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= 042463
(490 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 61/204 (29%), Positives = 88/204 (43%), Gaps = 45/204 (22%)
Query: 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDYNEGPK----------LVH 253
++ Y D ILVLNKP + G S+ EG + LVH
Sbjct: 6 VILYEDDHILVLNKPSGTAVHG------------GSGLSFGVIEGLRALRPEARFLELVH 53
Query: 254 RLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKE 313
RLDR++SG+LL+ + + ++ +SL + + + M + Y ALV G +
Sbjct: 54 RLDRDTSGVLLVAKKRSAL-------------RSLHEQLRE--KGMQKDYLALVRGQWQS 98
Query: 314 KQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTC 373
+ APL K +L G ERI+ G + E R + CS P+T
Sbjct: 99 HVKSVQAPLLKNILQSG--ERIVRVSQEGKPSETRFKVEERYAFATLVRCS-----PVTG 151
Query: 374 RKHQLRVHCAEALGTPIVGDYKYG 397
R HQ+RVH A G PI D +YG
Sbjct: 152 RTHQIRVHTQYA-GHPIAFDDRYG 174
>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 = 65.1 bits (157), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 60/204 (29%), Positives = 83/204 (40%), Gaps = 45/204 (22%)
Query: 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDYNEGPK----------LVH 253
++ Y D ILVLNKP + G S+ EG + LVH
Sbjct: 3 VIXYEDDHILVLNKPSGTAVHG------------GSGLSFGVIEGLRALRPEARFLELVH 50
Query: 254 RLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKE 313
RLDR++SG+LL+ + + ++ L + K Y ALV G +
Sbjct: 51 RLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKD---------------YLALVRGQWQS 95
Query: 314 KQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTC 373
+ APL K +L G ERI+ G + E R + CS P+T
Sbjct: 96 HVKSVQAPLLKNILQSG--ERIVRVSQEGKPSETRFKVEERYAFATLVRCS-----PVTG 148
Query: 374 RKHQLRVHCAEALGTPIVGDYKYG 397
R HQ+RVH A G PI D +YG
Sbjct: 149 RTHQIRVHTQYA-GHPIAFDDRYG 171
>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 = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 59/195 (30%), Positives = 87/195 (44%), Gaps = 28/195 (14%)
Query: 204 LVKYRDSAILVLNKPPKV-PLKGHLPVHNSMDXXXXXXXSYDYNEGPKLVHRLDRESSGL 262
++ Y+D I V+NKP + + G L H DY + + VHRLD +SG+
Sbjct: 13 VILYQDDHIXVVNKPSGLLSVPGRLEEHKD---SVXTRIQRDYPQA-ESVHRLDXATSGV 68
Query: 263 LLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPL 322
+++ TK + L F + K +Y A V G P +G++ PL
Sbjct: 69 IVVALTKAAERELKRQFREREPKK---------------QYVARVWGHPSPAEGLVDLPL 113
Query: 323 SKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHC 382
+ K Q E + A TEY V+ + + + L+P+T R HQLRVH
Sbjct: 114 ICDWPNRPK-------QKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHX 166
Query: 383 AEALGTPIVGDYKYG 397
ALG PI+GD Y
Sbjct: 167 L-ALGHPILGDRFYA 180
>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 = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 51/198 (25%), Positives = 91/198 (45%), Gaps = 34/198 (17%)
Query: 205 VKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDY---NEGPK--LVHRLDRES 259
+ Y D I+++NKP + + P + D + Y + P+ +VHRLD+++
Sbjct: 85 IVYEDEDIIIINKPRDLVVH---PGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 141
Query: 260 SGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIH 319
+GL+++ +T V T L + + + + + Y A+ IG G +
Sbjct: 142 TGLMVVAKT---VPAQTRLVESLQRRE------------ITREYEAVAIGH-MTAGGTVD 185
Query: 320 APLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLR 379
P+S+ T+R +A + + A+T YR++ + + LR T R HQ+R
Sbjct: 186 EPISR-----HPTKRTHMAVHP---MGKPAVTHYRIM-EHFRVHTRLRLRLETGRTHQIR 236
Query: 380 VHCAEALGTPIVGDYKYG 397
VH A + P+VGD YG
Sbjct: 237 VHMAH-ITHPLVGDPVYG 253
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 52/198 (26%), Positives = 88/198 (44%), Gaps = 34/198 (17%)
Query: 205 VKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDY---NEGPK--LVHRLDRES 259
+ Y D I+V+NKP + + P + D + Y + P+ +VHRLD+++
