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= psy9878
(338 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 68.6 bits (166), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 40/120 (33%), Positives = 64/120 (53%), Gaps = 4/120 (3%)
Query: 179 PGIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRP-PGDSSFLLVQRFGEL 237
PG+ GL N+ + N LQ L + PL DYFL++ A + R P + + + EL
Sbjct: 6 PGLCGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAEL 65
Query: 238 MRKLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKK 297
++++W+ R+ +HV+P M + V QF +Q D + L++ L+ LH LN KKK
Sbjct: 66 IKQMWSGRD--AHVAP-RMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKK 122
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 58/123 (47%), Gaps = 4/123 (3%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G VGL N+ + N +LQ L PLRD+ LR R + P G + L + F +++
Sbjct: 15 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRD--FRQEVPGGGRAQELTEAFADVIG 72
Query: 240 KLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDS 299
LW+P + ++ V+P +AV F Q D +FL + LH +N ++
Sbjct: 73 ALWHPDSCEA-VNP-TRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAP 130
Query: 300 SIV 302
I+
Sbjct: 131 PIL 133
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G+ GL N+ + N ILQ L + LRDY L+ + Y R ++ LV+ F +L++
Sbjct: 8 GLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQ 66
Query: 240 KLW--NPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALN 292
+W +P + VSP E + ++ + + +Q D +FL + L+ LH +N
Sbjct: 67 TIWTSSPNDV---VSPSEFKTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVN 117
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 58/123 (47%), Gaps = 4/123 (3%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G VGL N+ + N +LQ L PLRD+ LR R + P G + L + F +++
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRD--FRQEVPGGGRAQELTEAFADVIG 59
Query: 240 KLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDS 299
LW+P + ++ V+P +AV F Q D +FL + LH +N ++
Sbjct: 60 ALWHPDSCEA-VNPTR-FRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAP 117
Query: 300 SIV 302
I+
Sbjct: 118 PIL 120
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 36/123 (29%), Positives = 58/123 (47%), Gaps = 4/123 (3%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G VGL N+ + N +LQ L PLRD+ LR R + P G + L + F +++
Sbjct: 21 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRD--FRQEVPGGGRAQELTEAFADVIG 78
Query: 240 KLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDS 299
LW+P + ++ V+P +AV F Q D +FL + LH +N ++
Sbjct: 79 ALWHPDSCEA-VNPTR-FRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAP 136
Query: 300 SIV 302
I+
Sbjct: 137 PIL 139
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 39/131 (29%), Positives = 61/131 (46%), Gaps = 15/131 (11%)
Query: 179 PGIVGLNNIKANDYCNVILQALCHVTPLRDYFLR-----EINYARVKRPPGDSSFLLVQR 233
P + GL N+ Y N ILQ LC+ L DYF R +IN + + G+ + +
Sbjct: 60 PALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGE----VAEE 115
Query: 234 FGELMRKLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNG 293
FG +M+ LW + ++SP + + + QF Q D + L + ++ LH LN
Sbjct: 116 FGIIMKALWTGQ--YRYISPKD-FKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLN- 171
Query: 294 TKKKDSSIVYK 304
K D+ YK
Sbjct: 172 --KADNRKRYK 180
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G+ GL N+ + N ILQ L + LRDY L+ + Y R ++ LV+ F +L++
Sbjct: 8 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQ 66
Query: 240 KLW--NPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALN 292
+W +P + VSP E + ++ + + +Q D +FL + L+ LH +N
Sbjct: 67 TIWTSSPNDV---VSPSEFKTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVN 117
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G+ GL N+ + N ILQ L + LRDY L+ + Y R ++ LV+ F +L++
Sbjct: 27 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQ 85
Query: 240 KLW--NPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALN 292
+W +P + VSP E + ++ + + +Q D +FL + L+ LH +N
Sbjct: 86 TIWTSSPNDV---VSPSEFKTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVN 136
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 180 GIVGLNNIKANDYCNVILQALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMR 239
G+ GL N+ + N ILQ L + LRDY L+ + Y R ++ LV+ F +L++
Sbjct: 34 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQ 92
Query: 240 KLW--NPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALN 292
+W +P + VSP E + ++ + + +Q D +FL + L+ LH +N
Sbjct: 93 TIWTSSPNDV---VSPSEFKTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVN 143
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/131 (29%), Positives = 59/131 (45%), Gaps = 15/131 (11%)
Query: 179 PGIVGLNNIKANDYCNVILQALCHVTPLRDYFLR-----EINYARVKRPPGDSSFLLVQR 233
P + GL N+ Y N ILQ LC+ L DYF R +IN + + G+ + +
