RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780669|ref|YP_003065082.1| 2-dehydro-3-deoxyphosphooctonate aldolase [Candidatus Liberibacter asiaticus str. psy62] (301 letters) >gnl|CDD|32704 COG2877, KdsA, 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]. Length = 279 Score = 416 bits (1070), Expect = e-117 Identities = 156/265 (58%), Positives = 196/265 (73%) Query: 35 NQVTFSNEQRFVLIAGPCQIESHDHAFMIAEKLYAICQSLNIGLVYKSSFDKANRSSLAG 94 + N+ FVLIAGPC IES D A IAE L + + L I V+KSSFDKANRSS+ Sbjct: 8 GDIVIGNDLPFVLIAGPCVIESRDLALEIAEHLKELTEKLGIPYVFKSSFDKANRSSIHS 67 Query: 95 KRGVGLKKGREIFRDLKKKYGFPILTDVHTEQQCEAIADSVDILQIPALLCRQTDLLTAA 154 RG GL++G +I +++K+++G PILTDVH Q + +A+ VD+LQIPA LCRQTDLL AA Sbjct: 68 YRGPGLEEGLKILQEVKEEFGVPILTDVHEPSQAQPVAEVVDVLQIPAFLCRQTDLLVAA 127 Query: 155 AQTGRVINVKKGQFLSPWEMHNILQKLHAHGAKDVLFCERGTSFGYNTLVTDMRSIPIMT 214 A+TG V+NVKKGQFL+PW+M NI++K G V+ CERG SFGYN LV DMRS+PIM Sbjct: 128 AKTGAVVNVKKGQFLAPWDMKNIVEKFLETGNNKVILCERGASFGYNNLVVDMRSLPIMK 187 Query: 215 SMGVPVIFDASHSVQQPGIHGNCSGGERQYIVPLAKAAVAIGIAGIFLETHQDPDNAPSD 274 G PVIFDA+HSVQQPG G SGG R+++ LA+AAVA+G+AG+F+ETH DPDNA SD Sbjct: 188 EFGAPVIFDATHSVQQPGGQGGSSGGRREFVPTLARAAVAVGVAGLFIETHPDPDNAKSD 247 Query: 275 GPNMINIKDLPKLLSQLLAIDKIIK 299 GPNM+ + L LL QL AID ++K Sbjct: 248 GPNMLPLDKLEALLEQLKAIDDLVK 272 >gnl|CDD|144404 pfam00793, DAHP_synth_1, DAHP synthetase I family. Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. Length = 271 Score = 263 bits (674), Expect = 5e-71 Identities = 83/271 (30%), Positives = 135/271 (49%), Gaps = 12/271 (4%) Query: 34 KNQVTFSNEQRFVLIAGPCQIESHDHAFMIAEKLYAICQSLNIGLVYKSSFDKANRSSLA 93 ++ + + R ++IAGPC IES + A AE+L + L + ++ ++ F+K S + Sbjct: 7 ESDILIGEDDRLLVIAGPCSIESPEAAMEYAERLKELGAKLKLPIIMRAYFEKPRTSPV- 65 Query: 94 GKRGVGLKKGREIFRDLKKKYGFPILTDVHTEQQCEAIADSVDILQIPALLCRQTDLLTA 153 G +G+G G +I +K G PI T+V + +A+ DI QI A DLL A Sbjct: 66 GFKGLGNDPGLKILFRVKDGLGLPIATEVLDPIDPQYVAEVADIGQIGARTTESQDLLEA 125 Query: 154 AAQTGRVINVKKGQFLSPWEMHNILQKLHAHGA-KDVLFCERGTSFGY--NTLVTDMRSI 210 A+ T + + +K+G L+ EM + G + CERG GY N L D+ ++ Sbjct: 126 ASGTSKPVGLKRGTDLAIDEMLAAAEYHLFLGNTPGNILCERGIRGGYGPNRLTLDVSAV 185 Query: 211 PIMTSMG--VPVIFDASHSVQQPGIHGNCSGGERQYIVPLAKAAVAIGIAGIFLETHQDP 268 PI+ +PV+ D SHS + GG + + PLA+AA+A+G G+ +E H +P Sbjct: 186 PILKEETGHLPVMVDPSHSNGRKD------GGRQPLVPPLARAAIAVGADGLMIEVHPNP 239 Query: 269 DNAPSDGPNMINIKDLPKLLSQLLAIDKIIK 299 NA SDGP + L + +++ Sbjct: 240 GNALSDGPQQLKYGVSETDACILWELTELVL 270 >gnl|CDD|32703 COG2876, AroA, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]. Length = 286 Score = 131 bits (331), Expect = 2e-31 Identities = 75/258 (29%), Positives = 124/258 (48%), Gaps = 25/258 (9%) Query: 45 FVLIAGPCQIESHDHAFMIAEKLYAICQSLNIGLVYKSSFDKANRSSLAGKRGVGLKKGR 104 +IAGPC +ES + AE + A G +K R+S +G+G + G Sbjct: 46 LRVIAGPCSVESEEQVRETAESVKAAGAKALRGGAFKP------RTSPYSFQGLGEE-GL 98 Query: 105 EIFRDLKKKYGFPILTDVHTEQQCEAIADSVDILQIPALLCRQTDLLTAAAQTGRVINVK 164 ++ + + G P++T+V + EA A+ DILQ+ A + LL + + + +K Sbjct: 99 KLLKRAADETGLPVVTEVMDVRDVEAAAEYADILQVGARNMQNFALLKEVGRQNKPVLLK 158 Query: 165 KGQFLSPWEMHNILQKLHAHGAKDVLFCERG----TSFGYNTLVTDMRSIPIMTSMG-VP 219 +G + E N + + +HG +V+ CERG NTL D+ ++PI+ +P Sbjct: 159 RGLSATIEEWLNAAEYILSHGNGNVILCERGIRTFEKATRNTL--DISAVPILKQETHLP 216 Query: 220 VIFDASHSVQQPGIHGNCSGGERQYIVPLAKAAVAIGIAGIFLETHQDPDNAPSDGPNMI 279 VI D SH+ G R + PLAKAA+A G G+ +E H DP+ A SD + Sbjct: 217 VIVDPSHA-----------TGRRDLVEPLAKAAIAAGADGLMIEVHPDPEKALSDAKQQL 265 Query: 280 NIKDLPKLLSQLLAIDKI 297 ++ +L+ +L A+ Sbjct: 266 TPEEFEELVKELRALADA 283 >gnl|CDD|32361 COG2178, COG2178, Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]. Length = 204 Score = 29.1 bits (65), Expect = 1.7 Identities = 30/150 (20%), Positives = 56/150 (37%), Gaps = 35/150 (23%) Query: 55 ESHDHAFMIAEKLYAICQSLNIGLVYKSSFDKANRSSLAGKRGVGLKKGREIFRDLKKKY 114 ++ + A ++ ++ + I L+++ F++A + LKK E LK+ Sbjct: 17 KAREEALKLSREIVRLSGEA-IFLLHRGDFEEAEKK---------LKKASEAVEKLKRLL 66 Query: 115 -GFPIL---TDVHTEQQ--CEAIA-------------DSVDILQIPALLCRQTDLLTAAA 155 GFP L V T Q EA + + + I +L L A Sbjct: 67 AGFPELYFAGFVTTALQEYVEATLLYSILKDGRLPSPEELGVPPIAYIL----GLADAVG 122 Query: 156 QTGR--VINVKKGQFLSPWEMHNILQKLHA 183 + R + ++KG F ++KL+ Sbjct: 123 ELRRHVLELLRKGSFEEAERFLKFMEKLYE 152 >gnl|CDD|31066 COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]. Length = 351 Score = 28.3 bits (63), Expect = 2.8 Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 15/94 (15%) Query: 42 EQRFVLIAGPCQIESHDHAFMIAEKLYAICQSL--NIGLVYKSSFDK----------ANR 89 + R +++ GPC I + A A +L A+ + L + +V + F+K N Sbjct: 51 DDRLLVVIGPCSIHDPEAALEYARRLKALREELKDRLEIVMRVYFEKPRTTVGWKGLIND 110 Query: 90 SSLAGKRGV--GLKKGREIFRDLKKKYGFPILTD 121 L G + GL+ R++ D+ + G P T+ Sbjct: 111 PDLDGSFDINKGLRIARKLLLDVNEL-GLPTATE 143 >gnl|CDD|145282 pfam02016, Peptidase_S66, LD-carboxypeptidase. Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein. This family corresponds to Merops family S66. Length = 281 Score = 27.5 bits (62), Expect = 4.3 Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 3/28 (10%) Query: 104 REIFRDLKKKYGFPILTDV---HTEQQC 128 E+ R++ G P+L + HT Sbjct: 243 EEVLREVLGDLGIPVLYGLPFGHTPPNL 270 >gnl|CDD|145083 pfam01740, STAS, STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. Length = 106 Score = 27.6 bits (62), Expect = 4.6 Identities = 5/36 (13%), Positives = 17/36 (47%) Query: 199 GYNTLVTDMRSIPIMTSMGVPVIFDASHSVQQPGIH 234 ++ D+ +P + S G+ + + +++ G+ Sbjct: 39 EIRHVILDLSGVPFIDSSGLGALLELYKELRRRGVE 74 >gnl|CDD|36479 KOG1265, KOG1265, KOG1265, Phospholipase C [Lipid transport and metabolism]. Length = 1189 Score = 26.9 bits (59), Expect = 6.3 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%) Query: 78 LVYKSSFDKANRSSLAGKRGVGLK--KGREIFRDLKKKYGFPILTDVHTEQQCEAIADS 134 L KSS + + L+G R V L G+ + +GF + T++ + EAIA++ Sbjct: 338 LGGKSSVEMYRQVLLSGCRCVELDCWDGKGEDEEPVITHGFTMTTEIFFKDVLEAIAET 396 >gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein. LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide bond that links the dibasic amino acids to C-terminal D-amino acids. The physiological substrates of LD-carboxypeptidase are tetrapeptide fragments (such as UDP-MurNAc-tetrapeptides) that are produced when bacterial cell walls are degraded; they contain an L-configured residue (L-lysine or meso-diaminopimelic acid residue) as the penultimate