RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9569
(156 letters)
>gnl|CDD|238463 cd00923, Cyt_c_Oxidase_Va, Cytochrome c oxidase subunit Va.
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 Va is one of three mammalian
subunits that lacks a transmembrane region. Subunit Va
is located on the matrix side of the membrane and binds
thyroid hormone T2, releasing allosteric inhibition
caused by the binding of ATP to subunit IV and allowing
high turnover at elevated intramitochondrial ATP/ADP
ratios.
Length = 103
Score = 178 bits (454), Expect = 3e-59
Identities = 65/104 (62%), Positives = 82/104 (78%), Gaps = 1/104 (0%)
Query: 40 VEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVNDYAL 99
EE+DEEF RY +FN+PDIDGW++RRGL NL D VP+P++I AAL+A RRVND+AL
Sbjct: 1 SEETDEEFDARYETYFNRPDIDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFAL 60
Query: 100 AIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQLGY 143
A+R LE + K G+H +I+PYI+QEI PTLKELGI TP +LGY
Sbjct: 61 AVRILEAIKDKC-GAHKEIYPYILQEIKPTLKELGISTPEELGY 103
>gnl|CDD|111202 pfam02284, COX5A, Cytochrome c oxidase subunit Va. 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 cytochrome c oxidase
subunit Va.
Length = 108
Score = 133 bits (335), Expect = 3e-41
Identities = 61/109 (55%), Positives = 80/109 (73%), Gaps = 1/109 (0%)
Query: 37 SHAVEESDEEFVKRYVAFFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRRVND 96
SH EE+DEEF RY +FN+ DID W++R+G+ L D VP+P+II AAL+A RRVND
Sbjct: 1 SHGSEETDEEFDARYEKYFNKEDIDAWELRKGMNTLVGYDLVPEPKIIEAALRACRRVND 60
Query: 97 YALAIRFLETTEFKTGGSHDKIWPYIVQEITPTLKELGIETPAQLGYDK 145
+A AIR LE + K G H +I+PY++QE+ PTL+ELGI TP +LG DK
Sbjct: 61 FASAIRILEVVKDKA-GPHKEIYPYVLQELRPTLQELGIPTPEELGLDK 108
>gnl|CDD|235320 PRK04926, dgt, deoxyguanosinetriphosphate triphosphohydrolase;
Provisional.
Length = 503
Score = 29.1 bits (66), Expect = 1.00
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 121 YIVQEITPTLKELGIETPAQLGYDKPELALESVYDM 156
YI +EI LKE + G D+ ES+ +M
Sbjct: 79 YIAKEILSRLKEQKL--LEAYGLDELTGPFESIVEM 112
>gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family
18) type II chitinases hydrolyze chitin, an abundant
polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc)
which is a major component of the cell wall of fungi and
the exoskeleton of arthropods. Chitinases have been
identified in viruses, bacteria, fungi, protozoan
parasites, insects, and plants. The structure of the
GH18 domain is an eight-stranded beta/alpha barrel with
a pronounced active-site cleft at the C-terminal end of
the beta-barrel. The GH18 family includes
chitotriosidase, chitobiase, hevamine, zymocin-alpha,
narbonin, SI-CLP (stabilin-1 interacting chitinase-like
protein), IDGF (imaginal disc growth factor), CFLE
(cortical fragment-lytic enzyme) spore hydrolase, the
type III and type V plant chitinases, the
endo-beta-N-acetylglucosaminidases, and the
chitolectins. The GH85 (glycosyl hydrolase, family 85)
ENGases (endo-beta-N-acetylglucosaminidases) are closely
related to the GH18 chitinases and are included in this
alignment model.
Length = 210
Score = 28.1 bits (63), Expect = 1.5
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 45 EEFVKRYVAFFNQPDIDGWDI 65
F V+F DG DI
Sbjct: 90 AAFANSLVSFLKTYGFDGVDI 110
>gnl|CDD|119365 cd06548, GH18_chitinase, The GH18 (glycosyl hydrolases, family 18)
type II chitinases hydrolyze chitin, an abundant polymer
of N-acetylglucosamine and have been identified in
bacteria, fungi, insects, plants, viruses, and protozoan
parasites. The structure of this domain is an
eight-stranded alpha/beta barrel with a pronounced
active-site cleft at the C-terminal end of the
beta-barrel.
