RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8787
(364 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 = 416 bits (1070), Expect = e-146
Identities = 146/245 (59%), Positives = 188/245 (76%), Gaps = 1/245 (0%)
Query: 121 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
E +LYANV C+SL G+ T ++DVD+V IRENTEGEYSG+EHE V GVV+S+K+IT + S
Sbjct: 88 ELDLYANVVHCKSLPGFKTRHEDVDIVIIRENTEGEYSGLEHESVPGVVESLKVITRDKS 147
Query: 181 SRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTVC 240
R+A +AFEYA+ N R KVTAVHKANIM+++DGLFL CR+ A+++P++ FE +D C
Sbjct: 148 ERIARYAFEYARKNGRKKVTAVHKANIMKLADGLFLNVCREVAKEYPDITFESMIVDNTC 207
Query: 241 LNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFE-SVHGTAPDI 299
+ +V P+Q+DV+VMPNLYG+ILS++ AGLVGG GL P NIG + A+FE V T PDI
Sbjct: 208 MQLVSRPSQFDVMVMPNLYGNILSNLGAGLVGGPGLVPGANIGRDYAVFEPGVRHTGPDI 267
Query: 300 AGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSEFTN 359
AG+++ANPTAL+LS+VMML HL L HAD IQKA L TI EGK RT DLGG A S+FT
Sbjct: 268 AGQNIANPTALILSSVMMLNHLGLKEHADRIQKAVLSTIAEGKNRTKDLGGTATTSDFTE 327
Query: 360 EICSK 364
+ +
Sbjct: 328 AVIKR 332
Score = 100 bits (251), Expect = 5e-24
Identities = 47/97 (48%), Positives = 57/97 (58%), Gaps = 3/97 (3%)
Query: 36 INTPSISQWSWRGLKVQGLGEFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGI 95
+ TP I + R L V E +LYANV C+SL G+ T ++DVD+V IRENTEGEYSG+
Sbjct: 69 LETP-IGKGGHRSLNVALRKELDLYANVVHCKSLPGFKTRHEDVDIVIIRENTEGEYSGL 127
Query: 96 EHEIVDGVCNS-NYATKWFSERGASVEFNL-YANVRP 130
EHE V GV S T+ SER A F N R
Sbjct: 128 EHESVPGVVESLKVITRDKSERIARYAFEYARKNGRK 164
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 417 bits (1073), Expect = e-146
Identities = 166/245 (67%), Positives = 203/245 (82%), Gaps = 1/245 (0%)
Query: 121 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
E LYANVRPC SL GY T YDDVD+VTIRENTEGEYSG+EH++V GVV+S+K+IT +AS
Sbjct: 127 ELGLYANVRPCYSLPGYKTRYDDVDLVTIRENTEGEYSGLEHQVVRGVVESLKIITRQAS 186
Query: 181 SRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTVC 240
RVAE+AF YAKT+ R +V+A+HKANIM+ +DGLFL+CCR+ AEK+PE+ +EE +D C
Sbjct: 187 LRVAEYAFHYAKTHGRKRVSAIHKANIMKKTDGLFLKCCREVAEKYPEIVYEEVIIDNCC 246
Query: 241 LNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG-ALFESVHGTAPDI 299
+ +V++P +DVLVMPNLYGDI+SD+CAGL+GGLGLTPS NIG NG AL E+VHG+APDI
Sbjct: 247 MMLVKNPALFDVLVMPNLYGDIISDLCAGLIGGLGLTPSCNIGENGLALAEAVHGSAPDI 306
Query: 300 AGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSEFTN 359
AGK+LANPTALLLSAVMMLRHL LN A+ I A L+TI EGKYRT DLGG + ++FT
Sbjct: 307 AGKNLANPTALLLSAVMMLRHLKLNEQAEQIHNAILNTIAEGKYRTADLGGSSTTTDFTK 366
Query: 360 EICSK 364
IC
Sbjct: 367 AICDH 371
Score = 93.8 bits (233), Expect = 2e-21
Identities = 45/72 (62%), Positives = 50/72 (69%), Gaps = 2/72 (2%)
Query: 56 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVCNS-NYATKWFS 114
E LYANVRPC SL GY T YDDVD+VTIRENTEGEYSG+EH++V GV S T+ S
Sbjct: 127 ELGLYANVRPCYSLPGYKTRYDDVDLVTIRENTEGEYSGLEHQVVRGVVESLKIITRQAS 186
Query: 115 ERGASVEFNLYA 126
R A F YA
Sbjct: 187 LRVAEYAF-HYA 197
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 365 bits (939), Expect = e-126
Identities = 124/260 (47%), Positives = 164/260 (63%), Gaps = 9/260 (3%)
Query: 114 SERGASV----EFNLYANVRPCRSLEGYPTLY-DDVDVVTIRENTEGEYSGIEHEIVDG- 167
ERG + E +LYAN+RP +SL G + VD+V +RENTEG Y G E I+ G
Sbjct: 85 PERGLLLALRKELDLYANLRPAKSLPGLKSPLVKGVDIVIVRENTEGLYFGEEGRILGGG 144
Query: 168 -VVQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKF 226
V K+IT + S R+A FAFE A+ R KVT+VHKAN++++SDGL+ + A+++
Sbjct: 145 EVAIDTKVITRKGSERIARFAFELARKRGRKKVTSVHKANVLKLSDGLWREVVEEVAKEY 204
Query: 227 PEVKFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG 286
P+V+ + Y+D + +V++P Q+DV+V NL+GDILSD A L G LGL PS N+G
Sbjct: 205 PDVELDHMYVDAAAMQLVRNPEQFDVIVTSNLFGDILSDEAAALTGSLGLAPSANLGDER 264
Query: 287 --ALFESVHGTAPDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYR 344
ALFE VHG+APDIAGK +ANP A +LSA MMLRHL AD I+ A + EG R
Sbjct: 265 GPALFEPVHGSAPDIAGKGIANPIATILSAAMMLRHLGEKEAADAIENAVEKVLAEGGIR 324
Query: 345 TGDLGGKAKCSEFTNEICSK 364
T DLGG A SE + I
Sbjct: 325 TPDLGGNATTSEVGDAIAKA 344
Score = 75.7 bits (187), Expect = 3e-15
Identities = 24/48 (50%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 56 EFNLYANVRPCRSLEGYPTLY-DDVDVVTIRENTEGEYSGIEHEIVDG 102
