RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780801|ref|YP_003065214.1| hypothetical protein CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62] (222 letters) >gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family. Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. Length = 229 Score = 134 bits (339), Expect = 1e-32 Identities = 78/223 (34%), Positives = 109/223 (48%), Gaps = 10/223 (4%) Query: 6 KLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKW 65 L+ K KIE + R V L+AVSK + I++A GQ F EN +QE +K Sbjct: 7 YLEDIKTKIEAANTHVNRNPSKVKLLAVSKTKPASAIQIAYDAGQRAFGENYVQELVEKI 66 Query: 66 IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQ 125 L ++ FIG LQSNK +V FD + T+ K A L+ + K L V +Q Sbjct: 67 KLLEDLGKLEWHFIGPLQSNKDRLVVENFDWVHTIDSLKIAKKLNEQREKLQPPLNVLLQ 126 Query: 126 VNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH----------FY 175 +N E KSGI P + + I + L + GLM I + + F+ Sbjct: 127 INISDEESKSGIQPEELLELAIQIEELKHLKLRGLMTIGAPTDSHEDQEENFRFMKLLFW 186 Query: 176 LLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218 + + + + LSMGM+ DFE AIA+GAT VRIG+ IFG R Sbjct: 187 QIKQDSPFGTIDTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229 >gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed. Length = 363 Score = 35.9 bits (84), Expect = 0.008 Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 5/59 (8%) Query: 106 ASLLSLEMIKQSRF---LPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLM 161 SL LE ++++ L V+++++TG + + G+ P + + + + +EG+ Sbjct: 103 HSLEQLEALEKAELGKPLKVHLKIDTG--MHRLGVRPEEAEAALERLLACPNVRLEGIF 159 >gnl|CDD|129583 TIGR00492, alr, alanine racemase. This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism. Length = 367 Score = 31.2 bits (71), Expect = 0.19 Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 3/74 (4%) Query: 89 EIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVIL 148 +I++ +D+ TV + L ++K+ + L V+++++TG + + G+ P++ FV Sbjct: 89 KILAAWDLTTTVHSVEQLQALEEALLKEPKRLKVHLKIDTG--MNRLGVKPDEAALFVQK 146 Query: 149 CRQKYQ-LNVEGLM 161 RQ + L +EG+ Sbjct: 147 LRQLKKFLELEGIF 160 >gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase; Validated. Length = 479 Score = 30.6 bits (70), Expect = 0.29 Identities = 11/18 (61%), Positives = 15/18 (83%) Query: 195 RDFELAIASGATSVRIGS 212 RD LA+A+GA++V IGS Sbjct: 343 RDVALALAAGASNVMIGS 360 >gnl|CDD|184518 PRK14119, gpmA, phosphoglyceromutase; Provisional. Length = 228 Score = 30.2 bits (68), Expect = 0.39 Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQS-NK 86 L E+K++WIP+ K W + R G LQ NK Sbjct: 69 LTESKQQWIPVYKSWRLNERHYGGLQGLNK 98 >gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice. Length = 1341 Score = 29.8 bits (67), Expect = 0.52 Identities = 28/145 (19%), Positives = 60/145 (41%), Gaps = 17/145 (11%) Query: 1 MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60 M K + ++ ++ +A++ + + + + V K I + C + + +E E Sbjct: 57 MEQEEKESLVRELLKMVHHVAEKNRYERVVDVLLRYVHQKIIPATMLCEEGLISEKLFYE 116 Query: 61 AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIV-----SLFDVIETVSREKTASLLSLEMI- 114 + WI +++ + + IG + V EI+ +VS E LL++E + Sbjct: 117 CSRFWI---EKFKLIRKVIGGVDYKGVREIMKYILEKALRFPYSVSPEIVPQLLAVEEVI 173 Query: 115 -----KQSRFLPVYIQVNTGYEIQK 134 + + LP Y +N EI + Sbjct: 174 LHIFDRNANLLPAYFTLN---EIMR 195 >gnl|CDD|130370 TIGR01303, IMP_DH_rel_1, IMP dehydrogenase family protein. This model represents a family of proteins, often annotated as a putative IMP dehydrogenase, related to IMP dehydrogenase and GMP reductase and restricted to the high GC Gram-positive bacteria. All species in which a member is found so far (Corynebacterium glutamicum, Mycobacterium tuberculosis, Streptomyces coelicolor, etc.) also have IMP dehydrogenase as described by TIGRFAMs entry TIGR01302. Length = 475 Score = 29.9 bits (67), Expect = 0.52 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 13/72 (18%) Query: 159 GLMCIPPAM-GNPKPHFYLLSEIARECKLTKLSMGM--------TRDFELAIASGATSVR 209 G MC M G +P F + E A E + KL + RD LA+A+GA++V Sbjct: 298 GAMCTTRMMTGVGRPQFSAVLECAAEAR--KLGGHVWADGGVRHPRDVALALAAGASNVM 355 Query: 210 IGSGIFG--ERP 219 +GS G E P Sbjct: 356 VGSWFAGTYESP 367 >gnl|CDD|184519 PRK14120, gpmA, phosphoglyceromutase; Provisional. Length = 249 Score = 30.0 bits (68), Expect = 0.56 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83 L A + WIP+R+ W + R G+LQ Sbjct: 72 LDAADRLWIPVRRSWRLNERHYGALQ 97 >gnl|CDD|130325 TIGR01258, pgm_1, phosphoglycerate mutase, BPG-dependent, family 1. Most members of this family are phosphoglycerate mutase (EC 5.4.2.1). