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= 042710
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
Length = 264
Score = 115 bits (287), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 8/208 (3%)
Query: 23 PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
P +K L I YDG++Y GWQ Q ++Q +EKAL +V E + + A RTD GVH
Sbjct: 2 PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 58
Query: 83 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
GQV HF T D ++ +N LP DI VR + +FHARFSA ++ Y Y I
Sbjct: 59 GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 116
Query: 142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
YN + H L+ M AA+ +G++DF++F +Q R P +++
Sbjct: 117 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 174
Query: 202 FDVIEMGALLQLEVEGSGFLYRQVRNMV 229
+V G + ++++ + F++ VRN+V
Sbjct: 175 INVTRHGPYVVVDIKANAFVHHMVRNIV 202
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
Length = 270
Score = 114 bits (286), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 8/208 (3%)
Query: 23 PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
P +K L I YDG++Y GWQ Q ++Q +EKAL +V E + + A RTD GVH
Sbjct: 8 PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 64
Query: 83 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
GQV HF T D ++ +N LP DI VR + +FHARFSA ++ Y Y I
Sbjct: 65 GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 122
Query: 142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
YN + H L+ M AA+ +G++DF++F +Q R P +++
Sbjct: 123 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 180
Query: 202 FDVIEMGALLQLEVEGSGFLYRQVRNMV 229
+V G + ++++ + F++ VRN+V
Sbjct: 181 INVTRHGPYVVVDIKANAFVHHMVRNIV 208
>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
Length = 249
Score = 87.8 bits (216), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 66/203 (32%), Positives = 92/203 (45%), Gaps = 6/203 (2%)
Query: 29 LVIGYDGTRYAGWQFQ-TSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQV 87
L+ YDGT +AG Q Q T+Q +E+AL + L + V A RTD GVHA
Sbjct: 6 LLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKA----VAAGRTDAGVHALAMP 61
Query: 88 AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 147
H + S +E + ALN LLP D++V P+FHAR A + Y Y+I
Sbjct: 62 FH-VDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHP 120
Query: 148 DPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM 207
P H A L+ M EA +G+H+F F + +++ + E
Sbjct: 121 SPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEA 180
Query: 208 GALLQLEVEGSGFLYRQVRNMVN 230
G ++L G FL QVR MV
Sbjct: 181 GLEVRLYFRGKSFLRGQVRGMVG 203
>pdb|3ETC|A Chain A, 2.1 A Structure Of Acyl-Adenylate Synthetase From
Methanosarcina Acetivorans Containing A Link Between
Lys256 And Cys298
pdb|3ETC|B Chain B, 2.1 A Structure Of Acyl-Adenylate Synthetase From
Methanosarcina Acetivorans Containing A Link Between
Lys256 And Cys298
Length = 580
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 174 FVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGA 209
FV K DF ++ + Q N + L P F +DV+++ A
Sbjct: 31 FVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYA 66
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
0.323 0.138 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,464,784
Number of Sequences: 62578
Number of extensions: 302870
Number of successful extensions: 645
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 5
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)