RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12750
(93 letters)
>gnl|CDD|239624 cd03567, VHS_GGA, VHS domain family, GGA subfamily; GGA
(Golgi-localized, Gamma-ear-containing, Arf-binding)
comprise a subfamily of ubiquitously expressed,
monomeric, motif-binding cargo/clathrin adaptor
proteins. The VHS domain has a superhelical structure
similar to the structure of the ARM (Armadillo) repeats
and is present at the N-termini of proteins. GGA
proteins have a multidomain structure consisting of an
N-terminal VHS domain linked by a short proline-rich
linker to a GAT (GGA and TOM) domain, which is followed
by a long flexible linker to the C-terminal appendage,
GAE (gamma-adaptin ear) domain. The VHS domain of GGA
proteins binds to the acidic-cluster dileucine (DxxLL)
motif found on the cytoplasmic tails of cargo proteins
trafficked between the trans-Golgi network and the
endosomal system.
Length = 139
Score = 144 bits (365), Expect = 3e-46
Identities = 55/84 (65%), Positives = 71/84 (84%)
Query: 8 ILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLWT 67
+ + VLEACM++CG +FH+EVGKFRFLNELIKL+SPKYLG+ T + V+T+IIELLY WT
Sbjct: 56 LQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWT 115
Query: 68 LEYPRESKIREAYEMLKKQQVVQA 91
LE P E KI+EAY+MLKKQ +++
Sbjct: 116 LELPHEPKIKEAYDMLKKQGIIKD 139
>gnl|CDD|216121 pfam00790, VHS, VHS domain. Domain present in VPS-27, Hrs and
STAM.
Length = 136
Score = 85.0 bits (211), Expect = 7e-23
Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 5/84 (5%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+L + +L+AC+++CG +FH E+ FLNEL+KLI K G V+ +I+EL+ W
Sbjct: 55 ALLALTLLDACVKNCGSKFHLEIASKEFLNELVKLIPNKPYGKPA--KVKKKILELIQEW 112
Query: 67 TLEY---PRESKIREAYEMLKKQQ 87
+ P IR+ Y++LK++
Sbjct: 113 ADAFKNDPDLKYIRDMYKLLKRKG 136
>gnl|CDD|197630 smart00288, VHS, Domain present in VPS-27, Hrs and STAM.
Unpublished observations. Domain of unknown function.
Length = 133
Score = 73.1 bits (180), Expect = 3e-18
Identities = 34/84 (40%), Positives = 52/84 (61%), Gaps = 7/84 (8%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+L + +L+AC+++CG +FH EV FLNEL+KLI PKY L V+ I+EL+ W
Sbjct: 54 ALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPL----VKKRILELIQEW 109
Query: 67 TLEY---PRESKIREAYEMLKKQQ 87
+ P S+I + Y++LKK+
Sbjct: 110 ADAFKNDPDLSQIVDVYDLLKKKG 133
>gnl|CDD|239623 cd03565, VHS_Tom1, VHS domain family, Tom1 subfamily; The VHS
domain is an essential part of Tom1 (Target of myb1 -
retroviral oncogene) protein. The VHS domain has a
superhelical structure similar to the structure of the
ARM repeats and is present at the very N-termini of
proteins. It is a right-handed superhelix of eight alpha
helices. The VHS domain has been found in a number of
proteins, some of which have been implicated in
intracellular trafficking and sorting. The VHS domain of
the Tom1 protein is essential for the negative
regulation of Interleukin-1 and Tumor Necrosis
Factor-induced signaling pathways.