E +LYAN+RP +SL G + VD+V +RENTEG Y G E I+ G
Sbjct: 96 ELDLYANLRPAKSLPGLKSPLVKGVDIVIVRENTEGLYFGEEGRILGG 143
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 318 bits (816), Expect = e-107
Identities = 107/258 (41%), Positives = 145/258 (56%), Gaps = 18/258 (6%)
Query: 121 EFNLYANVRPCRSLE--GYPTLY-----DDVDVVTIRENTEGEYSGIEHEIVDGV----- 168
E L+AN+RP + G + + VD+V +RE T G Y GI I
Sbjct: 93 ELGLFANLRPVKVFPSLGDASPLKREVVEGVDIVIVRELTGGIYFGIPKGIKGSGNGEEG 152
Query: 169 VQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPE 228
KL + + R+A AFE A+ R KVT+V KAN+++ S A ++P+
Sbjct: 153 AVDTKLYSRDEIERIARVAFELARKRGRKKVTSVDKANVLKSSRLWRKIVEEVAKAEYPD 212
Query: 229 VKFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG-A 287
V+ E +D + +V++P Q+DV+V NL+GDILSD + L G LGL PS ++G +G
Sbjct: 213 VELEHMLVDNAAMQLVKNPKQFDVIVTENLFGDILSDEASMLTGSLGLLPSASLGADGFG 272
Query: 288 LFESVHGTAPDIAGKDLANPTALLLSAVMMLRH-LDLNTHADVIQKAALDTIKEGKYRTG 346
LFE VHG+APDIAGK ANP A +LSA MMLRH L L AD I+ A L ++ G RTG
Sbjct: 273 LFEPVHGSAPDIAGKGKANPIATILSAAMMLRHSLGLEDEADKIEAAVLKVLEAG-IRTG 331
Query: 347 DLGGKA---KCSEFTNEI 361
DLGG A SEF + +
Sbjct: 332 DLGGNATYVSTSEFGDAV 349
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 304 bits (781), Expect = e-102
Identities = 121/245 (49%), Positives = 161/245 (65%), Gaps = 5/245 (2%)
Query: 121 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
+ YANVRP +S +G LY D+D V +RENTEG Y GIE EI DGV + ++IT +AS
Sbjct: 83 ILDTYANVRPVKSYKGVKCLYPDIDYVIVRENTEGLYKGIEAEIADGVTVATRVITRKAS 142
Query: 181 SRVAEFAFEYAK----TNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYL 236
R+ FAFE AK KVT HKAN+++ +DGLF + + A+++P++K E+ Y+
Sbjct: 143 ERIFRFAFEMAKRRKKMGKEGKVTCAHKANVLKKTDGLFKKTFYEVAKEYPDIKAEDYYV 202
Query: 237 DTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTA 296
D + + ++ P +DV+V NL+GDILSD AGLVGGLGL PS NIG LFE VHG+A
Sbjct: 203 DAMNMYIITRPQTFDVVVTSNLFGDILSDGAAGLVGGLGLAPSANIGDKYGLFEPVHGSA 262
Query: 297 PDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSE 356
PDIAGK +ANPTA +L+AV+MLRHL N AD ++KA + + G T DLGG E
Sbjct: 263 PDIAGKGIANPTATILTAVLMLRHLGENEEADKVEKALEEVLALGL-TTPDLGGNLSTME 321
Query: 357 FTNEI 361
E+
Sbjct: 322 MAEEV 326
Score = 73.2 bits (180), Expect = 2e-14
Identities = 33/70 (47%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 56 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVCNSNYA-TKWFS 114
+ YANVRP +S +G LY D+D V +RENTEG Y GIE EI DGV + T+ S
Sbjct: 83 ILDTYANVRPVKSYKGVKCLYPDIDYVIVRENTEGLYKGIEAEIADGVTVATRVITRKAS 142
Query: 115 ERGASVEFNL 124
ER F +
Sbjct: 143 ERIFRFAFEM 152
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 302 bits (774), Expect = e-101
Identities = 119/246 (48%), Positives = 173/246 (70%), Gaps = 2/246 (0%)
Query: 121 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIV-DG-VVQSIKLITEE 178
+F+LYANVRP S G YD++D++T+RENTEG YSG + DG ++ +IT +
Sbjct: 88 KFDLYANVRPVLSFPGTKARYDNIDIITVRENTEGMYSGEGQTVSEDGETAEATSIITRK 147
Query: 179 ASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDT 238
+ R+ FA+E A+ R KVTAVHKANIM+ + GLFL+ R+ A ++P+++FEE +D
Sbjct: 148 GAERIVRFAYELARKEGRKKVTAVHKANIMKSTSGLFLKVAREVALRYPDIEFEEMIVDA 207
Query: 239 VCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPD 298
C+ +V +P Q+DV+V NL+GDILSD+CAGLVGGLG+ P NIG + A+FE+VHG+APD
Sbjct: 208 TCMQLVMNPEQFDVIVTTNLFGDILSDLCAGLVGGLGMAPGANIGRDAAIFEAVHGSAPD 267
Query: 299 IAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSEFT 358
IAGK+LANPT+++L+A+ ML +L + A+ I+KA + I+ G T DLGG ++FT
Sbjct: 268 IAGKNLANPTSVILAAIQMLEYLGMPDKAERIRKAIVAVIEAGDRTTRDLGGTHGTTDFT 327
Query: 359 NEICSK 364
+ +
Sbjct: 328 QAVIDR 333
Score = 64.0 bits (156), Expect = 2e-11
Identities = 23/46 (50%), Positives = 32/46 (69%)
Query: 56 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVD 101
+F+LYANVRP S G YD++D++T+RENTEG YSG + +
Sbjct: 88 KFDLYANVRPVLSFPGTKARYDNIDIITVRENTEGMYSGEGQTVSE 133
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 293 bits (752), Expect = 2e-97
Identities = 121/248 (48%), Positives = 172/248 (69%), Gaps = 4/248 (1%)
Query: 121 EFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
E +L+A++ C +L G PT +++VD+V IRENTEGEYSG+EHE+V GVV+S+K+IT+ S
