BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 008575
(561 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 265 bits (678), Expect = 4e-71, Method: Compositional matrix adjust.
Identities = 154/412 (37%), Positives = 242/412 (58%), Gaps = 15/412 (3%)
Query: 151 FYRVTCKDNGKGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIE 210
Y+V DNG G+P ++PN FGRVL +KY +QTRG +GLG K A+++S+M PIE
Sbjct: 70 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIE 129
Query: 211 ISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTTYRSKIL 270
I +S + I KL IDI++N P + EN +HG + + I G+W +S+I
Sbjct: 130 IETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIY 189
Query: 271 HYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSVDLLLIKG 330
Y+++ +ITPYA+F+FK E NVT + R T+ +P P E K HP VD IK
Sbjct: 190 EYIKRTYIITPYAEFIFK----DPEGNVTY-YPRLTNKIPKPPQEVKPHPYGVDREEIKI 244
Query: 331 LIAETSKG-TLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVRIHQLFR 389
LI + T+ +FL +EF +IG + A++++ G P VK+LT ++I R+ + F+
Sbjct: 245 LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG--LKPNKKVKNLTEEEITRLVETFK 302
Query: 390 QAK-FDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGK 448
+ + F PS LS GE + LG+ K +PD A+ + + ++GHPFIVEAGV+ GG
Sbjct: 303 KYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGS 362
Query: 449 -DVKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGVFVSIVSTKI 507
V + + R+AN+IPL++++ DV+ + ++ ++W Y I Q ++ V V + STKI
Sbjct: 363 IPVGEEPIVLRYANKIPLIYDEKSDVIWKV-VEELDWKRYGIESDQYQMVVMVHLCSTKI 421
Query: 508 PFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERKRNL 559
P+K GKE I + ++I +K+A+ + +LK + K R++QE K+ L
Sbjct: 422 PYKSAGKESIA-EVEDIEKEIKNALMEVARKLKQYLSEK---RKEQEAKKKL 469
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 27 SPAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIEEIGKSKFNS 86
SPAEFF N +AGF NP ++LY TVREL+ENSLD+ + LP ++ITI+ I ++
Sbjct: 12 SPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIY 71
Query: 87 MIGLVD 92
+ +VD
Sbjct: 72 KVNVVD 77
>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
Length = 469
Score = 265 bits (678), Expect = 4e-71, Method: Compositional matrix adjust.
Identities = 154/412 (37%), Positives = 242/412 (58%), Gaps = 15/412 (3%)
Query: 151 FYRVTCKDNGKGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIE 210
Y+V DNG G+P ++PN FGRVL +KY +QTRG +GLG K A+++S+M PIE
Sbjct: 68 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIE 127
Query: 211 ISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTTYRSKIL 270
I +S + I KL IDI++N P + EN +HG + + I G+W +S+I
Sbjct: 128 IETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIY 187
Query: 271 HYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSVDLLLIKG 330
Y+++ +ITPYA+F+FK E NVT + R T+ +P P E K HP VD IK
Sbjct: 188 EYIKRTYIITPYAEFIFK----DPEGNVTY-YPRLTNKIPKPPQEVKPHPYGVDREEIKI 242
Query: 331 LIAETSKG-TLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVRIHQLFR 389
LI + T+ +FL +EF +IG + A++++ G P VK+LT ++I R+ + F+
Sbjct: 243 LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG--LKPNKKVKNLTEEEITRLVETFK 300
Query: 390 QAK-FDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGK 448
+ + F PS LS GE + LG+ K +PD A+ + + ++GHPFIVEAGV+ GG
Sbjct: 301 KYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGS 360
Query: 449 -DVKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGVFVSIVSTKI 507
V + + R+AN+IPL++++ DV+ + ++ ++W Y I Q ++ V V + STKI
Sbjct: 361 IPVGEEPIVLRYANKIPLIYDEKSDVIWKV-VEELDWKRYGIESDQYQMVVMVHLCSTKI 419
Query: 508 PFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERKRNL 559
P+K GKE I + ++I +K+A+ + +LK + K R++QE K+ L
Sbjct: 420 PYKSAGKESIA-EVEDIEKEIKNALMEVARKLKQYLSEK---RKEQEAKKKL 467
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 27 SPAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIEEIGKSKFNS 86
SPAEFF N +AGF NP ++LY TVREL+ENSLD+ + LP ++ITI+ I ++
Sbjct: 10 SPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIY 69
Query: 87 MIGLVD 92
+ +VD
Sbjct: 70 KVNVVD 75
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 530
Score = 265 bits (676), Expect = 6e-71, Method: Compositional matrix adjust.
