RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus Liberibacter asiaticus str. psy62] (240 letters) >gnl|CDD|30948 COG0603, COG0603, Predicted PP-loop superfamily ATPase [General function prediction only]. Length = 222 Score = 223 bits (569), Expect = 4e-59 Identities = 93/234 (39%), Positives = 128/234 (54%), Gaps = 29/234 (12%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A++L SGG DS+TCL+WA V L+FDYGQR++ ELE K++ + Sbjct: 5 AVVLLSGGLDSTTCLAWAKKEGYEVHALTFDYGQRHRKELEAA----KELAKK------- 53 Query: 71 LG-EDHILPLAILGDISHSSLTKNVAMKIQDNN----LPNTFVPGRNIIFLVFAATLAYR 125 LG HI+ + +LG+I S+LT + + +P TFVP RN+IFL AA A Sbjct: 54 LGVPHHIIDVDLLGEIGGSALTDDSIDVPKYEFAEEEIPATFVPARNLIFLSIAAAYAEA 113 Query: 126 LGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHV-TVHTPLMWLKKYETWKLA 184 LG I+IGV E D+SGYPDCR + I A+ A+NLG E V +H PLM L K E KLA Sbjct: 114 LGADAIIIGVNEEDFSGYPDCRPEFIEALNEALNLGTEKGVRIIHAPLMELTKAEIVKLA 173 Query: 185 QDIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEFKEKY 238 ++G + LE + +CY G G C C +C LR++ + E + Sbjct: 174 DELG------VPLELTWSCYNG------GEGDHCGECESCVLRERAFKEAGLED 215 >gnl|CDD|73293 cd01995, ExsB, ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown. Length = 169 Score = 200 bits (509), Expect = 4e-52 Identities = 81/223 (36%), Positives = 107/223 (47%), Gaps = 55/223 (24%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 A++L SGG DS+TCL+WA V LSFDYGQR+ E E K I E Sbjct: 2 AVVLLSGGLDSTTCLAWAKKEGYEVHALSFDYGQRHAKEEEAA----KLIAEK------- 50 Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130 LG P+T+VP RN+IFL AA A LG Sbjct: 51 -----------LG--------------------PSTYVPARNLIFLSIAAAYAEALGAEA 79 Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190 I+IGV DYSGYPDCR + I A+ A+NLG E+ + +H PL+ L K E +L ++G Sbjct: 80 IIIGVNAEDYSGYPDCRPEFIEAMNKALNLGTENGIKIHAPLIDLSKAEIVRLGGELG-- 137 Query: 191 DLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWME 233 + LE + +CY G C C +C LR++ + E Sbjct: 138 ----VPLELTWSCYNGGE-------KHCGECDSCLLRKRAFEE 169 >gnl|CDD|73292 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group... Length = 103 Score = 37.1 bits (85), Expect = 0.004 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 1/76 (1%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 L+ FSGG+DSS + +V ++ D+G ++E + ++ E + Sbjct: 1 VLVAFSGGKDSSVAAALLKKLGYQVIAVTVDHGISPRLEDAKEIA-KEAREEAAKRIAKE 59 Query: 71 LGEDHILPLAILGDIS 86 G + I D++ Sbjct: 60 KGAETIATGTRRDDVA 75 >gnl|CDD|109807 pfam00764, Arginosuc_synth, Arginosuccinate synthase. This family contains a PP-loop motif. Length = 389 Score = 36.2 bits (84), Expect = 0.008 Identities = 12/32 (37%), Positives = 20/32 (62%) Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQ 44 L +SGG D+S C+ W +++ V ++ D GQ Sbjct: 2 LAYSGGLDTSVCIPWLKEKYYEVIAVAVDVGQ 33 >gnl|CDD|30186 cd01999, Argininosuccinate_Synthase, Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity. Length = 385 Score = 33.2 bits (76), Expect = 0.071 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%) Query: 12 LLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELECRLCVRKKIVEL 63 +L +SGG D+S L W ++ V ++ D GQ + + +K ++L Sbjct: 2 VLAYSGGLDTSVILKWLKEKGGYEVIAVTADVGQPEEEIEA----IEEKALKL 50 >gnl|CDD|30486 COG0137, ArgG, Argininosuccinate synthase [Amino acid transport and metabolism]. Length = 403 Score = 30.9 bits (70), Expect = 0.29 Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%) Query: 12 LLLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQ 44 +L +SGG D+S + W ++ V ++ D GQ Sbjct: 8 VLAYSGGLDTSVAIKWLKEKGGAEVIAVTADVGQ 41 >gnl|CDD|30386 COG0037, MesJ, Predicted ATPase of the PP-loop superfamily implicated in cell cycle control [Cell division and chromosome partitioning]. Length = 298 Score = 30.6 bits (68), Expect = 0.35 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 2/48 (4%) Query: 12 LLLFSGGQDSSTCLSWALDRFDR--VETLSFDYGQRNKVELECRLCVR 