RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781149|ref|YP_003065562.1| replicative DNA helicase
[Candidatus Liberibacter asiaticus str. psy62]
(266 letters)
>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 99.5 bits (248), Expect = 8e-22
Identities = 67/266 (25%), Positives = 108/266 (40%), Gaps = 27/266 (10%)
Query: 5 IISHFESQTKISFSTYLNNLLTLASSISSEV-INAARRVVQQWA--R--ITISQEAKALA 59
+ + ++ N L TL S I+ ++V++ A R I E L
Sbjct: 63 VSEELSDRGLLTRIGGANYLATLIDRTPSAANIDYYAKIVKEKALLRELIEAGNEIVNLG 122
Query: 60 LHTSDPTCNTATLIRKSMQSFEDIISEVHLTKNQCTGSSCISIANAATTAMKSAEQQKKE 119
+ + + + E I +V KN + I + M E + +
Sbjct: 123 YESEKDL------DEEVLDAAEKKIFDVAERKNS---EDFVHIGDLLKETMDEIEARFEN 173
Query: 120 GENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSL 178
G + G +D + G + +LI++ ARP MGKT AL+ AL+ A G VA FSL
Sbjct: 174 GGLIGVPTGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSL 233
Query: 179 EMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPS 238
EM E+L R LS S S I L G ++ +++ +L + P+ IDD P
Sbjct: 234 EMSEEQLVMRLLS-----SESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDTPG 288
Query: 239 PGIMEFVHVANGLRNKHTKMVQLYRL 264
I E +R+K ++ + L
Sbjct: 289 LTITE-------IRSKARRLKLKHNL 307
>gnl|CDD|29985 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis..
Length = 242
Score = 98.3 bits (245), Expect = 2e-21
Identities = 50/125 (40%), Positives = 74/125 (59%), Gaps = 8/125 (6%)
Query: 133 DHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLGARALS 191
D+L GG+Q +LI+I ARPSMGKT FAL+ A ++A G V FFSLEM +E+L R L+
Sbjct: 4 DNLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQRLLA 63
Query: 192 NLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRPSPGIMEFVHVANG 250
+ S I L G ++ E + R+++ I E L++ P+ IDD S + + A
Sbjct: 64 SE-----SGISLSKLRTGSLSDEDWERLAEAIGE-LKELPIYIDDSSSLTVSDIRSRARR 117
Query: 251 LRNKH 255
L+ +H
Sbjct: 118 LKKEH 122
>gnl|CDD|146436 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerization of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 186
Score = 96.9 bits (242), Expect = 5e-21
Identities = 51/138 (36%), Positives = 72/138 (52%), Gaps = 13/138 (9%)
Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186
G +D L GG+Q +LI+I ARPSMGKT FAL+ A + A+ V FFSLEM E+L
Sbjct: 5 GFTDLDQLTGGLQKGDLIIIAARPSMGKTAFALNIARNAALKQDKPVLFFSLEMSAEQLA 64
Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPSPGIMEFVH 246
R LS+ SRI L G+++ E + +L + PL IDD P + E
Sbjct: 65 ERLLSSE-----SRISSSKLRSGQLSDEDWERLAEAAGELSEAPLYIDDTPGLSLSE--- 116
Query: 247 VANGLRNKHTKMVQLYRL 264
LR + ++ + + L
Sbjct: 117 ----LRAQARRLKREHGL 130
>gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands..
