RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254781017|ref|YP_003065430.1| GHMP kinase [Candidatus
Liberibacter asiaticus str. psy62]
         (324 letters)



>gnl|CDD|161922 TIGR00549, mevalon_kin, mevalonate kinase.  Paracoccus exhibits two
           genes within the phosphomevalonate/mevalonate kinase
           family, one of which falls between trusted and noise
           cutoffs of this model. The degree of divergence is high,
           but if the trees created from this model are correct,
           the proper names of these genes have been swapped.
          Length = 273

 Score =  148 bits (376), Expect = 2e-36
 Identities = 83/283 (29%), Positives = 142/283 (50%), Gaps = 17/283 (6%)

Query: 12  APGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDRLINIDSSLGQYCGSLDLAMFHP 71
           APG ++L GEH V++G  A+   I  R  + +    D    I+S L    GSLD A    
Sbjct: 1   APGKIILFGEHAVVYGEPAIAAPIPLRTTVTVIESSDG-SFIESDL--GRGSLDDAPQEL 57

Query: 72  S--FSFIIMAIN--HIKPSCGFDLKVISQLDSQLGLGSSAAITVAITAALLTLQYH-KEP 126
               S+I  A++          ++++ S++    GLGSSAA+ VA+  AL    Y   E 
Sbjct: 58  DGLVSYIAEALSYFSELNPPPLEIEIDSEIPPGRGLGSSAAVAVALIRALA--DYFGSEL 115

Query: 127 SPDEILTTAHAIVLKVQGISSGIDLAASIHGGLICYQ--MPKYSIEKIDFIFPIHLIYSG 184
           S +E+   A+       G  SGID A S +GG + ++    +++   I       +  +G
Sbjct: 116 SKEELAKLANEAEKIAHGKPSGIDTATSTYGGPVYFEKGEGEFTKL-ISLDGYFVIADTG 174

Query: 185 YKTPTAQVLKKISYIEIEYPEINEINQKIYALMGKLSQISCQALRNKNLKVLAQAMNRQQ 244
               T + + ++  +   +PE+ +    I   +G+L+  +  AL++ +++ L + MN  Q
Sbjct: 175 VSGSTKEAVARVRQLLERFPELID---SIMDAIGELTLEAKAALQDGDVESLGELMNINQ 231

Query: 245 GLLETLGVSDSKLSEIVWKLREQPHIMASKISGSGLGDCVIAL 287
           GLL+ LGVS  KL ++V   R+    + +K++G+G G C+IAL
Sbjct: 232 GLLKALGVSHPKLDQLVETARKA-GALGAKLTGAGGGGCMIAL 273


>gnl|CDD|179677 PRK03926, PRK03926, mevalonate kinase; Provisional.
          Length = 302

 Score =  141 bits (357), Expect = 3e-34
 Identities = 92/282 (32%), Positives = 138/282 (48%), Gaps = 17/282 (6%)

Query: 7   KICVSAPGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDRLINIDSSLGQYCGSLDL 66
            +  SAPG + L GEH V++G  A+  AI+ R  +      D  I I+S  G        
Sbjct: 1   MVLCSAPGKIYLFGEHAVVYGKPAIACAIDLRTYVRAEFNDDS-IYIESDYG------KT 53

Query: 67  AMFHPSFSFIIMAINHIKPSCGFDLKVISQLDSQLGLGSSAAITVAITAALLTLQYHKEP 126
              HP  S  I  +       G  + + SQ+    GLGSSAA+TVA   AL  L      
Sbjct: 54  GEKHPYVSAAIEKMREEADKDGVTVSITSQIPVGSGLGSSAAVTVATIGALNRL-LGLGL 112

Query: 127 SPDEILTTAHAIVLKVQGISSGIDLAASIHGGLICYQMPKYSIEKIDFI-FPIHLIYSGY 185
           S +EI    H + L VQG +S  D   S  GG +     K    K+ F    I + Y+G 
Sbjct: 113 SLEEIAKLGHKVELLVQGAASPTDTYVSTMGGFVTIPDRK----KLPFPECGIVVGYTGS 168

Query: 186 KTPTAQVLKKISYIEIEYPEINEINQKIYALMGKLSQISCQALRNKNLKVLAQAMNRQQG 245
              T +++  +  ++ EYPE+ E    I + +GK+S+   + + + +   L + MN  QG
Sbjct: 169 SGSTKELVANVRKLKEEYPELIE---PILSSIGKISEKGEELILSGDYVSLGELMNINQG 225

