RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019635
(338 letters)
>gnl|CDD|215285 PLN02521, PLN02521, galactokinase.
Length = 497
Score = 567 bits (1463), Expect = 0.0
Identities = 241/336 (71%), Positives = 272/336 (80%), Gaps = 23/336 (6%)
Query: 26 GSGLSSSTAFVCSSTVALMAAFGVEVPK-----------------------AISIMAKSG 62
GSGLSSS A VCS+ +A+MAA G+ K AISIMA+ G
Sbjct: 161 GSGLSSSAALVCSAAIAIMAALGLNFTKKEVAQFTCKCERHIGTQSGGMDQAISIMAQQG 220
Query: 63 FAELIDFNPIRTTDVQLPAGGTFVVAHSLAESLKAITAASNYNNRVVECRLTAIVLAIKL 122
A+LIDFNP+R TDVQLPAGGTFV+A+SLAES KA+TAA+NYNNRVVECRL AIVLA+KL
Sbjct: 221 VAKLIDFNPVRATDVQLPAGGTFVIANSLAESNKAVTAATNYNNRVVECRLAAIVLAVKL 280
Query: 123 GMKPQEAISKVKTLSDVEGLCVAFACKNGSSDPVFAVKEFLRKEPYTALDIEKITEEKLT 182
GM +EAISKVKTLSDVEGLCV+FA +GSSDP AVKE L + PYTA +IE+I E LT
Sbjct: 281 GMSAEEAISKVKTLSDVEGLCVSFAGSHGSSDPAVAVKELLHEGPYTAEEIEEILGESLT 340
Query: 183 SIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGDLMN 242
SIF NS +SL VL AAK +KLHQRA HVYSEAKRVHAF+DTVSS+LSEE+KLKKLGDLMN
Sbjct: 341 SIFKNSPTSLAVLKAAKHFKLHQRAVHVYSEAKRVHAFRDTVSSSLSEEEKLKKLGDLMN 400
Query: 243 DSHHSCSVLYECSCPELEELVNVCRNNGALGARLTGAGWGGCVVALVKESIDSQFILNLK 302
+SH+SCSVLYECSCPELEELV VCR+NGALGARLTGAGWGGC VALVKE+I QFIL LK
Sbjct: 401 ESHYSCSVLYECSCPELEELVKVCRDNGALGARLTGAGWGGCAVALVKEAIVPQFILALK 460
Query: 303 EQFYQSRIDRGVINNNDLGLYVFASKPSSGAAKFKF 338
E+FY+SRI++GVI DLGLYVFASKPSSGAA KF
Sbjct: 461 EKFYKSRIEKGVIKEEDLGLYVFASKPSSGAAILKF 496
>gnl|CDD|223231 COG0153, GalK, Galactokinase [Carbohydrate transport and
metabolism].
Length = 390
Score = 134 bits (339), Expect = 3e-36
Identities = 84/339 (24%), Positives = 123/339 (36%), Gaps = 100/339 (29%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPKA------------------------ISIMAK 60
+G+GLSSS A + +AL F + + KA S K
Sbjct: 126 IGAGLSSSAALEVAVALALQRLFNLPLDKAELAKIAQVAENQFVGVNCGIMDQLASAFGK 185
Query: 61 SGFAELIDFNPIRTTDVQLPAGG-TFVVAHSLAESLKAITAASNYNNRVVECRLTAIVLA 119
A L+D + V P GG + V+ +S K A S YN R EC A L
Sbjct: 186 KDHALLLDCRTLEYEPVPFPVGGVSIVIVNSNV---KRELADSEYNERRAECEEAAEFLG 242
Query: 120 IKLGMKPQEAISKVKTLSDVEGLCVAFACKNGSSDPVFAVKEFLRKEPYTALDIEKITEE 179
+ + K+L DV + + A++ + +P
Sbjct: 243 VSI-----------KSLRDV------------TDEEFAALQAEIEVDP------------ 267
Query: 180 KLTSIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGD 239
K+ +RA HV +E +RV + L + G+
Sbjct: 268 ----------------------KIARRARHVVTENQRV---LEAA--KALRSGDLTEFGE 300
Query: 240 LMNDSHHSCSVLYECSCPELEELVN-VCRNNGALGARLTGAGWGGCVVALVKESIDSQFI 298
LMN+SH S YE +CPEL+ LV GA GAR+TGAG+GGCV+ALV
Sbjct: 301 LMNESHESLRDDYEVTCPELDTLVEIALAAGGAYGARMTGAGFGGCVIALVPNDDVEAVA 360
Query: 299 LNLKEQFYQSRIDRGVINNNDLGLYVFASKPSSGAAKFK 337
+ E++ + L + + S GA
Sbjct: 361 EAVAEEYEKVT---------GLKAAFYVVEASQGAGVCD 390
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.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 [Energy
metabolism, Sugars].
