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= psy12968
(402 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 = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 70/111 (63%), Gaps = 4/111 (3%)
Query: 81 EHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVE 140
E+P FNFVG++LGP+G + ++L+ ET K+ + GKGSMRD+ KEE+ R G P HL E
Sbjct: 12 EYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNE 69
Query: 141 DLHVQVSALAPPAEAHARIAYALSELRKYIIP--DVNDEIRQEQFREMGYV 189
DLHV ++ A ++ A+ E++K ++P + D +++ + E+ +
Sbjct: 70 DLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAIL 120
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 34/116 (29%), Positives = 60/116 (51%), Gaps = 22/116 (18%)
Query: 81 EHPRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRD----RSKEEELRKEGDPKNA 136
E+P NFVG L+GP+GN+L+ +++E K+ I GKGS+++ R + L E +P
Sbjct: 17 EYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEP--- 73
Query: 137 HLVEDLHVQVSALAPPAEAHARIAYALSELRKYI-----IPDVNDEIRQEQFREMG 187
LH V+ A + A+ ++R + P+ +++R+ Q RE+
Sbjct: 74 -----LHALVT-----ANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELA 119
>pdb|3NUI|A Chain A, Crystal Structure Of Omega-Transferase From Vibrio
Fluvialis Js17
pdb|3NUI|B Chain B, Crystal Structure Of Omega-Transferase From Vibrio
Fluvialis Js17
Length = 478
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 121 RSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELRKYIIPDVNDEI 178
R EE +++EG A + + + PPA+ + + L LRKY IP ++DE+
Sbjct: 217 RELEETIQREGADTIAGFFAEPVMGAGGVIPPAKGYFQAI--LPILRKYDIPVISDEV 272
>pdb|4E3R|A Chain A, Plp-Bound Aminotransferase Mutant Crystal Structure From
Vibrio Fluvialis
pdb|4E3R|B Chain B, Plp-Bound Aminotransferase Mutant Crystal Structure From
Vibrio Fluvialis
pdb|4E3R|C Chain C, Plp-Bound Aminotransferase Mutant Crystal Structure From
Vibrio Fluvialis
pdb|4E3R|D Chain D, Plp-Bound Aminotransferase Mutant Crystal Structure From
Vibrio Fluvialis
Length = 473
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 121 RSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELRKYIIPDVNDEI 178
R EE +++EG A + + + PPA+ + + L LRKY IP ++DE+
Sbjct: 223 RELEETIQREGADTIAGFFAEPVMGAGGVIPPAKGYFQAI--LPILRKYDIPVISDEV 278
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 85 FNFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLV-EDLH 143
+ VG ++GPKG +++R+Q+ T T + G R KE G P+N E++
Sbjct: 18 YRVVGLVVGPKGATIKRIQQRTHTYIVTPG------RDKEPVFAVTGMPENVDRAREEIE 71
Query: 144 VQVSALAPPA 153
++ + P+
Sbjct: 72 AHITLRSGPS 81
>pdb|4E3Q|A Chain A, Pmp-Bound Form Of Aminotransferase Crystal Structure From
Vibrio Fluvialis
pdb|4E3Q|B Chain B, Pmp-Bound Form Of Aminotransferase Crystal Structure From
Vibrio Fluvialis
pdb|4E3Q|C Chain C, Pmp-Bound Form Of Aminotransferase Crystal Structure From
Vibrio Fluvialis
pdb|4E3Q|D Chain D, Pmp-Bound Form Of Aminotransferase Crystal Structure From
Vibrio Fluvialis
Length = 473
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 121 RSKEEELRKEGDPKNAHLVEDLHVQVSALAPPAEAHARIAYALSELRKYIIPDVNDEI 178
R EE +++EG A + + PPA+ + + L LRKY IP ++DE+
Sbjct: 223 RELEETIQREGADTIAGFFAEPVXGAGGVIPPAKGYFQAI--LPILRKYDIPVISDEV 278
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 28.9 bits (63), Expect = 5.2, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 26/60 (43%)
Query: 86 NFVGKLLGPKGNSLRRLQEETMTKMSILGKGSMRDRSKEEELRKEGDPKNAHLVEDLHVQ 145
N VG +LG G +L QE T ++ I KG ++ ++ G P + L Q
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLITQ 71
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 81 EH--PRFNFVGKLLGPKGNSLRRLQEETMTKMSILGKGS 117
EH P FN K+ GP + L+ +Q ET K+ + GKGS
Sbjct: 21 EHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGS 59
>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|B Chain B, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|C Chain C, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|D Chain D, Human Alpha Polyc Binding Protein Kh1
Length = 74
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 88 VGKLLGPKGNSLRRLQEETMTKMSI 112
VG ++G KG S++R++EE+ +++I
Sbjct: 14 VGSIIGKKGESVKRIREESGARINI 38
>pdb|3O19|A Chain A, Structure-Function Analysis Of Human L-Prostaglandin D
Synthase Bound With Fatty Acid
pdb|3O22|A Chain A, Structure-Function Analysis Of Human L-Prostaglandin D
Synthase Bound With Fatty Acid
pdb|3O2Y|A Chain A, Structure-Function Analysis Of Human L-Prostaglandin D
Synthase Bound With Fatty Acid
pdb|3O2Y|B Chain B, Structure-Function Analysis Of Human L-Prostaglandin D
Synthase Bound With Fatty Acid
Length = 162
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 254 RAAMEKPAPSAGVYEYEDPHAAHAYYETTASYDPAMYDPYA 294
R + +PA S G Y Y PH Y + D YD YA
Sbjct: 64 RTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETD---YDQYA 101
>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|B Chain B, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|C Chain C, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|D Chain D, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
Length = 76
Score = 28.5 bits (62), Expect = 7.8, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 88 VGKLLGPKGNSLRRLQEETMTKMSI 112
VG ++G KG S++R++EE+ +++I
Sbjct: 14 VGSIIGKKGESVKRIREESGARINI 38
>pdb|2WWP|A Chain A, Crystal Structure Of The Human Lipocalin-Type
Prostaglandin D Synthase Crystallised With The Substrate
Analog
9,11-Dideoxy-9alpha,11alpha-Epoxymethanoprostaglandin
F2alpha
pdb|2WWP|B Chain B, Crystal Structure Of The Human Lipocalin-Type
Prostaglandin D Synthase Crystallised With The Substrate
Analog
9,11-Dideoxy-9alpha,11alpha-Epoxymethanoprostaglandin
F2alpha
Length = 176
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 254 RAAMEKPAPSAGVYEYEDPHAAHAYYETTASYDPAMYDPYA 294
R + +PA S G Y Y PH Y + D YD YA
Sbjct: 71 RTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETD---YDQYA 108
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 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,370,836
Number of Sequences: 62578
Number of extensions: 327537
Number of successful extensions: 558
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 548
Number of HSP's gapped (non-prelim): 15
length of query: 402
length of database: 14,973,337
effective HSP length: 101
effective length of query: 301
effective length of database: 8,652,959
effective search space: 2604540659
effective search space used: 2604540659
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: 52 (24.6 bits)