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|15645501|ref|NP_207676.1| Holliday junction DNA
helicase (ruvA) [Helicobacter pylori 26695]
(183 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|1C7Y|A Chain A, E.Coli Ruva-Holliday Junction Complex >... 103 2e-23
pdb|1CUK| Escherichia Coli Ruva Protein At Ph 4.9 And Roo... 101 6e-23
pdb|1D8L|A Chain A, E. Coli Holliday Junction Binding Prote... 93 2e-20
pdb|1IXR|A Chain A, Ruva-Ruvb Complex >gi|24987360|pdb|1IXR... 84 1e-17
pdb|1BVS|B Chain B, Ruva Complexed To A Holliday Junction. ... 79 4e-16
pdb|1IXS|A Chain A, Structure Of Ruvb Complexed With Ruva D... 32 0.056
pdb|1KIJ|A Chain A, Crystal Structure Of The 43k Atpase Dom... 28 0.82
pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 3... 27 1.8
pdb|1J5E|D Chain D, Structure Of The Thermus Thermophilus 3... 27 1.8
pdb|1IBL|D Chain D, Structure Of The Thermus Thermophilus 3... 27 1.8
pdb|1QMN|A Chain A, Alpha1-Antichymotrypsin Serpin In The D... 26 3.1
pdb|3CAA|A Chain A, Cleaved Antichymotrypsin A347r 26 3.1
pdb|1QO2|A Chain A, Crystal Structure Of N-((5'-Phosphoribo... 26 3.1
pdb|2ACH|A Chain A, Alpha1 Antichymotrypsin 26 3.1
pdb|1AS4|A Chain A, Cleaved Antichymotrypsin A349r 26 3.1
pdb|4CAA|A Chain A, Cleaved Antichymotrypsin T345r 26 3.1
>pdb|1C7Y|A Chain A, E.Coli Ruva-Holliday Junction Complex
pdb|1HJP| Holliday Junction Binding Protein Ruva From E. Coli
pdb|1BDX|A Chain A, E. Coli Ruva With Bound Dna Holliday Junction, Alpha
Carbons And Phosphate Atoms Only
pdb|1BDX|B Chain B, E. Coli Ruva With Bound Dna Holliday Junction, Alpha
Carbons And Phosphate Atoms Only
pdb|1BDX|C Chain C, E. Coli Ruva With Bound Dna Holliday Junction, Alpha
Carbons And Phosphate Atoms Only
pdb|1BDX|D Chain D, E. Coli Ruva With Bound Dna Holliday Junction, Alpha
Carbons And Phosphate Atoms Only
Length = 203
Score = 103 bits (256), Expect = 2e-23
Identities = 74/200 (37%), Positives = 108/200 (54%), Gaps = 21/200 (10%)
Query: 1 MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTA-ALLEAGQKARLKILQVIKEDAHLL 59
MI L G++ + V IEV GV Y V + M L EAGQ+A + V++EDA LL
Sbjct: 1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60
Query: 60 YGFLEEGEKILFERLLKINGVGGRIALAILSSFSPNEFESIIATKEVKRLQQVPGIGKKL 119
YGF + E+ LF+ L+K NGVG ++ALAILS S +F + + +EV L ++PGIGKK
Sbjct: 61 YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120
Query: 120 ADKIMVDLIGFF-------------------IQDENRPARNEVFLALESLGFKSAEINQ- 159
A++++V++ F A E AL +LG+K E ++
Sbjct: 121 AERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVAALVALGYKPQEASRM 180
Query: 160 VLKTLKPNLSIEAAIKEALQ 179
V K +P+ S E I+EAL+
Sbjct: 181 VSKIARPDASSETLIREALR 200
>pdb|1CUK| Escherichia Coli Ruva Protein At Ph 4.9 And Room Temperature
Length = 203
Score = 101 bits (251), Expect = 6e-23
Identities = 73/200 (36%), Positives = 107/200 (53%), Gaps = 21/200 (10%)
Query: 1 MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTA-ALLEAGQKARLKILQVIKEDAHLL 59
MI L G++ + V IEV GV Y V + M L EAGQ+A + V++EDA LL
Sbjct: 1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60
Query: 60 YGFLEEGEKILFERLLKINGVGGRIALAILSSFSPNEFESIIATKEVKRLQQVPGIGKKL 119
YGF + E+ LF+ L+K NGVG ++ALAILS S +F + + +EV L ++PGIGKK
Sbjct: 61 YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120
Query: 120 ADKIMVDLIGFF-------------------IQDENRPARNEVFLALESLGFKSAEINQ- 159
A++++V++ F A E L +LG+K E ++
Sbjct: 121 AERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVARLVALGYKPQEASRM 180
Query: 160 VLKTLKPNLSIEAAIKEALQ 179
V K +P+ S E I+EAL+
Sbjct: 181 VSKIARPDASSETLIREALR 200
>pdb|1D8L|A Chain A, E. Coli Holliday Junction Binding Protein Ruva Nh2 Region
Lacking Domain Iii
pdb|1D8L|B Chain B, E. Coli Holliday Junction Binding Protein Ruva Nh2 Region
Lacking Domain Iii
Length = 149
Score = 92.8 bits (229), Expect = 2e-20
Identities = 56/128 (43%), Positives = 82/128 (63%), Gaps = 1/128 (0%)
Query: 1 MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTA-ALLEAGQKARLKILQVIKEDAHLL 59
MI L G++ + V IEV GV Y V + M L EAGQ+A + V++EDA LL
Sbjct: 1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60
