RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15302
(68 letters)
>gnl|CDD|197984 smart00916, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 /
S25 / CI-B8 domain. Proteins containing this domain
are located in the mitochondrion and include ribosomal
protein L51, and S25. This domain is also found in
mitochondrial NADH-ubiquinone oxidoreductase B8 subunit
(CI-B8) . It is not known whether all members of this
family form part of the NADH-ubiquinone oxidoreductase
and whether they are also all ribosomal proteins.
Length = 70
Score = 66.4 bits (163), Expect = 9e-17
Identities = 22/40 (55%), Positives = 25/40 (62%)
Query: 21 GSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
GSS+G R FL + LK NP PILVRE SGV P + A
Sbjct: 1 GSSAGARKFLESNLPTLKFKNPDVPILVRERSGVVPKLTA 40
>gnl|CDD|191176 pfam05047, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 /
S25 / CI-B8 domain. The proteins in this family are
located in the mitochondrion. The family includes
ribosomal protein L51, and S25. This family also
includes mitochondrial NADH-ubiquinone oxidoreductase
B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether
all members of this family form part of the
NADH-ubiquinone oxidoreductase and whether they are
also all ribosomal proteins.
Length = 52
Score = 55.7 bits (135), Expect = 9e-13
Identities = 18/35 (51%), Positives = 22/35 (62%)
Query: 26 VRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWA 60
RDFL ++ LK NP+ PILVRE SG P + A
Sbjct: 1 ARDFLEKNLPTLKYKNPQVPILVRERSGKHPRLLA 35
>gnl|CDD|188566 TIGR04051, rSAM_NirJ, heme d1 biosynthesis radical SAM protein
NirJ. Heme d1 occurs in the cytochrome cd1 subunit of
nitrite reductase in species such as Pseudomonas
stutzeri. NirJ is a radical SAM protein involved in its
bioynthesis. In a number of species, distinct genes
NirJ1 and NirJ2 are found in similar genomic regions;
this model describe authentic NirJ from genomes with
NirJ only [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 354
Score = 27.3 bits (61), Expect = 0.54
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 2 AARFGSKLKELRIHLCQKGGSSSGV 26
RF +L LR L GG++SGV
Sbjct: 235 KRRFPEQLAHLRARLAAWGGNASGV 259
>gnl|CDD|223628 COG0554, GlpK, Glycerol kinase [Energy production and conversion].
Length = 499
Score = 26.4 bits (59), Expect = 1.1
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 1 MAARFGSKLKELRIHLCQKGGSSSGVRDFLAQ 32
M G KL LR+ GG+S +FL Q
Sbjct: 395 MEKDSGIKLTRLRV----DGGASRN--NFLMQ 420
>gnl|CDD|233486 TIGR01595, cas_CT1132, CRISPR-associated protein, CT1132 family.
This protein is found in at least five widely species
that contain CRISPR loci. Four cas (CRISPR-associated)
proteins that are widely distributed and found near the
CRISPR repeats. This protein is found exclusively next
to other cas proteins. Its function is unknown [Mobile
and extrachromosomal element functions, Other].
Length = 265
Score = 26.0 bits (57), Expect = 1.5
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 3/67 (4%)
Query: 2 AARFGSKLKELRIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPVVWAS 61
+ +K + C K VR F A K P+ + + PVV +S
Sbjct: 82 SQHATAKDPDKEEKACAK---YIDVRLFGAVITYLKKSIGITGPVQISMAKSLEPVVISS 138
Query: 62 GKGTHNF 68
+GT
Sbjct: 139 LQGTRAT 145
>gnl|CDD|219330 pfam07201, HrpJ, HrpJ-like domain. This family represents a
conserved region approximately 200 residues long within
a number of bacterial hypersensitivity response
secretion protein HrpJ and similar proteins. HrpJ forms
part of a type III secretion system through which, in
phytopathogenic bacterial species, virulence factors
are thought to be delivered to plant cells. This family
also includes the InvE invasion protein from
Salmonella. This protein is involved in host parasite
interactions and mutations in the InvE gene render
Salmonella typhimurium non-invasive. InvE S.
typhimurium mutants fail to elicit a rapid Ca2+
increase in cultured cells, an important event in the
infection procedure and internalisation of S.
typhimurium into epithelial cells. This family includes
bacterial SepL and SsaL proteins. SepL plays an
essential role in the infection process of
enterohemorrhagic Escherichia coli and is thought to be
responsible for the secretion of EspA, EspD, and EspB.