Identities = 154/412 (37%), Positives = 241/412 (58%), Gaps = 15/412 (3%)
Query: 151 FYRVTCKDNGKGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIE 210
Y+V DNG G+P ++PN FGRVL +KY +QTRG +GLG K A+++S+M PIE
Sbjct: 69 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIE 128
Query: 211 ISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTTYRSKIL 270
I +S + I KL IDI++N P + EN +HG + + I G+W +S+I
Sbjct: 129 IETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIY 188
Query: 271 HYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSVDLLLIKG 330
Y+++ +ITPYA+F+FK E NVT + R T+ +P P E K HP VD IK
Sbjct: 189 EYIKRTYIITPYAEFIFK----DPEGNVTY-YPRLTNKIPKPPQEVKPHPYGVDREEIKI 243
Query: 331 LIAETSKG-TLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVRIHQLFR 389
LI + T+ +FL +EF +IG + A++++ G P VK+LT ++I R+ + F+
Sbjct: 244 LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG--LKPNKKVKNLTEEEITRLVETFK 301
Query: 390 QAK-FDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGK 448
+ + F PS LS GE + LG+ K +PD A+ + + ++GHPFIVEAGV+ GG
Sbjct: 302 KDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGS 361
Query: 449 -DVKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGVFVSIVSTKI 507
V + + R+AN+IPL++++ DV+ + ++ ++W Y I Q ++ V V + STKI
Sbjct: 362 IPVGEEPIVLRYANKIPLIYDEKSDVIWKV-VEELDWKRYGIESDQYQMVVMVHLCSTKI 420
Query: 508 PFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERKRNL 559
P+K GKE I + + I +K+A+ + +LK + K R++QE K+ L
Sbjct: 421 PYKSAGKESIA-EVENIEKEIKNALMEVARKLKQYLSEK---RKEQEAKKKL 468
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 27 SPAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIEEIGKSKFNS 86
SPAEFF N +AGF NP ++LY TVREL+ENSLD+ + LP ++ITI+ I ++
Sbjct: 11 SPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIY 70
Query: 87 MIGLVD 92
+ +VD
Sbjct: 71 KVNVVD 76
>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
Length = 472
Score = 262 bits (669), Expect = 5e-70, Method: Compositional matrix adjust.
Identities = 153/412 (37%), Positives = 240/412 (58%), Gaps = 15/412 (3%)
Query: 151 FYRVTCKDNGKGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIE 210
Y+V DNG G+P ++PN FGRVL +KY +QTRG +GLG K A+++S+ PIE
Sbjct: 71 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGXYGLGVKAAVLYSQXHQDKPIE 130
Query: 211 ISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTTYRSKIL 270
I +S + I KL IDI++N P + EN +HG + + I G+W +S+I
Sbjct: 131 IETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIY 190
Query: 271 HYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSVDLLLIKG 330
Y+++ +ITPYA+F+FK E NVT + R T+ +P P E K HP VD IK
Sbjct: 191 EYIKRTYIITPYAEFIFK----DPEGNVTY-YPRLTNKIPKPPQEVKPHPYGVDREEIKI 245
Query: 331 LIAETSKG-TLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVRIHQLFR 389
LI + T+ +FL +EF +IG + A++++ G P VK+LT ++I R+ + F+
Sbjct: 246 LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG--LKPNKKVKNLTEEEITRLVETFK 303
Query: 390 QAK-FDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGK 448
+ + F PS LS GE + LG+ K +PD A+ + + ++GHPFIVEAGV+ GG
Sbjct: 304 KYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGS 363
Query: 449 -DVKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGVFVSIVSTKI 507
V + + R+AN+IPL++++ DV+ + ++ ++W Y I Q + V V + STKI
Sbjct: 364 IPVGEEPIVLRYANKIPLIYDEKSDVIWKV-VEELDWKRYGIESDQYQXVVXVHLCSTKI 422
Query: 508 PFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERKRNL 559
P+K GKE I + ++I +K+A+ + +LK + K R++QE K+ L
Sbjct: 423 PYKSAGKESIA-EVEDIEKEIKNALXEVARKLKQYLSEK---RKEQEAKKKL 470
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 27 SPAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIEEIGKSKFNS 86
SPAEFF N +AGF NP ++LY TVREL+ENSLD+ + LP ++ITI+ I ++
Sbjct: 13 SPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIY 72
Query: 87 MIGLVD 92
+ +VD
Sbjct: 73 KVNVVD 78
>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
Length = 469
Score = 262 bits (669), Expect = 5e-70, Method: Compositional matrix adjust.