Query: 246 LLETLGVSDSKLSEIVWKLREQPHIMASKISGSGLGDCVIAL 287
           LL+ LGVS  +LSE+++  R    + A KI+G+G G C++AL
Sbjct: 226 LLDALGVSTKELSELIYAARTAGALGA-KITGAGGGGCMVAL 266


>gnl|CDD|130287 TIGR01220, Pmev_kin_Gr_pos, phosphomevalonate kinase, ERG8-type,
           Gram-positive branch.  This enzyme is part of the
           mevalonate pathway, one of two alternative pathways for
           the biosynthesis of IPP. In an example of nonorthologous
           gene displacement, two different types of
           phosphomevalonate kinase are found - the animal type and
           this ERG8 type. This model represents the low GC
           Gram-positive organism forms of the ERG8 type of
           phosphomevalonate kinase.
          Length = 358

 Score = 71.1 bits (174), Expect = 4e-13
 Identities = 53/181 (29%), Positives = 79/181 (43%), Gaps = 24/181 (13%)

Query: 8   ICVSAPGSLVLMGEHGVLH-GHAALVFAINKRVILYLTLRKDRLINIDSSLGQYC----- 61
           I V APG L + GE+ V+  G+ A++ A+++ V + +         I SS          
Sbjct: 1   IVVHAPGKLFVAGEYAVVEPGNPAILVAVDRFVTVTVEDADGAADVIISSDLGPQPVGWR 60

Query: 62  ---GSLDL--AMFHPSFSFIIMAINHIKP---SCG-----FDLKVISQLDS----QLGLG 104
              G L +       + ++++ AI  ++              L V S+LD     + GLG
Sbjct: 61  RHDGRLVVRDPDARSALAYVVSAIETVERYAGERNQKLPALHLSVSSRLDEADGRKYGLG 120

Query: 105 SSAAITVAITAALLTLQYHKEPSPDEILTTAHAIVLKVQGISSGIDLAASIHGGLICYQM 164
           SS A+TVA   AL    Y  E S DEI   A     ++Q   S  D+AAS +GG I Y  
Sbjct: 121 SSGAVTVATVKALNAF-YDLELSNDEIFKLAMLATAELQPKGSCGDIAASTYGGWIAYST 179

Query: 165 P 165
            
Sbjct: 180 F 180


>gnl|CDD|140319 PTZ00298, PTZ00298, mevalonate kinase; Provisional.
          Length = 328

 Score = 64.1 bits (156), Expect = 4e-11
 Identities = 74/290 (25%), Positives = 128/290 (44%), Gaps = 30/290 (10%)

Query: 14  GSLVLMGEHGVLHGHAALVFAINKRVILYLTLRK--------DRLINIDSSLGQYCGSLD 65
           G ++L GEH V++G  A+V  I++     L L K        D+   +   + +      
Sbjct: 17  GKVILFGEHFVVYGAEAIVAGIDEYTECRLELTKGVPGLQVVDQRPAVPGYIVEKREEQR 76

Query: 66  LAMFHPSFSFIIMAINHIKPSC---GFDLKVISQLDSQLGLGSSAAITVAITAALLTLQY 122
            A  H       + + H+       G  + +   L    G+G+SA+  V+++ AL  L Y
Sbjct: 77  KA--HQ------LVLRHLNIDTSVDGLKMHLGGPLVPSSGIGASASDVVSLSRALSEL-Y 127

Query: 123 HKEPSPDEILTTAHAIVLKVQGISSGIDLAASIHGGLICYQ--MPKYSIEKIDFIFPIHL 180
               + +E+  +A        G  SG D  A+ +GGLI Y+    K   ++I F  P++L
Sbjct: 128 QLNLTEEEVNLSAFVGEGGYHGTPSGADNTAATYGGLISYRRVNGKSVFKRIAFQQPLYL 187

Query: 181 IY--SGYKTPTAQVLKKISYIEIEYPE-INEINQKIYALMGKLSQISCQALRNKNLKVLA 237
           +   +G    T +V+  +  ++   P   N + +   A + +  +    AL+  NL  + 
Sbjct: 188 VVCSTGITASTTKVVGDVRKLKENQPTWFNRLLENYNACVSEAKE----ALQKGNLFRVG 243

Query: 238 QAMNRQQGLLETLGVSDSKLSEIVWKLREQPHIMASKISGSGLGDCVIAL 287
           + MN    L + L VS  +L  IV   R    + A K+SG+G G  V+AL
Sbjct: 244 ELMNANHDLCQKLTVSCRELDSIVQTCRTYGALGA-KMSGTGRGGLVVAL 292


