RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9726
(381 letters)
>gnl|CDD|232856 TIGR00175, mito_nad_idh, isocitrate dehydrogenase, NAD-dependent,
mitochondrial type. Several NAD- or NADP-dependent
dehydrogenases, including 3-isopropylmalate
dehydrogenase, tartrate dehydrogenase, and the
multimeric forms of isocitrate dehydrogenase, share a
nucleotide binding domain unrelated to that of lactate
dehydrogenase and its homologs. These enzymes
dehydrogenate their substates at a H-C-OH site adjacent
to a H-C-COOH site; the latter carbon, now adjacent to a
carbonyl group, readily decarboxylates. Mitochondrial
NAD-dependent isocitrate dehydrogenases (IDH) resemble
prokaryotic NADP-dependent IDH and 3-isopropylmalate
dehydrogenase (an NAD-dependent enzyme) more closely
than they resemble eukaryotic NADP-dependent IDH. The
mitochondrial NAD-dependent isocitrate dehydrogenase is
believed to be an alpha(2)-beta-gamma heterotetramer.
All subunits are homologous and found by this model. The
NADP-dependent IDH of Thermus aquaticus thermophilus
strain HB8 resembles these NAD-dependent IDH, except for
the residues involved in cofactor specificity, much more
closely than it resembles other prokaryotic
NADP-dependent IDH, including that of Thermus aquaticus
strain YT1 [Energy metabolism, TCA cycle].
Length = 333
Score = 466 bits (1202), Expect = e-166
Identities = 184/311 (59%), Positives = 226/311 (72%), Gaps = 2/311 (0%)
Query: 71 GRTKCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTMSAPLETVADSIARN 130
G+ TLIPGDG+GPE+ SV+++F+AANVP++FE S + + +SI RN
Sbjct: 2 GKYTVTLIPGDGIGPEISGSVKKIFRAANVPIEFEEIDVSPQTDGKTEIPDEAVESIKRN 61
Query: 131 GICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVKVRHSNVDCVIIREQ 190
+ LKG L TP G ++LN+ LRK LDLYANVVH KSLPG K RH +VD VIIRE
Sbjct: 62 KVALKGPLETP--IGKGGHRSLNVALRKELDLYANVVHCKSLPGFKTRHEDVDIVIIREN 119
Query: 191 TEGEYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGD 250
TEGEYS LEHE VPGVVE LK++T +KS RIA++AF+YA KN RKKVTAVHKANIMKL D
Sbjct: 120 TEGEYSGLEHESVPGVVESLKVITRDKSERIARYAFEYARKNGRKKVTAVHKANIMKLAD 179
Query: 251 GLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVG 310
GLFLN C+E+AK YP I FE MIVDN MQ+VS P QFDVMVMPNLYGNI+ NL +GLVG
Sbjct: 180 GLFLNVCREVAKEYPDITFESMIVDNTCMQLVSRPSQFDVMVMPNLYGNILSNLGAGLVG 239
Query: 311 GAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIR 370
G G+V GA+ + VFEPG RHT + G+N+ANPTA++L S ML+H+ L+ + D I+
Sbjct: 240 GPGLVPGANIGRDYAVFEPGVRHTGPDIAGQNIANPTALILSSVMMLNHLGLKEHADRIQ 299
Query: 371 NAVNRVLKAGK 381
AV + GK
Sbjct: 300 KAVLSTIAEGK 310
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 376 bits (966), Expect = e-129
Identities = 167/309 (54%), Positives = 214/309 (69%), Gaps = 9/309 (2%)
Query: 76 TLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTMSAPLETVADSIARNGICLK 135
TLIPGDG+GP + +V++V +A + PV FE + EV+ M E V +SI RN +CLK
Sbjct: 34 TLIPGDGIGPLVTGAVEQVMEAMHAPVYFERY---EVHGDMKKVPEEVLESIRRNKVCLK 90
Query: 136 GVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVKVRHSNVDCVIIREQTEGEY 195
G L+TP G + +LN++LRK LDL+A++V+ +LPG+ RH NVD V+IRE TEGEY
Sbjct: 91 GGLATP---VGGGVSSLNVQLRKELDLFASLVNCFNLPGLPTRHENVDIVVIRENTEGEY 147
Query: 196 SALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLN 255
S LEHE VPGVVE LK++T S RIAK+AF+YA NNRKKVTAVHKANIMKL DGLFL
Sbjct: 148 SGLEHEVVPGVVESLKVITKFCSERIAKYAFEYAYLNNRKKVTAVHKANIMKLADGLFLE 207
Query: 256 SCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGVV 315
SC+E+AK YP I++ ++IVDNC MQ+VS P QFDVMV PNLYGN+V N A+G+ GG GV+
Sbjct: 208 SCREVAKKYPGIKYNEIIVDNCCMQLVSKPEQFDVMVTPNLYGNLVANTAAGIAGGTGVM 267
Query: 316 AGASWSPECVVFEPGARH---TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNA 372
G + + VFE GA + V + ANP A+LL S ML H+ + D + A
Sbjct: 268 PGGNVGADHAVFEQGASAGNVGNEKLVEQKKANPVALLLSSAMMLRHLQFPSFADRLETA 327
Query: 373 VNRVLKAGK 381
V RV+ GK
Sbjct: 328 VKRVIAEGK 336
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 329 bits (845), Expect = e-111
Identities = 152/317 (47%), Positives = 210/317 (66%), Gaps = 19/317 (5%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFF-SEVNP-TMSAPLETVADSIARNG 131
TL PGDG+GPE+ SV++VF AA VP+++E + + V+P T S +S+ RN
Sbjct: 43 TATLFPGDGIGPEIAESVKQVFTAAGVPIEWEEHYVGTTVDPRTGSFLTWESLESVRRNK 102
Query: 132 ICLKGVLSTPDYSHTGE-LQTLNMKLRKALDLYANVVHVKSLPGVKVRHSNVDCVIIREQ 190
+ LKG ++TP G+ ++LN+ LRK L LYANV SLPG K R+ +VD V IRE
Sbjct: 103 VGLKGPMATP----IGKGHRSLNLTLRKELGLYANVRPCYSLPGYKTRYDDVDLVTIREN 158
Query: 191 TEGEYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGD 250
TEGEYS LEH+ V GVVE LKI+T + S R+A++AF YA + RK+V+A+HKANIMK D
Sbjct: 159 TEGEYSGLEHQVVRGVVESLKIITRQASLRVAEYAFHYAKTHGRKRVSAIHKANIMKKTD 218
Query: 251 GLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVG 310
