RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780795|ref|YP_003065208.1| homoserine kinase [Candidatus Liberibacter asiaticus str. psy62] (316 letters) >gnl|CDD|179968 PRK05231, PRK05231, homoserine kinase; Provisional. Length = 319 Score = 372 bits (958), Expect = e-104 Identities = 126/321 (39%), Positives = 193/321 (60%), Gaps = 7/321 (2%) Query: 1 MAVYTHPPQKEIQSFVQEYAIGQLNSVQPIIHGVENSNFVIQTSKGTFILTIYEKRMNEK 60 MAVYT E+ +F+ Y +G+L S++ I G+ENSNF + T++G ++LT++E R+ + Sbjct: 1 MAVYTDVSDDELAAFLAPYDLGELLSLKGIAEGIENSNFFLTTTQGEYVLTLFE-RLTAE 59 Query: 61 DLPVFIELLHYISRNKLPCPIPIPRNDGKLYGFLCKKPANIFSFIKGSPLNHISDIHCEE 120 DLP F+ L+ +++ +P P P+ R DG G L KPA I +F++G + HC E Sbjct: 60 DLPFFLGLMQHLAARGVPVPAPVARRDGAALGELAGKPAAIVTFLEGKWPRAPTAAHCAE 119 Query: 121 IGSMLASMHQKTKNFHLYRKNTLSPLNLKFLWAKCFDKVDED----LKKEIDHEFCFLKE 176 +G MLA MH ++F L R N + L + + ++ L+ E+ + FL Sbjct: 120 VGEMLARMHLAGRDFPLERPNLRGLAWWRELAPRLLPFLADEQAALLEAELAAQLAFLAS 179 Query: 177 S-WPKNLPTGIIHADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLSICINAWCFDENNT 235 + WP LP G+IHADLF DNVLF +++ G IDFYF+CND L+YD++I +N WCF+ + + Sbjct: 180 AAWPA-LPRGVIHADLFRDNVLFEGDRLSGFIDFYFACNDKLLYDVAITLNDWCFEADGS 238 Query: 236 YNPSRGFSILNGYNKVRKISENELQSLPTLLRGAALRFFLTRLYDSQNMPCNALTITKDP 295 + ++ ++L Y VR ++ E +LP +LRGAALRF+L+RLYD AL KDP Sbjct: 239 LDATKARALLAAYQSVRPLTAAERAALPVMLRGAALRFWLSRLYDWLLPRAGALVKPKDP 298 Query: 296 MEYILKTRFHKQISSISEYGF 316 +E+ K RF + + S YG Sbjct: 299 LEFERKLRFRRAVVSALPYGL 319 >gnl|CDD|162121 TIGR00938, thrB_alt, homoserine kinase, Neisseria type. Homoserine kinase is required in the biosynthesis of threonine from aspartate.The member of this family from Pseudomonas aeruginosa was shown by direct assay and complementation to act specifically as a homoserine kinase. Length = 307 Score = 311 bits (798), Expect = 2e-85 Identities = 126/307 (41%), Positives = 192/307 (62%), Gaps = 3/307 (0%) Query: 1 MAVYTHPPQKEIQSFVQEYAIGQLNSVQPIIHGVENSNFVIQTSKGTFILTIYEKRMNEK 60 MAVYT +E+ SF+ Y +G+L S++ I GVENSN+++ T G +ILT+YEKR+ + Sbjct: 1 MAVYTSVSDEEMSSFLDGYDLGELLSLKGIAEGVENSNYLLTTDVGRYILTLYEKRVKAE 60 Query: 61 DLPVFIELLHYISRNKLPCPIPIPRNDGKLYGFLCKKPANIFSFIKGSPLNHISDIHCEE 120 +LP F+ L +++ LP P P+ DG+ L KPA + F++G + + +HC Sbjct: 61 ELPFFLALTTHLAARGLPVPKPVKSRDGRQLSTLAGKPACLVEFLQGLSVGRPTAMHCRP 120 Query: 121 IGSMLASMHQKTKNFHLYRKNTLSPLNLKFLWAKCFD---KVDEDLKKEIDHEFCFLKES 177 +G +LA MH +F RKN+L L KCF+ +++ + E+D E +L + Sbjct: 121 VGEVLAWMHLAGAHFPENRKNSLRLEAWHILAEKCFEAAPQLEAHMGAELDKELDYLDKF 180 Query: 178 WPKNLPTGIIHADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLSICINAWCFDENNTYN 237 WP++LP G+IHADLFPDNVLF + + G+IDFYF+C D YDL+I +NAWCFD ++ ++ Sbjct: 181 WPRDLPRGVIHADLFPDNVLFDGDSVKGVIDFYFACTDARAYDLAITVNAWCFDADDHFD 240 Query: 238 PSRGFSILNGYNKVRKISENELQSLPTLLRGAALRFFLTRLYDSQNMPCNALTITKDPME 297 +++ GY++ R ++E E + P LLRGAA+RF LTRL+D P AL + KDP + Sbjct: 241 ADHAKALIKGYHQSRPLTEEEKAAFPVLLRGAAMRFLLTRLWDWVFTPAGALVVPKDPRD 300 Query: 298 YILKTRF 304 + + RF Sbjct: 301 FERRLRF 307 >gnl|CDD|178464 PLN02876, PLN02876, acyl-CoA dehydrogenase. Length = 822 Score = 33.6 bits (77), Expect = 0.076 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 7/77 (9%) Query: 173 FLKESWPKN----LPTGIIHADLFPDNVLFY--NNKIMGLIDFYFSCNDFLMYDLSICIN 226 +L+E+ P TGI+H D DN++F+ ++++G++D+ S M D++ Sbjct: 210 WLRENIPAEDSTGAGTGIVHGDFRIDNLVFHPTEDRVIGILDWELSTLGNQMCDVAYSCL 269 Query: 227 AWCFDEN-NTYNPSRGF 242 + D N + +GF Sbjct: 270 PYIVDINLDNQQVGKGF 286 >gnl|CDD|184879 PRK14879, PRK14879, serine/threonine protein kinase; Provisional. Length = 211 Score = 33.0 bits (76), Expect = 0.11 Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%) Query: 185 GIIHADLFPDNVLFYNNKIMGLIDF 209 GIIH DL N++ KI LIDF Sbjct: 115 GIIHGDLTTSNMILSGGKIY-LIDF 138 >gnl|CDD|185545 PTZ00296, PTZ00296, choline kinase; Provisional. Length = 442 Score = 32.9 bits (75), Expect = 0.12 Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 15/116 (12%) Query: 121 IGSMLASMHQKTKNFHLYRKNTLSPLNLKFL--WA------KCFDKVDEDLKKEIDHEFC 172 I ++L H ++ HL +P K + W K +K D+ K I Sbjct: 207 IANVLGKFHTLSRKRHLPEHWDRTPCIFKMMEKWKNQLSKYKNIEKYQRDIHKYIKESEK 266 Query: 173 FLK----ESWPKNLPTGII--HADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLS 222 F+K S NL I+ H DL +N++ NK + LIDF +S +FL D++ Sbjct: 267 FIKFMKVYSKSDNLANDIVFCHNDLQENNII-NTNKCLRLIDFEYSGYNFLATDIA 321 >gnl|CDD|131952 TIGR02906, spore_CotS, spore coat protein, CotS family. Members of this family include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologs that are more closely related to these two than to the spore coat proteins YutH and YsxE. The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers. Length = 313 Score = 32.6 bits (75), Expect = 0.12 Identities = 51/257 (19%), Positives = 97/257 (37%), Gaps = 43/257 (16%) Query: 39 FVIQTSKGTFILTIYEKRMN-EKDLPVFIELLH-YISRNKLPCPIPIPRNDGKLYGFLCK 96 + ++T G L K++N + +FI ++ +N P + DG+LY Sbjct: 13 YKVETDSGNKCL----KKINYPPERLLFILGAQEHLRKNGFNIPKILKTKDGELYVKYNG 68 Query: 97 KPANIFSFIKGSPLNHISDIHCEEIGSMLASMHQKTKNFHLYRKNTLSPLNLKFLWAKCF 156 + +I+G + + I ++ LA H +K + + + L W K F Sbjct: 69 DLYVLTEWIEGRECDFNNPIDLKKAAKGLALFHHASKGY-VPPDGSKIRSKL-GKWPKQF 126 Query: 157 DKVDEDL--------KKEIDHEF--CFLKE---------------------SWPKNLPT- 184 +K ++L +K+ EF +LKE K Sbjct: 127 EKRLKELERFKKIALEKKYKDEFDKLYLKEVDYFLERGKKALELLNKSKYYDLCKEAKKI 186 Query: 185 -GIIHADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLSICINAWCFDENNTYNPSRGFS 243 G H D N+L +N++ +IDF + D + DL I +N ++ + Sbjct: 187 RGFCHQDYAYHNILLKDNEVY-VIDFDYCTIDLPVRDLRKLIIK-LMKKNGVWDLEKAKE 244 Query: 244 ILNGYNKVRKISENELQ 260 I+ Y+ + +S+ E + Sbjct: 245 IIEAYSSINPLSKEEKE 261 >gnl|CDD|128517 smart00221, STYKc, Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase. Length = 225 Score = 32.7 bits (75), Expect = 0.15 Identities = 11/29 (37%), Positives = 18/29 (62%) Query: 185 GIIHADLFPDNVLFYNNKIMGLIDFYFSC 213 GI+H DL P+N+L + ++ L DF + Sbjct: 118 GIVHRDLKPENILLGMDGLVKLADFGLAR 146 >gnl|CDD|163436 TIGR03724, arch_bud32, Kae1-associated kinase Bud32. Members of this protein family are the Bud32 protein associated with Kae1 (kinase-associated endopeptidase 1) in the Archaea. In many Archaeal genomes, Kae1 and Bud32 are fused. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex, an apparently ancient protein kinase-containing molecular machine. Length = 199 Score = 31.8 bits (73), Expect = 0.25 Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 4/32 (12%) Query: 185 GIIHADLFPDNVLFYNNKIMGLIDF---YFSC 213 GI+H DL N++ ++K+ LIDF +S Sbjct: 110 GIVHGDLTTSNIIVRDDKLY-LIDFGLGKYSD 140 >gnl|CDD|128516 smart00220, S_TKc, Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily. Length = 244 Score = 31.4 bits (72), Expect = 0.30 Identities = 12/25 (48%), Positives = 16/25 (64%) Query: 185 GIIHADLFPDNVLFYNNKIMGLIDF 209 GIIH DL P+N+L + + L DF Sbjct: 107 GIIHRDLKPENILLDEDGHVKLADF 131 >gnl|CDD|152392 pfam11957, efThoc1, THO complex subunit 1 transcription elongation factor. The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. Length = 464 Score = 30.5 bits (69), Expect = 0.53 Identities = 9/28 (32%), Positives = 13/28 (46%) Query: 139 RKNTLSPLNLKFLWAKCFDKVDEDLKKE 166 R+ + L L LW D + + LKK Sbjct: 383 RRFPMGSLELSRLWNDEPDNILQALKKP 410 >gnl|CDD|181985 PRK09605, PRK09605, bifunctional UGMP family protein/serine/threonine protein kinase; Validated. Length = 535 Score = 30.2 bits (69), Expect = 0.75 Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 4/32 (12%) Query: 185 GIIHADLFPDNVLFYNNKIMGLIDF---YFSC 213 GI+H DL N + ++++ LIDF +S Sbjct: 448 GIVHGDLTTSNFIVRDDRLY-LIDFGLGKYSD 478 Score = 27.9 bits (63), Expect = 3.7 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 15/67 (22%) Query: 68 LLHYISRNKLPCPI--PIPRNDGKLYGFLCKKPANIFSFIKGSPLNHI---SDIHCEEIG 122 LL R +P P+ + + + + +I G L + + ++G Sbjct: 389 LLSEARRAGVPTPVIYDVDPEEKTI----------VMEYIGGKDLKDVLEGNPELVRKVG 438 Query: 123 SMLASMH 129 ++A +H Sbjct: 439 EIVAKLH 445 >gnl|CDD|163308 TIGR03529, GldK_short, gliding motility-associated lipoprotein GldK. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldK abolish the gliding phenotype. GldK is homologous to GldJ. This model represents a GldK homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture than that found in Flavobacterium johnsoniae and related species (represented by (TIGR03525). Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. Length = 344 Score = 29.5 bits (66), Expect = 1.0 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 24/84 (28%) Query: 185 GIIHADLFPDNVLFYNNKIM--GLIDFYFSCNDFLMYDLSICINAWCFDE---------- 232 G + A+ P +Y++ + YF NDF +YD++ + W D Sbjct: 227 GCMLANFKPGRGNYYDDGFPYTAPVAVYFP-NDFGLYDMAGNVAEWVLDAYAATSVPIVW 285 Query: 233 --NNTYNPSRGFSILNGYNKVRKI 254 N Y N+VRKI Sbjct: 286 DLNPVYEDP---------NEVRKI 300 >gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein; Provisional. Length = 865 Score = 28.9 bits (65), Expect = 1.8 Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 23 QLNSVQPIIHGVENSNFVIQTSKGTFILTIYE 54 L S PII GV NSN + ++ + IYE Sbjct: 279 