Sbjct: 111 ELDLFASLVNCFNLPGLPTRHENVDIVVIRENTEGEYSGLEHEVVPGVVESLKVITKFCS 170
Query: 181 SRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTVC 240
R+A++AFEYA NNR KVTAVHKANIM+++DGLFL CR+ A+K+P +K+ E +D C
Sbjct: 171 ERIAKYAFEYAYLNNRKKVTAVHKANIMKLADGLFLESCREVAKKYPGIKYNEIIVDNCC 230
Query: 241 LNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTA---- 296
+ +V P Q+DV+V PNLYG+++++ AG+ GG G+ P GN+G + A+FE
Sbjct: 231 MQLVSKPEQFDVMVTPNLYGNLVANTAAGIAGGTGVMPGGNVGADHAVFEQGASAGNVGN 290
Query: 297 PDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSE 356
+ + ANP ALLLS+ MMLRHL + AD ++ A I EGKYRT DLGG + E
Sbjct: 291 EKLVEQKKANPVALLLSSAMMLRHLQFPSFADRLETAVKRVIAEGKYRTKDLGGSSTTQE 350
Query: 357 FTNEICSK 364
+ + +
Sbjct: 351 VVDAVIAN 358
Score = 84.9 bits (210), Expect = 2e-18
Identities = 42/83 (50%), Positives = 54/83 (65%), Gaps = 2/83 (2%)
Query: 49 LKVQGLGEFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHEIVDGVCNS-N 107
L VQ E +L+A++ C +L G PT +++VD+V IRENTEGEYSG+EHE+V GV S
Sbjct: 104 LNVQLRKELDLFASLVNCFNLPGLPTRHENVDIVVIRENTEGEYSGLEHEVVPGVVESLK 163
Query: 108 YATKWFSERGASVEFNL-YANVR 129
TK+ SER A F Y N R
Sbjct: 164 VITKFCSERIAKYAFEYAYLNNR 186
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 292 bits (749), Expect = 2e-95
Identities = 108/247 (43%), Positives = 156/247 (63%), Gaps = 8/247 (3%)
Query: 122 FNLYANVRPCRSLEGY-PTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
LYANVRPC S + T + ++DVV IREN E Y+GIEH V Q +KLI+ S
Sbjct: 92 LGLYANVRPCVSYHPFVETKHPNLDVVIIRENEEDLYAGIEHRQTPDVYQCLKLISRPGS 151
Query: 181 SRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTVC 240
++ +AFEYA+ N R KVT + K NIM+++DGLF + + A+++P+++ E +D
Sbjct: 152 EKIIRYAFEYARANGRKKVTCLTKDNIMKLTDGLFHKVFDEIAKEYPDIEAEHYIVDIGA 211
Query: 241 LNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIA 300
+ +P +DV+V PNLYGDILSD+ A + G +GL S NIG A+FE+VHG+APDIA
Sbjct: 212 ARLATNPENFDVIVTPNLYGDILSDIAAEISGSVGLAGSANIGEEYAMFEAVHGSAPDIA 271
Query: 301 GKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGG------KAKC 354
GK++ANP+ LL +AVMML H+ A++I+ A L T+++G + T D+ K
Sbjct: 272 GKNIANPSGLLNAAVMMLVHIGQFDIAELIENAWLKTLEDGIH-TADIYNEGVSKKKVGT 330
Query: 355 SEFTNEI 361
EF +
Sbjct: 331 KEFAEAV 337
Score = 65.7 bits (161), Expect = 8e-12
Identities = 24/48 (50%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 57 FNLYANVRPCRSLEGY-PTLYDDVDVVTIRENTEGEYSGIEHEIVDGV 103
LYANVRPC S + T + ++DVV IREN E Y+GIEH V
Sbjct: 92 LGLYANVRPCVSYHPFVETKHPNLDVVIIRENEEDLYAGIEHRQTPDV 139
>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 = 284 bits (728), Expect = 2e-94
Identities = 120/242 (49%), Positives = 162/242 (66%), Gaps = 5/242 (2%)
Query: 121 EFNLYANVRPCRSLEGYPTLY-DDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEA 179
E +LYANVRP +SL G P LY + D+V +RENTEG Y+G E +I++IT E
Sbjct: 84 ELDLYANVRPAKSLPGIPDLYPNGKDIVIVRENTEGLYAGFE-FGFSDRAIAIRVITREG 142
Query: 180 SSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTV 239
S R+A FAF AK NR KVT VHKAN+++ +DGLF CR+ A+++ V++ + Y+D+
Sbjct: 143 SERIARFAFNLAKERNR-KVTCVHKANVLKGTDGLFREVCREIAKRYG-VEYRDMYVDSA 200
Query: 240 CLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDI 299
+N+V+DP ++DV+V N++GDILSD+ + L G LGL PS NIG ALFE VHG+APDI
Sbjct: 201 AMNLVKDPWRFDVIVTTNMFGDILSDLASALAGSLGLAPSANIGDRKALFEPVHGSAPDI 260
Query: 300 AGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLGGKAKCSEFTN 359
AGK +ANPTA +LS MML +L ++ +A I EG +T DLGG AK E +
Sbjct: 261 AGKGIANPTAAILSVAMMLDYLGELEKGKLVWEAVEYYIIEG-KKTPDLGGTAKTKEVGD 319
Query: 360 EI 361
EI
Sbjct: 320 EI 321
>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 = 239 bits (612), Expect = 3e-75
Identities = 100/247 (40%), Positives = 151/247 (61%), Gaps = 12/247 (4%)
Query: 124 LYANVRPCRSLEGYP---TLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEAS 180
LYAN+RPC S +P T ++++V +REN E Y+GIE+ + KLIT S
Sbjct: 90 LYANIRPCVSY--HPFIETKSPNLNIVIVRENEEDLYTGIEYRQTPDTYECTKLITRSGS 147
Query: 181 SRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEKYLDTVC 240
++ +AFEYA+ +NR KVT + K NIM+M+DG+F + A ++P+++ E +D
Sbjct: 148 EKICRYAFEYARKHNRKKVTCLTKDNIMKMTDGIFHKIFDKIAAEYPDIESEHYIVDIGM 207
Query: 241 LNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIA 300
+ +P +DV+V PNLYGDILSD+ A + G +GL S NIG A+FE+VHG+APDIA