GLFL C+E+A+ YP+I +E++I+DNC M +V NP FDV+VMPNLYG+I+ +L +GL+G
Sbjct: 219 GLFLKCCREVAEKYPEIVYEEVIIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLIG 278
Query: 311 GAGVVAGASWSPECVVFEPG-----ARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQY 364
G G+ +P C + E G A H + + GKN+ANPTA+LL + ML H+ L
Sbjct: 279 GLGL------TPSCNIGENGLALAEAVHGSAPDIAGKNLANPTALLLSAVMMLRHLKLNE 332
Query: 365 YGDMIRNAVNRVLKAGK 381
+ I NA+ + GK
Sbjct: 333 QAEQIHNAILNTIAEGK 349
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 320 bits (822), Expect = e-108
Identities = 126/323 (39%), Positives = 179/323 (55%), Gaps = 14/323 (4%)
Query: 71 GRTKCTLIPGDGVGPELVYSVQEVFKAAN---VPVDFEPFFFS-EVNPTMSAPL--ETVA 124
+IPGDG+GPE++ + +V +AA + +FE E PL ET+
Sbjct: 2 KTYTIAVIPGDGIGPEVMAAALKVLEAAAEFGLDFEFEEAEVGGEAYDKHGEPLPEETL- 60
Query: 125 DSIARNGICLKGVLSTPDYSHTGE-LQTLNMKLRKALDLYANVVHVKSLPGVK-VRHSNV 182
+S+ + L G + P + + L + LRK LDLYAN+ KSLPG+K V
Sbjct: 61 ESLKKADAILFGAVGGPKWDPLPRPERGLLLALRKELDLYANLRPAKSLPGLKSPLVKGV 120
Query: 183 DCVIIREQTEGEYSALEHECVPG--VVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAV 240
D VI+RE TEG Y E + G V K++T + S RIA+FAF+ A K RKKVT+V
Sbjct: 121 DIVIVRENTEGLYFGEEGRILGGGEVAIDTKVITRKGSERIARFAFELARKRGRKKVTSV 180
Query: 241 HKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNI 300
HKAN++KL DGL+ +E+AK YP ++ + M VD MQ+V NP QFDV+V NL+G+I
Sbjct: 181 HKANVLKLSDGLWREVVEEVAKEYPDVELDHMYVDAAAMQLVRNPEQFDVIVTSNLFGDI 240
Query: 301 VDNLASGLVGGAGVVAGASWSPEC--VVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLS 358
+ + A+ L G G+ A+ E +FEP + + GK +ANP A +L + ML
Sbjct: 241 LSDEAAALTGSLGLAPSANLGDERGPALFEP-VHGSAPDIAGKGIANPIATILSAAMMLR 299
Query: 359 HVNLQYYGDMIRNAVNRVLKAGK 381
H+ + D I NAV +VL G
Sbjct: 300 HLGEKEAADAIENAVEKVLAEGG 322
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 293 bits (752), Expect = 1e-97
Identities = 131/317 (41%), Positives = 188/317 (59%), Gaps = 20/317 (6%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTMSA------PLETVADSI 127
T+IPGDG+GP ++ + ++ ++E F++ T P T+ D I
Sbjct: 4 TITVIPGDGIGPSIIDATLKILDKLGCDFEYE---FADAGLTALEKHGELLPQRTL-DLI 59
Query: 128 ARNGICLKGVLSTPDYSHTGE-LQTLNMKLRKALDLYANVVHVKSLPGVKVRHSNVDCVI 186
+N I LKG L+TP GE ++N+ LRK DLYANV V S PG K R+ N+D +
Sbjct: 60 EKNKIALKGPLTTP----VGEGFTSINVTLRKKFDLYANVRPVLSFPGTKARYDNIDIIT 115
Query: 187 IREQTEGEYSALEHECVP--GVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKAN 244
+RE TEG YS E I+T + + RI +FA++ A K RKKVTAVHKAN
Sbjct: 116 VRENTEGMYSGEGQTVSEDGETAEATSIITRKGAERIVRFAYELARKEGRKKVTAVHKAN 175
Query: 245 IMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNL 304
IMK GLFL +E+A YP I+FE+MIVD MQ+V NP QFDV+V NL+G+I+ +L
Sbjct: 176 IMKSTSGLFLKVAREVALRYPDIEFEEMIVDATCMQLVMNPEQFDVIVTTNLFGDILSDL 235
Query: 305 ASGLVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQ 363
+GLVGG G+ GA+ + +FE A H + + GKN+ANPT+++L + +ML ++ +
Sbjct: 236 CAGLVGGLGMAPGANIGRDAAIFE--AVHGSAPDIAGKNLANPTSVILAAIQMLEYLGMP 293
Query: 364 YYGDMIRNAVNRVLKAG 380
+ IR A+ V++AG
Sbjct: 294 DKAERIRKAIVAVIEAG 310
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 265 bits (679), Expect = 1e-84
Identities = 121/319 (37%), Positives = 183/319 (57%), Gaps = 14/319 (4%)
Query: 69 PEGRTKCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPF-----FFSEVNPTMSAPLETV 123
+T T+ GDG+GPE++ +V ++ +AA P++ E + + + +P
Sbjct: 1 MAEKTPITVAYGDGIGPEIMEAVLKILEAAGAPLEIETIEIGEKVYKKGWTSGISP-SAW 59
Query: 124 ADSIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSL-PGVKVRHSNV 182
+SI R + LK ++TP G ++LN+ LRK L LYANV S P V+ +H N+
Sbjct: 60 -ESIRRTKVLLKAPITTP---QGGGYKSLNVTLRKTLGLYANVRPCVSYHPFVETKHPNL 115
Query: 183 DCVIIREQTEGEYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHK 242
D VIIRE E Y+ +EH P V +CLK+++ S +I ++AF+YA N RKKVT + K
Sbjct: 116 DVVIIRENEEDLYAGIEHRQTPDVYQCLKLISRPGSEKIIRYAFEYARANGRKKVTCLTK 175
Query: 243 ANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVD 302
NIMKL DGLF E+AK YP I+ E IVD ++ +NP FDV+V PNLYG+I+
Sbjct: 176 DNIMKLTDGLFHKVFDEIAKEYPDIEAEHYIVDIGAARLATNPENFDVIVTPNLYGDILS 235
Query: 303 NLASGLVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVN 361
++A+ + G G+ A+ E +FE A H + + GKN+ANP+ +L + ML H+
Sbjct: 236 DIAAEISGSVGLAGSANIGEEYAMFE--AVHGSAPDIAGKNIANPSGLLNAAVMMLVHIG 293
Query: 362 LQYYGDMIRNAVNRVLKAG 380
++I NA + L+ G
Sbjct: 294 QFDIAELIENAWLKTLEDG 312
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 249 bits (638), Expect = 3e-80
Identities = 112/332 (33%), Positives = 165/332 (49%), Gaps = 28/332 (8%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTMSA--------PLETVAD 125
K ++PGDG+GPE+ + +V KAA E F F E +A P ET+ +
Sbjct: 1 KIAVLPGDGIGPEVTEAALKVLKAALEKAPLE-FEFEEGLAGGAAIDETGTPLPEETL-E 58
Query: 126 SIARNGICLKGVLSTPDYSHTGELQTLN--MKLRKALDLYANVVHVKSLPGVKV------ 177
+ + L G + P ++ G ++ N + LRK L L+AN+ VK P +
