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= psy11202
(360 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SHQ|A Chain A, Crystal Structure Of Ublcp1
Length = 320
Score = 375 bits (963), Expect = e-104, Method: Compositional matrix adjust.
Identities = 182/304 (59%), Positives = 231/304 (75%), Gaps = 3/304 (0%)
Query: 11 WNSKEYKTSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLADTNATDG 70
W+ KEY L+ +TV L+ EI ++T V PERQKLLNLK+ GK +D+ K++
Sbjct: 12 WSGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPN 71
Query: 71 FKLMVMGSLEQSIQEASTKPLDIPEIVDDFD-IEEDQVAIENKDIYLAKIDKRIQDYQID 129
FKLM++GS E I++A + P +I E+VDDFD +E + ++ + +YLAK+ +R++DY+I
Sbjct: 72 FKLMMVGSTEADIEDACSLPDNIGEVVDDFDDADEREESVAHSAVYLAKVQRRVRDYKIK 131
Query: 130 ILNEPRPGKKLLVLDIDYTLFDHRSAAEQGYELMRPYLHEFLTSAYKNYDIAIWSATGMK 189
L PR GKKLLVLDIDYTLFDHRS AE G ELMRPYLHEFLTSAY++YDI IWSAT M+
Sbjct: 132 ELAPPREGKKLLVLDIDYTLFDHRSPAETGTELMRPYLHEFLTSAYEDYDIVIWSATSMR 191
Query: 190 WIEEKMKLLGVTVNPNYKIAFYVDYSAMISVHLPKYGVVEVKPLGVIWGKFPSLYNPTNT 249
WIEEKM+LLGV N NYK+ FY+D +AMISVH+P+ GVV+VKPLGVIW + YN +NT
Sbjct: 192 WIEEKMRLLGVASNDNYKVMFYLDSTAMISVHVPERGVVDVKPLGVIWALYKQ-YNSSNT 250
Query: 250 IMFDDIRRNFLMNPRNGLRIRPFREAHLNRGSDRELKRLGRYLDEIA-TVEDLTALNHRN 308
IMFDDIRRNFLMNP++GL+IRPFR+AHLNRG+D EL +L YL +IA D +LNHR
Sbjct: 251 IMFDDIRRNFLMNPKSGLKIRPFRQAHLNRGTDTELLKLSDYLRKIAHHCPDFNSLNHRK 310
Query: 309 WEKY 312
WE Y
Sbjct: 311 WEHY 314
>pdb|2KX3|A Chain A, The Solution Structure Of The Mutant Of Ubl Domain Of
Ublcp1, I5m
Length = 81
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/80 (47%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 4 SLNLIIKWNSKEYK-TSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKL 62
+L +I+KW +EY T+LS+ +TVL+LKQ + TGV PERQKLL LK GK +D KL
Sbjct: 2 ALPMIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKL 61
Query: 63 ADTNATDGFKLMVMGSLEQS 82
K+M+MG+ E+S
Sbjct: 62 GALKLKPNTKIMMMGTREES 81
>pdb|2LGD|A Chain A, The High Resolution Structure Of Ubiquitin Like Domain
Of Ublcp1
Length = 83
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/80 (47%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 4 SLNLIIKWNSKEYK-TSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKL 62
+L +I+KW +EY T+LS+ +TVL+LKQ + TGV PERQKLL LK GK +D KL
Sbjct: 4 ALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKL 63
Query: 63 ADTNATDGFKLMVMGSLEQS 82
K+M+MG+ E+S
Sbjct: 64 GALKLKPNTKIMMMGTREES 83
>pdb|1V5T|A Chain A, Solution Structure Of The Ubiquitin-Like Domain From
Mouse Hypothetical 8430435i17rik Protein
Length = 90
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 37/81 (45%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 3 DSLNLIIKWNSKEYK-TSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTK 61
L +I+KW +EY T+LS+ +TVL+LKQ + TGV PERQKLL LK GK +D K
Sbjct: 6 SGLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVK 65
Query: 62 LADTNATDGFKLMVMGSLEQS 82
L K+M+MG+ E
Sbjct: 66 LGALKLKPNTKIMMMGTRESG 86
>pdb|1V86|A Chain A, Solution Structure Of The Ubiquitin Domain From Mouse
D7wsu128e Protein
Length = 95
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 5 LNLIIKWNSKEYKTSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLAD 64
++L I WN ++ + +T ELKQ+I TG+ P QK++ + G +P D T L +
