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= psy2620
(441 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LV0|A Chain A, Crystal Structure Of The Rab Effector Guanine Nucleotide
Dissociation Inhibitor (Gdi) In Complex With A
Geranylgeranyl (Gg) Peptide
Length = 449
Score = 622 bits (1603), Expect = e-178, Method: Compositional matrix adjust.
Identities = 292/438 (66%), Positives = 355/438 (81%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFGSTL 60
MDEEYD IVLGTGL ECILSG++SV+GKKVLH+DRN YYGGES+SITPLEEL+ +F
Sbjct: 3 MDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLE 62
Query: 61 PDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKISKVP 120
T GRGRDWNVDLIPKFLMANG LVK+L++T VTRYL+FK VEGS+V+KGGKI KVP
Sbjct: 63 GPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVP 122
Query: 121 VDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFGLDPN 180
+ EALAS+LMG+FEKRRFR FLV++ F E DPKT++ ++PQ+ + +Y KF L +
Sbjct: 123 STETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQD 182
Query: 181 TKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQSFAR 240
DFTGHALALYR D+Y++ + TI RIKLYS+SLARYGKSPYLYP+YGLGELPQ FAR
Sbjct: 183 VIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFAR 242
Query: 241 LSAIYGGTYMLDKPVDEIVIENGKVVGVRSGTEIARCKQVYCDPSYVQDRVKKLNQVIRC 300
LSAIYGGTYML+KPVD+I++ENGKVVGV+S E+ARCKQ+ CDPSYV DRV+K QVIR
Sbjct: 243 LSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRI 302
Query: 301 ICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGWFIAMVSTTVETD 360
IC++ HPI NT DA SCQIIIPQ QVNRKSDIYV ++SY H V+A+G +IA+ STTVET
Sbjct: 303 ICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETT 362
Query: 361 NPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATTHFETVCTDVVNL 420
+PE E++P L+LL +KFV +SD YEP D G+ESQ+F S SYDATTHFET C D+ ++
Sbjct: 363 DPEKEVEPALELLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDI 422
Query: 421 FKRGTGEDFDFSKIKLEE 438
+KR G FDF +K ++
Sbjct: 423 YKRMAGSAFDFENMKRKQ 440
>pdb|1GND|A Chain A, Guanine Nucleotide Dissociation Inhibitor, Alpha-Isoform
Length = 447
Score = 621 bits (1602), Expect = e-178, Method: Compositional matrix adjust.
Identities = 292/438 (66%), Positives = 355/438 (81%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFGSTL 60
MDEEYD IVLGTGL ECILSG++SV+GKKVLH+DRN YYGGES+SITPLEEL+ +F
Sbjct: 1 MDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLE 60
Query: 61 PDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKISKVP 120
T GRGRDWNVDLIPKFLMANG LVK+L++T VTRYL+FK VEGS+V+KGGKI KVP
Sbjct: 61 GPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVP 120
Query: 121 VDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFGLDPN 180
+ EALAS+LMG+FEKRRFR FLV++ F E DPKT++ ++PQ+ + +Y KF L +
Sbjct: 121 STETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQD 180
Query: 181 TKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQSFAR 240
DFTGHALALYR D+Y++ + TI RIKLYS+SLARYGKSPYLYP+YGLGELPQ FAR
Sbjct: 181 VIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFAR 240
Query: 241 LSAIYGGTYMLDKPVDEIVIENGKVVGVRSGTEIARCKQVYCDPSYVQDRVKKLNQVIRC 300
LSAIYGGTYML+KPVD+I++ENGKVVGV+S E+ARCKQ+ CDPSYV DRV+K QVIR
Sbjct: 241 LSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRI 300
Query: 301 ICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGWFIAMVSTTVETD 360
IC++ HPI NT DA SCQIIIPQ QVNRKSDIYV ++SY H V+A+G +IA+ STTVET
Sbjct: 301 ICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETT 360
Query: 361 NPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATTHFETVCTDVVNL 420
+PE E++P L+LL +KFV +SD YEP D G+ESQ+F S SYDATTHFET C D+ ++
Sbjct: 361 DPEKEVEPALELLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDI 420
Query: 421 FKRGTGEDFDFSKIKLEE 438
+KR G FDF +K ++
Sbjct: 421 YKRMAGSAFDFENMKRKQ 438
>pdb|1D5T|A Chain A, Guanine Nucleotide Dissociation Inhibitor, Alpha-Isoform
Length = 433
Score = 617 bits (1591), Expect = e-177, Method: Compositional matrix adjust.