Sbjct: 59 ACKKADAVLLGAVGGPKWN-PGGVRPENGLLALRKELGLFANLRPVKVFPSLGDASPLKR 117
Query: 178 -RHSNVDCVIIREQTEGEYSALEHECVPGVVEC-----LKIVTAEKSRRIAKFAFDYATK 231
VD VI+RE T G Y + K+ + ++ RIA+ AF+ A K
Sbjct: 118 EVVEGVDIVIVRELTGGIYFGIPKGIKGSGNGEEGAVDTKLYSRDEIERIARVAFELARK 177
Query: 232 NNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVM 291
RKKVT+V KAN++K + YP ++ E M+VDN MQ+V NP QFDV+
Sbjct: 178 RGRKKVTSVDKANVLKSSRLWRKIVEEVAKAEYPDVELEHMLVDNAAMQLVKNPKQFDVI 237
Query: 292 VMPNLYGNIVDNLASGLVGGAGVVAGASWSPECV-VFEPGARHTYSEAVGKNVANPTAML 350
V NL+G+I+ + AS L G G++ AS + +FEP + + GK ANP A +
Sbjct: 238 VTENLFGDILSDEASMLTGSLGLLPSASLGADGFGLFEP-VHGSAPDIAGKGKANPIATI 296
Query: 351 LCSTKMLSH-VNLQYYGDMIRNAVNRVLKAGK 381
L + ML H + L+ D I AV +VL+AG
Sbjct: 297 LSAAMMLRHSLGLEDEADKIEAAVLKVLEAGI 328
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 228 bits (584), Expect = 2e-72
Identities = 113/319 (35%), Positives = 166/319 (52%), Gaps = 24/319 (7%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVPVDF-------EPFFFSEVNPTMSAPLETVADS 126
K +I GDG+G E+V + V +A +P +F E F + + P ET+ +
Sbjct: 3 KICVIEGDGIGKEVVPAALHVLEATGLPFEFVYAEAGDEVFEKTGK----ALPEETIEAA 58
Query: 127 IARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVKVRHSNVDCVI 186
+ + T + +KLR+ LD YANV VKS GVK + ++D VI
Sbjct: 59 KEADAVLFGAAGETA--------ADVIVKLRRILDTYANVRPVKSYKGVKCLYPDIDYVI 110
Query: 187 IREQTEGEYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATK----NNRKKVTAVHK 242
+RE TEG Y +E E GV +++T + S RI +FAF+ A + KVT HK
Sbjct: 111 VRENTEGLYKGIEAEIADGVTVATRVITRKASERIFRFAFEMAKRRKKMGKEGKVTCAHK 170
Query: 243 ANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVD 302
AN++K DGLF + E+AK YP I+ E VD M I++ P FDV+V NL+G+I+
Sbjct: 171 ANVLKKTDGLFKKTFYEVAKEYPDIKAEDYYVDAMNMYIITRPQTFDVVVTSNLFGDILS 230
Query: 303 NLASGLVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNL 362
+ A+GLVGG G+ A+ + +FEP + + GK +ANPTA +L + ML H+
Sbjct: 231 DGAAGLVGGLGLAPSANIGDKYGLFEP-VHGSAPDIAGKGIANPTATILTAVLMLRHLGE 289
Query: 363 QYYGDMIRNAVNRVLKAGK 381
D + A+ VL G
Sbjct: 290 NEEADKVEKALEEVLALGL 308
>gnl|CDD|233717 TIGR02088, LEU3_arch, isopropylmalate/isohomocitrate
dehydrogenases. This model represents a group of
archaeal decarboxylating dehydrogenases which include
the leucine biosynthesis enzyme 3-isopropylmalate
dehydrogenase (LeuB, LEU3) and the methanogenic cofactor
CoB biosynthesis enzyme isohomocitrate dehydrogenase
(AksF). Both of these have been characterized in
Methanococcus janaschii. Non-methanogenic archaea have
only one hit to this model and presumably this is LeuB,
although phylogenetic trees cannot establish which gene
is which in the methanogens. The AksF gene is capable of
acting on isohomocitrate, iso(homo)2-citrate and
iso(homo)3-citrate in the successive elongation cycles
of coenzyme B (7-mercaptoheptanoyl-threonine phosphate).
This family is closely related to both the LeuB genes
found in TIGR00169 and the mitochondrial eukaryotic
isocitrate dehydratases found in TIGR00175. All of these
are included within the broader subfamily model,
pfam00180.
Length = 322
Score = 227 bits (581), Expect = 4e-72
Identities = 112/310 (36%), Positives = 171/310 (55%), Gaps = 14/310 (4%)
Query: 77 LIPGDGVGPELVYSVQEVFKAANVPVDFEPF--FFSEVNPTMSAPLETVADSIARNGICL 134
+IPGDG+GPE++ + + + ++F F + SA E + I + L
Sbjct: 3 VIPGDGIGPEVIEAAIRILNKLGLEIEFIEFEAGDEALKKYGSALPEDTLEEIRKADAIL 62
Query: 135 KGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK-VRHSNVDCVIIREQTEG 193
G ++TP +++ + LRK LDLYANV KSLPG+ + + D VI+RE TEG
Sbjct: 63 FGAVTTP---ANPGYKSVIVTLRKELDLYANVRPAKSLPGIPDLYPNGKDIVIVRENTEG 119
Query: 194 EYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLF 253
Y+ E ++++T E S RIA+FAF+ A + NRK VT VHKAN++K DGLF
Sbjct: 120 LYAGFE-FGFSDRAIAIRVITREGSERIARFAFNLAKERNRK-VTCVHKANVLKGTDGLF 177
Query: 254 LNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAG 313
C+E+AK Y +++ M VD+ M +V +P +FDV+V N++G+I+ +LAS L G G
Sbjct: 178 REVCREIAKRYG-VEYRDMYVDSAAMNLVKDPWRFDVIVTTNMFGDILSDLASALAGSLG 236
Query: 314 VVAGASWSPECVVFEP--GARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRN 371
+ A+ +FEP G+ + GK +ANPTA +L ML ++ G ++
Sbjct: 237 LAPSANIGDRKALFEPVHGSA---PDIAGKGIANPTAAILSVAMMLDYLGELEKGKLVWE 293
Query: 372 AVNRVLKAGK 381
AV + GK
Sbjct: 294 AVEYYIIEGK 303
>gnl|CDD|234062 TIGR02924, ICDH_alpha, isocitrate dehydrogenase. This family of
mainly alphaproteobacterial enzymes is a member of the
isocitrate/isopropylmalate dehydrogenase superfamily
described by pfam00180. Every member of the seed of this
model appears to have a TCA cycle lacking only a
determined isocitrate dehydrogenase. The precise
identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH --
1.1.1.42) is unclear [Energy metabolism, TCA cycle].
