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= 003922
(786 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 55/144 (38%), Positives = 86/144 (59%), Gaps = 3/144 (2%)
Query: 2 EDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLN 61
ED+Y+++L++KG K + ES DY++VE+L GDN+Y G + +A + +K +LP VL+
Sbjct: 307 EDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLH 365
Query: 62 FQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLI-YDLSAVLIHKGTAVNS 120
QL R ++ P+T KI F FP +L + L + D Y L AVL+H G +
Sbjct: 366 LQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDN-HG 424
Query: 121 GHYIALIKDENTGQWWEFDDEHVS 144
GHY+ + + G+W +FDD+ VS
Sbjct: 425 GHYVVYLNPKGDGKWCKFDDDVVS 448
>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 = 98.2 bits (243), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 55/144 (38%), Positives = 86/144 (59%), Gaps = 3/144 (2%)
Query: 2 EDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLN 61
ED+Y+++L++KG K + ES DY++VE+L GDN+Y G + +A + +K +LP VL+
Sbjct: 138 EDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLH 196
Query: 62 FQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLI-YDLSAVLIHKGTAVNS 120
QL R ++ P+T KI F FP +L + L + D Y L AVL+H G +
Sbjct: 197 LQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDN-HG 255
Query: 121 GHYIALIKDENTGQWWEFDDEHVS 144
GHY+ + + G+W +FDD+ VS
Sbjct: 256 GHYVVYLNPKGDGKWCKFDDDVVS 279
>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 = 97.4 bits (241), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 55/144 (38%), Positives = 85/144 (59%), Gaps = 3/144 (2%)
Query: 2 EDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLN 61
ED+Y+++L++KG K + ES DY++VE+L GDN+Y G + +A + +K +LP VL+
Sbjct: 138 EDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLH 196
Query: 62 FQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLI-YDLSAVLIHKGTAVNS 120
QL R + P+T KI F FP +L + L + D Y L AVL+H G +
Sbjct: 197 LQLXRFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDN-HG 255
Query: 121 GHYIALIKDENTGQWWEFDDEHVS 144
GHY+ + + G+W +FDD+ VS
Sbjct: 256 GHYVVYLNPKGDGKWCKFDDDVVS 279
>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 = 82.8 bits (203), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 57/155 (36%), Positives = 84/155 (54%), Gaps = 13/155 (8%)
Query: 1 MEDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVL 60
++ F +L L++K K L E LD + E+L D Y C C + DA + + + LP VL
Sbjct: 305 IDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVL 363
Query: 61 NFQLKRCVFLPKTTMKKKITSPFCFPGELNMQR--------RLSEPSQL-DLIYDLSAVL 111
QLKR L + +K+ FP LNM+ + SE ++ D+IY+L ++
Sbjct: 364 VLQLKRFEHLLNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIV 422
Query: 112 IHKGTAVNSGHYIALIKDENTGQWWEFDDEHVSNL 146
HKGT VN GHYIA K GQW++F+D VS++
Sbjct: 423 SHKGT-VNEGHYIAFCKISG-GQWFKFNDSMVSSI 455
>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 = 82.4 bits (202), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 57/155 (36%), Positives = 84/155 (54%), Gaps = 13/155 (8%)
Query: 1 MEDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVL 60
++ F +L L++K K L E LD + E+L D Y C C + DA + + + LP VL
Sbjct: 305 IDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVL 363
Query: 61 NFQLKRCVFLPKTTMKKKITSPFCFPGELNMQR--------RLSEPSQL-DLIYDLSAVL 111
QLKR L + +K+ FP LNM+ + SE ++ D+IY+L ++
Sbjct: 364 VLQLKRFEHLLNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIV 422