residue and D-alanine as the ultimate residue. A possible role of LD-carboxypeptidase is in peptidoglycan recycling whereby the resulting tripeptide (precursor for murein synthesis) can be reconverted into peptidoglycan by attachment of preformed D-Ala-D-Ala dipeptides. Some enzymes possessing LD-carboxypeptidase activity also act as LD-transpeptidase by replacing the terminal D-Ala with another D-amino acid. MccF contributes to self-immunity towards microcin C7 (MccC7), a ribosomally encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. Its possible biological role is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that MccF is involved in microcin degradation or sequestration in the periplasm. Length = 282 Score = 27.1 bits (61), Expect = 6.8 Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 3/28 (10%) Query: 104 REIFRDLKKKYGFPILTDV---HTEQQC 128 E+ +++ G P+L + HT Sbjct: 246 EEVLKEVLGDLGIPVLYGLPIGHTPPNL 273 >gnl|CDD|107209 cd06448, L-Ser-dehyd, Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- , D-serine, or L-threonine to pyruvate/ketobutyrate and ammonia.. Length = 316 Score = 26.9 bits (60), Expect = 8.1 Identities = 24/111 (21%), Positives = 40/111 (36%), Gaps = 21/111 (18%) Query: 202 TLVTDMRSIPIMTSMGVPVIFD-ASHSVQQPGIHG-------------NCSGGERQYIVP 247 LVT + + TS+G + A Q+ I + ER + P Sbjct: 206 KLVTLPKITSVATSLGAKTVSSQALEYAQEHNIKSEVVSDRDAVQACLRFADDERILVEP 265 Query: 248 LAKAAVAIGIAGIFLETHQDPDNAPSD-------GPNMINIKDLPKLLSQL 291 AA+A+ +G L+ + P D G + I ++ L + QL Sbjct: 266 ACGAALAVVYSGKILDLQLEVLLTPLDNVVVVVCGGSNITLEQLKEYKKQL 316 >gnl|CDD|173802 cd07476, Peptidases_S8_thiazoline_oxidase_subtilisin-like_protease, Peptidase S8 family domain in Thiazoline oxidase/subtilisin-like proteases. Thiazoline oxidase/subtilisin-like protease is produced by the symbiotic bacteria Prochloron spp. that inhabit didemnid family ascidians. The cyclic peptides of the patellamide class found in didemnid extracts are now known to be synthesized by the Prochloron spp. The prepatellamide is heterocyclized to form thiazole and oxazoline rings and the peptide is cleaved to form the two cyclic patellamides A and C. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Length = 267 Score = 26.5 bits (59), Expect = 9.2 Identities = 18/61 (29%), Positives = 21/61 (34%), Gaps = 9/61 (14%) Query: 129 EAIADSVDILQIPALL-----CRQTDL----LTAAAQTGRVINVKKGQFLSPWEMHNILQ 179 E IA L IP C Q DL A Q +IN+ G+ E IL Sbjct: 69 EGIAPLCRGLNIPIFAEDRRGCSQLDLARAINLALEQGAHIINISGGRLTQTGEADPILA 128 Query: 180 K 180 Sbjct: 129 N 129 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 0.321 0.137 0.404 Gapped Lambda K H 0.267 0.0812 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,595,902 Number of extensions: 185646 Number of successful extensions: 458 Number of sequences better than 10.0: 1 Number of HSP's gapped: 450 Number of HSP's successfully gapped: 14 Length of query: 301 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 208 Effective length of database: 4,254,100 Effective search space: 884852800 Effective search space used: 884852800 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: 57 (25.6 bits)