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|15646131|ref|NP_208313.1| DNA recombinase (recG)
[Helicobacter pylori 26695]
(623 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|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dn... 248 2e-66
pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Pro... 40 0.001
pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Pro... 40 0.001
pdb|1M6N|A Chain A, Crystal Structure Of The Seca Transloca... 37 0.009
pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb... 32 0.27
pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide... 32 0.27
pdb|1FYX|A Chain A, Crystal Structure Of P681h Mutant Of Ti... 30 1.0
pdb|1J96|A Chain A, Human 3alpha-Hsd Type 3 In Ternary Comp... 29 1.8
pdb|1IHI|A Chain A, Crystal Structure Of Human Type Iii 3-A... 29 1.8
pdb|1GWN|C Chain C, The Crystal Structure Of The Core Domai... 27 5.2
pdb|1DQ3|A Chain A, Crystal Structure Of An Archaeal Intein... 27 5.2
pdb|1CXZ|A Chain A, Crystal Structure Of Human Rhoa Complex... 27 6.8
pdb|1DPF|A Chain A, Crystal Structure Of A Mg-Free Form Of ... 27 6.8
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 248 bits (632), Expect = 2e-66
Identities = 207/637 (32%), Positives = 318/637 (49%), Gaps = 43/637 (6%)
Query: 8 LKTLNVKSLLEALLVYTPKGYKDLNLLERFETGLSGVL-----EVGILEKRNYAKVLKIF 62
LK L +++L + LL + P+ Y+D + + L G ++ +E + + + +
Sbjct: 131 LKKLGIETLRD-LLEFFPRDYEDRRKIFKLNDLLPGEKVTTQGKIVSVETKKFQNMNILT 189
Query: 63 AYSKRFYKNLELVFFNYSAFH-HSQFKTGESLFIYGKLEQSSFNQAYIINTPKIITKFG- 120
A ++ L +FN + + TG+ +F+ G ++ +++ Y I+ ++ K G
Sbjct: 190 AVLSDGLVHVPLKWFNQDYLQTYLKQLTGKEVFVTGTVKSNAYTGQYEIHNAEVTPKEGE 249
Query: 121 ---KISLIFKKV-----KNHKKI-QENLQKLI-SLENLKKEGVKENIAHLLLEIFFPTPH 170
+I I++ K +KI +EN+ L SL+ E + E L ++ + H
Sbjct: 250 YVRRILPIYRLTSGISQKQMRKIFEENIPSLCCSLKETLPERILEKRKLLGVKDAYYGMH 309
Query: 171 FVKDF-ETNKNFPSQHLNALKYIEMLFYMKNLERKKLQFGAKIACPNNNERLKAFIASLP 229
F K F K L +++ F ER+K I + + FI SLP
Sbjct: 310 FPKTFYHLEKARERLAYEELFVLQLAFQKIRKEREK---HGGIPKKIEGKLAEEFIKSLP 366
Query: 230 FKLTRDQQNAIKEIQNDLTSSIACKRLIIGDVGCGKTMVILASMVLTYPN--KTLLMAPT 287
FKLT Q+ A +EI+ND+ S RL+ GDVG GKT+V +++ Y +T M PT
Sbjct: 367 FKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPT 426
Query: 288 SILAKQLYNEALKFLPPY-FEVELLLGGSYKKRSNHLFETITH----VVIGTQALLFDKR 342
SILA Q Y ++ + V LL+G + + + + VVIGT AL+ +
Sbjct: 427 SILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDV 486
Query: 343 DLNEFALVITDEQHRFGTKQRYQLEKMASSKGNKPHSLQFSATPIPRTLALAKSAFVKTT 402
LVI DEQHRFG KQR L +KG +L SATPIPR++ALA + T
Sbjct: 487 HFKNLGLVIIDEQHRFGVKQREAL----MNKGKMVDTLVMSATPIPRSMALAFYGDLDVT 542
Query: 403 MIREIPYP-KEIETLVLHKRDFKIVMEKISEEIAKNHQVIVVYPLVNESEKIPYLSLSEG 461
+I E+P KE++T+++ V E + +E+ + Q +VYPL+ ES+K+ S E
Sbjct: 543 VIDEMPPGRKEVQTMLVPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEM 602
Query: 462 ASFWQKRFK---KVYTTSGQ--DKNKEEVIEEFRESG-SILLATTLIEVGISLPRLSVMV 515
+ K K+ G+ + K+ V+ EF E IL++TT+IEVGI +PR +VMV
Sbjct: 603 YEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMV 662
Query: 516 ILAPERLGLATLHQLRGRVSRNGLKGYCFLC---TIQEENERLEKFADELDGFKIAELDL 572
I PER GLA LHQLRGRV R G + YCFL +E ERL F DGFKIAE DL
Sbjct: 663 IENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGFKIAEYDL 722
Query: 573 EYRKSGDLLQGGEQSGNSFEYIDLAKDENIIAEVKRD 609
+ R G+ + + F+ DL +D ++ + D
Sbjct: 723 KTRGPGEFFGVKQHGLSGFKVADLYRDLKLLEWARED 759