Query: 112 IHKGTAVNSGHYIALIKDENTGQWWEFDDEHVSNL 146
HKGT VN GHYIA K GQW++F+D VS++
Sbjct: 423 SHKGT-VNEGHYIAFCKISG-GQWFKFNDSMVSSI 455
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 82.4 bits (202), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 57/155 (36%), Positives = 84/155 (54%), Gaps = 13/155 (8%)
Query: 1 MEDFYELELNVKGLKTLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVL 60
++ F +L L++K K L E LD + E+L D Y C C + DA + + + LP VL
Sbjct: 300 IDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGIHKLPSVL 358
Query: 61 NFQLKRCVFLPKTTMKKKITSPFCFPGELNMQR--------RLSEPSQL-DLIYDLSAVL 111
QLKR L + +K+ FP LNM+ + SE ++ D+IY+L ++
Sbjct: 359 VLQLKRFEHLLNGS-NRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIV 417
Query: 112 IHKGTAVNSGHYIALIKDENTGQWWEFDDEHVSNL 146
HKGT VN GHYIA K GQW++F+D VS++
Sbjct: 418 SHKGT-VNEGHYIAFCKISG-GQWFKFNDSMVSSI 450
>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 = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/130 (33%), Positives = 66/130 (50%), Gaps = 4/130 (3%)
Query: 16 TLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLNFQLKRCVFLPKTTM 75
L + ++ + ++E L + ++C +C AT+ L SLP +L LKR F
Sbjct: 212 ALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKR--FSYNRYW 269
Query: 76 KKKITSPFCFPGE-LNMQRRLSEPSQLDLIYDLSAVLIHKGTAVNSGHYIALIKDENTGQ 134
+ K+ + FP LNM + S +YDL AV H G A+ GHY A K++ G+
Sbjct: 270 RDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYG-AMGVGHYTAYAKNKLNGK 328
Query: 135 WWEFDDEHVS 144
W+ FDD +VS
Sbjct: 329 WYYFDDSNVS 338
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 59.3 bits (142), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 40/127 (31%), Positives = 66/127 (51%), Gaps = 4/127 (3%)
Query: 16 TLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLNFQLKRCVFLPKTTM 75
TL + L + E+L +N+++C C R D+ + I++ LP VL LKR F
Sbjct: 249 TLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR--FSYDGRW 306
Query: 76 KKKITSPFCFPGE-LNMQRRLSEPSQLDLIYDLSAVLIHKGTAVNSGHYIALIKDENTGQ 134
K+K+ + FP E L++ + + P Y+L +V H G ++ GHY A K+ +
Sbjct: 307 KQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQR 365
Query: 135 WWEFDDE 141
W++FDD
Sbjct: 366 WFKFDDH 372
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 59.3 bits (142), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 40/127 (31%), Positives = 66/127 (51%), Gaps = 4/127 (3%)
Query: 16 TLDESLDDYLSVEELHGDNQYFCDSCGTRVDATRSIKLRSLPDVLNFQLKRCVFLPKTTM 75
TL + L + E+L +N+++C C R D+ + I++ LP VL LKR F
Sbjct: 249 TLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR--FSYDGRW 306
Query: 76 KKKITSPFCFPGE-LNMQRRLSEPSQLDLIYDLSAVLIHKGTAVNSGHYIALIKDENTGQ 134
K+K+ + FP E L++ + + P Y+L +V H G ++ GHY A K+ +
Sbjct: 307 KQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQR 365
Query: 135 WWEFDDE 141
W++FDD
Sbjct: 366 WFKFDDH 372
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 66/150 (44%), Gaps = 11/150 (7%)
Query: 1 MEDFYELELNV--KGLKTLDESLDDYLSV----EELHGDNQYFCDSCGTRVDATRSIKLR 54
E F +L L + KG SL D ++ EEL +N CD C + +T+ + ++
Sbjct: 205 FEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQ 264
Query: 55 SLPDVLNFQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLIYDLSAVLIHK 114
P +L L R F KK + FP + + +Y L A+ H
Sbjct: 265 RFPRILVLHLNR--FSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHS 322
Query: 115 GTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
G+ V+ GHY AL + + TG W ++D VS
Sbjct: 323 GS-VHYGHYTALCRCQ-TG-WHVYNDSRVS 349
