RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6184
(156 letters)
>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 = 146 bits (370), Expect = 6e-46
Identities = 53/107 (49%), Positives = 78/107 (72%), Gaps = 1/107 (0%)
Query: 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG 66
+ P +A+ ++KK+L + NP++ LYALL+LESCVKNCG HDEV ++ FM+++K+L++
Sbjct: 36 DVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKT 95
Query: 67 TQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGFKNPSK 112
T++EEV+ KILELIQAWA AFRN P+ + V T + +G K P
Sbjct: 96 TKNEEVRQKILELIQAWALAFRNKPQLKYVVDTYQILKAEGHKFPEL 142
>gnl|CDD|197630 smart00288, VHS, Domain present in VPS-27, Hrs and STAM.
Unpublished observations. Domain of unknown function.
Length = 133
Score = 100 bits (250), Expect = 8e-28
Identities = 39/91 (42%), Positives = 57/91 (62%), Gaps = 1/91 (1%)
Query: 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQ 68
P A+ +KK+L N NPH+ L AL +L++CVKNCG+ H EV +K F+ ++ +L++
Sbjct: 34 GPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKY 93
Query: 69 -HEEVKAKILELIQAWAHAFRNSPKYRAVPT 98
VK +ILELIQ WA AF+N P +
Sbjct: 94 PLPLVKKRILELIQEWADAFKNDPDLSQIVD 124
>gnl|CDD|216121 pfam00790, VHS, VHS domain. Domain present in VPS-27, Hrs and
STAM.
Length = 136
Score = 98.5 bits (246), Expect = 3e-27
Identities = 38/90 (42%), Positives = 59/90 (65%), Gaps = 3/90 (3%)
Query: 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQH 69
P A+ IKK++ + NPH+ L AL +L++CVKNCG+ H E+ +K F+ ++ +L+ +
Sbjct: 36 PKEAVRLIKKRINSPNPHVALLALTLLDACVKNCGSKFHLEIASKEFLNELVKLIPNKPY 95
Query: 70 ---EEVKAKILELIQAWAHAFRNSPKYRAV 96
+VK KILELIQ WA AF+N P + +
Sbjct: 96 GKPAKVKKKILELIQEWADAFKNDPDLKYI 125
>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 = 83.8 bits (208), Expect = 2e-21
Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 2/86 (2%)
Query: 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQ- 68
P A +I+KK+ NPH+ L AL +LE VKNCG H +V K F+ ++ ++ + +
Sbjct: 35 PKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPK 94
Query: 69 -HEEVKAKILELIQAWAHAFRNSPKY 93
+V+ K LELI AW+ +F +
Sbjct: 95 YDPKVREKALELILAWSESFGGHSED 120
>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 = 79.3 bits (196), Expect = 1e-19
Identities = 29/86 (33%), Positives = 52/86 (60%)
Query: 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEV 72
L +I K+L + +P++ L AL +L++C +NCG H EV ++ F +++K+L+ H V
Sbjct: 38 CLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTV 97
Query: 73 KAKILELIQAWAHAFRNSPKYRAVPT 98
K K+ E+++ WA F+N P +
Sbjct: 98 KEKLREVVKQWADEFKNDPSLSLMSD 123
>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 = 72.5 bits (178), Expect = 3e-17
Identities = 32/80 (40%), Positives = 46/80 (57%), Gaps = 5/80 (6%)
Query: 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG--- 66
P A+ +IKK++ N NPH+VL AL +LE CVKNCG H EV + F ++ + +
Sbjct: 35 PKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDFAVELLKFDKSKLL 94
Query: 67 --TQHEEVKAKILELIQAWA 84
V+ K +EL+Q WA
Sbjct: 95 GDDVSTNVREKAIELVQLWA 114
>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 = 70.1 bits (172), Expect = 4e-16
Identities = 38/88 (43%), Positives = 52/88 (59%), Gaps = 8/88 (9%)
Query: 10 PSHALASIKKKLT-NSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQ 68
P A+ ++KK+L N N V+ L VLE+CVKNCG+ H V K F++ + LV+
Sbjct: 36 PKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVLVAKKDFIKDV--LVKLIN 93
Query: 69 HE-----EVKAKILELIQAWAHAFRNSP 91
+ V+ K+L LIQAWA AFR SP
Sbjct: 94 PKNNPPTIVQEKVLALIQAWADAFRGSP 121
>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 = 58.1 bits (141), Expect = 1e-11
Identities = 32/90 (35%), Positives = 50/90 (55%), Gaps = 5/90 (5%)
Query: 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV----R 65
P A+ + K+ + L AL VLE+C+KNCG H EVG F+ ++ +LV
Sbjct: 36 PQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYL 95
Query: 66 GTQ-HEEVKAKILELIQAWAHAFRNSPKYR 94
G++ E+VK KI+EL+ +W + PK +
Sbjct: 96 GSRTSEKVKTKIIELLYSWTLELPHEPKIK 125
>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
present in several RNA-processing factors such as Pcf11
and Nrd1. Pcf11 is a conserved and essential subunit of
the yeast cleavage factor IA, which is required for
polyadenylation-dependent 3'-RNA processing and
transcription termination. Nrd1 is implicated in
polyadenylation-independent 3'-RNA processing. CID binds
tightly to the carboxy-terminal domain (CTD) of RNA
polymerase (Pol) II. During transcription, Pol II
synthesizes eukaryotic messenger RNA. Transcription is
coupled to RNA processing through the CTD, which
consists of up to 52 repeats of the sequence Tyr 1-Ser
2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
alpha-helices in a right-handed superhelical
arrangement, which closely resembles that of the VHS
domains and ARM (Armadillo) repeat proteins, except for
its two amino-terminal helices.