Length = 386
Score = 120 bits (302), Expect = 4e-31
Identities = 93/338 (27%), Positives = 130/338 (38%), Gaps = 104/338 (30%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEV------------------------PKAISIMAK 60
GSGLSSS AF C+ L + + +A S++ K
Sbjct: 121 TGSGLSSSAAFECAVGAVLQNMGHLPLDSKQILLRIQVAENHFVGVNCGIMDQAASVLGK 180
Query: 61 SGFAELIDFNPIRTTDVQLPAGG-TFVVAHSLAESLKAITAASNYNNRVVECRLTAIVLA 119
A L++ ++ T + P G FV+A++ +K A SNYN R EC A LA
Sbjct: 181 EDHALLVECRSLKATPFKFPQLGIAFVIANTN---VKRTLAPSNYNTRRQECTTAANFLA 237
Query: 120 IKLGMKPQEAISKVKTLSDVEGLCVAFACKNGSSDPVFAVKEFLRKEPYTALDIEKITEE 179
L D Y A I ++T+
Sbjct: 238 ATD----------KGALRDF-------------------------MNEYFARYIARLTK- 261
Query: 180 KLTSIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRV----HAFKDTVSSNLSEEDKLK 235
+ L +RA HV SE RV A KD D K
Sbjct: 262 ------------MLPLVE-------ERAKHVVSENLRVLKAVKAMKD--------ND-FK 293
Query: 236 KLGDLMNDSHHSCSVLYECSCPELEELV-NVCRNNGALGARLTGAGWGGCVVALVKESID 294
+ G LMN+SH SC YEC+CPE++ELV + NG+ G+R+TGAG+GGC V LV
Sbjct: 294 QFGALMNESHASCDDDYECTCPEIDELVCSAALVNGSGGSRMTGAGFGGCTVHLVPNENV 353
Query: 295 SQFILNLKEQFYQSRIDRGVINNNDLGLYVFASKPSSG 332
+ + ++ Y + +L YV SKP +G
Sbjct: 354 DKVRQAVADK-YPKKTGL------ELTFYVIVSKPGAG 384
>gnl|CDD|235163 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 80.0 bits (198), Expect = 6e-17
Identities = 40/104 (38%), Positives = 56/104 (53%), Gaps = 5/104 (4%)
Query: 203 LHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGDLMNDSHHSCSVLYECSCPELEEL 262
L +RA +V E +RV +D L E D ++ LG+L+ +SH + YE SC EL+
Sbjct: 231 LRKRAGYVLRENERVLKVRDA----LKEGD-IETLGELLTESHWDLADNYEVSCEELDFF 285
Query: 263 VNVCRNNGALGARLTGAGWGGCVVALVKESIDSQFILNLKEQFY 306
V GA GARLTGAG+GG +ALV + L E++
Sbjct: 286 VEFALELGAYGARLTGAGFGGSAIALVDKGKFESIGEELLEEYK 329
Score = 30.3 bits (69), Expect = 1.2
Identities = 27/111 (24%), Positives = 38/111 (34%), Gaps = 27/111 (24%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFG-------------------VEVPKAI-----SIMAK 60
+G+GLSSS + + AL A+ V VP I K
Sbjct: 97 IGAGLSSSASLEVAVAYALNEAYNLNLSKLELALLAREAENEFVGVPCGIMDQFAVAFGK 156
Query: 61 SGFAELIDFNPIRTTDVQLPAGGTFVVAHSLAESLKAITAASNYNNRVVEC 111
A +D + V P +V + +K A+S YN R EC
Sbjct: 157 KDHAIFLDTMTLEYEYVPFPEDYEILVFDT---GVKRELASSEYNERRQEC 204
>gnl|CDD|235407 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 76.1 bits (188), Expect = 2e-15
Identities = 41/110 (37%), Positives = 56/110 (50%), Gaps = 15/110 (13%)
