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= 037167
(353 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
Synthase Rlud From Escherichia Coli
pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
Length = 325
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 75/249 (30%), Positives = 116/249 (46%), Gaps = 40/249 (16%)
Query: 75 IALNKPSGLQVLPGGLFQQRTVLNQLQWRXXXXXXXXXXXXXHPVPVHRLGRGTSGILLC 134
I +NKP L V PG TVLN L VHRL + T+G+++
Sbjct: 93 IIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI-----VHRLDKDTTGLMVV 147
Query: 135 AKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGI 194
AKT A+T + V L +R+IT+ Y A+ G + + +PI
Sbjct: 148 AKTVPAQTRL----------------VESLQRREITREYEAVAIGHMTAGGTV-DEPIS- 189
Query: 195 VRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHP 254
R+P + V P GKPA++ ++E R T +++ +++GR HQIR+H+A + HP
Sbjct: 190 -RHPTKRTHMAV-HPMGKPAVTHYRIMEH--FRVHTRLRLRLETGRTHQIRVHMAHITHP 245
Query: 255 LLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNE 314
L+GDP+Y GG+P+ G E ++ + LHA L L HP +
Sbjct: 246 LVGDPVY--GGRPRP-----------PKGASEAFISTLRKFDRQALHATMLRLYHPISGI 292
Query: 315 VIKITAPLP 323
++ AP+P
Sbjct: 293 EMEWHAPIP 301
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 74/249 (29%), Positives = 110/249 (44%), Gaps = 40/249 (16%)
Query: 75 IALNKPSGLQVLPGGLFQQRTVLNQLQWRXXXXXXXXXXXXXHPVPVHRLGRGTSGILLC 134
I +NKP L V PG TVLN L VHRL + T+G+ +
Sbjct: 20 IVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI-----VHRLDKDTTGLXVV 74
Query: 135 AKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGI 194
AKT A+T + V L +R+IT+ Y A+ G + +PI
Sbjct: 75 AKTVPAQTRL----------------VESLQRREITREYEAVAIGHXTAGGTV-DEPIS- 116
Query: 195 VRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHP 254
R+P + P GKPA++ + E R T +++ +++GR HQIR+H A + HP
Sbjct: 117 -RHP-TKRTHXAVHPXGKPAVTHYRIXEH--FRVHTRLRLRLETGRTHQIRVHXAHITHP 172
Query: 255 LLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNE 314
L+GDP+Y GG+P+ G E ++ + LHA L L HP +
Sbjct: 173 LVGDPVY--GGRPRP-----------PKGASEAFISTLRKFDRQALHATXLRLYHPISGI 219
Query: 315 VIKITAPLP 323
+ AP+P
Sbjct: 220 EXEWHAPIP 228
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 74/249 (29%), Positives = 110/249 (44%), Gaps = 40/249 (16%)
Query: 75 IALNKPSGLQVLPGGLFQQRTVLNQLQWRXXXXXXXXXXXXXHPVPVHRLGRGTSGILLC 134
I +NKP L V PG TVLN L VHRL + T+G+ +
Sbjct: 117 IIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI-----VHRLDKDTTGLXVV 171
Query: 135 AKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGI 194
AKT A+T + V L +R+IT+ Y A+ G + +PI
Sbjct: 172 AKTVPAQTRL----------------VESLQRREITREYEAVAIGHXTAGGTV-DEPIS- 213
Query: 195 VRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHP 254
R+P + P GKPA++ + E R T +++ +++GR HQIR+H A + HP
Sbjct: 214 -RHP-TKRTHXAVHPMGKPAVTHYRIXEH--FRVHTRLRLRLETGRTHQIRVHXAHITHP 269
Query: 255 LLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNE 314
L+GDP+Y GG+P+ G E ++ + LHA L L HP +
Sbjct: 270 LVGDPVY--GGRPRP-----------PKGASEAFISTLRKFDRQALHATXLRLYHPISGI 316
Query: 315 VIKITAPLP 323
+ AP+P
Sbjct: 317 EXEWHAPIP 325
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
Length = 231
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 60/208 (28%), Positives = 89/208 (42%), Gaps = 39/208 (18%)
Query: 121 VHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGI 180
VHRL R TSG+LL AK + A + +K D + V Q + + L+ I
Sbjct: 52 VHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNI 111
Query: 181 VDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGR 240
+ + I++ S GKP+ ++ V ER TLV+ +GR
Sbjct: 112 LQSGERIVR-----------------VSQEGKPSETRFKVEERYA--FATLVRCSPVTGR 152
Query: 241 PHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPV-PGDCGYY 299
HQIR+H + GHP+ +FD + D F +R + G +
Sbjct: 153 THQIRVHTQYAGHPI-------------AFDDRYGDREF------DRQLTEAGTGLNRLF 193
