BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|15646079|ref|NP_208261.1| DNA polymerase I (polA)
[Helicobacter pylori 26695]
(892 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1TAU|A Chain A, Structure Of Dna Polymerase 397 e-111
pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An ... 395 e-110
pdb|1TAQ| Structure Of Taq Dna Polymerase 392 e-110
pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of... 290 6e-79
pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bo... 290 6e-79
pdb|1JXE| Stoffel Fragment Of Taq Dna Polymerase I >gi|67... 290 6e-79
pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of... 290 6e-79
pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragm... 290 6e-79
pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of... 290 6e-79
pdb|2BDP|A Chain A, Crystal Structure Of Bacillus Dna Polym... 274 3e-74
pdb|1XWL| Bacillus Stearothermophilus (Newly Identified S... 274 4e-74
pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna... 265 1e-71
pdb|1KLN|A Chain A, Dna Polymerase I (Klenow Fragment) (E.C... 265 2e-71
pdb|1KFD| Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7... 264 3e-71
pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Su... 264 3e-71
pdb|1T7P|A Chain A, T7 Dna Polymerase Complexed To Dna Prim... 72 4e-13
pdb|1EXN|B Chain B, T5 5'-Exonuclease >gi|2392326|pdb|1EXN|... 64 1e-10
pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a >gi|14719... 63 1e-10
pdb|1C7N|A Chain A, Crystal Structure Of Cystalysin From Tr... 30 1.2
pdb|1MMU|A Chain A, Crystal Structure Of Galactose Mutarota... 29 2.6
pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-... 28 4.5
pdb|1UOR| X-Ray Study Of Recombinant Human Serum Albumin.... 28 4.5
pdb|1BKE| Human Serum Albumin In A Complex With Myristic ... 28 4.5
pdb|1JIL|A Chain A, Crystal Structure Of S. Aureus Tyrrs In... 28 4.5
pdb|1ENV|A Chain A, Atomic Structure Of The Ectodomain From... 27 7.6
>pdb|1TAU|A Chain A, Structure Of Dna Polymerase
Length = 832
Score = 397 bits (1020), Expect = e-111
Identities = 307/898 (34%), Positives = 450/898 (49%), Gaps = 92/898 (10%)
Query: 9 EGTLALIDTFAYLFRSYYMSAKNKPLTNDKGFPTGLLTGLVGMVKKFYKDRKNMPFIVFA 68
+G + L+D +R+++ K LT +G P + G + K K+ + +VF
Sbjct: 11 KGRVLLVDGHHLAYRTFHAL---KGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVF- 66
Query: 69 LESQTKTKRAEKLGEYKQNRKDAPKEMLLQIPIALEWLQKMGFVCVEVNGFEADDVIASL 128
+++ + R E G YK R P++ Q+ + E + +G +EV G+EADDV+ASL
Sbjct: 67 -DAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASL 125
Query: 129 ATLSP---YKTRIYSKDKDFNQLLSDKIALFDGKTEFLAKDCV-EKYGILPSQFTDYQGI 184
A + Y+ RI + DKD QLLSD+I + + + + EKYG+ P Q+ DY+ +
Sbjct: 126 AKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRAL 185
Query: 185 VGDSSDNYKGVKGIGSKNAKELLQRLGSLEKIYENLDLAKNLLSPKMYRALIHDKASAFL 244
GD SDN GVKGIG K A++LL+ GSLE + +NLD K + K+ + K L
Sbjct: 186 TGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLK----L 241
Query: 245 SKELATLERGCIKEFDFLSCAFPSENPLLKIKDELKEYGFISTLRDLENSPTPLILDNAP 304
S +LA + E DF P L + L E+G + L
Sbjct: 242 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERL-EFGSL--------------LHEFG 286
Query: 305 LLDNTPALDNTPKKSCMIVLESAAPLSAFLEKLEKTNARVFARLVLDKEKKVLALAFLYE 364
LL++ AL+ P P AF+ + ++A L LALA
Sbjct: 287 LLESPKALEEAPWPP---------PEGAFVGFVLSRKEPMWADL--------LALAAARG 329
Query: 365 DQGYFLPLEEALFSPFSLEFLQNAFFKMLQHAQIIGHDLKPLLSFLKAKYQVPLENIRIQ 424
+ + P P+ A + + ++ DL L L+ +P +
Sbjct: 330 GRVHRAP------EPYK------ALRDLKEARGLLAKDLSVLA--LREGLGLPPGD---- 371
Query: 425 DTQILAFLKNPEKVGFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLCEY 484
D +LA+L +P + V + Y E + +A + LS L A
Sbjct: 372 DPMLLAYLLDPSNTTPEGVARRYGGE----------WTEEAGERAALSERLFA-----NL 416
Query: 485 FEKGGLEENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILE 544
+ + EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++
Sbjct: 417 WGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFR 476
Query: 545 LIGVDFNLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYR 598
L G FNLNS QL VL+D+LGLP K ST L + + HP + IL+YR
Sbjct: 477 LAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYR 536
Query: 599 ELNKLFNTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRK 657
EL KL +TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+
Sbjct: 537 ELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRR 596
Query: 658 GFIASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLA 714
GFIA + + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E +
Sbjct: 597 GFIA-EEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVD 655
Query: 715 KEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEIL 774
R AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE
Sbjct: 656 PLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGR 715
Query: 775 KTSKAFTLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNN 833
+ TL GR R V D V+ R N QG+A+DL+KL M+K+ R +
Sbjct: 716 RRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-E 774
Query: 834 PSVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
R+LLQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 775 MGARMLLQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 831
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1CMW|A Chain A, Crystal Structure Of Taq Dna-Polymerase Shows A New
Orientation For The Structure-Specific Nuclease Domain
Length = 832
Score = 395 bits (1014), Expect = e-110
Identities = 306/898 (34%), Positives = 449/898 (49%), Gaps = 92/898 (10%)
Query: 9 EGTLALIDTFAYLFRSYYMSAKNKPLTNDKGFPTGLLTGLVGMVKKFYKDRKNMPFIVFA 68