Query: 206 RAAHVYSEAKRV----HAFKDTVSSNLSEEDKLKKLGDLMNDSHHSCSVLYECSCPELEE 261
RA H +E +R A K L+K G LMN SH S YE + EL+
Sbjct: 270 RARHAVTENQRTLKAVKALKA---------GDLEKFGRLMNASHVSLRDDYEVTGLELDT 320
Query: 262 LVNVC-RNNGALGARLTGAGWGGCVVALVKESIDSQFILNLKEQFYQSRI 310
LV + G LGAR+TGAG+GGC +A+VK+ F N+ + Y+ +I
Sbjct: 321 LVEAAWKQEGVLGARMTGAGFGGCAIAIVKKDKVEAFKENVGKA-YEEKI 369
>gnl|CDD|224493 COG1577, ERG12, Mevalonate kinase [Lipid metabolism].
Length = 307
Score = 68.1 bits (167), Expect = 5e-13
Identities = 30/64 (46%), Positives = 41/64 (64%), Gaps = 7/64 (10%)
Query: 230 EEDKLKKLGDLMNDSHHSCSVLYEC---SCPELEELVNVCRNNGALGARLTGAGWGGCVV 286
+ ++LG+LMN + L + S PEL+ELV R+ GALGA+LTGAG GGC++
Sbjct: 221 QTGDFEELGELMNINQG----LLKALGVSTPELDELVEAARSLGALGAKLTGAGGGGCII 276
Query: 287 ALVK 290
AL K
Sbjct: 277 ALAK 280
Score = 28.0 bits (63), Expect = 6.6
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPK-AISIMAKSGFAELI 67
+G+GL SS A + AL A FGVE+ ++ +A ELI
Sbjct: 94 IGAGLGSSAAVSVAVIKALSAYFGVELSPEELAKLAN--KVELI 135
>gnl|CDD|240351 PTZ00298, PTZ00298, mevalonate kinase; Provisional.
Length = 328
Score = 68.3 bits (167), Expect = 5e-13
Identities = 33/91 (36%), Positives = 46/91 (50%), Gaps = 12/91 (13%)
Query: 202 KLHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGDLMNDSHHSCSVLYECSCPELEE 261
+L + SEAK ++ L ++G+LMN +H C L SC EL+
Sbjct: 218 RLLENYNACVSEAKEA-----------LQKGNLFRVGELMNANHDLCQKL-TVSCRELDS 265
Query: 262 LVNVCRNNGALGARLTGAGWGGCVVALVKES 292
+V CR GALGA+++G G GG VVAL
Sbjct: 266 IVQTCRTYGALGAKMSGTGRGGLVVALAASE 296
>gnl|CDD|179063 PRK00555, PRK00555, galactokinase; Provisional.
Length = 363
Score = 66.8 bits (163), Expect = 2e-12
Identities = 35/112 (31%), Positives = 54/112 (48%), Gaps = 5/112 (4%)
Query: 181 LTSIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGDL 240
++S+ A L L A +RA HV +E +RV F ++ + G L
Sbjct: 221 VSSLRAVQDRGLAALGAIADPIDARRARHVLTENQRVLDFAAALADS-----DFTAAGQL 275
Query: 241 MNDSHHSCSVLYECSCPELEELVNVCRNNGALGARLTGAGWGGCVVALVKES 292
+ SH S +E + ++ + + GALGAR+TG G+GGCV+ALV
Sbjct: 276 LTASHASMRDDFEITTERIDLIADSAVRAGALGARMTGGGFGGCVIALVPAD 327
Score = 31.8 bits (72), Expect = 0.53
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEV 51
+GSGLSSS A C+ A+ AA G +
Sbjct: 102 IGSGLSSSAALECAVLGAVGAATGTRI 128
>gnl|CDD|233017 TIGR00549, mevalon_kin, mevalonate kinase. This model represents
mevalonate kinase, the third step in the mevalonate
pathway of isopentanyl pyrophosphate (IPP) biosynthesis.
