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)