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|15644929|ref|NP_207099.1| dipeptide ABC transporter,
ATP-binding protein (dppD) [Helicobacter pylori 26695]
(287 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|1B0U|A Chain A, Atp-Binding Subunit Of The Histidine Pe... 122 5e-29
pdb|1L2T|A Chain A, Dimeric Structure Of Mj0796, A Bacteria... 99 6e-22
pdb|1F3O|A Chain A, Crystal Structure Of Mj0796 Atp-Binding... 98 1e-21
pdb|1G29|1 Chain 1, Malk >gi|12084695|pdb|1G29|2 Chain 2, Malk 97 2e-21
pdb|1JJ7|A Chain A, Crystal Structure Of The C-Terminal Atp... 81 1e-16
pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformati... 77 3e-15
pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free ... 75 1e-14
pdb|1JI0|A Chain A, Crystal Structure Analysis Of The Abc T... 75 1e-14
pdb|1JSQ|A Chain A, Structure Of Msba From Escherichia Coli... 72 6e-14
pdb|1L7V|C Chain C, Bacterial Abc Transporter Involved In B... 49 9e-07
pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Pro... 36 0.006
pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Pro... 36 0.006
pdb|1TRE|A Chain A, Triosephosphate Isomerase Tim (E.C.5.3.... 28 1.2
pdb|1PSD|A Chain A, D-3-Phosphoglycerate Dehydrogenase (Pho... 27 2.1
pdb|2AT2|A Chain A, Aspartate Transcarbamoylase (E.C.2.1.3.... 27 2.1
pdb|4UBP|C Chain C, Structure Of Bacillus Pasteurii Urease ... 27 2.7
pdb|3DAA|A Chain A, Crystallographic Structure Of D-Amino A... 27 2.7
pdb|1DAA|A Chain A, Crystallographic Structure Of D-Amino A... 27 2.7
pdb|5DAA|A Chain A, E177k Mutant Of D-Amino Acid Aminotrans... 27 2.7
pdb|1A0G|B Chain B, L201a Mutant Of D-Amino Acid Aminotrans... 27 2.7
pdb|1G2W|A Chain A, E177s Mutant Of The Pyridoxal-5'-Phosph... 27 2.7
pdb|2MYS|A Chain A, Myosin Subfragment-1, Alpha Carbon Coor... 26 4.6
pdb|1M8Q|A Chain A, Molecular Models Of Averaged Rigor Cros... 26 4.6
pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of... 25 7.9
pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bo... 25 7.9
pdb|1JXE| Stoffel Fragment Of Taq Dna Polymerase I >gi|67... 25 7.9
pdb|1PBV| Sec7 Domain Of The Exchange Factor Arno 25 7.9
pdb|1TAQ| Structure Of Taq Dna Polymerase 25 7.9
pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of... 25 7.9
pdb|1TAU|A Chain A, Structure Of Dna Polymerase 25 7.9
pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragm... 25 7.9
pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An ... 25 7.9
pdb|1G6O|A Chain A, Crystal Structure Of The Helicobacter P... 25 7.9
pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of... 25 7.9
>pdb|1B0U|A Chain A, Atp-Binding Subunit Of The Histidine Permease From
Salmonella Typhimurium
Length = 262
Score = 122 bits (306), Expect = 5e-29
Identities = 77/247 (31%), Positives = 139/247 (56%), Gaps = 18/247 (7%)
Query: 17 GVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLLQ 76
G ++ + GVS + + I+G SGSGKS T L + +EKP + G+I GQ++
Sbjct: 17 GGHEVLKGVSLQARAGDVISIIGSSGSGKS-TFLRCINFLEKPSE---GAIIVNGQNINL 72
Query: 77 LKEKQMQKEIRGK--------KIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPNLNKKER 128
