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= psy14778
(210 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VJV|A Chain A, Crystal Structure Of Ubiquitin Carboxyl-terminal Hydrolase
6 (yfr010w) From Saccharomyces Cerevisiae At 1.74 A
Resolution
Length = 415
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 71 LIGVTVHTG-TADGGHYYSFIRDR---DKWLLFNDAEVKHFDSSQLAAECFGGE 120
LIGV H G ++ GHY +FIRD +KW FND +V + ++ + GGE
Sbjct: 348 LIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGE 401
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 20/103 (19%)
Query: 14 KVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARXXXXXXXXXXXXXXXXXXXXLIG 73
K++ FP L+M Y +H + K+ LIG
Sbjct: 375 KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPD-------------------IIYELIG 415
Query: 74 VTVHTGTADGGHYYSFIR-DRDKWLLFNDAEVKHFDSSQLAAE 115
+ H GT + GHY +F + +W FND+ V ++ E
Sbjct: 416 IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKE 458
>pdb|3MHH|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE
pdb|3MHS|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND
Ubiquitin Aldehyde
pdb|4FJC|A Chain A, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
pdb|4FJC|E Chain E, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
Length = 476
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 20/103 (19%)
Query: 14 KVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARXXXXXXXXXXXXXXXXXXXXLIG 73
K++ FP L+M Y +H + K+ LIG
Sbjct: 380 KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPD-------------------IIYELIG 420
Query: 74 VTVHTGTADGGHYYSFIR-DRDKWLLFNDAEVKHFDSSQLAAE 115
+ H GT + GHY +F + +W FND+ V ++ E
Sbjct: 421 IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKE 463
>pdb|4FIP|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FIP|E Chain E, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FK5|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11SUS1SGF73 DUB MODULE
Length = 476
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 20/103 (19%)
Query: 14 KVNTHFSFPMRLDMSGYVEKHLMPQHYQEEKLKSEARXXXXXXXXXXXXXXXXXXXXLIG 73
K++ FP L+M Y +H + K+ LIG
Sbjct: 380 KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPD-------------------IIYELIG 420
Query: 74 VTVHTGTADGGHYYSFIR-DRDKWLLFNDAEVKHFDSSQLAAE 115
+ H GT + GHY +F + +W FND+ V ++ E
Sbjct: 421 IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKE 463
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQL 112
L V+ H+GT GGHY ++ R +W FND+ V SSQ+
Sbjct: 286 LYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 329
>pdb|3V6C|A Chain A, Crystal Structure Of Usp2 In Complex With Mutated
Ubiquitin
pdb|3V6E|A Chain A, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin
Length = 367
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQL 112
L V+ H+GT GGHY ++ R +W FND+ V SSQ+
Sbjct: 305 LYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 348
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQL 112
L V+ H+GT GGHY ++ R +W FND+ V SSQ+
Sbjct: 286 LYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 329
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAEVKHFDSSQL 112
L V+ H+GT GGHY ++ R +W FND+ V SSQ+
Sbjct: 312 LYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 355
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 33.9 bits (76), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAE 103
L V+ H G DGGHY ++ ++ R +W F+D E
Sbjct: 339 LFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHE 373
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 33.5 bits (75), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 71 LIGVTVHTGTADGGHYYSFIRD--RDKWLLFNDAE 103
L V+ H G DGGHY ++ ++ R +W F+D E
Sbjct: 339 LFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHE 373