57 L+ SGG+DS L + R VE + D+G R + E L + Sbjct: 25 LVAVSGGKDSLALLHLLKELGRRIEVEAVHVDHGLRGYSDQEAELVEK 72 >gnl|CDD|145913 pfam03016, Exostosin, Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia. EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities. The nature of the defect in heparan sulphate biosynthesis in HME is unclear. Length = 289 Score = 30.5 bits (69), Expect = 0.39 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 10/65 (15%) Query: 59 KIVELMPKWKDSLGEDHILPLAILGDISHSSLTKN--------VAMKIQDNNLPNTFVPG 110 K + +P W S G DHI+ + S+ + + + F PG Sbjct: 86 KWLSSLPYWNRSGGRDHIIVNS--HPFGGSAFDRLPALNNPTILVVLAGGGFSERQFRPG 143 Query: 111 RNIIF 115 +++ Sbjct: 144 KDVPL 148 >gnl|CDD|144677 pfam01171, ATP_bind_3, PP-loop family. This family of proteins belongs to the PP-loop superfamily. Length = 182 Score = 27.6 bits (62), Expect = 2.9 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 16/75 (21%) Query: 12 LLLFSGGQDSSTCLSWALDRF-----DRVETLSFDYGQRNKVELE----CRLCVRKKI-- 60 L+ SGG D S L + L + + D+G R + + E LC + I Sbjct: 3 LVAVSGGPD-SMALLYLLKKLKPKFGIDLTAAHVDHGLREESDREAQFVKELCRQLNIPL 61 Query: 61 ----VELMPKWKDSL 71 V++ K +L Sbjct: 62 EVLRVDVAKKSGLNL 76 >gnl|CDD|146412 pfam03759, PRONE, PRONE (Plant-specific Rop nucleotide exchanger). This is a functional guanine exchange factor (GEF) of plant Rho GTPase. Length = 360 Score = 27.7 bits (62), Expect = 3.1 Identities = 10/33 (30%), Positives = 17/33 (51%) Query: 34 RVETLSFDYGQRNKVELECRLCVRKKIVELMPK 66 R+E L+ + + E++ L V IVE +P Sbjct: 51 RLEPLAPEKKAMWRREMDWLLSVTDYIVEFVPS 83 >gnl|CDD|30167 cd01712, ThiI, ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide.. Length = 177 Score = 27.5 bits (61), Expect = 3.8 Identities = 41/183 (22%), Positives = 60/183 (32%), Gaps = 34/183 (18%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70 AL L SGG DS + R V+ L F+ G + R+K+ +L K Sbjct: 2 ALALLSGGIDSPVAAWLLMKRGIEVDALHFNSGPFTSEK------AREKVEDLARKLAR- 54 Query: 71 LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130 H L + I + + A LA LG Sbjct: 55 YSPGHKLVVIIFTFFVQKEIYGYG-----KEKYRCILC---KRMMYRIAEKLAEELGADA 106 Query: 131 IVIGVCETDYSGYPDCRHDTI--RAIETAINLGMESHVT---VHTPLMWLKKYETWKLAQ 185 IV G +++ A +T NL + S T + PL+ K E +A+ Sbjct: 107 IVTG--------------ESLGQVASQTLENLLVISSGTDLPILRPLIGFDKEEIIGIAR 152 Query: 186 DIG 188 IG Sbjct: 153 RIG 155 >gnl|CDD|73291 cd01984, AANH_like, Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide.. Length = 86 Score = 26.9 bits (59), Expect = 4.4 Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 1/38 (2%) Query: 11 ALLLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQRNK 47 L+ SGG DSS L A E ++ + Sbjct: 1 ILVALSGGLDSSVLLHLAKRLKSGGPEVVALVVVAFVR 38 >gnl|CDD|176542 cd08600, GDPD_EcGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli periplasmic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), GlpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the E. coli glp operon codes for a periplasmic phosphodiesterase GlpQ, which is the prototype of this family. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for the enzymatic activity of GlpQ. This family also includes a surface-exposed lipoprotein, protein D (HPD), from Haemophilus influenza Type b and nontypeable strains, which shows very high sequence similarity with E. coli GlpQ. HPD has been characterized as a human immunoglobulin D-binding protein with glycerophosphodiester phosphodiesterase activity. It can hydrolyze phosphatidylcholine from host membranes to produce free choline on the lipopolysaccharides on the surface of pathogenic bacteria. Length = 318 Score = 27.0 bits (60), Expect = 5.0 Identities = 9/37 (24%), Positives = 20/37 (54%), Gaps = 2/37 (5%) Query: 35 VETLSFDYGQRNKVELECRLCVRKKIVELMP--KWKD 69 ++T + +R K EL ++ + K+V+L+ W + Sbjct: 177 LQTFDPNELKRIKNELLPKMGMDLKLVQLIAYTDWGE 213 >gnl|CDD|31794 