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= 047631
(1232 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WH2|A Chain A, Solution Structure Of The Gyf Domain Of A Hypothetical
Protein From Arabidopsis Thaliana
Length = 78
Score = 65.1 bits (157), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 652 ESEKI-WHYQDPSGKVQGPFSMVQLRKWNNTGYFPANLRIWRSNEKQDDSILLTDAL 707
+ EK+ W Y+DP G VQGPFS+ QL+ W++ YF R+W + E + ++LLTD L
Sbjct: 14 DKEKLNWLYKDPQGLVQGPFSLTQLKAWSDAEYFTKQFRVWMTGESMESAVLLTDVL 70
>pdb|1V32|A Chain A, Solution Structure Of The SwibMDM2 DOMAIN OF THE
Hypothetical Protein At5g08430 From Arabidopsis Thaliana
Length = 101
Score = 57.4 bits (137), Expect = 5e-08, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%)
Query: 164 VEWASKELLDLVMHMRNGDKSALSQFDVQTLLLEYIKKYKLRDPQRRTHVICDARLQNLF 223
V W S++L++ + + +S++DV + +YI K L DP + V+CD RL LF
Sbjct: 13 VGWGSRQLIEFLHSLGKDTSEMISRYDVSDTIAKYISKEGLLDPSNKKKVVCDKRLVLLF 72
Query: 224 GKPRVGHFEMLKLLESHFLTKEDS 247
G + ++ LLE H+ +DS
Sbjct: 73 GTRTIFRMKVYDLLEKHYKENQDS 96
>pdb|2DB9|A Chain A, Solution Structure Of The Plus-3 Domain Of Human Kiaa0252
Protein
Length = 149
Score = 57.4 bits (137), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 59/106 (55%), Gaps = 2/106 (1%)
Query: 328 FHDKVVGTFARIRISGSAHQKQDLYRLVQVTGTSKGTEPYKVGKRTTDILLEILNLNKTE 387
F V G F RI I H + +YR+ ++TG + + Y++G T+ L++ + N
Sbjct: 39 FAKTVTGCFVRIGIGN--HNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQR 96
Query: 388 VISIDIISNQEFTEDECKRLRQSIKCGLINRLTVGDIQEKAMALQE 433
V ++ +SNQEFTE E + ++++ + T+ +I +K ++++E
Sbjct: 97 VFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKE 142
>pdb|2BZE|A Chain A, Nmr Structure Of Human Rtf1 Plus3 Domain
Length = 153
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 59/106 (55%), Gaps = 2/106 (1%)
Query: 328 FHDKVVGTFARIRISGSAHQKQDLYRLVQVTGTSKGTEPYKVGKRTTDILLEILNLNKTE 387
F V G F RI I H + +YR+ ++TG + + Y++G T+ L++ + N
Sbjct: 47 FAKTVTGCFVRIGIGN--HNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQR 104
Query: 388 VISIDIISNQEFTEDECKRLRQSIKCGLINRLTVGDIQEKAMALQE 433
V ++ +SNQEFTE E + ++++ + T+ +I +K ++++E
Sbjct: 105 VFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKE 150
>pdb|3U1U|A Chain A, Crystal Structure Of Rna Polymerase-Associated Protein
Rtf1 Homolog Plus-3 Domain
pdb|3U1U|B Chain B, Crystal Structure Of Rna Polymerase-Associated Protein
Rtf1 Homolog Plus-3 Domain
Length = 137
Score = 54.3 bits (129), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 57/106 (53%), Gaps = 2/106 (1%)
Query: 328 FHDKVVGTFARIRISGSAHQKQDLYRLVQVTGTSKGTEPYKVGKRTTDILLEILNLNKTE 387
F V G F RI I H + +YR+ ++TG + + Y++G T+ L++ + N
Sbjct: 33 FAKTVTGCFVRIGIGN--HNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQR 90
Query: 388 VISIDIISNQEFTEDECKRLRQSIKCGLINRLTVGDIQEKAMALQE 433
V ++ +SNQEFTE E + +++ T+ +I +K ++++E
Sbjct: 91 VFRLEFVSNQEFTESEFXKWKEAXFSAGXQLPTLDEINKKELSIKE 136
>pdb|1UHR|A Chain A, Solution Structure Of The Swib Domain Of Mouse Brg1-
Associated Factor 60a
Length = 93
Score = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 195 LLEYIKKYKLRDPQRRTHVICDARLQNLFGKPRVGHFEMLKLLESHFLTKEDS 247