Identities = 291/431 (67%), Positives = 350/431 (81%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFGSTL 60
MDEEYD IVLGTGL ECILSG++SV+GKKVLH+DRN YYGGES+SITPLEEL+ +F
Sbjct: 3 MDEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESSSITPLEELYKRFQLLE 62
Query: 61 PDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKISKVP 120
T GRGRDWNVDLIPKFLMANG LVK+L++T VTRYL+FK VEGS+V+KGGKI KVP
Sbjct: 63 GPPETMGRGRDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVVEGSFVYKGGKIYKVP 122
Query: 121 VDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFGLDPN 180
+ EALAS+LMG+FEKRRFR FLV++ F E DPKT++ ++PQ+ + +Y KF L +
Sbjct: 123 STETEALASNLMGMFEKRRFRKFLVFVANFDENDPKTFEGVDPQNTSMRDVYRKFDLGQD 182
Query: 181 TKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQSFAR 240
DFTGHALALYR D+Y++ + TI RIKLYS+SLARYGKSPYLYP+YGLGELPQ FAR
Sbjct: 183 VIDFTGHALALYRTDDYLDQPCLETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFAR 242
Query: 241 LSAIYGGTYMLDKPVDEIVIENGKVVGVRSGTEIARCKQVYCDPSYVQDRVKKLNQVIRC 300
LSAIYGGTYML+KPVD+I++ENGKVVGV+S E+ARCKQ+ CDPSYV DRV+K QVIR
Sbjct: 243 LSAIYGGTYMLNKPVDDIIMENGKVVGVKSEGEVARCKQLICDPSYVPDRVRKAGQVIRI 302
Query: 301 ICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGWFIAMVSTTVETD 360
IC++ HPI NT DA SCQIIIPQ QVNRKSDIYV ++SY H V+A+G +IA+ STTVET
Sbjct: 303 ICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISYAHNVAAQGKYIAIASTTVETT 362
Query: 361 NPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATTHFETVCTDVVNL 420
+PE E++P L LL +KFV +SD YEP D G+ESQ+F S SYDATTHFET C D+ ++
Sbjct: 363 DPEKEVEPALGLLEPIDQKFVAISDLYEPIDDGSESQVFCSCSYDATTHFETTCNDIKDI 422
Query: 421 FKRGTGEDFDF 431
+KR G FDF
Sbjct: 423 YKRMAGSAFDF 433
>pdb|3CPH|G Chain G, Crystal Structure Of Sec4 In Complex With Rab-Gdi
pdb|3CPH|H Chain H, Crystal Structure Of Sec4 In Complex With Rab-Gdi
pdb|3CPI|G Chain G, Crystal Structure Of Yeast Rab-Gdi
pdb|3CPI|H Chain H, Crystal Structure Of Yeast Rab-Gdi
pdb|3CPJ|G Chain G, Crystal Structure Of Ypt31 In Complex With Yeast Rab-Gdi
Length = 451
Score = 471 bits (1212), Expect = e-133, Method: Compositional matrix adjust.
