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= 022748
(292 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DDG|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|J Chain J, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|K Chain K, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDG|L Chain L, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|A Chain A, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|B Chain B, Crystal Structure Of Human Otub1UBCH5B~UBUB
pdb|4DDI|C Chain C, Crystal Structure Of Human Otub1UBCH5B~UBUB
Length = 399
Score = 193 bits (490), Expect = 1e-49, Method: Compositional matrix adjust.
Identities = 115/270 (42%), Positives = 158/270 (58%), Gaps = 26/270 (9%)
Query: 21 DEDIMQQQSDIKAEEAQKVPFVADKEPLSALASEYQSGSPILLEKIKVLGEQYAAIRRTR 80
DE IM QQ I+ E A + P V+++ LS L EY I +KIK L ++Y+ IR+TR
Sbjct: 155 DEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTR 214
Query: 81 GDGNCFFRSFMFSYLEHILASQDQAEVDRIKAKVEECRRTLQSLGHADFTFEDFFALFLE 140
DGN F+R+F FS+LE +L D E+ R KA + + L S G +FT EDF F++
Sbjct: 215 PDGNSFYRAFGFSHLEALL--DDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMD 272
Query: 141 QLDNVLQGNEFSISHGELVVRSRDQSVSDYVVMFFRFVTSGEIRKRSEFFEPFILGLTNA 200
++ V E S +L+ DQS SDY+V++ R +TSG +++ S+FFE FI G
Sbjct: 273 LIEQV----EKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEG--GR 326
Query: 201 TVEQFCKSSVEPMGEESDHVHITALSDALGVPIRVVYLDRSSCDSGGASVNHHDFIPTPG 260
TV++FC+ VEPM +ESDH+HI AL+ AL V I+V Y+DR G + N H F
Sbjct: 327 TVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGE----GGTTNPHIF----- 377
Query: 261 DCPNATSGSTETTIPFITLLYRPGHYDILY 290
E + P + LLYRPGHYDILY
Sbjct: 378 ---------PEGSEPKVYLLYRPGHYDILY 398
>pdb|2ZFY|A Chain A, Crystal Structure Of Human Otubain 1
Length = 234
Score = 185 bits (470), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 109/258 (42%), Positives = 152/258 (58%), Gaps = 26/258 (10%)
Query: 33 AEEAQKVPFVADKEPLSALASEYQSGSPILLEKIKVLGEQYAAIRRTRGDGNCFFRSFMF 92
+E A + P V+++ LS L EY I +KIK L ++Y+ IR+TR DGNCF+R+F F
Sbjct: 2 SEIAVQNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGF 61
Query: 93 SYLEHILASQDQAEVDRIKAKVEECRRTLQSLGHADFTFEDFFALFLEQLDNVLQGNEFS 152
S+LE +L D E+ R KA + + L S G +FT EDF F++ ++ V E
Sbjct: 62 SHLEALL--DDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQV----EKQ 115
Query: 153 ISHGELVVRSRDQSVSDYVVMFFRFVTSGEIRKRSEFFEPFILGLTNATVEQFCKSSVEP 212
S +L+ DQS SDY+V++ R +TSG +++ S+FFE FI G TV++FC+ VEP
Sbjct: 116 TSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEG--GRTVKEFCQQEVEP 173
Query: 213 MGEESDHVHITALSDALGVPIRVVYLDRSSCDSGGASVNHHDFIPTPGDCPNATSGSTET 272
M +ESDH+HI AL+ AL V I+V Y+DR G + N H F E
Sbjct: 174 MCKESDHIHIIALAQALSVSIQVEYMDRGE----GGTTNPHIF--------------PEG 215
Query: 273 TIPFITLLYRPGHYDILY 290
+ P + LLYRPGHYDILY
Sbjct: 216 SEPKVYLLYRPGHYDILY 233
>pdb|3VON|A Chain A, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|H Chain H, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|O Chain O, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|V Chain V, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|CC Chain c, Crystalstructure Of The Ubiquitin Protease
pdb|3VON|JJ Chain j, Crystalstructure Of The Ubiquitin Protease
Length = 228
Score = 184 bits (467), Expect = 5e-47, Method: Compositional matrix adjust.