Identities = 153/412 (37%), Positives = 240/412 (58%), Gaps = 15/412 (3%)
Query: 151 FYRVTCKDNGKGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIE 210
Y+V DNG G+P ++PN FGRVL +KY +QTRG +GLG K A+++S+ PIE
Sbjct: 68 IYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGXYGLGVKAAVLYSQXHQDKPIE 127
Query: 211 ISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTTYRSKIL 270
I +S + I KL IDI++N P + EN +HG + + I G+W +S+I
Sbjct: 128 IETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIY 187
Query: 271 HYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSVDLLLIKG 330
Y+++ +ITPYA+F+FK E NVT + R T+ +P P E K HP VD IK
Sbjct: 188 EYIKRTYIITPYAEFIFK----DPEGNVTY-YPRLTNKIPKPPQEVKPHPYGVDREEIKI 242
Query: 331 LIAETSKG-TLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVRIHQLFR 389
LI + T+ +FL +EF +IG + A++++ G P VK+LT ++I R+ + F+
Sbjct: 243 LINNLKRDYTIKEFLVNEFQSIGDTTADKILELAG--LKPNKKVKNLTEEEITRLVETFK 300
Query: 390 QAK-FDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGK 448
+ + F PS LS GE + LG+ K +PD A+ + + ++GHPFIVEAGV+ GG
Sbjct: 301 KYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGS 360
Query: 449 -DVKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGVFVSIVSTKI 507
V + + R+AN+IPL++++ DV+ + ++ ++W Y I Q + V V + STKI
Sbjct: 361 IPVGEEPIVLRYANKIPLIYDEKSDVIWKV-VEELDWKRYGIESDQYQXVVXVHLCSTKI 419
Query: 508 PFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERKRNL 559
P+K GKE I + ++I +K+A+ + +LK + K R++QE K+ L
Sbjct: 420 PYKSAGKESIA-EVEDIEKEIKNALXEVARKLKQYLSEK---RKEQEAKKKL 467
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 27 SPAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIEEIGKSKFNS 86
SPAEFF N +AGF NP ++LY TVREL+ENSLD+ + LP ++ITI+ I ++
Sbjct: 10 SPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIY 69
Query: 87 MIGLVD 92
+ +VD
Sbjct: 70 KVNVVD 75
>pdb|2Q2E|B Chain B, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
Methanosarcina Mazei
Length = 621
Score = 182 bits (463), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 121/419 (28%), Positives = 212/419 (50%), Gaps = 18/419 (4%)
Query: 146 RGEASFYRVTCKDNGKGMPHDDIPNMFGRVLSGTKY-GLKQTRGKFGLGAKMALIWSKMS 204
R + V +DNG G+ + IP +F ++L G+++ LKQ+RG+ G+G A+++++M+
Sbjct: 68 RTGPDYVTVIIEDNGPGIVREQIPKVFAKLLYGSRFHALKQSRGQQGIGISAAVLYAQMT 127
Query: 205 TGLPIEISSSMRSHNFISFCKLDIDIHRNIPHVHLHEKRENKDRWHGAEIQVVIEGNWTT 264
G +I S + +L I+ N P + + E R + R HG +I++ + +
Sbjct: 128 AGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVR-DWFRPHGTQIELEMRAAYVK 186
Query: 265 -YRSKILHYMRQMAVITPYAQFLFKFVSEVAEKNVTIRFSRRTDVMPPVPVETKHHPSSV 323
R I Y++ A++ P+A+ + + V F R TD MP E HP +
Sbjct: 187 GRRQSIYEYLKATAIVNPHARI--TLIDPDGNEEV---FERATDKMPEPAEEILPHPEGI 241
Query: 324 DLLLIKGLIAETSKGTLLQFLQHEFVNIGKSLAERLIGEMGPEFSPKMAVKSLTSQQIVR 383
+L + ++ T + L FL++ F IG AE + G P++ +L + +
Sbjct: 242 ELGTLMKMLHYTERQKLAPFLRYSFCKIGLLTAEEICKAAG--LDPEIDPHALGRHEARK 299
Query: 384 IHQLFRQAKFDDPSGGCLSPAGEYNLRLGIIKELHPDMVATYSGSAQVFEGHPFIVEAGV 443
+ + F + K P CLSP GE + G+ KE D +AT + V+ G+PF+VE G+
Sbjct: 300 LIEAFEKVKIMAPPTDCLSPIGEDLIYRGLEKETTVDFIATSTRKPAVYSGNPFVVEVGM 359