Query: 300 LHAYQLFLSHPTTNEVIKITAPLPSVLK 327
LHA L +HP T EV++I AP+ LK
Sbjct: 194 LHAAALKFTHPGTGEVMRIEAPMDEGLK 221
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
Length = 228
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 60/208 (28%), Positives = 87/208 (41%), Gaps = 39/208 (18%)
Query: 121 VHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGI 180
VHRL R TSG+LL AK + A + +K D + V Q + + L+ I
Sbjct: 49 VHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNI 108
Query: 181 VDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGR 240
+ + I++ S GKP+ ++ V ER TLV+ +GR
Sbjct: 109 LQSGERIVR-----------------VSQEGKPSETRFKVEERYA--FATLVRCSPVTGR 149
Query: 241 PHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPV-PGDCGYY 299
HQIR+H + GHP+ +FD + D F +R + G +
Sbjct: 150 THQIRVHTQYAGHPI-------------AFDDRYGDREF------DRQLTEAGTGLNRLF 190
Query: 300 LHAYQLFLSHPTTNEVIKITAPLPSVLK 327
LHA L +HP T EV +I AP LK
Sbjct: 191 LHAAALKFTHPGTGEVXRIEAPXDEGLK 218
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
Length = 217
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 56/188 (29%), Positives = 86/188 (45%), Gaps = 31/188 (16%)
Query: 77 LNKPSGLQVLPGGLFQQR-TVLNQLQWRXXXXXXXXXXXXXHPVPVHRLGRGTSGILLCA 135
+NKPSGL +PG L + + +V ++Q VHRL TSG+++ A
Sbjct: 24 VNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAES-----------VHRLDXATSGVIVVA 72
Query: 136 KTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIV 195
TK A+ + F +R+ K Y A V G + ++ P+ I
Sbjct: 73 LTKAAERELKRQF----------------REREPKKQYVARVWGHPSPAEGLVDLPL-IC 115
Query: 196 RYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPL 255
+P K V +GKPA ++ +V+E +V I +GR HQ+R+H LGHP+
Sbjct: 116 DWPNRPKQ-KVCYETGKPAQTEYEVVEYAADNTARVVLKPI-TGRSHQLRVHXLALGHPI 173
Query: 256 LGDPLYVA 263
LGD Y +
Sbjct: 174 LGDRFYAS 181
>pdb|3FHJ|B Chain B, Independent Saturation Of Three Trprs Subsites Generates A
Partially-Assembled State Similar To Those Observed In
Molecular Simulations
Length = 292
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 14/78 (17%)
Query: 180 IVDEDKVI---IKQPIGIVRYPGVAKGLYVASP-SGKPALSKVDVLERDVQ------RNC 229
++D+ K I IK G +RYPG++ L + S SG+ ++ LER +
Sbjct: 180 LLDDAKTIEKKIKSSEGTIRYPGISNLLNIYSTLSGQ----SIEELERQYEGKGYGVFKA 235
Query: 230 TLVQVEIQSGRPHQIRIH 247
L QV I++ RP Q R H
Sbjct: 236 DLAQVVIETLRPIQERYH 253
>pdb|1LI1|A Chain A, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|B Chain B, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|D Chain D, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
pdb|1LI1|E Chain E, The 1.9-A Crystal Structure Of The Noncollagenous (Nc1)
Domain Of Human Placenta Collagen Iv Shows Stabilization
Via A Novel Type Of Covalent Met-Lys Cross-Link
Length = 229
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 30/75 (40%), Gaps = 10/75 (13%)
Query: 263 AGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPL 322
A P S EF F + G G C YY +AY +L+ +E+ K P
Sbjct: 157 ALASPGSCLEEFRSAPFIECHGR--------GTCNYYANAYSFWLATIERSEMFK--KPT 206
Query: 323 PSVLKTREEGREVDK 337
PS LK E V +
Sbjct: 207 PSTLKAGELRTHVSR 221
>pdb|3FHJ|A Chain A, Independent Saturation Of Three Trprs Subsites Generates A
Partially-Assembled State Similar To Those Observed In
Molecular Simulations
Length = 300
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 14/78 (17%)
Query: 180 IVDEDKVI---IKQPIGIVRYPGVAKGLYVASP-SGKPALSKVDVLERDVQ------RNC 229
++D+ K I IK G +RYPG++ L + S SG+ ++ LER +
Sbjct: 188 LLDDAKTIEKKIKSSEGTIRYPGISNLLNIYSTLSGQ----SIEELERQYEGKGYGVFKA 243
Query: 230 TLVQVEIQSGRPHQIRIH 247
L QV I++ RP Q R H
Sbjct: 244 DLAQVVIETLRPIQERYH 261
>pdb|1M3D|A Chain A, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|B Chain B, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|D Chain D, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|E Chain E, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|G Chain G, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|H Chain H, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|J Chain J, Structure Of Type Iv Collagen Nc1 Domains
