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= 034809
(82 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SE9|A Chain A, Structure Of At3g01050, A Ubiquitin-Fold Protein From
Arabidopsis Thaliana
Length = 126
Score = 68.9 bits (167), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 52/77 (67%), Gaps = 1/77 (1%)
Query: 6 YLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLRPSLPDKKG 65
+ EKENGPKTV V+LI AGK+LE++ T+ + R PV L G TMHV+++ + +K+
Sbjct: 51 WPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEKE- 109
Query: 66 EKLLSDSSKSRCLCSIL 82
+K D ++C+CS++
Sbjct: 110 KKPKGDPKMNKCVCSVM 126
>pdb|2GOW|A Chain A, Solution Structure Of Bc059385 From Homo Sapiens
Length = 125
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 11/85 (12%)
Query: 4 HIY----LAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLRPS 59
H+Y + +E + N ++LI+ G+ L N+T+ +LP G MH+V R +
Sbjct: 46 HVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPF----GKTTVMHLVARET 101
Query: 60 LPD--KKGEKLLSDSSKSRCLCSIL 82
LP+ +G++ + +S C C IL
Sbjct: 102 LPEPNSQGQRNREKTGESNC-CVIL 125
>pdb|1WGH|A Chain A, Solution Structure Of Mouse Ubiquitin-Like 3 Protein
Length = 116
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 4 HIY----LAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLRPS 59
H+Y + +E + N ++LI+ G+ L N+T+ +LP G MH+V R +
Sbjct: 45 HVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPF----GKTTVMHLVARET 100
Query: 60 LPDKKGEKLLSDSS 73
LP+ + S S
Sbjct: 101 LPEPNSQGQRSGPS 114
>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core
Mutant Of Ubiquitin, 1d7
Length = 76
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 2 NFHIYLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLR 57
NF + +KE P + +LI AGK LED T+++ + T+H+VLR
Sbjct: 25 NFKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLSDYNIQ------KESTIHLVLR 72
>pdb|2WYQ|A Chain A, The Crystal Structure Of The Ubiquitin-Like (Ubl) Domain
Of Hhr23a (Human Homologue A Of Rad23)
Length = 85
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 8 AEKENGPKTVNNVQLIHAGKILEDNMTIAESRL 40
AEK V +LI+AGKIL D++ I + R+
Sbjct: 37 AEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRI 69
>pdb|1P98|A Chain A, High-Resolution Nmr Structure Of The Ubl-Domain Of
Hhr23a
pdb|1P9D|U Chain U, High-Resolution Structure Of The Complex Of Hhr23a
Ubiquitin-Like Domain And The C-Terminal Ubiquitin-
Interacting Motif Of Proteasome Subunit S5a
Length = 78
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 8 AEKENGPKTVNNVQLIHAGKILEDNMTIAESRL 40
AEK V +LI+AGKIL D++ I + R+
Sbjct: 34 AEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRI 66
>pdb|3M62|B Chain B, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
Length = 106
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 18/20 (90%)
Query: 18 NNVQLIHAGKILEDNMTIAE 37
+ ++LI++GK+L+D+ T++E
Sbjct: 40 SQIKLIYSGKVLQDSKTVSE 59
>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy
pdb|2KX0|A Chain A, The Solution Structure Of Ubb+1, Frameshift Mutant Of
Ubiquitin B
Length = 103
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 2 NFHIYLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLR 57
N + +KE P + +LI AGK LED T++E + T+H+VLR
Sbjct: 33 NVKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLSEYNIQ------KESTLHLVLR 80
>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural
Specificity
Length = 76
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 2 NFHIYLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLR 57
N + +KE P + +LI AGK LED T+++ L T+H+VLR
Sbjct: 25 NLKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLSDYNLQ------KESTIHLVLR 72
>pdb|3H7S|A Chain A, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin
Reveal A Highly Extended Chain Architecture
pdb|3H7S|B Chain B, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin
Reveal A Highly Extended Chain Architecture
Length = 76
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 2 NFHIYLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLR 57
N + +KE P + +LI AGK LED T+++ + E T+H+VLR
Sbjct: 25 NVKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLSDYNIQKRE-----STLHLVLR 73
>pdb|1EX0|A Chain A, Human Factor Xiii, Mutant W279f Zymogen
pdb|1EX0|B Chain B, Human Factor Xiii, Mutant W279f Zymogen
Length = 731
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 5 IYLAEKENGPKTVNNVQLIHAGKIL 29
IY+ K++G V NV H GK++
Sbjct: 440 IYITAKKDGTHVVENVDATHIGKLI 464
>pdb|1EVU|A Chain A, Human Factor Xiii With Calcium Bound In The Ion Site
pdb|1EVU|B Chain B, Human Factor Xiii With Calcium Bound In The Ion Site
Length = 731
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 5 IYLAEKENGPKTVNNVQLIHAGKIL 29
IY+ K++G V NV H GK++
Sbjct: 440 IYITAKKDGTHVVENVDATHIGKLI 464
>pdb|1FIE|A Chain A, Recombinant Human Coagulation Factor Xiii
pdb|1FIE|B Chain B, Recombinant Human Coagulation Factor Xiii
Length = 731
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 5 IYLAEKENGPKTVNNVQLIHAGKIL 29
IY+ K++G V NV H GK++
Sbjct: 440 IYITAKKDGTHVVENVDATHIGKLI 464
>pdb|1GGT|A Chain A, Three-Dimensional Structure Of A Transglutaminase: Human
Blood Coagulation Factor Xiii
pdb|1GGT|B Chain B, Three-Dimensional Structure Of A Transglutaminase: Human
Blood Coagulation Factor Xiii
pdb|1F13|A Chain A, Recombinant Human Cellular Coagulation Factor Xiii
pdb|1F13|B Chain B, Recombinant Human Cellular Coagulation Factor Xiii
pdb|1GGU|A Chain A, Human Factor Xiii With Calcium Bound In The Ion Site
pdb|1GGY|A Chain A, Human Factor Xiii With Ytterbium Bound In The Ion Site
pdb|1GGY|B Chain B, Human Factor Xiii With Ytterbium Bound In The Ion Site
pdb|1QRK|A Chain A, Human Factor Xiii With Strontium Bound In The Ion Site
pdb|1QRK|B Chain B, Human Factor Xiii With Strontium Bound In The Ion Site
pdb|1GGU|B Chain B, Human Factor Xiii With Calcium Bound In The Ion Site
Length = 731
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 5 IYLAEKENGPKTVNNVQLIHAGKIL 29
IY+ K++G V NV H GK++
Sbjct: 440 IYITAKKDGTHVVENVDATHIGKLI 464
>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant
Of Ubiquitin
Length = 88
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 2 NFHIYLAEKENGPKTVNNVQLIHAGKILEDNMTIAESRLPVVELPGTAITMHVVLR 57
N + +KE P + +LI AGK LED T+++ + T+H+VLR
Sbjct: 34 NLKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLSDYNIQ------KESTLHLVLR 81
>pdb|1OQY|A Chain A, Structure Of The Dna Repair Protein Hhr23a
pdb|1QZE|A Chain A, Hhr23a Protein Structure Based On Residual Dipolar
Coupling Data
Length = 368
Score = 25.4 bits (54), Expect = 7.9, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 8 AEKENGPKTVNNVQLIHAGKILEDNMTIAESRL 40
AEK V +LI+AGKIL D++ I + R+
Sbjct: 39 AEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRI 71
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 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,316,740
Number of Sequences: 62578
Number of extensions: 74852
Number of successful extensions: 246
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: 231
Number of HSP's gapped (non-prelim): 20
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)