>gnl|CDD|178281 PLN02677, PLN02677, mevalonate kinase.
          Length = 387

 Score = 54.8 bits (132), Expect = 3e-08
 Identities = 81/359 (22%), Positives = 141/359 (39%), Gaps = 103/359 (28%)

Query: 12  APGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDRLINIDSSLGQYCGSLDLAMFHP 71
           APG ++L GEH V+HG  A+  AI+  +  Y++LR       D +L      L L     
Sbjct: 7   APGKIILAGEHAVVHGSTAVAAAID--LYTYVSLRFPPSAENDDTL-----KLQLKDLGL 59

Query: 72  SFSFIIMAINHIKP-----------SCGFD-LKVISQL---------------------- 97
            FS+ +  I    P           SC  + LK I+ L                      
Sbjct: 60  EFSWPLARIKEALPDLGTPCPSTPTSCSEETLKSIAALVEEQNIPEAKIWLSSGVSAFLW 119

Query: 98  ---------------DSQL----GLGSSAAITVAITAALLTLQYHKEPSPDEI-LTTAHA 137
                           S+L    GLGSSAA  VA++AALL          D I ++T   
Sbjct: 120 LYTSILGFNPATVVVTSELPLGSGLGSSAAFCVALSAALLAAS-------DSISVSTGGN 172

Query: 138 IVLKV-------------------QGISSGIDLAASIHGGLICYQMPKYSIEKIDFIFPI 178
               +                    G  SGID   S +G +I ++     + ++    P+
Sbjct: 173 GWSSLDETDLELVNKWAFEGEKIIHGKPSGIDNTVSTYGNMIKFK--SGELTRLQSNMPL 230

Query: 179 HLIYSGYKT--PTAQVLKKISYIEIEYPE--------INEINQKIYALMGKLSQISCQAL 228
            ++ +  +    T  ++  +S   + +P+        ++ I++++  ++ +       ++
Sbjct: 231 KMLITNTRVGRNTKALVAGVSERALRHPDAMKSVFNAVDSISEELATII-QSPAEDELSI 289

Query: 229 RNKNLKVLAQAMNRQQGLLETLGVSDSKLSEIVWKLREQPHIMASKISGSGLGDCVIAL 287
             K  K L + M   QGLL+ +GVS S +  ++       + + SK++G+G G CV+ L
Sbjct: 290 TEKEEK-LKELMEMNQGLLQCMGVSHSSIETVL--RTTLKYKLVSKLTGAGGGGCVLTL 345


>gnl|CDD|149558 pfam08544, GHMP_kinases_C, GHMP kinases C terminal.  This family
           includes homoserine kinases, galactokinases and
           mevalonate kinases.
          Length = 82

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 226 QALRNKNLKVLAQAMNRQQGLLETLGVSDSKLSEIVWKLREQPHIMASKISGSGLGDCVI 285
           +ALR  +L++L + +N    LL   G+   +L E++ +LRE    + +K+SGSG G  V 
Sbjct: 3   EALREGDLELLGELLNENALLLYL-GILSPELDELLEELRELG-ALGAKLSGSGGGPTVF 60

Query: 286 ALGK 289
           AL K
Sbjct: 61  ALFK 64


>gnl|CDD|179653 PRK03817, PRK03817, galactokinase; Provisional.
          Length = 351

 Score = 40.8 bits (96), Expect = 6e-04
 Identities = 69/320 (21%), Positives = 114/320 (35%), Gaps = 41/320 (12%)

Query: 8   ICVSAPGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDRLINIDSSLGQYCGSLDLA 67
           + V +PG + L+GEH   +    L FAIN    L   + K       S       + +L 
Sbjct: 1   MKVKSPGRVNLIGEHTDYNDGYVLPFAINLYTFL--EIEKSEKFIFYSENFNEEKTFELD 58

Query: 68  MFHPSFSFI--IMAI------NHIKPSCGFDLKVISQLDSQLGLGSSAAITVAITAALLT 119
                 S+   I  +         +   G   KV S L    GL SSA++ VA+  AL  
Sbjct: 59  KLEKLNSWADYIKGVIWVLEKRGYEVG-GVKGKVSSNLPIGAGLSSSASLEVAVAYALNE 117

Query: 120 LQYHKEPSPDEILTTAHAIVLKVQGISSGI-DLAASIHGG---LICYQMPKYSIEKIDFI 175
             Y+   S  E+   A     +  G+  GI D  A   G     I         E + F 
Sbjct: 118 A-YNLNLSKLELALLAREAENEFVGVPCGIMDQFAVAFGKKDHAIFLDTMTLEYEYVPFP 176