+G + L+D +R+++ K LT +G P + G + K K+ + +VF
Sbjct: 11 KGRVLLVDGHHLAYRTFHAL---KGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVF- 66
Query: 69 LESQTKTKRAEKLGEYKQNRKDAPKEMLLQIPIALEWLQKMGFVCVEVNGFEADDVIASL 128
+++ + R E G YK R P++ Q+ + E + +G +EV G+EADDV+ASL
Sbjct: 67 -DAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASL 125
Query: 129 ATLSP---YKTRIYSKDKDFNQLLSDKIALFDGKTEFLAKDCV-EKYGILPSQFTDYQGI 184
A + Y+ RI + DKD QLLSD+I + + + + EKYG+ P Q+ DY+ +
Sbjct: 126 AKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRAL 185
Query: 185 VGDSSDNYKGVKGIGSKNAKELLQRLGSLEKIYENLDLAKNLLSPKMYRALIHDKASAFL 244
GD SDN GVKGIG K A++LL+ GSLE + +NLD K + K+ + K L
Sbjct: 186 TGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLK----L 241
Query: 245 SKELATLERGCIKEFDFLSCAFPSENPLLKIKDELKEYGFISTLRDLENSPTPLILDNAP 304
S +LA + E DF P L + L E+G + L
Sbjct: 242 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERL-EFGSL--------------LHEFG 286
Query: 305 LLDNTPALDNTPKKSCMIVLESAAPLSAFLEKLEKTNARVFARLVLDKEKKVLALAFLYE 364
LL++ AL+ P P AF+ + ++A L LALA
Sbjct: 287 LLESPKALEEAPWPP---------PEGAFVGFVLSRKEPMWADL--------LALAAARG 329
Query: 365 DQGYFLPLEEALFSPFSLEFLQNAFFKMLQHAQIIGHDLKPLLSFLKAKYQVPLENIRIQ 424
+ + P P+ A + + ++ DL L L+ +P +
Sbjct: 330 GRVHRAP------EPYK------ALRDLKEARGLLAKDLSVLA--LREGLGLPPGD---- 371
Query: 425 DTQILAFLKNPEKVGFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLCEY 484
D +LA+L +P + V + Y E + +A + LS L A
Sbjct: 372 DPMLLAYLLDPSNTTPEGVARRYGGE----------WTEEAGERAALSERLFA-----NL 416
Query: 485 FEKGGLEENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILE 544
+ + EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++
Sbjct: 417 WGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFR 476
Query: 545 LIGVDFNLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYR 598
L G FNLNS QL VL+D+LGLP K ST L + + HP + IL+YR
Sbjct: 477 LAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYR 536
Query: 599 ELNKLFNTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRK 657
EL KL +TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+
Sbjct: 537 ELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRR 596
Query: 658 GFIASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLA 714
FIA + + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E +
Sbjct: 597 AFIA-EEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVD 655
Query: 715 KEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEIL 774
R AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE
Sbjct: 656 PLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGR 715
Query: 775 KTSKAFTLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNN 833
+ TL GR R V D V+ R N QG+A+DL+KL M+K+ R +
Sbjct: 716 RRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-E 774
Query: 834 PSVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
R+LLQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 775 MGARMLLQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 831
>pdb|1TAQ| Structure Of Taq Dna Polymerase
Length = 832
Score = 392 bits (1008), Expect = e-110
Identities = 305/898 (33%), Positives = 448/898 (48%), Gaps = 92/898 (10%)
Query: 9 EGTLALIDTFAYLFRSYYMSAKNKPLTNDKGFPTGLLTGLVGMVKKFYKDRKNMPFIVFA 68
+G + L+D +R+++ K LT +G P + G + K K+ + +VF
Sbjct: 11 KGRVLLVDGHHLAYRTFHAL---KGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVF- 66
Query: 69 LESQTKTKRAEKLGEYKQNRKDAPKEMLLQIPIALEWLQKMGFVCVEVNGFEADDVIASL 128
+++ + R E G YK R P++ Q+ + E + +G +EV G+EADDV+ASL
Sbjct: 67 -DAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASL 125
Query: 129 ATLSP---YKTRIYSKDKDFNQLLSDKIALFDGKTEFLAKDCV-EKYGILPSQFTDYQGI 184
A + Y+ RI + DKD QLLSD+I + + + + EKYG+ P Q+ DY+ +
Sbjct: 126 AKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRAL 185
Query: 185 VGDSSDNYKGVKGIGSKNAKELLQRLGSLEKIYENLDLAKNLLSPKMYRALIHDKASAFL 244
GD SDN GVKGIG K A++LL+ GSLE + +NLD K + K+ + K L
Sbjct: 186 TGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLK----L 241
Query: 245 SKELATLERGCIKEFDFLSCAFPSENPLLKIKDELKEYGFISTLRDLENSPTPLILDNAP 304
S +LA + E DF P L + L E+G + L
Sbjct: 242 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERL-EFGSL--------------LHEFG 286
Query: 305 LLDNTPALDNTPKKSCMIVLESAAPLSAFLEKLEKTNARVFARLVLDKEKKVLALAFLYE 364
LL++ AL+ P P AF+ + ++A L LALA
Sbjct: 287 LLESPKALEEAPWPP---------PEGAFVGFVLSRKEPMWADL--------LALAAARG 329
Query: 365 DQGYFLPLEEALFSPFSLEFLQNAFFKMLQHAQIIGHDLKPLLSFLKAKYQVPLENIRIQ 424
+ + P P+ A + + ++ DL L L+ +P +
Sbjct: 330 GRVHRAP------EPYK------ALRDLKEARGLLAKDLSVLA--LREGLGLPPGD---- 371
Query: 425 DTQILAFLKNPEKVGFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLCEY 484
D +LA+L +P + V + Y E + +A + LS L A
Sbjct: 372 DPMLLAYLLDPSNTTPEGVARRYGGE----------WTEEAGERAALSERLFA-----NL 416
Query: 485 FEKGGLEENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILE 544
+ + EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++
Sbjct: 417 WGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFR 476
Query: 545 LIGVDFNLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYR 598
L G FNLNS QL VL+D+LGLP K ST L + + HP + IL+YR
Sbjct: 477 LAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYR 536
Query: 599 ELNKLFNTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRK 657
EL KL +TY PL L + ++HT F QT TATGRL PNLQNIPVR+P G IR+
Sbjct: 537 ELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLCCCDPNLQNIPVRTPLGQRIRR 596
Query: 658 GFIASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLA 714
GFIA + + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E +