Length = 322
Score = 28.0 bits (63), Expect = 2.2
Identities = 20/70 (28%), Positives = 25/70 (35%), Gaps = 12/70 (17%)
Query: 36 FSHAV--EESDEEFVKRYVAFFNQPDIDGWDI-------RRGLMNLAHDDCVPDPEIIIA 86
FS A E S +F V F + DG DI N+A + D E
Sbjct: 100 FSDAAATEASRAKFADSAVDFIRKYGFDGIDIDWEYPGSGGAPGNVARPE---DKENFTL 156
Query: 87 ALKAIRRVND 96
LK +R D
Sbjct: 157 LLKELREALD 166
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 27.2 bits (61), Expect = 4.2
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 81 PEIIIAALKAIRRVNDYALAIRFLETTEFKTGGSHDK 117
PE++ AALK + ++ L F E + GG
Sbjct: 16 PEVMAAALKVLEAAAEFGLDFEF---EEAEVGGEAYD 49
>gnl|CDD|235928 PRK07079, PRK07079, hypothetical protein; Provisional.
Length = 469
Score = 27.2 bits (61), Expect = 4.3
Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 8/56 (14%)
Query: 90 AIRRVNDYALAIRFLET--------TEFKTGGSHDKIWPYIVQEITPTLKELGIET 137
AI R Y + F TE + + Y+ EI P L LG
Sbjct: 6 AIARAAAYFDSGAFFADLARRVAYRTESQNPDRAPALRAYLTDEIAPALAALGFTC 61
>gnl|CDD|183514 PRK12414, PRK12414, putative aminotransferase; Provisional.
Length = 384
Score = 27.1 bits (60), Expect = 4.6
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 5 LASRLAASSSQVLRQTAVSKVKPLTFAPIRSFSHAVEESDEEFVKRYV 52
LA LA S ++L +F + F H +ESD +FV R +
Sbjct: 300 LARELAGSRFELLPSEG-------SFFMLARFRHFSDESDSDFVLRLI 340
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 25.4 bits (55), Expect = 5.2
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 40 VEESDEEFVKRYVAFFNQPDIDG 62
VE DEEFVK+ + N+ D++G
Sbjct: 46 VEFKDEEFVKKALEVMNKYDLNG 68
>gnl|CDD|180426 PRK06148, PRK06148, hypothetical protein; Provisional.
Length = 1013
Score = 26.5 bits (59), Expect = 8.4
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 24 KVKPLTFAPIRSFSHAVEESDEEFVKRYVAFFNQP----DIDGWDIRRGLMNLAHDDCVP 79
+ P T A + + A+ D R + F P D+D WD+R +
Sbjct: 122 EAAPRTEALLDNLGRALGRLD-----RALQGFMHPGALRDLD-WDLRHAGRARDRLHFID 175
Query: 80 DPE 82
DPE
Sbjct: 176 DPE 178
>gnl|CDD|211388 cd11302, O-FucT-1, GDP-fucose protein O-fucosyltransferase 1. The
protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds
O-fucose to EGF (epidermal growth factor-like) repeats.
The O-fucsosylation of the Notch receptor signaling
protein is dependent on this enzyme, which requires
GDP-fucose as a substrate. O-fucose residues added to
the target of O-FucT-1 may be further elongated by other
glycosyltransferases. On top of O-fucosylation, O-FucT-1
may have other functions such as the regulation of the
Notch receptor exit from the ER. Six highly conserved
cysteines are present in O-FucT-1, which is a soluble ER
protein, as well as a DXD-like motif (ERD), conserved in
mammals, Drosophila, and C. elegans. Both features are
characteristic of several glycosyltransferase families.
The membrane-bound pre-protein is released by
proteolysis and, as for most glycosyltransferases, is
strongly activated by manganese. O-FucT-1 is similar to
family 1 glycosyltransferases (GT1).
Length = 347
Score = 26.0 bits (58), Expect = 9.3
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 46 EFVKRYVA-FFNQPDIDGWDIRRGLMNLAHDDCVPDPEIIIAALKAIRR 93
E VK P G+ RG + C+P E I+ +K +
Sbjct: 220 EHVKGTSRNLMASPQCLGYGNERGTLTKEM--CLPSKEEILKQVKRAVK 266
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
0.320 0.136 0.397
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,331,994
Number of extensions: 796782
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 856
Number of HSP's successfully gapped: 25
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 55 (24.9 bits)