+++K Q ++ K ++ M+FQ +L TV + E I L+K +
Sbjct: 73 VRDKDGQLKVADKNQLRLLRTRLTMVFQH--FNLWSHMTVLENVMEA-PIQVLGLSKHDA 129
Query: 129 LERVVYELERVGIPHAGDKYHEYPFNLSGGQRQRVMIAMAMVCEPEILIADEPTTALDVT 188
ER + L +VGI +YP +LSGGQ+QRV IA A+ EP++L+ DEPT+ALD
Sbjct: 130 RERALKYLAKVGIDERAQG--KYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPE 187
Query: 189 IQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQASAKELFADPRH 248
+ ++L +M++L + +G +++ +TH++G ++ V+ +++G + E+ +++F +P+
Sbjct: 188 LVGEVLRIMQQLAE-EGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQS 246
Query: 249 PYTKALL 255
P + L
Sbjct: 247 PRLQQFL 253
>pdb|1L2T|A Chain A, Dimeric Structure Of Mj0796, A Bacterial Abc Transporter
Cassette
pdb|1L2T|B Chain B, Dimeric Structure Of Mj0796, A Bacterial Abc Transporter
Cassette
Length = 235
Score = 99.0 bits (245), Expect = 6e-22
Identities = 70/234 (29%), Positives = 132/234 (55%), Gaps = 13/234 (5%)
Query: 2 ILEVKDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQ 61
++++K++ + + + A+ V+ +K+ + + I+G SGSGKS T L+I+G ++KP +
Sbjct: 1 MIKLKNVTKTYKMGEEIIYALKNVNLNIKEGEFVSIMGPSGSGKS-TMLNIIGCLDKPTE 59
Query: 62 IVGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHP 121
G + L + ++ K IR KIG +FQ+ +L P T + L +
Sbjct: 60 ---GEVYIDNIKTNDLDDDELTK-IRRDKIGFVFQQ--FNLIPLLTALENVELPLIFKYR 113
Query: 122 N-LNKKERLERVVYELERVGIPHAGDKYHEY-PFNLSGGQRQRVMIAMAMVCEPEILIAD 179
++ +ER +R LE + + +++ + P LSGGQ+QRV IA A+ P I++AD
Sbjct: 114 GAMSGEERRKRA---LECLKMAELEERFANHKPNQLSGGQQQRVAIARALANNPPIILAD 170
Query: 180 EPTTALDVTIQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHV 233
+PT ALD +I++L+K+L ++ G +++ +THD+ VA+ + ++ + G V
Sbjct: 171 QPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDIN-VARFGERIIYLKDGEV 223
>pdb|1F3O|A Chain A, Crystal Structure Of Mj0796 Atp-Binding Cassette
Length = 235
Score = 97.8 bits (242), Expect = 1e-21
Identities = 71/232 (30%), Positives = 124/232 (52%), Gaps = 11/232 (4%)
Query: 3 LEVKDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQI 62
+++K++ + + + A+ V+ +K+ + + I G SGSGKS T L+I+G ++KP +
Sbjct: 2 IKLKNVTKTYKXGEEIIYALKNVNLNIKEGEFVSIXGPSGSGKS-TXLNIIGCLDKPTE- 59
Query: 63 VGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPN 122
G + L + ++ K IR KIG +FQ+ +L P T + L +
Sbjct: 60 --GEVYIDNIKTNDLDDDELTK-IRRDKIGFVFQQ--FNLIPLLTALENVELPLIFKYRG 114
Query: 123 LNKKERLERVVYELERVGIPHAGDKYHEY-PFNLSGGQRQRVMIAMAMVCEPEILIADEP 181
E ER LE + +++ + P LSGGQ+QRV IA A+ P I++ADEP
Sbjct: 115 AXSGE--ERRKRALECLKXAELEERFANHKPNQLSGGQQQRVAIARALANNPPIILADEP 172
Query: 182 TTALDVTIQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHV 233
T ALD +I +L+K+L ++ G +++ +THD+ VA+ + ++ + G V
Sbjct: 173 TGALDSKTGEKIXQLLKKLNEEDGKTVVVVTHDIN-VARFGERIIYLKDGEV 223
>pdb|1G29|1 Chain 1, Malk
pdb|1G29|2 Chain 2, Malk
Length = 372
Score = 97.4 bits (241), Expect = 2e-21
Identities = 76/267 (28%), Positives = 135/267 (50%), Gaps = 18/267 (6%)
Query: 21 AVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKP-GQIVGGSIQFLGQDLLQLKE 79
AV +S +K + + ++G SG GK+ T I GL E GQI ++G L+ E
Sbjct: 18 AVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI------YIGDKLVADPE 71