Sbjct: 597 GFIA-EEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVD 655
Query: 715 KEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEIL 774
R AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE
Sbjct: 656 PLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGR 715
Query: 775 KTSKAFTLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNN 833
+ TL GR R V D V+ R N QG+A+DL+KL M+K+ R +
Sbjct: 716 RRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-E 774
Query: 834 PSVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
R+LLQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 775 MGARMLLQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 831
>pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 131 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 190
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 191 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 250
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 251 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 309
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 310 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 369
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 370 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 429
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 430 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 488
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 489 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 539
>pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bound To Dctp
pdb|1KTQ| Dna Polymerase
Length = 543
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 134 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 193
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 194 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 253
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 254 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 312
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 313 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 372
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 373 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 432
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 433 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 491
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 492 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 542
>pdb|1JXE| Stoffel Fragment Of Taq Dna Polymerase I
pdb|3KTQ|A Chain A, Crystal Structure Of An Active Ternary Complex Of The
Large Fragment Of Dna Polymerase I From Thermus
Aquaticus
Length = 540
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 131 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 190
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 191 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 250
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 251 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 309
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 310 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 369
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 370 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 429
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 430 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 488
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 489 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 539
>pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
pdb|1QSS|A Chain A, Ddgtp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 131 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 190
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 191 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 250
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 251 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 309
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 310 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 369
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 370 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 429
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 430 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 488
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 489 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 539
>pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus
Length = 538
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 129 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 188
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 189 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 248
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 249 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 307
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 308 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 367
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 368 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 427
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 428 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 486
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 487 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 537
>pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of Dna Polymerase I
From T. Aquaticus Bound To A PrimerTEMPLATE DNA
Length = 539
Score = 290 bits (741), Expect = 6e-79
Identities = 177/412 (42%), Positives = 242/412 (57%), Gaps = 14/412 (3%)
Query: 491 EENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDF 550
