RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14516
(76 letters)
>gnl|CDD|197632 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like
zinc finger.
Length = 50
Score = 44.7 bits (106), Expect = 3e-08
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 44 PCVDCASVAENWVCLICYQVRCGRYIEEHS 73
C C ++ W+CL C QV CGRY H+
Sbjct: 1 RCSVCGTIENLWLCLTCGQVGCGRYQNGHA 30
>gnl|CDD|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other
protein.
Length = 63
Score = 40.1 bits (94), Expect = 3e-06
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 45 CVDCASVAENWVCLICYQVRCGRYIEEHSNE 75
C +C S W+CL C V CGRY H+ +
Sbjct: 1 CSECGSTENLWLCLTCGHVGCGRYSNGHALK 31
>gnl|CDD|227532 COG5207, UBP14, Isopeptidase T [Posttranslational modification,
protein turnover, chaperones].
Length = 749
Score = 29.3 bits (65), Expect = 0.16
Identities = 15/48 (31%), Positives = 17/48 (35%), Gaps = 3/48 (6%)
Query: 22 LADCPHT-PLVAPVPQSGVDVKAPCVDCASVAEN-WVCLICYQVRCGR 67
C H + G C C + N WVCL C V CGR
Sbjct: 152 EVTCVHGCNEGPSSIEMGNIGGLKCSLC-DLKTNLWVCLSCGYVGCGR 198
Score = 24.3 bits (52), Expect = 9.9
Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 6/55 (10%)
Query: 25 CPHTPLVAPVPQ--SGVDVKAPCVDCASVAENW----VCLICYQVRCGRYIEEHS 73
H+ + V V + C C + VCL C+Q C ++ H
Sbjct: 3 FSHSEMAEMVLPNLPAVRFREECCYCFRSIGDEHSISVCLNCFQSFCEKHRGIHL 57
>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 28.0 bits (63), Expect = 0.41
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 21/57 (36%)
Query: 18 LVTPLADCPHTPLV--APVPQSGVDVKAPCVDCASV----------AENWVCLICYQ 62
L TPL P P++ P+ C C +V A+ W+C C+Q
Sbjct: 36 LYTPLKPLPELPVLPYDPLR---------CRTCRAVLNPYCRVDFQAKIWICPFCFQ 83
>gnl|CDD|235974 PRK07229, PRK07229, aconitate hydratase; Validated.
Length = 646
Score = 25.9 bits (58), Expect = 2.1
Identities = 8/15 (53%), Positives = 9/15 (60%), Gaps = 1/15 (6%)
Query: 21 PLADCPHTP-LVAPV 34
PL PH+P V PV
Sbjct: 267 PLIAGPHSPDNVVPV 281
>gnl|CDD|147559 pfam05434, Tmemb_9, TMEM9. This family contains several
eukaryotic transmembrane proteins which are homologous
to human transmembrane protein 9. The TMEM9 gene
encodes a 183 amino-acid protein that contains an
N-terminal signal peptide, a single transmembrane
region, three potential N-glycosylation sites and three
conserved cys-rich domains in the N-terminus, but no
known functional domains. The protein is highly
conserved between species from Caenorhabditis elegans
to man and belongs to a novel family of transmembrane
proteins. The exact function of TMEM9 is unknown
although it has been found to be widely expressed and
localised to the late endosomes and lysosomes. Members
of this family contain pfam03128 repeats in their
N-terminal region.
Length = 149
Score = 25.2 bits (55), Expect = 3.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 21 PLADCPHTPLVAPVPQSGVDVKAPCVDC 48
DC +V P+P G DV+A C+ C
Sbjct: 15 SQKDCNCLHVVEPMPVPGKDVEAYCLRC 42
>gnl|CDD|233059 TIGR00627, tfb4, transcription factor tfb4. All proteins in this
family are part of the TFIIH complex which is involved
in the initiation of transcription and nucleotide
excision repair.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 279
Score = 25.6 bits (56), Expect = 3.1
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 22 LADCPHTPLVAPVPQSGVDVKAPCVDCAS--VAENWVCLICYQVRC 65
L D +++ + VD +A C C V+ +VC +C V C
Sbjct: 222 LPDPTLRAVLSKPNHNSVDYRASCF-CHHQLVSIGFVCSVCLSVLC 266
>gnl|CDD|144451 pfam00859, CTF_NFI, CTF/NF-I family transcription modulation
region.
Length = 295
Score = 24.7 bits (53), Expect = 5.4
Identities = 14/29 (48%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 17 FLVTP-LADCPHTPLVAPVPQSGVDVKAP 44
FL TP LA P P+ PVP D K P
Sbjct: 220 FLPTPMLAPPPPPPMARPVPLPMPDTKPP 248
>gnl|CDD|233054 TIGR00615, recR, recombination protein RecR. All proteins in
this family for which functions are known are involved
in the initiation of recombination and recombinational
repair. RecF is also required. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 195
Score = 24.6 bits (54), Expect = 6.1
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 43 APCVDCASVAENWVCLIC 60
C C ++++ VC IC
Sbjct: 54 RTCSVCGAISDQEVCNIC 71
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.452
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,658,778
Number of extensions: 257843
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 11
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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: 53 (24.2 bits)