Query: 80 KQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERV 139
K + + + I M+FQ +L P TV I LK+ + ++E +RV E +
Sbjct: 72 KGIFVPPKDRDIAMVFQS--YALYPHMTVYDNIAFPLKLR--KVPRQEIDQRVREVAELL 127
Query: 140 GIPHAGDKYHEYPFNLSGGQRQRVMIAMAMVCEPEILIADEPTTALDVTIQAQILELMKE 199
G+ + + P LSGGQRQRV + A+V +P++ + DEP + LD ++ ++ +K+
Sbjct: 128 GLT---ELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKK 184
Query: 200 LQQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQASAKELFADPRHPYTKALLSAIP 259
LQ++ G + +++THD + D + VM +G + + S E++ P + + + + P
Sbjct: 185 LQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSPP 244
Query: 260 KPGKEYRKKRLETVDENVDYLSFQKEL 286
+ + T D VD+ F+ +L
Sbjct: 245 MNFLD----AIVTEDGFVDFGEFRLKL 267
>pdb|1JJ7|A Chain A, Crystal Structure Of The C-Terminal Atpase Domain Of Human
Tap1
Length = 260
Score = 81.3 bits (199), Expect = 1e-16
Identities = 63/229 (27%), Positives = 112/229 (48%), Gaps = 28/229 (12%)
Query: 22 VDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLLQLKEKQ 81
+ G++F L+ + +VG +GSGKS ++ L++ Q GG + G+ L Q + +
Sbjct: 33 LQGLTFTLRPGEVTALVGPNGSGKS----TVAALLQNLYQPTGGQLLLDGKPLPQYEHRY 88
Query: 82 MQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERVG- 140
+ +++ + QEP G + E + L +K +E + + G
Sbjct: 89 LHRQVAA-----VGQEPQV-------FGRSLQENIAY---GLTQKPTMEEITAAAVKSGA 133
Query: 141 ------IPHAGD-KYHEYPFNLSGGQRQRVMIAMAMVCEPEILIADEPTTALDVTIQAQI 193
+P D + E LSGGQRQ V +A A++ +P +LI D+ T+ALD Q Q+
Sbjct: 134 HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV 193
Query: 194 LELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQASAKEL 242
+L+ E ++ S+L IT L +V Q AD ++ + G + E + ++L
Sbjct: 194 EQLLYESPERYSRSVLLITQHLSLVEQ-ADHILFLEGGAIREGGTHQQL 241
>pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformation Of Mj1267, An
Atp- Binding Cassette Of An Abc Transporter
Length = 257
Score = 76.6 bits (187), Expect = 3e-15
Identities = 69/260 (26%), Positives = 113/260 (42%), Gaps = 31/260 (11%)
Query: 2 ILEVKDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQ 61
IL +++ YF G KA+DGVS + K I+G +GSGKS I G ++
Sbjct: 7 ILRTENIVKYF----GEFKALDGVSISVNKGDVTLIIGPNGSGKSTLINVITGFLKAD-- 60
Query: 62 IVGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHP 121
G + F +D+ + E+ I FQ P + I E+ P
Sbjct: 61 --EGRVYFENKDI----TNKEPAELYHYGIVRTFQTPQPLKEMTVLENLLIGEICPGESP 114
Query: 122 NLN----------KKERLERVVYELERVGIPHAGDKYHEYPFNLSGGQRQRVMIAMAMVC 171
LN ++E +E+ LE + + H Y LSGGQ + V I A++
Sbjct: 115 -LNSLFYKKWIPKEEEMVEKAFKILEFLKLSHL---YDRKAGELSGGQMKLVEIGRALMT 170
Query: 172 EPEILIADEPTTALDVTIQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKG 231
P++++ DEP + + I + EL + KG + L I H L +V D + VM+ G
Sbjct: 171 NPKMIVMDEPIAGVAPGLAHDIFNHVLEL-KAKGITFLIIEHRLDIVLNYIDHLYVMFNG 229
Query: 232 HVVEQASAKE----LFADPR 247
++ + +E + +DP+
Sbjct: 230 QIIAEGRGEEEIKNVLSDPK 249
>pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free Atp-Binding
Cassette From An Abc Transporter
Length = 257
Score = 74.7 bits (182), Expect = 1e-14
Identities = 68/260 (26%), Positives = 113/260 (43%), Gaps = 31/260 (11%)
Query: 2 ILEVKDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQ 61