Identities = 231/434 (53%), Positives = 313/434 (72%), Gaps = 8/434 (1%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFG--- 57
+D +YD IVLGTG+ ECILSG+LSV GKKVLHID+ +YGGE+AS+T L +L+ KF
Sbjct: 6 IDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVT-LSQLYEKFKQNP 64
Query: 58 -STLPDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKI 116
S E FG+ RDWNVDLIPKFLMANG L +LIHT VTRY++FK V GSYVFK GKI
Sbjct: 65 ISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKI 124
Query: 117 SKVPVDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFG 176
KVP ++ EA++S LMG+FEKRR + FL +I + E D T + ++ T ++Y KFG
Sbjct: 125 YKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFG 184
Query: 177 LDPNTKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQ 236
L +TK+F GHA+AL+ +D+Y+ A + RI LY S+ARYGKSPYLYPMYGLGELPQ
Sbjct: 185 LGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQ 244
Query: 237 SFARLSAIYGGTYMLDKPVDEIVI--ENGKVVGVRSGTEIARCKQVYCDPSYVQDRVKKL 294
FARLSAIYGGTYMLD P+DE++ + GK GV++ + V DP+Y ++ K
Sbjct: 245 GFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKST 304
Query: 295 NQ-VIRCICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGWFIAMV 353
Q VIR IC+++HP+PNT +A S QIIIPQ Q+ RKSDIYV++VS H V +KG ++A++
Sbjct: 305 GQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAII 364
Query: 354 STTVETDNPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATTHFETV 413
ST +ETD P +E++P LLG ++KF+ +++ +EP + G++ I++S SYDA++HFE++
Sbjct: 365 STIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESM 424
Query: 414 CTDVVNLFKRGTGE 427
DV +++ R TG
Sbjct: 425 TDDVKDIYFRVTGH 438
>pdb|1UKV|G Chain G, Structure Of Rabgdp-Dissociation Inhibitor In Complex With
Prenylated Ypt1 Gtpase
pdb|2BCG|G Chain G, Structure Of Doubly Prenylated Ypt1:gdi Complex
Length = 453
Score = 471 bits (1212), Expect = e-133, Method: Compositional matrix adjust.
Identities = 231/434 (53%), Positives = 313/434 (72%), Gaps = 8/434 (1%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFG--- 57
+D +YD IVLGTG+ ECILSG+LSV GKKVLHID+ +YGGE+AS+T L +L+ KF
Sbjct: 8 IDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVT-LSQLYEKFKQNP 66
Query: 58 -STLPDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKI 116
S E FG+ RDWNVDLIPKFLMANG L +LIHT VTRY++FK V GSYVFK GKI
Sbjct: 67 ISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKI 126
Query: 117 SKVPVDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFG 176
KVP ++ EA++S LMG+FEKRR + FL +I + E D T + ++ T ++Y KFG
Sbjct: 127 YKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFG 186
Query: 177 LDPNTKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQ 236
L +TK+F GHA+AL+ +D+Y+ A + RI LY S+ARYGKSPYLYPMYGLGELPQ
Sbjct: 187 LGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQ 246
Query: 237 SFARLSAIYGGTYMLDKPVDEIVI--ENGKVVGVRSGTEIARCKQVYCDPSYVQDRVKKL 294
FARLSAIYGGTYMLD P+DE++ + GK GV++ + V DP+Y ++ K
Sbjct: 247 GFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKST 306
Query: 295 NQ-VIRCICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGWFIAMV 353
Q VIR IC+++HP+PNT +A S QIIIPQ Q+ RKSDIYV++VS H V +KG ++A++
Sbjct: 307 GQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAII 366
Query: 354 STTVETDNPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATTHFETV 413
ST +ETD P +E++P LLG ++KF+ +++ +EP + G++ I++S SYDA++HFE++
Sbjct: 367 STIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESM 426
Query: 414 CTDVVNLFKRGTGE 427
DV +++ R TG
Sbjct: 427 TDDVKDIYFRVTGH 440
>pdb|3P1W|A Chain A, Crystal Structure Of Rab Gdi From Plasmodium Falciparum,
Pfl2060c
Length = 475
Score = 429 bits (1103), Expect = e-120, Method: Compositional matrix adjust.