Sbjct: 18 VDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVM---YKGLVPEDKT-LRE 73
Query: 65 TNATDGFKLMVMGS 78
T G K+MV+GS
Sbjct: 74 IKVTSGAKIMVVGS 87
>pdb|2KD0|A Chain A, Nmr Solution Structure Of O64736 Protein From
Arabidopsis Thaliana. Northeast Structural Genomics
Consortium Mega Target Ar3445a
Length = 85
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 4 SLNLIIKWNSKEYKTSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLA 63
++ L +K+ K S+S TV +LK ++ T V P QKL+ GK+ + + L
Sbjct: 12 TIKLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLI---FKGKVLVETSTLK 68
Query: 64 DTNATDGFKLMVMGS 78
++ G KLM+M S
Sbjct: 69 QSDVGSGAKLMLMAS 83
>pdb|3M63|B Chain B, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 101
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 4 SLNLIIKWNSKEYKTSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLA 63
SLN+ IK +++ +++ +TVL+ K+ I K G+ Q+L+ ++GKI DD +
Sbjct: 28 SLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLI---YSGKILKDDQTVE 84
Query: 64 DTNATDGFKLMVMGS 78
+ DG + ++ S
Sbjct: 85 SYHIQDGHSVHLVKS 99
>pdb|2BWE|S Chain S, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWE|T Chain T, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWE|U Chain U, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWF|A Chain A, Crystal Sturcture Of The Ubl Domain Of Dsk2 From S.
Cerevisiae
pdb|2BWF|B Chain B, Crystal Sturcture Of The Ubl Domain Of Dsk2 From S.
Cerevisiae
Length = 77
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 4 SLNLIIKWNSKEYKTSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLA 63
SLN+ IK +++ +++ +TVL+ K+ I K G+ Q+L+ ++GKI DD +
Sbjct: 4 SLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLI---YSGKILKDDQTVE 60
Query: 64 DTNATDGFKLMVMGS 78
+ DG + ++ S
Sbjct: 61 SYHIQDGHSVHLVKS 75
>pdb|1WGG|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like
Domain Of Mouse Ubiquitin Specific Protease 14 (Usp14)
Length = 96
Score = 34.7 bits (78), Expect = 0.096, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 7 LIIKWNSKEYK-TSLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLADT 65
+ +KW ++++ L+ + K ++ TGV P RQK+ + G + DD +
Sbjct: 10 VTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKV--MVKGGTLKDDD--WGNI 65
Query: 66 NATDGFKLMVMGSLEQSIQEASTK 89
+G +++MGS + +E S K
Sbjct: 66 KMKNGMTVLMMGSADALPEEPSAK 89
>pdb|2HHL|A Chain A, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|B Chain B, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|C Chain C, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
pdb|2HHL|D Chain D, Crystal Structure Of The Human Small Ctd Phosphatase 3
Isoform 1
Length = 195
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 16/78 (20%)
Query: 137 GKKLLVLDIDYTL----FDHRSAAE------------QGYELMRPYLHEFLTSAYKNYDI 180
GKK +V+D+D TL F S A+ Q Y L RP++ EFL + ++
Sbjct: 27 GKKCVVIDLDETLVHSSFKPISNADFIVPVEIDGTIHQVYVLKRPHVDEFLQRMGQLFEC 86
Query: 181 AIWSATGMKWIEEKMKLL 198
+++A+ K+ + LL
Sbjct: 87 VLFTASLAKYADPVADLL 104
>pdb|2BHV|A Chain A, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
pdb|2BHV|B Chain B, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
pdb|2BHV|C Chain C, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
pdb|2BHV|D Chain D, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