Query: 176 --FPIHLIYSGYKTPTA---------------QVLKKISYIEIEYPEINEINQKIYALMG 218
             + I +  +G K   A               ++L K S  E+   +++++   +    G
Sbjct: 177 EDYEILVFDTGVKRELASSEYNERRQECEEALKILGKKSSKEVTEEDLSKLPPLLRKRAG 236

Query: 219 ------KLSQISCQALRNKNLKVLAQAMNR-QQGLLETLGVSDSKLSEIVWKLREQPHIM 271
                 +       AL+  +++ L + +      L +   VS  +L   V    E     
Sbjct: 237 YVLRENERVLKVRDALKEGDIETLGELLTESHWDLADNYEVSCEELDFFVEFALEL-GAY 295

Query: 272 ASKISGSGLGDCVIALGKGD 291
            ++++G+G G   IAL    
Sbjct: 296 GARLTGAGFGGSAIALVDKG 315


>gnl|CDD|161727 TIGR00131, gal_kin, galactokinase.  The galactokinases found by
           this model are divided into two sets. Prokaryotic forms
           are generally shorter. The eukaryotic forms are longer
           because of additional central regions and in some cases
           are known to be bifunctional, with regulatory activities
           that are independent of galactokinase activity.
          Length = 386

 Score = 37.5 bits (87), Expect = 0.005
 Identities = 65/339 (19%), Positives = 117/339 (34%), Gaps = 58/339 (17%)

Query: 8   ICVSAPGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDR-----LINIDSSLGQYCG 62
               APG + L+GEH   +  + L  AI+   +  + +R D+     L N D+   +   
Sbjct: 18  FTARAPGRVNLIGEHTDYNDGSVLPCAIDFGTLCAVAVRDDKNVRIYLANADNKFAER-- 75

Query: 63  SLDLAMFHPSFS----FIIMAINHIKP-----SCGFDLKVISQLDSQLGLGSSAAITVAI 113
           SLDL +     S    +    ++  +        G D+     + +  GL SSAA   A+
Sbjct: 76  SLDLPLDGSEVSDWANYFKGVLHVAQERFNSFPLGADIVCSGNVPTGSGLSSSAAFECAV 135

Query: 114 TAALLTLQYHKEPSPDEILTTAHAIVLKVQGISSGI-DLAASIHG-------------GL 159
            A L  +  H      +IL           G++ GI D AAS+ G               
Sbjct: 136 GAVLQNM-GHLPLDSKQILLRIQVAENHFVGVNCGIMDQAASVLGKEDHALLVECRSLKA 194

Query: 160 ICYQMPKYSIEKI--DFIFPIHLIYSGYKT------PTAQVLKKISYIEIEYPEINEINQ 211
             ++ P+  I  +  +      L  S Y T        A  L       +         +
Sbjct: 195 TPFKFPQLGIAFVIANTNVKRTLAPSNYNTRRQECTTAANFLAATDKGALRDFMNEYFAR 254

Query: 212 KIYALMGKLSQI-----------------SCQALRNKNLKVLAQAMNRQQGLLETL-GVS 253
            I A + K+  +                 + +A+++ + K     MN      +     +
Sbjct: 255 YI-ARLTKMLPLVEERAKHVVSENLRVLKAVKAMKDNDFKQFGALMNESHASCDDDYECT 313

Query: 254 DSKLSEIVWKLREQPHIMASKISGSGLGDCVIALGKGDL 292
             ++ E+V           S+++G+G G C + L   + 
Sbjct: 314 CPEIDELVCSAALVNGSGGSRMTGAGFGGCTVHLVPNEN 352


>gnl|CDD|129249 TIGR00144, beta_RFAP_syn, beta-RFAP synthase.  This protein family
           contains several archaeal examples of
           beta-ribofuranosylaminobenzene 5-prime-phosphate
           synthase (beta-RFAP synthase), an enzyme involved in
           methanopterin biosynthesis. In some species, two members
           of this family are found. It is unclear whether both act
           as beta-RFAP synthase. This family is related to the
           GHMP kinases (Galactokinase, Homoserine kinase,
           Mevalonate kinase, Phosphomevalonate kinase). Members
           are found so far only in the Archaea and in
           Methylobacterium extorquens.
          Length = 324