EE LL L RE+E P VL ME G ++D Y + L E E+ LE ++ L G F
Sbjct: 130 EERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPF 189
Query: 551 NLNSPKQLSEVLYDKLGLP------KNKSHSTDEKSLLKILDKHPSIALILEYRELNKLF 604
NLNS QL VL+D+LGLP K ST L + + HP + IL+YREL KL
Sbjct: 190 NLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLK 249
Query: 605 NTYTTPLLRL-KDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASS 663
+TY PL L + ++HT F QT TATGRLSS PNLQNIPVR+P G IR+ FIA
Sbjct: 250 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIA-E 308
Query: 664 KEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSI 720
+ + L+ +DYSQIELR+LAH S D++L+ F +GRDIH ET+ +FG E + R
Sbjct: 309 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 368
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
AK+INFG++YGM + +LS+ L I EA+++IE YF+ FP ++ ++ + EE +
Sbjct: 369 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 428
Query: 781 TLLGRYR-VFDFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNNPSVRLL 839
TL GR R V D V+ R N QG+A+DL+KL M+K+ R + R+L
Sbjct: 429 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLE-EMGARML 487
Query: 840 LQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LQVHDEL+ E ++ A + + + ++ + VYPL VPLE I + W K
Sbjct: 488 LQVHDELVLEAPKERAEAVARLAKEVM-EGVYPLAVPLEVEVGIGEDWLSAK 538
>pdb|2BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna
pdb|3BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To Duplex Dna After The Incorporation Of +ttp
By The Enzyme
pdb|4BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 11 Base Pairs Of Duplex Dna After Addition
Of Two Datp Residues
Length = 580
Score = 274 bits (701), Expect = 3e-74
Identities = 174/479 (36%), Positives = 260/479 (53%), Gaps = 19/479 (3%)
Query: 423 IQDTQILAFLKNPEKVGFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLC 482
+ D + A +K E V DE + + +P E + AE L + + L+R
Sbjct: 111 VDDVRAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVL-----AEHLVRKAAAIWELERPF 165
Query: 483 EYFEKGGLEENLLSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQI 542
+ ++ LL E+E P +L MEF G K+D +++ +E +L +E++I
Sbjct: 166 LDELRRNEQDRLLV---ELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRI 222
Query: 543 LELIGVDFNLNSPKQLSEVLYDKLGLPKNKSHSTDEKSLLKILDK----HPSIALILEYR 598
EL G +FN+NSPKQL +L++KL LP K T + +L+K H + IL YR
Sbjct: 223 YELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYR 282
Query: 599 ELNKLFNTYTTPLLRLKDKDDK-IHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRK 657
+L KL +TY LL++ D K +HT F Q T TGRLSS PNLQNIP+R +G IR+
Sbjct: 283 QLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQ 342
Query: 658 GFIASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALF---GEYLA 714
F+ S ++ + DYSQIELR+LAH ++D +LMEAF + DIH +T+ +F + +
Sbjct: 343 AFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVT 402
Query: 715 KEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEIL 774
R AK++NFG+VYG+ L++ LNIS EA +IE YF+ FP +K Y+ + +E
Sbjct: 403 PNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAK 462
Query: 775 KTSKAFTLLGRYRVF-DFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFKNN 833
+ TLL R R D T N V+ R +N QGSA+D++K M+ ++ R K
Sbjct: 463 QKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEE 522
Query: 834 P-SVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNELK 891
LLLQVHDELI E ++ L + + ++ ++ LRVPL+ W + K
Sbjct: 523 RLQAHLLLQVHDELILEAPKEEMERLCRLVPEVM-EQAVTLRVPLKVDYHYGSTWYDAK 580
>pdb|1XWL| Bacillus Stearothermophilus (Newly Identified Strain As Yet
Unnamed) Dna Polymerase Fragment
Length = 580
Score = 274 bits (700), Expect = 4e-74
Identities = 193/563 (34%), Positives = 290/563 (51%), Gaps = 45/563 (7%)
Query: 356 VLALAFLYEDQGYFLPLEEALFSPFSLEFLQNAFFKMLQHAQIIGHDLKPLLSFLKAKYQ 415
++ +A + E +FL E AL P Q +G + K F +
Sbjct: 36 IVGIAVVNEHGRFFLRPETALADP--------------QFVAWLGDETKKKSMFDSKRAA 81
Query: 416 VPLENIRIQ------DTQILAFLKNPEKVGFDEV-----LKEYLKEELIPHEKI--KDFK 462
V L+ I+ D + A+L +P + G D+V +K+Y E + P E + K K
Sbjct: 82 VALKWKGIELCGVSFDLLLAAYLLDPAQ-GVDDVAAAAKMKQY--EAVRPDEAVYGKGAK 138
Query: 463 TKAEKLELLSVELNALKRLCEYFEKGGLEENLLS----LAREIETPFMKVLMGMEFQGFK 518
+L+ L E+ L+E + L E+E P +L MEF G K
Sbjct: 139 RAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVK 198
Query: 519 IDAPYFKRLEQEFKNELHVLERQILELIGVDFNLNSPKQLSEVLYDKLGLPKNKSHSTDE 578
+D +++ +E +L +E++I EL G +FN+NSPKQL +L++KL LP K T
Sbjct: 199 VDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGY 258
Query: 579 KSLLKILDK----HPSIALILEYRELNKLFNTYTTPLLRLKDKDDK-IHTTFIQTGTATG 633
+ +L+K H + IL YR+L KL +TY LL++ D K +HT F Q T TG
Sbjct: 259 STSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTG 318
Query: 634 RLSSHSPNLQNIPVRSPKGLLIRKGFIASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEA 693
RLSS PNLQNIP+R +G IR+ F+ S ++ + DYSQIELR+LAH ++D +LMEA
Sbjct: 319 RLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEA 378
Query: 694 FLKGRDIHLETSKALF---GEYLAKEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKS 750
F + DIH +T+ +F + + R AK++NFG+VYG+ L++ LNIS EA
Sbjct: 379 FRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAE 438
Query: 751 YIEAYFKRFPSIKDYLNRMKEEILKTSKAFTLLGRYRVF-DFTGANDYVKGNYLREGVNA 809
+IE YF+ FP +K Y+ + +E + TLL R R D T N V+ R +N
Sbjct: 439 FIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNT 498
Query: 810 IFQGSASDLLKLGMLKVSERFKNNP-SVRLLLQVHDELIFEIEEKNAPELQQEIQRILND 868
QGSA+D++K M+ ++ R K LLLQVHDELI E ++ L + + ++ +
Sbjct: 499 PIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVM-E 557
Query: 869 EVYPLRVPLETSAFIAKRWNELK 891
