RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2656
(85 letters)
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 90.0 bits (223), Expect = 1e-23
Identities = 33/53 (62%), Positives = 46/53 (86%)
Query: 1 MHTKLAQTFLPTAVKFHYIWNLRDLDNVFQGMLFASGDCVRSSSQLVRLWMHE 53
+H K+A TFLPTA+KFHY++NLRDL N+FQG+LF+S +C++S L+RLW+HE
Sbjct: 220 LHQKIATTFLPTAIKFHYVFNLRDLSNIFQGLLFSSVECLKSPWDLIRLWLHE 272
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 32.3 bits (73), Expect = 0.017
Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 12 TAVKFHYIWNLRDLDNVFQGMLFASGDCVRSSS-QLVRLWMHEASRVYGDKMVDKKDIET 70
++ +Y + R+L + + + + + L+ W EA R D++V +K+ T
Sbjct: 1692 FFLQMNYGYKPRELTRSLRAIFGYAETRIDTPDVSLIIDWYCEAIREKIDRLVQQKESST 1751
Query: 71 FNKMLVENIKKVF 83
+ L + +
Sbjct: 1752 SRQDLYDFGLRAI 1764
>gnl|CDD|213305 cd05939, hsFATP4_like, Fatty acid transport proteins (FATP),
including FATP4 and FATP1, and similar proteins. Fatty
acid transport protein (FATP) transports long-chain or
very-long-chain fatty acids across the plasma membrane.
At least five copies of FATPs are identified in
mammalian cells. This family includes FATP4, FATP1, and
homologous proteins. Each FATP has unique patterns of
tissue distribution. FATP4 is mainly expressed in the
brain, testis, colon and kidney. FATPs also have fatty
acid CoA synthetase activity, thus playing dual roles
as fatty acid transporters and its activation enzymes.
FATPs are the key players in the trafficking of
exogenous fatty acids into the cell and in
intracellular fatty acid homeostasis.
Length = 474
Score = 27.0 bits (60), Expect = 1.1
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 11/43 (25%)
Query: 20 WNLRDLD-------NVFQGMLFASGDCV----RSSSQLVRLWM 51
W R+L+ N FQ + SGD V + + V LW+
Sbjct: 4 WTFRELNEYSNKVANFFQAQGYRSGDVVALFMENRLEFVALWL 46
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 26.3 bits (58), Expect = 1.6
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 11 PTAVKFHYIWNLRDLDNVFQGMLFASGDCVRSSS 44
P+A K H + DN F G + GDC + S
Sbjct: 176 PSAGKKHQVVQDLPPDNTFVGGCDSLGDCSSTGS 209
>gnl|CDD|225277 COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy
production and conversion].
Length = 614
Score = 26.5 bits (59), Expect = 1.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 57 VYGDKMVDKKDIETFNKMLVENIKKV 82
V G K V D E K++ E KK+
Sbjct: 202 VRGTKRVPVADPEKLKKIVEEIYKKI 227
>gnl|CDD|171821 PRK12937, PRK12937, short chain dehydrogenase; Provisional.
Length = 245
Score = 25.5 bits (56), Expect = 3.3
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 63 VDKKDIETFNKMLVENIKKVFAV 85
+ D+E F++ + N++ F V
Sbjct: 99 IADFDLEDFDRTIATNLRGAFVV 121
>gnl|CDD|222817 PHA00965, PHA00965, tail protein.
Length = 588
Score = 25.3 bits (55), Expect = 5.1
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 14 VKFHYIWNLRDLDNVFQGML---FASGDCVRSSSQLVRLWMHEASRV 57
+K + L ++D + ML SG VRLW ++ +
Sbjct: 539 LKCTGTYTLPNIDPMLMEMLRAILESG---------VRLWHNDGPML 576
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 25.1 bits (55), Expect = 5.8
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 56 RVYGDKMVDKKDIETFNKMLV-ENIKKVF 83
R YG M D E + +L IKK +
Sbjct: 308 REYGKPMSDISITEEYYNLLANPAIKKTY 336
>gnl|CDD|218676 pfam05649, Peptidase_M13_N, Peptidase family M13. M13 peptidases
are well-studied proteases found in a wide range of
organisms including mammals and bacteria. In mammals
they participate in processes such as cardiovascular
development, blood-pressure regulation, nervous control
of respiration, and regulation of the function of
neuropeptides in the central nervous system. In bacteria
they may be used for digestion of milk.
Length = 380
Score = 25.0 bits (55), Expect = 6.5
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 45 QLVRLWMHEA-SRVYGDKMVD---KKDIETFNKMLVENIKKVF 83
LV + EA R+Y +K K D+E +V+NIKK F
Sbjct: 310 SLVNGLLGEALGRLYVEKYFPPEAKADVEE----MVKNIKKAF 348
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 24.9 bits (55), Expect = 6.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 57 VYGDKMVDKKDIETFNKMLVENIKKVFA 84
V G+ + K+D E N+ E +K FA
Sbjct: 158 VRGEVFMPKEDFEALNEERREQGEKPFA 185
>gnl|CDD|176050 cd08405, C2B_Synaptotagmin-7, C2 domain second repeat present in
Synaptotagmin 7. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 7, a member of
class 2 synaptotagmins, is located in presynaptic
plasma membranes in neurons, dense-core vesicles in
endocrine cells, and lysosomes in fibroblasts. It has
been shown to play a role in regulation of
Ca2+-dependent lysosomal exocytosis in fibroblasts and
may also function as a vesicular Ca2+-sensor. It is
distinguished from the other synaptotagmins by having
over 12 splice forms. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that
can adopt 2 structural arrangements: Type I and Type
II, distinguished by a circular permutation involving
their N- and C-terminal beta strands. Many C2 domains
are Ca2+-dependent membrane-targeting modules that bind
a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 24.3 bits (53), Expect = 9.3
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 42 SSSQLVRLWMHEASRVYGDKMVDKKDIETFNKML 75
+S V++W+ Y DK V+KK + L
Sbjct: 35 TSDPYVKVWLM-----YKDKRVEKKKTVIKKRTL 63
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
0.326 0.136 0.414
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,123,107
Number of extensions: 306920
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 14
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.5 bits)