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= 003997
(780 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 33/98 (33%), Positives = 51/98 (52%), Gaps = 7/98 (7%)
Query: 173 IPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKA-DTGEKVEISTSDANVQST 231
+PVKEYP +NF+G I GP T K+LE ET I V G + +K E + N +
Sbjct: 8 VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHL 67
Query: 232 YEEFHISISA-DSYEKVD-----AATDLIELLVTSVSG 263
E+ H+ I+ D+ + + A ++ +LLV + G
Sbjct: 68 NEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEG 105
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 171 VPIPVKEYPGYNFLGLIFGPASDTQKRLEKETRTVIKVYGTKADTGEKVEISTSDANVQS 230
V IP EYP NF+GL+ GP +T K +EKE I + G + KV D +
Sbjct: 11 VMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV--GRKDGQMLP 68
Query: 231 TYEE-FHISISADSYEKVDAATDLI 254
+E H ++A++ E V A + I
Sbjct: 69 GEDEPLHALVTANTMENVKKAVEQI 93
>pdb|4FXX|A Chain A, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|B Chain B, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|C Chain C, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|D Chain D, Structure Of Sf1 Coiled-coil Domain
Length = 112
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 8/84 (9%)
Query: 87 RALAYQTRVDQIVQQLESGSLEAEENQVPEVAA------QNADQKSPNPQVDRELECLEL 140
RA Q +++ + ++L +G L N PE + N++ K N + R + LE
Sbjct: 30 RAYIVQLQIEDLTRKLRTGDLGIPPN--PEDRSPSPEPIYNSEGKRLNTREFRTRKKLEE 87
Query: 141 EKQEVIGEILKLNPSYRTPPDYKP 164
E+ +I E++ LNP ++ P DYKP
Sbjct: 88 ERHNLITEMVALNPDFKPPADYKP 111
>pdb|2M0G|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 145
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 8/84 (9%)
Query: 87 RALAYQTRVDQIVQQLESGSLEAEENQVPEVAA------QNADQKSPNPQVDRELECLEL 140
RA Q +++ + ++L +G L N PE + N++ K N + R + LE
Sbjct: 50 RAYIVQLQIEDLTRKLRTGDLGIPPN--PEDRSPSPEPIYNSEGKRLNTREFRTRKKLEE 107
Query: 141 EKQEVIGEILKLNPSYRTPPDYKP 164
E+ +I E++ LNP ++ P DYKP
Sbjct: 108 ERHNLITEMVALNPDFKPPADYKP 131
>pdb|2M09|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 121
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 8/84 (9%)
Query: 87 RALAYQTRVDQIVQQLESGSLEAEENQVPEVAA------QNADQKSPNPQVDRELECLEL 140
RA Q +++ + ++L +G L N PE + N++ K N + R + LE
Sbjct: 26 RAYIVQLQIEDLTRKLRTGDLGIPPN--PEDRSPSPEPIYNSEGKRLNTREFRTRKKLEE 83
Query: 141 EKQEVIGEILKLNPSYRTPPDYKP 164
E+ +I E++ LNP ++ P DYKP
Sbjct: 84 ERHNLITEMVALNPDFKPPADYKP 107
>pdb|4FXW|B Chain B, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|D Chain D, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 124
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 87 RALAYQTRVDQIVQQLESGSL----EAEENQVPEVAAQNADQKSPNPQVDRELECLELEK 142
RA Q +++ + ++L +G L E+ N++ K N + R + LE E+
Sbjct: 42 RAYIVQLQIEDLTRKLRTGDLGIPPNPEDRXPXPEPIYNSEGKRLNTREFRTRKKLEEER 101
Query: 143 QEVIGEILKLNPSYRTPPDYKP 164
+I E + LNP ++ P DYKP
Sbjct: 102 HNLITEXVALNPDFKPPADYKP 123
>pdb|3U1N|A Chain A, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|B Chain B, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|C Chain C, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|D Chain D, Structure Of The Catalytic Core Of Human Samhd1
Length = 528
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 416 QPQPTGPIHIGRPSMPSLPQAVSSVGPRPLPDRPL 450
+ QPTG I I R SLP+ V+S P+ L D L
Sbjct: 361 ETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKL 395
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
0.311 0.129 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,567,927
Number of Sequences: 62578
Number of extensions: 904488
Number of successful extensions: 1367
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1313
Number of HSP's gapped (non-prelim): 29
length of query: 780
length of database: 14,973,337
effective HSP length: 106
effective length of query: 674
effective length of database: 8,340,069
effective search space: 5621206506
effective search space used: 5621206506
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)