Length = 473
Score = 214 bits (546), Expect = 4e-65
Identities = 112/316 (35%), Positives = 177/316 (56%), Gaps = 16/316 (5%)
Query: 73 TKCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTM------SAPLETVADS 126
T+ GDG+GPE++ +V + K A P+D E E+ + S + +S
Sbjct: 1 IPITVAYGDGIGPEIMEAVLLILKEAEAPIDIETI---EIGEKVYKKGWPSGISPSSWES 57
Query: 127 IARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSL-PGVKVRHSNVDCV 185
I R + LK ++TP G ++LN+ LRK L LYAN+ S P ++ + N++ V
Sbjct: 58 IRRTKVLLKAPITTP---QGGGHKSLNVTLRKTLGLYANIRPCVSYHPFIETKSPNLNIV 114
Query: 186 IIREQTEGEYSALEHECVPGVVECLKIVTAEKSRRIAKFAFDYATKNNRKKVTAVHKANI 245
I+RE E Y+ +E+ P EC K++T S +I ++AF+YA K+NRKKVT + K NI
Sbjct: 115 IVRENEEDLYTGIEYRQTPDTYECTKLITRSGSEKICRYAFEYARKHNRKKVTCLTKDNI 174
Query: 246 MKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLA 305
MK+ DG+F ++A YP I+ E IVD ++ +NP FDV+V PNLYG+I+ ++A
Sbjct: 175 MKMTDGIFHKIFDKIAAEYPDIESEHYIVDIGMARLATNPENFDVIVTPNLYGDILSDVA 234
Query: 306 SGLVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQY 364
+ + G G+ A+ E +FE A H + + G+N+ANP+ +L + +ML H+
Sbjct: 235 AEISGSVGLAGSANIGEEYAMFE--AVHGSAPDIAGQNIANPSGLLNAAIQMLVHIGQSD 292
Query: 365 YGDMIRNAVNRVLKAG 380
+I NA + L+ G
Sbjct: 293 IAQLIYNAWLKTLEDG 308
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 172 bits (438), Expect = 3e-50
Identities = 112/350 (32%), Positives = 165/350 (47%), Gaps = 67/350 (19%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEV-----------NPTMSAPLET 122
K ++PGDG+GPE++ +V A F+ F F E P P ET
Sbjct: 4 KIAVLPGDGIGPEVMAEAVKVLDAVAEKFGFD-FEFEEALVGGAAIDAHGVP---LPEET 59
Query: 123 V-----ADSIARNGICLKGVLSTPDYSH--------TGELQTLNMKLRKALDLYANVVHV 169
+ AD++ L G + P + + G L LRK L L+AN+
Sbjct: 60 LEACRAADAV------LLGAVGGPKWDNLPPDVRPERGLL-----ALRKELGLFANLRPA 108
Query: 170 KSLPGVK-------VRHSNVDCVIIREQTEGEYSALEHECVPGVVECLK---------IV 213
K PG+ + +D +I+RE T G Y P E L +
Sbjct: 109 KLYPGLADASPLKPEIVAGLDILIVRELTGGIYFG-----EPRGREGLGGEERAFDTMVY 163
Query: 214 TAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMI 273
T E+ RIA+ AF+ A + RKKVT+V KAN+++ L+ E+AK YP ++ M
Sbjct: 164 TREEIERIARVAFELA-RKRRKKVTSVDKANVLE-SSRLWREVVTEVAKEYPDVELSHMY 221
Query: 274 VDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWSPECV-VFEPGAR 332
VDN MQ+V NP QFDV+V NL+G+I+ + A+ L G G++ AS ++EP
Sbjct: 222 VDNAAMQLVRNPKQFDVIVTENLFGDILSDEAAMLTGSLGMLPSASLGESGPGLYEPI-- 279
Query: 333 H-TYSEAVGKNVANPTAMLLCSTKMLSH-VNLQYYGDMIRNAVNRVLKAG 380
H + + GK +ANP A +L + ML + + L+ D I AV +VL G
Sbjct: 280 HGSAPDIAGKGIANPIATILSAAMMLRYSLGLEEAADAIEAAVEKVLAQG 329
Score = 28.9 bits (66), Expect = 5.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 45 KCTLIPGDGVGPELV 59
K ++PGDG+GPE++
Sbjct: 4 KIAVLPGDGIGPEVM 18
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 150 bits (380), Expect = 2e-41
Identities = 106/360 (29%), Positives = 162/360 (45%), Gaps = 62/360 (17%)
Query: 78 IPGDGVGPELVYSVQEVFKAA-------NVPVDFEPFFFSEVNPTMSA---PLETVADSI 127
I GDG+G E+ ++ +V AA ++++ E + P+ET ++I
Sbjct: 24 IEGDGIGDEITRAIWKVIDAAVEKAYGGERKIEWKEVDAGEKARDKTGDQLPIET-LEAI 82
Query: 128 ARNGICLKGVLSTPDYSHTGE-LQTLNMKLRKALDLYANVVHVKSLPGVK--VRHS-NVD 183
+ G+ +KG L+TP G+ ++LN+ LR+ LDLY V+ PGV V+ VD
Sbjct: 83 KKYGVAIKGPLTTP----VGKGWRSLNVTLRQILDLYVFRRPVRYFPGVPSPVKRPEKVD 138
Query: 184 CVIIREQTEGEYSA----------------LEHECVPGVVE-------CLKIVTAEKSRR 220
VI RE TE Y+ LE E + +K ++ E S R
Sbjct: 139 MVIFRENTEDIYAGIEWKAGSPEALKLIFFLEDEMGVKKIRFPEDSGIGIKPISKEGSIR 198
Query: 221 IAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMA------------------- 261
+ + A +YA +N RK VT VHK NIMK +G F + E+A
Sbjct: 199 LVRAAIEYAIENKRKSVTLVHKGNIMKFTEGAFKDWGYEVAEEEEFGDEVVTGKEKFELK 258
Query: 262 KLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWS 321
KI ++ I D+ QI+ P ++DV+ NL G+ + + + VGG G+ GA+
Sbjct: 259 GPKGKIVYKDRIADDMLQQILLRPGEYDVIATKNLNGDYISDALAAQVGGLGLAPGANIG 318
Query: 322 PECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKAGK 381
FE T + GK+ NP A +L T ML H D+I AV +++GK
Sbjct: 319 DGTAEFEA-THGTAPKYAGKDSTNPIASILSGTMMLRHRGWLEAADLIEKAVEDTIESGK 377
>gnl|CDD|233718 TIGR02089, TTC, tartrate dehydrogenase. Tartrate dehydrogenase
catalyzes the oxidation of both meso- and (+)-tartrate
as well as a D-malate. These enzymes are closely related
to the 3-isopropylmalate and isohomocitrate
dehydrogenases found in TIGR00169 and TIGR02088,
respectively [Energy metabolism, Other].
