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= 047404
(291 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LBC|A Chain A, Solution Structure Of Tandem Uba Of Usp13
Length = 126
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%)
Query: 248 EPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNIL 285
+PPE+ +A++ SMGF RN A QAL N++ A + +
Sbjct: 76 QPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWI 113
>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
Ubiquitin Specific Protease 5 (Isopeptidase 5)
Length = 63
Score = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATN 283
PPED + +VSMGF R+ A +AL N + A +
Sbjct: 8 PPEDCVTTIVSMGFSRDQALKALRATNNSLERAVD 42
>pdb|1VG5|A Chain A, Solution Structure Of Rsgi Ruh-014, A Uba Domain From
Arabidopsis Cdna
Length = 73
Score = 35.8 bits (81), Expect = 0.030, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 30/69 (43%), Gaps = 14/69 (20%)
Query: 218 APSRNVLGSIPSHAGRQAESNYPLPVPSTIEPPEDSIAMLVSMGFDRNSARQALVQARND 277
AP N +P GR A S E+ I LV+MGFDR AL A +D
Sbjct: 11 APIANA-AVLPQSQGRVAAS-------------EEQIQKLVAMGFDRTQVEVALAAADDD 56
Query: 278 INAATNILL 286
+ A IL+
Sbjct: 57 LTVAVEILM 65
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNIL 285
PPED + +VSMGF R+ A +AL N + A + +
Sbjct: 719 PPEDCVTTIVSMGFSRDQALKALRATNNSLERAVDWI 755
>pdb|1WJI|A Chain A, Solution Structure Of The Uba Domain Of Human Tudor Domain
Containing Protein 3
Length = 63
Score = 34.3 bits (77), Expect = 0.087, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 25/38 (65%)
Query: 251 EDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288
E ++ + MGF + ++RQAL+ N++ AA N+LL +
Sbjct: 10 EKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTS 47
>pdb|1Z96|A Chain A, Crystal Structure Of The Mud1 Uba Domain
pdb|1Z96|B Chain B, Crystal Structure Of The Mud1 Uba Domain
Length = 40
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/33 (54%), Positives = 21/33 (63%)
Query: 254 IAMLVSMGFDRNSARQALVQARNDINAATNILL 286
IA LVSMGFD A QAL A D++ A + LL
Sbjct: 8 IAQLVSMGFDPLEAAQALDAANGDLDVAASFLL 40
>pdb|2PWQ|A Chain A, Crystal Structure Of A Putative Ubiquitin Conjugating
Enzyme From Plasmodium Yoelii
Length = 216
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 248 EPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLE 287
EP E I + MGF + A+ AL++A + A N LLE
Sbjct: 175 EPREVIIKKITEMGFSEDQAKNALIKANWNETLALNTLLE 214
>pdb|2G3Q|A Chain A, Solution Structure Of Ede1 Uba-Ubiquitin Complex
Length = 43
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 249 PPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILLEA 288
P ++ L MGF A AL + D+ AATN LL++
Sbjct: 3 PKSLAVEELSGMGFTEEEAHNALEKCNWDLEAATNFLLDS 42
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 253 SIAMLVSMGFDRNSARQALVQARNDINAATNILL 286
I L +MGFDRN+ AL D+ AT +LL
Sbjct: 167 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 200
>pdb|3K9O|A Chain A, The Crystal Structure Of E2-25k And Ubb+1 Complex
Length = 201
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 253 SIAMLVSMGFDRNSARQALVQARNDINAATNILL 286
I L +MGFDRN+ AL D+ AT +LL
Sbjct: 166 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 199
>pdb|2HAK|A Chain A, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|B Chain B, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|C Chain C, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|D Chain D, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|E Chain E, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|F Chain F, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|G Chain G, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|H Chain H, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
Length = 328
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 230 HAGRQAESNYPLPVPSTIEPPEDSIAMLVSMGFDRNSARQALVQARNDINAATNILL 286
+ G + E P P I ++V+MGF R+ AL+ + D AT ILL
Sbjct: 269 NVGHEEEELKPYTEPDPDFNDTKRIDIMVTMGFARDEINDALINQKYDEVMATYILL 325
>pdb|3K9P|A Chain A, The Crystal Structure Of E2-25k And Ubiquitin Complex
Length = 217
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 253 SIAMLVSMGFDRNSARQALVQARNDINAATNILL 286
I L +MGFDRN+ AL D+ AT +LL
Sbjct: 182 KIENLCAMGFDRNAVIVALSSKSWDVETATELLL 215
>pdb|2OO9|A Chain A, Crystal Structure Of The Uba Domain From Human C-cbl
Ubiquitin Ligase
pdb|2OO9|B Chain B, Crystal Structure Of The Uba Domain From Human C-cbl
Ubiquitin Ligase
pdb|2OO9|C Chain C, Crystal Structure Of The Uba Domain From Human C-cbl
Ubiquitin Ligase
Length = 46
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 254 IAMLVSMGFDRNSARQALVQARNDINAATNILLE 287
I L S G+ ++ALV A+N+I A NIL E
Sbjct: 8 IENLXSQGYSYQDIQKALVIAQNNIEXAKNILRE 41
>pdb|2D9S|A Chain A, Solution Structure Of Rsgi Ruh-049, A Uba Domain From
Mouse Cdna
pdb|2D9S|B Chain B, Solution Structure Of Rsgi Ruh-049, A Uba Domain From
Mouse Cdna
Length = 53
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 254 IAMLVSMGFDRNSARQALVQARNDINAATNILLE 287
I L+S G+ ++ALV A N+I A NIL E
Sbjct: 13 IERLMSQGYSYQDIQKALVIAHNNIEMAKNILRE 46
>pdb|2JUJ|A Chain A, Solution Structure Of The Uba Domain From C-Cbl
Length = 56
Score = 28.5 bits (62), Expect = 4.1, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 254 IAMLVSMGFDRNSARQALVQARNDINAATNILLE 287
I L+S G+ ++ALV A+N+I A NIL E
Sbjct: 11 IENLMSQGYSYQDIQKALVIAQNNIEMAKNILRE 44
>pdb|2KNZ|A Chain A, Nmr Structure Of Cip75 Uba Domain
Length = 53
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 251 EDSIAMLVSMGF-DRNSARQALVQARNDINAATNILLEAQ 289
+ + L SMGF +R + QAL+ DINAA LL +Q
Sbjct: 12 QQQLEQLNSMGFINREANLQALIATGGDINAAIERLLGSQ 51
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
0.328 0.142 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,213,685
Number of Sequences: 62578
Number of extensions: 323455
Number of successful extensions: 837
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 822
Number of HSP's gapped (non-prelim): 16
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)