RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780402|ref|YP_003064815.1| 3-deoxy-D-manno-octulosonic-acid transferase [Candidatus Liberibacter asiaticus str. psy62] (440 letters) >gnl|CDD|180233 PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed. Length = 425 Score = 459 bits (1183), Expect = e-130 Identities = 165/424 (38%), Positives = 244/424 (57%), Gaps = 6/424 (1%) Query: 8 ILLGIYRWGGIFFMPFLSVSLSLYRVFNRERGRKFGERLGYPT-ALRPIGPLIWFHASSV 66 +L +Y +P + + L L + +++GER G+ P GPLIWFHA SV Sbjct: 1 MLRLLYTALLYLALPLILLRLLLRSRKAPKYRKRWGERFGFRKPNPPPKGPLIWFHAVSV 60 Query: 67 GETMALIGLIPAIRSR--HVNVLLTTMTATSAKVARKYLGQYAIHQYAPLDIQPAVSRFL 124 GET A I LI A+R R + +L+TTMT T ++ A+ G H+Y P D+ AV RFL Sbjct: 61 GETRAAIPLIRALRKRYPDLPILVTTMTPTGSERAQALFGDDVEHRYLPYDLPGAVRRFL 120 Query: 125 KYWKPDCMILSESDIWPLTVFELSKQRIPQVLVNARMSRRSFKNWKTVLSFSKKIFSQFS 184 ++W+P +I+ E+++WP + EL ++ IP VL NAR+S RSFK ++ F + +F Sbjct: 121 RFWRPKLVIIMETELWPNLIAELKRRGIPLVLANARLSERSFKRYQKFKRFYRLLFKNID 180 Query: 185 LVIVQSERYFRRYKELGAQK-LIVSGNLKIDTESLPCDKELLSLYQESIAG-RYTWAAIS 242 LV+ QSE R+ LGA+ + V+GNLK D E P + + +A R W A S Sbjct: 181 LVLAQSEEDAERFLALGAKNEVTVTGNLKFDIEVPPELAARAATLRRQLAPNRPVWIAAS 240 Query: 243 TFEGEEDKAVYVH-NFIKCRTDVLTIIVPRHPRRCDAIERRLIAKGLKVARRSRGDVINA 301 T EGEE+ + H +K ++L I+VPRHP R +E L GL RRS+G+ +A Sbjct: 241 THEGEEELVLDAHRALLKQFPNLLLILVPRHPERFKEVEELLKKAGLSYVRRSQGEPPSA 300 Query: 302 EVDIFLGDTIGEMGFYLRMTEIAFIGRSFCASGGQNPLEAAMLGCAILSGPNVENFRDIY 361 + D+ LGDT+GE+G + +IAF+G S GG NPLE A G ++SGP+ NF++I+ Sbjct: 301 DTDVLLGDTMGELGLLYAIADIAFVGGSLVKRGGHNPLEPAAFGVPVISGPHTFNFKEIF 360 Query: 362 RRMVSSGAVRIVEEVGTLADMVYSLLSEPTIRYEMINAAINEVKKMQGPLKITLRSLDSY 421 R++ +GA VE+ LA V LL++P R A + +K+ QG L+ TL+ L+ Y Sbjct: 361 ERLLQAGAAIQVEDAEDLAKAVTYLLTDPDARQAYGEAGVAFLKQNQGALQRTLQLLEPY 420 Query: 422 VNPL 425 + PL Sbjct: 421 LPPL 424 >gnl|CDD|179146 PRK00865, PRK00865, glutamate racemase; Provisional. Length = 261 Score = 32.8 bits (76), Expect = 0.18 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 13/48 (27%) Query: 73 IGLIPAI-------RSRHVNVLLTTMTATSAKVARKYLGQYAIHQYAP 113 +G++PAI R+ + VL T T SA I ++AP Sbjct: 95 VGIVPAIKPAAALTRNGRIGVLATPGTVKSAAYRD------LIARFAP 136 >gnl|CDD|132039 TIGR02994, ectoine_eutE, ectoine utilization protein EutE. Members of this family, part of the succinylglutamate desuccinylase / aspartoacylase family (pfam04952), belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it the operon is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. Length = 325 Score = 30.5 bits (69), Expect = 0.88 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%) Query: 90 TMTATSAKVARKYLGQYAIHQYAPL-DIQPAVSRFLKYWKPDCMILSESD 138 T +A + K+A++ + H +++ A + +L DC I +E D Sbjct: 214 TASARTIKIAKRGVRNVLRHAGILKGELEIAPTIWLDMPSDDCFIFAEDD 263 >gnl|CDD|180935 PRK07333, PRK07333, 