RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= 537021.9.peg.1074_1
(169 letters)
>gnl|CDD|146637 pfam04106, APG5, Autophagy protein Apg5. Apg5 is directly required
for the import of aminopeptidase I via the
cytoplasm-to-vacuole targeting pathway.
Length = 195
Score = 31.9 bits (73), Expect = 0.091
Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 2 TIVNNTFITSSSTTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHP------EWVVDDL 55
++ S ++L D +S + PE P + K H I +W+ ++L
Sbjct: 122 PVIQALIPPLSEEGQPQTLGDALSELLPELFPSSEELAKPIIHGIEVPLDAPLQWLYENL 181
Query: 56 ASP 58
+ P
Sbjct: 182 SYP 184
>gnl|CDD|48517 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II..
Length = 142
Score = 28.6 bits (64), Expect = 0.96
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 76 TPERMGNYTQIMRKSWI-LSGTQEAVDDV 103
TPE + Y + WI L+GT E ++ +
Sbjct: 73 TPEVLKAYAKAFGPGWIGLTGTPEEIEAL 101
>gnl|CDD|133117 cd06907, M14_AGBL2-3_like, Peptidase M14-like domain of ATP/GTP
binding protein_like (AGBL)-2, and related proteins.
The Peptidase M14 family of metallocarboxypeptidases
are zinc-binding carboxypeptidases (CPs) which
hydrolyze single, C-terminal amino acids from
polypeptide chains, and have a recognition site for the
free C-terminal carboxyl group, which is a key
determinant of specificity. This subgroup includes the
human AGBL-2, and -3, and the mouse cytosolic
carboxypeptidase (CCPs)-2, and -3. ATP/GTP binding
protein (AGTPBP-1/Nna1)-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje
cell degeneration (pcd). AGTPBP-1/Nna1 however does not
belong to this subgroup. AGTPBP-1/Nna1-like proteins
from the different phyla are highly diverse, but they
all contain a unique N-terminal conserved domain right
before the CP domain. It has been suggested that this
N-terminal domain might act as a folding domain.
Length = 261
Score = 26.2 bits (58), Expect = 4.6
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 9 ITSSSTTNKESLSD---VVS-RITPEDTPIYSMIKKGTTHSIHPEWVVDDLASPGPNAQL 64
ITS S+ + + V++ R+ P +T S + KG +D L S P+AQL
Sbjct: 33 ITSPSSNPSLAAAKKAVVLTARVHPGETNA-SWMMKG---------FLDFLTSNSPDAQL 82
Query: 65 EGDEYSFKTI 74
D + FK +
Sbjct: 83 LRDTFIFKIV 92
>gnl|CDD|73140 cd04642, CBS_pair_29, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase)..
Length = 126
Score = 26.0 bits (57), Expect = 5.4
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 2 TIVNNTFITSSSTTNKESLSDVVSRITPEDTPIYSMIKKGTTHSIHPEWVVDDLASP 58
TI + ++ +++ TP T + +I K + +H WVVD+ P
Sbjct: 60 TITFKELSEKFTDSDGVKSRPLIT-CTPSST-LKEVITKLVANKVHRVWVVDEEGKP 114
>gnl|CDD|31089 COG0746, MobA, Molybdopterin-guanine dinucleotide biosynthesis
protein A [Coenzyme metabolism].
Length = 192
Score = 25.7 bits (56), Expect = 6.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 65 EGDEYSFKTINTPERMGNYTQI 86
+ +E SF INTPE + +
Sbjct: 170 DLEEDSFFNINTPEDLARAREK 191
>gnl|CDD|36824 KOG1611, KOG1611, KOG1611, Predicted short chain-type dehydrogenase
[General function prediction only].
Length = 249
Score = 25.6 bits (56), Expect = 7.5
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 45 SIHPEWVVDDLASPGPNAQLEGDEYSFKTINTPERMGN 82
SIHP WV D+ G A L +E + K + + ++ N
Sbjct: 198 SIHPGWVQTDMG--GKKAALTVEESTSKLLASINKLKN 233
>gnl|CDD|30123 cd00295, RNA_Cyclase, RNA 3' phosphate cyclase domain - RNA
phosphate cyclases are enzymes that catalyze the
ATP-dependent conversion of 3'-phosphate at the end of
RNA into 2', 3'-cyclic phosphodiester bond. The enzymes
are conserved in eucaryotes, bacteria and archaea. The
exact biological role of this enzyme is unknown, but it
has been proposed that it is likely to function in
cellular RNA metabolism and processing. RNA phosphate
cyclase has been characterized in human (with at least
three isozymes), and E. coli, and it seems to be
taxonomically widespread. The crystal structure of RNA
phospate cyclase shows that it consists of two domains.
The larger domain contains three repeats of a fold
originally identified in the bacterial translation
initiation factor IF3..
Length = 338
Score = 25.4 bits (55), Expect = 7.5
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 56 ASPGPNAQLEGDEYSFKTINTPERMGNYTQIMRKSWILSGTQ 97
A+ G A+ SFK + ER + + R I +GT+
Sbjct: 156 AAGGGGAEENFLCASFKELLLGERGSEFGRQFRGEGIAAGTR 197
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.310 0.126 0.351
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,922,624
Number of extensions: 90886
Number of successful extensions: 159
Number of sequences better than 10.0: 1
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 10
Length of query: 169
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,383,754
Effective search space: 359467828
Effective search space used: 359467828
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.5 bits)