L +YIK +KL+DP R V+CD LQ +F R+ E+ + L + + E S
Sbjct: 36 LWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEPS 88
>pdb|3K3V|A Chain A, Crystal Structure The Gyf Domain Of S. Cerevisiae Smy2
Length = 100
Score = 39.3 bits (90), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 639 ASTGVTQSAPKINESEKIWHYQDPSGKVQGPFSMVQLRKWNNTGYFPANLRIWR 692
S G++Q P E W Y D G++ GPF+ + +W GYF + L+I R
Sbjct: 1 GSNGMSQ-LPAPVSVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISR 53
>pdb|3FMA|A Chain A, Crystal Structure Of The Gyf Domain Of Smy2 In Complex
With A Proline- Rich Peptide From BbpSCSF1
pdb|3FMA|B Chain B, Crystal Structure Of The Gyf Domain Of Smy2 In Complex
With A Proline- Rich Peptide From BbpSCSF1
pdb|3FMA|C Chain C, Crystal Structure Of The Gyf Domain Of Smy2 In Complex
With A Proline- Rich Peptide From BbpSCSF1
pdb|3FMA|D Chain D, Crystal Structure Of The Gyf Domain Of Smy2 In Complex
With A Proline- Rich Peptide From BbpSCSF1
pdb|3FMA|E Chain E, Crystal Structure Of The Gyf Domain Of Smy2 In Complex
With A Proline- Rich Peptide From BbpSCSF1
Length = 100
Score = 37.4 bits (85), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 654 EKIWHYQDPSGKVQGPFSMVQLRKWNNTGYFPANLRIWR 692
E W Y D G++ GPF+ +W GYF + L+I R
Sbjct: 15 ESSWRYIDTQGQIHGPFTTQXXSQWYIGGYFASTLQISR 53
>pdb|3OW7|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli.
pdb|3OW7|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli.
pdb|3OOC|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3OOC|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3NE5|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli
pdb|3NE5|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli
pdb|3OPO|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3OPO|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|4DNT|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, Mutant
pdb|4DNT|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, Mutant
pdb|4DOP|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, R Mutant
pdb|4DOP|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, R Mutant
pdb|4DNR|B Chain B, Crystal Structure Of The Cusba Heavy-metal Efflux Complex
From Escherichia Coli, E716f Mutant
pdb|4DNR|C Chain C, Crystal Structure Of The Cusba Heavy-metal Efflux Complex
From Escherichia Coli, E716f Mutant
Length = 413
Score = 33.1 bits (74), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 29/101 (28%)
Query: 407 LRQSIKCGLINR---LTVGDIQEKAMALQEVRVKDWMEAEILRLSHLRDRASDLGRRKEY 463
+ Q+ G I++ LTVGD +K L ++ + DW+EA+ EY
Sbjct: 123 IVQARAAGFIDKVYPLTVGDKVQKGTPLLDLTIPDWVEAQ-----------------SEY 165
Query: 464 PLLYEE---------CVEKLQLLKTPEERQRRLEEIPEIHS 495
LL E +E+L+L PE RRL +I +
Sbjct: 166 LLLRETGGTATQTEGILERLRLAGMPEADIRRLIATQKIQT 206
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 32.0 bits (71), Expect = 2.2, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 1212 VCKFHESGHCKKGSQCDYLH 1231
VCK G CKKG QC++LH
Sbjct: 18 VCKHWLRGLCKKGDQCEFLH 37
>pdb|1V31|A Chain A, Solution Structure Of The SwibMDM2 DOMAIN OF THE