Identities = 107/251 (42%), Positives = 148/251 (58%), Gaps = 26/251 (10%)
Query: 40 PFVADKEPLSALASEYQSGSPILLEKIKVLGEQYAAIRRTRGDGNCFFRSFMFSYLEHIL 99
P V+++ LS L EY I +KIK L ++Y+ IR+TR DGNCF+R+F FS+LE +L
Sbjct: 3 PLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALL 62
Query: 100 ASQDQAEVDRIKAKVEECRRTLQSLGHADFTFEDFFALFLEQLDNVLQGNEFSISHGELV 159
D E+ R KA + + L S G +FT EDF F++ ++ V E S +L+
Sbjct: 63 --DDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQV----EKQTSVADLL 116
Query: 160 VRSRDQSVSDYVVMFFRFVTSGEIRKRSEFFEPFILGLTNATVEQFCKSSVEPMGEESDH 219
DQS SDY+V++ R +TSG +++ S+FFE FI G TV++FC+ VEPM +ESDH
Sbjct: 117 ASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEG--GRTVKEFCQQEVEPMCKESDH 174
Query: 220 VHITALSDALGVPIRVVYLDRSSCDSGGASVNHHDFIPTPGDCPNATSGSTETTIPFITL 279
+HI AL+ AL V I+V Y+DR G + N H F E + P + L
Sbjct: 175 IHIIALAQALSVSIQVEYMDRGE----GGTTNPHIF--------------PEGSEPKVYL 216
Query: 280 LYRPGHYDILY 290
LYRPGHYDILY
Sbjct: 217 LYRPGHYDILY 227
>pdb|4I6L|A Chain A, Crystal Structure Of Otub1 In Complex With Ubiquitin
Variant
Length = 229
Score = 181 bits (458), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 106/251 (42%), Positives = 147/251 (58%), Gaps = 26/251 (10%)
Query: 40 PFVADKEPLSALASEYQSGSPILLEKIKVLGEQYAAIRRTRGDGNCFFRSFMFSYLEHIL 99
P V+++ LS L EY I +KIK L ++Y+ IR+TR DGN F+R+F FS+LE +L
Sbjct: 4 PLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNSFYRAFGFSHLEALL 63
Query: 100 ASQDQAEVDRIKAKVEECRRTLQSLGHADFTFEDFFALFLEQLDNVLQGNEFSISHGELV 159
D E+ R KA + + L S G +FT EDF F++ ++ V E S +L+
Sbjct: 64 --DDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQV----EKQTSVADLL 117
Query: 160 VRSRDQSVSDYVVMFFRFVTSGEIRKRSEFFEPFILGLTNATVEQFCKSSVEPMGEESDH 219
DQS SDY+V++ R +TSG +++ S+FFE FI G TV++FC+ VEPM +ESDH
Sbjct: 118 ASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEG--GRTVKEFCQQEVEPMCKESDH 175
Query: 220 VHITALSDALGVPIRVVYLDRSSCDSGGASVNHHDFIPTPGDCPNATSGSTETTIPFITL 279
+HI AL+ AL V I+V Y+DR G + N H F E + P + L
Sbjct: 176 IHIIALAQALSVSIQVEYMDRGE----GGTTNPHIF--------------PEGSEPKVYL 217
Query: 280 LYRPGHYDILY 290
LYRPGHYDILY
Sbjct: 218 LYRPGHYDILY 228
>pdb|4DHZ|A Chain A, The Structure Of HCEOTUB1-Ubiquitin Aldehyde-Ubc13~ub
Length = 288
Score = 174 bits (441), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 109/294 (37%), Positives = 159/294 (54%), Gaps = 27/294 (9%)
Query: 2 QNQEKCGASCEFDDWSNFEDEDIMQQQSDIKAEEAQKVPFVADKEPLSALASEYQS-GSP 60
Q QE G+ E + + DE IM QQ I+ E A + P VA P S L +EY + S
Sbjct: 9 QKQEPLGSDSEGVNCLAY-DEAIMAQQDRIQQEIAVQNPLVATLAPFSILCAEYDNETSA 67
Query: 61 ILLEKIKVLGEQYAAIRRTRGDGNCFFRSFMFSYLEHILASQDQAEVDRIKAKVEECRRT 120
L K L E Y IR RGDGNCF+R+ + +E +L +D+A +++ A + RT
Sbjct: 68 AFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIML--KDRARLEKFIASSRDWTRT 125
Query: 121 LQSLGHADFTFEDFFALFLEQLDNVLQGNEFSISHGELVVRS--RDQSVSDYVVMFFRFV 178
L LG D+T DF F+E L+ + G H E V + D ++Y++MFFR +
Sbjct: 126 LVELGFPDWTCTDFCDFFIEFLEKIHSG-----VHTEEAVYTILNDDGSANYILMFFRLI 180
Query: 179 TSGEIRKRSEFFEPFILGLTNATVEQFCKSSVEPMGEESDHVHITALSDALGVPIRVVYL 238
TS +++ SE + PFI TV Q+C+ +EPM +++DH+ I +L A G +R+ Y+
Sbjct: 181 TSAFLKQNSEEYAPFID--EGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYM 238
Query: 239 DRSSCDSGGASVNHHDFIPTPGDCPNATSGSTETTIPFITLLYRPGHYDILYPK 292
DR++ +GG H+D P D + P ITLLYRPGHYD++Y K
Sbjct: 239 DRTAAPNGGW---HYDI---PSD--------DQQIAPEITLLYRPGHYDVIYKK 278
>pdb|4DHI|B Chain B, Structure Of C. Elegans Otub1 Bound To Human Ubc13