Length = 271
Score = 40.3 bits (94), Expect = 5e-04
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 114 EQQKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHG 172
E+ ++ N ++ W ++ L G++ ELI++ A +GKTTF AL + G
Sbjct: 2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQHGVR 61
Query: 173 VAFFSLEMDREKLGARALS 191
V SLE + R L
Sbjct: 62 VGTISLEEPVVRTARRLLG 80
>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 40.5 bits (94), Expect = 5e-04
Identities = 19/53 (35%), Positives = 25/53 (47%)
Query: 133 DHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKL 185
+ L GG+ ++LI P GKT FAL A G V + S E E+L
Sbjct: 14 EILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEEL 66
>gnl|CDD|31265 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 39.4 bits (92), Expect = 0.001
Identities = 36/136 (26%), Positives = 61/136 (44%), Gaps = 14/136 (10%)
Query: 95 TGSSCISIANAATTAMKSAEQQK-------KEGENPDIKWGLQSVDHLMGGVQLR-ELIL 146
+S N + +E K + E P I G++ +D ++GG + +IL
Sbjct: 38 LAASPGGAPNKRRSGKAGSEPSKVLKLSDIELEEEPRISTGIEELDRVLGGGLVPGSVIL 97
Query: 147 IGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLLYPSSSR--IPYL 204
IG P +GK+T L A +A G V + S E +++ RA L P+++ +
Sbjct: 98 IGGDPGIGKSTLLLQVAARLAKRGK-VLYVSGEESLQQIKLRA-DRLGLPTNNLYLLAET 155
Query: 205 NL--IRGEINQEQYRI 218
NL I E+ QE+ +
Sbjct: 156 NLEDIIAELEQEKPDL 171
>gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 38.7 bits (90), Expect = 0.002
Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 9/102 (8%)
Query: 100 ISIANAATTAMKSAEQQKKEGENPDIKWGLQSVDHLMG-GVQLRELILIGARPSMGKTTF 158
+ + A+ E+++ + I G ++D +G G+ + I S GKTT
Sbjct: 20 KAFGKGSIMALGGDERRE---DIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTL 76
Query: 159 ALSTALHMAMSGHGVAFF----SLEMDR-EKLGARALSNLLY 195
AL + G AF +L+ +R ++LG L NLL
Sbjct: 77 ALQLVANAQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLV 118
>gnl|CDD|29987 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules..
Length = 372
Score = 38.7 bits (90), Expect = 0.002
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 118 KEGENPDIKWGLQSVDH-LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFF 176
+ E I G++ +D L GG+ +ILIG P +GK+T L A +A G V +
Sbjct: 57 EAEEEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYV 116
Query: 177 SLEMDREKLGARA 189
S E E++ RA
Sbjct: 117 SGEESPEQIKLRA 129
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion..
Length = 165
Score = 35.1 bits (80), Expect = 0.021
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 1/93 (1%)
Query: 144 LILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLLYPSSSRIPY 203
LIL+ GKTT AL AL++A G V + +E + E+L R + L + +
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60
Query: 204 LNLIRGEINQEQYRISQGI-CEKLQDFPLIIDD 235
+ + + E+ D +I+D+
Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDE 93
>gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear..
Length = 218
Score = 34.1 bits (78), Expect = 0.042
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 128 GLQSVDHLMGG-VQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
G + +D L+GG V+ + + P GKT A+ A+ A G VA+ E
Sbjct: 4 GCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE 56
>gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB..
Length = 226
Score = 32.9 bits (75), Expect = 0.100
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 125 IKWGLQSVDHLM-GGVQLRELILIGARPSMGKTTFALSTALHMAMSGH 171
I G +++D L+ GG+ + I GKT L A+ + G
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGE 48
>gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea..
Length = 187
Score = 32.2 bits (73), Expect = 0.15
Identities = 16/48 (33%), Positives = 20/48 (41%)
Query: 144 LILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALS 191
L+ P GKTTFAL G + +LE E+L A S
Sbjct: 1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAES 48
>gnl|CDD|37584 KOG2373, KOG2373, KOG2373, Predicted mitochondrial DNA helicase
twinkle [Replication, recombination and repair].
Length = 514
Score = 31.9 bits (72), Expect = 0.20
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 132 VDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALS 191
++ + G + EL ++ GKTTF +L + G + S E+ ++L L
Sbjct: 263 LNKYLKGHRPGELTVLTGPTGSGKTTFLSEYSLDLFTQGVNTLWGSFEIPNKRLAHWMLV 322
Query: 192 NLL-YPSSSRI 201
Y R+
Sbjct: 323 QYAGYRLLDRL 333
>gnl|CDD|30201 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK)..
Length = 179
Score = 30.6 bits (69), Expect = 0.41
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 144 LILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
++ I GKTTFA + + ++G G SL+
Sbjct: 1 VVGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLD 36
>gnl|CDD|35071 COG5512, COG5512, Zn-ribbon-containing, possibly RNA-binding
protein and truncated derivatives [General function
prediction only].