+ LRVPL+ W + K
Sbjct: 558 QAVTLRVPLKVDYHYGSTWYDAK 580
>pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna
Length = 605
Score = 265 bits (678), Expect = 1e-71
Identities = 200/595 (33%), Positives = 313/595 (51%), Gaps = 42/595 (7%)
Query: 330 LSAFLEKLEKTNARVFARLV--LDK-EKKVLALAFLYED--QGYFLPLEEALFSP--FSL 382
L A++ KLEK FA LD ++ L+F E Y + L +P S
Sbjct: 16 LKAWIAKLEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISR 75
Query: 383 EFLQNAFFKMLQHAQI--IGHDLKPLLSFLKAKYQVPLENIRIQDTQILAFLKNPE--KV 438
E +L+ + +G +LK L A Y + L I DT + +++ N +
Sbjct: 76 ERALELLKPLLEDEKALKVGQNLKYDRGIL-ANYGIELRGIAF-DTMLESYILNSVAGRH 133
Query: 439 GFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLCEYFEKGGLEENL---- 494
D + + +LK + I E+I K K +L + L R L+ +L
Sbjct: 134 DMDSLAERWLKHKTITFEEIAG-KGK-NQLTFNQIALEEAGRYAAEDADVTLQLHLKMWP 191
Query: 495 --------LSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELI 546
L++ IE P + VL +E G KID +E L LE++ E+
Sbjct: 192 DLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIA 251
Query: 547 GVDFNLNSPKQLSEVLYDKLGLPKNK-----SHSTDEKSLLKILDKHPSIALILEYRELN 601
G +FNL+S KQL +L++K G+ K + ST E+ L ++ +P +ILEYR L
Sbjct: 252 GEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLA 311
Query: 602 KLFNTYTTPL-LRLKDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFI 660
KL +TYT L L + K ++HT++ Q TATGRLSS PNLQNIPVR+ +G IR+ FI
Sbjct: 312 KLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFI 371
Query: 661 ASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEK 717
A ++Y ++ DYSQIELR++AH S+DK L+ AF +G+DIH T+ +FG E + E+
Sbjct: 372 AP-EDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQ 430
Query: 718 RSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTS 777
R AK+INFGL+YGM + L+ LNI EA+ Y++ YF+R+P + +Y+ R + + +
Sbjct: 431 RRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQG 490
Query: 778 KAFTLLGRYRVF--DFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFK-NNP 834
TL GR R++ D +N + R +NA QG+A+D++K M+ V + P
Sbjct: 491 YVETLDGR-RLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQP 549
Query: 835 SVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNE 889
VR+++QVHDEL+FE+ + + + ++I +++ + L VPL + W++
Sbjct: 550 RVRMIMQVHDELVFEVHKDDVDAVAKQIHQLM-ENCTRLDVPLLVEVGSGENWDQ 603
>pdb|1KLN|A Chain A, Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7) Mutant
With Asp 355 Replaced By Ala (D355a) Complexed With Dna
Length = 605
Score = 265 bits (676), Expect = 2e-71
Identities = 200/595 (33%), Positives = 313/595 (51%), Gaps = 42/595 (7%)
Query: 330 LSAFLEKLEKTNARVFARLV--LDK-EKKVLALAFLYED--QGYFLPLEEALFSP--FSL 382
L A++ KLEK FA LD ++ L+F E Y + L +P S
Sbjct: 16 LKAWIAKLEKAPVFAFATETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISR 75
Query: 383 EFLQNAFFKMLQHAQI--IGHDLKPLLSFLKAKYQVPLENIRIQDTQILAFLKNPE--KV 438
E +L+ + +G +LK L A Y + L I DT + +++ N +
Sbjct: 76 ERALELLKPLLEDEKALKVGQNLKYDRGIL-ANYGIELRGIAF-DTMLESYILNSVAGRH 133
Query: 439 GFDEVLKEYLKEELIPHEKIKDFKTKAEKLELLSVELNALKRLCEYFEKGGLEENL---- 494
D + + +LK + I E+I K K +L + L R L+ +L
Sbjct: 134 DMDSLAERWLKHKTITFEEIAG-KGK-NQLTFNQIALEEAGRYAAEDADVTLQLHLKMWP 191
Query: 495 --------LSLAREIETPFMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELI 546
L++ IE P + VL +E G KID +E L LE++ E+
Sbjct: 192 DLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIA 251
Query: 547 GVDFNLNSPKQLSEVLYDKLGLPKNK-----SHSTDEKSLLKILDKHPSIALILEYRELN 601
G +FNL+S KQL +L++K G+ K + ST E+ L ++ +P +ILEYR L
Sbjct: 252 GEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLA 311
Query: 602 KLFNTYTTPL-LRLKDKDDKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFI 660
KL +TYT L L + K ++HT++ Q TATGRLSS PNLQNIPVR+ +G IR+ FI
Sbjct: 312 KLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFI 371
Query: 661 ASSKEYCLLGVDYSQIELRLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEK 717
A ++Y ++ DYSQIELR++AH S+DK L+ AF +G+DIH T+ +FG E + E+
Sbjct: 372 AP-EDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQ 430
Query: 718 RSIAKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTS 777
R AK+INFGL+YGM + L+ LNI EA+ Y++ YF+R+P + +Y+ R + + +
Sbjct: 431 RRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQG 490
Query: 778 KAFTLLGRYRVF--DFTGANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFK-NNP 834
TL GR R++ D +N + R +NA QG+A+D++K M+ V + P
Sbjct: 491 YVETLDGR-RLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQP 549
Query: 835 SVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNE 889
VR+++QVHDEL+FE+ + + + ++I +++ + L VPL + W++
Sbjct: 550 RVRMIMQVHDELVFEVHKDDVDAVAKQIHQLM-ENCTRLDVPLLVEVGSGENWDQ 603
>pdb|1KFD| Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7) Complexed With
Dctp
pdb|1DPI| DNA Polymerase I (Klenow Fragment) (E.C.2.7.7.7) - dCMP Complex
Length = 605
Score = 264 bits (675), Expect = 3e-71
Identities = 181/517 (35%), Positives = 284/517 (54%), Gaps = 33/517 (6%)
Query: 399 IGHDLKPLLSFLKAKYQVPLENIRIQDTQILAFLKNPE--KVGFDEVLKEYLKEELIPHE 456
+G +LK L A Y + L I DT + +++ N + D + + +LK + I E
Sbjct: 94 VGQNLKYDRGIL-ANYGIELRGIAF-DTMLESYILNSVAGRHDMDSLAERWLKHKTITFE 151
Query: 457 KIKDFKTKAEKLELLSVELNALKRLCEYFEKGGLEENL------------LSLAREIETP 504
+I K K +L + L R L+ +L L++ IE P
Sbjct: 152 EIAG-KGK-NQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMP 209
Query: 505 FMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDFNLNSPKQLSEVLYD 564
+ VL +E G KID +E L LE++ E+ G +FNL+S KQL +L++
Sbjct: 210 LVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFE 269
Query: 565 KLGLPKNK-----SHSTDEKSLLKILDKHPSIALILEYRELNKLFNTYTTPL-LRLKDKD 618