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 66/150 (44%), Gaps = 11/150 (7%)
Query: 1 MEDFYELELNV--KGLKTLDESLDDYLSV----EELHGDNQYFCDSCGTRVDATRSIKLR 54
E F +L L + KG SL D ++ EEL +N CD C + +T+ + ++
Sbjct: 186 FEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQ 245
Query: 55 SLPDVLNFQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLIYDLSAVLIHK 114
P +L L R F KK + FP + + +Y L A+ H
Sbjct: 246 RFPRILVLHLNR--FSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHS 303
Query: 115 GTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
G+ V+ GHY AL + + TG W ++D VS
Sbjct: 304 GS-VHYGHYTALCRCQ-TG-WHVYNDSRVS 330
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 5/97 (5%)
Query: 49 RSIKLRSLPDVLNFQLKRCVFLPKTTMKKKITSPFCFP-GELNMQRRLSEPSQLDLIYDL 107
+ ++ P +L LKR F K+T+ FP +L+++ SE + +Y+L
Sbjct: 256 KKFSIQRFPKILVLHLKR--FSESRIRTSKLTTFVNFPLRDLDLREFASENTN-HAVYNL 312
Query: 108 SAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
AV H GT + GHY A + TG+W F+D V+
Sbjct: 313 YAVSNHSGTTM-GGHYTAYCRSPGTGEWHTFNDSSVT 348
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 5/97 (5%)
Query: 49 RSIKLRSLPDVLNFQLKRCVFLPKTTMKKKITSPFCFP-GELNMQRRLSEPSQLDLIYDL 107
+ ++ P +L LKR F K+T+ FP +L+++ SE + +Y+L
Sbjct: 230 KKFSIQRFPKILVLHLKR--FSESRIRTSKLTTFVNFPLRDLDLREFASENTN-HAVYNL 286
Query: 108 SAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
AV H GT + GHY A + TG+W F+D V+
Sbjct: 287 YAVSNHSGTTM-GGHYTAYCRSPGTGEWHTFNDSSVT 322
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 66/150 (44%), Gaps = 11/150 (7%)
Query: 1 MEDFYELELNV--KGLKTLDESLDDYLSV----EELHGDNQYFCDSCGTRVDATRSIKLR 54
E F +L L + KG SL D ++ EEL +N CD C + +T+ + ++
Sbjct: 199 FEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQ 258
Query: 55 SLPDVLNFQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLIYDLSAVLIHK 114
P +L L R F KK + FP + + +Y L A+ H
Sbjct: 259 RFPRILVLHLNR--FSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHS 316
Query: 115 GTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
G+ V+ GHY AL + + TG W ++D VS
Sbjct: 317 GS-VHYGHYTALCRCQ-TG-WHVYNDSRVS 343
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 5/97 (5%)
Query: 49 RSIKLRSLPDVLNFQLKRCVFLPKTTMKKKITSPFCFP-GELNMQRRLSEPSQLDLIYDL 107
+ ++ P +L LKR F K+T+ FP +L+++ SE + +Y+L
Sbjct: 249 KKFSIQRFPKILVLHLKR--FSESRIRTSKLTTFVNFPLRDLDLREFASENTN-HAVYNL 305
Query: 108 SAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
AV H GT + GHY A + TG+W F+D V+
Sbjct: 306 YAVSNHSGTTM-GGHYTAYCRSPGTGEWHTFNDSSVT 341
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 5/97 (5%)
Query: 49 RSIKLRSLPDVLNFQLKRCVFLPKTTMKKKITSPFCFP-GELNMQRRLSEPSQLDLIYDL 107
+ ++ P +L LKR F K+T+ FP +L+++ SE + +Y+L
Sbjct: 230 KKFSIQRFPKILVLHLKR--FSESRIRTSKLTTFVNFPLRDLDLREFASENTN-HAVYNL 286
Query: 108 SAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
AV H GT + GHY A + TG+W F+D V+
Sbjct: 287 YAVSNHSGTTM-GGHYTAYCRSPGTGEWHTFNDSSVT 322
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 29/42 (69%), Gaps = 1/42 (2%)
Query: 104 IYDLSAVLIHKGTAVNSGHYIALIKDE-NTGQWWEFDDEHVS 144
+Y+L V+ H+G SGHY A I+DE + +W++F+D+ VS
Sbjct: 345 VYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVS 386
>pdb|2AYN|A Chain A, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|B Chain B, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|C Chain C, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYO|A Chain A, Structure Of Usp14 Bound To Ubquitin Aldehyde