IL +++ YF G KA+DGVS + K I+G +GSGKS I G ++
Sbjct: 7 ILRTENIVKYF----GEFKALDGVSISVNKGDVTLIIGPNGSGKSTLINVITGFLKAD-- 60
Query: 62 IVGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHP 121
G + F +D+ + E+ I FQ P + I E+ P
Sbjct: 61 --EGRVYFENKDI----TNKEPAELYHYGIVRTFQTPQPLKEMTVLENLLIGEINPGESP 114
Query: 122 NLN----------KKERLERVVYELERVGIPHAGDKYHEYPFNLSGGQRQRVMIAMAMVC 171
LN ++E +E+ LE + + H Y LSGGQ + V I A++
Sbjct: 115 -LNSLFYKKWIPKEEEMVEKAFKILEFLKLSHL---YDRKAGELSGGQMKLVEIGRALMT 170
Query: 172 EPEILIADEPTTALDVTIQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKG 231
P++++ D+P + + I + EL + KG + L I H L +V D + VM+ G
Sbjct: 171 NPKMIVMDQPIAGVAPGLAHDIFNHVLEL-KAKGITFLIIEHRLDIVLNYIDHLYVMFNG 229
Query: 232 HVVEQASAKE----LFADPR 247
++ + +E + +DP+
Sbjct: 230 QIIAEGRGEEEIKNVLSDPK 249
>pdb|1JI0|A Chain A, Crystal Structure Analysis Of The Abc Transporter From
Thermotoga Maritima
Length = 240
Score = 74.7 bits (182), Expect = 1e-14
Identities = 62/244 (25%), Positives = 115/244 (46%), Gaps = 24/244 (9%)
Query: 1 MILEVKDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPG 60
++LEV+ L Y+ G A+ G+ + + Q + ++G +G+GK+ T +I GL+
Sbjct: 5 IVLEVQSLHVYY----GAIHAIKGIDLKVPRGQIVTLIGANGAGKTTTLSAIAGLVRAQK 60
Query: 61 QIVGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHH 120
G I F GQD+ + + G+ + P TV E L
Sbjct: 61 ----GKIIFNGQDITNKPAHVINRX------GIALVPEGRRIFPELTV----YENLXXGA 106
Query: 121 PNLNKKERLERVVYELERVG--IPHAGDKYHEYPFNLSGGQRQRVMIAMAMVCEPEILIA 178
N KE ++R +LE + P ++ + LSGG++Q + I A+ P++L
Sbjct: 107 YNRKDKEGIKR---DLEWIFSLFPRLKERLKQLGGTLSGGEQQXLAIGRALXSRPKLLXX 163
Query: 179 DEPTTALDVTIQAQILELMKELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQAS 238
DEP+ L + +++ E+++++ Q +GT+IL + + ++A V+ G +V +
Sbjct: 164 DEPSLGLAPILVSEVFEVIQKINQ-EGTTILLVEQNALGALKVAHYGYVLETGQIVLEGK 222
Query: 239 AKEL 242
A EL
Sbjct: 223 ASEL 226
>pdb|1JSQ|A Chain A, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|B Chain B, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|C Chain C, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|D Chain D, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|E Chain E, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|F Chain F, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|G Chain G, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
pdb|1JSQ|H Chain H, Structure Of Msba From Escherichia Coli: A Homolog Of The
Multidrug Resistance Atp Binding Cassette (Abc)
Transporters
Length = 582
Score = 72.4 bits (176), Expect = 6e-14
Identities = 65/224 (29%), Positives = 104/224 (46%), Gaps = 18/224 (8%)
Query: 21 AVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLLQLKEK 80
A+ ++ + +T+ +VG SGSGKS +I LI + I G I G DL +
Sbjct: 358 ALRNINLKIPAGKTVALVGRSGSGKS----TIASLITRFYDIDEGEILMDGHDLREYTLA 413
Query: 81 QMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERVG 140
++ ++ + + N +Y Q + + E R+ Y ++ +
Sbjct: 414 SLRNQVALVSQNVHLFNDTVANNIAYARTEQYSR---------EQIEEAARMAYAMDFIN 464
Query: 141 IPHAG--DKYHEYPFNLSGGQRQRVMIAMAMVCEPEILIADEPTTALDVTIQAQILELMK 198
G E LSGGQRQR+ IA A++ + ILI DE T+ALD + I +