Identities = 218/443 (49%), Positives = 299/443 (67%), Gaps = 15/443 (3%)
Query: 3 EEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASITPLEELFSKFGSTLPD 62
E YD I+LGTGLKECILSG+LS GKK+L +DRN YYGGE+AS+ L L++ F
Sbjct: 19 EHYDVIILGTGLKECILSGLLSHYGKKILVLDRNPYYGGETASLN-LTNLYNTFKPKENI 77
Query: 63 EVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGK------- 115
+G R WNVDLIPKF++ G+LVK+L T VT YLE+ VEGSYV++ K
Sbjct: 78 PSKYGENRHWNVDLIPKFILVGGNLVKILKKTRVTNYLEWLVVEGSYVYQHQKKGFLTSE 137
Query: 116 --ISKVPVDQKEALASDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYD 173
I KVP EAL S L+ L EK R +NF Y+ E+ TW +++P T ++Y
Sbjct: 138 KFIHKVPATDMEALVSPLLSLMEKNRCKNFYQYVSEWDANKRNTWDNLDPYKLTMLEIYK 197
Query: 174 KFGLDPNTKDFTGHALALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGE 233
F L T DF GHA+ALY +D+Y+ A T+ RIKLY S++ +GKSP++YP+YGLG
Sbjct: 198 HFNLCQLTIDFLGHAVALYLNDDYLKQPAYLTLERIKLYMQSISAFGKSPFIYPLYGLGG 257
Query: 234 LPQSFARLSAIYGGTYMLDKPVDEIVIEN-GKVVGVRSGT-EIARCKQVYCDPSYV---Q 288
+P+ F+R+ AI GGT+ML+K V + V ++ KV G++S EIA C +V CDPSYV +
Sbjct: 258 IPEGFSRMCAINGGTFMLNKNVVDFVFDDDNKVCGIKSSDGEIAYCDKVICDPSYVMHLK 317
Query: 289 DRVKKLNQVIRCICLMDHPIPNTKDALSCQIIIPQKQVNRKSDIYVSLVSYTHQVSAKGW 348
+++KK+ QVIRCIC++ +PIP T SCQIIIPQ Q+NRKSDIY++LVS+ H V+ KG
Sbjct: 318 NKIKKIGQVIRCICILSNPIPETNQTNSCQIIIPQNQLNRKSDIYINLVSFQHGVTLKGK 377
Query: 349 FIAMVSTTVETDNPELEIKPGLDLLGSYKKKFVTVSDYYEPTDLGTESQIFISTSYDATT 408
+IA+VS TVET+NP EI+ L+LLG+ ++KFV +SD Y T IF+++SYDAT+
Sbjct: 378 YIAIVSATVETNNPIKEIEKPLELLGTIEEKFVKISDLYVSTSKKPADNIFVTSSYDATS 437
Query: 409 HFETVCTDVVNLFKRGTGEDFDF 431
HFET D++ +++ G+ +F
Sbjct: 438 HFETATNDLLQIWENLWGQKLNF 460
>pdb|1LTX|R Chain R, Structure Of Rab Escort Protein-1 In Complex With Rab
Geranylgeranyl Transferase And Isoprenoid
Length = 650
Score = 124 bits (312), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 62/193 (32%), Positives = 104/193 (53%), Gaps = 6/193 (3%)
Query: 69 GRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKISKVPVDQKEALA 128
GR +N+DL+ K L + G L+ LLI + V+RY EFK++ F+ G + +VP + +
Sbjct: 221 GRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFN 280
Query: 129 SDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFGLDPNTKDFTGHA 188
S + + EKR FL + E+ E P ++ + T ++ L PN + F H+
Sbjct: 281 SKQLTMVEKRMLMKFLTFCVEYEE-HPDEYRAY--EGTTFSEYLKTQKLTPNLQYFVLHS 337
Query: 189 LALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQSFARLSAIYGGT 248
+A+ + + ++ K + L RYG +P+L+P+YG GELPQ F R+ A++GG
Sbjct: 338 IAMTSE---TTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGI 394
Query: 249 YMLDKPVDEIVIE 261
Y L V +V++
Sbjct: 395 YCLRHSVQCLVVD 407
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 32/47 (68%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASIT 47
+ ++D IV+GTGL E I++ S SG++VLH+D YYGG AS +
Sbjct: 5 LPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFS 51
>pdb|1VG0|A Chain A, The Crystal Structures Of The Rep-1 Protein In Complex
With Monoprenylated Rab7 Protein
pdb|1VG9|A Chain A, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|C Chain C, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|E Chain E, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|G Chain G, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
Length = 650
Score = 124 bits (312), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 62/193 (32%), Positives = 104/193 (53%), Gaps = 6/193 (3%)