Sbjct: 12 IVYEDEDIIVINKPRDLVVH---PGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 68
Query: 260 SGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIH 319
+GL ++ +T V T L + + + + + Y A+ IG G +
Sbjct: 69 TGLXVVAKT---VPAQTRLVESLQRRE------------ITREYEAVAIGH-XTAGGTVD 112
Query: 320 APLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLR 379
P+S+ T+R A + + A+T YR+ + + LR T R HQ+R
Sbjct: 113 EPISR-----HPTKRTHXAVHP---XGKPAVTHYRIXE-HFRVHTRLRLRLETGRTHQIR 163
Query: 380 VHCAEALGTPIVGDYKYG 397
VH A + P+VGD YG
Sbjct: 164 VHXAH-ITHPLVGDPVYG 180
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 51/198 (25%), Positives = 88/198 (44%), Gaps = 34/198 (17%)
Query: 205 VKYRDSAILVLNKPPKVPLKGHLPVHNSMDXXXXXXXSYDY---NEGPK--LVHRLDRES 259
+ Y D I+++NKP + + P + D + Y + P+ +VHRLD+++
Sbjct: 109 IVYEDEDIIIINKPRDLVVH---PGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 165
Query: 260 SGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIH 319
+GL ++ +T V T L + + + + + Y A+ IG G +
Sbjct: 166 TGLXVVAKT---VPAQTRLVESLQRRE------------ITREYEAVAIGH-XTAGGTVD 209
Query: 320 APLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLR 379
P+S+ T+R A + + A+T YR+ + + LR T R HQ+R
Sbjct: 210 EPISR-----HPTKRTHXAVHP---MGKPAVTHYRIX-EHFRVHTRLRLRLETGRTHQIR 260
Query: 380 VHCAEALGTPIVGDYKYG 397
VH A + P+VGD YG
Sbjct: 261 VHXAH-ITHPLVGDPVYG 277
>pdb|1OGC|A Chain A, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGC|B Chain B, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGC|C Chain C, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGC|D Chain D, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGC|E Chain E, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGD|A Chain A, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGD|B Chain B, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGD|C Chain C, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGD|D Chain D, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGD|E Chain E, The Structure Of Bacillus Subtilis Rbsd Complexed With
D-Ribose
pdb|1OGE|A Chain A, The Structure Of Bacillus Subtilis Rbsd Complexed With
Ribose 5-Phosphate
pdb|1OGE|B Chain B, The Structure Of Bacillus Subtilis Rbsd Complexed With
Ribose 5-Phosphate
pdb|1OGE|C Chain C, The Structure Of Bacillus Subtilis Rbsd Complexed With
Ribose 5-Phosphate
pdb|1OGE|D Chain D, The Structure Of Bacillus Subtilis Rbsd Complexed With
Ribose 5-Phosphate
pdb|1OGE|E Chain E, The Structure Of Bacillus Subtilis Rbsd Complexed With
Ribose 5-Phosphate
pdb|1OGF|A Chain A, The Structure Of Bacillus Subtilis Rbsd Complexed With
Glycerol
pdb|1OGF|B Chain B, The Structure Of Bacillus Subtilis Rbsd Complexed With
Glycerol
pdb|1OGF|C Chain C, The Structure Of Bacillus Subtilis Rbsd Complexed With
Glycerol
pdb|1OGF|D Chain D, The Structure Of Bacillus Subtilis Rbsd Complexed With
Glycerol
pdb|1OGF|E Chain E, The Structure Of Bacillus Subtilis Rbsd Complexed With
Glycerol
Length = 131
Score = 29.3 bits (64), Expect = 5.0, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 313 EKQGIIHAPLSKVLLDDGKTERIILAQNSGL 343
+K GI+++ L+K+L D G T++I++A ++GL
Sbjct: 2 KKHGILNSHLAKILADLGHTDKIVIA-DAGL 31
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 0.136 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,619,206
Number of Sequences: 62578
Number of extensions: 670972
Number of successful extensions: 1394
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1376
Number of HSP's gapped (non-prelim): 7
length of query: 490
length of database: 14,973,337
effective HSP length: 103
effective length of query: 387
effective length of database: 8,527,803
effective search space: 3300259761
effective search space used: 3300259761
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)