Length = 352
Score = 146 bits (371), Expect = 7e-41
Identities = 101/330 (30%), Positives = 158/330 (47%), Gaps = 28/330 (8%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAA-----NVPVDFEPF-----FFSEVNPTMSAP-LET 122
+ IPGDG+G E+V + +V +AA + F F ++ E M LE
Sbjct: 5 RIAAIPGDGIGKEVVAAALQVLEAAAKRHGGFSLHFTEFPWSCDYYKEHGKMMPEDGLEK 64
Query: 123 VADSIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK--VRH- 179
+ + I L V L L +K+R+ D YANV K LPGV +R+
Sbjct: 65 LKK---FDAIFLGAVGWPALVPDHISLWGLLLKIRREFDQYANVRPAKLLPGVTSPLRNC 121
Query: 180 --SNVDCVIIREQTEGEYSALEHECVPGVVECLKIVTAEKSR----RIAKFAFDYATKNN 233
+ D V++RE +EGEYS + G E + A +R RI +FAF+ A K
Sbjct: 122 GPGDFDFVVVRENSEGEYSGVGGRIHRGTDEEVATQNAIFTRKGVERIMRFAFELAQKR- 180
Query: 234 RKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVM 293
RK +T+ K+N ++ + E+A YP ++++ +D + V P FDV+V
Sbjct: 181 RKHLTSATKSNGIRHSMPFWDEVFAEVAAEYPDVEWDSYHIDALAARFVLKPETFDVIVA 240
Query: 294 PNLYGNIVDNLASGLVGGAGVVAGASWSPE---CVVFEPGARHTYSEAVGKNVANPTAML 350
NL+G+I+ +L + L+G GV A+ +PE +FEP + + GK +ANP +
Sbjct: 241 SNLFGDILSDLGAALMGSLGVAPSANINPEGKFPSMFEP-VHGSAPDIAGKGIANPIGAI 299
Query: 351 LCSTKMLSHVNLQYYGDMIRNAVNRVLKAG 380
+ ML H+ + G I +A+ RV AG
Sbjct: 300 WTAAMMLEHLGEKEAGAKIMDAIERVTAAG 329
>gnl|CDD|232853 TIGR00169, leuB, 3-isopropylmalate dehydrogenase. Several NAD- or
NADP-dependent dehydrogenases, including
3-isopropylmalate dehydrogenase, tartrate dehydrogenase,
and the dimeric forms of isocitrate dehydrogenase, share
a nucleotide binding domain unrelated to that of lactate
dehydrogenase and its homologs. These enzymes
dehydrogenate their substates at a H-C-OH site adjacent
to a H-C-COOH site; the latter carbon, now adjacent to a
carbonyl group, readily decarboxylates.Among these
decarboxylating dehydrogenases of hydroxyacids, overall
sequence homology indicates evolutionary history rather
than actual substrate or cofactor specifity, which may
be toggled experimentally by replacement of just a few
amino acids. 3-isopropylmalate dehydrogenase is an
NAD-dependent enzyme and should have a sequence
resembling HGSAPDI around residue 340. The subtrate
binding loop should include a sequence resembling
E[KQR]X(0,1)LLXXR around residue 115. Other contacts of
importance are known from crystallography but not
detailed here.This model will not find all
isopropylmalate dehydrogenases; the enzyme from
Sulfolobus sp. strain 7 is more similar to mitochondrial
NAD-dependent isocitrate dehydrogenases than to other
known isopropylmalate dehydrogenases and was omitted to
improve the specificity of the model. It scores below
the cutoff and below some enzymes known not to be
isopropylmalate dehydrogenase [Amino acid biosynthesis,
Pyruvate family].
Length = 346
Score = 146 bits (370), Expect = 1e-40
Identities = 106/336 (31%), Positives = 162/336 (48%), Gaps = 40/336 (11%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAA----NVPVDFEPFFFSEV------NPTMSAPLETV 123
K ++PGDG+GPE++ +V KA + +FE P P ET+
Sbjct: 1 KIAVLPGDGIGPEVMAQALKVLKAVAERFGLKFEFEEHLIGGAAIDATGQPL---PEETL 57
Query: 124 ADSIARNGICLKGVLSTPDYSH--------TGELQTLNMKLRKALDLYANVVHVKSLPGV 175
+ + L G + P + + G L KLRK+LDL+AN+ K PG+
Sbjct: 58 KGCKEADAVLL-GAVGGPKWDNLPRDQRPEQGLL-----KLRKSLDLFANLRPAKVFPGL 111
Query: 176 KVRHS--------NVDCVIIREQTEGEYSALEHEC-VPGVVECLKIVTAEKSRRIAKFAF 226
S VD V++RE T G Y G ++ T + RIA+ AF
Sbjct: 112 -EDLSPLKPEIAKGVDFVVVRELTGGIYFGEPKGREGEGEAWDTEVYTVPEIERIARVAF 170
Query: 227 DYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPH 286
+ A K RKKVT+V KAN+++ L+ + +E+AK YP ++ E +DN MQ+V +P
Sbjct: 171 EMARKR-RKKVTSVDKANVLESSR-LWRKTVEEIAKEYPDVELEHQYIDNAAMQLVKSPT 228
Query: 287 QFDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANP 346
QFDV+V NL+G+I+ + AS + G G++ AS + + + GK +ANP
Sbjct: 229 QFDVVVTSNLFGDILSDEASVITGSLGMLPSASLGSDGFGLFEPVHGSAPDIAGKGIANP 288
Query: 347 TAMLLCSTKMLSH-VNLQYYGDMIRNAVNRVLKAGK 381
A +L + +L + NL+ D I AV +VL G
Sbjct: 289 IAQILSAAMLLRYSFNLEEAADAIEAAVKKVLAEGY 324
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 145 bits (369), Expect = 2e-40
Identities = 102/334 (30%), Positives = 160/334 (47%), Gaps = 42/334 (12%)
Query: 74 KCTLIPGDGVGPELVYSVQEVFKAANVP-VDFEPFFFS----------EVNPTMSAPLET 122
K +IPGDG+GPE+V +V A E + E P ++
Sbjct: 6 KLAVIPGDGIGPEVVAEALKVLDAVAAGGPGVETTEYDLGARRYLRTGETLP------DS 59
Query: 123 VADSIARNGICLKGVLSTPDYSHTGELQT-LNMKLRKALDLYANVVHVKSLPGVKVRHSN 181
V + ++ L G + P +G L+ L +KLR ALD Y N+ K PGV +
Sbjct: 60 VLAELRQHDAILLGAIGDPSVP-SGVLERGLLLKLRFALDHYVNLRPSKLYPGVTSPLAG 118
Query: 182 ---VDCVIIREQTEGEYS----AL----EHECVPGVVECLKIVTAEKSRRIAKFAFDYAT 230
+D V++RE TEG Y+ AL HE V + + TA R+ + AF+ A
Sbjct: 119 PGDIDFVVVREGTEGPYTGNGGALRVGTPHE----VATEVSVNTAFGVERVVRDAFERAQ 174
Query: 231 KNNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDV 290
K RK +T VHK N++ L+ + E+A YP + + VD T+ +V++P +FDV
Sbjct: 175 KRPRKHLTLVHKTNVLTFAGDLWQRTVDEVAAEYPDVTVDYQHVDAATIFMVTDPSRFDV 234