pdb|2BHV|E Chain E, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
pdb|2BHV|F Chain F, Structure Of Comb10 Of The Com Type Iv Secretion System Of
Helicobacter Pylori
Length = 246
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 82 SIQEASTKPLDIPEIVDDF-DIEEDQVAI-ENKDIYLAKIDKRIQDYQIDILNEPRPGKK 139
SIQE P+D P+ +D F +++E +A ENK + DK I + I ++ GK
Sbjct: 5 SIQENLIFPMDNPKGIDGFTNLKEKDIATNENKLLRTITADKMIPAFLITPISSQIAGK- 63
Query: 140 LLVLDIDYTLFDHRSAA 156
++ ++ +F H A
Sbjct: 64 -VIAQVESDIFAHMGKA 79
>pdb|3ZHE|B Chain B, Structure Of The C. Elegans Smg5-smg7 Complex
pdb|3ZHE|D Chain D, Structure Of The C. Elegans Smg5-smg7 Complex
Length = 395
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 162 LMRPYLHEFLTSAYKNYDIAIWS--ATGMKWIEEKM---KLLGVTVNPNYKIAFYVDYSA 216
LM+ ++ +F T+ K +D+ W+ + M I + M +L+ V N I F D S
Sbjct: 29 LMKMFVADFETAVSKRFDVKFWNKLKSMMDEITKAMENDRLVNHNVQ-NLAIGFLTDLSL 87
Query: 217 MISVH--LPKYG 226
++ H +P YG
Sbjct: 88 LVHYHYEIPNYG 99
>pdb|3M62|B Chain B, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
Length = 106
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 20 LSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLADTNATDGFKLMVMGSL 79
L SNT+LE K ++ + + KL+ ++GK+ D +++ DG +++ M S
Sbjct: 18 LEPSNTILETKTKLAQSISCEESQIKLI---YSGKVLQDSKTVSECGLKDGDQVVFMVSQ 74
Query: 80 EQSIQEASTK 89
++S + T+
Sbjct: 75 KKSTKTKVTE 84
>pdb|1WX7|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like
Domain In The Human Ubiquilin 3 (Ubqln3)
Length = 106
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 19 SLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLADTNATDGFKL 73
S++ + T+ +LK+EI ++ +P++ L L AGKI D LA DG +
Sbjct: 32 SVTDTCTIQQLKEEISQRFKAHPDQ---LVLIFAGKILKDPDSLAQCGVRDGLTV 83
>pdb|1YQB|A Chain A, Human Ubiquilin 3
Length = 100
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 19 SLSKSNTVLELKQEILKQTGVNPERQKLLNLKHAGKIPSDDTKLADTNATDGFKL 73
S++ + T+ +LK+EI ++ +P++ L L AGKI D LA DG +
Sbjct: 37 SVTDTCTIQQLKEEISQRFKAHPDQ---LVLIFAGKILKDPDSLAQCGVRDGLTV 88
>pdb|2Q5E|A Chain A, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|B Chain B, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|C Chain C, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|D Chain D, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|E Chain E, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|F Chain F, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|G Chain G, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|H Chain H, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
Length = 187
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 18/79 (22%)
Query: 137 GKKLLVLDIDYTLFDHRS-----------------AAEQGYELMRPYLHEFLTSAYKNYD 179
G+ +V+D+D TL H S Q Y L RPY+ EFL + ++
Sbjct: 16 GRICVVIDLDETLV-HSSFKPINNADFIVPIEIEGTTHQVYVLKRPYVDEFLRRMGELFE 74
Query: 180 IAIWSATGMKWIEEKMKLL 198
+++A+ K+ + LL
Sbjct: 75 CVLFTASLAKYADPVTDLL 93
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 0.136 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,304,500
Number of Sequences: 62578
Number of extensions: 430011
Number of successful extensions: 1174
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1150
Number of HSP's gapped (non-prelim): 29
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)