Sbjct: 465 KMDNGLDTVIGENGVLLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALD 524
Query: 199 ELQQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQASAKEL 242
ELQ K + L I H L + + ADE+VV+ G +VE+ + +L
Sbjct: 525 ELQ--KNRTSLVIAHRLSTIEK-ADEIVVVEDGVIVERGTHNDL 565
>pdb|1L7V|C Chain C, Bacterial Abc Transporter Involved In B12 Uptake
pdb|1L7V|D Chain D, Bacterial Abc Transporter Involved In B12 Uptake
Length = 249
Score = 48.5 bits (114), Expect = 9e-07
Identities = 57/226 (25%), Positives = 95/226 (41%), Gaps = 32/226 (14%)
Query: 29 LKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVG-GSIQFLGQDLLQLKEKQMQKEIR 87
++ + L +VG +G+GKS L G G GSIQF GQ L E ++
Sbjct: 23 VRAGEILHLVGPNGAGKSTL------LARXAGXTSGKGSIQFAGQPL----EAWSATKLA 72
Query: 88 GKKIGMIFQEPMTSLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERVGIPHAGDK 147
+ + Q+ P + L +H + + E L V G DK
Sbjct: 73 LHRAYLSQQQTPPFATPVW-------HYLTLHQHDKTRTELLNDVA------GALALDDK 119
Query: 148 YHEYPFNLSGGQRQRVMIAMAMV-----CEP--EILIADEPTTALDVTIQAQILELMKEL 200
LSGG+ QRV +A ++ P ++L+ DEP +LDV Q+ + +++ L
Sbjct: 120 LGRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDEPXNSLDVAQQSALDKILSAL 179
Query: 201 QQKKGTSILFITHDLGVVAQIADEVVVMYKGHVVEQASAKELFADP 246
Q +G +I+ +HDL + A ++ G + +E+ P
Sbjct: 180 CQ-QGLAIVXSSHDLNHTLRHAHRAWLLKGGKXLASGRREEVLTPP 224
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 35.8 bits (81), Expect = 0.006
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 16 KGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLL 75
+ + K VDG+ G+K QTL +G +G+GK+ T +++ + KP ++ + GQ
Sbjct: 19 QAIAKLVDGLRRGVKH-QTL--LGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYS 75
Query: 76 QLKE 79
+LKE
Sbjct: 76 ELKE 79
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 35.8 bits (81), Expect = 0.006
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 16 KGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLL 75
+ + K VDG+ G+K QTL +G +G+GK+ T +++ + KP ++ + GQ
Sbjct: 19 QAIAKLVDGLRRGVKH-QTL--LGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYS 75
Query: 76 QLKE 79
+LKE
Sbjct: 76 ELKE 79
>pdb|1TRE|A Chain A, Triosephosphate Isomerase Tim (E.C.5.3.1.1)
pdb|1TRE|B Chain B, Triosephosphate Isomerase Tim (E.C.5.3.1.1)
Length = 255
Score = 28.1 bits (61), Expect = 1.2
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 213 HDLGVVAQIADEVVVMYKGHVVEQASAKELFADP 246
H V A IA++V++ Y G V ++A ELFA P
Sbjct: 193 HIAKVDANIAEQVIIQYGGSV-NASNAAELFAQP 225
>pdb|1PSD|A Chain A, D-3-Phosphoglycerate Dehydrogenase (Phosphoglycerate
Dehydrogenase) (E.C.1.1.1.95)
pdb|1PSD|B Chain B, D-3-Phosphoglycerate Dehydrogenase (Phosphoglycerate
Dehydrogenase) (E.C.1.1.1.95)
Length = 409
Score = 27.3 bits (59), Expect = 2.1
Identities = 29/130 (22%), Positives = 56/130 (42%), Gaps = 8/130 (6%)
Query: 38 VGESGSGKSITSLSILGLIEKPGQIVGGSIQFLGQDLLQLKEKQMQKEIRGKKIGMIFQE 97
V E+ S K++ + L+ KPG ++ + + D+ L + K + G I + E
Sbjct: 210 VPENPSTKNMMGAKEISLM-KPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTE 268
Query: 98 PMTSLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERVGIPHAGD-------KYHE 150
