RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14516
(76 letters)
>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding,
chromatin regulator, cytoplasm, hydrolase,
metal-binding, nucleus, phosphoprotein; 1.55A {Homo
sapiens} PDB: 3gv4_A 3phd_A
Length = 109
Score = 60.4 bits (146), Expect = 6e-14
Identities = 31/56 (55%), Positives = 38/56 (67%)
Query: 20 TPLADCPHTPLVAPVPQSGVDVKAPCVDCASVAENWVCLICYQVRCGRYIEEHSNE 75
+PL CPH V P+P +G+DV PC DC ++ ENWVCL CYQV CGRYI H +
Sbjct: 2 SPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQ 57
>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase;
1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A
Length = 129
Score = 43.5 bits (102), Expect = 3e-07
Identities = 9/47 (19%), Positives = 12/47 (25%), Gaps = 2/47 (4%)
Query: 25 CPHTPLV--APVPQSGVDVKAPCVDCASVAENWVCLICYQVRCGRYI 69
H + P C C W+ L + CGR
Sbjct: 15 SKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRY 61
>2ida_A Hypothetical protein; zinc binding protein, structural genomics,
PSI-2, protein structure initiative; NMR
{Rhodopseudomonas palustris} SCOP: g.44.1.5
Length = 102
Score = 42.3 bits (99), Expect = 5e-07
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 9/54 (16%)
Query: 25 CPHTPLVAPVPQSGVDVKAPCVDCASVAENWV----CLICYQVRCGRY-IEEHS 73
C H + V S C +C + WV C C V C +H+
Sbjct: 5 CRHVAGIRTVTPSA----LGCEECLKIGSPWVHLRICRTCGHVGCCDDSPHKHA 54
>2uzg_A Ubiquitin carboxyl-terminal hydrolase 33; UBL conjugation
pathway, DE-ubiquitination, alternative splicing,
metal-binding, thiol protease; NMR {Homo sapiens} SCOP:
g.44.1.5
Length = 97
Score = 40.0 bits (93), Expect = 3e-06
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 24 DCPHTPLVAPVPQSGVDVKAP--CVDCASVAEN-WVCL--ICYQVRCGRYIEEHSNE 75
CPH V + + + K+ C DC N W CL C V CG +HS
Sbjct: 5 HCPHLDSVGEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTI 61
>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger,
ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding
protein, USP; NMR {Homo sapiens}
Length = 126
Score = 37.8 bits (87), Expect = 4e-05
Identities = 8/37 (21%), Positives = 11/37 (29%)
Query: 36 QSGVDVKAPCVDCASVAENWVCLICYQVRCGRYIEEH 72
+ W+CL C CGR +E
Sbjct: 36 TDNKVKDKAEEETEEKPSVWLCLKCGHQGCGRNSQEQ 72
>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 = 33.0 bits (74), Expect = 0.004
Identities = 9/52 (17%), Positives = 14/52 (26%), Gaps = 2/52 (3%)
Query: 25 CPHTPLVAPVPQSGVDVKAP--CVDCASVAENWVCLICYQVRCGRYIEEHSN 74
H + + C C W+ L + CGR + S
Sbjct: 196 SKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSG 247
Score = 24.5 bits (52), Expect = 3.9
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 15 EMFLVTPLADCPHTPLVAPVPQSGVDV-KAPCVDCASVAEN----WVCLICYQVRCGRYI 69
M ++ A P + VP++G V K C E+ ++C+ + +Y+
Sbjct: 19 SMAELSEEALLSVLPTI-RVPKAGDRVHKDECAFSFDTPESEGGLYICMNTFLGFGKQYV 77
Query: 70 EEHSN 74
E H N
Sbjct: 78 ERHFN 82
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.9 bits (64), Expect = 0.11
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 9/44 (20%)
Query: 39 VDVKAPCVDCASVAEN---------WVCLICYQVRCGRYIEEHS 73
+++ C +C VC +C V + ++ S
Sbjct: 18 LNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRS 61
>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 = 27.3 bits (60), Expect = 0.50
Identities = 13/68 (19%), Positives = 19/68 (27%), Gaps = 22/68 (32%)
Query: 17 FLVTPLADCP-HTPLVAPVPQSGVDVKAPCVDCASVAENW--------VCLICYQVRCGR 67
FL P+A P H+ L+ P D ++ V Y G
