RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3162
(91 letters)
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol
protease, UBL conjugation pathway, metal-binding,
zinc-finger,structural genomics; 2.80A {Homo sapiens}
Length = 854
Score = 73.4 bits (179), Expect = 4e-17
Identities = 36/63 (57%), Positives = 48/63 (76%)
Query: 29 TLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLRGSGPQPGEEMLP 88
++TTR ASFPDYL+ +KKFT DW KLDV +EMP+ +D++ LRG+G QPGEE LP
Sbjct: 575 AVKTTRFASFPDYLVIQIKKFTFGLDWVPKKLDVSIEMPEELDISQLRGTGLQPGEEELP 634
Query: 89 EVA 91
++A
Sbjct: 635 DIA 637
>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex,
hydrolase-transcription regulator-Pro binding complex,
acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae}
PDB: 3mhh_A 3m99_A
Length = 476
Score = 44.9 bits (106), Expect = 4e-07
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 31 RTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTP 74
+ + P L+ LK+F + + KLD +E P +++
Sbjct: 352 KQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKN 395
>2ayn_A Ubiquitin carboxyl-terminal hydrolase 14; deubiquitinating enzymes,
DUB, USP14, proteasome, enzyme mechanism; 3.20A {Homo
sapiens} SCOP: d.3.1.9 PDB: 2ayo_A
Length = 404
Score = 40.8 bits (95), Expect = 1e-05
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 31 RTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTPL 75
++++++ P YL + +F KE AK+ +V+ P +D+ L
Sbjct: 223 KSSKISRLPAYLTIQMVRFFYKEKESVNAKVLKDVKFPLMLDMYEL 268
>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination,
hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9
PDB: 1nbf_A
Length = 353
Score = 40.6 bits (95), Expect = 1e-05
Identities = 9/61 (14%), Positives = 18/61 (29%), Gaps = 10/61 (16%)
Query: 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFT-MKEDWTLAKLDVEVEMPDTIDLT 73
G + + + P L L +F + K++ E P+ + L
Sbjct: 177 HGLQ---------EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLD 227
Query: 74 P 74
Sbjct: 228 E 228
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 39.6 bits (92), Expect = 4e-05
Identities = 9/61 (14%), Positives = 18/61 (29%), Gaps = 10/61 (16%)
Query: 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFT-MKEDWTLAKLDVEVEMPDTIDLT 73
G + + + P L L +F + K++ E P+ + L
Sbjct: 346 HGLQ---------EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLD 396
Query: 74 P 74
Sbjct: 397 E 397
>3nhe_A Ubiquitin carboxyl-terminal hydrolase 2; cysteine protease,
substrate ENZY complex, hydrolase-protein binding
complex; HET: CME; 1.26A {Homo sapiens} PDB: 2hd5_A
2ibi_A
Length = 348
Score = 34.8 bits (80), Expect = 0.002
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 31 RTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLTPLRGSGPQPGEEML 87
+ + FP L+ HLK+F+ T +KL V P +DL L
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIRT-SKLTTFVNFPLRDLDLREFASENTNHAVYNL 286
>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9
Length = 415
Score = 34.5 bits (78), Expect = 0.002
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 31 RTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTPL 75
+++ P +L +F K +K+ +V P +D+ +
Sbjct: 215 VEKKISRLPKFLTVQYVRFFWKRSTNKKSKILRKVVFPFQLDVADM 260
>3i3t_A Ubiquitin carboxyl-terminal hydrolase 21; hydrolase, structural
genomics consortium, SGC, activator, alternative
splicing, chromatin regulator, nucleus, polymorphism,
protease; 2.59A {Homo sapiens} PDB: 2y5b_A 3mtn_A
Length = 355
Score = 34.2 bits (78), Expect = 0.003
Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 31 RTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLTPLRGSGPQP 82
+ + FP L+ HL +F+ K V V+ P + L
Sbjct: 240 KKLTVQRFPRILVLHLNRFSASRGSI-KKSSVGVDFPLQRLSLGDFASDKAGS 291
>2gfo_A Ubiquitin carboxyl-terminal hydrolase 8; protease, thiol protease,
UBL conjugation pathway deubiquitinating enzyme, DUB,
zinc ribbon; 2.00A {Homo sapiens} SCOP: d.3.1.9 PDB:
3n3k_A
Length = 396
Score = 32.6 bits (74), Expect = 0.010
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 34 RLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLTP 74
+ P L+ HLK+F+ W KL V+ P + +DL+
Sbjct: 285 EIWKLPPVLLVHLKRFSYDGRWK-QKLQTSVDFPLENLDLSQ 325