Length = 141
Score = 60.1 bits (146), Expect = 3e-13
Identities = 32/88 (36%), Positives = 53/88 (60%), Gaps = 7/88 (7%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNE-LIKLISPKYLGNLTPDAVRTEIIELL 63
+ V+LT+ VLE C+++CG +FH V K F+ + L+KLI+PK N P V+ +++ L+
Sbjct: 54 KEVMLTLTVLETCVKNCGHRFHVLVAKKDFIKDVLVKLINPKN--NP-PTIVQEKVLALI 110
Query: 64 YLWTLEY---PRESKIREAYEMLKKQQV 88
W + P + + E YE LKK+ +
Sbjct: 111 QAWADAFRGSPDLTGVVEVYEELKKKGI 138
>gnl|CDD|238118 cd00197, VHS_ENTH_ANTH, VHS, ENTH and ANTH domain superfamily;
composed of proteins containing a VHS, ENTH or ANTH
domain. The VHS domain is present in Vps27 (Vacuolar
Protein Sorting), Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and STAM
(Signal Transducing Adaptor Molecule). It is located at
the N-termini of proteins involved in intracellular
membrane trafficking. The epsin N-terminal homology
(ENTH) domain is an evolutionarily conserved protein
module found primarily in proteins that participate in
clathrin-mediated endocytosis. A set of proteins
previously designated as harboring an ENTH domain in
fact contains a highly similar, yet unique module
referred to as an AP180 N-terminal homology (ANTH)
domain. VHS, ENTH and ANTH domains are structurally
similar and are composed of a superhelix of eight alpha
helices. ENTH adnd ANTH (E/ANTH) domains bind both
inositol phospholipids and proteins and contribute to
the nucleation and formation of clathrin coats on
membranes. ENTH domains also function in the development
of membrane curvature through lipid remodeling during
the formation of clathrin-coated vesicles. E/ANTH
domain-bearing proteins have recently been shown to
function with adaptor protein-1 and GGA adaptors at the
trans-Golgi network, which suggests that E/ANTH domains
are universal components of the machinery for
clathrin-mediated membrane budding.
Length = 115
Score = 58.6 bits (142), Expect = 1e-12
Identities = 23/55 (41%), Positives = 32/55 (58%)
Query: 13 VLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLWT 67
+LE C+++CG +FH EV F EL+K K LG+ VR + IEL+ LW
Sbjct: 60 LLEYCVKNCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLWA 114
>gnl|CDD|239620 cd03561, VHS, VHS domain family; The VHS domain is present in Vps27
(Vacuolar Protein Sorting), Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and STAM
(Signal Transducing Adaptor Molecule). It has a
superhelical structure similar to that of the ARM
(Armadillo) repeats and is present at the N-termini of
proteins involved in intracellular membrane trafficking.
There are four general groups of VHS domain containing
proteins based on their association with other domains.
The first group consists of proteins of the
STAM/EAST/Hbp family which has the domain composition
VHS-SH3-ITAM. The second consists of proteins with a
FYVE domain C-terminal to VHS. The third consists of GGA
proteins with a domain composition VHS-GAT (GGA and
TOM)-GAE (gamma-adaptin ear) domain. The fourth consists
of proteins with a VHS domain alone or with domains
other than those mentioned above. In GGA proteins, VHS
domains are involved in cargo recognition in
trans-Golgi, thereby having a general membrane
targeting/cargo recognition role in vesicular
trafficking.
Length = 133
Score = 56.5 bits (137), Expect = 7e-12
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 8 ILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLWT 67
+L + +LE +++CG FH +V FL EL+K+ VR + +EL+ W+
Sbjct: 55 LLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNS---PKYDPKVREKALELILAWS 111
Query: 68 LEY----PRESKIREAYEMLK 84
+ I +AY++LK
Sbjct: 112 ESFGGHSEDLPGIEDAYKLLK 132
>gnl|CDD|239626 cd03569, VHS_Hrs_Vps27p, VHS domain family, Hrs and Vps27p
subfamily; composed of Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and its
yeast homolog Vps27p (vacuolar protein sorting). The VHS
domain, an essential part of Hrs/Vps27p, has a
superhelical structure similar to the structure of ARM
(Armadillo) repeats and is present at the N-termini of
proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p,
and EEA1) zinc finger domain C-terminal to VHS, as well
as two coiled-coil domains. Hrs has been proposed to
play a role in at least three vesicle trafficking
events: exocytosis, endocytosis, and endosome to
lysosome trafficking. Hrs is involved in promoting rapid
recycling of endocytosed signaling receptors to the
plasma membrane.
