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|15645867|ref|NP_208045.1| tryptophanyl-tRNA
synthetase (trpS) [Helicobacter pylori 26695]
(339 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|1I6M|A Chain A, 1.7 High Resolution Experimental Phases... 325 3e-90
pdb|1D2R|A Chain A, 2.9 A Crystal Structure Of Ligand-Free ... 322 4e-89
pdb|1I6L|A Chain A, 1.7 High Resolution Experimental Phases... 313 2e-86
pdb|1H3F|A Chain A, Tyrosyl-Trna Synthetase From Thermus Th... 33 0.036
pdb|1BIH|A Chain A, Crystal Structure Of The Insect Immune ... 30 0.51
pdb|1JWB|B Chain B, Structure Of The Covalent Acyl-Adenylat... 28 2.0
pdb|1DCI|A Chain A, Dienoyl-Coa Isomerase >gi|4699608|pdb|1... 28 2.0
pdb|1T7P|A Chain A, T7 Dna Polymerase Complexed To Dna Prim... 27 2.5
pdb|1IRX|B Chain B, Crystal Structure Of Class I Lysyl-Trna... 27 3.3
pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus >... 27 3.3
pdb|1BPX|A Chain A, Human Dna Polymerase Beta Complexed Wit... 26 7.4
pdb|1JDC| Mutant (E219q) Maltotetraose-Forming Exo-Amylas... 25 9.7
pdb|1QPK|A Chain A, Mutant (D193g) Maltotetraose-Forming Ex... 25 9.7
pdb|1QI4|A Chain A, Mutant (E219g) Maltotetraose-Forming Ex... 25 9.7
pdb|1GCW|B Chain B, Co Form Hemoglobin From Mustelus Griseu... 25 9.7
pdb|1GCV|B Chain B, Deoxy Form Hemoglobin From Mustelus Gri... 25 9.7
pdb|2AMG| Structure Of Hydrolase (Glycosidase) 25 9.7
pdb|1QI3|A Chain A, Mutant (D193n) Maltotetraose-Forming Ex... 25 9.7
pdb|1GCY|A Chain A, High Resolution Crystal Structure Of Ma... 25 9.7
pdb|1QI5|A Chain A, Mutant (D294n) Maltotetraose-Forming Ex... 25 9.7
>pdb|1I6M|A Chain A, 1.7 High Resolution Experimental Phases For Tryptophanyl-
Trna Synthetase Complexed With Tryptophanyl-5'amp
Length = 328
Score = 325 bits (834), Expect = 3e-90
Identities = 171/324 (52%), Positives = 225/324 (68%), Gaps = 3/324 (0%)
Query: 17 KRVFSGIQPTGQIHLGNYLGAIKHWVEMQDEYENLFCVVNSHAITLPIDPAFLKSQSYEL 76
K +FSGIQP+G I +GNY+GA++ +VE+Q EY FC+V+ HAIT+ DP L+ L
Sbjct: 2 KTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRL 61
Query: 77 VKLLLACGIDPKQSGLFIQSEVDEHPALAWLLNCQVSMGEMQRMTQFKDKSLKNPKSVNV 136
L LA GIDP Q+ LFIQSEV H AW+L C V +GE++RMTQFK+KS ++V+
Sbjct: 62 AALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSA-GKEAVSA 120
Query: 137 GLFNYPILMASDILLYQSDLVPVGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVG 196
GL YP LMA+DILLY +D+VPVGEDQKQH+ELTR++AE+FN+ +G F +PE I KVG
Sbjct: 121 GLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVG 180
Query: 197 ARVMGLDDPKVKMSKSHQGANHAIFLLDEPDIIVKKIKKAATDSMGVIAFD-EKREGIFN 255
AR+M L DP KMSKS I LLD+ I KKIK A TDS G I +D E + GI N
Sbjct: 181 ARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISN 240
Query: 256 LLNIYMLLSNESPENIEERFKNKGYGDFKKELAEVMIQALKPIQERYKE-ISDDEVKAIL 314
LLNIY LS +S E +E +++ KGYG FK +LA+V+I+ L+PIQERY + +E+ +L
Sbjct: 241 LLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVL 300
Query: 315 NGGAEKARPLARATYQKAKELMGL 338
+ GAEKA +A +K ++ MGL
Sbjct: 301 DEGAEKANRVASEMVRKMEQAMGL 324
>pdb|1D2R|A Chain A, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site.
pdb|1D2R|B Chain B, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site.
pdb|1D2R|C Chain C, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site.