K G+ K + ST E+ L ++ +P +ILEYR L KL +TYT L L + K
Sbjct: 270 KQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKT 329
Query: 619 DKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASSKEYCLLGVDYSQIEL 678
++HT++ Q TATGRLSS PNLQNIPVR+ +G IR+ FIA ++Y ++ DYSQIEL
Sbjct: 330 GRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAP-EDYVIVSADYSQIEL 388
Query: 679 RLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSIAKSINFGLVYGMGSK 735
R++AH S+DK L+ AF +G+DIH T+ +FG E + E+R AK+INFGL+YGM +
Sbjct: 389 RIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAF 448
Query: 736 KLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAFTLLGRYRVF--DFTG 793
L+ LNI EA+ Y++ YF+R+P + +Y+ R + + + TL GR R++ D
Sbjct: 449 GLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGR-RLYLPDIKS 507
Query: 794 ANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFK-NNPSVRLLLQVHDELIFEIEE 852
+N + R +NA QG+A+D++K M+ V + P VR+++QVHDEL+FE+ +
Sbjct: 508 SNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHK 567
Query: 853 KNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNE 889
+ + ++I +++ + L VPL + W++
Sbjct: 568 DDVDAVAKQIHQLM-ENCTRLDVPLLVEVGSGENWDQ 603
>pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And
Manganese
pdb|2KFZ|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And Zinc
Only
pdb|1KFS|A Chain A, All-Oxygen Dna Complexed To The 3'-5' Exonuclease Of Dna
Polymerase I From E. Coli
pdb|1D9D|A Chain A, Crystall Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Short Dna Fragment Carrying 2'-0-
Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'
pdb|1KRP|A Chain A, Rp Isomer Phosphorothioate Dna Complexed To The 3'-5'
Exonuclease Of Dna Polymerase I From E. Coli
pdb|1QSL|A Chain A, Klenow Fragment Complexed With Single-Stranded Substrate
And Europium (Iii) Ion
pdb|2KZZ|A Chain A, Klenow Fragment With Normal Substrate And Zinc Only
pdb|1KSP|A Chain A, Sp Isomer Phosphorothioate Dna Complexed To The 3'-5'
Exonuclease Of Dna Polymerase I From E. Coli
pdb|2KZM|A Chain A, Klenow Fragment With Normal Substrate And Zinc And
Manganese
pdb|1D9F|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna Tetramer Carrying
2'-O-(3-Aminopropyl)- Rna Modification
5'-D(Tt)-Ap(U)-D(T)-3'
Length = 605
Score = 264 bits (675), Expect = 3e-71
Identities = 181/517 (35%), Positives = 284/517 (54%), Gaps = 33/517 (6%)
Query: 399 IGHDLKPLLSFLKAKYQVPLENIRIQDTQILAFLKNPE--KVGFDEVLKEYLKEELIPHE 456
+G +LK L A Y + L I DT + +++ N + D + + +LK + I E
Sbjct: 94 VGQNLKYDRGIL-ANYGIELRGIAF-DTMLESYILNSVAGRHDMDSLAERWLKHKTITFE 151
Query: 457 KIKDFKTKAEKLELLSVELNALKRLCEYFEKGGLEENL------------LSLAREIETP 504
+I K K +L + L R L+ +L L++ IE P
Sbjct: 152 EIAG-KGK-NQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMP 209
Query: 505 FMKVLMGMEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDFNLNSPKQLSEVLYD 564
+ VL +E G KID +E L LE++ E+ G +FNL+S KQL +L++
Sbjct: 210 LVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFE 269
Query: 565 KLGLPKNK-----SHSTDEKSLLKILDKHPSIALILEYRELNKLFNTYTTPL-LRLKDKD 618
K G+ K + ST E+ L ++ +P +ILEYR L KL +TYT L L + K
Sbjct: 270 KQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKT 329
Query: 619 DKIHTTFIQTGTATGRLSSHSPNLQNIPVRSPKGLLIRKGFIASSKEYCLLGVDYSQIEL 678
++HT++ Q TATGRLSS PNLQNIPVR+ +G IR+ FIA ++Y ++ DYSQIEL
Sbjct: 330 GRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAP-EDYVIVSADYSQIEL 388
Query: 679 RLLAHFSQDKDLMEAFLKGRDIHLETSKALFG---EYLAKEKRSIAKSINFGLVYGMGSK 735
R++AH S+DK L+ AF +G+DIH T+ +FG E + E+R AK+INFGL+YGM +
Sbjct: 389 RIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAF 448
Query: 736 KLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAFTLLGRYRVF--DFTG 793
L+ LNI EA+ Y++ YF+R+P + +Y+ R + + + TL GR R++ D
Sbjct: 449 GLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGR-RLYLPDIKS 507
Query: 794 ANDYVKGNYLREGVNAIFQGSASDLLKLGMLKVSERFK-NNPSVRLLLQVHDELIFEIEE 852
+N + R +NA QG+A+D++K M+ V + P VR+++QVHDEL+FE+ +
Sbjct: 508 SNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHK 567
Query: 853 KNAPELQQEIQRILNDEVYPLRVPLETSAFIAKRWNE 889
+ + ++I +++ + L VPL + W++
Sbjct: 568 DDVDAVAKQIHQLM-ENCTRLDVPLLVEVGSGENWDQ 603
>pdb|1T7P|A Chain A, T7 Dna Polymerase Complexed To Dna PrimerTEMPLATE,A
Nucleoside Triphosphate, And Its Processivity Factor
Thioredoxin
Length = 698
Score = 71.6 bits (174), Expect = 4e-13
Identities = 83/332 (25%), Positives = 134/332 (40%), Gaps = 39/332 (11%)
Query: 586 DKHPSIALILEYRELNKLFNTYTT---PLLRLKDKDDKIHTTFIQTGTATGRLSSHSPNL 642
+K +I LI EY + K LR +D KIH + G TGR + PNL
Sbjct: 372 EKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNL 431
Query: 643 QNIP-VRSPKGLLIRKGFIA-------SSKEYCLLGVDYSQIELRLLAHFSQDKDLME-- 692
IP VRSP G R F A + K + G+D S +ELR LAHF D E
Sbjct: 432 AQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYA 491
Query: 693 -AFLKGRDIHLETSKALFGEYLAKEKRSIAKSINFGLVYGMGSKKLSETLNISLNEAKSY 751
L G DIH T + E ++ AK+ +G +YG G +K+ + + K
Sbjct: 492 HEILNG-DIH--TKNQIAAELPTRDN---AKTFIYGFLYGAGDEKIGQIVGAGKERGKEL 545
Query: 752 IEAYFKRFPSIKDYLNRMKEEILKTS-----KAFTLLGRYRVFDFTGANDYVKGNYLREG 806
+ + + P+I +++ ++++S + R + G +V+ +
Sbjct: 546 KKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPH--AA 603
Query: 807 VNAIFQGSASDLLKLGMLKVSERFKN-------NPSVRLLLQVHDELIFEIEEKNAP--- 856
+N + Q + + + KL ++K E + + VHDE+ +
Sbjct: 604 LNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVV 663
Query: 857 -ELQQEIQRILNDEVYPLRVPLETSAFIAKRW 887
E QE R + D + R L+T + W
Sbjct: 664 IETAQEAMRWVGDH-WNFRCLLDTEGKMGPNW 694
>pdb|1EXN|B Chain B, T5 5'-Exonuclease