>pdb|1NBF|A Chain A, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|B Chain B, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|E Chain E, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
Length = 353
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 28/123 (22%), Positives = 45/123 (36%), Gaps = 33/123 (26%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKH--LMPQHYQEEKLKSEARXXXXXXXX 58
MR+ ++ T K+N F FP +L + +++K P +Y
Sbjct: 200 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANY------------------ 241
Query: 59 XXXXXXXXXXXXLIGVTVHTGTADGGHYYSFI--RDRDKWLLFNDAEVKHFDSSQLAAEC 116
L V VH+G GGHY ++ + KW F+D V +
Sbjct: 242 -----------ILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHN 290
Query: 117 FGG 119
+GG
Sbjct: 291 YGG 293
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 28/123 (22%), Positives = 45/123 (36%), Gaps = 33/123 (26%)
Query: 1 MRYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKH--LMPQHYQEEKLKSEARXXXXXXXX 58
MR+ ++ T K+N F FP +L + +++K P +Y
Sbjct: 369 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANY------------------ 410
Query: 59 XXXXXXXXXXXXLIGVTVHTGTADGGHYYSFI--RDRDKWLLFNDAEVKHFDSSQLAAEC 116
L V VH+G GGHY ++ + KW F+D V +
Sbjct: 411 -----------ILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHN 459
Query: 117 FGG 119
+GG
Sbjct: 460 YGG 462
>pdb|3I3T|A Chain A, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|C Chain C, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|E Chain E, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|G Chain G, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
Length = 355
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 71 LIGVTVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQLAA 114
L + H+G+ GHY + R + W ++ND+ V +Q+A+
Sbjct: 296 LYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQVAS 339
>pdb|3MTN|A Chain A, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
pdb|3MTN|C Chain C, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
Length = 373
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 71 LIGVTVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQLAA 114
L + H+G+ GHY + R + W ++ND+ V +Q+A+
Sbjct: 315 LYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQVAS 358
>pdb|2Y5B|A Chain A, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
pdb|2Y5B|E Chain E, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
Length = 370
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 71 LIGVTVHTGTADGGHYYSFIRDRDKWLLFNDAEVKHFDSSQLAA 114
L + H+G+ GHY + R + W ++ND+ V +Q+A+
Sbjct: 309 LYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQVAS 352
>pdb|1NB8|A Chain A, Structure Of The Catalytic Domain Of Usp7 (Hausp)
pdb|1NB8|B Chain B, Structure Of The Catalytic Domain Of Usp7 (Hausp)
Length = 353
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 27/122 (22%), Positives = 44/122 (36%), Gaps = 33/122 (27%)
Query: 2 RYTFNMVTMLKEKVNTHFSFPMRLDMSGYVEKH--LMPQHYQEEKLKSEARXXXXXXXXX 59
R+ ++ T K+N F FP +L + +++K P +Y
Sbjct: 201 RFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANY------------------- 241
Query: 60 XXXXXXXXXXXLIGVTVHTGTADGGHYYSFI--RDRDKWLLFNDAEVKHFDSSQLAAECF 117
L V VH+G GGHY ++ + KW F+D V + +
Sbjct: 242 ----------ILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNY 291
Query: 118 GG 119
GG
Sbjct: 292 GG 293
>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
Length = 367
Score = 30.0 bits (66), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 71 LIGVTVHTGTADGGHYYSFIRDR--DKWLLFNDAEVKHFDSSQLAAE 115
LI V+ H G GHY ++ +++ KW F+D+ V Q+ +
Sbjct: 302 LIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTK 348
>pdb|2H21|A Chain A, Structure Of Rubisco Lsmt Bound To Adomet
pdb|2H21|B Chain B, Structure Of Rubisco Lsmt Bound To Adomet