Sbjct: 208 ARLATNPENFDVIVTPNLYGDILSDVAAEISGSVGLAGSANIGEEYAMFEAVHGSAPDIA 267
Query: 301 GKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDL------GGKAKC 354
G+++ANP+ LL +A+ ML H+ + A +I A L T+++G + T D+ K
Sbjct: 268 GQNIANPSGLLNAAIQMLVHIGQSDIAQLIYNAWLKTLEDGVH-TADIYNEKTSKQKVGT 326
Query: 355 SEFTNEI 361
EF +
Sbjct: 327 KEFAEAV 333
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 229 bits (588), Expect = 9e-73
Identities = 101/257 (39%), Positives = 146/257 (56%), Gaps = 19/257 (7%)
Query: 121 EFNLYANVRPCR---SLEGYPTLYDDV----DVVTIRENTEGEYSG----IEHEIVDGVV 169
E L+AN+RP + L L ++ D++ +RE T G Y G E +
Sbjct: 98 ELGLFANLRPAKLYPGLADASPLKPEIVAGLDILIVRELTGGIYFGEPRGREGLGGEERA 157
Query: 170 QSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEV 229
+ T E R+A AFE A+ R KVT+V KAN++ S L+ + A+++P+V
Sbjct: 158 FDTMVYTREEIERIARVAFELARKR-RKKVTSVDKANVLE-SSRLWREVVTEVAKEYPDV 215
Query: 230 KFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG-AL 288
+ Y+D + +V++P Q+DV+V NL+GDILSD A L G LG+ PS ++G +G L
Sbjct: 216 ELSHMYVDNAAMQLVRNPKQFDVIVTENLFGDILSDEAAMLTGSLGMLPSASLGESGPGL 275
Query: 289 FESVHGTAPDIAGKDLANPTALLLSAVMMLRH-LDLNTHADVIQKAALDTIKEGKYRTGD 347
+E +HG+APDIAGK +ANP A +LSA MMLR+ L L AD I+ A + +G YRT D
Sbjct: 276 YEPIHGSAPDIAGKGIANPIATILSAAMMLRYSLGLEEAADAIEAAVEKVLAQG-YRTAD 334
Query: 348 L---GGKAKCSEFTNEI 361
+ GGK SE + I
Sbjct: 335 IAEGGGKVSTSEMGDAI 351
Score = 48.2 bits (116), Expect = 3e-06
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 52 QGL----GEFNLYANVRPCR---SLEGYPTLYDDV----DVVTIRENTEGEYSG 94
+GL E L+AN+RP + L L ++ D++ +RE T G Y G
Sbjct: 90 RGLLALRKELGLFANLRPAKLYPGLADASPLKPEIVAGLDILIVRELTGGIYFG 143
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 206 bits (527), Expect = 3e-63
Identities = 113/295 (38%), Positives = 143/295 (48%), Gaps = 57/295 (19%)
Query: 121 EFNLYANVRPCRSLEGYPTL---YDDVDVVTIRENTEGEYSGIE--------HEIVD--- 166
+LY RP R G P+ + VD+V RENTE Y+GIE +++
Sbjct: 111 ILDLYVFRRPVRYFPGVPSPVKRPEKVDMVIFRENTEDIYAGIEWKAGSPEALKLIFFLE 170
Query: 167 --------------GVVQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSD 212
G+ IK I++E S R+ A EYA N R VT VHK NIM+ ++
Sbjct: 171 DEMGVKKIRFPEDSGIG--IKPISKEGSIRLVRAAIEYAIENKRKSVTLVHKGNIMKFTE 228
Query: 213 GLFLRCCRDAAEKFP----EVKFEEK-----------YLDTVCLNMVQD----PTQYDVL 253
G F + AE+ V +EK Y D + +M+Q P +YDV+
Sbjct: 229 GAFKDWGYEVAEEEEFGDEVVTGKEKFELKGPKGKIVYKDRIADDMLQQILLRPGEYDVI 288
Query: 254 VMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLANPTALLLS 313
NL GD +SD A VGGLGL P NIG A FE+ HGTAP AGKD NP A +LS
Sbjct: 289 ATKNLNGDYISDALAAQVGGLGLAPGANIGDGTAEFEATHGTAPKYAGKDSTNPIASILS 348
Query: 314 AVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLG---GKA----KCSEFTNEI 361
MMLRH AD+I+KA DTI+ GK T DL G A SEF + I
Sbjct: 349 GTMMLRHRGWLEAADLIEKAVEDTIESGKV-TYDLARLMGGAKRYLSTSEFADAI 402
>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 = 192 bits (489), Expect = 2e-58
Identities = 98/255 (38%), Positives = 141/255 (55%), Gaps = 14/255 (5%)
Query: 121 EFNLYANVRPCRSLEGYPT-----LYDDVDVVTIRENTEGEYSGIEHEIVDG----VVQS 171
EF+ YANVRP + L G + D D V +REN+EGEYSG+ I G V
Sbjct: 98 EFDQYANVRPAKLLPGVTSPLRNCGPGDFDFVVVRENSEGEYSGVGGRIHRGTDEEVATQ 157
Query: 172 IKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKF 231
+ T + R+ FAFE A+ R +T+ K+N +R S + + A ++P+V++
Sbjct: 158 NAIFTRKGVERIMRFAFELAQKR-RKHLTSATKSNGIRHSMPFWDEVFAEVAAEYPDVEW 216
Query: 232 EEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG---AL 288
+ ++D + V P +DV+V NL+GDILSD+ A L+G LG+ PS NI G ++
Sbjct: 217 DSYHIDALAARFVLKPETFDVIVASNLFGDILSDLGAALMGSLGVAPSANINPEGKFPSM 276
Query: 289 FESVHGTAPDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDL 348
FE VHG+APDIAGK +ANP + +A MML HL I A++ + T D+
Sbjct: 277 FEPVHGSAPDIAGKGIANPIGAIWTAAMMLEHLGEKEAGAKIM-DAIERVTAAGILTPDV 335
Query: 349 GGKAKCSEFTNEICS 363
GGKA SE T +C+
Sbjct: 336 GGKATTSEVTEAVCN 350
Score = 53.3 bits (128), Expect = 7e-08
Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 8/61 (13%)
Query: 40 SISQWSWRGLKVQGLGEFNLYANVRPCRSLEGYPT-----LYDDVDVVTIRENTEGEYSG 94
IS W GL ++ EF+ YANVRP + L G + D D V +REN+EGEYSG
Sbjct: 85 HISLW---GLLLKIRREFDQYANVRPAKLLPGVTSPLRNCGPGDFDFVVVRENSEGEYSG 141
Query: 95 I 95
+
Sbjct: 142 V 142
>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 = 190 bits (485), Expect = 9e-58