SsaL of Salmonella typhimurium is thought to be a
component of the type III secretion system.
Length = 161
Score = 25.8 bits (57), Expect = 1.7
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 8 KLKELRIHLCQKGGSSSGVRDFLAQHY 34
KL+ELR L S + +L +
Sbjct: 43 KLRELRQLLKSGRSSLPQLLAYLESLF 69
>gnl|CDD|217552 pfam03429, MSP1b, Major surface protein 1B. The major surface
protein (MSP1) of the cattle pathogen Anaplasma is a
heterodimer comprised of MSP1a and MSP1b. This family is
the MSP1b chain. There MSP1 proteins are putative
adhesins for bovine erythrocytes.
Length = 726
Score = 25.8 bits (56), Expect = 1.8
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 16 LCQKGGSSSGVRDFLAQHYVPLKQANPKFPILVRECSGVTPV 57
L Q GG S RD L Q + P A I+ + C+ V
Sbjct: 506 LAQIGGLSQAERDALVQSFTPKPPARTTKEIVSQMCNSVKSA 547
>gnl|CDD|234447 TIGR04046, MSMEG_0569_nitr, flavin-dependent oxidoreductase,
MSMEG_0569 family. Members of this protein family
belong to a conserved seven-gene biosynthetic cluster
found sparsely in Cyanobacteria, Proteobacteria, and
Actinobacteria. Distant homologies to characterized
proteins suggest that members are enzymes dependent on a
flavinoid cofactor.
Length = 400
Score = 25.0 bits (55), Expect = 3.0
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 31 AQHYVPLKQANPKFPILVRECSGVTPVVWASG 62
Y P+ + + L +G+T V+W +G
Sbjct: 308 ESPYQPVWEPEEEPTELDLAAAGITSVIWCTG 339
>gnl|CDD|241265 cd01231, PH_SH2B_family, SH2B adapter protein 1, 2, and 3
Pleckstrin homology (PH) domain. SH2B family/APS
proteins are a family of intracellular adaptor proteins
that influences a variety of signaling pathways
mediated by Janus kinase (JAK) and receptor tyrosine
kinases (RTKs) including receptors for insulin,
insulin-like growth factor-1, Janus kinase 2 (Jak2),
platelet derived growth factor, fibroblast growth
factor and nerve growth factor. They function in
glucose homeostasis, energy metabolism, hematopoesis
and reproduction. Mutations in human SH2B orthologs are
associated with metabolic disregulation and obesity.