Sbjct: 420 FL--PVA-SPFHSHLLVPASDLINK------DLVKNNVSFNAKDIQIPV----YDTFDGS 466
Query: 68 YIEEHSNE 75
+ S
Sbjct: 467 DLRVLSGS 474
>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 = 26.1 bits (57), Expect = 1.0
Identities = 11/75 (14%), Positives = 21/75 (28%), Gaps = 8/75 (10%)
Query: 8 LQALVNEEMFLVTPLADCPHTPLVAPVPQSGVDVKAPCVDCA-----SVAENWVCLICYQ 62
+Q + E L C + + + C + ++CL C
Sbjct: 12 IQQVFQNEKSKDGVLKTCNAARYI-LNHSVPKEKFLNTMKCGTCHEINSGATFMCLQCGF 70
Query: 63 VRC--GRYIEEHSNE 75
C + HS +
Sbjct: 71 CGCWNHSHFLSHSKQ 85
>3efo_B SEC24 related gene family, member D; copii, coat protein, transport
signal, disease mutation, endoplasmic reticulum,
ER-golgi transport, golgi apparatus, membrane; 2.70A
{Homo sapiens} PDB: 3eg9_B
Length = 770
Score = 25.2 bits (54), Expect = 2.3
Identities = 9/59 (15%), Positives = 16/59 (27%)
Query: 18 LVTPLADCPHTPLVAPVPQSGVDVKAPCVDCASVAENWVCLICYQVRCGRYIEEHSNEF 76
++ P A P + G C C + ++ I R N+
Sbjct: 74 VIKPFATIPSNESPLYLVNHGESGPVRCNRCKAYMCPFMQFIEGGRRYQCGFCNCVNDV 132
>3eh2_A Protein transport protein SEC24C; copii-coat protein, vesicle
transport, cytoplasm, endoplasmic reticulum, ER-golgi
transport, golgi apparatus; 2.35A {Homo sapiens}
Length = 766
Score = 24.1 bits (51), Expect = 5.4
Identities = 10/56 (17%), Positives = 15/56 (26%), Gaps = 10/56 (17%)
Query: 18 LVTPLADCPHTPLVAPVPQSGVDVKAPCVDCASV----------AENWVCLICYQV 63
++ PLA P V G C C + + C C +
Sbjct: 70 VIKPLARLPPEEASPYVVDHGESGPLRCNRCKAYMCPFMQFIEGGRRFQCCFCSCI 125
>4feg_A Pyruvate oxidase; carbanion, structure activity relationship,
oxidation-reduct umpolung, thiamine diphosphate,
reaction intermediate; HET: TDM FAD GOL; 1.09A
{Lactobacillus plantarum} PDB: 4fee_A* 1y9d_A* 2ez9_A*
2ez4_A* 2ez8_A* 2ezt_A* 2ezu_A* 1pow_A* 1pox_A*
Length = 603
Score = 23.7 bits (52), Expect = 7.6
Identities = 6/17 (35%), Positives = 9/17 (52%), Gaps = 2/17 (11%)
Query: 18 LVTPLADCP--HTPLVA 32
L+ L D H P++A
Sbjct: 90 LMNGLYDAREDHVPVLA 106
>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB,
RAB27B, effector, SLP homology domain, acetylation,
lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus}
Length = 153
Score = 23.8 bits (50), Expect = 7.8
Identities = 6/23 (26%), Positives = 9/23 (39%), Gaps = 3/23 (13%)
Query: 45 CVDCASVAEN---WVCLICYQVR 64
C C+ W+C C+ R
Sbjct: 96 CKSCSHAHPEEQGWLCDPCHLAR 118
>2nut_A Protein transport protein SEC23A; human copii SEC23/24 complexed
with SEC22, protein transport; 2.30A {Homo sapiens}
PDB: 2nup_A 3egd_A 3eg9_A 3egx_A 3efo_A
Length = 769
Score = 23.7 bits (50), Expect = 8.0
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 15/55 (27%)
Query: 18 LVTPLADCPHTPLVAPVPQSGVDVKAPCVDCASV----------AENWVCLICYQ 62
L TPL + P P + P V C +V A+ W C CYQ
Sbjct: 45 LFTPLKERPDLPPIQYEP-----VLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQ 94
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
0.322 0.136 0.452
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,120,447
Number of extensions: 50463
Number of successful extensions: 83
Number of sequences better than 10.0: 1
Number of HSP's gapped: 76
Number of HSP's successfully gapped: 17
Length of query: 76
Length of database: 6,701,793
Length adjustment: 45
Effective length of query: 31
Effective length of database: 5,445,348
Effective search space: 168805788
Effective search space used: 168805788
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 (21.9 bits)
S2: 51 (23.3 bits)