Query: 444 SVGGKDVK-QGLNIFRFANRIPLLFEQGGDVVTRTAMKRINWSSYKINQTQDKIGV---- 498
+ GG K + ++I RFANR+PLL++QGG VT A++ I W Y +NQ I V
Sbjct: 360 AYGGNLPKEEKISIMRFANRVPLLYQQGG-CVTTHAVEDIKWKQYGLNQPGGGIPVGPVI 418
Query: 499 -FVSIVSTKIPFKGTGKEYIGDDTKEIASAVKSAIQQCCIQLKSKIVRKIQDREQQERK 556
+ + S +PF K+ I D I + AI++ +LK + ++ ++++E++
Sbjct: 419 LLIHVASINVPFTSESKDAIA-DIPVIKEEIDLAIKEVARKLKHYLSKQSNLKKRREKE 476
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 20 ESALKQKS--PAEFFAENKNIAGFDNPGKSLYTTVRELVENSLDSAESISELPVVEITIE 77
E A KQKS AEFF +N+ I GFD+ +SL TTV+E V+N+LD+ E LP + + +E
Sbjct: 8 ELAKKQKSISVAEFFEKNRQILGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVE 67
Query: 78 EIGKSKFNSMI 88
G +I
Sbjct: 68 RTGPDYVTVII 78
>pdb|1LRT|A Chain A, Crystal Structure Of Ternary Complex Of Tritrichomonas
Foetus Inosine-5'-Monophosphate Dehydrogenase:
Structural Characterization Of Nad+ Site In Microbial
Enzyme
pdb|1LRT|B Chain B, Crystal Structure Of Ternary Complex Of Tritrichomonas
Foetus Inosine-5'-Monophosphate Dehydrogenase:
Structural Characterization Of Nad+ Site In Microbial
Enzyme
pdb|1LRT|C Chain C, Crystal Structure Of Ternary Complex Of Tritrichomonas
Foetus Inosine-5'-Monophosphate Dehydrogenase:
Structural Characterization Of Nad+ Site In Microbial
Enzyme
pdb|1LRT|D Chain D, Crystal Structure Of Ternary Complex Of Tritrichomonas
Foetus Inosine-5'-Monophosphate Dehydrogenase:
Structural Characterization Of Nad+ Site In Microbial
Enzyme
Length = 376
Score = 32.0 bits (71), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 450 VKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRIN-WSSYKINQTQDKIGVFVSIVSTKIP 508
V G+N F R+P L E G DV+ + + W I +DK G V + + I
Sbjct: 107 VGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIRDKYGDKVKVGAGNI- 165
Query: 509 FKGTGKEYIGD 519
G G Y+ D
Sbjct: 166 VDGEGFRYLAD 176
>pdb|1KXD|A Chain A, Sindbis Virus Capsid (N222l Mutant), Tetragonal Crystal
Form
Length = 159
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDLSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|3T1E|A Chain A, The Structure Of The Newcastle Disease Virus
Hemagglutinin- Neuraminidase (Hn) Ectodomain Reveals A
4-Helix Bundle Stalk
pdb|3T1E|B Chain B, The Structure Of The Newcastle Disease Virus
Hemagglutinin- Neuraminidase (Hn) Ectodomain Reveals A
4-Helix Bundle Stalk
pdb|3T1E|E Chain E, The Structure Of The Newcastle Disease Virus
Hemagglutinin- Neuraminidase (Hn) Ectodomain Reveals A
4-Helix Bundle Stalk
pdb|3T1E|F Chain F, The Structure Of The Newcastle Disease Virus
Hemagglutinin- Neuraminidase (Hn) Ectodomain Reveals A
4-Helix Bundle Stalk
Length = 537
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 479 MKRINWSSYKINQTQDKIGVFVSIVSTKIPFKGTGKEYIGDDTKEIASAVKSAIQQ 534
M I SY+IN + G + G GKE I DDT ++ S SA Q+
Sbjct: 71 MNAITSLSYQINGAANNSGCGAPVHDPDY-IGGIGKELIVDDTSDVTSFYPSAFQE 125
>pdb|1PVN|A Chain A, The Crystal Structure Of The Complex Between Imp
Dehydrogenase Catalytic Domain And A Transition State
Analogue Mzp
pdb|1PVN|B Chain B, The Crystal Structure Of The Complex Between Imp
Dehydrogenase Catalytic Domain And A Transition State
Analogue Mzp