pdb|1EXN|A Chain A, T5 5'-Exonuclease
Length = 290
Score = 63.5 bits (153), Expect = 1e-10
Identities = 50/165 (30%), Positives = 79/165 (47%), Gaps = 9/165 (5%)
Query: 66 VFALES--QTKTKRAEKLGEYKQNRKDAPKEMLLQIPIALEWLQKMGFVCVEVNGFEADD 123
VF LE + K R EK + + K ++ + A E L K F + G EADD
Sbjct: 72 VFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFE-LCKTTFPTFTIRGVEADD 130
Query: 124 VIASLATLSPY---KTRIYSKDKDFNQLLSDKIALFDGKT--EFLAKDCVEKYGILP-SQ 177
A + L + + S D D++ LL+DK++ F T E+ +D E + + Q
Sbjct: 131 XAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDXYEHHNVDDVEQ 190
Query: 178 FTDYQGIVGDSSDNYKGVKGIGSKNAKELLQRLGSLEKIYENLDL 222
F + I GD DN +GV+GIG+K +++ G++ I + L L
Sbjct: 191 FISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL 235
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a
pdb|1XO1|B Chain B, T5 5'-Exonuclease Mutant K83a
Length = 291
Score = 63.2 bits (152), Expect = 1e-10
Identities = 49/165 (29%), Positives = 80/165 (47%), Gaps = 9/165 (5%)
Query: 66 VFALES--QTKTKRAEKLGEYKQNRKDAPKEMLLQIPIALEWLQKMGFVCVEVNGFEADD 123
VF LE + R EK + + K ++ + A E L K F + G EADD
Sbjct: 73 VFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFE-LCKTTFPTFTIRGVEADD 131
Query: 124 VIASLATLSPY---KTRIYSKDKDFNQLLSDKIALFDGKT--EFLAKDCVEKYGILP-SQ 177
+ A + L + + S D D++ LL+DK++ F T E+ +D E + + Q
Sbjct: 132 MAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQ 191
Query: 178 FTDYQGIVGDSSDNYKGVKGIGSKNAKELLQRLGSLEKIYENLDL 222
F + I+GD DN +GV+GIG+K +++ G++ I + L L
Sbjct: 192 FISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL 236
>pdb|1C7N|A Chain A, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|B Chain B, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|C Chain C, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|D Chain D, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|E Chain E, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|F Chain F, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|G Chain G, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7N|H Chain H, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal 5'-Phosphate Cofactor
pdb|1C7O|A Chain A, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|B Chain B, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|C Chain C, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|D Chain D, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|E Chain E, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|F Chain F, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|G Chain G, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
pdb|1C7O|H Chain H, Crystal Structure Of Cystalysin From Treponema Denticola
Contains A Pyridoxal
5'-Phosphate-L-Aminoethoxyvinylglycine Complex
Length = 399
Score = 30.0 bits (66), Expect = 1.2
Identities = 20/67 (29%), Positives = 32/67 (46%), Gaps = 2/67 (2%)
Query: 821 LGMLKVSERFKNNPSVRLLLQVHDELIFEIEEKNAPELQQEIQRILNDEVYPLRVPLETS 880
LG LK + NP V +V + ++E KN PEL + +++ L++ V P E
Sbjct: 14 LGSLKWDLMYSQNPEVGN--EVVPLSVADMEFKNPPELIEGLKKYLDETVLGYTGPTEEY 71
Query: 881 AFIAKRW 887
K+W
Sbjct: 72 KKTVKKW 78
>pdb|1MMU|A Chain A, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Glucose
pdb|1MMU|B Chain B, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Glucose
pdb|1MMX|A Chain A, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Fucose
pdb|1MMX|B Chain B, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Fucose
pdb|1MMY|A Chain A, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Quinovose
pdb|1MMY|B Chain B, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Quinovose
pdb|1MMZ|A Chain A, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With L-Arabinose
pdb|1MMZ|B Chain B, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With L-Arabinose
pdb|1MN0|A Chain A, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Xylose
pdb|1MN0|B Chain B, Crystal Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With D-Xylose
pdb|1L7K|B Chain B, X-Ray Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With Galactose
pdb|1L7K|A Chain A, X-Ray Structure Of Galactose Mutarotase From Lactococcus
Lactis Complexed With Galactose
pdb|1L7J|A Chain A, X-Ray Structure Of Galactose Mutarotase From Lactococcus
Lactis (Apo)
pdb|1L7J|B Chain B, X-Ray Structure Of Galactose Mutarotase From Lactococcus
Lactis (Apo)
Length = 347
Score = 28.9 bits (63), Expect = 2.6
Identities = 24/113 (21%), Positives = 47/113 (41%), Gaps = 23/113 (20%)
Query: 512 MEFQGFKIDAPYFKRLEQEFKNELHVLERQILELIGVDFNLNSPKQLSEV---------- 561
+E G ++ A F L K++ ++ I+++ D + KQLS
Sbjct: 183 VENHGLRLAASRFVPL----KDQTEIVRGDIVDIKNTDLDFRQEKQLSNAFNSNMEQVQL 238
Query: 562 --------LYDKLGLPKNKSHSTDEKSLLKILDKHPSIALI-LEYRELNKLFN 605
L D+LGL K ++ T + + + + PSI + + +L L++
Sbjct: 239 VKGIDHPFLLDQLGLDKEQARLTLDDTSISVFTDQPSIVIFTANFGDLGTLYH 291
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
pdb|1MC8|B Chain B, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
Pyrococcus Horikoshii
Length = 343
Score = 28.1 bits (61), Expect = 4.5
Identities = 59/231 (25%), Positives = 91/231 (38%), Gaps = 50/231 (21%)
Query: 20 YLFRSYYMSAKNKPLTNDKGFPTGLLTGL---------VGMVKKFYKDRKNMPFIVFALE 70
Y F S PL + KG T L+GL G+ + D K F LE
Sbjct: 33 YQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAYVFDGKPPEFKRKELE 92
Query: 71 --------SQTKTKRAEKLGEYKQNRKDAPK-----EMLLQIPIALEWLQKMGFVCVEVN 117
++ K K A G ++ RK A + EML++ A + LQ MG ++
Sbjct: 93 KRREAREEAELKWKEALAKGNLEEARKYAQRATKVNEMLIED--AKKLLQLMGIPIIQAP 150
Query: 118 GFEADDVIASLATLSPYKTRIY-SKDKDFNQLLSDKIALF-----DGKTEFLAKDC---- 167