Query: 291 MVMPNLYGNIVDNLASGLVGGAGVVAGASWSPECV---VFEP--GARHTYSEAVGKNVAN 345
+V NL+G+I+ +LA+ + GG G+ A + +P +FEP G+ + G+ +A+
Sbjct: 235 IVTDNLFGDIITDLAAAVTGGIGLAASGNINPTGTNPSMFEPVHGSAPDIA---GQGIAD 291
Query: 346 PTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKA 379
PTA +L +L H+ + I AV L
Sbjct: 292 PTAAILSVALLLDHLGEEDAAARIEAAVEADLAE 325
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 141 bits (357), Expect = 3e-38
Identities = 104/368 (28%), Positives = 167/368 (45%), Gaps = 79/368 (21%)
Query: 78 IPGDGVGPELVYSVQEVFKAANVPVDFEPFFFS-------EVNPTMSA--------PLET 122
+ GDG+GPE+ ++ +V A E + S EV A P E+
Sbjct: 29 VEGDGIGPEITHAAMKVINKA-----VEKAYGSDREIKWVEVLAGDKAEKLTGNRFPKES 83
Query: 123 VADSIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK--VRHS 180
+ I + + LKG L TP +++N+ +R LDLYAN+ VK +PG++ +++
Sbjct: 84 E-ELIEKYRVLLKGPLETPI---GKGWKSINVAIRLMLDLYANIRPVKYIPGIESPLKNP 139
Query: 181 N-VDCVIIREQTEGEYSALEH------------------------ECVPGVVECLKIVTA 215
+D +I RE T+ Y +E+ + G +K+++
Sbjct: 140 EKIDLIIFRENTDDLYRGIEYPYDSEEAKKIRDFLRKELGVEVEDDTGIG----IKLISK 195
Query: 216 EKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMA-------------- 261
K++RIA+ A YA + RKKVT +HK N+MK +G F E+A
Sbjct: 196 FKTQRIARMAIKYAIDHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEFRDYVVTEEEV 255
Query: 262 -KLYP------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGV 314
K Y K+ I DN QI+ P ++D+++ PN+ G+ + + A LVG G+
Sbjct: 256 TKNYNGVPPSGKVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISDAAGALVGNIGM 315
Query: 315 VAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAV 373
+ GA+ +FE A H T + GKNVANPT ++ ML + D+I A+
Sbjct: 316 LGGANIGDTGGMFE--AIHGTAPKYAGKNVANPTGIIKGGELMLRFMGWDKAADLIDKAI 373
Query: 374 NRVLKAGK 381
+K K
Sbjct: 374 MESIKQKK 381
>gnl|CDD|232862 TIGR00183, prok_nadp_idh, isocitrate dehydrogenase, NADP-dependent,
prokaryotic type. Several NAD- or NADP-dependent
dehydrogenases, including 3-isopropylmalate
dehydrogenase, tartrate dehydrogenase, and the
multimeric forms of isocitrate dehydrogenase, share a
nucleotide binding domain unrelated to that of lactate
dehydrogenase and its homologs. These enzymes
dehydrogenate their substates at a H-C-OH site adjacent
to a H-C-COOH site; Prokaryotic NADP-dependent
isocitrate dehydrogenases resemble their NAD-dependent
counterparts and 3-isopropylmalate dehydrogenase (an
NAD-dependent enzyme) more closely than they resemble
eukaryotic NADP-dependent isocitrate dehydrogenases
[Energy metabolism, TCA cycle].
Length = 416
Score = 138 bits (350), Expect = 3e-37
Identities = 101/364 (27%), Positives = 167/364 (45%), Gaps = 67/364 (18%)
Query: 78 IPGDGVGPELV--------YSVQEVFKAANVPVDFEPFF----FSEVNPTMSAPLETVAD 125
I GDG+G ++ +V++ +K V FE + + P +T+ D
Sbjct: 32 IEGDGIGVDVTPAAIKVLDAAVEKAYKGEKKIVWFEVYAGEKAYQLYGQDQWLPADTL-D 90
Query: 126 SIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK--VRH-SNV 182
+I + +KG L+TP G +++LN+ LR+ LDLY + V+ GV V+H V
Sbjct: 91 AIKEYRVAIKGPLTTPV---GGGIRSLNVALRQELDLYVCLRPVRYYKGVPSPVKHPEKV 147
Query: 183 DCVIIREQTEGEYSALEHECVPGVVECLKI-------------------------VTAEK 217
D VI RE TE Y+ +E G E K+ ++ E
Sbjct: 148 DMVIFRENTEDIYAGIEWA--EGSEEAKKLIRFLQNELGVKKIRFPEDSGIGIKPISEEG 205
Query: 218 SRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMAK-----------LYPK 266
++R+ + A +YA +N+RK VT VHK NIMK +G F + E+AK L+ K
Sbjct: 206 TKRLVRAAIEYAIENDRKSVTLVHKGNIMKFTEGAFRDWGYELAKKEFGAECITWGLWDK 265
Query: 267 ---------IQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGVVAG 317
I + I D QI++ P ++DV+ NL G+ + + + VGG G+ G
Sbjct: 266 YKNPNPGKEIVIKDRIADAFLQQILTRPDEYDVIATMNLNGDYISDALAAQVGGIGIAPG 325
Query: 318 ASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVL 377
A+ E +FE T + G++ NP +++L ML H+ + D+I+ A+ + +
Sbjct: 326 ANIGDEIGIFEA-THGTAPKYAGQDKVNPGSIILSGEMMLEHMGWKEAADLIKKAMEKAI 384
Query: 378 KAGK 381
+
Sbjct: 385 ASKI 388
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 127 bits (320), Expect = 2e-33
Identities = 90/336 (26%), Positives = 154/336 (45%), Gaps = 51/336 (15%)
Query: 78 IPGDGVGPELVYSVQEVFKAA-----NVPVDFEPFFFS--------EVNPTMSAPLETVA 124
IPGDGVG E+V + V KA + +F F +S E+ P LE +
Sbjct: 9 IPGDGVGKEVVPAAVRVLKAVAEVHGGLKFEFTEFPWSCEYYLEHGEMMP--EDGLEQLK 66
Query: 125 DSIARNGICLKGVLS---TPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK--VRH 179
+ I L V + PD+ L L +K+R+ + N+ K L G+K + +
Sbjct: 67 QF---DAIFLGAVGNPKLVPDHI---SLWGLLIKIRREFEQVINIRPAKQLRGIKSPLAN 120
Query: 180 SN-VDCVIIREQTEGEYSAL-------EHECVPGVVECLKIVTAEKSRRIAKFAFDYATK 231
D +++RE +EGEYS + E E + + T + + R ++AF+ A
Sbjct: 121 PKDFDLLVVRENSEGEYSEVGGRIHRGEDE----IAIQNAVFTRKGTERAMRYAFELA-A 175
Query: 232 NNRKKVTAVHKAN----IMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPHQ 287
RK VT+ K+N M D +F +E+ K YP+I+ + +D V+ P +
Sbjct: 176 KRRKHVTSATKSNGIVHSMPFWDEVF----QEVGKDYPEIETDSQHIDALAAFFVTRPEE 231
Query: 288 FDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWSPEC---VVFEPGARHTYSEAVGKNVA 344
