RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5800
(152 letters)
>gnl|CDD|241513 cd13359, PH_ELMO1_CED-12, Engulfment and cell motility protein 1
pleckstrin homology (PH) domain. DOCK2 (Dedicator of
cytokinesis 2), a hematopoietic cell-specific, atypical
GEF, controls lymphocyte migration through Rac
activation. A DOCK2-ELMO1 complex s necessary for
DOCK2-mediated Rac signaling. DOCK2 contains a SH3
domain at its N-terminus, followed by a lipid binding
DHR1 domain, and a Rac-binding DHR2 domain at its
C-terminus. ELMO1, a mammalian homolog of C. elegans
CED-12, contains the N-terminal RhoG-binding region, the
ELMO domain, the PH domain, and the C-terminal sequence
with three PxxP motifs. The C-terminal region of ELMO1,
including the Pro-rich sequence, binds the
SH3-containing region of DOCK2 forming a intermolecular
five-helix bundle along with the PH domain of ELMO1.
Autoinhibition of ELMO1 and DOCK2 is accomplished by the
interactions of the EID and EAD domains and SH3 and DHR2
domains, respectively. The interaction of DOCK2 and
ELMO1 mutually relieve their autoinhibition and results
in the activation of Rac1. The PH domain of ELMO1 does
not bind phosphoinositides due to the absence of key
binding residues. It more closely resembles the FERM
domain rather than other PH domains. 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 = 126
Score = 140 bits (355), Expect = 7e-44
Identities = 56/84 (66%), Positives = 66/84 (78%), Gaps = 4/84 (4%)
Query: 69 DLIQQQRLGYLVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVFQYGDCDEKSIP-QLDH 127
+LI+QQRL +LVEGT F KY++R + DKFWY RLSPNHKV YGDC+E + P L+
Sbjct: 1 ELIKQQRLNFLVEGTLFPKYNARRRK---DKFWYCRLSPNHKVLHYGDCEESAQPAPLES 57
Query: 128 LPNKLPVADIKALLVGKDCPHMKE 151
LP KLPVADIKAL+ GKDCPHMKE
Sbjct: 58 LPEKLPVADIKALVTGKDCPHMKE 81
>gnl|CDD|241279 cd01248, PH_PLC_ELMO1, Phospholipase C and Engulfment and cell
motility protein 1 pleckstrin homology domain. The
C-terminal region of ELMO1, the PH domain and Pro-rich
sequences, binds the SH3-containing region of DOCK2
forming a intermolecular five-helix bundle allowing for
DOCK mediated Rac1 activation. ELMO1, a mammalian
homolog of C. elegans CED-12, contains an N-terminal
RhoG-binding region, a ELMO domain, a PH domain, and a
C-terminal sequence with three PxxP motifs. Specificaly,
PLCs catalyze the cleavage of
phosphatidylinositol-4,5-bisphosphate (PIP2) and result
in the release of 1,2-diacylglycerol (DAG) and inositol
1,4,5-triphosphate (IP3). These products trigger the
activation of protein kinase C (PKC) and the release of
Ca2+ from intracellular stores. There are fourteen kinds
of mammalian phospholipase C which are are classified
into six isotypes (beta, gamma, delta, epsilon, zeta,
eta). All PLCs, except for PLCzeta, have a PH domain
which is for most part N-terminally located, though
lipid binding specificity is not conserved between them.
In addition PLC gamma contains a split PH domain within
its catalytic domain that is separated by 2 SH2 domains
and a single SH3 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 = 108
Score = 44.2 bits (105), Expect = 1e-06
Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 10/73 (13%)
Query: 79 LVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVFQYGDCDEKSIPQLDHLPNKLPVADIK 138
L +GT KY + K L P+ + +KS + + ++DIK
Sbjct: 1 LQQGTLLLKYREGSK----PKERTFYLDPDGTQITWESSKKKSEKK------SIDISDIK 50
Query: 139 ALLVGKDCPHMKE 151
+ GKD K
Sbjct: 51 EVRPGKDTKGFKR 63
>gnl|CDD|176488 cd08667, APC10-ZZEF1, APC10/DOC1-like domain of uncharacterized
Zinc finger ZZ-type and EF-hand domain-containing
protein 1 (ZZEF1) and homologs. This model represents
the APC10/DOC1-like domain present in the
uncharacterized Zinc finger ZZ-type and EF-hand
domain-containing protein 1 (ZZEF1) of Mus musculus.