P T+ +P + + + VL H + +E E + E+ I ++ + + E
Sbjct: 269 PATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPE 328
Query: 151 YPFNLSGGQR 160
L GG+R
Sbjct: 329 VSLPLHGGRR 338
>pdb|2AT2|A Chain A, Aspartate Transcarbamoylase (E.C.2.1.3.2) (Aspartate
Carbamoyltransferase)
pdb|2AT2|B Chain B, Aspartate Transcarbamoylase (E.C.2.1.3.2) (Aspartate
Carbamoyltransferase)
pdb|2AT2|C Chain C, Aspartate Transcarbamoylase (E.C.2.1.3.2) (Aspartate
Carbamoyltransferase)
Length = 300
Score = 27.3 bits (59), Expect = 2.1
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 13/92 (14%)
Query: 72 QDLLQ----LKEKQMQKEIRGKKIGMIFQEPMTSLNPSYTVGFQI--NEVLKIH--HPNL 123
+DLLQ LK + ++ GK +F EP T S+ V + VL + ++
Sbjct: 16 KDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSV 75
Query: 124 NKKERLERVVYELERVG-----IPHAGDKYHE 150
K E L + LE +G I H+ D+Y+E
Sbjct: 76 QKGETLYDTIRTLESIGVDVCVIRHSEDEYYE 107
>pdb|4UBP|C Chain C, Structure Of Bacillus Pasteurii Urease Inhibited With
Acetohydroxamic Acid At 1.55 A Resolution
pdb|1UBP|C Chain C, Crystal Structure Of Urease From Bacillus Pasteurii
Inhibited With Beta-Mercaptoethanol At 1.65 Angstroms
Resolution
pdb|2UBP|C Chain C, Structure Of Native Urease From Bacillus Pasteurii
pdb|3UBP|C Chain C, Diamidophosphate Inhibited Bacillus Pasteurii Urease
Length = 570
Score = 26.9 bits (58), Expect = 2.7
Identities = 31/146 (21%), Positives = 57/146 (38%), Gaps = 27/146 (18%)
Query: 101 SLNPSYTVGFQINEVLKIHHPNLNKKERLERVVYELERVGIPHAGDKYHEYPFNLSGGQR 160
S++ S TV + + + IH LN+ LE + + G H + +GG
Sbjct: 231 SIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAIN-------GRVIHSFHVEGAGGGH 283
Query: 161 QRVMIAMAMVCEPEILIAD----EPTTALDVTIQAQILELMKELQQKKGTSILF------ 210
++AMA P +L + P T + +L + L+Q + F
Sbjct: 284 APDIMAMAG--HPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIR 341
Query: 211 --------ITHDLGVVAQIADEVVVM 228
I HDLG+++ ++ + + M
Sbjct: 342 PETIAAEDILHDLGIISMMSTDALAM 367
>pdb|3DAA|A Chain A, Crystallographic Structure Of D-Amino Acid
Aminotransferase Inactivated By Pyridoxyl-D-Alanine
pdb|3DAA|B Chain B, Crystallographic Structure Of D-Amino Acid
Aminotransferase Inactivated By Pyridoxyl-D-Alanine
pdb|4DAA|A Chain A, Crystallographic Structure Of D-Amino Acid
Aminotransferase In Pyridoxal-5'-Phosphate (Plp) Form
pdb|4DAA|B Chain B, Crystallographic Structure Of D-Amino Acid
Aminotransferase In Pyridoxal-5'-Phosphate (Plp) Form
Length = 277
Score = 26.9 bits (58), Expect = 2.7
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 106 YTVGFQINEVLKIHHPNL-NKKERLERVVYELE--RVGIPHAGDKYHE 150
Y G + EV+K+++ + E ++R+ E R+ IP+ DK+H+
Sbjct: 24 YQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQ 71
>pdb|1DAA|A Chain A, Crystallographic Structure Of D-Amino Acid
Aminotransferase Complexed With Pyridoxal-5'-Phosphate
pdb|1DAA|B Chain B, Crystallographic Structure Of D-Amino Acid
Aminotransferase Complexed With Pyridoxal-5'-Phosphate
pdb|2DAA|A Chain A, Crystallographic Structure Of D-Amino Acid
Aminotransferase Inactivated By D-Cycloserine
pdb|2DAA|B Chain B, Crystallographic Structure Of D-Amino Acid