FDV+V NL+G+I+ ++ + ++G G+ A+ + +FEP + + GK +A
Sbjct: 232 FDVIVASNLFGDILTDIGAAIMGSIGIAPAANINVNGKYPSMFEP-VHGSAPDIAGKGIA 290
Query: 345 NPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKAG 380
NP + + ML H + G + + + V + G
Sbjct: 291 NPIGQIWTAKLMLDHFGEEELGSHLLDVIEDVTEDG 326
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 120 bits (303), Expect = 1e-30
Identities = 102/365 (27%), Positives = 166/365 (45%), Gaps = 73/365 (20%)
Query: 78 IPGDGVGPELVYSVQEVFKAANVPVD-----------FEPFF----FSEVNPTMSAPLET 122
I GDG+GP++ ++ +V AA V+ E + + P ET
Sbjct: 25 IEGDGIGPDITPAMLKVVDAA---VEKAYKGERKISWMEIYAGEKATKVYGEDVWLPEET 81
Query: 123 VADSIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVK--VRH- 179
+ D I + +KG L+TP G +++LN+ LR+ LDLY + V+ GV V+
Sbjct: 82 L-DLIREYRVAIKGPLTTPV---GGGIRSLNVALRQELDLYVCLRPVRYFKGVPSPVKRP 137
Query: 180 SNVDCVIIREQTEGEYSALEHEC----VPGVVECL-------------------KIVTAE 216
+ D VI RE +E Y+ +E + V++ L K V+ E
Sbjct: 138 EDTDMVIFRENSEDIYAGIEWKAGSAEAKKVIKFLQEEMGVKKIRFPETSGIGIKPVSEE 197
Query: 217 KSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMA------KLYP----- 265
+ R+ + A +YA N+RK VT VHK NIMK +G F + ++A +L
Sbjct: 198 GTERLVRAAIEYAIDNDRKSVTLVHKGNIMKFTEGAFKDWGYQLAEEEFGDELIDGGPWD 257
Query: 266 ---------KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGN-IVDNLASGLVGGAGVV 315
+I + I D QI+ P ++DV+ NL G+ I D LA+ VGG G+
Sbjct: 258 KIKNPETGKEIIVKDSIADAFLQQILLRPAEYDVIATMNLNGDYISDALAAQ-VGGIGIA 316
Query: 316 AGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVN 374
GA+ + +FE A H T + G + NP +++L + ML H+ D+I ++
Sbjct: 317 PGANINDGHAIFE--ATHGTAPKYAGLDKVNPGSVILSAEMMLRHMGWTEAADLIIKSME 374
Query: 375 RVLKA 379
+ + +
Sbjct: 375 KTIAS 379
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 101 bits (253), Expect = 7e-24
Identities = 94/336 (27%), Positives = 152/336 (45%), Gaps = 34/336 (10%)
Query: 72 RTKCTLIPGDGVGPELVYSVQEVFKAANVPVDFEPFFFSEVNPTMSAPLETV-------- 123
R L+PGDG+GPE++ + V + A E F F E+ P A L+ V
Sbjct: 46 RYNIALLPGDGIGPEVISVAKNVLQKAGSLEGLE-FDFQEM-PVGGAALDLVGVPLPEET 103
Query: 124 ADSIARNGICLKGVLSTPDYSHTG-----ELQTLNMKLRKALDLYANVVHVKSLPGV--- 175
+ ++ L G + + E+ LR+ L ++AN+ LP +
Sbjct: 104 FTAAKQSDAILLGAIGGYKWDKNEKHLRPEMALFY--LRRDLKVFANLRPATVLPQLVDA 161
Query: 176 ----KVRHSNVDCVIIREQTEGEYSALE-----HECVPGVVECLKIVTAEKSRRIAKFAF 226
K VD +I+RE T G Y +E V +I A + RIA+ AF
Sbjct: 162 STLKKEVAEGVDMMIVRELTGGIYFGEPRGITINENGEEVGVSTEIYAAHEIDRIARVAF 221
Query: 227 DYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQMIVDNCTMQIVSNPH 286
+ A K R K+ +V KAN++ L+ +A YP ++ M VDN MQ++ +P
Sbjct: 222 ETARKR-RGKLCSVDKANVLD-ASILWRKRVTALASEYPDVELSHMYVDNAAMQLIRDPK 279
Query: 287 QFDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWSPECV-VFEPGARHTYSEAVGKNVAN 345
QFD +V N++G+I+ + AS + G G++ AS +FEP + + G++ AN
Sbjct: 280 QFDTIVTNNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEP-IHGSAPDIAGQDKAN 338
Query: 346 PTAMLLCSTKMLSH-VNLQYYGDMIRNAVNRVLKAG 380
P A +L + +L + + + I +AV L G
Sbjct: 339 PLATILSAAMLLKYGLGEEKAAKRIEDAVVDALNKG 374
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 61.7 bits (150), Expect = 2e-10
Identities = 50/176 (28%), Positives = 82/176 (46%), Gaps = 37/176 (21%)
Query: 119 PLETVADSIARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLPGVKVR 178
P +T+ ++I G+ +KG L+TP G +++LN+ LR+ DLY+ V + G
Sbjct: 87 PEDTL-EAIREYGVAIKGPLTTPI---GGGIRSLNVALRQIFDLYSCVRPCRYYAGTPSP 142
Query: 179 HSN---VDCVIIREQTEGEYSALE----------------HECVPGVVEC---------- 209
H N +D ++ RE TE Y +E E +P E
Sbjct: 143 HKNPEKLDVIVYRENTEDIYMGIEWEAGDEIGDKLIKHLNEEVIPASPELGKRQIPLGSG 202
Query: 210 --LKIVTAEKSRRIAKFAFDYATK--NNRKKVTAVHKANIMKLGDGLFLNSCKEMA 261
+K V+ S+R + A ++A + +++ VT VHK NIMK +G F + E+A
Sbjct: 203 IGIKPVSKTGSQRHIRRAIEHALRLPGDKRHVTLVHKGNIMKYTEGAFRDWGYELA 258
Score = 53.2 bits (128), Expect = 1e-07
Identities = 37/170 (21%), Positives = 75/170 (44%), Gaps = 9/170 (5%)
Query: 213 VTAEKSRRIAKFAFDYATKNNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPKIQFEQM 272
++ E + R+ + +D T + + A K + + KE + +
Sbjct: 284 ISIEDNARMIEPGYDSLTPEKKAAICAEVKEVLDSIWSSHGNGKWKEK------VLVDDR 337
Query: 273 IVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASGLVGGAGVVAGASWSPECVVFEPGAR 332
I D+ QI + P ++ ++ NL G+ + + A+ +VGG G+ GA+ +FE A
Sbjct: 338 IADSIFQQIQTRPQEYSILATLNLNGDYISDAAAAIVGGLGMAPGANIGDNAAIFE--AT 395
Query: 333 H-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKAGK 381
H T + G + NP +++L ML ++ Q D+I ++ + +
Sbjct: 396 HGTAPKHAGLDRINPGSVILSGVMMLEYLGWQEAADLITKGLSAAIANKQ 445
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 30.8 bits (70), Expect = 1.1
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 128 ARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSL-PGVKVRHSNV 182
R GI L GVLS P+ + L + LR L L A V+ V+ + G V + +
Sbjct: 213 VRPGILLYGVLSDPN-----DPTKLGLDLRPVLSLKAKVILVRKVAKGEAVGYGRL 263
>gnl|CDD|182165 PRK09954, PRK09954, putative kinase; Provisional.