Members of this family contain EF-hand, APC10, CUB, and
zinc finger ZZ-type domains. ZZEF1-like APC10 domains
are homologous to the APC10 subunit/DOC1 domains
present in E3 ubiquitin ligases, which mediate
substrate ubiquitination (or ubiquitylation), and are
components of the ubiquitin-26S proteasome pathway for
selective proteolytic degradation.
Length = 131
Score = 34.9 bits (80), Expect = 0.005
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 25 ANISRLTYSEITNLWQQERTSREEW-ESHAKPIVELKEL 62
A+I R+T E + WQ + ++R W KP V L+ L
Sbjct: 14 ADIDRMTDGETSTYWQSDGSARSHWIRLKMKPDVVLRHL 52
>gnl|CDD|197642 smart00306, HintN, Hint (Hedgehog/Intein) domain N-terminal region.
Hedgehog/Intein domain, N-terminal region. Domain has
been split to accommodate large insertions of
endonucleases.
Length = 100
Score = 31.5 bits (72), Expect = 0.059
Identities = 13/70 (18%), Positives = 23/70 (32%)
Query: 54 KPIVELKELITPEIVDLIQQQRLGYLVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVFQ 113
K I EL+E +D + V R K + I + + L+P+H +
Sbjct: 17 KKIEELEEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLV 76
Query: 114 YGDCDEKSIP 123
+
Sbjct: 77 RDGGKLVWVF 86
>gnl|CDD|238035 cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins
as well as proteins which contain inteins and undergo
protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In
protein splicing an intervening polypeptide sequence -
the intein - is excised from a protein, and the flanking
polypeptide sequences - the exteins - are joined by a
peptide bond. In addition to the autocatalytic splicing
domain, many inteins contain an inserted endonuclease
domain, which plays a role in spreading inteins.
Hedgehog proteins are a major class of intercellular
signaling molecules, which control inductive
interactions during animal development. The mature
signaling forms of hedgehog proteins are the N-terminal
fragments, which are covalently linked to cholesterol at
their C-termini. This modification is the result of an
autoprocessing step catalyzed by the C-terminal
fragments, which are aligned here.
Length = 136
Score = 30.3 bits (69), Expect = 0.18
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 54 KPIVELKELITPEIVDLIQQQRLGYLVEGTRFTKYSSRGQV--IILDKFWYVRLSPNHKV 111
K I EL E +++ L + +L + + + + + I + + L+P+H +
Sbjct: 16 KKIEELVEKKGDKVLALDETGKLVF-SKVLKVLRRDYEKKFYKIKTESGREITLTPDHLL 74
Query: 112 FQYGDCDEKSIPQLD 126
F D + K + D
Sbjct: 75 FVLEDGELKWVFASD 89
>gnl|CDD|199864 cd06240, M14-like_1_3, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 274
Score = 28.8 bits (65), Expect = 0.90
Identities = 27/101 (26%), Positives = 37/101 (36%), Gaps = 19/101 (18%)
Query: 6 REQITRALSSQP--ASLDKFRANISRLTYSEITNLWQQERTSREEWESHAKPIVELKELI 63
REQI A+SS A LD ++A + +L + Q + + E K IV I
Sbjct: 12 REQIMAAISSPENLAKLDHYKAILRKLADPRGLSEEQARKLAAE-----GKAIV----WI 62
Query: 64 T-----PEIVDLIQQQRLGY--LVEGTRFTKYSSRGQVIIL 97
T E L Y E + K VI+L
Sbjct: 63 TGGLHSTETGPPQMLMELAYRLASEESPEIK-RILDNVILL 102
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 27.8 bits (62), Expect = 2.5
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 10/73 (13%)
Query: 23 FRANISRLTYSEITNLWQQERTSREEWESHAKPIVELKELITPEIVDLIQQQRLGYLVEG 82
FRA R+ Y+E+ + +Q RE W A EL ++ + R +
Sbjct: 488 FRAIAERIGYAELETIRRQ----REAWARQAS-----LELARGDVEKALAAYRDHGHITI 538
Query: 83 TRFTKYSSRGQVI 95
T+ + QV+
Sbjct: 539 HD-TREEAIEQVV 550
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 27.8 bits (62), Expect = 2.7
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 28 SRLTYSEITNLWQQERTSREEWESHAKPIVELKEL 62
+RLTY+++ ++ Q ++ RE++ K + EL L
Sbjct: 379 ARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNL 413
>gnl|CDD|225674 COG3132, COG3132, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 26.7 bits (59), Expect = 4.8
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 42 ERTSREEWESHAKPIVELKELITPEIVDLIQQQRLGYLVEGTRFTKYSSR 91
++T+R+ P++ L E E +D ++++ L V G+R TKY R
Sbjct: 40 QKTNRD-------PVMNLSESEVQEQLDNLEKRHLVRTVSGSRVTKYEHR 82
>gnl|CDD|204573 pfam10990, DUF2809, Protein of unknown function (DUF2809). Some
members in this family of proteins are annotated as
yjgA however currently no function for the protein is
known.