Length = 194
Score = 29.6 bits (66), Expect = 0.88
Identities = 26/135 (19%), Positives = 38/135 (28%), Gaps = 33/135 (24%)
Query: 23 NLLTLASSISSEVINAARRVVQQWARITISQEAKALALHTSDPTCNTATLIRKSMQSFED 82
LL L + + A V+ QW + +A HT
Sbjct: 82 VLLELLNKQGWSPLVALGFVLSQWREEVGWRPCPVIAEHTRPEPLR-------------- 127
Query: 83 IISEVHLTKNQCTGSSCISIANAATTAMKSAEQQK----KEGENP--DIKWGLQSVDHLM 136
+ +C A A T + A+ + G NP +K G
Sbjct: 128 ---------DGVLSVTCDLTAWATTLRRRQAQLLACIAERVGNNPGESLKIGGPRAP--- 175
Query: 137 GGVQLRELILIGARP 151
QL L + G RP
Sbjct: 176 -SWQLGPLHIAGRRP 189
>gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence..
Length = 217
Score = 28.7 bits (64), Expect = 1.6
Identities = 25/108 (23%), Positives = 38/108 (35%), Gaps = 14/108 (12%)
Query: 144 LILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLLYPSSSRIPY 203
+I + +GKTT A +TA+ +A G V S + A LS+ P+ S
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTD------PAHNLSDKGLPNLSDA-- 52
Query: 204 LNLIRGEINQEQYRIS------QGICEKLQDFPLIIDDRPSPGIMEFV 245
+ EI YR + ++ PGI E
Sbjct: 53 FIVEDPEIAPNLYREEVDATRRVERAWGGEGGLMLELAAALPGIEELA 100
>gnl|CDD|73214 cd00550, ArsA_ATPase, Oxyanion-translocating ATPase (ArsA). This
ATPase is involved in transport of arsenite, antimonite
or other oxyanions across biological membranes in all
three kingdoms of life. ArsA contains a highly
conserved AAA motif present in the AAA+ ATPase
superfamily associated with a variety of cellular
activities. To form a functional ATP-driven pump, ArsA
interacts with the permease ArsB, which is a
channel-forming integral membrane protein. One of the
most interesting features of ArsA is the allosteric
activation by its transport substrates. A divalent
cation, typically Mg2+, is required for its enzymatic
activity..
Length = 254
Score = 28.7 bits (64), Expect = 1.8
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 143 ELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
I G + +GKTT + +TA+ +A G V S +
Sbjct: 1 RYIFFGGKGGVGKTTISAATAVRLAEQGKKVLLVSTD 37
>gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 28.4 bits (63), Expect = 1.9
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 143 ELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
++ + +GKTT A +TA+ +A SG V S +
Sbjct: 3 RIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTD 39
>gnl|CDD|36647 KOG1434, KOG1434, KOG1434, Meiotic recombination protein Dmc1
[Energy production and conversion, Replication,
recombination and repair].
Length = 335
Score = 28.4 bits (63), Expect = 2.0
Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 12/104 (11%)
Query: 83 IISEVHLTKNQCTGSSCISIANAATTAMKSAEQQKKEGENPDIKWGLQSVDHLMGG-VQL 141
ISEV + K + + SI++ TA++ EQ+K I G ++D ++GG +
Sbjct: 60 GISEVKVDKLKEAANK--SISHGFCTALELLEQRKTV---GSITTGSSALDDILGGGIPS 114
Query: 142 RELILIGARPSMGKT----TFALSTALHMAMSGHG--VAFFSLE 179
+ I GKT T ++ L M G G F E
Sbjct: 115 MSITEIFGEFRCGKTQLSHTLCVTVQLPREMGGVGGKAIFIDTE 158
>gnl|CDD|34146 COG4468, GalT, Galactose-1-phosphate uridyltransferase
[Carbohydrate transport and metabolism].
Length = 503
Score = 28.0 bits (62), Expect = 2.5
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 23 NLLTLASSISSEVINAARRVVQQWARITISQEAKALALHTSDPTCNTATLI-RKSMQSFE 81
++L L S E+I A +++++W S E + +T D NT T I RK +E
Sbjct: 310 SVLRLQSKNKVELIKLADKILKKWR--EYSDEEVQILAYTGDTPHNTITPIARKRGGLYE 367
Query: 82 -DII 84
D++
Sbjct: 368 LDLV 371
>gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 ..
