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= 032940
(130 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AQ5|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 488
Score = 28.1 bits (61), Expect = 1.4, Method: Composition-based stats.
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 9 PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
P E+ QP+ R FG++ K ++Y+++
Sbjct: 338 PSEETPEKPQPRRRSSFGIMIKAEEYILK 366
>pdb|3OOQ|A Chain A, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|B Chain B, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|C Chain C, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|D Chain D, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|E Chain E, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|F Chain F, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|G Chain G, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|H Chain H, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|I Chain I, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
pdb|3OOQ|J Chain J, Crystal Structure Of Amidohydrolase From Thermotoga
Maritima Msb8
Length = 396
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 9 PRRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPD 61
P+R + ER Q S + G +DY + K Y KK+E + KE F D
Sbjct: 158 PKRVYGERKQTPSTRX-GTAGVIRDYFTKVKNYXKKKELAQ--KEGKEFTETD 207
>pdb|1OED|E Chain E, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 260
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 9 PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
P E+ QP+ R FG++ K ++Y+++
Sbjct: 121 PSEETPEKPQPRRRSSFGIMIKAEEYILK 149
>pdb|4HOQ|A Chain A, Crystal Structure Of Full-length Human Ifit5
Length = 482
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 54 KAAFRNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQ 97
KA NPD Y+K+ + VH E+E KY +E L + +Q
Sbjct: 206 KAVTLNPDNSYIKVFLALKLQDVHA-EAEGEKYIEEILDQISSQ 248
>pdb|3ZGQ|A Chain A, Crystal Structure Of Human Interferon-induced Protein
Ifit5
pdb|4HOR|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligocytidine
pdb|4HOS|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligouridine
pdb|4HOT|A Chain A, Crystal Structure Of Full-length Human Ifit5 With
5`-triphosphate Oligoadenine
pdb|4J0U|A Chain A, Crystal Structure Of Ifit5/isg58
Length = 482
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 54 KAAFRNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQ 97
KA NPD Y+K+ + VH E+E KY +E L + +Q
Sbjct: 206 KAVTLNPDNSYIKVFLALKLQDVHA-EAEGEKYIEEILDQISSQ 248
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 72 IVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQSERN-------GRDKRNKIYI 121
I D VH + + EE+I+M Q + +IL GR K+ IY+
Sbjct: 152 IFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYV 208
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 0.133 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,512,817
Number of Sequences: 62578
Number of extensions: 125094
Number of successful extensions: 404
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 394
Number of HSP's gapped (non-prelim): 26
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
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: 45 (21.9 bits)