Length = 91
Score = 25.6 bits (57), Expect = 5.0
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 57 VELKELITPEIVDLIQQQRLGYLVEGTRFT 86
+E +L + I+ LG LV G+ F
Sbjct: 50 IEFLQLYHLPWLLGIRNTTLGRLVLGSTFD 79
>gnl|CDD|201726 pfam01320, Colicin_Pyocin, Colicin immunity protein / pyocin
immunity protein.
Length = 85
Score = 25.3 bits (56), Expect = 5.8
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 22 KFRANISRLTYSE----ITNLWQQERTSREEWESHAKPIVELKELITPEIVDLI 71
+ + IS T SE + ++ E + EE + + ++ E P+ DLI
Sbjct: 2 ELKKKISDYTESEFLEFVKEIFNAELDTEEEHDDLVEHFEKITE--HPDGSDLI 53
>gnl|CDD|184416 PRK13955, mscL, large-conductance mechanosensitive channel;
Provisional.
Length = 130
Score = 25.9 bits (57), Expect = 7.0
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 43 RTSREEWESHAKPIVELKELITPEIVDLIQQQ 74
+ +EE + P +E + EI DL++QQ
Sbjct: 94 TSKKEEEKEEEIPEPTKEEELLGEIRDLLKQQ 125
>gnl|CDD|224879 COG1968, BacA, Undecaprenyl pyrophosphate phosphatase [Lipid
transport and metabolism].
Length = 270
Score = 26.0 bits (58), Expect = 7.8
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 66 EIVDLIQQQRLGYLVEG-TRFTKYSSRGQVIILDKFWYVRLSPNHKVF 112
++++L+Q LG +VEG T F SS G +I++ S K F
Sbjct: 2 DMMELLQAIILG-IVEGITEFLPISSTGHLILVGHLL--GFSDAGKSF 46
>gnl|CDD|188450 TIGR03935, fragilysin, fragilysin. Members of this family are
fragilysin, the Bacteroides fragilis enterotoxin. This
enzyme is a Zn metalloprotease. Three distinct subtypes
included in this family all are produced by
enterotoxigenic (by definition) strains of Bacteroides
fragilis [Cellular processes, Pathogenesis].
Length = 386
Score = 26.1 bits (57), Expect = 8.5
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 3/58 (5%)
Query: 59 LKELITPEIVDLIQQQRLGYLVEGTRFTKYSSRGQVIIL---DKFWYVRLSPNHKVFQ 113
+ I P + I Q + Y T+ S G+ IIL V +S + +
Sbjct: 21 VTTTIDPPVTASINLQSVDYTDLATQLNDVSDFGKTIILKDNGFNRQVHVSMDKRTKI 78
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 0.134 0.398
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,764,817
Number of extensions: 689172
Number of successful extensions: 606
Number of sequences better than 10.0: 1
Number of HSP's gapped: 602
Number of HSP's successfully gapped: 29
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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 (21.7 bits)
S2: 55 (24.9 bits)