Length = 404
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 29/40 (72%), Gaps = 1/40 (2%)
Query: 105 YDLSAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHVS 144
YDL AVL H+G + +SGHY++ +K + +W +FDD+ VS
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRKQ-DEWIKFDDDKVS 366
>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 = 0.36, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 105 YDLSAVLIHKGTAVNSGHYIALIKDENTGQWWEFDDEHV 143
Y L A + H GT+ GHY+ IK E G+W ++D+ V
Sbjct: 797 YQLFAFISHMGTSTMCGHYVCHIKKE--GRWVIYNDQKV 833
>pdb|4FFH|A Chain A, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Sucrose
pdb|4FFH|B Chain B, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Sucrose
pdb|4FFH|C Chain C, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Sucrose
pdb|4FFH|D Chain D, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Sucrose
pdb|4FFI|A Chain A, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Levanbiose
pdb|4FFI|B Chain B, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Levanbiose
pdb|4FFI|C Chain C, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Levanbiose
pdb|4FFI|D Chain D, Crystal Structure Of Levan Fructotransferase D54n Mutant
From Arthrobacter Ureafaciens In Complex With Levanbiose
Length = 492
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 406 GKLVEGTYYVSKSWLQQWTRRKNLDAPSEADGGPTTSIRCP 446
G+L +Y S + L+ WT R+N D P+ A GG I CP
Sbjct: 164 GRLRYAAFYTSPN-LRDWTLRRNFDYPNHALGG----IECP 199
>pdb|4FFG|A Chain A, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens In Complex With Dfa-Iv
pdb|4FFG|B Chain B, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens In Complex With Dfa-Iv
pdb|4FFG|C Chain C, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens In Complex With Dfa-Iv
pdb|4FFG|D Chain D, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens In Complex With Dfa-Iv
Length = 492
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 406 GKLVEGTYYVSKSWLQQWTRRKNLDAPSEADGGPTTSIRCP 446
G+L +Y S + L+ WT R+N D P+ A GG I CP
Sbjct: 164 GRLRYAAFYTSPN-LRDWTLRRNFDYPNHALGG----IECP 199
>pdb|4FFF|A Chain A, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens
pdb|4FFF|B Chain B, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens
pdb|4FFF|C Chain C, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens
pdb|4FFF|D Chain D, Crystal Structure Of Levan Fructotransferase From
Arthrobacter Ureafaciens
Length = 490
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 406 GKLVEGTYYVSKSWLQQWTRRKNLDAPSEADGGPTTSIRCP 446
G+L +Y S + L+ WT R+N D P+ A GG I CP
Sbjct: 164 GRLRYAAFYTSPN-LRDWTLRRNFDYPNHALGG----IECP 199
>pdb|2Y9K|A Chain A, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|B Chain B, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|C Chain C, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|D Chain D, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|E Chain E, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|F Chain F, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|G Chain G, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|H Chain H, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|I Chain I, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|J Chain J, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|K Chain K, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|L Chain L, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|M Chain M, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|N Chain N, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9K|O Chain O, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