Query: 60 YGFLEEGEKILFERLLKINGVGGRIALAILSSFSPNEFESIIATKEVKRLQQVPGIGKKL 119
YGF + E+ LF+ L+K NGVG ++ALAILS S +F + + +EV L ++PGIGKK
Sbjct: 61 YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120
Query: 120 ADKIMVDL 127
A++++V++
Sbjct: 121 AERLIVEM 128
>pdb|1IXR|A Chain A, Ruva-Ruvb Complex
pdb|1IXR|B Chain B, Ruva-Ruvb Complex
Length = 191
Score = 84.0 bits (206), Expect = 1e-17
Identities = 61/191 (31%), Positives = 96/191 (49%), Gaps = 9/191 (4%)
Query: 1 MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTAALLEAGQKARLKILQVIKEDAHLLY 60
MI L G+V K A + GV + +Q LE G++ + ++KE+ LY
Sbjct: 1 MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQALEEGKEVGVHTHLLLKEEGLSLY 60
Query: 61 GFLEEGEKILFERLLKINGVGGRIALAILSSFSPNEFESIIATKEVKRLQQVPGIGKKLA 120
GF +E LFE LL ++GVG ++ALA+LS+ P + + + L G+G++LA
Sbjct: 61 GFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLA 120
Query: 121 DKIMVDLIG------FFIQDENRPARNEVFLALESLGFKSAEINQVLKTL---KPNLSIE 171
++I ++L G + A E +AL +LGFK A+ V+ L P +
Sbjct: 121 ERIALELKGKVPPHLLAGEKVESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQ 180
Query: 172 AAIKEALQQLR 182
IKEAL++LR
Sbjct: 181 DLIKEALKRLR 191
>pdb|1BVS|B Chain B, Ruva Complexed To A Holliday Junction.
pdb|1BVS|D Chain D, Ruva Complexed To A Holliday Junction.
pdb|1BVS|F Chain F, Ruva Complexed To A Holliday Junction.
pdb|1BVS|H Chain H, Ruva Complexed To A Holliday Junction.
pdb|1BVS|A Chain A, Ruva Complexed To A Holliday Junction.
pdb|1BVS|C Chain C, Ruva Complexed To A Holliday Junction.
pdb|1BVS|E Chain E, Ruva Complexed To A Holliday Junction.
pdb|1BVS|G Chain G, Ruva Complexed To A Holliday Junction
Length = 203
Score = 78.6 bits (192), Expect = 4e-16
Identities = 44/127 (34%), Positives = 71/127 (55%)
Query: 1 MIVGLIGVVEKISALEVHIEVQGVVYGVQVSMRTAALLEAGQKARLKILQVIKEDAHLLY 60
MI + G V +++ IE G+ Y V + A L G +ARL V++ED+ LY
Sbjct: 1 MIFSVRGEVLEVALDHAVIEAAGIGYRVNATPSALATLNQGSQARLVTAMVVREDSMTLY 60
Query: 61 GFLEEGEKILFERLLKINGVGGRIALAILSSFSPNEFESIIATKEVKRLQQVPGIGKKLA 120
GF + + LF LL ++GVG R+A+A L+ +A +V L +VPGIG++ A
Sbjct: 61 GFSDAENRDLFLALLSVSGVGPRLAMATLAVHDAAALRQALADSDVASLTRVPGIGRRGA 120
Query: 121 DKIMVDL 127
++I+++L
Sbjct: 121 ERIVLEL 127
>pdb|1IXS|A Chain A, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 62
Score = 31.6 bits (70), Expect = 0.056
Identities = 19/47 (40%), Positives = 26/47 (54%), Gaps = 3/47 (6%)
Query: 139 ARNEVFLALESLGFKSAEINQVLKTL---KPNLSIEAAIKEALQQLR 182
A E +AL +LGFK A+ V+ L P + IKEAL++LR
Sbjct: 16 AAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALKRLR 62
>pdb|1KIJ|A Chain A, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
pdb|1KIJ|B Chain B, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
Length = 390
Score = 27.7 bits (60), Expect = 0.82
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 28 VQVSMRTAALLEAGQKARLKILQVIKEDAHLLYG-------FLEEGEKILFERLLKINGV 80
++ +R A L AG K + Q KE+ L G L EGE +L+E+ I G
Sbjct: 185 IRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGT 244
Query: 81 GGRIALAI 88
G + + +
Sbjct: 245 HGEVEVEV 252
>pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin And Paromomycin
pdb|1HR0|D Chain D, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1JGQ|G Chain G, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgq, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
pdb|1GIX|G Chain G, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1JGO|G Chain G, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgo, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
pdb|1JGP|G Chain G, The Path Of Messenger Rna Through The Ribosome. This
File, 1jgp, Contains The 30s Ribosome Subunit, Three
Trna, And Mrna Molecules. 50s Ribosome Subunit Is In
The File 1giy
Length = 209
Score = 26.6 bits (57), Expect = 1.8
Identities = 14/39 (35%), Positives = 19/39 (47%)
Query: 53 KEDAHLLYGFLEEGEKILFERLLKINGVGGRIALAILSS 91
K+ +YG E + LFE K GV G + L +L S
Sbjct: 61 KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLES 99