 Score = 37.2 bits (86), Expect = 0.005
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 88  GFDLKVISQLDSQLGLGSSAAITVAITAALLTLQYHKEPSPDEILTTAHAIVLKVQGISS 147
           GF   V S   +  GLGS   +++A    L++  Y  +       T      +  +G +S
Sbjct: 82  GFHFTVRSMFPAHSGLGSGTQLSLA-VGRLVSEYYGMK------FTAREIAHIVGRGGTS 134

Query: 148 GIDLAASIHGGLI 160
           GI +A+   GG I
Sbjct: 135 GIGVASFEDGGFI 147


>gnl|CDD|179937 PRK05101, PRK05101, galactokinase; Provisional.
          Length = 382

 Score = 35.7 bits (83), Expect = 0.018
 Identities = 37/140 (26%), Positives = 58/140 (41%), Gaps = 12/140 (8%)

Query: 3   QCLHKICVSAPGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKDRLIN---IDSSLGQ 59
                  + APG + L+GEH   +    L  AI+ + ++    R DR++     D    Q
Sbjct: 16  GYPPTHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAKRDDRIVRVIAADYDNQQ 75

Query: 60  YCGSLDLAM-FHPSFS---FIIMAINHIKPSC----GFDLKVISQLDSQLGLGSSAAITV 111
              SLD  +  HP      ++   + H++       G DL +   +    GL SSA++ V
Sbjct: 76  DEFSLDAPIVPHPEQQWANYVRGVVKHLQERNPDFGGADLVISGNVPQGAGLSSSASLEV 135

Query: 112 AITAALLTLQYHKEPSPDEI 131
           A+      L YH   S  EI
Sbjct: 136 AVGQTFQQL-YHLPLSGAEI 154


>gnl|CDD|179248 PRK01212, PRK01212, homoserine kinase; Provisional.
          Length = 301

 Score = 35.1 bits (82), Expect = 0.026
 Identities = 29/112 (25%), Positives = 43/112 (38%), Gaps = 30/112 (26%)

Query: 102 GLGSSAAITVAITAALLTL-QYHKEP-SPDEILTTA-----HAIVLKVQGISSGID-LAA 153
           GLGSSAA   +I A L+   +    P S +E+L  A     H             D +A 
Sbjct: 95  GLGSSAA---SIVAGLVAANELAGLPLSKEELLQLATEGEGHP------------DNVAP 139

Query: 154 SIHGGL-ICYQMPKYSIEKIDFIFPIHLI--YSGYKTPTA---QVL-KKISY 198
           ++ GGL +  +       KI     +  +      +  TA    VL K+ S 
Sbjct: 140 ALLGGLVLALEENGVISVKIPVFDDLKWVVAIPNIELSTAEARAVLPKQYSL 191


>gnl|CDD|178456 PLN02865, PLN02865, galactokinase.
          Length = 423

 Score = 32.5 bits (74), Expect = 0.17
 Identities = 57/244 (23%), Positives = 96/244 (39%), Gaps = 60/244 (24%)

Query: 97  LDSQLGLGSSAAITVAITAAL-----LTLQYHKEPSPDEILTTAHAIVLKVQGISSGI-D 150
           LDS  GL SSAA+ VA   AL     LT+      SP++ +     I  +  G+ +GI D
Sbjct: 141 LDSS-GLSSSAAVGVAYLLALENANNLTV------SPEDNIELDRLIENEYLGLRNGILD 193

Query: 151 LAA---SIHGGLIC---------YQMPKYSIEKIDFIFPIHLIYSGYKTP---------- 188
            +A   S +G L               ++     +  F I L +SG +            
Sbjct: 194 QSAILLSRYGCLTFMDCKTLDHKLVSLQFQQPGGEKPFKILLAFSGLRHALTNKPGYNLR 253

Query: 189 ------TAQVLKKISYIEIEYPEINEINQKIY-ALMGKLSQI---SCQALRNKNLKVLAQ 238
                  A+ L + S  +   P +  +  ++Y A   KL  +     +   ++N++V+  
Sbjct: 254 VSECQEAARFLLEASGNDELEPLLCNVEPEVYEAHKCKLEAVLARRAEHYFSENMRVIKG 313

Query: 239 AMNRQQGLLETLG--VSDSKLSEI------------VWK-LREQPHIMASKISGSGLGDC 283
                 G LE  G  +S S LS I            +++ L + P +  ++ SG+G   C
Sbjct: 314 VEAWASGNLEEFGKLISASGLSSIENYECGCEPLIQLYEILLKAPGVYGARFSGAGFRGC 373