pdb|1PVN|C Chain C, The Crystal Structure Of The Complex Between Imp
Dehydrogenase Catalytic Domain And A Transition State
Analogue Mzp
pdb|1PVN|D Chain D, The Crystal Structure Of The Complex Between Imp
Dehydrogenase Catalytic Domain And A Transition State
Analogue Mzp
Length = 376
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 450 VKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRIN-WSSYKINQTQDKIGVFVSIVSTKIP 508
V G+N F R+P L E G DV+ + + W I ++K G V + + I
Sbjct: 107 VGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNI- 165
Query: 509 FKGTGKEYIGD 519
G G Y+ D
Sbjct: 166 VDGEGFRYLAD 176
>pdb|1ME8|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Rvp Bound
pdb|1ME9|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Imp Bound
pdb|1MEH|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Imp And Moa Bound
Length = 503
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 450 VKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRIN-WSSYKINQTQDKIGVFVSIVSTKIP 508
V G+N F R+P L E G DV+ + + W I ++K G V + + I
Sbjct: 234 VGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNI- 292
Query: 509 FKGTGKEYIGD 519
G G Y+ D
Sbjct: 293 VDGEGFRYLAD 303
>pdb|1ME7|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Rvp And Moa Bound
pdb|1MEI|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Xmp And Mycophenolic Acid
Bound
pdb|1MEW|A Chain A, Inosine Monophosphate Dehydrogenase (Impdh) From
Tritrichomonas Foetus With Xmp And Nad Bound
pdb|1AK5|A Chain A, Inosine Monophosphate Dehydrogenase (impdh) From
Tritrichomonas Foetus
Length = 503
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 450 VKQGLNIFRFANRIPLLFEQGGDVVTRTAMKRIN-WSSYKINQTQDKIGVFVSIVSTKIP 508
V G+N F R+P L E G DV+ + + W I ++K G V + + I
Sbjct: 234 VGAGINTRDFRERVPALVEAGADVLCIDSSDGFSEWQKITIGWIREKYGDKVKVGAGNI- 292
Query: 509 FKGTGKEYIGD 519
G G Y+ D
Sbjct: 293 VDGEGFRYLAD 303
>pdb|1W07|A Chain A, Arabidopsis Thaliana Acyl-Coa Oxidase 1
pdb|1W07|B Chain B, Arabidopsis Thaliana Acyl-Coa Oxidase 1
Length = 659
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 30/66 (45%)
Query: 414 IKELHPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDV 473
+EL D+V Q+ FI + +GGK VK+ LN + + LL + GD
Sbjct: 512 FQELLADLVEAAIAHCQLIVVSKFIAKLEQDIGGKGVKKQLNNLCYIYALYLLHKHLGDF 571
Query: 474 VTRTAM 479
++ +
Sbjct: 572 LSTNCI 577
>pdb|2SNW|A Chain A, Sindbis Virus Capsid Protein, Type3 Crystal Form
pdb|2SNW|B Chain B, Sindbis Virus Capsid Protein, Type3 Crystal Form
Length = 158
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 78 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 134
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 135 ALSVVTWNS 143
>pdb|1KXA|A Chain A, Sindbis Virus Capsid, (Wild-Type) Residues 106-264,
Tetragonal Crystal Form
Length = 159
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|1KXE|A Chain A, Sindbis Virus Capsid (Y180s, E183g Double Mutant),
Tetragonal Crystal Form
Length = 159
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|1WYK|A Chain A, Sindbis Virus Capsid Protein (114-264)
pdb|1WYK|B Chain B, Sindbis Virus Capsid Protein (114-264)