GLASYAPIIRGVANSNAKVTITQSGY--KIYE 308 >gnl|CDD|132519 TIGR03479, DMSO_red_II_alp, DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane. Length = 912 Score = 28.6 bits (64), Expect = 2.4 Identities = 15/79 (18%), Positives = 23/79 (29%), Gaps = 17/79 (21%) Query: 177 SWPKNLPTGIIHADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLSICINAWCFDENNTY 236 +L TG H + + +D+ D I W + + T Sbjct: 197 DDYGDLYTGAFHT---------FGKAHDS-----ATSDDWFNADY---IIMWGSNPSVTR 239 Query: 237 NPSRGFSILNGYNKVRKIS 255 P F YN R +S Sbjct: 240 IPDAHFLSEARYNGARVVS 258 >gnl|CDD|178764 PLN03225, PLN03225, Serine/threonine-protein kinase SNT7; Provisional. Length = 566 Score = 28.2 bits (63), Expect = 3.0 Identities = 8/15 (53%), Positives = 12/15 (80%) Query: 184 TGIIHADLFPDNVLF 198 TGI+H D+ P N++F Sbjct: 274 TGIVHRDVKPQNIIF 288 >gnl|CDD|178046 PLN02426, PLN02426, cytochrome P450, family 94, subfamily C protein. Length = 502 Score = 27.0 bits (60), Expect = 6.5 Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 7/29 (24%) Query: 290 TITKDP--MEYILKTRFH-----KQISSI 311 TIT +P +EY+LKTRF K S+I Sbjct: 86 TITANPENVEYMLKTRFDNYPKGKPFSAI 114 >gnl|CDD|178737 PLN03195, PLN03195, fatty acid omega-hydroxylase; Provisional. Length = 516 Score = 27.1 bits (60), Expect = 7.0 Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%) Query: 284 MPCNALTITKDP--MEYILKTRF 304 MP T DP +E++LKT F Sbjct: 72 MPFTTYTYIADPVNVEHVLKTNF 94 >gnl|CDD|140300 PTZ00274, PTZ00274, cytochrome b5 reductase; Provisional. Length = 325 Score = 26.8 bits (59), Expect = 7.4 Identities = 11/40 (27%), Positives = 17/40 (42%) Query: 2 AVYTHPPQKEIQSFVQEYAIGQLNSVQPIIHGVENSNFVI 41 A++ + + F Q Y QL V PI H F++ Sbjct: 35 ALHFRNKPRPGRVFSQRYEPYQLGEVIPITHDTALFRFLL 74 >gnl|CDD|173576 PTZ00384, PTZ00384, choline kinase; Provisional. Length = 383 Score = 26.7 bits (59), Expect = 9.2 Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 1/35 (2%) Query: 188 HADLFPDNVLFYNNKIMGLIDFYFSCNDFLMYDLS 222 H DLF N+L +N I IDF F+ +++ ++++ Sbjct: 231 HNDLFFTNILDFNQGIY-FIDFDFAGFNYVGWEIA 264 >gnl|CDD|129562 TIGR00470, sepS, O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys. Length = 533 Score = 26.4 bits (58), Expect = 9.6 Identities = 14/45 (31%), Positives = 22/45 (48%) Query: 135 FHLYRKNTLSPLNLKFLWAKCFDKVDEDLKKEIDHEFCFLKESWP 179 FHLY+K + +L F AK + +E K ++ F K+ P Sbjct: 134 FHLYKKGAIDGDDLVFEIAKALNVSNEMGLKVLETVFPEFKDLKP 178 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 0.323 0.140 0.436 Gapped Lambda K H 0.267 0.0778 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,169,678 Number of extensions: 326966 Number of successful extensions: 555 Number of sequences better than 10.0: 1 Number of HSP's gapped: 551 Number of HSP's successfully gapped: 32 Length of query: 316 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 223 Effective length of database: 3,984,929 Effective search space: 888639167 Effective search space used: 888639167 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: 41 (22.0 bits) S2: 57 (25.6 bits)