Query: 284 VIAL 287
            +A 
Sbjct: 374 CVAF 377


>gnl|CDD|162257 TIGR01219, Pmev_kin_ERG8, phosphomevalonate kinase, ERG8-type,
           eukaryotic branch.  This enzyme is part of the
           mevalonate pathway, one of two alternative pathways for
           the biosynthesis of IPP. In an example of nonorthologous
           gene displacement, two different types of
           phosphomevalonate kinase are found - the animal type and
           this ERG8 type. This model represents plant and fungal
           forms of the ERG8 type of phosphomevalonate kinase.
          Length = 454

 Score = 32.2 bits (73), Expect = 0.17
 Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 19/85 (22%)

Query: 102 GLGSSAAITVAITAALLT-LQYHKEPSPDE--------------ILTTAHAIVLKVQG-I 145
           GLGSSAA+T A+ AALL  L       PD+              +  TAH      QG +
Sbjct: 154 GLGSSAAMTTALVAALLHYLGVVDLSDPDKEGKFGCSDLDVIHNLAQTAHC---LAQGKV 210

Query: 146 SSGIDLAASIHGGLICYQMPKYSIE 170
            SG D++A+++G     +     I 
Sbjct: 211 GSGFDVSAAVYGSQRYRRFSPELIS 235


>gnl|CDD|162602 TIGR01920, Shik_kin_archae, shikimate kinase.  This model
           represents the shikimate kinase (SK) gene found in
           archaea which is only distantly related to homoserine
           kinase (thrB) and not atr all to the bacterial SK
           enzyme. The SK from M. janaschii has been overexpressed
           in E. coli and characterized. SK catalyzes the fifth
           step of the biosynthesis of chorismate from
           D-erythrose-4-phosphate and phosphoenolpyruvate.
          Length = 261

 Score = 30.4 bits (69), Expect = 0.63
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 86  SCGFDLKVI--SQLDSQLGLGSSAAITVAITAALLTLQYHKEPSPDEILTTAHAIVLKVQ 143
                L+V   S++ +  GL SS+A+  A+  A   L+       D  +    A + K  
Sbjct: 60  GIVDGLEVEVESEIPAGSGLKSSSALVNALVEA--VLKAKGVEIDDIDILRLGARLSKDA 117

Query: 144 GIS-SGI--DLAASIHGGL 159
           G+S +G   D AAS  GG+
Sbjct: 118 GLSVTGAFDDAAASYLGGI 136


>gnl|CDD|178136 PLN02521, PLN02521, galactokinase.
          Length = 497

 Score = 29.7 bits (67), Expect = 0.94
 Identities = 33/136 (24%), Positives = 54/136 (39%), Gaps = 36/136 (26%)

Query: 12  APGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKD------RLINIDS---------- 55
           +PG + L+GEH    G++ L  AI +  I+   +R+       R+ N++           
Sbjct: 53  SPGRVNLIGEHIDYEGYSVLPMAIRQDTIV--AIRRAEGSKKLRIANVNDKYTTCTFPAD 110

Query: 56  ----------SLGQYCGSLDLAMFHPSFSFIIMAINHIKPSCGFDLKVISQLDSQLGLGS 105
                       G Y     +  +   F F+      + P  G D+ V   + +  GL S
Sbjct: 111 PDQEVDLANHKWGNYF----ICGYKGVFEFLKSKGVDVGPPVGLDVVVDGTVPTGSGLSS 166

Query: 106 SAAI----TVAITAAL 117
           SAA+     +AI AAL
Sbjct: 167 SAALVCSAAIAIMAAL 182


>gnl|CDD|178029 PLN02407, PLN02407, diphosphomevalonate decarboxylase.
          Length = 343

 Score = 29.8 bits (67), Expect = 1.1
 Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 9/65 (13%)

Query: 102 GLGSSAAITVAITAALLTLQYHKEPSPDEILTTAHAIVLKVQGISSGIDLAASIHGGLIC 161
           GL SSAA    +  AL  L   KE  P E+   A       QG  S      S++GG + 
Sbjct: 119 GLASSAAGFACLVFALAKLMNVKEDFPGELSAIAR------QGSGSA---CRSLYGGFVK 169

Query: 162 YQMPK 166
           + M K
Sbjct: 170 WNMGK 174


>gnl|CDD|129295 TIGR00191, thrB, homoserine kinase.  P.aeruginosa homoserine kinase
           seems not to be homologous (see PROSITE:PDOC0054).
          Length = 302

