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= 027823
(218 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 = 133 bits (335), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 58/122 (47%), Positives = 92/122 (75%)
Query: 73 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGY 132
+L +PV YP+FNFVGR+LGPRG + K++EA TGC++ +RGKGS++D KE++ RG+P +
Sbjct: 5 KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNW 64
Query: 133 EHLNDPLHILIEADLPANIVDIRLRQAQEIIEELLKPVDESQDYIKRQQLRELAMLNSNF 192
EHLN+ LH+LI + N +++L++A E +++LL P E +D +K+ +L ELA+LN +
Sbjct: 65 EHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAAEGEDSLKKMKLMELAILNGTY 124
Query: 193 RE 194
R+
Sbjct: 125 RD 126
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 86.7 bits (213), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 54/129 (41%), Positives = 76/129 (58%), Gaps = 16/129 (12%)
Query: 73 RLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPDKEDKLRGRPGY 132
++ IP D YP NFVG L+GPRGN+LK +E ++ IRGKGS+ KE K+ GR
Sbjct: 10 KVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSV----KEGKV-GRKDG 64
Query: 133 EHL---NDPLHILIEADLPANIVDIRLRQAQEIIEELLK---PVDESQDYIKRQQLRELA 186
+ L ++PLH L+ A+ N+ ++A E I +LK E Q+ +++ QLRELA
Sbjct: 65 QMLPGEDEPLHALVTANTMENV-----KKAVEQIRNILKQGIETPEDQNDLRKMQLRELA 119
Query: 187 MLNSNFRED 195
LN RED
Sbjct: 120 RLNGTLRED 128
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 15/91 (16%)
Query: 82 PNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS-IKDPDKEDKLRGRPGYEHLNDPLH 140
P FN ++ GP + L+ ++ TG +V++RGKGS +P GR +E P++
Sbjct: 25 PTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPAS-----GREAFE----PMY 75
Query: 141 ILIEADLPANIVDIRLRQAQEIIEELLKPVD 171
I I P L A+++ E LL+ V
Sbjct: 76 IYISHPKPEG-----LAAAKKLCENLLQTVH 101
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 115
N VG +LG G +L + TGCR+ I KG
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGCRIQISKKG 42
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 31.2 bits (69), Expect = 0.42, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 12/61 (19%)
Query: 57 QSAPASPSSYTVKRILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGS 116
+ +P +P RI+ ++IPVD +G ++GP+ + +++ TG + I G+
Sbjct: 591 EXSPNAP------RIITVKIPVDK------IGEVIGPKRQXINQIQEDTGAEITIEDDGT 638
Query: 117 I 117
I
Sbjct: 639 I 639
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 30.4 bits (67), Expect = 0.70, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 70 RILRLEIPVDTYPNFNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSI 117
RI+ ++IPVD +G ++GP+ + +++ TG + I G+I
Sbjct: 598 RIITVKIPVDK------IGEVIGPKRQMINQIQEDTGAEITIEDDGTI 639
>pdb|1DU5|A Chain A, The Crystal Structure Of Zeamatin.
pdb|1DU5|B Chain B, The Crystal Structure Of Zeamatin
Length = 206
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 89 RLLGPRGNSLKRVEATTGCRVYIRGKGSIKDPD 121
R+ P G + R+ A TGC+ G+GS + D
Sbjct: 33 RITAPAGTTAARIWARTGCKFDASGRGSCRTGD 65
>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|C Chain C, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|D Chain D, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
Length = 76
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 115
N VG +LG G +L + TG R+ I KG
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKG 42
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 85 NFVGRLLGPRGNSLKRVEATTGCRVYIRGKG 115
N VG +LG G +L + TG R+ I KG
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKG 42
>pdb|3UOR|A Chain A, The Structure Of The Sugar-Binding Protein Male From The
Phytopathogen Xanthomonas Citri
pdb|3UOR|B Chain B, The Structure Of The Sugar-Binding Protein Male From The
Phytopathogen Xanthomonas Citri
Length = 458
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 5 QGFGDFDRLRHRSPSPMASSNLMSNVAGTGLGG---------WNGLPQERLGGPPGMTMD 55
+ G +D + + +P S +SNV G WN + + +L PPGM +
Sbjct: 225 KALGFYDNMYQQGWAPKVSETQVSNVWYEFFNGYYAFYLSGPWN-VREFKLRQPPGMEGN 283
Query: 56 WQSAP 60
W +AP
Sbjct: 284 WGTAP 288
>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 = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 87 VGRLLGPRGNSLKRVEATTGCRVYI 111
VG ++G +G S+KR+ +G R+ I
Sbjct: 14 VGSIIGKKGESVKRIREESGARINI 38
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 84 FNFVGRLLGPRGNSLKRVEATTGCRVYIRGKGSIKDP 120
+ VG ++GP+G ++KR++ T YI G K+P
Sbjct: 18 YRVVGLVVGPKGATIKRIQQRT--HTYIVTPGRDKEP 52
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 27.3 bits (59), Expect = 6.8, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 149 ANIVDIRLRQAQEI-IEELLKPVDESQDYIKRQQLRELAMLNSNFREDSPGPSGSVSPF 206
A + DI + E+ E+L + +DES+D +R+Q +L + + F +SP + +S F
Sbjct: 466 AKLYDIEFKSIDEVDFEKLSRELDESRDRYRRRQEFDL-IKPALFIVESPTKARQISRF 523
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 27.3 bits (59), Expect = 6.9, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 149 ANIVDIRLRQAQEI-IEELLKPVDESQDYIKRQQLRELAMLNSNFREDSPGPSGSVSPF 206
A + DI + E+ E+L + +DES+D +R+Q +L + + F +SP + +S F
Sbjct: 466 AKLYDIEFKSIDEVDFEKLSRELDESRDRYRRRQEFDL-IKPALFIVESPTKARQISRF 523
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
0.316 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,410,550
Number of Sequences: 62578
Number of extensions: 333807
Number of successful extensions: 694
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 684
Number of HSP's gapped (non-prelim): 16
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 49 (23.5 bits)