Query: 69 GRDWNVDLIPKFLMANGSLVKLLIHTGVTRYLEFKSVEGSYVFKGGKISKVPVDQKEALA 128
GR +N+DL+ K L + G L+ LLI + V+RY EFK++ F+ G + +VP + +
Sbjct: 221 GRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFN 280
Query: 129 SDLMGLFEKRRFRNFLVYIQEFSEADPKTWKDINPQSATTAQLYDKFGLDPNTKDFTGHA 188
S + + EKR FL + E+ E P ++ + T ++ L PN + F H+
Sbjct: 281 SKQLTMVEKRMLMKFLTFCVEYEE-HPDEYRAY--EGTTFSEYLKTQKLTPNLQYFVLHS 337
Query: 189 LALYRDDEYINDLAIHTIRRIKLYSDSLARYGKSPYLYPMYGLGELPQSFARLSAIYGGT 248
+A+ + + ++ K + L RYG +P+L+P+YG GELPQ F R+ A++GG
Sbjct: 338 IAMTSE---TTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGI 394
Query: 249 YMLDKPVDEIVIE 261
Y L V +V++
Sbjct: 395 YCLRHSVQCLVVD 407
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 32/47 (68%)
Query: 1 MDEEYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESASIT 47
+ ++D IV+GTGL E I++ S SG++VLH+D YYGG AS +
Sbjct: 5 LPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFS 51
>pdb|3HDQ|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDQ|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase
(Oxidized Form) In Complex With Substrate
pdb|3HDY|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HDY|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase (Reduced
Form) In Complex With Substrate
pdb|3HE3|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3HE3|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Udp
pdb|3MJ4|A Chain A, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|B Chain B, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|C Chain C, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|D Chain D, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|E Chain E, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|F Chain F, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|G Chain G, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|H Chain H, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|I Chain I, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
pdb|3MJ4|J Chain J, Crystal Structure Of Udp-Galactopyranose Mutase In
Complex With Phosphonate Analog Of Udp-Galactopyranose
Length = 397
Score = 35.0 bits (79), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGES 43
+D +++G G +L+ L+ SG++VL +DR + GG +
Sbjct: 30 FDYLIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGNA 68
>pdb|1MO9|A Chain A, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE Complexed With 2-Ketopropyl
Coenzyme M
pdb|1MO9|B Chain B, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE Complexed With 2-Ketopropyl
Coenzyme M
pdb|1MOK|A Chain A, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE
pdb|1MOK|B Chain B, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE
pdb|1MOK|C Chain C, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE
pdb|1MOK|D Chain D, Nadph Dependent 2-Ketopropyl Coenzyme M
OxidoreductaseCARBOXYLASE
pdb|2C3D|A Chain A, 2.15 Angstrom Crystal Structure Of 2-Ketopropyl Coenzyme M
Oxidoreductase Carboxylase With A Coenzyme M Disulfide
Bound At The Active Site
pdb|2C3D|B Chain B, 2.15 Angstrom Crystal Structure Of 2-Ketopropyl Coenzyme M
Oxidoreductase Carboxylase With A Coenzyme M Disulfide
Bound At The Active Site
pdb|2C3C|A Chain A, 2.01 Angstrom X-Ray Crystal Structure Of A Mixed Disulfide
Between Coenzyme M And Nadph-Dependent Oxidoreductase 2-
Ketopropyl Coenzyme M Carboxylase