 Score = 29.3 bits (66), Expect = 1.4
 Identities = 43/194 (22%), Positives = 68/194 (35%), Gaps = 46/194 (23%)

Query: 102 GLGSSAAITVAITAALLTLQYHKEP-SPDEILTTAHAIVLKVQGISSGIDLAASIHGG-- 158
           GLGSSAA  VA  A     +    P S + +L  A  +      +      A ++ GG  
Sbjct: 94  GLGSSAAAIVA--ALAAANELCGLPLSKERLLDYASELEGHPDNV------APALLGGFQ 145

Query: 159 --------LICYQMPKYSIEKIDFIFPIHLIYSGYKTPTAQ---VLKKISYIEIEYPEIN 207
                   L   ++P +S  K+D++    L     +  TA+   VL K       YP  +
Sbjct: 146 LAFVEDDKLEVLKIPIFS--KLDWV----LAIPNIEVSTAEARAVLPK------AYPRQD 193

Query: 208 EINQKIYALMGKLSQISCQALRNKNLKVLAQAMNRQ--QGLLETLGVSDSKLSEIVWKLR 265
            +                 A+  K   + A  M  +  Q   E+L  +  K+ +      
Sbjct: 194 LVFN------LSHLAGLVHAIYQKKPDLGAIMMKDRIHQPYRESLIPNLFKIKQAA---- 243

Query: 266 EQPHIMASKISGSG 279
            +       ISGSG
Sbjct: 244 LEKGAYGITISGSG 257


>gnl|CDD|180014 PRK05322, PRK05322, galactokinase; Provisional.
          Length = 387

 Score = 29.1 bits (66), Expect = 1.4
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 226 QALRNKNLKVLAQAMNRQQGLL----ETLGVSDSKLSEIVWKLREQPHIMASKISGSGLG 281
           +AL+  +L+   + MN     L    E  G+    L E  WK   Q  ++ ++++G+G G
Sbjct: 286 KALKAGDLEKFGRLMNASHVSLRDDYEVTGLELDTLVEAAWK---QEGVLGARMTGAGFG 342

Query: 282 DCVIALGKGD 291
            C IA+ K D
Sbjct: 343 GCAIAIVKKD 352


>gnl|CDD|184056 PRK13446, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
          Length = 136

 Score = 29.2 bits (66), Expect = 1.5
 Identities = 18/39 (46%), Positives = 21/39 (53%), Gaps = 6/39 (15%)

Query: 10 VSAPGSLVLMGEHGVLHGHAALVFAINKRVILYLTLRKD 48
          V APG L   GE GVL GHA  + A+    I  LT +K 
Sbjct: 24 VGAPGVL---GEFGVLPGHAPFLTALK---IGELTYKKG 56


>gnl|CDD|179070 PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated.
          Length = 135

 Score = 29.3 bits (67), Expect = 1.5
 Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 3/26 (11%)

Query: 10 VSAPGSLVLMGEHGVLHGHAALVFAI 35
          V  PG+    GE G+L GHA L+ A+
Sbjct: 23 VVVPGT---EGELGILPGHAPLLTAL 45


>gnl|CDD|180473 PRK06213, PRK06213, enoyl-CoA hydratase; Provisional.
          Length = 229

 Score = 28.4 bits (64), Expect = 2.8
 Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 13/56 (23%)

Query: 86  SCGFDLKVISQLDSQLGLGSSAAI---TVAITAALLTLQYHKEPSPDEILTTAHAI 138
           S GFDLKV++        G+ AAI   T   T A   L +   P P  +  T HAI
Sbjct: 58  SGGFDLKVMTS-------GAQAAIALLTAGSTLARRLLSH---PKPVIVACTGHAI 103


>gnl|CDD|140312 PTZ00290, PTZ00290, galactokinase; Provisional.
          Length = 468

 Score = 27.9 bits (62), Expect = 3.8
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 219 KLSQISCQALRNKNLKVLAQAMNR-QQGLLETLGVSDSKLSEIVWKLREQPHIMASKISG 277
           KL+       R +  +   + +N   QG+ + + ++  +L  I   + E+  +   ++ G
Sbjct: 348 KLNDPELPLSREERFRKAGEILNAGHQGMRDLMKITTPELDFIHELINEEKGVAGGRMMG 407

Query: 278 SGLGDCVIALGKGDLNSLPYQSVNCHMHAK 307
            G G C+I L    L       V  H+  K
Sbjct: 408 GGFGGCIILL----LKKNAVDRVVAHVREK 433


