RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12189
(131 letters)
>gnl|CDD|240441 cd13433, Na_channel_gate, Inactivation gate of the voltage-gated
sodium channel alpha subunits. This region is part of
the intracellular linker between domains III and IV of
the alpha subunits of voltage-gated sodium channels. It
is responsible for fast inactivation of the channel and
essential for proper physiological function.
Length = 54
Score = 36.8 bits (86), Expect = 2e-04
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 63 LLTVDQRRWCDLKKRLKIAQPLHLPPRPDAFKYRARIYD 101
LT Q+++ + K+L +P PRP K++ I+D
Sbjct: 17 FLTESQKKYYNAMKKLGSKKPQKPIPRP-KNKFQGFIFD 54
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 34.6 bits (80), Expect = 0.007
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 1 MLTLFEVLSFKGWLDVRDILKTQLGDAHVIYIHVYIFLGCMIGLTLFVGVV 51
+L LF L+ +GW DV I+ ++I LG ++ L L +GV+
Sbjct: 144 LLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLIGVI 194
>gnl|CDD|224828 COG1916, COG1916, Uncharacterized homolog of PrgY (pheromone
shutdown protein) [Function unknown].
Length = 388
Score = 30.4 bits (69), Expect = 0.23
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 1 MLTLFEVLSFKGWLDVRDILKTQLGDAHVIYIHVYIFLGCMIGLTLFVGVVIAN 54
TL + LSFKG + V+ + + LG MIG + + V++
Sbjct: 341 FETLADDLSFKGMYKNK--------FFRVLLVVAFTNLGSMIGTFIGLPVLLNV 386
>gnl|CDD|198182 cd09928, SH2_Cterm_SPT6_like, C-terminal Src homology 2 (SH2)
domain found in Spt6. Spt6 is an essential
transcription elongation factor and histone chaperone
that binds the C-terminal repeat domain (CTD) of RNA
polymerase II. Spt6 contains a tandem SH2 domain with a
novel structure and CTD-binding mode. The tandem SH2
domain binds to a serine 2-phosphorylated CTD peptide in
vitro, whereas its N-terminal SH2 subdomain does not.
CTD binding requires a positively charged crevice in the
C-terminal SH2 subdomain, which lacks the canonical
phospho-binding pocket of SH2 domains. The tandem SH2
domain is apparently required for transcription
elongation in vivo as its deletion in cells is lethal in
the presence of 6-azauracil. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 89
Score = 26.4 bits (59), Expect = 2.0
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 90 PDAFKYRARIYDVTQNL--WFKRLI 112
PD F++R +++ +L WFK
Sbjct: 65 PDGFRFRGQVFPSVDSLLNWFKEHF 89
>gnl|CDD|192980 pfam12304, BCLP, Beta-casein like protein. This protein is found
in eukaryotes. Proteins in this family are typically
between 216 to 240 amino acids in length. This protein
has two conserved sequence motifs: VLR and TRIY. BCLP is
associated with cell morphology and a regulation of
growth pattern of tumor. It is found in adenocarcinomas
of uterine cervical tissues.
Length = 188
Score = 25.8 bits (57), Expect = 7.4
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 38 LGCMIGLTLFVGVVIANYSENKGTALLTVDQRRWCDLKKRLKIAQPLHLPPRPDAFKYRA 97
C +GL + V + +A N G LL + +L L IA P
Sbjct: 89 AACAVGLLVSVALTVA----NGGRNLLA--GCNFTNLASLLTIANECPFDP--------T 134
Query: 98 RIYDVTQNLWFKRLIAAVV 116
RIY T LW ++ + V
Sbjct: 135 RIYSTTLCLWAPSILLSAV 153
>gnl|CDD|132770 cd06860, PX_SNX7_30_like, The phosphoinositide binding Phox
Homology domain of Sorting Nexins 7 and 30. The PX
domain is a phosphoinositide (PI) binding module
present in many proteins with diverse functions.
Sorting nexins (SNXs) make up the largest group among
PX domain containing proteins. They are involved in
regulating membrane traffic and protein sorting in the
endosomal system. The PX domain of SNXs binds PIs and
targets the protein to PI-enriched membranes. SNXs
differ from each other in PI-binding specificity and
affinity, and the presence of other protein-protein
interaction domains, which help determine subcellular
localization and specific function in the endocytic
pathway. Some SNXs are localized in early endosome
structures such as clathrin-coated pits, while others
are located in late structures of the endocytic
pathway. This subfamily consists of SNX7, SNX30, and
similar proteins. They harbor a Bin/Amphiphysin/Rvs
(BAR) domain, which detects membrane curvature,
C-terminal to the PX domain, similar to the sorting
nexins SNX1-2, SNX4-6, SNX8, and SNX32. Both domains
have been shown to determine the specific
membrane-targeting of SNX1. The specific function of
the sorting nexins in this subfamily has yet to be
elucidated.
Length = 116
Score = 25.4 bits (56), Expect = 7.7
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 68 QRRWCD---LKKRLKIAQPLHL-PPRPDAFKYRARI 99
+RR+ D L+++L+ + P H+ PP P+ + +
Sbjct: 40 RRRYQDFLWLRQKLEESHPTHIIPPLPEKHSVKGLL 75
>gnl|CDD|241382 cd13228, PHear_NECAP, NECAP (adaptin-ear-binding coat-associated
protein) Plextrin Homology (PH) fold with ear-like
function (PHear) domain. NECAPs are alpha-ear-binding
proteins that enrich on clathrin-coated vesicles (CCVs).
NECAP 1 is expressed in brain and non-neuronal tissues
and cells while NECAP 2 is ubiquitously expressed. The
PH-like domain of NECAPs is a protein-binding interface
that mimics the FxDxF motif binding properties of the
alpha-ear and is called PHear (PH fold with ear-like
function) domain. 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 = 120
Score = 25.2 bits (56), Expect = 9.2
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 86 LPPRPDAFKYRARIYDVTQNLWFKRL 111
+PPR A YRA + + + LW RL
Sbjct: 14 IPPRASARGYRAADWGLEKPLWTGRL 39
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
0.331 0.144 0.449
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,895,693
Number of extensions: 622399
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 813
Number of HSP's successfully gapped: 25
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.2 bits)