pdb|2C3C|B Chain B, 2.01 Angstrom X-Ray Crystal Structure Of A Mixed Disulfide
Between Coenzyme M And Nadph-Dependent Oxidoreductase 2-
Ketopropyl Coenzyme M Carboxylase
pdb|3Q6J|A Chain A, Structural Basis For Carbon Dioxide Binding By
2-Ketopropyl Coenzyme M OxidoreductaseCARBOXYLASE
pdb|3Q6J|B Chain B, Structural Basis For Carbon Dioxide Binding By
2-Ketopropyl Coenzyme M OxidoreductaseCARBOXYLASE
Length = 523
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 4 EYDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESA--SITPLEELFSKFGSTLP 61
EYDAI +G G S L G + L +DR + GG + P LFS + L
Sbjct: 43 EYDAIFIGGGAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVP-HHLFSDCAAELM 101
Query: 62 DEVTFGRGRDWNVDLIPKFL 81
TF G+ W D+ K +
Sbjct: 102 LARTF-SGQYWFPDMTEKVV 120
>pdb|1I8T|A Chain A, Strcuture Of Udp-Galactopyranose Mutase From E.Coli
pdb|1I8T|B Chain B, Strcuture Of Udp-Galactopyranose Mutase From E.Coli
Length = 367
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGES 43
YD I++G+GL + + L KKVL I++ + GG +
Sbjct: 2 YDYIIVGSGLFGAVCANELKKLNKKVLVIEKRNHIGGNA 40
>pdb|1H79|A Chain A, Structural Basis For Allosteric Substrate Specificity
Regulation In Class Iii Ribonucleotide Reductases: Nrdd
In Complex With Dttp
pdb|1H7A|A Chain A, Structural Basis For Allosteric Substrate Specificity
Regulation In Class Iii Ribonucleotide Reductases: Nrdd
In Complex With Datp
pdb|1H7B|A Chain A, Structural Basis For Allosteric Substrate Specificity
Regulation In Class Iii Ribonucleotide Reductases,
Native Nrdd
pdb|1H78|A Chain A, Structural Basis For Allosteric Substrate Specificity
Regulation In Class Iii Ribonucleotide Reductases: Nrdd
In Complex With Dctp.
pdb|1HK8|A Chain A, Structural Basis For Allosteric Substrate Specificity
Regulation In Class Iii Ribonucleotide Reductases: Nrdd
In Complex With Dgtp
Length = 605
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 52 LFSKFGSTLPDEVTFGRGRDWNVDLIPKFLMANGSLVKLLIHTGVT 97
LFS G T +TFG G DW +I K ++ N +K L G+T
Sbjct: 185 LFSSNGQTPFVTITFGTGTDWTERMIQKAILKN--RIKGLGRDGIT 228
>pdb|3K7M|X Chain X, Crystal Structure Of 6-Hydroxy-L-Nicotine Oxidase From
Arthrobacter Nicotinovorans
pdb|3K7Q|X Chain X, Crystal Structure Of Substrate-Bound
6-Hydroxy-L-Nicotine Oxidase From Arthrobacter
Nicotinovorans
pdb|3NG7|X Chain X, Complex Of Dithionite-Reduced 6-Hydroxy-L-Nicotine
Oxidase With Substrate Bound At Active Site And
Inhibitor At Exit Cavity
pdb|3NGC|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With
Intermediate Methylmyosmine Product Formed During
Catalytic Turnover
pdb|3NH3|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Final
Ketone Product Formed During Catalytic Turnover
pdb|3NHO|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Product
Bound At Active Site
pdb|3NK0|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Inhibitor
Bound At Active Site And Turnover Product At Exit
Cavity
pdb|3NK1|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Serotonin
pdb|3NK2|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Dopamine
pdb|3NN6|X Chain X, Crystal Structure Of Inhibitor-Bound In Active Centre
6-Hydroxy-L- Nicotine Oxidase From Arthrobacter
Nicotinovorans
pdb|3NN0|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With
Nicotinamide
Length = 431
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESAS 45