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional. Length = 403 Score = 30.3 bits (69), Expect = 1.1 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 9/48 (18%) Query: 33 VFNRERGRKFGERLGYPTALRPIG-----PLIWFHASS-VGETMALIG 74 VF E ++FG RLG L+ +G PL A S V AL+G Sbjct: 242 VFEAELEQRFGHRLG---ELKVLGKRRAFPLGLTLARSFVAPRFALVG 286 >gnl|CDD|180314 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed. Length = 455 Score = 29.8 bits (68), Expect = 1.5 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 9/58 (15%) Query: 239 AAISTFEGEEDKAVYVHNFIKCRTDVLTII---VPRHPRRCDAIERRLIAKGLKVARR 293 +A+ST G E + + IK +I P+ P I L +G+ VARR Sbjct: 384 SAVSTDGGGEASSTAIRALIK------KLIAAENPKKPLSDSKIAELLKEQGIDVARR 435 >gnl|CDD|181663 PRK09126, PRK09126, hypothetical protein; Provisional. Length = 392 Score = 29.1 bits (66), Expect = 2.5 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 9/47 (19%) Query: 34 FNRERGRKFGERLGYPTALRPIG-----PLIWFHASS-VGETMALIG 74 F E +F RLG A+R + PL+ +A V + ALIG Sbjct: 243 FAAEVTARFKGRLG---AMRLVSSRHAYPLVAVYAHRFVAKRFALIG 286 >gnl|CDD|185627 PTZ00448, PTZ00448, hypothetical protein; Provisional. Length = 373 Score = 28.8 bits (64), Expect = 2.7 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 14/100 (14%) Query: 142 LTVFELSKQRIPQVLVNARMSRRSFKNWKTVLSFSKKI--FSQFSLVIVQSE-------- 191 L F++ K+RIP + A+M + + + +KK+ F+ F + + Sbjct: 155 LKAFDILKKRIPDQIERAKMMLKLSVDIVNKQNITKKLNEFNVFPISSEEKHNTYSITFL 214 Query: 192 ---RYFRRYKELGAQKLIVSGNLK-IDTESLPCDKELLSL 227 RY+R +L + L++ N+K ID S + E + L Sbjct: 215 CEPRYYREIDQLDCKLLLLDSNVKTIDKNSNQDNVEAIQL 254 >gnl|CDD|132132 TIGR03088, stp2, sugar transferase, PEP-CTERM/EpsH1 system associated. Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate. Length = 374 Score = 28.5 bits (64), Expect = 3.8 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%) Query: 72 LIGLIPAIRSRHVNVLLTTMTATSAKVARKYLGQYAIHQYAPLD--IQPAVSRFLKYWKP 129 LI +PA R RH V LT ++A ++ R + YA+H+ D + P + R L+ +P Sbjct: 23 LINHLPADRYRHAVVALTEVSAFRKRIQRPDVAFYALHKQPGKDVAVYPQLYRLLRQLRP 82 Query: 130 D 130 D Sbjct: 83 D 83 >gnl|CDD|132616 TIGR03577, EF_0830, conserved hypothetical protein EF_0830/AHA_3911. Members of this family of small (about 120 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. Length = 115 Score = 27.9 bits (62), Expect = 5.0 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 8/59 (13%) Query: 284 IAKGLKVARRSRGDVINAEVDIFLGDTIGEMGFYLRMTEIAFIGRSFCASGGQNPLEAA 342 +AKG++ A + D+ LGD + E A +G SFC SGG + A Sbjct: 15 VAKGVEAAGGRAVVIPGMAADMKLGDVMK--------QENADLGISFCGSGGAGAITAQ 65 >gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. Length = 654 Score = 27.8 bits (62), Expect = 5.7 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 6/76 (7%) Query: 159 ARMSRRSFKNWKTVLSFSKKIFSQFSLVIVQSERY--FRRYKELGAQKLI-VSGNLKIDT 215 AR + R +W K+ ++FS I R+ F R + G LI +S + Sbjct: 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHIS---TLHN 608 Query: 216 ESLPCDKELLSLYQES 231 + D+E ++L + Sbjct: 609 DYYVFDQEKMALIGKG 624 >gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated. Length = 562 Score = 27.8 bits (62), Expect = 6.1 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 11/54 (20%) Query: 356 NFRDIYRRMVSSGAVR--IVEEVGTLADMVYSLLSEPTIRYEMINAAINEVKKM 407 N + +++ V+ IV EV DM+ P ++ +INA + VKKM Sbjct: 131 NMAHLAEKVLPKTGVKHVIVTEVA---DML------PPLKRLLINAVVKHVKKM 175 >gnl|CDD|184461 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional. Length = 241 Score = 27.6 bits (62), Expect = 6.2 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 17/60 (28%) Query: 339 LEAAMLGCA-----------ILSGPNVENFRDIYRR----MVSSGAVRIVEEVGTLADMV 383 L++A GC+ L+GPN+E R++ R +V+SG V ++++ LA++V Sbjct: 155 LDSA--GCSRYVVTDVTKDGTLTGPNLELLREVCARTDAPVVASGGVSSLDDLRALAELV 212 >gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism associated alcohol dehydrogenase. This clade of zinc-binding alcohol dehydrogenases (members of pfam00107) are repeatedly associated with genes proposed to be involved with the catabolism of phosphonate compounds. Length = 280 Score = 27.5 bits (61), Expect = 7.7 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%) Query: 97 KVARKYLGQYAIHQYAPLDIQPAVSRFLK 125 +V R++L +H Y P + AV RFL Sbjct: 232 QVVRRWLTIRGVHNYEPRHLDQAV-RFLA 259 >gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional. Length = 430 Score = 27.4 bits (61), Expect = 8.5 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%) Query: 189 QSERYFRRYKELGAQKLIVSGNLKIDTESLPCDKELLSLYQE 230 SE FR +K LGAQ ++V GN+ L L ++ E Sbjct: 84 ASEVIFRDWKALGAQYVMV-GNIVPAGGRLQVQYALFNVATE 124 >gnl|CDD|130031 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein (MRP). This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved. Length = 1522 Score = 27.2 bits (60), Expect = 9.3 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%) Query: 120 VSRFLKYWKPDCMI------LSESDIWPLTVFELSKQRIPQVLVNARMSRRSFKNWKTVL 173 +SR +W + L ESD+W L + S+ +P ++ N + + + Sbjct: 210 LSRITFWWITGMAVYGYRQPLEESDLWSLNKEDTSEMVVPVLVENWKKECKKTRKQPVSA 269 Query: 174 SFSKKIFSQ 182 + KK S+ Sbjct: 270 VYGKKDPSK 278 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 0.325 0.139 0.414 Gapped Lambda K H 0.267 0.0632 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,216,761 Number of extensions: 474775 Number of successful extensions: 1305 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1298 Number of HSP's successfully gapped: 16 Length of query: 440 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 344 Effective length of database: 3,920,105 Effective search space: 1348516120 Effective search space used: 1348516120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 59 (26.7 bits)