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= 030404
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WFL|A Chain A, Solution Structure Of The Zf-An1 Domain From Mouse Zinc
Finger Protein 216
Length = 74
Score = 77.0 bits (188), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 34/52 (65%), Positives = 39/52 (75%)
Query: 106 EKEANVEKRVVNRCSGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYDYKS 157
EK + K NRC CR+KVGLTGF CRCG LFCG HRYSD+H+C YDYK+
Sbjct: 15 EKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKA 66
>pdb|1WFH|A Chain A, Solution Structrue Of The Zf-An1 Domain From Arabidopsis
Thaliana At2g36320 Protein
Length = 64
Score = 68.2 bits (165), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 28/43 (65%), Positives = 35/43 (81%)
Query: 117 NRCSGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYDYKSAG 159
NRC+ CR++VGLTGF CRCG FCG HRY + H C++D+KSAG
Sbjct: 16 NRCTVCRKRVGLTGFMCRCGTTFCGSHRYPEVHGCTFDFKSAG 58
>pdb|1WFF|A Chain A, Solution Structure Of The Zf-An1 Domain From Mouse Riken
Cdna 2810002d23 Protein
Length = 85
Score = 67.4 bits (163), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 30/60 (50%), Positives = 39/60 (65%), Gaps = 1/60 (1%)
Query: 111 VEKRVVNRCSGCRRKVGL-TGFRCRCGELFCGEHRYSDRHDCSYDYKSAGRDAIARENPV 169
+K+++ C C +K GL T F CRCG FC HRY++ H C+YDYKSAGR + NPV
Sbjct: 20 TKKKIMKHCFLCGKKTGLATSFECRCGNNFCASHRYAEAHGCNYDYKSAGRRYLEEANPV 79
>pdb|1WG2|A Chain A, Solution Structure Of Zf-An1 Domain From Arabidopsis
Thaliana
Length = 64
Score = 64.7 bits (156), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 34/46 (73%)
Query: 114 RVVNRCSGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYDYKSAG 159
R NRC C +KVG+ GF+C+CG FCG HRY ++H+CS+D+K G
Sbjct: 13 RPNNRCFSCNKKVGVMGFKCKCGSTFCGSHRYPEKHECSFDFKEVG 58
>pdb|1WFP|A Chain A, Solution Structure Of The Zf-an1 Domain From Arabiopsis
Thaliana F5o11.17 Protein
Length = 74
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 24/47 (51%), Positives = 32/47 (68%)
Query: 110 NVEKRVVNRCSGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYDYK 156
+ K RC C +KVG+TGF+CRCG FCG HRY + H+C +D+K
Sbjct: 19 DPPKSTATRCLSCNKKVGVTGFKCRCGSTFCGTHRYPESHECQFDFK 65
>pdb|1X4W|A Chain A, Solution Structure Of The Zf-An1 Domain From Human
Hypothetical Protein Flj13222
Length = 67
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 118 RCSGCRRKVGLTGFR---CRCGELFCGEHRYSDRHDCSYDYKSAG 159
RC C+ K+ L CRCG +FC HR ++HDC++D+ G
Sbjct: 17 RCFQCQTKLELVQQELGSCRCGYVFCMLHRLPEQHDCTFDHMGRG 61
>pdb|2FID|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
With Ubiquitin
pdb|2FIF|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
With Ubiquitin
pdb|2FIF|D Chain D, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
With Ubiquitin
pdb|2FIF|F Chain F, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
With Ubiquitin
Length = 70
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 14 VPETLTLCVNNCGFTGNPATNNMCQKCF 41
V ++ LC CG+ GNPA C KC+
Sbjct: 9 VDQSELLCKKGCGYYGNPAWQGFCSKCW 36
>pdb|2C7M|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|C Chain C, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|E Chain E, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|G Chain G, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|I Chain I, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
pdb|2C7N|K Chain K, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
Length = 74
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 14 VPETLTLCVNNCGFTGNPATNNMCQKCF 41
V ++ LC CG+ GNPA C KC+
Sbjct: 12 VDQSDLLCKKGCGYYGNPAWQGFCSKCW 39
>pdb|2KZY|A Chain A, Solution Nmr Structure Of The Znf216 A20 Zinc Finger
pdb|2L00|A Chain A, Solution Structure Of The Non-Covalent Complex Of The
Znf216 A20 Domain With Ubiquitin
Length = 62
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 1 MAQKTEKEETEFKVPETLTLCVNNCGFTGNPATNNMCQKCF 41
MAQ+T + LC CGF GNP TN MC C+
Sbjct: 3 MAQETNQTPGPM-------LCSTGCGFYGNPRTNGMCSVCY 36
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
0.318 0.132 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,325,676
Number of Sequences: 62578
Number of extensions: 134796
Number of successful extensions: 366
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 353
Number of HSP's gapped (non-prelim): 21
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
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: 48 (23.1 bits)