YDAIV+G G + L+ +GKKVL ++ + GG + S
Sbjct: 2 YDAIVVGGGFSGLKAARDLTNAGKKVLLLEGGERLGGRAYS 42
>pdb|1KDG|A Chain A, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
pdb|1KDG|B Chain B, Crystal Structure Of The Flavin Domain Of Cellobiose
Dehydrogenase
Length = 546
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGES 43
YD I++G G I + LS +GKKVL ++R GG S
Sbjct: 8 YDYIIVGAGPGGIIAADRLSEAGKKVLLLER----GGPS 42
>pdb|1NAA|A Chain A, Cellobiose Dehydrogenase Flavoprotein Fragment In
Complex With Cellobionolactam
pdb|1NAA|B Chain B, Cellobiose Dehydrogenase Flavoprotein Fragment In
Complex With Cellobionolactam
Length = 541
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGES 43
YD I++G G I + LS +GKKVL ++R GG S
Sbjct: 3 YDYIIVGAGPGGIIAADRLSEAGKKVLLLER----GGPS 37
>pdb|3K7T|A Chain A, Crystal Structure Of Apo-Form 6-Hydroxy-L-Nicotine
Oxidase, Crystal Form P3121
pdb|3K7T|B Chain B, Crystal Structure Of Apo-Form 6-Hydroxy-L-Nicotine
Oxidase, Crystal Form P3121
Length = 425
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 5 YDAIVLGTGLKECILSGMLSVSGKKVLHIDRNKYYGGESAS 45
YDAIV+G G + L+ +GKKVL ++ + GG + S
Sbjct: 2 YDAIVVGGGFSGLKAARDLTNAGKKVLLLEGGERLGGRAYS 42
>pdb|1M7S|A Chain A, Crystal Structure Analysis Of Catalase Catf Of Pseudomonas
Syringae
pdb|1M7S|B Chain B, Crystal Structure Analysis Of Catalase Catf Of Pseudomonas
Syringae
pdb|1M7S|C Chain C, Crystal Structure Analysis Of Catalase Catf Of Pseudomonas
Syringae
pdb|1M7S|D Chain D, Crystal Structure Analysis Of Catalase Catf Of Pseudomonas
Syringae
Length = 484
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 79 KFLMANG-SLVKLLIHTGVTRYLEF--KSVEGSYVFKGGKISKVPVDQKEALASDLMGLF 135
+F+ NG KL+ G Y++F KS++G ++++V L +DL+G
Sbjct: 186 RFMDGNGVHAYKLVNAKGEVHYVKFHWKSLQGIKNLDPKEVAQVQSKDYSHLTNDLVGAI 245
Query: 136 EKRRFRNFLVYIQ 148
+K F + +Y+Q
Sbjct: 246 KKGDFPKWDLYVQ 258
>pdb|2JH8|A Chain A, The Structure Of Bluetongue Virus Vp4 Reveals A
Multifunctional Rna-capping Production-line
pdb|2JH9|A Chain A, The Structure Of Bluetongue Virus Vp4 Reveals A
Multifunctional Rna-Capping Production-Line
pdb|2JHA|A Chain A, The Structure Of Bluetongue Virus Vp4 Reveals A
Multifunctional Rna-Capping Production-Line
pdb|2JHC|A Chain A, The Structure Of Bluetongue Virus Vp4 Reveals A
Multifunctional Rna-Capping Production-Line
pdb|2JHP|A Chain A, The Structure Of Bluetongue Virus Vp4 Reveals A
Multifunctional Rna-Capping Production-Line
Length = 644
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 19/79 (24%)
Query: 199 NDLAIHTIRRIKLYSDSLARYG-----------------KSPYLYPMYGLGELPQSFARL 241
N++ IR K + D+L Y +P L+ +YG+ E+P +
Sbjct: 104 NEIGRRRIRMRKGFGDALRNYAFKMAIEFHGSEAETLNDANPRLHKIYGMPEIPPLYMEY 163
Query: 242 SAIYGGTYMLDKPVDEIVI 260
+ I GT D+P DE ++
Sbjct: 164 AEI--GTRFDDEPTDEKLV 180
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
0.318 0.137 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,935,291
Number of Sequences: 62578
Number of extensions: 621489
Number of successful extensions: 1504
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1473
Number of HSP's gapped (non-prelim): 21
length of query: 441
length of database: 14,973,337
effective HSP length: 102
effective length of query: 339
effective length of database: 8,590,381
effective search space: 2912139159
effective search space used: 2912139159
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)