Length = 362
Score = 29.9 bits (67), Expect = 2.1
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 329 PGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMI 369
PG H + VG+N+A+ A+L +LS + +YG+ +
Sbjct: 85 PGTIHCSAGGVGRNIAHNLALLGRDVHLLSAIGDDFYGETL 125
>gnl|CDD|234600 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 29.8 bits (68), Expect = 2.3
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 128 ARNGICLKGVLSTPDYSHTGELQTLNMKLRKALDLYANVVHVKSLP 173
R GI L G+ +P G + L+ A+ L ++++ V+ L
Sbjct: 214 VRPGIALYGL--SPSGEPLGL----DFGLKPAMTLKSSLIAVRELK 253
>gnl|CDD|199990 TIGR00072, hydrog_prot, hydrogenase maturation protease. HycI
and HoxM are well-characterized as responsible for
C-terminal protease activity on their respective
hydrogenase large chains. A large number of homologous
proteins appear responsible for the maturation of
various forms of hydrogenase.
Length = 145
Score = 28.6 bits (65), Expect = 2.6
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 52 DGVGPELVYSVQEHQSVPEGRTKCTLIPGDGVGPELVYSVQEV 94
DG GP + ++E P G ++ G +G EL+ +++
Sbjct: 13 DGFGPRVAERLEERYEFPPG---VEVLDGGTLGLELLDAIEGA 52
>gnl|CDD|225226 COG2351, COG2351, Transthyretin-like protein [General function
prediction only].
Length = 124
Score = 28.1 bits (63), Expect = 3.6
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 12/71 (16%)
Query: 49 IPGDGVGPELVYSVQEHQSVP--------EGRTKCTLIPGDGVGP---ELVYSVQEVFKA 97
P GV EL Y ++ +Q +GR L+ G+ + ELV+ + FK+
Sbjct: 22 KPAAGVKVEL-YRLEGNQWELLKTVVTNADGRIDAPLLAGETLATGIYELVFHTGDYFKS 80
Query: 98 ANVPVDFEPFF 108
V + PF
Sbjct: 81 RGVQLADPPFL 91
>gnl|CDD|115006 pfam06319, DUF1052, Protein of unknown function (DUF1052). This
family consists of several bacterial proteins of unknown
function.
Length = 158
Score = 28.6 bits (64), Expect = 3.8
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 36 HQSVPEG--RTKCTLIPGDGVGPELVYSVQEHQSVPEGRTKCTL 77
H VP +C LI DG G ++ EH+ P R TL
Sbjct: 95 HPDVPLEIFPEECGLILSDGYGAHMLREAPEHRLAPATRKALTL 138
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 29.1 bits (66), Expect = 4.3
Identities = 16/26 (61%), Positives = 18/26 (69%), Gaps = 4/26 (15%)
Query: 307 GLVGGAGVVAGASWSPECVVFEPGAR 332
G +GG GVVAGAS+ E VF GAR
Sbjct: 35 GGLGGRGVVAGASY--EARVF--GAR 56
>gnl|CDD|218901 pfam06110, DUF953, Eukaryotic protein of unknown function (DUF953).
This family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 119
Score = 27.4 bits (61), Expect = 5.5
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 317 GASWSPECVVFEPGARHTYSEA 338
G SW P+CV EP R A
Sbjct: 34 GESWCPDCVRAEPVIREALKHA 55
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 28.3 bits (64), Expect = 6.8
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 188 REQTEGEYSALEHECVPGVVE 208
RE E+S E + V GVV+
Sbjct: 123 REIIYNEFSEREGDIVTGVVQ 143
>gnl|CDD|99983 cd03812, GT1_CapH_like, This family is most closely related to the
GT1 family of glycosyltransferases. capH in
Staphylococcus aureus has been shown to be required for
the biosynthesis of the type 1 capsular polysaccharide
(CP1).
Length = 358
Score = 28.0 bits (63), Expect = 8.7
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 16/57 (28%)
Query: 248 LGDGLFLNSCKEMAK---LYPKIQFEQMIVDNCTMQIVSNPHQ----FDVMVMPNLY 297
+GDG K+ K L K+ F + + ++ + DV + P+LY
Sbjct: 229 VGDGELEEEIKKKVKELGLEDKVIF---------LGVRNDVPELLQAMDVFLFPSLY 276
>gnl|CDD|240439 PTZ00491, PTZ00491, major vault protein; Provisional.
Length = 850
Score = 28.1 bits (63), Expect = 9.6
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 54 VGPELVYSVQEHQSVPEGRTKCTLIP 79
VGP ++ Q+H+ V ++P
Sbjct: 29 VGP-QTFTRQDHERVLHPPQPMVVVP 53
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 0.134 0.394
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,752,056
Number of extensions: 1763164
Number of successful extensions: 1440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1358
Number of HSP's successfully gapped: 63
Length of query: 381
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 282
Effective length of database: 6,546,556
Effective search space: 1846128792
Effective search space used: 1846128792
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: 60 (27.1 bits)