There are several SH2B members in mammals: SH2B1
(splice variants: SH2B1alpha, SH2B1beta, SH2B1gamma,
and SH2B1delta), SH2B2 (APS) and SH2B3 (Lnk). They
contain a PH domain, a SH2 domain, a proline rich
region, multiple consensus sites for tyrosine and
serine/threonine phosphorylation and a highly conserved
c-Cbl recognition motif. These domains function as
protein-protein interaction motifs which allows SH2B
proteins to integrate and transduce intracellular
signals from multiple signaling networks in the absence
of intrinsic catalytic activity. SH2B proteins bind via
their SH2 domains to phosphotyrosine residues within
the intracellular tails of several activated RTKs
thereby contributing to receptor activation. SH2B
proteins have been shown to interact with insulin
receptor substrates IRS1 and IRS2, Grb2, Shc and c-Cbl
which may or may not require RTK-stimulated tyrosine
phosphorylation of SH2B. positively and negatively
regulating RTK signaling. Understanding the
physiological functions of SH2B proteins in mammals has
been complicated by the presence of multiple SH2B
isoforms and conflicting data. Both SH2-Bbeta and APS
associate with JAKs, but the former facilitates
JAK/STAT signaling while the latter inhibits it. Lnk
plays a role in cell growth and proliferation with
mutations resulting in growth reduction, developmental
delay and female sterility. Recently Lnk Drosophila has
been shown to be an important regulator of the
insulin/insulin-like growth factor (IGF)-1 signaling
(IIS) pathway during growth. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold,
which is electrostatically polarized. Less than 10% of
PH domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 115
Score = 24.6 bits (54), Expect = 3.3
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 13 RIHLCQKGGSSSGVRDFLAQHYVPLKQANPKFPIL------VRECS 52
R+ L + G G ++L + YVP K + PK I VRE +
Sbjct: 28 RLVLRKAAG---GDGEYLLEFYVPPKASKPKLGIFCSLIQEVRETT 70
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 25.0 bits (55), Expect = 3.8
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 30 LAQHYVPLKQANPKFPILVRECSGVTPVVWASGK 63
LAQ LK+ NPK PI V+ SG A+G
Sbjct: 189 LAQLIYDLKEINPKAPISVKLVSGHGVGTIAAGV 222
>gnl|CDD|235426 PRK05352, PRK05352, Na(+)-translocating NADH-quinone reductase
subunit A; Provisional.
Length = 448
Score = 24.8 bits (55), Expect = 3.9
Identities = 6/17 (35%), Positives = 13/17 (76%)
Query: 7 SKLKELRIHLCQKGGSS 23
S+L + ++H+C+ G+S
Sbjct: 183 SRLTDGKVHVCKAPGAS 199
>gnl|CDD|218801 pfam05896, NQRA, Na(+)-translocating NADH-quinone reductase subunit
A (NQRA). This family consists of several bacterial
Na(+)-translocating NADH-quinone reductase subunit A
(NQRA) proteins. The Na(+)-translocating NADH:
ubiquinone oxidoreductase (Na(+)-NQR) generates an
electrochemical Na(+) potential driven by aerobic
respiration.
Length = 257
Score = 24.4 bits (54), Expect = 4.7
Identities = 6/18 (33%), Positives = 13/18 (72%)
Query: 7 SKLKELRIHLCQKGGSSS 24
SKL + ++H+C+ G++
Sbjct: 182 SKLTDGKVHVCKAPGAAL 199
>gnl|CDD|176210 cd08248, RTN4I1, Human Reticulon 4 Interacting Protein 1. Human
Reticulon 4 Interacting Protein 1 is a member of the
medium chain dehydrogenase/ reductase (MDR) family.
Riticulons are endoplasmic reticulum associated
proteins involved in membrane trafficking and
neuroendocrine secretion. The MDR/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins
related to the first identified member, class I
mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P) binding-Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES.
Length = 350
Score = 24.1 bits (53), Expect = 5.8
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 38 KQANPKFP-ILVRECSGVTPVVWASGKGTHNF 68
K + +FP L R+CSG VV G G +F
Sbjct: 67 KYSGIEFPLTLGRDCSG---VVVDIGSGVKSF 95
>gnl|CDD|218679 pfam05661, DUF808, Protein of unknown function (DUF808). This
family consists of several bacterial proteins of
unknown function.
Length = 293
Score = 23.7 bits (52), Expect = 8.5
Identities = 10/18 (55%), Positives = 10/18 (55%), Gaps = 5/18 (27%)
Query: 52 SGVT-----PVVWASGKG 64
SGV PVVWA KG
Sbjct: 47 SGVKADRELPVVWAVAKG 64
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 0.137 0.430
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,503,144
Number of extensions: 251448
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 14
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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 (24.0 bits)