Length = 235
Score = 28.2 bits (63), Expect = 2.7
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 125 IKWGLQSVDHLM-GGVQLRELILIGARPSMGKTTFALSTALH 165
+ G +++D L+ GG++ + I GKT A+
Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVT 42
>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 27.5 bits (61), Expect = 3.5
Identities = 14/31 (45%), Positives = 16/31 (51%)
Query: 143 ELILIGARPSMGKTTFALSTALHMAMSGHGV 173
E ILI P GK+TFA + A A G V
Sbjct: 264 EGILIAGAPGAGKSTFAQALAEFYASQGKIV 294
>gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 27.6 bits (62), Expect = 3.7
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 132 VDHLMGG--VQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179
+ L G ++ E +L+ P +GKT A + +G+ V F
Sbjct: 35 IAELAGLDWIEQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTP 84
>gnl|CDD|72878 cd04702, ASRGL1_like, ASRGL1_like domains, a subfamily of the
L-Asparaginase type 2-like enzymes. The wider family
includes Glycosylasparaginase, Taspase 1 and
L-Asparaginase type 2 enzymes. The proenzymes undergo
autoproteolytic cleavage before a threonine to generate
alpha and beta subunits. The threonine becomes the
N-terminal residue of the beta subunit and is the
catalytic residue. ASRGL1, or asparaginase-like 1, has
been cloned from mammalian testis cDNA libraries. It has
been identified as a sperm antigen that may induce the
production of autoantibodies following obstruction of
the male reproductive tract, e.g. vasectomy..
Length = 261
Score = 27.5 bits (61), Expect = 4.3
Identities = 23/103 (22%), Positives = 37/103 (35%), Gaps = 19/103 (18%)
Query: 101 SIANAATTAMKSAEQQKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTT--- 157
S +A A++ E ++P G SV + G V++ I+ G G
Sbjct: 41 SALDAVEAAVRVME------DDPIFNAGYGSVLNEDGEVEMDASIMDGKTLRAGAVAAVR 94
Query: 158 ----------FALSTALHMAMSGHGVAFFSLEMDREKLGARAL 190
+ H+ + G G F+ EM +GA AL
Sbjct: 95 DIMNPISLARKVMEKTDHVLLVGEGAERFAREMGLGTVGAVAL 137
>gnl|CDD|176163 cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 5. The LTTRs are acting as
both auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis showed
that the CrgA-like regulators form a subclass of the
LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 202
Score = 27.0 bits (61), Expect = 4.9
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 13/53 (24%)
Query: 163 ALHMAMSGHGVAFFSLEMDREKLGARALS-------------NLLYPSSSRIP 202
L A+ G G+A+ ++ E L + L L YPS R+P
Sbjct: 140 MLDAALDGLGIAYLFEDLVAEHLASGRLVRVLEDWSPPFPGGYLYYPSRRRVP 192
>gnl|CDD|32701 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 27.1 bits (60), Expect = 5.2
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 118 KEGENPDIKWGLQSVD-HLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFF 176
E IK G +D L GG+ + LILI GK+ + A M+G+ V +
Sbjct: 3 VEELKKIIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYV 62
Query: 177 SLEM 180
S E+
Sbjct: 63 STEL 66
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 27.0 bits (59), Expect = 5.9
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 144 LILIGARPSMGKTTFALSTALHMAMSGHGVA 174
+I++ + +GKTT A + A +A G V
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVL 31
>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
(PDR1-15), ABC superfamily [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 1391
Score = 26.8 bits (59), Expect = 6.3
Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 2/91 (2%)
Query: 73 IRKSMQSFEDIISEVHLTKNQCTGSSCISIANAATTAMKSAEQQKKEGENPDIKWGLQSV 132
+R+ + E EV + + E + K +Q +
Sbjct: 74 LRERIDRVELPTIEVRFS-ALGVEADVTYGPTLVNILSNPLESILRML-GKRKKKKIQIL 131
Query: 133 DHLMGGVQLRELILIGARPSMGKTTFALSTA 163
+ G ++ E+ L+ P GKTT + A
Sbjct: 132 KDISGIIKPGEMTLVLGPPGSGKTTLLKALA 162
>gnl|CDD|111283 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam
family represents a conserved domain, which is sometimes
repeated, in an anion-transporting ATPase. The ATPase is
involved in the removal of arsenate, antimonite, and
arsenate from the cell.
Length = 304
Score = 26.9 bits (60), Expect = 6.4
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 145 ILIGARPSMGKTTFALSTALHMAMSGHGV 173
I G + +GKTT + +TA+ ++ G V
Sbjct: 4 IFFGGKGGVGKTTVSCATAVRLSEQGKKV 32
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.130 0.364
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,932,330
Number of extensions: 141504
Number of successful extensions: 399
Number of sequences better than 10.0: 1
Number of HSP's gapped: 393
Number of HSP's successfully gapped: 38
Length of query: 266
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 174
Effective length of database: 4,275,709
Effective search space: 743973366
Effective search space used: 743973366
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.2 bits)