Hypothetical Protein At5g14170 From Arabidopsis Thaliana
Length = 93
Score = 31.6 bits (70), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 197 EYIKKYKLRDPQRRTHVICDARLQNLFGKPRVGHFEMLKLLESHFL 242
Y+K KL++P + CDA LQ +FG+ ++ F M+ SH L
Sbjct: 38 HYVKARKLQNPNDPSFFNCDAALQKVFGEEKL-KFTMVSQKISHHL 82
>pdb|3T51|B Chain B, Crystal Structures Of The Pre-Extrusion And Extrusion
States Of The Cusba Adaptor-Transporter Complex
pdb|3T51|C Chain C, Crystal Structures Of The Pre-Extrusion And Extrusion
States Of The Cusba Adaptor-Transporter Complex
pdb|3T53|B Chain B, Crystal Structures Of The Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T53|C Chain C, Crystal Structures Of The Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T56|B Chain B, Crystal Structure Of The Pre-Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T56|C Chain C, Crystal Structure Of The Pre-Extrusion State Of The Cusba
Adaptor- Transporter Complex
Length = 336
Score = 31.2 bits (69), Expect = 3.6, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 42/92 (45%), Gaps = 15/92 (16%)
Query: 409 QSIKCGLINR---LTVGDIQEKAMALQEVRVKDWMEA--EILRLSHLRDRASDLGRRKEY 463
Q+ G I++ LTVGD +K L ++ + DW+EA E L L A+
Sbjct: 48 QARAAGFIDKVYPLTVGDKVQKGTPLLDLTIPDWVEAQSEYLLLRETGGTATQT------ 101
Query: 464 PLLYEECVEKLQLLKTPEERQRRLEEIPEIHS 495
E +E+L+L PE RRL +I +
Sbjct: 102 ----EGILERLRLAGMPEADIRRLIATQKIQT 129
>pdb|3H94|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3H94|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
Length = 407
Score = 31.2 bits (69), Expect = 3.6, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 42/92 (45%), Gaps = 15/92 (16%)
Query: 409 QSIKCGLINR---LTVGDIQEKAMALQEVRVKDWMEA--EILRLSHLRDRASDLGRRKEY 463
Q+ G I++ LTVGD +K L ++ + DW+EA E L L A+
Sbjct: 125 QARAAGFIDKVYPLTVGDKVQKGTPLLDLTIPDWVEAQSEYLLLRETGGTATQT------ 178
Query: 464 PLLYEECVEKLQLLKTPEERQRRLEEIPEIHS 495
E +E+L+L PE RRL +I +
Sbjct: 179 ----EGILERLRLAGMPEADIRRLIATQKIQT 206
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 30.8 bits (68), Expect = 4.5, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 1195 GSRGGDSSRPHFNKGQRVCKFHESGHCKKGSQCDYLH 1231
GS G P K + +CKF+ +G C + C Y+H
Sbjct: 1 GSSGSSGELP---KKRELCKFYITGFCARAENCPYMH 34
>pdb|2D9N|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 2 In
Cleavage And Polyadenylation Specificity Factor
Length = 77
Score = 30.4 bits (67), Expect = 6.0, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 1212 VCKFHESGHCKKGSQCDYLH 1231
VCK G CKKG QC++LH
Sbjct: 12 VCKHWLRGLCKKGDQCEFLH 31
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 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,005,893
Number of Sequences: 62578
Number of extensions: 1385176
Number of successful extensions: 2070
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2059
Number of HSP's gapped (non-prelim): 17
length of query: 1232
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1122
effective length of database: 8,089,757
effective search space: 9076707354
effective search space used: 9076707354
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: 57 (26.6 bits)