pdb|1D2R|D Chain D, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site.
pdb|1D2R|E Chain E, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site.
pdb|1D2R|F Chain F, 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna
Synthetase: Domain Movements Fragment The Adenine
Nucleotide Binding Site
Length = 326
Score = 322 bits (825), Expect = 4e-89
Identities = 170/324 (52%), Positives = 222/324 (68%), Gaps = 3/324 (0%)
Query: 17 KRVFSGIQPTGQIHLGNYLGAIKHWVEMQDEYENLFCVVNSHAITLPIDPAFLKSQSYEL 76
K +FSGIQP+G I +GNY+GA++ +VE+Q EY FC+V+ HAIT+ DP L+ L
Sbjct: 2 KTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRL 61
Query: 77 VKLLLACGIDPKQSGLFIQSEVDEHPALAWLLNCQVSMGEMQRMTQFKDKSLKNPKSVNV 136
L LA GIDP Q+ LFIQSEV H AW+L C V +GE++RMTQFK+KS +
Sbjct: 62 AALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSA-GAAAAAA 120
Query: 137 GLFNYPILMASDILLYQSDLVPVGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVG 196
GL YP LMA+DILLY +D+VPVGEDQKQH+ELTR++AE+FN+ +G F +PE I KVG
Sbjct: 121 GLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVG 180
Query: 197 ARVMGLDDPKVKMSKSHQGANHAIFLLDEPDIIVKKIKKAATDSMGVIAFD-EKREGIFN 255
AR+M L DP KMSKS I LLD+ I KKIK A TDS G I +D E + GI N
Sbjct: 181 ARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISN 240
Query: 256 LLNIYMLLSNESPENIEERFKNKGYGDFKKELAEVMIQALKPIQERYKE-ISDDEVKAIL 314
LLNIY LS +S E +E +++ KGYG FK +LA+V+I+ L+PIQERY + +E+ +L
Sbjct: 241 LLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVL 300
Query: 315 NGGAEKARPLARATYQKAKELMGL 338
+ GAEKA +A +K ++ MGL
Sbjct: 301 DEGAEKANRVASEMVRKMEQAMGL 324
>pdb|1I6L|A Chain A, 1.7 High Resolution Experimental Phases For Tryptophanyl-
Trna Synthetase Complexed With Tryptophanyl-5'amp
pdb|1I6K|A Chain A, 1.7 High Resolution Experimental Phases For Tryptophanyl-
Trna Synthetase Complexed With Tryptophanyl-5'amp
Length = 328
Score = 313 bits (801), Expect = 2e-86
Identities = 166/324 (51%), Positives = 218/324 (67%), Gaps = 3/324 (0%)
Query: 17 KRVFSGIQPTGQIHLGNYLGAIKHWVEMQDEYENLFCVVNSHAITLPIDPAFLKSQSYEL 76
K +FSGIQP+G I +GNY+GA++ +VE+Q EY FC+V+ HAIT+ DP L+ L
Sbjct: 2 KTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRL 61
Query: 77 VKLLLACGIDPKQSGLFIQSEVDEHPALAWLLNCQVSMGEMQRMTQFKDKSLKNPKSVNV 136
L LA GIDP Q+ LFIQSEV H AW L C V +GE++R TQFK+KS ++V+
Sbjct: 62 AALYLAVGIDPTQATLFIQSEVPAHAQAAWXLQCIVYIGELERXTQFKEKSA-GKEAVSA 120
Query: 137 GLFNYPILMASDILLYQSDLVPVGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVG 196
GL YP L A+DILLY +D+VPVGEDQKQH+ELTR++AE+FN+ +G F +PE I KVG
Sbjct: 121 GLLTYPPLXAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVG 180
Query: 197 ARVMGLDDPKVKMSKSHQGANHAIFLLDEPDIIVKKIKKAATDSMGVIAFD-EKREGIFN 255
AR+ L DP K SKS I LLD+ I KKIK A TDS G I +D E + GI N
Sbjct: 181 ARIXSLVDPTKKXSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISN 240
Query: 256 LLNIYMLLSNESPENIEERFKNKGYGDFKKELAEVMIQALKPIQERYKE-ISDDEVKAIL 314
LLNIY LS +S E +E +++ KGYG FK +LA+V+I+ L+PIQERY +E+ +L
Sbjct: 241 LLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWXESEELDRVL 300
Query: 315 NGGAEKARPLARATYQKAKELMGL 338
+ GAEKA +A +K ++ GL
Sbjct: 301 DEGAEKANRVASEXVRKXEQAXGL 324
>pdb|1H3F|A Chain A, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Tyrosinol
pdb|1H3F|B Chain B, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Tyrosinol
pdb|1H3E|A Chain A, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Wild-Type Trnatyr(Gua) And With Atp And
Tyrosinol
Length = 432
Score = 33.5 bits (75), Expect = 0.036
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 13/95 (13%)
Query: 141 YPILMASDILLYQSDLVPVGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVGARVM 200
YP A D + ++D+ G DQ+ +L + R + + + CF +P ++
Sbjct: 175 YPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMP---------LLV 225
Query: 201 GLDDPKVKMSKSHQGANHAIFLLDEPDIIVKKIKK 235
GLD + KMSKS ++ I L + P+ + KK+ +
Sbjct: 226 GLDG-REKMSKS---LDNYIGLTEPPEAMFKKLMR 256
>pdb|1BIH|A Chain A, Crystal Structure Of The Insect Immune Protein Hemolin: A
New Domain Arrangement With Implications For Homophilic
Adhesion
pdb|1BIH|B Chain B, Crystal Structure Of The Insect Immune Protein Hemolin: A
New Domain Arrangement With Implications For Homophilic
Adhesion
Length = 395