pdb|4DHJ|A Chain A, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|E Chain E, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|I Chain I, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
pdb|4DHJ|L Chain L, The Structure Of A Ceotub1 Ubiquitin Aldehyde Ubc13~ub
Complex
Length = 284
Score = 169 bits (428), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 103/277 (37%), Positives = 152/277 (54%), Gaps = 27/277 (9%)
Query: 20 EDEDIMQQQSDIKAEEAQK-VPFVADKEPLSALASEYQS-GSPILLEKIKVLGEQYAAIR 77
+DE ++Q Q E+ QK VP VA P S L +EY + S L K L E Y IR
Sbjct: 21 DDEIVLQDQQLKTIEDEQKSVPLVATLAPFSILCAEYDNETSAAFLSKATELSEVYGEIR 80
Query: 78 RTRGDGNCFFRSFMFSYLEHILASQDQAEVDRIKAKVEECRRTLQSLGHADFTFEDFFAL 137
RGDGNCF+R+ + +E +L +D+A +++ A + RTL LG D+T DF
Sbjct: 81 YIRGDGNCFYRAILVGLIEIML--KDRARLEKFIASSRDWTRTLVELGFPDWTCTDFCDF 138
Query: 138 FLEQLDNVLQGNEFSISHGELVVRS--RDQSVSDYVVMFFRFVTSGEIRKRSEFFEPFIL 195
F+E L+ + G H E V + D ++Y++MFFR +TS +++ SE + PFI
Sbjct: 139 FIEFLEKIHSG-----VHTEEAVYTILNDDGSANYILMFFRLITSAFLKQNSEEYAPFID 193
Query: 196 GLTNATVEQFCKSSVEPMGEESDHVHITALSDALGVPIRVVYLDRSSCDSGGASVNHHDF 255
TV Q+C+ +EPM +++DH+ I +L A G +R+ Y+DR++ +GG H+D
Sbjct: 194 --EGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAPNGGW---HYDI 248
Query: 256 IPTPGDCPNATSGSTETTIPFITLLYRPGHYDILYPK 292
P D + P ITLLYRPGHYD++Y K
Sbjct: 249 ---PSD--------DQQIAPEITLLYRPGHYDVIYKK 274
>pdb|1TFF|A Chain A, Structure Of Otubain-2
Length = 234
Score = 127 bits (320), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 81/230 (35%), Positives = 120/230 (52%), Gaps = 27/230 (11%)
Query: 61 ILLEKIKVLGEQYAAIRRTRGDGNCFFRSFMFSYLEHILASQDQAEVDRIKAKVEECRRT 120
I KI+ L +++ AIR+T+GD NCF+R+ +SYLE +L E+ + K +V +
Sbjct: 27 IYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGK--SREIFKFKERVLQTPND 84
Query: 121 LQSLGHADFTFEDFFALFLEQLDNVLQGNEFSISHGELVVRSRDQSVSDYVVMFFRFVTS 180
L + G + F +FF F ++ V + S L+ DQS SD++V F R +TS
Sbjct: 85 LLAAGFEEHKFRNFFNAFYSVVELVEKDGSVS----SLLKVFNDQSASDHIVQFLRLLTS 140
Query: 181 GEIRKRSEFFEPFILGLTNATVEQFCKSSVEPMGEESDHVHITALSDALGVPIRVVYLDR 240
IR R++FF FI ++ FC VEP E DH+ ITALS AL + ++V Y+
Sbjct: 141 AFIRNRADFFRHFI--DEEXDIKDFCTHEVEPXATECDHIQITALSQALSIALQVEYV-- 196
Query: 241 SSCDSGGASVNHHDFIPTPGDCPNATSGSTETTIPFITLLYRPGHYDILY 290
D ++NHH F P A + P + LLY+ HY+ILY
Sbjct: 197 ---DEMDTALNHHVF-------PEAAT-------PSVYLLYKTSHYNILY 229
>pdb|2X7X|A Chain A, Fructose Binding Periplasmic Domain Of Hybrid Two
Component System Bt1754
pdb|2X7X|B Chain B, Fructose Binding Periplasmic Domain Of Hybrid Two
Component System Bt1754
Length = 325
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 26/93 (27%)
Query: 9 ASCEFDDWSNFEDEDIMQQQ-------------SDIKAEEAQKVPFVADK---------- 45
A C D W + +++I+++ D +++A+ V + D+
Sbjct: 12 AQCSDDSWRHKMNDEILREAMFYNGVSVEIRSAGDDNSKQAEDVHYFMDEGVDLLIISAN 71
Query: 46 --EPLSALASE-YQSGSPILLEKIKVLGEQYAA 75
P++ + E YQ G P++L K+L ++Y A
Sbjct: 72 EAAPMTPIVEEAYQKGIPVILVDRKILSDKYTA 104
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
0.320 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,709,212
Number of Sequences: 62578
Number of extensions: 345829
Number of successful extensions: 922
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 881
Number of HSP's gapped (non-prelim): 15
length of query: 292
length of database: 14,973,337
effective HSP length: 98
effective length of query: 194
effective length of database: 8,840,693
effective search space: 1715094442
effective search space used: 1715094442
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)