E + A +A+ K +Y S +D++ LL L GK + KD
Sbjct: 151 S-EGEAQAAYMAS----KGDVYASASQDYDSLLFGAPRLIRNLTITGKRKMPGKDVYVEI 205
Query: 168 ----------VEKYGILPSQFTDYQGIVGDSSDNYKGVKGIGSKNAKELLQ 208
+++ I + + +VG + N GVKGIG K A E+++
Sbjct: 206 KPELVVLDEVLKELKITREKLIELAILVG-TDYNPGGVKGIGPKKALEIVR 255
>pdb|1UOR| X-Ray Study Of Recombinant Human Serum Albumin. Phases Determined
By Molecular Replacement Method, Using Low Resolution
Structure Model Of Tetragonal Form Of Human Serum
Albumin
pdb|1AO6|A Chain A, Crystal Structure Of Human Serum Albumin
pdb|1AO6|B Chain B, Crystal Structure Of Human Serum Albumin
pdb|1BM0|A Chain A, Crystal Structure Of Human Serum Albumin
pdb|1BM0|B Chain B, Crystal Structure Of Human Serum Albumin
pdb|1H9Z|A Chain A, Human Serum Albumin Complexed With Myristic Acid And The
R-(+) Enantiomer Of Warfarin
pdb|1HA2|A Chain A, Human Serum Albumin Complexed With Myristic Acid And The
S- (-) Enantiomer Of Warfarin
pdb|1GNJ|A Chain A, Human Serum Albumin Complexed With
Cis-5,8,11,14-Eicosatetraenoic Acid (Arachidonic Acid)
pdb|1GNI|A Chain A, Human Serum Albumin Complexed With Cis-9-Octadecenoic Acid
(Oleic Acid)
pdb|1E7A|B Chain B, Crystal Structure Of Human Serum Albumin Complexed With
The General Anesthetic Propofol
pdb|1E7A|A Chain A, Crystal Structure Of Human Serum Albumin Complexed With
The General Anesthetic Propofol
pdb|1E7G|A Chain A, Human Serum Albumin Complexed With Tetradecanoic Acid
(Myristic Acid) Human Serum Albumin Complexed With
Myristic Acid
pdb|1E7C|A Chain A, Human Serum Albumin Complexed With Myristic Acid And The
General Anesthetic Halothane
pdb|1BJ5| Human Serum Albumin Complexed With Myristic Acid
pdb|1E7I|A Chain A, Human Serum Albumin Complexed With Octadecanoic Acid
(Stearic Acid)
pdb|1E7E|A Chain A, Human Serum Albumin Complexed With Decanoic Acid (Capric
Acid)
pdb|1E7H|A Chain A, Human Serum Albumin Complexed With Hexadecanoic Acid
(Palmitic Acid)
pdb|1E7F|A Chain A, Human Serum Albumin Complexed With Dodecanoic Acid (Lauric
Acid)
pdb|1E78|A Chain A, Crystal Structure Of Human Serum Albumin
pdb|1E7B|A Chain A, Crystal Structure Of Human Serum Albumin Complexed With
The General Anesthetic Halothane
pdb|1E78|B Chain B, Crystal Structure Of Human Serum Albumin
pdb|1E7B|B Chain B, Crystal Structure Of Human Serum Albumin Complexed With
The General Anesthetic Halothane
Length = 585
Score = 28.1 bits (61), Expect = 4.5
Identities = 28/127 (22%), Positives = 52/127 (40%), Gaps = 13/127 (10%)
Query: 664 KEYCLLGVDYSQIEL---RLLAHFSQDKDLMEAFLKGRDIHLETSKALFGEYLAKEKRSI 720
K +C+ V+ ++ L A F + KD+ + + + +D+ L G +L + R
Sbjct: 286 KSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFL-------GMFLYEYAR-- 336
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
+ ++ +V + K ET A E Y K F K + + I + + F
Sbjct: 337 -RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELF 395
Query: 781 TLLGRYR 787
LG Y+
Sbjct: 396 EQLGEYK 402
>pdb|1BKE| Human Serum Albumin In A Complex With Myristic Acid And
Tri-Iodobenzoic Acid
Length = 581
Score = 28.1 bits (61), Expect = 4.5
Identities = 28/127 (22%), Positives = 52/127 (40%), Gaps = 13/127 (10%)
Query: 664 KEYCLLGVDYSQIEL---RLLAHFSQDKDLMEAFLKGRDIHLETSKALFGEYLAKEKRSI 720
K +C+ V+ ++ L A F + KD+ + + + +D+ L G +L + R
Sbjct: 283 KSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFL-------GMFLYEYAR-- 333
Query: 721 AKSINFGLVYGMGSKKLSETLNISLNEAKSYIEAYFKRFPSIKDYLNRMKEEILKTSKAF 780
+ ++ +V + K ET A E Y K F K + + I + + F
Sbjct: 334 -RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELF 392
Query: 781 TLLGRYR 787
LG Y+
Sbjct: 393 EQLGEYK 399
>pdb|1JIL|A Chain A, Crystal Structure Of S. Aureus Tyrrs In Complex With
Sb284485
pdb|1JIK|A Chain A, Crystal Structure Of S. Aureus Tyrrs In Complex With Sb-
243545
pdb|1JII|A Chain A, Crystal Structure Of S. Aureus Tyrrs In Complex With Sb-
219383
pdb|1JIJ|A Chain A, Crystal Structure Of S. Aureus Tyrrs In Complex With Sb-
239629
Length = 420
Score = 28.1 bits (61), Expect = 4.5
Identities = 30/129 (23%), Positives = 53/129 (40%), Gaps = 25/129 (19%)
Query: 765 YLNRMKEEILKTSKAFTLLGR---------------YRVFDFTGANDYVKGNYLREGVN- 808
++N+ E+++K K FT LG+ R T A + K + + +N
Sbjct: 256 WINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALND 315
Query: 809 ------AIFQGSASDLLKLGMLKVSERFKNNPSVRLLLQVHDELIFEIEEKNAPELQQEI 862
A+F G DL L ++ + FK+ P V L + + IE +P +Q
Sbjct: 316 AIRISQALFSG---DLKSLSAKELKDGFKDVPQVTLSNDTTNIVEVLIETGISPSKRQAR 372
Query: 863 QRILNDEVY 871
+ + N +Y
Sbjct: 373 EDVNNGAIY 381
>pdb|1ENV|A Chain A, Atomic Structure Of The Ectodomain From Hiv-1 Gp41
Length = 123
Score = 27.3 bits (59), Expect = 7.6
Identities = 13/48 (27%), Positives = 27/48 (56%)
Query: 52 VKKFYKDRKNMPFIVFALESQTKTKRAEKLGEYKQNRKDAPKEMLLQI 99
V+++ KD+ NM ++ + E T L E QN+++ ++ LL++
Sbjct: 74 VERYLKDQNNMTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEL 121
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.319 0.138 0.385
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,978,287
Number of Sequences: 13198
Number of extensions: 211841
Number of successful extensions: 722
Number of sequences better than 10.0: 25
Number of HSP's better than 10.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 594
Number of HSP's gapped (non-prelim): 28
length of query: 892
length of database: 2,899,336
effective HSP length: 97
effective length of query: 795
effective length of database: 1,619,130
effective search space: 1287208350
effective search space used: 1287208350
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)