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= 011530
(483 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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/196 (27%), Positives = 84/196 (42%), Gaps = 42/196 (21%)
Query: 220 IIAVTESHV-VLDKPAGT-SVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCV 277
+I + H+ V++KP+G SV G + ++S T R + H++D T G +
Sbjct: 13 VILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQA---ESVHRLDXATSGVI 69
Query: 278 VLARTQEYCSIFHRKIREKKVKKLYLALTTA-PLPVGIMTHYMRPINIAPRLVSEGWYLC 336
V+A T+ R+ RE++ KK Y+A P P +EG L
Sbjct: 70 VVALTKAAERELKRQFREREPKKQYVARVWGHPSP------------------AEG--LV 109
Query: 337 QLEVMECKKVPWPDATVGKAYSIEDCGWPSR----------DYAYECKIKLLTGRTHQVR 386
L ++ C WP+ K + G P++ D +K +TGR+HQ+R
Sbjct: 110 DLPLI-CD---WPNRPKQKV--CYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLR 163
Query: 387 AQLAACGAPIVGDSMY 402
A G PI+GD Y
Sbjct: 164 VHXLALGHPILGDRFY 179
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 52/200 (26%), Positives = 82/200 (41%), Gaps = 49/200 (24%)
Query: 220 IIAVTESHV-VLDKPAGTSVGGTTD---NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
+I + H+ VL+KP+GT+V G + + E A L H++D T G
Sbjct: 6 VILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA----RFLELVHRLDRDTSG 61
Query: 276 CVVLARTQEYCSIFHRKIREKKVKKLYLAL-----------TTAPLPVGIMTHYMRPINI 324
+++A+ + H ++REK ++K YLAL APL I+ R +
Sbjct: 62 VLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIV-- 119
Query: 325 APRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKL--LTGRT 382
R+ EG P T + +E+ YA+ ++ +TGRT
Sbjct: 120 --RVSQEG---------------KPSET---RFKVEE------RYAFATLVRCSPVTGRT 153
Query: 383 HQVRAQLAACGAPIVGDSMY 402
HQ+R G PI D Y
Sbjct: 154 HQIRVHTQYAGHPIAFDDRY 173
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 52/200 (26%), Positives = 81/200 (40%), Gaps = 49/200 (24%)
Query: 220 IIAVTESHV-VLDKPAGTSVGGTTD---NIEESCATFASRALGLTTPLRTTHQIDNCTEG 275
+I + H+ VL+KP+GT+V G + + E A L H++D T G
Sbjct: 3 VIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEA----RFLELVHRLDRDTSG 58
Query: 276 CVVLARTQEYCSIFHRKIREKKVKKLYLAL-----------TTAPLPVGIMTHYMRPINI 324
+++A+ + H ++REK +K YLAL APL I+ R +
Sbjct: 59 VLLVAKKRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIV-- 116
Query: 325 APRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKL--LTGRT 382
R+ EG P T + +E+ YA+ ++ +TGRT
Sbjct: 117 --RVSQEG---------------KPSET---RFKVEE------RYAFATLVRCSPVTGRT 150
Query: 383 HQVRAQLAACGAPIVGDSMY 402
HQ+R G PI D Y
Sbjct: 151 HQIRVHTQYAGHPIAFDDRY 170
>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 = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 373 CKIKLLTGRTHQVRAQLAACGAPIVGDSMY 402
+++L TGRTHQ+R +A P+VGD +Y
Sbjct: 223 LRLRLETGRTHQIRVHMAHITHPLVGDPVY 252
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 373 CKIKLLTGRTHQVRAQLAACGAPIVGDSMY 402
+++L TGRTHQ+R A P+VGD +Y
Sbjct: 150 LRLRLETGRTHQIRVHXAHITHPLVGDPVY 179
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 373 CKIKLLTGRTHQVRAQLAACGAPIVGDSMY 402
+++L TGRTHQ+R A P+VGD +Y
Sbjct: 247 LRLRLETGRTHQIRVHXAHITHPLVGDPVY 276
>pdb|3AQO|A Chain A, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|B Chain B, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|C Chain C, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
pdb|3AQO|D Chain D, Structure And Function Of A Membrane Component Secdf That
Enhances Protein Export
Length = 229
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 123 PPLFV-ADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSI 172
PPL ADL AV+ P+ LT TPE + F+EVT ++ KR +I
Sbjct: 123 PPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNI-GKRLAI 172
>pdb|3AQP|A Chain A, Crystal Structure Of Secdf, A Translocon-Associated
Membrane Protein, From Thermus Thrmophilus
pdb|3AQP|B Chain B, Crystal Structure Of Secdf, A Translocon-Associated
Membrane Protein, From Thermus Thrmophilus
Length = 741
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 123 PPLFV-ADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSI 172
PPL ADL AV+ P+ LT TPE + F+EVT ++ KR +I
Sbjct: 157 PPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNI-GKRLAI 206
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
0.321 0.135 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,598,551
Number of Sequences: 62578
Number of extensions: 591935
Number of successful extensions: 1135
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1119
Number of HSP's gapped (non-prelim): 14
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)