RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9563
(192 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 = 90.4 bits (224), Expect = 3e-22
Identities = 44/127 (34%), Positives = 64/127 (50%), Gaps = 2/127 (1%)
Query: 20 DVQFVAAMAQPGGGRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYNAKRGFPIE 79
+ Q+V+ M P G I SRL+R FC+F P A+ I+++I H A
Sbjct: 148 NCQYVSCM-NPTAGSFTINSRLQRHFCVFALSFPGQDALSTIYNIILTQHL-ALGSVSAA 205
Query: 80 VRNLVKQLIPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSEKVL 139
++ L+ L + LPT KFHYVF+LRDLS I+QG++ + + S L
Sbjct: 206 LQKSSPPLVDAALALHQKIATTFLPTAIKFHYVFNLRDLSNIFQGLLFSSVECLKSPWDL 265
Query: 140 MLLWKHE 146
+ LW HE
Sbjct: 266 IRLWLHE 272
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 54.2 bits (130), Expect = 7e-09
Identities = 29/146 (19%), Positives = 53/146 (36%), Gaps = 6/146 (4%)
Query: 33 GRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYNAKRGFPIEVRNLVKQLIPLTR 92
GR R R+ C P ++ NI+ + G Y F + + L
Sbjct: 1625 GRVKYYERFIRKPVFVFCCYPELASLRNIYEAVLMGSYLCFDEFNRLSEETMSASVELYL 1684
Query: 93 LLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSEKV-LMLLWKHEVTRVF 151
T+ L + +Y + R+L+R + + G T ID+ V L++ W E R
Sbjct: 1685 SSKDKTKFFL-----QMNYGYKPRELTRSLRAIFGYAETRIDTPDVSLIIDWYCEAIREK 1739
Query: 152 SDRFTIMSDKHWFDDEVLNLVEQNLG 177
DR + ++ + + +
Sbjct: 1740 IDRLVQQKESSTSRQDLYDFGLRAIR 1765
>gnl|CDD|225612 COG3070, TfoX, Regulator of competence-specific genes
[Transcription].
Length = 121
Score = 28.1 bits (63), Expect = 1.7
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 158 MSDKHWFDDEVLNLVEQNLGVKYREMAGTDPVFVD 192
M+ + V L+ V YR M G ++VD
Sbjct: 1 MASSKMRLEFVQELLAGLGAVTYRSMFGGYGLYVD 35
>gnl|CDD|234005 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and
in alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1076
Score = 29.0 bits (65), Expect = 1.9
Identities = 29/104 (27%), Positives = 44/104 (42%), Gaps = 14/104 (13%)
Query: 71 NAKRGFPIEVRNLVKQ--LIPLTRLLWKSTRAQL-LPTPAKFHYVFSLRDLSRIWQGMVG 127
N F ++ N+++Q L PL L +R QL KF L++ Q +
Sbjct: 427 NHHGKFDLDRLNVLRQRILAPLEELF--KSRKQLGEKLLNKFSVFLKEIALTKNLQDLAT 484
Query: 128 TLSTVIDSEKVLMLLWKHEVTRVFSDRFTIMSDKHWFDDEVLNL 171
TLS V + EK + EV + F+D + F E L+L
Sbjct: 485 TLSEV-EQEK------QEEVWKTFTDILEQFA--TIFGQEKLSL 519
>gnl|CDD|220524 pfam10021, DUF2263, Uncharacterized protein conserved in bacteria
(DUF2263). This domain, found in various hypothetical
bacterial and eukaryotic proteins, has no known
function.
Length = 149
Score = 27.3 bits (61), Expect = 3.8
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 63 SVIGEGHYNAKRGFPIEVRNLVKQLIPLTRLLWKSTRAQLLPTPAKF 109
+++ G Y G PI+++ + I LTRL + L +
Sbjct: 6 AILAAGLYLTPDGPPIDIKYQLDAAIQLTRLYCPNLLESLPEIASSV 52
>gnl|CDD|99857 cd06103, ScCS-like, Saccharomyces cerevisiae (Sc) citrate synthase
(CS)-like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) with oxaloacetate (OAA) to form
citrate and coenzyme A (CoA), the first step in the
citric acid cycle (TCA or Krebs cycle). Some CS proteins
function as 2-methylcitrate synthase (2MCS). 2MCS
catalyzes the condensation of propionyl-coenzyme A
(PrCoA) and OAA to form 2-methylcitrate and CoA during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). This group includes three S.
cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a
nuclear-encoded mitochondrial CS with highly specificity
for AcCoA; in addition to having activity with AcCoA, it
plays a part in the construction of the TCA cycle
metabolon. Yeast cells deleted for Cit1 are
hyper-susceptible to apoptosis induced by heat and aging
stress. ScCit2 is a peroxisomal CS involved in the
glyoxylate cycle; in addition to having activity with
AcCoA, it may have activity with PrCoA. ScCit3 is a
mitochondrial CS and functions in the metabolism of
PrCoA; it is a dual specificity CS and 2MCS, having
similar catalytic efficiency with both AcCoA and PrCoA.
The pattern of expression of the ScCIT3 gene follows
that of the ScCIT1 gene and its expression is increased
in the presence of a ScCIT1 deletion. Included in this
group is the Tetrahymena 14 nm filament protein which
functions as a CS in mitochondria and as a cytoskeletal
component in cytoplasm and Geobacter sulfurreducens
(GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks
2MCS activity and is inhibited by ATP. In contrast to
eukaryotic and other prokaryotic CSs, GSuCIT is not
stimulated by K+ ions. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS.
Length = 426
Score = 26.9 bits (60), Expect = 7.8
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 145 HEVTRVFSDRFTIMSD---KHWFDDEVLNLVEQ 174
H V R RFT + KH DD + LV Q
Sbjct: 316 HAVLRKTDPRFTCQREFALKHLPDDPLFKLVAQ 348
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
0.325 0.140 0.431
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: 10,062,384
Number of extensions: 928189
Number of successful extensions: 918
Number of sequences better than 10.0: 1
Number of HSP's gapped: 914
Number of HSP's successfully gapped: 9
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.7 bits)