Length = 114
Score = 29.1 bits (66), Expect = 0.42
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 16 SIKKKLTNSNPHIVLYALLVLESCVKNCG---NLIHDEVGTKAFMEQMKELVRGTQHEEV 72
I+K + P L L +L+S VKN G E F++ +++ E+
Sbjct: 41 IIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSEFLVPLFLDAYEKV-----DEKT 95
Query: 73 KAKILELIQAWAHAFRNSP 91
+ K+ L+ W F
Sbjct: 96 RKKLERLLNIWEERFVFGS 114
>gnl|CDD|221133 pfam11554, DUF3232, Protein of unknown function (DUF3232). This
bacterial family of proteins has no known function.
Length = 149
Score = 28.5 bits (63), Expect = 0.96
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 52 GTKAFMEQMKELVRGTQHEEVKAKILE-LIQAWAHAF 87
++ M++ K +V + +EV +LE LI A+ F
Sbjct: 15 ASEETMDRYKRVVCIAKGDEVALSLLEGLIDAFTRYF 51
>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-C subtype; also
known as Csd1 family.
Length = 569
Score = 28.8 bits (65), Expect = 1.3
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 54 KAFMEQMKELVRGTQHEEVKAKILELIQAW-AHAFRNSPKYRAVPTK 99
+AF+E ++E + T+ VKA +L ++ W + V +
Sbjct: 100 EAFIELLEEWLAETEDPGVKA-VLRFLKKWELEEDLIEAIKKEVEEE 145
>gnl|CDD|188684 cd08729, RGS_PX, Regulator of G protein signaling domain. These
uncharacterized RGS-like domains are found in proteins
that also contain one or more PX domains. The RGS domain
is an essential part of the Regulator of G-protein
Signaling (RGS) protein family, a diverse group of
multifunctional proteins that regulate cellular
signaling events downstream of G-protein coupled
receptors (GPCRs). RGS proteins play critical regulatory
role as GTPase activating proteins (GAPs) of the
heterotrimeric G-protein G-alpha-subunits. As a major
G-protein regulator, the RGS domain containing proteins
that are involves in many crucial cellular processes.
RGS proteins regulate intracellular trafficking and
provide vital support for signal transduction. RGS
proteins play critical regulatory role as GTPase
activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins regulate many
aspects of embryonic development such as glial
differentiation, embryonic axis formation, skeletal and
muscle development, cell migration during early
embryogenesis, as well as apoptosis, cell proliferation,
and modulation of cardiac development. Several RGS
proteins can fine-tune immune responses, others RGS
proteins play important role in neuronal signals
modulation. Some RGS proteins are the principal elements
needed for proper vision.
Length = 136
Score = 27.4 bits (61), Expect = 1.9
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 92 KYRAVPTKSWMTDKGFKNPSKS--SDSLGLELQIFRICHIHFSEIKGIDQIVDSSSSVAL 149
+ R+ + W+ +GFKNP + +D Q +I I + S S +L
Sbjct: 17 RNRSQLVQFWLVVEGFKNPLEDTENDYSLDSSQSRSWIDSDKEDIAMIYETYFSDPSPSL 76
>gnl|CDD|234559 TIGR04358, XXXCH_domain, XXXCH domain. Members of this family
show C-terminal sequence similarity, perhaps indicating
distant homology, to cytochrome c-prime (see
pfam01322). However, the motif CxxCH is replaced by
xxxCH. Genes for this protein occur in a sporadically
distributed genome context, largely in
deltaProteobacteria, in which an ATP-grasp family
glutamate ligase homolog and a CofD (LPPG:FO
2-phospho-L-lactate transferase) homolog suggest a
novel biosynthesis.
Length = 90
Score = 25.8 bits (57), Expect = 4.2
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 58 EQMKELVRGTQHEEVKAKILELIQAWAHAFRN 89
+Q++ V+ E A + EL QA
Sbjct: 59 DQLQAAVKNGDLEAAVAAVDELEQAKKFCHER 90
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 26.5 bits (59), Expect = 7.0
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 85 HAFRNSPKYRAVPTKSWMTDKGFKN 109
H P+ R P S + G +N
Sbjct: 260 HPLYTHPRVRLSPHTSAIAPDGRRN 284
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 26.1 bits (58), Expect = 7.1
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 13 ALASIKKKLTNSNPHIVLY 31
L+ IK+ L +VLY
Sbjct: 101 ILSIIKRFLKKKTIDVVLY 119
>gnl|CDD|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional.
Length = 172
Score = 26.1 bits (58), Expect = 7.1
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 97 PTKSWMTDKGFKNPSKSSDSLGLEL 121
P W+T+ GF++ S D LG+E+
Sbjct: 18 PVSQWLTENGFEHESLGPDHLGVEI 42
>gnl|CDD|220356 pfam09709, Cas_Csd1, CRISPR-associated protein (Cas_Csd1). CRISPR
loci appear to be mobile elements with a wide host
range. This entry represents proteins that tend to be
found near CRISPR repeats. The species range, so far, is
exclusively bacterial and mesophilic, although CRISPR
loci are particularly common among the archaea and
thermophilic bacteria. Clusters of short DNA repeats
with nonhomologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins.
Length = 572
Score = 26.1 bits (58), Expect = 9.8
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 54 KAFMEQMKELVRGTQHEEVKAKILELIQAWA 84
+AF+E ++E + VKA +L ++ W
Sbjct: 100 RAFIELLEEWAESEEDPGVKA-VLRFLKKWG 129
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
0.320 0.132 0.406
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,751,621
Number of extensions: 656711
Number of successful extensions: 662
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 29
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 55 (24.9 bits)