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= 026204
(241 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 = 114 bits (286), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 76/214 (35%), Positives = 107/214 (50%), Gaps = 36/214 (16%)
Query: 28 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
V GG+ V + R E +DIPLDIVYED++++++NKP +VVHP GN GT++N
Sbjct: 57 KVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN 116
Query: 88 GILHHCSLPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAK 147
+LH+ P +A R GIVHRLDK T+GL+VVAK
Sbjct: 117 ALLHY--YPPIADVP-------------------------RAGIVHRLDKDTTGLMVVAK 149
Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
+ L E + I R Y ++ G + + G ++ PISR P R MA H
Sbjct: 150 TVPAQTRLVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAV------HP 202
Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
+ A + Y+++E + RLETGRTHQ
Sbjct: 203 MGKPAVTHYRIMEHFR--VHTRLRLRLETGRTHQ 234
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 109 bits (273), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 75/214 (35%), Positives = 104/214 (48%), Gaps = 36/214 (16%)
Query: 28 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
V GG+ V + R E +DIPLDIVYED++++++NKP +VVHP GN GT++N
Sbjct: 81 KVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN 140
Query: 88 GILHHCSLPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAK 147
+LH+ P +A R GIVHRLDK T+GL VVAK
Sbjct: 141 ALLHY--YPPIADVP-------------------------RAGIVHRLDKDTTGLXVVAK 173
Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
+ L E + I R Y ++ G + + G ++ PISR P R A H
Sbjct: 174 TVPAQTRLVESLQRREITREYEAVAIGHXT-AGGTVDEPISRHPTKRTHXAV------HP 226
Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
+ A + Y++ E + RLETGRTHQ
Sbjct: 227 MGKPAVTHYRIXEHFR--VHTRLRLRLETGRTHQ 258
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 72/196 (36%), Positives = 98/196 (50%), Gaps = 36/196 (18%)
Query: 46 RAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXX 105
R E +DIPLDIVYED++++V+NKP +VVHP GN GT++N +LH+ P +A
Sbjct: 2 RFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYY--PPIADVP--- 56
Query: 106 XXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIE 165
R GIVHRLDK T+GL VVAK + L E + I
Sbjct: 57 ----------------------RAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREIT 94
Query: 166 RVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGG 225
R Y ++ G + + G ++ PISR P R A H + A + Y++ E
Sbjct: 95 REYEAVAIGHXT-AGGTVDEPISRHPTKRTHXAV------HPXGKPAVTHYRIXEHFR-- 145
Query: 226 GSALVEWRLETGRTHQ 241
+ RLETGRTHQ
Sbjct: 146 VHTRLRLRLETGRTHQ 161
>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 = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 52/188 (27%), Positives = 83/188 (44%), Gaps = 38/188 (20%)
Query: 54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXX 113
L I+Y+DD++ VVNKP+ ++ P G L H S+ T +
Sbjct: 12 LVILYQDDHIXVVNKPSGLLSVP------GRLEE---HKDSVXTRIQRDYPQAES----- 57
Query: 114 XXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173
VHRLD TSG++VVA + + L QF+ ++ Y++
Sbjct: 58 ------------------VHRLDXATSGVIVVALTKAAERELKRQFREREPKKQYVARVW 99
Query: 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWR 233
G PS + G +++P+ D NR + + K Q + Y+V+E A +A V +
Sbjct: 100 GHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQ-----TEYEVVE-YAADNTARVVLK 153
Query: 234 LETGRTHQ 241
TGR+HQ
Sbjct: 154 PITGRSHQ 161
>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 = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 85/194 (43%), Gaps = 53/194 (27%)
Query: 56 IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXXXX 115
I+YEDD++LV+NKP+ VH G + G ++ G+
Sbjct: 7 ILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGL-------------------------- 39
Query: 116 XXXXXXXXGASIRPG-----IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYIS 170
++RP +VHRLD+ TSG+L+VAK + L EQ + +++ Y++
Sbjct: 40 ---------RALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLA 90
Query: 171 LTSGVPSQSSGRIEVPISRD---PNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 227
L G ++ P+ ++ RI + G + + +R+KV E A +
Sbjct: 91 LVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEG-------KPSETRFKVEERYA--FA 141
Query: 228 ALVEWRLETGRTHQ 241
LV TGRTHQ
Sbjct: 142 TLVRCSPVTGRTHQ 155
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 83/194 (42%), Gaps = 53/194 (27%)
Query: 56 IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXXXX 115
I YEDD++LV+NKP+ VH G + G ++ G+
Sbjct: 4 IXYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGL-------------------------- 36
Query: 116 XXXXXXXXGASIRPG-----IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYIS 170
++RP +VHRLD+ TSG+L+VAK + L EQ + ++ Y++
Sbjct: 37 ---------RALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKDYLA 87
Query: 171 LTSGVPSQSSGRIEVPISRD---PNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 227
L G ++ P+ ++ RI + G + + +R+KV E A +
Sbjct: 88 LVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEG-------KPSETRFKVEERYA--FA 138
Query: 228 ALVEWRLETGRTHQ 241
LV TGRTHQ
Sbjct: 139 TLVRCSPVTGRTHQ 152
>pdb|1HYU|A Chain A, Crystal Structure Of Intact Ahpf
Length = 521
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 24/37 (64%)
Query: 40 SELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHP 76
+E++ L AE ++ + +++DN L V KP+ ++ +P
Sbjct: 34 AEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNP 70
>pdb|1ZYN|A Chain A, Oxidized Structure Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
pdb|1ZYN|B Chain B, Oxidized Structure Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
pdb|1ZYP|A Chain A, Synchrotron Reduced Form Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
pdb|1ZYP|B Chain B, Synchrotron Reduced Form Of The N-Terminal Domain Of
Salmonella Typhimurium Ahpf
Length = 202
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 24/37 (64%)
Query: 40 SELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHP 76
+E++ L AE ++ + +++DN L V KP+ ++ +P
Sbjct: 34 AEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNP 70
>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 = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 30/55 (54%)
Query: 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRM 197
L + KD + A++ ++ K +E + S + + ++GR++ ++ PN +R+
Sbjct: 249 LKLIKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEMRI 303
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
0.316 0.132 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,655,191
Number of Sequences: 62578
Number of extensions: 242215
Number of successful extensions: 587
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 566
Number of HSP's gapped (non-prelim): 17
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)