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 27.7 bits (62), Expect = 4.1
 Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 205 EINEINQKIYALMGKLSQISCQALRNKNLKVLAQAMNRQQGLLE-TLGVSDSKLSEIVWK 263
           EINEI+ ++  L  +L ++  +    + LK   + + ++   LE +    + K+ E+  +
Sbjct: 208 EINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEER 267

Query: 264 LRE 266
           + E
Sbjct: 268 IEE 270


>gnl|CDD|179063 PRK00555, PRK00555, galactokinase; Provisional.
          Length = 363

 Score = 27.5 bits (61), Expect = 4.3
 Identities = 32/120 (26%), Positives = 54/120 (45%), Gaps = 20/120 (16%)

Query: 12  APGSLVLMGEHGVLHGHAALVFAINKRVILY--------LTLRKDRL-----INIDSSLG 58
           APG + L+GEH   +   AL  A+ +R ++         +T   DR      I +D++ G
Sbjct: 7   APGRINLIGEHTDYNLGFALPIALPQRTVVTFTPEHTDAITASSDRADGSARIPLDTTPG 66

Query: 59  QYCGSLDLAMFHPSFSFIIMAI-NHIKPSCGFDLKVISQLDSQLGLGSSAAITVAITAAL 117
           Q  G      +    + +I A+     P  G  + + S ++   GL SSAA+  A+  A+
Sbjct: 67  QVTG------WAAYAAGVIWALRGAGHPVPGGAMSITSDVEIGSGLSSSAALECAVLGAV 120


>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS.  A sigma
           factor is a DNA-binding protein protein that binds to
           the DNA-directed RNA polymerase core to produce the
           holoenzyme capable of initiating transcription at
           specific sites. Different sigma factors act in
           vegetative growth, heat shock, extracytoplasmic
           functions (ECF), etc. This model represents the clade of
           sigma factors called RpoS (also called sigma-38, KatF,
           etc.), found only in Proteobacteria. This sigma factor
           is induced in stationary phase (in response to the
           stress of nutrient limitation) and becomes the second
           prinicipal sigma factor at that time. RpoS is a member
           of the larger Sigma-70 subfamily (TIGR02937) and most
           closely related to RpoD (TIGR02393).
          Length = 285

 Score = 27.8 bits (62), Expect = 4.5
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 114 TAALLTLQYHKEPSPDEILTTAHAIVLKVQGISSGIDLAASI 155
            A  L  +  +EPS +EI   A  +   V+ +S  + L   I
Sbjct: 138 AARQLEKKLGREPSVEEI---AELLDKPVEDVSRVLALNERI 176


>gnl|CDD|183185 PRK11539, PRK11539, ComEC family competence protein; Provisional.
          Length = 755

 Score = 26.5 bits (59), Expect = 9.5
 Identities = 29/123 (23%), Positives = 43/123 (34%), Gaps = 37/123 (30%)

Query: 77  IMAINHIKPSCGFDLKVISQLDSQLGLGSSAAITVAIT-AALLTLQYHKEPSPDEILT-- 133
            +    I P+C    + ++ L+  L      AI +A+     L++       P EI    
Sbjct: 168 FLQAKVIDPNCSLRQQYLASLEQTLQPYPWRAIILALAFGERLSV-------PKEIKNLL 220

Query: 134 ----TAH--AIVLKVQGISSG--IDLAASIHGGLICYQMPKYSIEKIDFIFPIHLIYSGY 185
               TAH  AI        SG  I  AA +  GL              F  P+  I  G+
Sbjct: 221 RDTGTAHLMAI--------SGLHIAFAALLGWGL---------ARGGQFFLPVRWI--GW 261

Query: 186 KTP 188
           + P
Sbjct: 262 QFP 264


>gnl|CDD|181197 PRK08013, PRK08013, oxidoreductase; Provisional.
          Length = 400

 Score = 26.5 bits (59), Expect = 9.6
 Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 4/31 (12%)

Query: 238 QAMNRQ----QGLLETLGVSDSKLSEIVWKL 264
            A+ RQ     G+L  L +SD  L  IVW L
Sbjct: 199 DAVARQVFHGDGILAFLPLSDPHLCSIVWSL 229


  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
   0.322    0.137    0.400 

Gapped
Lambda     K      H
   0.267   0.0779    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,126,620
Number of extensions: 325980
Number of successful extensions: 707
Number of sequences better than 10.0: 1
Number of HSP's gapped: 688
Number of HSP's successfully gapped: 42
Length of query: 324
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 230
Effective length of database: 3,963,321
Effective search space: 911563830
Effective search space used: 911563830
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)