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 39.7 bits (91), Expect = 0.001
Identities = 36/130 (27%), Positives = 62/130 (47%), Gaps = 17/130 (13%)
Query: 229 PFKLTRDQQNAIKEIQNDLTSSIACKRLIIGDVGCGKTMVILASMVLTYPNK-TLLMAPT 287
P++ DQ AI ++ + L + + L+ G G GKT I S V+ NK TL++A
Sbjct: 10 PYEPQGDQPQAIAKLVDGLRRGVKHQTLL-GATGTGKTFTI--SNVIAQVNKPTLVIAHN 66
Query: 288 SILAKQLYNEALKFLP-----------PYFEVELLL--GGSYKKRSNHLFETITHVVIGT 334
LA QLY+E +F P Y++ E + +Y ++ + + I +
Sbjct: 67 KTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSA 126
Query: 335 QALLFDKRDL 344
+ LF++RD+
Sbjct: 127 TSALFERRDV 136
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 39.7 bits (91), Expect = 0.001
Identities = 36/130 (27%), Positives = 62/130 (47%), Gaps = 17/130 (13%)
Query: 229 PFKLTRDQQNAIKEIQNDLTSSIACKRLIIGDVGCGKTMVILASMVLTYPNK-TLLMAPT 287
P++ DQ AI ++ + L + + L+ G G GKT I S V+ NK TL++A
Sbjct: 10 PYEPQGDQPQAIAKLVDGLRRGVKHQTLL-GATGTGKTFTI--SNVIAQVNKPTLVIAHN 66
Query: 288 SILAKQLYNEALKFLP-----------PYFEVELLL--GGSYKKRSNHLFETITHVVIGT 334
LA QLY+E +F P Y++ E + +Y ++ + + I +
Sbjct: 67 KTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSA 126
Query: 335 QALLFDKRDL 344
+ LF++RD+
Sbjct: 127 TSALFERRDV 136
>pdb|1M6N|A Chain A, Crystal Structure Of The Seca Translocation Atpase From
Bacillus Subtilis
pdb|1M74|A Chain A, Crystal Structure Of Mg-Adp-Bound Seca From Bacillus
Subtilis
Length = 802
Score = 36.6 bits (83), Expect = 0.009
Identities = 36/146 (24%), Positives = 63/146 (42%), Gaps = 15/146 (10%)
Query: 423 FKIVMEKISEEIAKNHQVIVVYPLVNESEKIPYLSLSEGASFWQKRFKKVYTTSGQDKNK 482
FK V E +++ V+V V SE I L ++G K + +
Sbjct: 415 FKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKN-------HERE 467
Query: 483 EEVIEEFRESGSILLATTL------IEVGISLPRLSVMVILAPERLGLATL-HQLRGRVS 535
++IEE + G++ +AT + I++G + L + ++ ER + +QLRGR
Sbjct: 468 AQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSG 527
Query: 536 RNGLKGYCFLCTIQEENERLEKFADE 561
R G G + E+E + +F E
Sbjct: 528 RQGDPGITQF-YLSMEDELMRRFGAE 552
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 31.6 bits (70), Expect = 0.27
Identities = 33/135 (24%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 257 IIGDVGCGKTMVILASMVLTYPNKTLLMAPTSILAKQLYNEALKFLP-----------PY 305
++G G GKT V +A ++ L++AP ILA QL E + P Y
Sbjct: 34 LLGATGTGKT-VTMAKVIEALGRPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDY 92
Query: 306 FEVELLLGGS--YKKRSNHLFETITHVVIGTQALLFDKRDLNEFALVITDEQHRFGTKQR 363
++ E + G Y ++ + I + T L +RD+ A V + G +
Sbjct: 93 YQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASV--SAIYGLGDPRE 150
Query: 364 YQLEKMASSKGNKPH 378
Y+ + +G KP+
Sbjct: 151 YRARNLVVERG-KPY 164
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 31.6 bits (70), Expect = 0.27
Identities = 33/135 (24%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 257 IIGDVGCGKTMVILASMVLTYPNKTLLMAPTSILAKQLYNEALKFLP-----------PY 305
++G G GKT V +A ++ L++AP ILA QL E + P Y
Sbjct: 33 LLGATGTGKT-VTMAKVIEALGRPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDY 91
Query: 306 FEVELLLGGS--YKKRSNHLFETITHVVIGTQALLFDKRDLNEFALVITDEQHRFGTKQR 363
++ E + G Y ++ + I + T L +RD+ A V + G +
Sbjct: 92 YQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASV--SAIYGLGDPRE 149
Query: 364 YQLEKMASSKGNKPH 378
Y+ + +G KP+
Sbjct: 150 YRARNLVVERG-KPY 163
>pdb|1FYX|A Chain A, Crystal Structure Of P681h Mutant Of Tir Domain Of Human
Tlr2