IPP is a common intermediate for a number of pathways
including cholesterol biosynthesis. This model covers
enzymes from eukaryotes, archaea and bacteria. The
related enzyme from the same pathway, phosphmevalonate
kinase, serves as an outgroup for this clade. 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 [Central intermediary
metabolism, Other].
Length = 274
Score = 65.8 bits (161), Expect = 2e-12
Identities = 28/62 (45%), Positives = 41/62 (66%), Gaps = 7/62 (11%)
Query: 230 EEDKLKKLGDLMNDSH---HSCSVLYECSCPELEELVNVCRNNGALGARLTGAGWGGCVV 286
E+ ++ LG+LMN + + V S P+L++LV + R GALGA+LTGAG GGC++
Sbjct: 217 EDGDVESLGELMNINQGLLKALGV----SHPKLDQLVEIARKAGALGAKLTGAGGGGCMI 272
Query: 287 AL 288
AL
Sbjct: 273 AL 274
Score = 29.9 bits (68), Expect = 1.5
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 26 GSGLSSSTAFVCSSTVALMAAFGVEVPKAISIMAKSGFAELI 67
G GL SS A + AL FG E+ K + + AE I
Sbjct: 91 GRGLGSSAAVAVALIRALADYFGSELSKEE-LAELANEAEKI 131
>gnl|CDD|219894 pfam08544, GHMP_kinases_C, GHMP kinases C terminal. This family
includes homoserine kinases, galactokinases and
mevalonate kinases.
Length = 86
Score = 60.2 bits (146), Expect = 9e-12
Identities = 31/85 (36%), Positives = 48/85 (56%), Gaps = 4/85 (4%)
Query: 226 SNLSEEDKLKKLGDLMNDSHHSC--SVLYECSCPELEELVNVCRNNGALGARLTGAGWGG 283
L E D L+ LG+L+N++ S + PEL+EL+ R GALGA+L+G+G G
Sbjct: 3 EALREGD-LELLGELLNENALSLEPLLYLGILSPELDELLEELRELGALGAKLSGSGGGP 61
Query: 284 CVVALVKESIDSQFILN-LKEQFYQ 307
V AL K+ D++ + L+E +
Sbjct: 62 TVFALFKDEEDAEEVAEALREAYPL 86
>gnl|CDD|179937 PRK05101, PRK05101, galactokinase; Provisional.
Length = 382
Score = 63.4 bits (155), Expect = 4e-11
Identities = 45/136 (33%), Positives = 69/136 (50%), Gaps = 30/136 (22%)
Query: 191 SLDVLNAAKQ------YKLHQRAAHVYSEAKRVHAFKDTVSSNLSEEDKLKKLGDLMNDS 244
+L+ NA K RA HV +E R + S+ L+ D LK++G+LM +S
Sbjct: 246 TLEQFNAVAAELDPVVAK---RARHVITENART---LEAASA-LAAGD-LKRMGELMAES 297
Query: 245 HHSCSVLYECSCPELEELV----NVCRNNGALGARLTGAGWGGCVVAL--------VKES 292
H S +E + P+++ LV V + G G R+TG G+GGC+VAL V+++
Sbjct: 298 HASMRDDFEITVPQIDTLVEIVKAVIGDQG--GVRMTGGGFGGCIVALVPEELVEAVRQA 355
Query: 293 IDSQF--ILNLKEQFY 306
+ Q+ LKE FY
Sbjct: 356 VAEQYEAKTGLKETFY 371
>gnl|CDD|215466 PLN02865, PLN02865, galactokinase.