Length = 142
Score = 44.2 bits (105), Expect = 6e-07
Identities = 24/85 (28%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 5 RLVILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLY 64
+ + + +LE+C+++CG FH EV F++EL LI + VR +I+EL+
Sbjct: 56 NVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIK-----TTKNEEVRQKILELIQ 110
Query: 65 LWTLEYPRESK---IREAYEMLKKQ 86
W L + + + + + Y++LK +
Sbjct: 111 AWALAFRNKPQLKYVVDTYQILKAE 135
>gnl|CDD|239625 cd03568, VHS_STAM, VHS domain family, STAM subfamily; members
include STAM (Signal Transducing Adaptor Molecule), EAST
(EGFR-associated protein with SH3 and TAM domains) and
Hbp (Hrs-binding protein). Collectively, they are
referred to as STAM. All STAMs have at their N-termini a
VHS domain, which is involved in cytokine-mediated
intracellular signal transduction and has a superhelical
structure similar to the structure of ARM (Armadillo)
repeats, followed by a SH3 (Src homology 3) domain, a
well-established protein-protein interaction domain. At
the C-termini of most vertebrate STAMS, an ITAM
(Immunoreceptor Tyrosine-based Activation) motif is
present, which mediates the binding of HRS (hepatocyte
growth factor-regulated tyrosine kinase substrate) in
endocytic and exocytic machineries.
Length = 144
Score = 38.4 bits (90), Expect = 9e-05
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 7 VILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLW 66
+ + +L+AC ++CG +FH EV F EL KLI+ + V+ ++ E++ W
Sbjct: 54 QLRALTLLDACAENCGKRFHQEVASRDFTQELKKLIN-----DRVHPTVKEKLREVVKQW 108
Query: 67 TLEY---PRESKIREAYEMLKKQ 86
E+ P S + + Y+ LK +
Sbjct: 109 ADEFKNDPSLSLMSDLYKKLKNE 131
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 28.1 bits (63), Expect = 0.52
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 30 GKFRFLNELIKLISPKY 46
GKF LN+LI L+
Sbjct: 95 GKFLVLNDLINLLIRSE 111
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 27.7 bits (63), Expect = 0.71
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 53 DAVRTEIIELLYLWTLEYPRESKIREAYEMLKKQQV 88
DA++ E++E L E E +I+EA++ L+K+ V
Sbjct: 270 DAIKEEVLEALAAEEEEEEDEKEIKEAFKKLEKKIV 305
>gnl|CDD|182729 PRK10786, ribD, bifunctional
diaminohydroxyphosphoribosylaminopyrimidine
deaminase/5-amino-6-(5-phosphoribosylamino)uracil
reductase; Provisional.
Length = 367
Score = 27.0 bits (60), Expect = 1.2
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 8 ILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGN 49
I +IWV GP + + ++ELI I+PK LG+
Sbjct: 293 INSIWV------EAGPTLAGALLQAGLVDELIVYIAPKLLGS 328
>gnl|CDD|213540 TIGR00562, proto_IX_ox, protoporphyrinogen oxidase. This enzyme
oxidizes protoporphyrinogen IX to protoporphyrin IX, a
precursor of heme and chlorophyll. Bacillus subtilis
HemY also has coproporphyrinogen III to coproporphyrin
III oxidase activity in a heterologous expression
system, although the role for this activity in vivo is
unclear. This protein is a flavoprotein and has a
beta-alpha-beta dinucleotide binding motif near the
amino end [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 462
Score = 26.7 bits (59), Expect = 1.6
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 21 CGPQFHAEVGKFRFLNELIKLISPKYLG 48
PQ+H VG + L E +L+ Y G
Sbjct: 404 AIPQYH--VGHDQRLKEARELLESAYPG 429
>gnl|CDD|232920 TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD. This
model describes the ribD protein as found in Escherichia
coli. The N-terminal domain includes the conserved
zinc-binding site region captured in the model
dCMP_cyt_deam and shared by proteins such as cytosine
deaminase, mammalian apolipoprotein B mRNA editing
protein, blasticidin-S deaminase, and Bacillus subtilis
competence protein comEB. The C-terminal domain is
homologous to the full length of yeast HTP reductase, a
protein required for riboflavin biosynthesis. A number
of archaeal proteins believed related to riboflavin
biosynthesis contain only this C-terminal domain and are
not found as full-length matches to this model
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Riboflavin, FMN, and FAD].
