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= psy4260
(129 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 32/51 (62%), Positives = 38/51 (74%)
Query: 30 NAESTLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
+A STL+ G EY M+ I+ MGYER V ALRAS+NNP RAVEYL+TGI
Sbjct: 157 DAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 207
>pdb|1IFY|A Chain A, Solution Structure Of The Internal Uba Domain Of Hhr23a
Length = 49
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/47 (63%), Positives = 35/47 (74%)
Query: 34 TLLMGDEYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
TL+ G EY M+ I+ MGYER V ALRAS+NNP RAVEYL+TGI
Sbjct: 1 TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGI 47
>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 63
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 44 MVQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
V IV MG+ R +ALRA+ N+ +RAV+++ + I
Sbjct: 12 CVTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHI 48
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 33.9 bits (76), Expect = 0.028, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLITGI 80
V IV MG+ R +ALRA+ N+ +RAV+++ + I
Sbjct: 724 VTTIVSMGFSRDQALKALRATNNSLERAVDWIFSHI 759
>pdb|2LBC|A Chain A, Solution Structure Of Tandem Uba Of Usp13
Length = 126
Score = 32.3 bits (72), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
+V I MG++R+ +ALRA+ NN +RA++++ +
Sbjct: 80 EIVAIITSMGFQRNQAIQALRATNNNLERALDWIFS 115
>pdb|2DKL|A Chain A, Solution Structure Of The Uba Domain In The Human
Trinucleotide Repeat Containing 6c Protein (Htnrc6c)
Length = 85
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLI 77
R+++ + DMG+ R EAL+++ N D+A+ L+
Sbjct: 23 RLIKQLTDMGFPREPAEEALKSNNMNLDQAMSALL 57
>pdb|3K9P|A Chain A, The Crystal Structure Of E2-25k And Ubiquitin Complex
Length = 217
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
EY + ++N+ MG++R+AV AL + + + A E L++
Sbjct: 178 EYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLS 216
>pdb|1YLA|A Chain A, Ubiquitin-Conjugating Enzyme E2-25 Kda (Huntington
Interacting Protein 2)
pdb|1YLA|B Chain B, Ubiquitin-Conjugating Enzyme E2-25 Kda (Huntington
Interacting Protein 2)
pdb|2O25|A Chain A, Ubiquitin-Conjugating Enzyme E2-25 Kda Complexed With
Sumo-1- Conjugating Enzyme Ubc9
pdb|2O25|B Chain B, Ubiquitin-Conjugating Enzyme E2-25 Kda Complexed With
Sumo-1- Conjugating Enzyme Ubc9
Length = 202
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
EY + ++N+ MG++R+AV AL + + + A E L++
Sbjct: 163 EYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLS 201
>pdb|3K9O|A Chain A, The Crystal Structure Of E2-25k And Ubb+1 Complex
Length = 201
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
EY + ++N+ MG++R+AV AL + + + A E L++
Sbjct: 162 EYTKKIENLCAMGFDRNAVIVALSSKSWDVETATELLLS 200
>pdb|3E46|A Chain A, Crystal Structure Of Ubiquitin-Conjugating Enzyme E2-25kda
(Huntington Interacting Protein 2) M172a Mutant
pdb|3F92|A Chain A, Crystal Structure Of Ubiquitin-Conjugating Enzyme E2-25kda
(Huntington Interacting Protein 2) M172a Mutant
Crystallized At Ph 8.5
Length = 253
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 40 EYGRMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
EY + ++N+ G++R+AV AL + + + A E L++
Sbjct: 214 EYTKKIENLCAAGFDRNAVIVALSSKSWDVETATELLLS 252
>pdb|1VG5|A Chain A, Solution Structure Of Rsgi Ruh-014, A Uba Domain From
Arabidopsis Cdna
Length = 73
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 45 VQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
+Q +V MG++R+ V AL A+ ++ AVE L++
Sbjct: 33 IQKLVAMGFDRTQVEVALAAADDDLTVAVEILMS 66
>pdb|1WJI|A Chain A, Solution Structure Of The Uba Domain Of Human Tudor
Domain Containing Protein 3
Length = 63
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
+ +++I +MG+ + A +AL + NN + A+ L+T
Sbjct: 11 KALKHITEMGFSKEASRQALMDNGNNLEAALNVLLT 46
>pdb|1WGN|A Chain A, Solution Structure Of Uba Domain Of Human Ubiquitin
Associated Protein 1 (Ubap1)
Length = 63
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 43 RMVQNIVDMGYERSAVTEALRASFNNPDRAVEYLIT 78
+ V+ +V+MGY V A++ N ++ ++YL
Sbjct: 21 QCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFA 56
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
0.313 0.132 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,421,080
Number of Sequences: 62578
Number of extensions: 59510
Number of successful extensions: 129
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 116
Number of HSP's gapped (non-prelim): 14
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)