Length = 423
Score = 62.5 bits (152), Expect = 8e-11
Identities = 72/301 (23%), Positives = 100/301 (33%), Gaps = 100/301 (33%)
Query: 26 GSGLSSSTAFVCSSTVALMAAF-----------------------------GVEVPKAIS 56
SGLSSS A VA + A G+ AI
Sbjct: 143 SSGLSSSAAV----GVAYLLALENANNLTVSPEDNIELDRLIENEYLGLRNGILDQSAI- 197
Query: 57 IMAKSGFAELIDFNPIRTTDVQLPAGGT-----FVVAHSLAESLKAITAASNYNNRVVEC 111
++++ G +D + V L F + + + A+T YN RV EC
Sbjct: 198 LLSRYGCLTFMDCKTLDHKLVSLQFQQPGGEKPFKILLAFSGLRHALTNKPGYNLRVSEC 257
Query: 112 RLTAIVLAIKLGMKPQEAISKVKTLSDVEGLCVAFACKNGSSDPVFAVKEFLRKEPYTAL 171
+ A L G E + L +VE E Y A
Sbjct: 258 QEAARFLLEASGNDELEPL-----LCNVE------------------------PEVYEAH 288
Query: 172 DIEKITEEKLTSIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRVHA-FKDTVSSNLSE 230
+ KL ++ A +RA H +SE RV + S NL E
Sbjct: 289 ------KCKLEAVLA------------------RRAEHYFSENMRVIKGVEAWASGNLEE 324
Query: 231 EDKLKKLGDLMNDSHHSCSVLYECSCPELEELVNVC-RNNGALGARLTGAGWGGCVVALV 289
G L++ S S YEC C L +L + + G GAR +GAG+ GC VA V
Sbjct: 325 ------FGKLISASGLSSIENYECGCEPLIQLYEILLKAPGVYGARFSGAGFRGCCVAFV 378
Query: 290 K 290
Sbjct: 379 D 379
>gnl|CDD|179677 PRK03926, PRK03926, mevalonate kinase; Provisional.
Length = 302
Score = 58.5 bits (142), Expect = 9e-10
Identities = 27/58 (46%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 232 DKLKKLGDLMNDSHHSCSVLYECSCPELEELVNVCRNNGALGARLTGAGWGGCVVALV 289
LG+LMN + L S EL EL+ R GALGA++TGAG GGC+VAL
Sbjct: 211 GDYVSLGELMNINQGLLDAL-GVSTKELSELIYAARTAGALGAKITGAGGGGCMVALA 267
>gnl|CDD|240347 PTZ00290, PTZ00290, galactokinase; Provisional.
Length = 468
Score = 57.1 bits (138), Expect = 4e-09
Identities = 26/81 (32%), Positives = 49/81 (60%), Gaps = 5/81 (6%)
Query: 228 LSEEDKLKKLGDLMNDSHHSCSVLYECSCPELE---ELVNVCRNNGALGARLTGAGWGGC 284
LS E++ +K G+++N H L + + PEL+ EL+N G G R+ G G+GGC
Sbjct: 356 LSREERFRKAGEILNAGHQGMRDLMKITTPELDFIHELIN--EEKGVAGGRMMGGGFGGC 413
Query: 285 VVALVKESIDSQFILNLKEQF 305
++ L+K++ + + +++E+F
Sbjct: 414 IILLLKKNAVDRVVAHVREKF 434
>gnl|CDD|215839 pfam00288, GHMP_kinases_N, GHMP kinases N terminal domain. This
family includes homoserine kinases, galactokinases and
mevalonate kinases.
Length = 67
Score = 34.1 bits (79), Expect = 0.009
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPK 53
LG+GL SS A + +AL FG+ + K
Sbjct: 10 LGAGLGSSAALAVALLLALNELFGLPLSK 38
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 34.6 bits (81), Expect = 0.074
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPKAIS 56
L S SSS A VC S++ALM A GV + ++
Sbjct: 432 LESNGSSSMASVCGSSLALMDA-GVPIKAPVA 462
>gnl|CDD|225325 COG2605, COG2605, Predicted kinase related to galactokinase and
mevalonate kinase [General function prediction only].
