RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3396
(128 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 59.8 bits (146), Expect = 2e-13
Identities = 24/48 (50%), Positives = 29/48 (60%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRK 41
EQL ELE F K+ YP REELA +VWFQNRRAK+++
Sbjct: 10 EQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 54.9 bits (133), Expect = 2e-11
Identities = 24/50 (48%), Positives = 29/50 (58%), Gaps = 7/50 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQE 43
EQL ELE F K+ YP REELA ++WFQNRRAK ++ E
Sbjct: 10 EQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 53.0 bits (128), Expect = 8e-11
Identities = 24/47 (51%), Positives = 28/47 (59%), Gaps = 7/47 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYR 40
EQL ELE F K+ YP REELA +VWFQNRRAK++
Sbjct: 11 EQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 43.6 bits (103), Expect = 3e-06
Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 19/96 (19%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRK------------ 41
EQL LE F + YP R +L++L Q+WFQN+RAK +K
Sbjct: 61 EQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGE 120
Query: 42 QEKQLQKALTPSVIPTCNGAMMRNIYPTTSRGYQPY 77
+E L K + S + + G Y
Sbjct: 121 EEADLAKIGSLSTGQISIIETLEFSRTSYEEGGLQY 156
>gnl|CDD|217340 pfam03055, RPE65, Retinal pigment epithelial membrane protein.
This family represents a retinal pigment epithelial
membrane receptor which is abundantly expressed in
retinal pigment epithelium, and binds plasma retinal
binding protein. The family also includes the sequence
related neoxanthin cleavage enzyme in plants and
lignostilbene-alpha,beta-dioxygenase in bacteria.
Length = 469
Score = 26.8 bits (60), Expect = 3.6
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 29 QVWFQNRR---AKYRKQEKQLQKALTPSVIPTCNGAMMRNIYP 68
+V ++NR Y K E+ + L P T +NI+P
Sbjct: 63 RVTYRNRFVRTEGY-KAERAAGRRLYPGEFGTLKPDPCKNIFP 104
>gnl|CDD|132012 TIGR02967, guan_deamin, guanine deaminase. This model describes
guanine deaminase, which hydrolyzes guanine to xanthine
and ammonia. Xanthine can then be converted to urate by
xanthine dehydrogenase, and urate subsequently degraded.
In some bacteria, the guanine deaminase gene is found
near the xdhABC genes for xanthine dehydrogenase.
Non-homologous forms of guanine deaminase also exist, as
well as distantly related forms outside the scope of
this model [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 401
Score = 26.4 bits (59), Expect = 4.3
Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 15/57 (26%)
Query: 14 HYPDIYC------REELAILFQVWFQNRRAKYRKQEKQLQKALTPSVIPTCNGAMMR 64
+ PD +E L + W R Y A+TP PT + +
Sbjct: 142 NAPDYLRDTAESSYDESKALIERWHGKGRLLY---------AVTPRFAPTSSPEQLA 189
>gnl|CDD|213953 TIGR04340, rSAM_ACGX, radical SAM/SPASM domain protein, ACGX
system. Members of this protein family are radical
SAM/SPASM domain proteins likely to be involved in the
modification of small, Cys-rich peptides. Members of the
family of proposed target sequences, TIGR04341, average
75 amino acids in length and average six instances of
the motif ACGX, where X is A, S, or T.
Length = 341
Score = 25.6 bits (56), Expect = 8.4
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 27 LFQVWFQNRRAKYRKQEKQLQKALTPSVIPTCNGAMMRNIYPTTSRGY 74
L+ V+ N KYR+ +K +K ++ C G P +RGY
Sbjct: 286 LYDVFLGNEMDKYRQIDK-FEKCSRCELLRFCRGC------PAVARGY 326
>gnl|CDD|173653 cd05105, PTKc_PDGFR_alpha, Catalytic domain of the Protein Tyrosine
Kinase, Platelet Derived Growth Factor Receptor alpha.
Protein Tyrosine Kinase (PTK) family; Platelet Derived
Growth Factor Receptor (PDGFR) alpha; catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. PDGFR
alpha is a receptor tyr kinase (RTK) containing an
extracellular ligand-binding region with five
immunoglobulin-like domains, a transmembrane segment,
and an intracellular catalytic domain. The binding to
its ligands, the PDGFs, leads to receptor dimerization,
trans phosphorylation and activation, and intracellular
signaling. PDGFR alpha forms homodimers or heterodimers
with PDGFR beta, depending on the nature of the PDGF
ligand. PDGF-AA, PDGF-AB, and PDGF-CC induce PDGFR alpha
homodimerization. PDGFR signaling plays many roles in
normal embryonic development and adult physiology. PDGFR
alpha signaling is important in the formation of lung
alveoli, intestinal villi, mesenchymal dermis, and hair
follicles, as well as in the development of
oligodendrocytes, retinal astrocytes, neural crest
cells, and testicular cells. Aberrant PDGFR alpha
expression is associated with some human cancers.
Mutations in PDGFR alpha have been found within a subset
of gastrointestinal stromal tumors (GISTs). An active
fusion protein FIP1L1-PDGFR alpha, derived from
interstitial deletion, is associated with idiopathic
hypereosinophilic syndrome (HES) and chronic
eosinophilic leukemia (CEL).
Length = 400
Score = 25.8 bits (56), Expect = 8.7
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 90 ILVPGMSTEDEWYNKSLSALRMNSSHHS 117
PGM + +YNK S RM H+
Sbjct: 338 TPYPGMIVDSTFYNKIKSGYRMAKPDHA 365
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 25.3 bits (56), Expect = 9.6
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 3/28 (10%)
Query: 15 YPDIYCREELAILFQVWFQNRRAKYRKQ 42
Y D A L Q++F R K K+
Sbjct: 47 YEDPE---RYAFLLQIYFLLNRFKKIKK 71
>gnl|CDD|220337 pfam09669, Phage_pRha, Phage regulatory protein Rha (Phage_pRha).
Members of this protein family are found in temperate
phage and bacterial prophage regions. Members include
the product of the rha gene of the lambdoid phage
phi-80, a late operon gene. The presence of this gene
interferes with infection of bacterial strains that
lack integration host factor (IHF), which regulates the
rha gene. It is suggested that Rha is a phage
regulatory protein.
Length = 88
Score = 24.4 bits (54), Expect = 9.6
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 66 IYPTTSRGYQPYPHPNTINRQHFVILVPGMSTE 98
T SRG + YP + + F++LV G + +
Sbjct: 38 SSYTDSRG-RKYPMYL-LTKDGFMLLVMGFTGK 68
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
0.319 0.130 0.397
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,485,397
Number of extensions: 541616
Number of successful extensions: 481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 477
Number of HSP's successfully gapped: 15
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
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: 53 (24.1 bits)