Length = 137
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 32/69 (46%)
Query: 53 LRSLPDVLNFQLKRCVFLPKTTMKKKITSPFCFPGELNMQRRLSEPSQLDLIYDLSAVLI 112
LR+ D + QLK V + K +KKIT F F + +LS L +D A+ I
Sbjct: 9 LRTFFDAMALQLKEPVIVSKMAARKKITGNFEFHDPNALLEKLSLQLGLIWYFDGQAIYI 68
Query: 113 HKGTAVNSG 121
+ + + +
Sbjct: 69 YDASEMRNA 77
>pdb|3KLS|X Chain X, Structure Of Complement C5 In Complex With Ssl7
pdb|3KLS|Y Chain Y, Structure Of Complement C5 In Complex With Ssl7
pdb|3PRX|X Chain X, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PRX|Y Chain Y, Structure Of Complement C5 In Complex With Cvf And Ssl7
Length = 231
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 193 EYYNGSNVERFTSNDAYMLMYNLRRDKEDSK 223
E YNGSNV RF D ++ L +DKE K
Sbjct: 65 ENYNGSNVVRFNPKDQNHQLFLLGKDKEQYK 95
>pdb|2E7Z|A Chain A, Acetylene Hydratase From Pelobacter Acetylenicus
Length = 727
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 403 VLSGKLVEGTYYVSKSWLQQWTRRKNLDAPSEADGG-PTTSIRCPHGQLMPEKAGGAKRL 461
+L K + S W+ T L + DG P +IR PHG+ PE+ GG +
Sbjct: 628 LLHPKTAQSLGLPSGEWIWVETTHGRLKLLLKHDGAQPEGTIRIPHGRWCPEQEGGPETG 687
Query: 462 LVPEILWLFIYEDAMKVKPDD 482
+L + DAM + DD
Sbjct: 688 FSGAML----HNDAMVLSDDD 704
>pdb|1V1O|A Chain A, Staphylococcal Superantigen-Like Protein 7
pdb|1V1O|B Chain B, Staphylococcal Superantigen-Like Protein 7
pdb|1V1P|B Chain B, The Structure Ssl From Staphylococcus Aureus From An
Orthorhombic Crystal Form
Length = 213
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 193 EYYNGSNVERFTSNDAYMLMYNLRRDKEDSK 223
E YNGSNV RF D ++ L +DKE K
Sbjct: 47 ENYNGSNVVRFNPKDQNHQLFLLGKDKEQYK 77
>pdb|1VLJ|A Chain A, Crystal Structure Of Nadh-Dependent Butanol Dehydrogenase
A (Tm0820) From Thermotoga Maritima At 1.78 A Resolution
pdb|1VLJ|B Chain B, Crystal Structure Of Nadh-Dependent Butanol Dehydrogenase
A (Tm0820) From Thermotoga Maritima At 1.78 A Resolution
Length = 407
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 566 IEPEILDGVIDSLKCEKHLRLLERPPDLVCKRGSIYQKGSATDGLTIVTENDWKWFCEEW 625
I EI +G I ++ + RL+E+P D + + A +G V +W C
Sbjct: 224 ISNEIAEGTIRTI-MKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRI 282
Query: 626 GGIKEKGLSVIVDFSNNAGNELV 648
E LS + D ++ AG +V
Sbjct: 283 ----EHSLSALYDIAHGAGLAIV 301
>pdb|4GNS|B Chain B, Crystal Structure Of The Chs5-Chs6 Exomer Cargo Adaptor
Complex
Length = 754
Score = 29.3 bits (64), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 529 LGKSIPLSLDCKYYLLPSTWLTKWRNYISPSGKNASSIEPEILDGVIDSLK 579
L + +P SL+C + S T NY+ S K+ +I P ++D ID LK
Sbjct: 223 LCRFLPRSLNCGWDSTKSMQATIVNNYLMYSLKSFIAITPSLVDFTIDYLK 273
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
0.317 0.135 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,685,415
Number of Sequences: 62578
Number of extensions: 1062659
Number of successful extensions: 2325
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2282
Number of HSP's gapped (non-prelim): 31
length of query: 786
length of database: 14,973,337
effective HSP length: 107
effective length of query: 679
effective length of database: 8,277,491
effective search space: 5620416389
effective search space used: 5620416389
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)