Score = 29.6 bits (65), Expect = 0.51
Identities = 23/99 (23%), Positives = 41/99 (41%)
Query: 159 VGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVGARVMGLDDPKVKMSKSHQGANH 218
VG+ QK L+LT A K+ + V + + +V GL P V S + + +
Sbjct: 293 VGKPQKHSLKLTVVSAPKYEQKPEKVIVVKQGQDVTIPCKVTGLPAPNVVWSHNAKPLSG 352
Query: 219 AIFLLDEPDIIVKKIKKAATDSMGVIAFDEKREGIFNLL 257
+ + +++K +K G A +E + F L
Sbjct: 353 GRATVTDSGLVIKGVKNGDKGYYGCRATNEHGDKYFETL 391
>pdb|1JWB|B Chain B, Structure Of The Covalent Acyl-Adenylate Form Of The Moeb-
Moad Protein Complex
pdb|1JW9|B Chain B, Structure Of The Native Moeb-Moad Protein Complex
pdb|1JWA|B Chain B, Structure Of The Atp-Bound Moeb-Moad Protein Complex
Length = 249
Score = 27.7 bits (60), Expect = 2.0
Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 14/99 (14%)
Query: 112 VSMGEMQRMTQFKDKSLKNPK---------SVNVGLFNYPILMASDILLYQSDLVPVGED 162
VS+ +QR T D ++ PK +N + P+ + LL ++L + +
Sbjct: 66 VSLSNLQRQTLHSDATVGQPKVESARDALTRINPHIAITPV----NALLDDAELAALIAE 121
Query: 163 QKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVGARVMG 201
L+ T N+A + N+ CF PL++ R+ G
Sbjct: 122 HDLVLDCTDNVAVR-NQLNAGCFAAKVPLVSGAAIRMEG 159
>pdb|1DCI|A Chain A, Dienoyl-Coa Isomerase
pdb|1DCI|B Chain B, Dienoyl-Coa Isomerase
pdb|1DCI|C Chain C, Dienoyl-Coa Isomerase
Length = 275
Score = 27.7 bits (60), Expect = 2.0
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 6/84 (7%)
Query: 145 MASDILLYQSDLVPVGEDQKQHLELTRNIAEKFNRDFGNCFKVPEPLIAKVGARVMGLDD 204
MASDIL P G+D + R++ ++ + F K P+P+IA + +G
Sbjct: 70 MASDILQ------PPGDDVARIAWYLRDLISRYQKTFTVIEKCPKPVIAAIHGGCIGGGV 123
Query: 205 PKVKMSKSHQGANHAIFLLDEPDI 228
+ A F + E D+
Sbjct: 124 DLISACDIRYCTQDAFFQVKEVDV 147
>pdb|1T7P|A Chain A, T7 Dna Polymerase Complexed To Dna PrimerTEMPLATE,A
Nucleoside Triphosphate, And Its Processivity Factor
Thioredoxin
Length = 698
Score = 27.3 bits (59), Expect = 2.5
Identities = 20/78 (25%), Positives = 30/78 (37%), Gaps = 6/78 (7%)
Query: 182 GNCFKVPEPLIAKVGARVMGLDDPKVKMSKSHQGANHAIFLLDEPDIIVKKIKKAA---- 237
G FK P+ + G LD + + H +F D I KK+++A
Sbjct: 289 GGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPT 348
Query: 238 --TDSMGVIAFDEKREGI 253
TD + DE EG+
Sbjct: 349 KYTDKGAPVVDDEVLEGV 366
>pdb|1IRX|B Chain B, Crystal Structure Of Class I Lysyl-Trna Synthetase
pdb|1IRX|A Chain A, Crystal Structure Of Class I Lysyl-Trna Synthetase
Length = 523
Score = 26.9 bits (58), Expect = 3.3
Identities = 11/24 (45%), Positives = 15/24 (61%)
Query: 11 RNNMHKKRVFSGIQPTGQIHLGNY 34
R K V SGI P+G +H+GN+
Sbjct: 16 RGEKEKYVVESGITPSGYVHVGNF 39
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 26.9 bits (58), Expect = 3.3
Identities = 23/73 (31%), Positives = 33/73 (44%), Gaps = 2/73 (2%)
Query: 267 SPENIEERFKNKGYGDFKKELAEVMIQALKPIQERYKEISDDEVKAILNGGAEKARPLAR 326
SPEN++ER K + KE +I LKP + Y + S D + L+ E+ L
Sbjct: 85 SPENLDERMAAKTINEILKECYAEIILRLKP-EIAYVD-SPDVIPERLSRELEEITGLRV 142
Query: 327 ATYQKAKELMGLI 339
KA E L+
Sbjct: 143 VAEHKADEKYPLV 155
>pdb|1BPX|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
pdb|1BPZ|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
pdb|9ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Native Structure
pdb|9ICX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna (Non Gapped Dna Only)
pdb|9ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(0.1 Millimolar) And Zncl2 (0.2 Millimolar)
pdb|8ICK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mgcl2 (5 Millimolar), And Mncl2 (5
Millimolar)
pdb|8ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Azt-Tp (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|1ZQA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar) At Ph 7.5
pdb|1ZQI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar)
pdb|9ICK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Artificial Mother Liquor
pdb|8ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Atp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Pyrophosphate (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|7ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.01 Millimolar) And Mgcl2 (1 Millimolar)
pdb|8ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|1ZQP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Nacl (75 Millimolar)