Length = 344
Score = 25.9 bits (57), Expect = 3.4
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 6/41 (14%)
Query: 8 ILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLG 48
I ++ V GP ++ELI I+PK LG
Sbjct: 273 INSVLV------EGGPNLLGSFLDEGLVDELIIYIAPKLLG 307
>gnl|CDD|131210 TIGR02155, PA_CoA_ligase, phenylacetate-CoA ligase.
Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the
first step in aromatic catabolism of phenylacetic acid
(PA) into phenylacetyl-CoA (PA-CoA). Often located in a
conserved gene cluster with enzymes involved in
phenylacetic acid activation (paaG/H/I/J),
phenylacetate-CoA ligase has been found among the
proteobacteria as well as in gram positive prokaryotes.
In the B-subclass proteobacterium Azoarcus evansii,
phenylacetate-CoA ligase has been shown to be induced
under aerobic and anaerobic growth conditions. It
remains unclear however, whether this induction is due
to the same enzyme or to another isoenzyme restricted to
specific anaerobic growth conditions [Energy metabolism,
Other].
Length = 422
Score = 25.6 bits (56), Expect = 4.2
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 1 MFPLRLVILTIWVLEAC---MQHCGPQFHAEVGKFRFLNEL---IKLISPKYLGNLTPDA 54
M +R V + LE M P + E+ + ++EL ++L Y L A
Sbjct: 320 MLIIRGVNVFPTQLEEVILKMDELSPHYQLELTRNGHMDELTLKVELKPESYTLRLHEQA 379
>gnl|CDD|183511 PRK12411, PRK12411, cytidine deaminase; Provisional.
Length = 132
Score = 25.3 bits (55), Expect = 4.3
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 37 ELIKLISPKYLGNLTPDAVRTEIIELL 63
EL K + YL NL D T + ELL
Sbjct: 95 ELCKQDTKVYLSNLHGDVQETTVGELL 121
>gnl|CDD|218324 pfam04912, Dynamitin, Dynamitin. Dynamitin is a subunit of the
microtubule-dependent motor complex and in implicated in
cell adhesion by binding to macrophage-enriched
myristoylated alanine-rice C kinase substrate
(MacMARCKS).
Length = 376
Score = 25.5 bits (56), Expect = 4.7
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 69 EYPRESKIREAYEMLKKQQVV 89
+ ESKI E YE++KK V
Sbjct: 278 DANTESKISELYEIMKKWDPV 298
>gnl|CDD|234346 TIGR03756, conj_TIGR03756, integrating conjugative element protein,
PFL_4710 family. Members of this protein family are
found in genomic regions associated with conjugative
transfer and integrated TOL-like plasmids. The specific
function is unknown [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 297
Score = 25.0 bits (55), Expect = 5.9
Identities = 16/48 (33%), Positives = 17/48 (35%), Gaps = 18/48 (37%)
Query: 43 SPKYLGNLTPDAVRTEIIELLY------------------LWTLEYPR 72
P YL L A RT I ELLY +W YPR
Sbjct: 139 VPYYLSTLDALAWRTGIPELLYPEALIPGLREIGIGTSTNMWGNVYPR 186
>gnl|CDD|216753 pfam01872, RibD_C, RibD C-terminal domain. The function of this
domain is not known, but it is thought to be involved in
riboflavin biosynthesis. This domain is found in the C
terminus of RibD/RibG, in combination with pfam00383, as
well as in isolation in some archaebacterial proteins.
This family appears to be related to pfam00186.
Length = 201
Score = 24.7 bits (54), Expect = 7.7
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 8 ILTIWVLEACMQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTP 52
I ++ V G + + ++EL I+PK LG
Sbjct: 136 IRSLLV------EGGATLAGSLLRAGLVDELRLYIAPKLLGGGGR 174
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 23.9 bits (52), Expect = 9.0
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 18 MQHCGPQFHAEVGKFRFLNELIKLISPKYLGNLTPDAVRTEIIELLYLWTLEYPRES 74
+Q P+ E + + E KL S K+ + + + + E Y RE
Sbjct: 15 VQTMRPELKREGPQVPGVAEFSKLCSEKW-KAM-SEEEKEKYEEKAREDKKRYDREM 69
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
0.327 0.141 0.446
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,795,421
Number of extensions: 391516
Number of successful extensions: 546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 539
Number of HSP's successfully gapped: 28
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (24.2 bits)