Identities = 101/251 (40%), Positives = 148/251 (58%), Gaps = 13/251 (5%)
Query: 121 EFNLYANVRPCR---SLEGYPTLYDD----VDVVTIRENTEGEYSGIEHEI-VDGVVQSI 172
+L+AN+RP + LE L + VD V +RE T G Y G +G
Sbjct: 95 SLDLFANLRPAKVFPGLEDLSPLKPEIAKGVDFVVVRELTGGIYFGEPKGREGEGEAWDT 154
Query: 173 KLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFE 232
++ T R+A AFE A+ + KVT+V KAN++ S L+ + + A+++P+V+ E
Sbjct: 155 EVYTVPEIERIARVAFEMARKRRK-KVTSVDKANVLESSR-LWRKTVEEIAKEYPDVELE 212
Query: 233 EKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG-ALFES 291
+Y+D + +V+ PTQ+DV+V NL+GDILSD + + G LG+ PS ++G +G LFE
Sbjct: 213 HQYIDNAAMQLVKSPTQFDVVVTSNLFGDILSDEASVITGSLGMLPSASLGSDGFGLFEP 272
Query: 292 VHGTAPDIAGKDLANPTALLLSAVMMLRH-LDLNTHADVIQKAALDTIKEGKYRTGDLGG 350
VHG+APDIAGK +ANP A +LSA M+LR+ +L AD I+ A + EG YRT DLG
Sbjct: 273 VHGSAPDIAGKGIANPIAQILSAAMLLRYSFNLEEAADAIEAAVKKVLAEG-YRTPDLGS 331
Query: 351 KAKCSEFTNEI 361
A + T E+
Sbjct: 332 SATTAVGTAEM 342
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 187 bits (477), Expect = 2e-56
Identities = 89/246 (36%), Positives = 136/246 (55%), Gaps = 21/246 (8%)
Query: 121 EFNLYANVRPCRSLEGYPT-LYD--DVDVVTIRENTEGEYSGI--------EHEIVDGVV 169
+ Y N+RP + G + L D+D V +RE TEG Y+G HE+ V
Sbjct: 96 ALDHYVNLRPSKLYPGVTSPLAGPGDIDFVVVREGTEGPYTGNGGALRVGTPHEVATEV- 154
Query: 170 QSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEV 229
S+ T RV AFE A+ R +T VHK N++ + L+ R + A ++P+V
Sbjct: 155 -SVN--TAFGVERVVRDAFERAQKRPRKHLTLVHKTNVLTFAGDLWQRTVDEVAAEYPDV 211
Query: 230 KFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNI---GLNG 286
+ +++D + MV DP+++DV+V NL+GDI++D+ A + GG+GL SGNI G N
Sbjct: 212 TVDYQHVDAATIFMVTDPSRFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINPTGTNP 271
Query: 287 ALFESVHGTAPDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKE---GKY 343
++FE VHG+APDIAG+ +A+PTA +LS ++L HL A I+ A + E
Sbjct: 272 SMFEPVHGSAPDIAGQGIADPTAAILSVALLLDHLGEEDAAARIEAAVEADLAERGKMGR 331
Query: 344 RTGDLG 349
T ++G
Sbjct: 332 STAEVG 337
Score = 37.2 bits (87), Expect = 0.009
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 56 EFNLYANVRPCRSLEGYPT-LYD--DVDVVTIRENTEGEYSG 94
+ Y N+RP + G + L D+D V +RE TEG Y+G
Sbjct: 96 ALDHYVNLRPSKLYPGVTSPLAGPGDIDFVVVREGTEGPYTG 137
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 181 bits (461), Expect = 4e-54
Identities = 95/265 (35%), Positives = 152/265 (57%), Gaps = 35/265 (13%)
Query: 121 EFNLYANVRPCRSLEGY-PTLYD--DVDVVTIRENTEGEYSGI-------EHEIVDGVVQ 170
EF N+RP + L G L + D D++ +REN+EGEYS + E EI +Q
Sbjct: 98 EFEQVINIRPAKQLRGIKSPLANPKDFDLLVVRENSEGEYSEVGGRIHRGEDEIA---IQ 154
Query: 171 SIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKAN----IMRMSDGLFLRCCRDAAEKF 226
+ + T + + R +AFE A R VT+ K+N M D +F ++ + +
Sbjct: 155 N-AVFTRKGTERAMRYAFELAAKR-RKHVTSATKSNGIVHSMPFWDEVF----QEVGKDY 208
Query: 227 PEVKFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNG 286
PE++ + +++D + V P ++DV+V NL+GDIL+D+ A ++G +G+ P+ NI +NG
Sbjct: 209 PEIETDSQHIDALAAFFVTRPEEFDVIVASNLFGDILTDIGAAIMGSIGIAPAANINVNG 268
Query: 287 ---ALFESVHGTAPDIAGKDLANPTALLLSAVMMLRHL---DLNTHA-DVIQKAALDTIK 339
++FE VHG+APDIAGK +ANP + +A +ML H +L +H DVI+ D +
Sbjct: 269 KYPSMFEPVHGSAPDIAGKGIANPIGQIWTAKLMLDHFGEEELGSHLLDVIE----DVTE 324
Query: 340 EGKYRTGDLGGKAKCSEFTNEICSK 364
+G +T D+GG+A E T+EI S+
Sbjct: 325 DG-IKTPDIGGRATTDEVTDEIISR 348
Score = 48.6 bits (116), Expect = 2e-06
Identities = 34/99 (34%), Positives = 49/99 (49%), Gaps = 16/99 (16%)
Query: 41 ISQWSWRGLKVQGLGEFNLYANVRPCRSLEGY-PTLYD--DVDVVTIRENTEGEYSGI-- 95
IS W GL ++ EF N+RP + L G L + D D++ +REN+EGEYS +
Sbjct: 86 ISLW---GLLIKIRREFEQVINIRPAKQLRGIKSPLANPKDFDLLVVRENSEGEYSEVGG 142
Query: 96 -----EHEIVDGVCNSNYATKWFSERGASVEFNLYANVR 129
E EI + N+ + T+ +ER F L A R
Sbjct: 143 RIHRGEDEIA--IQNAVF-TRKGTERAMRYAFELAAKRR 178
>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 = 183 bits (465), Expect = 5e-54
Identities = 112/349 (32%), Positives = 152/349 (43%), Gaps = 78/349 (22%)
Query: 47 RGLKVQGLGEFNLYANVRPCRSLEGYPTLY---DDVDVVTIRENTEGEYSGIEHEIVDGV 103
R L V E +LY +RP R +G P+ + VD+V RENTE Y+GIE
Sbjct: 112 RSLNVALRQELDLYVCLRPVRYYKGVPSPVKHPEKVDMVIFRENTEDIYAGIE------- 164
Query: 104 CNSNYATKWFSERGASVEFNLYANVRPCRSLEGYPTLYDDVDVVTIRENTEGEYSGIEHE 163