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 31.1 bits (70), Expect = 0.026
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 34 RLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLTP 74
L S P L+ HLK+F+ W KLD VE P ++++
Sbjct: 248 DLWSLPKILVVHLKRFSYNRYW-RDKLDTVVEFPIRGLNMSE 288
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 31.0 bits (69), Expect = 0.039
Identities = 15/68 (22%), Positives = 21/68 (30%), Gaps = 14/68 (20%)
Query: 22 ALDFVLSTLRTTRLASFPDYL----------MFHLKKFTMKEDWTL-AK-LDVEVEM--P 67
A + L TTR D+L H T E +L K LD +
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 68 DTIDLTPL 75
+ + P
Sbjct: 321 EVLTTNPR 328
Score = 28.7 bits (63), Expect = 0.25
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 41 YLMFHLKKFTMKEDWTLAK---LD 61
++ HLK E TL + LD
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLD 499
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.7 bits (61), Expect = 0.57
Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 20/85 (23%)
Query: 4 PQPTKSF---------LGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED 54
P+PT+ F L V + L +V S + +++ F L L +F E+
Sbjct: 42 PEPTEGFAADDEPTTPAEL----VGKF-LGYVSSLVEPSKVGQFDQVLNLCLTEF---EN 93
Query: 55 WTLAKLDV---EVEMPDTIDLTPLR 76
L D+ ++ D T ++
Sbjct: 94 CYLEGNDIHALAAKLLQENDTTLVK 118
>2hr0_B Complement C3 alpha' chain; complement component C3B, immune
system; HET: THC; 2.26A {Homo sapiens} PDB: 2icf_B*
2wii_B* 2win_B* 3g6j_B 3l5n_B* 2a73_B* 2i07_B* 2xwj_B*
2xwb_B* 2a74_C* 2ice_C* 2qki_C* 3l3o_F* 3nms_C* 3nsa_C*
3ohx_C* 3t4a_C 2ice_B* 3l3o_B* 3nms_B* ...
Length = 915
Score = 26.6 bits (57), Expect = 1.3
Identities = 4/33 (12%), Positives = 16/33 (48%)
Query: 38 FPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTI 70
FP+ +++++ ++ + + + D+I
Sbjct: 19 FPESWLWNVEDLKEPPKNGISTKLMNIFLKDSI 51
>1vek_A UBP14, ubiquitin-specific protease 14, putative; UBA domain,
three helix bundle, ubiquitin associated domain,
structural genomics; NMR {Arabidopsis thaliana} SCOP:
a.5.2.1
Length = 84
Score = 25.6 bits (56), Expect = 1.3
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 78 SGPQPGEEMLPEVA 91
SG GEE+LP+
Sbjct: 3 SGSSGGEELLPDGV 16
>3r4d_B Spike glycoprotein; immunoglobulin, beta-sandwich, mceacam1A -
immunoglobulin FO spike NTD - galectin-like
beta-sandwich fold; HET: NAG; 3.10A {Murine hepatitis
virus}
Length = 288
Score = 25.6 bits (55), Expect = 2.7
Identities = 12/49 (24%), Positives = 15/49 (30%)
Query: 3 KPQPTKSFLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTM 51
KP T +Y G +LT T P Y + L K
Sbjct: 206 KPSATTFLFSVYIGDILTQYYVLPFICNPTAGSTFAPRYWVTPLVKRQY 254
>2r6i_A AGR_C_2717P, uncharacterized protein ATU1473; chaperone, structural
genomics, APC6123, PSI-2, protein STRU initiative; 2.59A
{Agrobacterium tumefaciens str} SCOP: d.381.1.1
Length = 284
Score = 24.7 bits (53), Expect = 5.8
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 3/65 (4%)
Query: 1 MPKPQPTKSFLGLYCGKVLTYALDFVLSTLR--TTRLASFPDYLMFHLKKFTMKEDWTLA 58
M + QP ++ + Y L+ L T+ S L + T++E W LA
Sbjct: 185 MHRDQPREAIAAF-AVTLKKYDTPIALAALHTMTSLTGSAILALALAEGELTLEEAWALA 243
Query: 59 KLDVE 63
LD +
Sbjct: 244 HLDED 248
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A
{Sulfolobus solfataricus} PDB: 2hix_A*
Length = 621
Score = 24.4 bits (53), Expect = 7.5
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 52 KEDWTLAKLDVEVEMPDTIDLTPL---RGSG 79
W K D + EM DT+DL + G G
Sbjct: 448 GWLWIKLKRDYQSEMADTVDLVVVGGFYGKG 478
>2c5u_A RNA ligase, T4 RNA ligase 1; nucleotidyl transferase, ATP-binding;
HET: APC; 2.21A {Bacteriophage T4}
Length = 375
Score = 24.0 bits (51), Expect = 8.8
Identities = 6/37 (16%), Positives = 12/37 (32%)
Query: 38 FPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTP 74
Y+ H K ++ L K ++ D +
Sbjct: 244 SDWYVSLHSTKSSLDNPEKLFKTIIDGASDDLKAMYA 280
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.138 0.420
Gapped
Lambda K H
0.267 0.0484 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,423,019
Number of extensions: 71299
Number of successful extensions: 97
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 20
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.0 bits)