Length = 149
Score = 29.6 bits (65), Expect = 1.0
Identities = 16/49 (32%), Positives = 28/49 (56%), Gaps = 3/49 (6%)
Query: 398 FVKTTMIREIPYPKEIETLVLHKRDF---KIVMEKISEEIAKNHQVIVV 443
+V+ M++E+ L LHKRDF K +++ I + I K+H+ + V
Sbjct: 19 WVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTVFV 67
>pdb|1J96|A Chain A, Human 3alpha-Hsd Type 3 In Ternary Complex With Nadp And
Testosterone
pdb|1J96|B Chain B, Human 3alpha-Hsd Type 3 In Ternary Complex With Nadp And
Testosterone
Length = 323
Score = 28.9 bits (63), Expect = 1.8
Identities = 15/52 (28%), Positives = 30/52 (56%), Gaps = 4/52 (7%)
Query: 124 LIFKKVKNHKKIQENLQ----KLISLENLKKEGVKENIAHLLLEIFFPTPHF 171
++ K N ++I++N+Q +L S E +G+ N+ +L L+IF P++
Sbjct: 266 VVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNY 317
>pdb|1IHI|A Chain A, Crystal Structure Of Human Type Iii 3-Alpha-Hydroxysteroid
DehydrogenaseBILE ACID BINDING PROTEIN (AKR1C2)
COMPLEXED With Nadp+ And Ursodeoxycholate
pdb|1IHI|B Chain B, Crystal Structure Of Human Type Iii 3-Alpha-Hydroxysteroid
DehydrogenaseBILE ACID BINDING PROTEIN (AKR1C2)
COMPLEXED With Nadp+ And Ursodeoxycholate
Length = 323
Score = 28.9 bits (63), Expect = 1.8
Identities = 15/52 (28%), Positives = 30/52 (56%), Gaps = 4/52 (7%)
Query: 124 LIFKKVKNHKKIQENLQ----KLISLENLKKEGVKENIAHLLLEIFFPTPHF 171
++ K N ++I++N+Q +L S E +G+ N+ +L L+IF P++
Sbjct: 266 VVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNY 317
>pdb|1GWN|C Chain C, The Crystal Structure Of The Core Domain Of RhoeRND3 - A
Constitutively Activated Small G Protein
pdb|1GWN|A Chain A, The Crystal Structure Of The Core Domain Of RhoeRND3 - A
Constitutively Activated Small G Protein
Length = 205
Score = 27.3 bits (59), Expect = 5.2
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 246 DLTSSIACKRLIIGDVGCGKTMVI 269
D ++ CK +++GD CGKT ++
Sbjct: 22 DPNQNVKCKIVVVGDSQCGKTALL 45
>pdb|1DQ3|A Chain A, Crystal Structure Of An Archaeal Intein-Encoded Homing
Endonuclease Pi-Pfui
Length = 454
Score = 27.3 bits (59), Expect = 5.2
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 565 FKIAELDLEYRKSGDLLQGGEQSGNSFEYI 594
FKI E + K GD+L GG G +++I
Sbjct: 108 FKIVEKRADELKEGDILIGGMPDGEDYKFI 137
>pdb|1CXZ|A Chain A, Crystal Structure Of Human Rhoa Complexed With The
Effector Domain Of The Protein Kinase PknPRK1
pdb|1A2B| Human Rhoa Complexed With Gtp Analogue
Length = 182
Score = 26.9 bits (58), Expect = 6.8
Identities = 10/22 (45%), Positives = 17/22 (76%)
Query: 249 SSIACKRLIIGDVGCGKTMVIL 270
++I K +I+GDV CGKT +++
Sbjct: 3 AAIRKKLVIVGDVACGKTCLLI 24
>pdb|1DPF|A Chain A, Crystal Structure Of A Mg-Free Form Of Rhoa Complexed With
Gdp
Length = 180
Score = 26.9 bits (58), Expect = 6.8
Identities = 10/22 (45%), Positives = 17/22 (76%)
Query: 249 SSIACKRLIIGDVGCGKTMVIL 270
++I K +I+GDV CGKT +++
Sbjct: 2 AAIRKKLVIVGDVACGKTCLLI 23
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 0.137 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: 3,310,030
Number of Sequences: 13198
Number of extensions: 134222
Number of successful extensions: 303
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 13
length of query: 623
length of database: 2,899,336
effective HSP length: 94
effective length of query: 529
effective length of database: 1,658,724
effective search space: 877464996
effective search space used: 877464996
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)