pdb|7ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(0.1 Millimolar)
pdb|7ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(0.1 Millimolar)
pdb|7ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Nicl2
(0.1 Millimolar)
pdb|7ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.001 Millimolar)
pdb|7ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar) And In The Absence Of Nacl
pdb|8ICC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna (No 5'-Phosphate)
pdb|9ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|8ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Datp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Ddctp
(10 Millimolar) And Mncl2 (10 Millimolar)
pdb|8ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dttp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|7ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.1 Millimolar) (Four-Day Soak)
pdb|8ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(10 Millimolar) And Mgcl2 (50 Millimolar)
pdb|8ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mncl2 (5 Millimolar), And Ammonium
Sulfate (75 Millimolar)
pdb|1ZQF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cscl
(150 Millimolar)
pdb|7ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cocl2
(0.1 Millimolar)
pdb|7ICK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mgcl2
(0.1 Millimolar)
pdb|9ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Double Stranded Dna (No 5'-Phosphate)
pdb|9ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dttp (1
Millimolar) And Mgcl2 (5 Millimolar)
pdb|9ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|8ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Ddatp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dctp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dgtp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cacl2 (5 Millimolar)
pdb|9ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Ddctp
(20 Millimolar) And Mgcl2 (20 Millimolar)
pdb|7ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.01 Millimolar)
pdb|7ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(1 Millimolar)
pdb|9ICA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Datp(Alpha)s (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICY|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna (Non Gapped Dna Only)
pdb|1ZQN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|7ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.01 Millimolar)
pdb|7ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(1.0 Millimolar)
pdb|8ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (0.1 Millimolar) And Mncl2 (0.5 Millimolar)
pdb|8ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Nicl2 (5 Millimolar)
pdb|8ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICY|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Crcl3 (5 Millimolar)
pdb|7ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar) (Four-Day Soak)
pdb|9ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|8ICZ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (1 Millimolar), Mncl2 (5 Millimolar), And Lithium
Sulfate (75 Millimolar)
pdb|9ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna
pdb|1ZQG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 6.5
pdb|1ZQH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 7.5
pdb|7ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar)
pdb|8ICB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Artificial Mother Liquor
pdb|9ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Pyrophosphate (1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cdcl2 (1 Millimolar)
pdb|9ICB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cocl2 (5 Millimolar)
pdb|8ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|1ZQB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(150 Millimolar)
pdb|1ZQC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar)
pdb|1ZQM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar)
pdb|1ZQK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Mgcl2 (75 Millimolar)
pdb|1ZQO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|8ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|1ZQQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|7ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.1 Millimolar)