W G+ L L +++ V IR E SGI
Sbjct: 165 --------W--AEGSEEAKKLIR------------FLQNELGVKKIR---FPEDSGI--- 196
Query: 164 IVDGVVQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAA 223
IK I+EE + R+ A EYA N+R VT VHK NIM+ ++G F RD
Sbjct: 197 -------GIKPISEEGTKRLVRAAIEYAIENDRKSVTLVHKGNIMKFTEGAF----RDWG 245
Query: 224 EKFPEVKFEEKYL--------------------DTVCLNMVQD----PTQYDVLVMPNLY 259
+ + +F + + D + +Q P +YDV+ NL
Sbjct: 246 YELAKKEFGAECITWGLWDKYKNPNPGKEIVIKDRIADAFLQQILTRPDEYDVIATMNLN 305
Query: 260 GDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLANPTALLLSAVMMLR 319
GD +SD A VGG+G+ P NIG +FE+ HGTAP AG+D NP +++LS MML
Sbjct: 306 GDYISDALAAQVGGIGIAPGANIGDEIGIFEATHGTAPKYAGQDKVNPGSIILSGEMMLE 365
Query: 320 HLDLNTHADVIQKAALDTIKEGK-----YRTGDLGGKAKCSEFTNEICS 363
H+ AD+I+KA I R D + KCSEF I
Sbjct: 366 HMGWKEAADLIKKAMEKAIASKIVTYDFARLMDGAKEVKCSEFAEAIIE 414
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 169 bits (429), Expect = 9e-49
Identities = 98/292 (33%), Positives = 142/292 (48%), Gaps = 51/292 (17%)
Query: 121 EFNLYANVRPCRSLEGYPTLY---DDVDVVTIRENTEGEYSGIEHEI----VDGVVQ--- 170
E +LY +RP R +G P+ +D D+V REN+E Y+GIE + V++
Sbjct: 114 ELDLYVCLRPVRYFKGVPSPVKRPEDTDMVIFRENSEDIYAGIEWKAGSAEAKKVIKFLQ 173
Query: 171 ----------------SIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGL 214
IK ++EE + R+ A EYA N+R VT VHK NIM+ ++G
Sbjct: 174 EEMGVKKIRFPETSGIGIKPVSEEGTERLVRAAIEYAIDNDRKSVTLVHKGNIMKFTEGA 233
Query: 215 FLRCCRDAAEK-----------FPEVKFEEKYLDTVCLNMVQD---------PTQYDVLV 254
F AE+ + ++K E + + + + D P +YDV+
Sbjct: 234 FKDWGYQLAEEEFGDELIDGGPWDKIKNPETGKEIIVKDSIADAFLQQILLRPAEYDVIA 293
Query: 255 MPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLANPTALLLSA 314
NL GD +SD A VGG+G+ P NI A+FE+ HGTAP AG D NP +++LSA
Sbjct: 294 TMNLNGDYISDALAAQVGGIGIAPGANINDGHAIFEATHGTAPKYAGLDKVNPGSVILSA 353
Query: 315 VMMLRHLDLNTHADVIQKAALDTIKEGK--Y---RTGDLGGKAKCSEFTNEI 361
MMLRH+ AD+I K+ TI Y R + + KCSEF + +
Sbjct: 354 EMMLRHMGWTEAADLIIKSMEKTIASKTVTYDFARLMEGATEVKCSEFGDAL 405
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 158 bits (400), Expect = 1e-44
Identities = 90/270 (33%), Positives = 140/270 (51%), Gaps = 45/270 (16%)
Query: 123 NLYANVRPCRSLEGYPTLY---DDVDVVTIRENTEGEYSGIEH----------------- 162
+LYAN+RP + + G + + +D++ RENT+ Y GIE+
Sbjct: 118 DLYANIRPVKYIPGIESPLKNPEKIDLIIFRENTDDLYRGIEYPYDSEEAKKIRDFLRKE 177
Query: 163 ---EIVDGVVQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCC 219
E+ D IKLI++ + R+A A +YA + R KVT +HK N+M+ ++G F
Sbjct: 178 LGVEVEDDTGIGIKLISKFKTQRIARMAIKYAIDHKRKKVTIMHKGNVMKYTEGAFREWA 237
Query: 220 RDAAEK---------------FPEVKFEEKYL--DTVCLNMVQD----PTQYDVLVMPNL 258
+ A K + V K + D + NM Q P +YD+++ PN+
Sbjct: 238 YEVALKEFRDYVVTEEEVTKNYNGVPPSGKVIINDRIADNMFQQIIIRPDEYDIILAPNV 297
Query: 259 YGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLANPTALLLSAVMML 318
GD +SD LVG +G+ NIG G +FE++HGTAP AGK++ANPT ++ +ML
Sbjct: 298 NGDYISDAAGALVGNIGMLGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKGGELML 357
Query: 319 RHLDLNTHADVIQKAALDTIKEGKYRTGDL 348
R + + AD+I KA +++IK+ K T DL
Sbjct: 358 RFMGWDKAADLIDKAIMESIKQKKV-TQDL 386
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 144 bits (365), Expect = 1e-39
Identities = 92/262 (35%), Positives = 144/262 (54%), Gaps = 27/262 (10%)
Query: 121 EFNLYANVRPCRSLEGYPTLYD----------DVDVVTIRENTEGEYSGIEHEIV----- 165
+ ++AN+RP L P L D VD++ +RE T G Y G I
Sbjct: 142 DLKVFANLRPATVL---PQLVDASTLKKEVAEGVDMMIVRELTGGIYFGEPRGITINENG 198
Query: 166 DGVVQSIKLITEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEK 225
+ V S ++ R+A AFE A+ R K+ +V KAN++ S L+ + A +
Sbjct: 199 EEVGVSTEIYAAHEIDRIARVAFETAR-KRRGKLCSVDKANVLDASI-LWRKRVTALASE 256
Query: 226 FPEVKFEEKYLDTVCLNMVQDPTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLN 285
+P+V+ Y+D + +++DP Q+D +V N++GDILSD + + G +G+ PS ++G +
Sbjct: 257 YPDVELSHMYVDNAAMQLIRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLGES 316
Query: 286 G-ALFESVHGTAPDIAGKDLANPTALLLSAVMMLRH-LDLNTHADVIQKAALDTIKEGKY 343
G LFE +HG+APDIAG+D ANP A +LSA M+L++ L A I+ A +D + +G +
Sbjct: 317 GPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVVDALNKG-F 375
Query: 344 RTGDL---GGK-AKCSEFTNEI 361
RTGD+ G K C E E+
Sbjct: 376 RTGDIYSPGNKLVGCKEMGEEV 397