Sbjct: 60 PALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGE----VAEE 115
Query: 234 FGELMRKLWNPRNFKSHVSPHEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNG 293
FG + + LW + ++SP + + + QF Q D + L + + LH LN
Sbjct: 116 FGIIXKALWTGQ--YRYISPKD-FKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLN- 171
Query: 294 TKKKDSSIVYK 304
K D+ YK
Sbjct: 172 --KADNRKRYK 180
>pdb|3B1C|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1D|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1E|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
Length = 392
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 255 EMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSI-----VYKTFLGS 309
E+LQAV+ W + + Q++ + I F+ + + A+ K+ ++ VY F S
Sbjct: 70 ELLQAVLDWEKSEHQYSFDKEDIVFVEGVVPAISIAIQAFTKEGEAVLINSPVYPPFARS 129
Query: 310 MKVKTRKIPPVELEEK 325
+++ RK+ L+E+
Sbjct: 130 VRLNNRKLVSNSLKEE 145
>pdb|1H2A|S Chain S, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris
Length = 317
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 80 CLPDNYEIVGTVAGPVVNRLCPYLDTINRQLLDF 113
C P+ Y +VGT+ + N+ P LD++NR + F
Sbjct: 200 CPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFF 233
>pdb|1H2R|S Chain S, Three-Dimensional Structure Of Ni-Fe Hydrogenase From
Desulfivibrio Vulgaris Miyazaki F In The Reduced Form At
1.4 A Resolution
pdb|1UBH|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBJ|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBK|S Chain S, Three-dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBL|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBM|S Chain S, Three-dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBO|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBR|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBT|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBU|S Chain S, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1WUH|S Chain S, Three-Dimensional Structure Of The Ni-A State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUI|S Chain S, Ultra-High Resolution Structure Of The Ni-A State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUJ|S Chain S, Three-Dimensional Structure Of The Ni-B State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUK|S Chain S, High Resolution Structure Of The Oxidized State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUL|S Chain S, High Resolution Structure Of The Reduced State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
Length = 267
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 80 CLPDNYEIVGTVAGPVVNRLCPYLDTINRQLLDF 113
C P+ Y +VGT+ + N+ P LD++NR + F
Sbjct: 150 CPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFF 183
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 11 CPYLDTINR----QLLDFDFEKLCSVSLSRINVYACLVCGKYFQGRGTNTFAYT--HSVA 64
CP+LD++ L+ + N++ACL + G G + ++ HS
Sbjct: 6 CPHLDSVGEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHSQE 65
Query: 65 ESHHVFLNLHTLKFYCLPDNYEI 87
H++ +NL TL+ +C + E+
Sbjct: 66 TKHYLTVNLTTLRVWCYACSKEV 88
>pdb|3IUF|A Chain A, Crystal Structure Of The C2h2-Type Zinc Finger Domain Of
Human Ubi-D4
Length = 48
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 40 YACLVCGKYFQGRGTNTFAYTHS 62
YAC +CGK ++ R ++ Y HS
Sbjct: 8 YACDICGKRYKNRPGLSYHYAHS 30
>pdb|1OH1|A Chain A, Solution Structure Of Staphostatin A Form Staphylococcus
Aureus Confirms The Discovery Of A Novel Class Of
Cysteine Proteinase Inhibitors
Length = 109
Score = 28.1 bits (61), Expect = 6.6, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 274 SDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFL 307
SD D++ ++NT H+ L K +SSIV + F+
Sbjct: 48 SDDSDYICKYINTEHKQLTLYNKNNSSIVIEIFI 81
>pdb|3DWL|D Chain D, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
pdb|3DWL|I Chain I, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
Length = 317
Score = 27.7 bits (60), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 261 VLWSRKQFQFTEQS--DPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRKIP 318
VL+ R FT Q+ D I + F NTLH + +K + K KV R P
Sbjct: 244 VLFER---HFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP 300
Query: 319 PVELEEK 325
VELE K
Sbjct: 301 DVELERK 307
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
0.325 0.140 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,248,060
Number of Sequences: 62578
Number of extensions: 420769
Number of successful extensions: 1134
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1107
Number of HSP's gapped (non-prelim): 26
length of query: 338
length of database: 14,973,337
effective HSP length: 99
effective length of query: 239
effective length of database: 8,778,115
effective search space: 2097969485
effective search space used: 2097969485
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)