RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14229
(119 letters)
>gnl|CDD|218070 pfam04408, HA2, Helicase associated domain (HA2). This presumed
domain is about 90 amino acid residues in length. It is
found is a diverse set of RNA helicases. Its function
is unknown, however it seems likely to be involved in
nucleic acid binding.
Length = 91
Score = 71.1 bits (175), Expect = 1e-17
Identities = 29/54 (53%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 14 EMKCLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGD-ALNIVAASASGS 66
E+ LD + ELTPLG+ +A LPL+PRLGKMLLL + F C D L I A + S
Sbjct: 8 ELGALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTIAAMLSVPS 61
>gnl|CDD|214852 smart00847, HA2, Helicase associated domain (HA2) Add an
annotation. This presumed domain is about 90 amino acid
residues in length. It is found is a diverse set of RNA
helicases. Its function is unknown, however it seems
likely to be involved in nucleic acid binding.
Length = 82
Score = 65.4 bits (160), Expect = 2e-15
Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 16/98 (16%)
Query: 14 EMKCLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGDALNIVAASASGSNEIFVTE 73
E+ LD + LTPLG+ +A LPL+PRL KMLL + F C D + + + + E
Sbjct: 1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEI-LTIVAMLSVGDPRPKE 59
Query: 74 RRLSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVI 111
+R A+R FA SD + ++
Sbjct: 60 KR--------------EDADAARRRFADPE-SDHLTLL 82
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 65.8 bits (161), Expect = 9e-14
Identities = 31/104 (29%), Positives = 48/104 (46%), Gaps = 8/104 (7%)
Query: 17 CLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNC-GDALNIVAA-SASGSNEIFVTER 74
LD + +LTPLGK ++ LPL+PRL +MLL C G+A I + S F +
Sbjct: 447 ALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASMLSEQDRESDFSRDV 506
Query: 75 RLSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFNMFI 118
+L + + + L +R A D + ++ AF I
Sbjct: 507 KLRKQRTAQD------LLKRLKRRNAADPRGDHLLLLEAFPDRI 544
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 53.2 bits (128), Expect = 2e-09
Identities = 29/98 (29%), Positives = 49/98 (50%), Gaps = 14/98 (14%)
Query: 20 ANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGDALNIVAASASGSNEIFVTERRLSYA 79
A +LTP+G+ LA+LP++PRL +MLL C + I+A++ S + ER +
Sbjct: 469 AEPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQD---PRERPMEKQ 525
Query: 80 QRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFNMF 117
Q +++ A F R SDF++ +N +
Sbjct: 526 QAADQ----------AHARFKDPR-SDFLSRVNLWRHI 552
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 51.2 bits (123), Expect = 1e-08
Identities = 33/108 (30%), Positives = 54/108 (50%), Gaps = 14/108 (12%)
Query: 8 DELTPLEMKCLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGDALNIVAASASGSN 67
+EL + + +LTPLG+ LA+LP++PRL +M+L C + I+ ++ S +
Sbjct: 466 EELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQD 525
Query: 68 EIFVTERRLSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFN 115
ER + Q S+E R FA + SDF+A +N +N
Sbjct: 526 P---RERPMDKQQASDE----------KHRRFA-DKESDFLAFVNLWN 559
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 34.0 bits (78), Expect = 0.013
Identities = 15/30 (50%), Positives = 16/30 (53%)
Query: 18 LDANDELTPLGKILARLPLEPRLGKMLLLG 47
LDA LT GK +A L PRL MLL
Sbjct: 396 LDAQGRLTAHGKAMAALGCHPRLAAMLLSA 425
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 31.8 bits (73), Expect = 0.060
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 18 LDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGDALNIVAA 61
LD LT G+ +A L +PRL ML+ +A AA
Sbjct: 399 LDGQGRLTARGRKMAALGNDPRLAAMLVAAK--EDDEAALATAA 440
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 28.6 bits (63), Expect = 0.90
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 53 GDALNIVAASASGSNEIFVTERRLSYAQRSNEIFVTE 89
G A++ AASASG + + V RR++ A R E E
Sbjct: 516 GAAVDPTAASASGDHPVLVGARRIARATRELEAAAKE 552
>gnl|CDD|212568 cd11695, DHR2_DOCK_C, Dock Homology Region 2, a GEF domain, of
Class C Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided into
four classes (A-D) based on sequence similarity and
domain architecture; class C, also called the
Zizimin-related (Zir) subfamily, includes Dock6, 7 and
8. Class C DOCKs have been shown to have GEF activity
for both Rac and Cdc42. Dock6 regulates neurite
outgrowth. Dock7 plays a critical roles in the early
stages of axon formation, neuronal polarity, and
myelination. Dock8 regulates T and B cell numbers and
functions, and plays essential roles in humoral immune
responses and the proper formation of B cell
immunological synapses. All DOCKs contain two homology
domains: the DHR-1 (Dock homology region-1), also called
CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and
DHR-2 (also called CZH2 or Docker). The DHR-1 domain
binds phosphatidylinositol-3,4,5-triphosphate. This
alignment model represents the DHR-2 domain of Class C
Docks, which contains the catalytic GEF activity for Rac
and Cdc42.
Length = 368
Score = 27.6 bits (62), Expect = 1.6
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 10 LTPLEMKCLDANDELTPLGKILARLPLEPRLGKMLLLGSI 49
LTP+E+ D + L + P +P++ +M+L GSI
Sbjct: 252 LTPIEVAIEDVQKKTRELAAATTQEPPDPKMLQMVLQGSI 291
>gnl|CDD|193529 cd05652, M20_ArgE_DapE_like_fungal, M20 Peptidases with similarity
to acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze
analogous reactions and share a common activator, the
metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad
range of substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly fungal, and have been inferred by
homology as being related to both ArgE and DapE.
Length = 335
Score = 26.8 bits (60), Expect = 2.8
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 20 ANDELTP-LGKILAR-LPLEPRLGKMLLLGSIFNCGDALNIVAASASGS 66
A ++L L K+ LP LG L + G A N++ A A S
Sbjct: 184 AIEKLLEALAKLRDADLPSSELLGPTTLNIGLIEGGVAANVIPAHAEAS 232
>gnl|CDD|236097 PRK07788, PRK07788, acyl-CoA synthetase; Validated.
Length = 549
Score = 26.0 bits (58), Expect = 6.2
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 24 LTPLGKILARLPLEPRLGKMLLLGSIF 50
L PL +L+R+P LL +F
Sbjct: 233 LAPLAGLLSRVPF-RAGETTLLPAPMF 258
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
0.323 0.137 0.389
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,067,871
Number of extensions: 530878
Number of successful extensions: 389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 21
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)