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 108 bits (271), Expect = 4e-26
Identities = 54/124 (43%), Positives = 67/124 (54%), Gaps = 8/124 (6%)
Query: 247 PTQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLAN 306
P +Y +L NL GD +SD A +VGGLG+ P NIG N A+FE+ HGTAP AG D N
Sbjct: 350 PQEYSILATLNLNGDYISDAAAAIVGGLGMAPGANIGDNAAIFEATHGTAPKHAGLDRIN 409
Query: 307 PTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYRTGDLG-------GKAKCSEFTN 359
P +++LS VMML +L AD+I K I + T DL CSEF
Sbjct: 410 PGSVILSGVMMLEYLGWQEAADLITKGLSAAIANKQV-TYDLARLMEPPVDPLSCSEFAE 468
Query: 360 EICS 363
I S
Sbjct: 469 AIIS 472
Score = 71.7 bits (176), Expect = 1e-13
Identities = 41/127 (32%), Positives = 56/127 (44%), Gaps = 33/127 (25%)
Query: 122 FNLYANVRPCRSLEGYPTLY---DDVDVVTIRENTEGEYSGIEHEIVDGVVQS------- 171
F+LY+ VRPCR G P+ + + +DV+ RENTE Y GIE E D +
Sbjct: 124 FDLYSCVRPCRYYAGTPSPHKNPEKLDVIVYRENTEDIYMGIEWEAGDEIGDKLIKHLNE 183
Query: 172 ---------------------IKLITEEASSRVAEFAFEYAKTNNRSK--VTAVHKANIM 208
IK +++ S R A E+A K VT VHK NIM
Sbjct: 184 EVIPASPELGKRQIPLGSGIGIKPVSKTGSQRHIRRAIEHALRLPGDKRHVTLVHKGNIM 243
Query: 209 RMSDGLF 215
+ ++G F
Sbjct: 244 KYTEGAF 250
>gnl|CDD|235402 PRK05312, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 37.6 bits (88), Expect = 0.008
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 293 HGTAPDIAGKDLANPTALL 311
HGTA DIAGK +A P +L+
Sbjct: 304 HGTAFDIAGKGIARPDSLI 322
>gnl|CDD|236226 PRK08299, PRK08299, isocitrate dehydrogenase; Validated.
Length = 402
Score = 36.8 bits (86), Expect = 0.013
Identities = 34/111 (30%), Positives = 47/111 (42%), Gaps = 24/111 (21%)
Query: 257 NLYGDILSDMCAGLVGGLGL------TPSGNIGLNGALFESVHGTAPD-----IAGKDLA 305
N GD+ SD A G LGL TP G E+ HGT G++ +
Sbjct: 269 NYDGDVQSDTVAQGFGSLGLMTSVLMTPDGKT----VEAEAAHGTVTRHYRQHQKGEETS 324
Query: 306 -NPTALLLSAVMMLRH---LDLNTH----ADVIQKAALDTIKEGKYRTGDL 348
NP A + + L H LD N AD ++K ++T++ G T DL
Sbjct: 325 TNPIASIFAWTRGLAHRGKLDGNPELVKFADTLEKVCIETVESGFM-TKDL 374
>gnl|CDD|129233 TIGR00127, nadp_idh_euk, isocitrate dehydrogenase, NADP-dependent,
eukaryotic type. This model describes a eukaryotic,
NADP-dependent form of isocitrate dehydrogenase. These
eukaryotic enzymes differ considerably from a fairly
tight cluster that includes all other related isocitrate
dehydrogenases, 3-isopropylmalate dehydrogenases, and
tartrate dehydrogenases. 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. This model does
not discriminate cytosolic, mitochondrial, and
chloroplast proteins. However, the model starts very
near the amino end of the cytosolic form; the finding of
additional amino-terminal sequence may indicate a
transit peptide [Energy metabolism, TCA cycle].
Length = 409
Score = 36.8 bits (85), Expect = 0.017
Identities = 42/167 (25%), Positives = 69/167 (41%), Gaps = 24/167 (14%)
Query: 204 KANIMRMSDGLFLRCCRDAAEKFPEVKFEE-------KYLDTVCLNMVQDPTQYDVLVMP 256
K I++ DG F ++ E + KFE + +D + ++ + +
Sbjct: 211 KNTILKKYDGRFKDIFQEVYEAQYKSKFEALGIWYEHRLIDDMVAQALKSEGGF-IWACK 269
Query: 257 NLYGDILSDMCAGLVGGLGLTPSGNIGLNGALFES--VHGTAP------DIAGKDLANPT 308
N GD+ SD+ A G LGL S I +G FE+ HGT + N
Sbjct: 270 NYDGDVQSDIVAQGFGSLGLMTSVLICPDGKTFEAEAAHGTVTRHYRMYQKGQETSTNSI 329
Query: 309 ALLLSAVMMLRH---LDLNTH----ADVIQKAALDTIKEGKYRTGDL 348
A + + L H LD N A++++ A ++T++ G T DL
Sbjct: 330 ASIFAWSRGLAHRAKLDNNPELSKFANILESACINTVEAGIM-TKDL 375
>gnl|CDD|233023 TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.
This model represents PdxA, an NAD+-dependent
4-hydroxythreonine 4-phosphate dehydrogenase (EC
1.1.1.262) active in pyridoxal phosphate biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridoxine].
Length = 320
Score = 35.5 bits (83), Expect = 0.029
Identities = 15/32 (46%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 291 SV-HGTAPDIAGKDLANPTALLLSAVMMLRHL 321
S HGTA DIAGK A+P + L++A+ + L
Sbjct: 289 SPDHGTAFDIAGKGKADPGS-LIAAIKLAIEL 319
>gnl|CDD|224906 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 332
Score = 33.8 bits (78), Expect = 0.12
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 293 HGTAPDIAGKDLANPTALL 311
HGTA DIAGK +A+P +L+
Sbjct: 298 HGTAFDIAGKGIADPGSLI 316
>gnl|CDD|234696 PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Reviewed.