pdb|1WYK|C Chain C, Sindbis Virus Capsid Protein (114-264)
pdb|1WYK|D Chain D, Sindbis Virus Capsid Protein (114-264)
Length = 152
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 72 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 128
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 129 ALSVVTWNS 137
>pdb|1Z8Y|Q Chain Q, Mapping The E2 Glycoprotein Of Alphaviruses
pdb|1Z8Y|R Chain R, Mapping The E2 Glycoprotein Of Alphaviruses
pdb|1Z8Y|S Chain S, Mapping The E2 Glycoprotein Of Alphaviruses
pdb|1Z8Y|T Chain T, Mapping The E2 Glycoprotein Of Alphaviruses
pdb|2SNV|A Chain A, The Refined Structure Of Sindbis Virus Core Protein In
Comparison With Other Chymotrypsin-Like Serine
Proteinase Structures
Length = 151
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 71 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 127
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 128 ALSVVTWNS 136
>pdb|1KXB|A Chain A, Sindbis Virus Capsid (S215a Mutant), Tetragonal Crystal
Form
Length = 159
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DAGRPIMDNSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|1SVP|A Chain A, Sindbis Virus Capsid Protein
pdb|1SVP|B Chain B, Sindbis Virus Capsid Protein
Length = 161
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DAGRPIMDNSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|1KXC|A Chain A, Sindbis Virus Capsid (N190k Mutant), Tetragonal Crystal
Form
Length = 159
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 79 HPEGFYKWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 135
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 136 ALSVVTWNS 144
>pdb|1KXF|A Chain A, Sindbis Virus Capsid, (Wild-Type) Residues 1-264,
Tetragonal Crystal Form (Form Ii)
Length = 264
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 184 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 240
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 241 ALSVVTWNS 249
>pdb|1LD4|A Chain A, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|B Chain B, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|C Chain C, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|D Chain D, Placement Of The Structural Proteins In Sindbis Virus
pdb|3J0F|A Chain A, Sindbis Virion
pdb|3J0F|B Chain B, Sindbis Virion
pdb|3J0F|C Chain C, Sindbis Virion
pdb|3J0F|D Chain D, Sindbis Virion
Length = 264
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 418 HPDMVATYSGSAQVFEGHPFIVEAGVSVGGKDVKQGLNIFRFANRIPLLFEQGGDVVTRT 477
HP+ + A + G F + GV GG+ G I + R+ + G D TRT
Sbjct: 184 HPEGFYNWHHGAVQYSGGRFTIPRGV--GGRG-DSGRPIMDNSGRVVAIVLGGADEGTRT 240
Query: 478 AMKRINWSS 486
A+ + W+S
Sbjct: 241 ALSVVTWNS 249
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.134 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,769,917
Number of Sequences: 62578
Number of extensions: 647865
Number of successful extensions: 1514
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1472
Number of HSP's gapped (non-prelim): 38
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
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)