pdb|7ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar)
pdb|1ZQL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Tlcl
(0.5 Millimolar)
pdb|8ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|9ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cucl2 (0.1 Millimolar)
pdb|1ZQT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(0.01 Millimolar) And Zncl2 (0.02 Millimolar)
pdb|7ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cucl2
(0.1 Millimolar)
pdb|1ZQD|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(150 Millimolar)
pdb|1ZQR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Nicl2
(15 Millimolar)
pdb|1ZQE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(Saturated Solution)
pdb|1BPY|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna And
Ddctp
Length = 335
Score = 25.8 bits (55), Expect = 7.4
Identities = 17/64 (26%), Positives = 29/64 (44%), Gaps = 4/64 (6%)
Query: 262 LLSNESPENIEERFKNKGYGDFKKEL-AEVMIQALKPIQERYKEISDDEVKAILNG---G 317
L NE N +R K +GDF+K + E M+Q + K++ + + + G
Sbjct: 125 LRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRG 184
Query: 318 AEKA 321
AE +
Sbjct: 185 AESS 188
>pdb|1JDC| Mutant (E219q) Maltotetraose-Forming Exo-Amylase Cocrystallized
With Maltotetraose (Crystal Type 1)
pdb|1JDD| Mutant (E219q) Maltotetraose-Forming Exo-Amylase Cocrystallized
With Maltotetraose (Crystal Type 2)
pdb|1JDA| Maltotetraose-Forming Exo-Amylase
Length = 429
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
>pdb|1QPK|A Chain A, Mutant (D193g) Maltotetraose-Forming Exo-Amylase In
Complex With Maltotetraose
Length = 418
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
>pdb|1QI4|A Chain A, Mutant (E219g) Maltotetraose-Forming Exo-Amylase In
Complex With Maltotetraose
Length = 429
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
>pdb|1GCW|B Chain B, Co Form Hemoglobin From Mustelus Griseus
pdb|1GCW|D Chain D, Co Form Hemoglobin From Mustelus Griseus
Length = 135
Score = 25.4 bits (54), Expect = 9.7
Identities = 14/39 (35%), Positives = 22/39 (55%), Gaps = 1/39 (2%)
Query: 29 IHLGNYLGAIKHWVEMQDEYENLF-CVVNSHAITLPIDP 66
IH G +GA++ V+ D+ + LF + HA L +DP
Sbjct: 52 IHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDP 90
>pdb|1GCV|B Chain B, Deoxy Form Hemoglobin From Mustelus Griseus
pdb|1GCV|D Chain D, Deoxy Form Hemoglobin From Mustelus Griseus
Length = 136
Score = 25.4 bits (54), Expect = 9.7
Identities = 14/39 (35%), Positives = 22/39 (55%), Gaps = 1/39 (2%)
Query: 29 IHLGNYLGAIKHWVEMQDEYENLF-CVVNSHAITLPIDP 66
IH G +GA++ V+ D+ + LF + HA L +DP
Sbjct: 52 IHAGIVVGALQDAVKHMDDVKTLFKDLSKKHADDLHVDP 90
>pdb|2AMG| Structure Of Hydrolase (Glycosidase)
Length = 415
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 308 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 348
>pdb|1QI3|A Chain A, Mutant (D193n) Maltotetraose-Forming Exo-Amylase In
Complex With Maltotetraose
Length = 429
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
>pdb|1GCY|A Chain A, High Resolution Crystal Structure Of Maltotetraose-Forming
Exo-Amylase
Length = 527
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
>pdb|1QI5|A Chain A, Mutant (D294n) Maltotetraose-Forming Exo-Amylase In
Complex With Maltotetraose
Length = 429
Score = 25.4 bits (54), Expect = 9.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 250 REGIFNLLNIYMLLSNESPENIEERFKNKGYGDFKKELAEV 290
++G+ Y+L S +P + + GYGDF ++L +V
Sbjct: 311 QDGLIRQAYAYILTSPGTPVVYWDHMYDWGYGDFIRQLIQV 351
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 0.136 0.389
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,898,733
Number of Sequences: 13198
Number of extensions: 80420
Number of successful extensions: 219
Number of sequences better than 10.0: 20
Number of HSP's better than 10.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 21
length of query: 339
length of database: 2,899,336
effective HSP length: 89
effective length of query: 250
effective length of database: 1,724,714
effective search space: 431178500
effective search space used: 431178500
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)