pdb|2H21|C Chain C, Structure Of Rubisco Lsmt Bound To Adomet
pdb|2H23|A Chain A, Structure Of Rubisco Lsmt Bound To Trimethyllysine And
Adohcy
pdb|2H23|B Chain B, Structure Of Rubisco Lsmt Bound To Trimethyllysine And
Adohcy
pdb|2H23|C Chain C, Structure Of Rubisco Lsmt Bound To Trimethyllysine And
Adohcy
pdb|2H2E|A Chain A, Structure Of Rubisco Lsmt Bound To Azaadomet And Lysine
pdb|2H2E|B Chain B, Structure Of Rubisco Lsmt Bound To Azaadomet And Lysine
pdb|2H2E|C Chain C, Structure Of Rubisco Lsmt Bound To Azaadomet And Lysine
pdb|2H2J|A Chain A, Structure Of Rubisco Lsmt Bound To Sinefungin And
Monomethyllysine
pdb|2H2J|B Chain B, Structure Of Rubisco Lsmt Bound To Sinefungin And
Monomethyllysine
pdb|2H2J|C Chain C, Structure Of Rubisco Lsmt Bound To Sinefungin And
Monomethyllysine
Length = 440
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 85 HYYSFI-RDRDKWLLFNDAEVKHFDSSQLAAECFGGEMTVLNACLKL---LSTAPQYIDA 140
HY+ + ++ D + +++ E++ SQL + V N CLKL + + +
Sbjct: 97 HYFGILPQETDSTIYWSEEELQELQGSQLLKTTVSVKEYVKNECLKLEQEIILPNKRLFP 156
Query: 141 TPPTSSRLVQYFTVL--NYFSMTRNEKLMLLPTS 172
P T F +L FS RNE L+++P +
Sbjct: 157 DPVTLDDFFWAFGILRSRAFSRLRNENLVVVPMA 190
>pdb|1MLV|A Chain A, Structure And Catalytic Mechanism Of A Set Domain Protein
Methyltransferase
pdb|1MLV|B Chain B, Structure And Catalytic Mechanism Of A Set Domain Protein
Methyltransferase
pdb|1MLV|C Chain C, Structure And Catalytic Mechanism Of A Set Domain Protein
Methyltransferase
pdb|1OZV|A Chain A, Crystal Structure Of The Set Domain Of Lsmt Bound To
Lysine And Adohcy
pdb|1OZV|B Chain B, Crystal Structure Of The Set Domain Of Lsmt Bound To
Lysine And Adohcy
pdb|1OZV|C Chain C, Crystal Structure Of The Set Domain Of Lsmt Bound To
Lysine And Adohcy
pdb|1P0Y|A Chain A, Crystal Structure Of The Set Domain Of Lsmt Bound To
Melysine And Adohcy
pdb|1P0Y|B Chain B, Crystal Structure Of The Set Domain Of Lsmt Bound To
Melysine And Adohcy
pdb|1P0Y|C Chain C, Crystal Structure Of The Set Domain Of Lsmt Bound To
Melysine And Adohcy
Length = 444
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 85 HYYSFI-RDRDKWLLFNDAEVKHFDSSQLAAECFGGEMTVLNACLKL---LSTAPQYIDA 140
HY+ + ++ D + +++ E++ SQL + V N CLKL + + +
Sbjct: 101 HYFGILPQETDSTIYWSEEELQELQGSQLLKTTVSVKEYVKNECLKLEQEIILPNKRLFP 160
Query: 141 TPPTSSRLVQYFTVL--NYFSMTRNEKLMLLPTS 172
P T F +L FS RNE L+++P +
Sbjct: 161 DPVTLDDFFWAFGILRSRAFSRLRNENLVVVPMA 194
>pdb|1KZH|A Chain A, Structure Of A Pyrophosphate-dependent Phosphofructokinase
From The Lyme Disease Spirochete Borrelia Burgdorferi
pdb|1KZH|B Chain B, Structure Of A Pyrophosphate-dependent Phosphofructokinase
From The Lyme Disease Spirochete Borrelia Burgdorferi
pdb|2F48|A Chain A, Crystal Structure Of A Novel Fructose 1,6-Bisphosphate And
Alf3 Containing Pyrophosphate-Dependent
Phosphofructo-1-Kinase Complex From Borrelia Burgdorferi
pdb|2F48|B Chain B, Crystal Structure Of A Novel Fructose 1,6-Bisphosphate And
Alf3 Containing Pyrophosphate-Dependent
Phosphofructo-1-Kinase Complex From Borrelia Burgdorferi
Length = 555
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 82 DGGHYYSFIRDRDKWLLFN----DAEVKHFDSSQLAAE 115
+G + F+++RDKW L N V++F SS++ E
Sbjct: 507 EGRPFKEFVKNRDKWALNNLYLYPGPVQYFGSSEIVDE 544
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 71 LIGVTVHTGTAD-GGHYYSFIRDRDKWLLFNDAEV 104
L H GT+ GHY I+ +W+++ND +V
Sbjct: 799 LFAFISHMGTSTMCGHYVCHIKKEGRWVIYNDQKV 833
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
0.323 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,702,621
Number of Sequences: 62578
Number of extensions: 190252
Number of successful extensions: 363
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 352
Number of HSP's gapped (non-prelim): 24
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)