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)