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= 026613
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 59/134 (44%), Gaps = 30/134 (22%)
Query: 17 VSSGIITVERVMYKDNDNEKRILQR----WYWALVVGTPRCSKGVISAPL---------G 63
+SG+I V + + +++ +R Y A V G P ++G++ PL
Sbjct: 64 ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQ 123
Query: 64 KVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCA 123
KV + GK A T Y+V++ + + L P+TGR HQLRVH
Sbjct: 124 KVCYETGKP----------------AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXL 167
Query: 124 EVLGTPIVGDYKYG 137
LG PI+GD Y
Sbjct: 168 -ALGHPILGDRFYA 180
>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 = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 55/99 (55%), Gaps = 8/99 (8%)
Query: 39 LQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKP 98
+Q+ Y ALV G + + APL K ++ +G +RI V+ + + + TR++V +
Sbjct: 84 MQKDYLALVRGQWQSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEER 137
Query: 99 SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
T ++ SP+TGR HQ+RVH + G PI D +YG
Sbjct: 138 YAFA-TLVRCSPVTGRTHQIRVHT-QYAGHPIAFDDRYG 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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 54/98 (55%), Gaps = 8/98 (8%)
Query: 40 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS 99
Q+ Y ALV G + + APL K ++ +G +RI V+ + + + TR++V +
Sbjct: 82 QKDYLALVRGQWQSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEERY 135
Query: 100 CHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
T ++ SP+TGR HQ+RVH + G PI D +YG
Sbjct: 136 AFA-TLVRCSPVTGRTHQIRVHT-QYAGHPIAFDDRYG 171
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 89 AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
AVT Y++++ +T L+L TGR HQ+RVH A + P+VGD YG
Sbjct: 207 AVTHYRIME-HFRVHTRLRLRLETGRTHQIRVHMAHIT-HPLVGDPVYG 253
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 89 AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 137
AVT Y++ + +T L+L TGR HQ+RVH A + P+VGD YG
Sbjct: 231 AVTHYRIXE-HFRVHTRLRLRLETGRTHQIRVHXAHIT-HPLVGDPVYG 277
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 89 AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 139
AVT Y++ + +T L+L TGR HQ+RVH A + P+VGD YG +
Sbjct: 134 AVTHYRIXE-HFRVHTRLRLRLETGRTHQIRVHXAHIT-HPLVGDPVYGGR 182
>pdb|2J0A|A Chain A, Structure Of The Catalytic Domain Of Mouse Manic Fringe
pdb|2J0B|A Chain A, Structure Of The Catalytic Domain Of Mouse Manic Fringe In
Complex With Udp And Manganese
Length = 280
Score = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 160 IPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKL 219
+P + T+ + ++ + G L+ P H H + + L +Q ++V LS G KL +KL
Sbjct: 188 LPDDCTVGYIIECKLGGRLQPSPLFHSHLETLQLLGAAQLPEQVTLSYGVFEGKLNVIKL 247
Query: 220 VAPL 223
P
Sbjct: 248 PGPF 251
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 0.132 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,399,596
Number of Sequences: 62578
Number of extensions: 307029
Number of successful extensions: 533
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 525
Number of HSP's gapped (non-prelim): 10
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
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: 50 (23.9 bits)