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]. Length = 269 Score = 26.8 bits (59), Expect = 5.1 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 7/70 (10%) Query: 1 MNDIIKKAPSALLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELE------CR 53 + IK+ ++ FSGG DSS A + D V ++ D + E+E Sbjct: 10 LKKAIKEKKKVVVAFSGGVDSSLLAKLAKEALGDNVVAVTVDSPYIPRREIEEAKNIAKE 69 Query: 54 LCVRKKIVEL 63 + +R + +++ Sbjct: 70 IGIRHEFIKM 79 >gnl|CDD|32300 COG2117, COG2117, Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]. Length = 198 Score = 26.8 bits (59), Expect = 5.3 Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 2/32 (6%) Query: 13 LLFSGGQDSSTCLSWALDRFD-RVETLSFDYG 43 +LFSGG+DSS + LD+ VE ++ ++G Sbjct: 5 VLFSGGKDSSLA-ALILDKLGYEVELVTVNFG 35 >gnl|CDD|32285 COG2102, COG2102, Predicted ATPases of PP-loop superfamily [General function prediction only]. Length = 223 Score = 26.3 bits (58), Expect = 7.2 Identities = 11/25 (44%), Positives = 14/25 (56%) Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38 L+SGG+DS L AL+ V L Sbjct: 6 LYSGGKDSFYALYLALEEGHEVVYL 30 >gnl|CDD|30178 cd01991, Asn_Synthase_B_C, The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. The three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase .. Length = 269 Score = 26.2 bits (57), Expect = 7.2 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%) Query: 13 LLFSGGQDSSTCLSWALDRF--DRVETLSFDYGQRNKVELE 51 +L SGG DSS ++ R + V+T S +G E E Sbjct: 20 VLLSGGLDSSL-VAALAARLLPEPVKTFSIGFGFEGSDERE 59 >gnl|CDD|145198 pfam01902, ATP_bind_4, ATP-binding region. This family of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.In some members of this family, this domain is associated with pfam01042. Length = 219 Score = 26.3 bits (58), Expect = 7.3 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%) Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38 L+SGG+DS+ L WAL + V L Sbjct: 6 LYSGGKDSNYALYWALKEIE-VPYL 29 >gnl|CDD|38147 KOG2936, KOG2936, KOG2936, Uncharacterized conserved protein [Function unknown]. Length = 301 Score = 26.4 bits (58), Expect = 7.3 Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 8/59 (13%) Query: 21 SSTCLSWALDRFDR----VETLSFD----YGQRNKVELECRLCVRKKIVELMPKWKDSL 71 C W+ + ++ V +LS + + ++ E R+ RK + + L Sbjct: 15 EKNCSPWSKEYLNQKLSGVSSLSGPFSCKITEVSSIDGEARVNQRKGKLISLFDLSIEL 73 >gnl|CDD|147621 pfam05544, Pro_racemase, Proline racemase. This family consists of proline racemase (EC 5.1.1.4) proteins which catalyse the interconversion of L- and D-proline in bacteria. This family also contains several similar eukaryotic proteins including a sequence with B-cell mitogenic properties which has been characterized as a co-factor-independent proline racemase. Length = 325 Score = 26.1 bits (58), Expect = 8.4 Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 7/38 (18%) Query: 141 SGYPD-CRHDTIRAIETAINLGM------ESHVTVHTP 171 SGY C H+TI + + G+ E+ + + TP Sbjct: 77 SGYLPMCGHNTIGVVTVLLETGIVPPQEPETRLNLETP 114 >gnl|CDD|144131 pfam00420, Oxidored_q2, NADH-ubiquinone/plastoquinone oxidoreductase chain 4L. Length = 96 Score = 26.3 bits (59), Expect = 8.4 Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%) Query: 112 NIIFLVFAATLAYRLG----ITNIVIGVCET 138 ++ ++F+ LA L +T +V CE Sbjct: 39 FLLLVLFSLLLADPLPQALPLTLLVFAACEA 69 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 0.322 0.138 0.438 Gapped Lambda K H 0.267 0.0736 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,022,433 Number of extensions: 153143 Number of successful extensions: 385 Number of sequences better than 10.0: 1 Number of HSP's gapped: 378 Number of HSP's successfully gapped: 25 Length of query: 240 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 149 Effective length of database: 4,297,318 Effective search space: 640300382 Effective search space used: 640300382 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 (21.9 bits) S2: 56 (25.3 bits)