pdb|1M3D|K Chain K, Structure Of Type Iv Collagen Nc1 Domains
pdb|1T60|A Chain A, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|B Chain B, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|D Chain D, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|E Chain E, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|G Chain G, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|H Chain H, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|J Chain J, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|K Chain K, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|M Chain M, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|N Chain N, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|P Chain P, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|Q Chain Q, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|S Chain S, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|T Chain T, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|V Chain V, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T60|W Chain W, Crystal Structure Of Type Iv Collagen Nc1 Domain From
Bovine Lens Capsule
pdb|1T61|A Chain A, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|B Chain B, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|D Chain D, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
pdb|1T61|E Chain E, Crystal Structure Of Collagen Iv Nc1 Domain From Placenta
Basement Membrane
Length = 229
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 30/75 (40%), Gaps = 10/75 (13%)
Query: 263 AGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPL 322
A P S EF F + G G C YY +AY +L+ +E+ K P
Sbjct: 157 ALASPGSCLEEFRSAPFIECHGR--------GTCNYYANAYSFWLATIERSEMFK--KPT 206
Query: 323 PSVLKTREEGREVDK 337
PS LK E V +
Sbjct: 207 PSTLKAGELRTHVSR 221
>pdb|3FHJ|F Chain F, Independent Saturation Of Three Trprs Subsites Generates A
Partially-Assembled State Similar To Those Observed In
Molecular Simulations
Length = 297
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 14/78 (17%)
Query: 180 IVDEDKVI---IKQPIGIVRYPGVAKGLYVASP-SGKPALSKVDVLERDVQ------RNC 229
++D+ K I IK G +RYPG++ L + S SG+ ++ LER +
Sbjct: 185 LLDDAKTIEKKIKSSEGTIRYPGISNLLNIYSTLSGQ----SIEELERQYEGKGYGVFKA 240
Query: 230 TLVQVEIQSGRPHQIRIH 247
L QV I++ RP Q R H
Sbjct: 241 DLAQVVIETLRPIQERYH 258
>pdb|3C5M|A Chain A, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
pdb|3C5M|B Chain B, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
pdb|3C5M|C Chain C, Crystal Structure Of Oligogalacturonate Lyase (Vpa0088)
From Vibrio Parahaemolyticus. Northeast Structural
Genomics Consortium Target Vpr199
Length = 396
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 16/86 (18%)
Query: 185 KVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQR---------------NC 229
+ + +Q I V G +VA+ S L +++L+RD Q C
Sbjct: 110 ETLEEQVIYTVDEEWKGYGTWVAN-SDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTC 168
Query: 230 TLVQVEIQSGRPHQIRIHLAFLGHPL 255
L++V+I++G I A+LGHP+
Sbjct: 169 RLIKVDIETGELEVIHQDTAWLGHPI 194
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
0.319 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,487,337
Number of Sequences: 62578
Number of extensions: 442690
Number of successful extensions: 869
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 844
Number of HSP's gapped (non-prelim): 15
length of query: 353
length of database: 14,973,337
effective HSP length: 100
effective length of query: 253
effective length of database: 8,715,537
effective search space: 2205030861
effective search space used: 2205030861
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: 52 (24.6 bits)