Length = 333
Score = 34.3 bits (79), Expect = 0.082
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 219 AFKDTVSSNLSEEDKLKKLGDLMNDSHHSCSVLYE-CSCPELEELVNVCRNNGALGARLT 277
KD + N + + G +++ + L S ++ + + NGA G +L+
Sbjct: 232 EMKDALVRN-----DIPEFGQILDRGWEAKKKLSSRISNDAIDRIYELALKNGAYGGKLS 286
Query: 278 GAGWGGCVVALVKES 292
GAG GG ++ S
Sbjct: 287 GAGGGGFLLFFCDPS 301
>gnl|CDD|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide
nucleotidyltransferase, repeat 2. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and in
quality control of ribosomal RNA precursors, with the
second repeat containing the active site. PNPase is part
of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 223
Score = 33.7 bits (78), Expect = 0.098
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPKAIS 56
L S SSS A VC ++ALM A GV + ++
Sbjct: 110 LESNGSSSMASVCGGSLALMDA-GVPIKAPVA 140
>gnl|CDD|107266 cd06271, PBP1_AglR_RafR_like, Ligand-binding domain of DNA
transcription repressors specific for raffinose (RafR)
and alpha-glucosides (AglR) which are members of the
LacI-GalR family of bacterial transcription regulators.
Ligand-binding domain of DNA transcription repressors
specific for raffinose (RafR) and alpha-glucosides
(AglR) which are members of the LacI-GalR family of
bacterial transcription regulators. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 268
Score = 31.4 bits (72), Expect = 0.52
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 33 TAFVCSSTVALMAAF------GVEVPKAISIMAKSGFAELIDFNPIRTTDVQLPAGGTFV 86
TA VCSS + + G+ + +S++ L+ F+P TT V+
Sbjct: 183 TAIVCSSELMALGVLAALAEAGLRPGRDVSVVGFDDSPPLLFFSPPLTT-VRSD---LRA 238
Query: 87 VAHSLAESL 95
LAE L
Sbjct: 239 AGRRLAELL 247
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 32.1 bits (74), Expect = 0.52
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 30 SSSTAFVCSSTVALMAAFGV 49
SSS A VC ++ALM A GV
Sbjct: 433 SSSMASVCGGSLALMDA-GV 451
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 30.6 bits (70), Expect = 1.3
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPKAIS 56
L S SSS A VC ++ALM A GV + ++
Sbjct: 430 LESNGSSSMASVCGGSLALMDA-GVPIKAPVA 460
>gnl|CDD|215363 PLN02677, PLN02677, mevalonate kinase.
Length = 387
Score = 30.2 bits (68), Expect = 1.4
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 229 SEEDKLKKLGDLMNDSHHSCSVLYECSCPELEELVNVCRNNGA--LGARLTGAGWGGCVV 286
+E+KLK+L + MN L +C + V R L ++LTGAG GGCV+
Sbjct: 291 EKEEKLKELME-MNQG------LLQCMGVSHSSIETVLRTTLKYKLVSKLTGAGGGGCVL 343
Query: 287 ALV 289
L+
Sbjct: 344 TLL 346
Score = 28.6 bits (64), Expect = 4.6
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGV 49
LGSGL SS AF + + AL+AA
Sbjct: 140 LGSGLGSSAAFCVALSAALLAASDS 164
>gnl|CDD|223099 COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid
metabolism].
Length = 245
Score = 29.2 bits (66), Expect = 2.5
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 121 KLGMKPQEAISKVKTLS-DVEGLCVAFACKNGS-SDPVFAVKEFLRKEPYTALDIEKITE 178
+L + +EAI K + + + GL + A G + V AV++ L E I E
Sbjct: 114 RLPEEVREAIEKAEEKTKNNTGLTLNIAVNYGGRDEIVDAVRKIAEDVAAGKLSPEDIDE 173
Query: 179 EKLTS 183
E ++S
Sbjct: 174 ELISS 178
>gnl|CDD|216923 pfam02190, LON, ATP-dependent protease La (LON) domain. This
domain has been shown to be part of the PUA superfamily.
