RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17942
(90 letters)
>gnl|CDD|216964 pfam02297, COX6B, Cytochrome oxidase c subunit VIb. Cytochrome c
oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
terminal oxidase in the mitochondrial electron
transport chain. This family is composed of the
potentially heme-binding subunit IVb of the oxidase.
Length = 66
Score = 55.4 bits (134), Expect = 5e-12
Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 6 KEERTKCWSARDKYWECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYHFLK 60
+ +R CW ARD +++CLD + + CK+F+ +YE CP WV++FD + L+
Sbjct: 6 QNQRKHCWQARDDFFKCLDKNGEDNSPCKKFKKNYESLCPASWVEYFDEQRVDLR 60
>gnl|CDD|238466 cd00926, Cyt_c_Oxidase_VIb, Cytochrome c oxidase subunit VIb.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is
a multi-chain transmembrane protein located in the
inner membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in
bacteria and up to 13 in mammalian mitochondria.
Subunits I, II, and III of mammalian CcO are encoded
within the mitochondrial genome and the remaining 10
subunits are encoded within the nuclear genome. Found
only in eukaryotes, subunit VIb is one of three
mammalian subunits that lacks a transmembrane region.
It is located on the cytosolic side of the membrane and
helps form the dimer interface with the corresponding
subunit on the other monomer complex.
Length = 75
Score = 44.2 bits (105), Expect = 1e-07
Identities = 18/63 (28%), Positives = 29/63 (46%)
Query: 2 SFLPKEERTKCWSARDKYWECLDSHEGNADSCKEFRTSYEQFCPGQWVKHFDRRYHFLKF 61
F + + CW Y C+ + +A CK+FR YE CP +W++ +D + F
Sbjct: 13 RFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTF 72
Query: 62 KNK 64
K
Sbjct: 73 PGK 75
>gnl|CDD|182651 PRK10692, PRK10692, hypothetical protein; Provisional.
Length = 92
Score = 26.5 bits (59), Expect = 1.2
Identities = 5/9 (55%), Positives = 8/9 (88%)
Query: 48 WVKHFDRRY 56
WV+H+D+R
Sbjct: 75 WVRHYDKRC 83
>gnl|CDD|236106 PRK07818, PRK07818, dihydrolipoamide dehydrogenase; Reviewed.
Length = 466
Score = 26.9 bits (60), Expect = 1.3
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 57 HFLKFKNKI-ETEGFEKFDSKQEYELPKGKSKAKT 90
HFL KNKI E G+ F E+ +T
Sbjct: 99 HFLMKKNKITEIHGYGTFTDANTLEVDLNDGGTET 133
>gnl|CDD|187696 cd09272, RNase_HI_RT_Ty1, Ty1/Copia family of RNase HI in long-term
repeat retroelements. Ribonuclease H (RNase H) enzymes
are divided into two major families, Type 1 and Type 2,
based on amino acid sequence similarities and
biochemical properties. RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner in the presence of divalent
cations. RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. RNase HI
has also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing and non-LTR retrotransposons. RNase HI in
LTR retrotransposons perform degradation of the original
RNA template, generation of a polypurine tract (the
primer for plus-strand DNA synthesis), and final removal
of RNA primers from newly synthesized minus and plus
strands. The catalytic residues for RNase H enzymatic
activity, three aspartatic acids and one glutamatic acid
residue (DEDD) are unvaried across all RNase H domains.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Ty1/Copia family is widely distributed
among the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 142
Score = 26.3 bits (59), Expect = 1.9
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 50 KHFDRRYHFLK 60
KH D RYHF++
Sbjct: 100 KHIDIRYHFIR 110
>gnl|CDD|119282 pfam10762, DUF2583, Protein of unknown function (DUF2583). Some
members in this family of proteins are annotated as
YchH however currently no function is known.
Length = 89
Score = 25.9 bits (57), Expect = 2.0
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 48 WVKHFDRRY 56
WVKHFD+R
Sbjct: 75 WVKHFDKRC 83
>gnl|CDD|220652 pfam10250, O-FucT, GDP-fucose protein O-fucosyltransferase. This
is a family of conserved proteins representing the
enzyme responsible for adding O-fucose to EGF (epidermal
growth factor-like) repeats. Six highly conserved
cysteines are present in O-FucT-1 as well as a DXD-like
motif (ERD), conserved in mammals, Drosophila, and C.
elegans. Both features are characteristic of several
glycosyltransferase families. The enzyme is a
membrane-bound protein released by proteolysis and, as
for most glycosyltransferases, is strongly activated by
manganese.
Length = 315
Score = 25.3 bits (56), Expect = 4.5
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 38 TSYEQFCPGQWVKHFDRRYHFLKFKNKIETEGFE 71
T ++ +R H L+F +IE G +
Sbjct: 118 TGAPARLANNYLPPDLQRLHALRFSPEIEELGNK 151
>gnl|CDD|185489 PTZ00160, PTZ00160, 60S ribosomal protein L27a; Provisional.
Length = 147
Score = 25.0 bits (55), Expect = 6.1
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 4/65 (6%)
Query: 28 GNADSCKEFRTSYEQFCPGQWVKHFDRRYHFLK---FKNKIETEGFEKFDSKQEYELPKG 84
GNA R +++++ PG + K R +H K + I + ++
Sbjct: 33 GNAGGQHHHRINFDKYHPGYFGKVGMRHFHLKKNKYYCPTINVDKLWSLVPEETRYK-YA 91
Query: 85 KSKAK 89
K K
Sbjct: 92 KKGDK 96
>gnl|CDD|217595 pfam03514, GRAS, GRAS family transcription factor. Sequence
analysis of the products of the GRAS (GAI, RGA, SCR)
gene family indicates that they share a variable
amino-terminus and a highly conserved carboxyl-terminus
that contains five recognisable motifs. Proteins in the
GRAS family are transcription factors that seem to be
involved in development and other processes. Mutation of
the SCARECROW (SCR) gene results in a radial pattern
defect, loss of a ground tissue layer, in the root. The
PAT1 protein is involved in phytochrome A signal
transduction.
Length = 372
Score = 24.5 bits (54), Expect = 9.7
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 9/62 (14%)
Query: 19 YWECLDSHEGNADSCKEFRTSYEQFCPGQWVK---------HFDRRYHFLKFKNKIETEG 69
Y DS E E R E+ G+ + +R F K++ ++ G
Sbjct: 262 YSALFDSLEATLPRDSEERRKVERELLGREIVNVVACEGAERVERHETFGKWRERMRRAG 321
Query: 70 FE 71
F
Sbjct: 322 FR 323
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
0.318 0.133 0.436
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,356,840
Number of extensions: 326020
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 14
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)