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC 5.4.2.4). This model is designated as a subfamily for this reason. The second and third paralogs in S. cerevisiae are somewhat divergent and apparently inactive (see PUBMED:9544241) but are also part of this subfamily phylogenetically. Length = 245 Score = 29.7 bits (67), Expect = 0.64 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83 L E + WIP++K W + R G+LQ Sbjct: 68 LDELDQLWIPVKKSWRLNERHYGALQ 93 >gnl|CDD|180614 PRK06546, PRK06546, pyruvate dehydrogenase; Provisional. Length = 578 Score = 28.0 bits (63), Expect = 2.1 Identities = 12/19 (63%), Positives = 13/19 (68%) Query: 199 LAIASGATSVRIGSGIFGE 217 LAIAS S +IGSG F E Sbjct: 96 LAIASHIPSAQIGSGFFQE 114 >gnl|CDD|185556 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain; Provisional. Length = 494 Score = 28.0 bits (63), Expect = 2.2 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%) Query: 62 KKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLP 121 KKKWI L K D ++ L + V + L ++ S+ + L+ +K+ + Sbjct: 112 KKKWIKLNKG-DKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKKRKL-- 168 Query: 122 VYIQVNTGYEIQK 134 ++ + + K Sbjct: 169 ATLEKIKYFVVTK 181 >gnl|CDD|172606 PRK14116, gpmA, phosphoglyceromutase; Provisional. Length = 228 Score = 28.0 bits (62), Expect = 2.2 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83 L+E+ + WIP K W + R G+LQ Sbjct: 69 LEESDQLWIPETKTWRLNERHYGALQ 94 >gnl|CDD|148843 pfam07467, BLIP, Beta-lactamase inhibitor (BLIP). The structure of BLIP reveals two structural domains, which form a polar, concave surface that docks onto a predominantly polar, convex protrusion on beta-lactamase. The ability of BLIP to adapt to a variety of class A beta-lactamases is thought to be due to flexibility between these two domains. Length = 183 Score = 27.6 bits (61), Expect = 2.5 Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%) Query: 185 KLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218 K T++ GMTR IA + G G FG+ Sbjct: 35 KYTQIQFGMTRQQVWDIAGAEQNCETG-GSFGDS 67 >gnl|CDD|172608 PRK14118, gpmA, phosphoglyceromutase; Provisional. Length = 227 Score = 27.6 bits (61), Expect = 2.6 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83 L+E+ + WIP K W + R G+LQ Sbjct: 68 LEESNQLWIPQVKNWRLNERHYGALQ 93 >gnl|CDD|178757 PLN03218, PLN03218, maturation of RBCL 1; Provisional. Length = 1060 Score = 27.2 bits (60), Expect = 3.5 Identities = 46/200 (23%), Positives = 73/200 (36%), Gaps = 42/200 (21%) Query: 31 VAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPL--------------RKEWDVQL 76 V ++ S + VA G + A LQ+A+K+ I L K W L Sbjct: 645 VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKAL 704 Query: 77 RFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSG 136 ++S K+ VS + + T E +LE++ E+++ G Sbjct: 705 ELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLS---------------EMKRLG 749 Query: 137 IMPNQTKDFVIL--CRQKYQLNVEGLMCIPPAMGNP-KPHFYLLSEIARECKLTKLSMGM 193 + PN ++L +K +V GL + A + KP+ + I C Sbjct: 750 LCPNTITYSILLVASERKDDADV-GLDLLSQAKEDGIKPNLVMCRCITGLCL-------- 800 Query: 194 TRDFELAIASGATSVRIGSG 213 R FE A A G V SG Sbjct: 801 -RRFEKACALGEPVVSFDSG 819 >gnl|CDD|132434 TIGR03393, indolpyr_decarb, indolepyruvate decarboxylase, Erwinia family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. Within the larger family, this model represents a clade of bacterial indolepyruvate decarboxylases, part of a pathway for biosynthesis of the plant hormone indole-3-acetic acid. Typically, these species interact with plants, as pathogens or as beneficial, root-associated bacteria. Length = 539 Score = 26.4 bits (58), Expect = 5.5 Identities = 11/36 (30%), Positives = 19/36 (52%) Query: 80 GSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIK 115 + +VSE L DV+E V+ + SL+ + + K Sbjct: 493 PQSECWRVSEAEQLADVLEKVAAHERLSLIEVVLPK 528 >gnl|CDD|148471 pfam06872, EspG, EspG protein. This family consists of several EspG like proteins from Citrobacter rodentium and Escherichia coli. EspG is secreted by the type III secretory system and is translocated into host epithelial cells. EspG is homologous with Shigella flexneri protein VirA and can rescue invasion in a Shigella virA mutant, indicating that these proteins are functionally equivalent in Shigella. EspG plays an accessory but as yet undefined role in EPEC virulence that may involve intestinal colonisation. Length = 336 Score = 26.4 bits (58), Expect = 6.8 Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 3/67 (4%) Query: 114 IKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH 173 I QS +Y+ +TG I PN R Y++ G C + Sbjct: 269 ISQSSGGAIYVTSHTGVLIMAPEDRPNGVGMLTN--RTSYEVP-AGTKCEIEELVRAIKP 325 Query: 174 FYLLSEI 180 Y SE Sbjct: 326 RYASSET 332 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.320 0.134 0.378 Gapped Lambda K H 0.267 0.0725 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,354,946 Number of extensions: 197507 Number of successful extensions: 360 Number of sequences better than 10.0: 1 Number of HSP's gapped: 358 Number of HSP's successfully gapped: 26 Length of query: 222 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 132 Effective length of database: 4,049,753 Effective search space: 534567396 Effective search space used: 534567396 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 (21.8 bits) S2: 55 (25.0 bits)