Length = 191
Score = 28.5 bits (64), Expect = 3.4
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 6/85 (7%)
Query: 157 FAVKEFLRKEPYTALDIEKITEEKLTSIF----ANSSSSLDVLNAAKQYKLHQRAAHVYS 212
F + E ++EPY ++E + EE+L + A ++ + L
Sbjct: 87 FRILELEQEEPYLVAEVEDLPEEELEELLEALEALVKELIEKIKELLPLLLPLELLLKID 146
Query: 213 EAKRVHAFKDTVSSNL--SEEDKLK 235
+ + D ++S L S E+K +
Sbjct: 147 DIEDPGRLADLIASLLPLSPEEKQE 171
>gnl|CDD|226917 COG4542, PduX, Protein involved in propanediol utilization, and
related proteins (includes coumermycin biosynthetic
protein), possible kinase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 293
Score = 29.0 bits (65), Expect = 3.5
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 26 GSGLSSSTAFVCSSTVALMAAFGVEV 51
G G++SSTA + ++ A G E+
Sbjct: 95 GKGMASSTADLVATARATARFLGREL 120
>gnl|CDD|188029 TIGR00154, ispE, 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.
Members of this family of GHMP kinases were previously
designated as conserved hypothetical protein YchB or as
isopentenyl monophosphate kinase. It is now known, in
tomato and E. coli, to encode
4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an
enzyme of the deoxyxylulose phosphate pathway of
terpenoid biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 294
Score = 29.0 bits (65), Expect = 3.5
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 257 PELEELVNVCRNNGALGARLTGAGWGGCVVALVKESIDSQFILNLKEQFYQSRIDRGV 314
E+ + +N G R++G+ G CV AL +++ +L ++ + +G
Sbjct: 229 TEVAQALNWLLEYGLAPERMSGS--GPCVFALFDMESEAEQVLEQAPEWLNGFVAKGY 284
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 28.9 bits (66), Expect = 3.6
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 161 EFLRKE-PY-TALDIEKITEEKLTSIFAN 187
L E PY A++IEK E L I A
Sbjct: 201 RLLGDELPYSVAVEIEKFEERGLVRIEAT 229
>gnl|CDD|224599 COG1685, COG1685, Archaeal shikimate kinase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 278
Score = 28.8 bits (65), Expect = 3.7
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVP 52
+GSGL SS+A + A++ A G E+
Sbjct: 81 VGSGLKSSSAASNALVKAVLKALGEEID 108
>gnl|CDD|234920 PRK01212, PRK01212, homoserine kinase; Provisional.
Length = 301
Score = 29.0 bits (66), Expect = 3.9
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 257 PELEELVNVCRNNGALGARLTGAGWGGCVVAL--------VKESIDSQFILNLKEQFYQS 308
P E+ GALGA ++GA G V AL V +++ F+ ++ +
Sbjct: 234 PGFAEVRQAALEAGALGAGISGA--GPTVFALCDKEDAEKVADALQKAFLQGIEGFVHVL 291
Query: 309 RIDRG 313
R+D
Sbjct: 292 RLDTA 296
>gnl|CDD|222027 pfam13288, DXPR_C, DXP reductoisomerase C-terminal domain. This is
the C-terminal domain of the
1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme.
This domain forms a left handed super-helix.
Length = 118
Score = 27.8 bits (63), Expect = 4.2
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 147 ACKNGSSDPVF-------AVKEFLRKE-PYTALDIEKITEEKLTSIFANSSSSL-DVLNA 197
A + G + P AV FL + + LDI +I E+ L + SL D+L A
Sbjct: 53 ALRAGGTAPAVLNAANEVAVAAFLEGKIGF--LDIARIVEKVLDAHEPIEPPSLEDILEA 110
>gnl|CDD|216392 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate
synthase. Previously known as uncharacterized protein
family UPF0015, a single member of this family has been
identified as an undecaprenyl diphosphate synthase.