Aminotransferase Inactivated By D-Cycloserine
Length = 282
Score = 26.9 bits (58), Expect = 2.7
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 106 YTVGFQINEVLKIHHPNL-NKKERLERVVYELE--RVGIPHAGDKYHE 150
Y G + EV+K+++ + E ++R+ E R+ IP+ DK+H+
Sbjct: 24 YQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQ 71
>pdb|5DAA|A Chain A, E177k Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxamine-5'-Phosphate
pdb|5DAA|B Chain B, E177k Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxamine-5'-Phosphate
Length = 277
Score = 26.9 bits (58), Expect = 2.7
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 106 YTVGFQINEVLKIHHPNL-NKKERLERVVYELE--RVGIPHAGDKYHE 150
Y G + EV+K+++ + E ++R+ E R+ IP+ DK+H+
Sbjct: 24 YQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQ 71
>pdb|1A0G|B Chain B, L201a Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxamine-5'-Phosphate
pdb|2DAB|B Chain B, L201a Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxal-5'-Phosphate
pdb|1A0G|A Chain A, L201a Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxamine-5'-Phosphate
pdb|2DAB|A Chain A, L201a Mutant Of D-Amino Acid Aminotransferase Complexed
With Pyridoxal-5'-Phosphate
Length = 282
Score = 26.9 bits (58), Expect = 2.7
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 106 YTVGFQINEVLKIHHPNL-NKKERLERVVYELE--RVGIPHAGDKYHE 150
Y G + EV+K+++ + E ++R+ E R+ IP+ DK+H+
Sbjct: 24 YQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQ 71
>pdb|1G2W|A Chain A, E177s Mutant Of The Pyridoxal-5'-Phosphate Enzyme D-Amino
Acid Aminotransferase
pdb|1G2W|B Chain B, E177s Mutant Of The Pyridoxal-5'-Phosphate Enzyme D-Amino
Acid Aminotransferase
Length = 282
Score = 26.9 bits (58), Expect = 2.7
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 106 YTVGFQINEVLKIHHPNL-NKKERLERVVYELE--RVGIPHAGDKYHE 150
Y G + EV+K+++ + E ++R+ E R+ IP+ DK+H+
Sbjct: 24 YQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQ 71
>pdb|2MYS|A Chain A, Myosin Subfragment-1, Alpha Carbon Coordinates Only For
The Two Light Chains
Length = 843
Score = 26.2 bits (56), Expect = 4.6
Identities = 8/24 (33%), Positives = 19/24 (78%)
Query: 30 KKSQTLCIVGESGSGKSITSLSIL 53
+++Q++ I GESG+GK++ + ++
Sbjct: 170 RENQSILITGESGAGKTVNTXRVI 193
>pdb|1M8Q|A Chain A, Molecular Models Of Averaged Rigor Crossbridges From
Tomograms Of Insect Flight Muscle
pdb|1M8Q|D Chain D, Molecular Models Of Averaged Rigor Crossbridges From
Tomograms Of Insect Flight Muscle
pdb|1M8Q|G Chain G, Molecular Models Of Averaged Rigor Crossbridges From
Tomograms Of Insect Flight Muscle
pdb|1M8Q|P Chain P, Molecular Models Of Averaged Rigor Crossbridges From
Tomograms Of Insect Flight Muscle
Length = 840
Score = 26.2 bits (56), Expect = 4.6
Identities = 8/24 (33%), Positives = 19/24 (78%)
Query: 30 KKSQTLCIVGESGSGKSITSLSIL 53
+++Q++ I GESG+GK++ + ++
Sbjct: 167 RENQSILITGESGAGKTVNTXRVI 190
>pdb|1QTM|A Chain A, Ddttp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 188 HPFNLNSRDQLERVLF--DELGLPAIG 212
>pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bound To Dctp
pdb|1KTQ| Dna Polymerase
Length = 543
