RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3738
(136 letters)
>gnl|CDD|218652 pfam05602, CLPTM1, Cleft lip and palate transmembrane protein 1
(CLPTM1). This family consists of several eukaryotic
cleft lip and palate transmembrane protein 1 sequences.
Cleft lip with or without cleft palate is a common birth
defect that is genetically complex. The nonsyndromic
forms have been studied genetically using linkage and
candidate-gene association studies with only partial
success in defining the loci responsible for orofacial
clefting. CLPTM1 encodes a transmembrane protein and has
strong homology to two Caenorhabditis elegans genes,
suggesting that CLPTM1 may belong to a new gene family.
This family also contains the human cisplatin resistance
related protein CRR9p which is associated with
CDDP-induced apoptosis.
Length = 437
Score = 159 bits (404), Expect = 4e-48
Identities = 54/98 (55%), Positives = 73/98 (74%)
Query: 37 PDQDSLKEALLETSPYLLAATVIVSILHSVFELLAFKNDIQFWNNRQSLEGLSVRSVFFN 96
+ D +KE LL+T+PYLLA T IVS+LH VFE LAFKNDIQFW N++S+ GLSVRS+ N
Sbjct: 282 KEADEVKEILLDTNPYLLALTAIVSLLHMVFEFLAFKNDIQFWRNKKSMVGLSVRSILAN 341
Query: 97 VFQSVVVLLYVLDNDANTLIRISCFVSVGIELWKINKI 134
VF +++ LY+LDN+ + +I +S + + IE WKI K
Sbjct: 342 VFCQIIIFLYLLDNETSWMILVSQGIGLLIEAWKITKA 379
>gnl|CDD|143474 cd07322, PriL_PriS_Eukaryotic, Eukaryotic core primase: Large
subunit, PriL. Primases synthesize the RNA primers
required for DNA replication. Primases are grouped into
two classes, bacteria/bacteriophage and
archaeal/eukaryotic. The proteins in the two classes
differ in structure and the replication apparatus
components. Archaeal/eukaryotic core primase is a
heterodimeric enzyme consisting of a small catalytic
subunit (PriS) and a large subunit (PriL). In eukaryotic
organisms, a heterotetrameric enzyme formed by DNA
polymerase alpha, the B subunit and two primase subunits
has primase activity. Although the catalytic activity
resides within PriS, the PriL subunit is essential for
primase function as disruption of the PriL gene in yeast
is lethal. PriL is composed of two structural domains.
Several functions have been proposed for PriL such as
stabilization of the PriS, involvement in synthesis
initiation, improvement of primase processivity,
determination of product size and transfer of the
products to DNA polymerase alpha.
Length = 390
Score = 27.2 bits (61), Expect = 2.6
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 32 CPFVFPDQDSLKEALLETSPYLLAATVIVSILHSV 66
CPF D DSLK+ L Y L+ + I I+ V
Sbjct: 323 CPFRHFDSDSLKQLLQS---YGLSDSDIEEIIDLV 354
>gnl|CDD|218677 pfam05652, DcpS, Scavenger mRNA decapping enzyme (DcpS)
N-terminal. This family consists of several scavenger
mRNA decapping enzymes (DcpS) and is the N-terminal
domain of these proteins. DcpS is a scavenger
pyrophosphatase that hydrolyses the residual cap
structure following 3' to 5' decay of an mRNA. The
association of DcpS with 3' to 5' exonuclease exosome
components suggests that these two activities are
linked and there is a coupled exonucleolytic
decay-dependent decapping pathway.
Length = 99
Score = 26.1 bits (58), Expect = 3.9
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 36 FPDQDSLKEALLETSPYLLAATVIVSILHSVFEL-LAFKNDIQFWNNRQSLEGLS 89
DQD++ +LE +P+ S+L + EL L F NDI W + L+
Sbjct: 26 IDDQDAI--LILEKTPFQEETLAEYSLLSGISELKLIFSNDIYGWYLSVPPQDLN 78
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 26.9 bits (60), Expect = 3.9
Identities = 27/104 (25%), Positives = 37/104 (35%), Gaps = 20/104 (19%)
Query: 19 ATTTFLLSCLTPSC------PFVFPDQDSLKEALLETSPYLLAATVIVSIL--HSVFELL 70
S L C P S+ E LL P + +S L V L
Sbjct: 409 QALKLFYSLLPGPCISGSSRPLGPA---SVLEHLLALCPPG-GLLLFLSALPEDVVSGLK 464
Query: 71 AFKNDIQFWNNRQSLEGLSVRSVFFNVFQSVVVLLYVLDNDANT 114
F +NR++ E + V+ F NV+ SVV L V+ N
Sbjct: 465 PFSA-----SNRETNEEI-VKQYFLNVYCSVVFL--VIKNTHEG 500
>gnl|CDD|205675 pfam13497, DUF4121, Domain of unknown function (DUF4121). Based
on Bacteroides thetaiotaomicron gene BT_2588, a
putative uncharacterized protein. As seen in gene
expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2
231), it appears to be upregulated in the presence of
host or vs when in culture.
Length = 262
Score = 26.2 bits (58), Expect = 5.8
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 27 CLTPSCPFVFPDQDSLK 43
CL P PFV+ D ++
Sbjct: 80 CLQPYVPFVWEDGGGIR 96
>gnl|CDD|215478 PLN02886, PLN02886, aminoacyl-tRNA ligase.
Length = 389
Score = 26.3 bits (58), Expect = 6.5
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 6 KNVLFVISSATAEATTTFLLSCLTP 30
K +FV S A A +LLSC TP
Sbjct: 119 KASVFVQSHVPAHAELMWLLSCSTP 143
>gnl|CDD|227714 COG5427, COG5427, Uncharacterized membrane protein [Function
unknown].
Length = 684
Score = 26.4 bits (58), Expect = 6.9
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 76 IQFWNNRQSLEGLSVRSVFFNVFQSVVVLLYVLD 109
+Q W R+S G SV+ V V V+ +V +
Sbjct: 316 VQRWTRRESAVGQSVQRVLLAVLAVVIAWPFVQN 349
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 25.6 bits (57), Expect = 8.3
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 96 NVFQSVVVLLYVLDNDANTLIR 117
++F++V VL+YV D ++ L +
Sbjct: 72 HIFRNVEVLIYVFDVESRELEK 93
>gnl|CDD|239977 cd04604, CBS_pair_KpsF_GutQ_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with KpsF/GutQ domains in the API
[A5P (D-arabinose 5-phosphate) isomerase] protein.
These APIs catalyze the conversion of the pentose
pathway intermediate D-ribulose 5-phosphate into A5P, a
precursor of 3-deoxy-D-manno-octulosonate, which is an
integral carbohydrate component of various glycolipids
coating the surface of the outer membrane of
Gram-negative bacteria, including lipopolysaccharide
and many group 2 K-antigen capsules. CBS is a small
domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
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. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 114
Score = 25.1 bits (56), Expect = 9.7
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 32 CPFVFPDQDSLKEALLETSPYLLAATVIV 60
P V PD SLK+ALLE S L T +V
Sbjct: 4 LPLVSPD-TSLKDALLEMSRKGLGMTAVV 31
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
0.324 0.136 0.404
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,607,562
Number of extensions: 569901
Number of successful extensions: 615
Number of sequences better than 10.0: 1
Number of HSP's gapped: 615
Number of HSP's successfully gapped: 29
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.7 bits)