>pdb|1J5E|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1I94|D Chain D, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I96|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1I95|D Chain D, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
Length = 208
Score = 26.6 bits (57), Expect = 1.8
Identities = 14/39 (35%), Positives = 19/39 (47%)
Query: 53 KEDAHLLYGFLEEGEKILFERLLKINGVGGRIALAILSS 91
K+ +YG E + LFE K GV G + L +L S
Sbjct: 60 KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLES 98
>pdb|1IBL|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1HNZ|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1IBM|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1IBK|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1HNW|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1FKA|D Chain D, Structure Of Functionally Activated Small Ribosomal
Subunit At 3.3 A Resolution
Length = 209
Score = 26.6 bits (57), Expect = 1.8
Identities = 14/39 (35%), Positives = 19/39 (47%)
Query: 53 KEDAHLLYGFLEEGEKILFERLLKINGVGGRIALAILSS 91
K+ +YG E + LFE K GV G + L +L S
Sbjct: 61 KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLES 99
>pdb|1QMN|A Chain A, Alpha1-Antichymotrypsin Serpin In The Delta Conformation
(Partial Loop Insertion)
Length = 401
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 138 PARNEVF--------LALESLGFKSAEINQVLKTLKPNL--SIEAAIKEALQQL 181
P +N +F LA SLG + + ++LK LK NL + EA I ++ Q L
Sbjct: 47 PDKNVIFSPPSISTALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHL 100
>pdb|3CAA|A Chain A, Cleaved Antichymotrypsin A347r
Length = 341
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 138 PARNEVF--------LALESLGFKSAEINQVLKTLKPNL--SIEAAIKEALQQL 181
P +N +F LA SLG + + ++LK LK NL + EA I ++ Q L
Sbjct: 27 PDKNVIFSPLSISTALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHL 80
>pdb|1QO2|A Chain A, Crystal Structure Of N-((5'-Phosphoribosyl)-Formimino)-5-
Aminoimidazol-4-Carboxamid Ribonucleotid Isomerase (Ec
3.1.3.15, Hisa)
pdb|1QO2|B Chain B, Crystal Structure Of N-((5'-Phosphoribosyl)-Formimino)-5-
Aminoimidazol-4-Carboxamid Ribonucleotid Isomerase (Ec
3.1.3.15, Hisa)
Length = 241
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/78 (24%), Positives = 40/78 (50%), Gaps = 8/78 (10%)
Query: 8 VVEKISALEVHIEVQGVVYGVQVSMRTAALLEAGQKARLKILQVIKEDAHLLYGFLEEGE 67
V+EK+S HI++ G G++ L + G + ++ +V+++ + FL+
Sbjct: 65 VLEKLSEFAEHIQIGG---GIRSLDYAEKLRKLGYRRQIVSSKVLEDPS-----FLKSLR 116
Query: 68 KILFERLLKINGVGGRIA 85
+I E + ++ GGR+A
Sbjct: 117 EIDVEPVFSLDTRGGRVA 134
>pdb|2ACH|A Chain A, Alpha1 Antichymotrypsin
Length = 360
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 138 PARNEVF--------LALESLGFKSAEINQVLKTLKPNL--SIEAAIKEALQQL 181
P +N +F LA SLG + + ++LK LK NL + EA I ++ Q L
Sbjct: 46 PDKNVIFSPLSISTALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHL 99
>pdb|1AS4|A Chain A, Cleaved Antichymotrypsin A349r
Length = 341
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 138 PARNEVF--------LALESLGFKSAEINQVLKTLKPNL--SIEAAIKEALQQL 181
P +N +F LA SLG + + ++LK LK NL + EA I ++ Q L
Sbjct: 27 PDKNVIFSPLSISTALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHL 80
>pdb|4CAA|A Chain A, Cleaved Antichymotrypsin T345r
Length = 341
Score = 25.8 bits (55), Expect = 3.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 138 PARNEVF--------LALESLGFKSAEINQVLKTLKPNL--SIEAAIKEALQQL 181
P +N +F LA SLG + + ++LK LK NL + EA I ++ Q L
Sbjct: 27 PDKNVIFSPLSISTALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHL 80
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
0.320 0.139 0.364
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 847,226
Number of Sequences: 13198
Number of extensions: 30142
Number of successful extensions: 84
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 75
Number of HSP's gapped (non-prelim): 16
length of query: 183
length of database: 2,899,336
effective HSP length: 83
effective length of query: 100
effective length of database: 1,803,902
effective search space: 180390200
effective search space used: 180390200
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: 51 (24.3 bits)