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= 023907
(275 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 = 70.9 bits (172), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 50/146 (34%), Positives = 79/146 (54%), Gaps = 22/146 (15%)
Query: 31 LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
LVHRLDRD+SG+L++ + +++ LH REK +Q+ Y ALV G
Sbjct: 51 LVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQKDYLALVRGQW 96
Query: 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
+ + APL K ++ +G +RI V+ + + + TR++V + T ++ SP+
Sbjct: 97 QSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEERYAFA-TLVRCSPV 149
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
TGR HQ+RVH + G PI D +YG
Sbjct: 150 TGRTHQIRVHT-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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 50/146 (34%), Positives = 78/146 (53%), Gaps = 22/146 (15%)
Query: 31 LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
LVHRLDRD+SG+L++ + +++ LH REK Q+ Y ALV G
Sbjct: 48 LVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------XQKDYLALVRGQW 93
Query: 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
+ + APL K ++ +G +RI V+ + + + TR++V + T ++ SP+
Sbjct: 94 QSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEERYAFA-TLVRCSPV 146
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
TGR HQ+RVH + G PI D +YG
Sbjct: 147 TGRTHQIRVHT-QYAGHPIAFDDRYG 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 = 60.8 bits (146), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 46/145 (31%), Positives = 69/145 (47%), Gaps = 22/145 (15%)
Query: 32 VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
VHRLD +SG++V+ T+ + L FRE R ++ Y A V G P
Sbjct: 58 VHRLDXATSGVIVVALTKAAERELKRQFRE--------------REPKKQYVARVWGHPS 103
Query: 92 CSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLT 151
++G++ PL + D + V + + A T Y+V++ + + L P+T
Sbjct: 104 PAEGLVDLPL---ICDWPNRPKQKVCYE----TGKPAQTEYEVVEYAADNTARVVLKPIT 156
Query: 152 GRKHQLRVHCAEVLGTPIVGDYKYG 176
GR HQLRVH LG PI+GD Y
Sbjct: 157 GRSHQLRVHXL-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 = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 41/146 (28%), Positives = 72/146 (49%), Gaps = 25/146 (17%)
Query: 31 LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
+VHRLD+D++G++V+ +T + T L ++R + R Y A+ +G
Sbjct: 133 IVHRLDKDTTGLMVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 177
Query: 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
+ G + P+ + + R + + + AVT Y++++ +T L+L
Sbjct: 178 MTAGGTVDEPISR-----HPTKRTHMAVHPM---GKPAVTHYRIME-HFRVHTRLRLRLE 228
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
TGR HQ+RVH A + P+VGD YG
Sbjct: 229 TGRTHQIRVHMAHIT-HPLVGDPVYG 253
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 41/146 (28%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 31 LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
+VHRLD+D++G+ V+ +T + T L ++R + R Y A+ +G
Sbjct: 60 IVHRLDKDTTGLXVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 104
Query: 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
+ G + P+ + + R + + AVT Y++ + +T L+L
Sbjct: 105 XTAGGTVDEPISR-----HPTKRTHXAVHP---XGKPAVTHYRIXE-HFRVHTRLRLRLE 155
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
TGR HQ+RVH A + P+VGD YG
Sbjct: 156 TGRTHQIRVHXAHIT-HPLVGDPVYG 180
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 41/146 (28%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 31 LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
+VHRLD+D++G+ V+ +T + T L ++R + R Y A+ +G
Sbjct: 157 IVHRLDKDTTGLXVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 201
Query: 91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
+ G + P+ + + R + + AVT Y++ + +T L+L
Sbjct: 202 XTAGGTVDEPISR-----HPTKRTHXAVHPM---GKPAVTHYRIXE-HFRVHTRLRLRLE 252
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
TGR HQ+RVH A + P+VGD YG
Sbjct: 253 TGRTHQIRVHXAHIT-HPLVGDPVYG 277
>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 = 0.077, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 199 IPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKL 258
+P + T+ + ++ + G L+ P H H + + L +Q ++V LS G KL +KL
Sbjct: 188 LPDDCTVGYIIECKLGGRLQPSPLFHSHLETLQLLGAAQLPEQVTLSYGVFEGKLNVIKL 247
Query: 259 VAPL 262
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 0.133 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,526,016
Number of Sequences: 62578
Number of extensions: 347825
Number of successful extensions: 648
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 7
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
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: 51 (24.3 bits)