Score = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 191 HPFNLNSRDQLERVLF--DELGLPAIG 215
>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 = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 188 HPFNLNSRDQLERVLF--DELGLPAIG 212
>pdb|1PBV| Sec7 Domain Of The Exchange Factor Arno
Length = 195
Score = 25.4 bits (54), Expect = 7.9
Identities = 32/153 (20%), Positives = 63/153 (40%), Gaps = 15/153 (9%)
Query: 6 KDLKTYFFTDKGVNKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIVGG 65
+++ + + +G+NK G G ++ L ++ T L+++ +
Sbjct: 43 EEIARFLYKGEGLNKTAIGDYLGEREELNLAVLHAFVDLHEFTDLNLVQALR-------- 94
Query: 66 SIQFLGQDLLQLKEKQMQK--EIRGKKIGMIFQEPMTSLNPSYTVGFQINEV-LKIHHPN 122
QFL L + +++ + E ++ + S + Y + F + + +H+PN
Sbjct: 95 --QFLWSFRLPGEAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSFAVIMLNTSLHNPN 152
Query: 123 LNKKERLERVVYELERVGIPHAGDKYHEYPFNL 155
+ K LER V + R GI GD E NL
Sbjct: 153 VRDKPGLERFV-AMNR-GINEGGDLPEELLRNL 183
>pdb|1TAQ| Structure Of Taq Dna Polymerase
Length = 832
Score = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 480 HPFNLNSRDQLERVLF--DELGLPAIG 504
>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 = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 188 HPFNLNSRDQLERVLF--DELGLPAIG 212
>pdb|1TAU|A Chain A, Structure Of Dna Polymerase
Length = 832
Score = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 480 HPFNLNSRDQLERVLF--DELGLPAIG 504
>pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus
Length = 538
Score = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 186 HPFNLNSRDQLERVLF--DELGLPAIG 210
>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 = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 480 HPFNLNSRDQLERVLF--DELGLPAIG 504
>pdb|1G6O|A Chain A, Crystal Structure Of The Helicobacter Pylori Atpase,
Hp0525, In Complex With Adp
pdb|1G6O|B Chain B, Crystal Structure Of The Helicobacter Pylori Atpase,
Hp0525, In Complex With Adp
Length = 330
Score = 25.4 bits (54), Expect = 7.9
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 12 FFTDKGV-------NKAVDGVSFGLKKSQTLCIVGESGSGKSITSLSILGLIEKPGQIV 63
FF ++G +A+ + G+ + + + G +GSGK+ SI I K +I+
Sbjct: 144 FFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIXEFIPKEERII 202
>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 = 25.4 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 20/27 (73%), Gaps = 3/27 (11%)
Query: 120 HP-NLNKKERLERVVYELERVGIPHAG 145
HP NLN +++LERV++ + +G+P G
Sbjct: 187 HPFNLNSRDQLERVLF--DELGLPAIG 211
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
0.318 0.137 0.379
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,601,825
Number of Sequences: 13198
Number of extensions: 63229
Number of successful extensions: 233
Number of sequences better than 10.0: 34
Number of HSP's better than 10.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 34
length of query: 287
length of database: 2,899,336
effective HSP length: 87
effective length of query: 200
effective length of database: 1,751,110
effective search space: 350222000
effective search space used: 350222000
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)