Length = 222
Score = 28.3 bits (64), Expect = 5.1
Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 142 LCVAFACKNGSSDPVFAVKEFLRKEPYTALDIEKITEEKLTS 183
L +A G + V AVK R L E I EE +
Sbjct: 116 LNIAL-NYGGRDEIVDAVKRLARDVADGKLSPEDIDEEVIEK 156
>gnl|CDD|215187 PLN02328, PLN02328, lysine-specific histone demethylase 1 homolog.
Length = 808
Score = 28.8 bits (64), Expect = 5.2
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 205 QRAAHVYSEA-KRVHAFKDTVSSNLSEEDKLKKLGDLMNDSHHSCSVLYECSCPELEEL 262
+ AA++ A +R D V+++ E+D L +L D + + S S+L++ + E L
Sbjct: 670 REAANILRVARRRSLCIDDKVNNDEEEDDCLDQLFDTPDLTFGSFSILFDPRSNDPESL 728
>gnl|CDD|215248 PLN02451, PLN02451, homoserine kinase.
Length = 370
Score = 28.2 bits (63), Expect = 6.4
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 25 LGSGLSSSTAFVCSSTVALMAAFGVEVPKAISIMA 59
LGSGL SS A ++ VA+ FG + K ++A
Sbjct: 145 LGSGLGSSAASAAAAAVAVNELFGSPLGKDDLVLA 179
>gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2.
Members of the HesA/MoeB/ThiF family of proteins
(pfam00899) include a number of members encoded in the
midst of thiamine biosynthetic operons. This mix of
known and putative ThiF proteins shows a deep split in
phylogenetic trees, with one the E. coli ThiF and the E.
coli MoeB proteins seemingly more closely related than
E. coli ThiF and Campylobacter (for example) ThiF. This
model represents the divergent clade of putative ThiF
proteins such found in Campylobacter [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 200
Score = 27.5 bits (61), Expect = 7.7
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 157 FAVKEFLRK-EPYTALDI--EKITEEKLTSIFANSSSSLDVLNAAKQYKLHQRAAH-VYS 212
A+KE + + PYT ++ EKITEE + F ++ + + A+ + A Y
Sbjct: 77 EALKENISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAKAMLVNAVLEKYK 136
Query: 213 EAKRVHA--FKDTVSSNLSEEDKLKK----LGDLMND 243
+ + A +N + K+ K GD +D
Sbjct: 137 DKYLIAASGLAGYDDANSIKTRKISKHFYLCGDGKSD 173
>gnl|CDD|223161 COG0083, ThrB, Homoserine kinase [Amino acid transport and
metabolism].
Length = 299
Score = 27.9 bits (63), Expect = 7.8
Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 257 PELEELVNVCRNNGALGARLTGAGWGGCVVALVKESIDSQFILNLKEQFYQSRIDRGV 314
P E+ GALGA L+GAG V AL ES D++ L E+ Y+ I V
Sbjct: 230 PGYAEVREAALEAGALGATLSGAGPT--VFALADES-DAEKAAALLEELYEQGIKGRV 284
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 28.0 bits (62), Expect = 9.8
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 178 EEKLTSIFANSSSSLDVLNAAKQYKLHQRAAHVYSEAKRVHAFKDTVSSNL--SEEDKLK 235
E+ + S LN K+YK+H++ HV + + S+L E + K
Sbjct: 557 EQLVQSTEIKLDELKVDLNR-KRYKIHKQVIHVIDITSKFKI---NIQSSLEDLENELGK 612
Query: 236 KLGDLMN 242
+ +L N
Sbjct: 613 VIEELRN 619
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.371
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,506,917
Number of extensions: 1552453
Number of successful extensions: 1546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1525
Number of HSP's successfully gapped: 58
Length of query: 338
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 240
Effective length of database: 6,590,910
Effective search space: 1581818400
Effective search space used: 1581818400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)