Length = 332
Score = 33.6 bits (78), Expect = 0.13
Identities = 16/31 (51%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 291 SV-HGTAPDIAGKDLANP----TALLLSAVM 316
SV HGTA D+AGK +A+ TAL L+ M
Sbjct: 296 SVDHGTALDLAGKGIADVGSFITALNLAIRM 326
>gnl|CDD|217937 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In
Escherichia coli the coenzyme pyridoxal 5'-phosphate is
synthesised de novo by a pathway that is thought to
involve the condensation of
4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose,
catalyzed by the enzymes PdxA and PdxJ, to form either
pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Length = 299
Score = 33.5 bits (77), Expect = 0.14
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 293 HGTAPDIAGKDLANPTALL 311
HGTA DIAGK A+P +L+
Sbjct: 274 HGTAFDIAGKGKADPGSLI 292
>gnl|CDD|178617 PLN03065, PLN03065, isocitrate dehydrogenase (NADP+); Provisional.
Length = 483
Score = 33.3 bits (76), Expect = 0.20
Identities = 51/194 (26%), Positives = 81/194 (41%), Gaps = 23/194 (11%)
Query: 176 TEEASSRVAEFAFEYAKTNNRSKVTAVHKANIMRMSDGLFLRCCRDAAEKFPEVKFEEK- 234
+E+ AE + A + + K I++ DG F ++ E+ + KFEE
Sbjct: 254 VDESIRAFAESSMAMALQK-KWPLYLSTKNTILKKYDGRFKDIFQEVYEEQWKQKFEEHS 312
Query: 235 --YLDTVCLNMVQDPTQYD---VLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLNGALF 289
Y + +MV + + V N GD+ SD+ A G LGL S + +G
Sbjct: 313 IWYEHRLIDDMVAYAVKSEGGYVWACKNYDGDVQSDLLAQGFGSLGLMTSVLLSSDGKTL 372
Query: 290 ES--VHGTAPD-----IAGKDLA-NPTALLLSAVMMLRH---LDLNTH-ADVIQK---AA 334
E+ HGT G++ + N A + + L H LD N D + K A
Sbjct: 373 EAEAAHGTVTRHFRLHQKGQETSTNSIASIFAWTRGLEHRAKLDKNEELLDFVHKLESAC 432
Query: 335 LDTIKEGKYRTGDL 348
++T++ GK T DL
Sbjct: 433 IETVESGKM-TKDL 445
>gnl|CDD|235066 PRK02746, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 345
Score = 33.0 bits (76), Expect = 0.20
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 293 HGTAPDIAGKDLANPTALL 311
HGTA DIAGK +A P ++
Sbjct: 312 HGTAFDIAGKGIARPQSMK 330
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 32.9 bits (76), Expect = 0.21
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 150 RENTEGEYSGIEHEIVDGVVQS 171
RE E+S E +IV GVVQ
Sbjct: 123 REIIYNEFSEREGDIVTGVVQR 144
Score = 28.3 bits (64), Expect = 7.8
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 85 RENTEGEYSGIEHEIVDGV 103
RE E+S E +IV GV
Sbjct: 123 REIIYNEFSEREGDIVTGV 141
>gnl|CDD|132322 TIGR03279, cyano_FeS_chp, putative FeS-containing
Cyanobacterial-specific oxidoreductase. Members of this
protein family are predicted FeS-containing
oxidoreductases of unknown function, apparently
restricted to and universal across the Cyanobacteria.
The high trusted cutoff score for this model, 700 bits,
excludes homologs from other lineages. This exclusion
seems justified because a significant number of sequence
positions are simultaneously unique to and invariant
across the Cyanobacteria, suggesting a specialized,
conserved function, perhaps related to photosynthesis. A
distantly related protein family, TIGR03278, in
universal in and restricted to archaeal methanogens, and
may be linked to methanogenesis.
Length = 433
Score = 32.4 bits (74), Expect = 0.39
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 288 LFESVHGTAPDIAGKDLANPTA-LLLSAVMMLRHLDLNTHADVI 330
L+ SVH T P + + L NP A L+L + + L HA V+
Sbjct: 142 LYVSVHATEPSLRARLLKNPRAGLILEQLKWFQERRLQLHAQVV 185
>gnl|CDD|234991 PRK01909, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Validated.
Length = 329
Score = 29.3 bits (66), Expect = 2.9
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 293 HGTAPDIAGKDLANPTALLL---SAVMMLRH 320
HGTA D+AG A+P +++ +AV M RH
Sbjct: 295 HGTALDLAGTGRADPGSMIAAIDTAVTMARH 325
>gnl|CDD|179641 PRK03743, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Validated.
Length = 332
Score = 28.8 bits (65), Expect = 4.6
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 291 SV-HGTAPDIAGKDLANPT----ALLLSA 314
SV HGTA DIAG A+ A+LL+A
Sbjct: 296 SVDHGTAFDIAGTGKASSVSMEEAILLAA 324
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 28.6 bits (64), Expect = 5.7
Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 10/79 (12%)
Query: 265 DMCAGLVGGLGLTPSGNIGLNGALFESVHGTAPDIAGKDLANPTALLLSAVMMLRHLDLN 324
M G+VGG G GL A+ + G I G + + L A + L+
Sbjct: 1 MMKVGIVGG------GLAGLTAAISLAKKGFDVTIIGPGIKKSNSYLAQAGIAFPILE-- 52
Query: 325 THADVIQKAALDTIKEGKY 343
D I+ LDTI+ GKY
Sbjct: 53 --GDSIRAHVLDTIRAGKY 69
>gnl|CDD|236287 PRK08561, rps15p, 30S ribosomal protein S15P; Reviewed.
Length = 151
Score = 27.5 bits (62), Expect = 6.2
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 293 HGTAPDIAGKDLANPTALLLSAVMMLRHLDLNTHADVIQKAALDTIKEGKYR 344
+G AP+I +DL N L+ AV + +HL+ N D+ K L I E K R
Sbjct: 78 NGLAPEIP-EDLRN---LIKKAVNLRKHLEENPK-DLHNKRGLQLI-ESKIR 123
>gnl|CDD|219458 pfam07539, DRIM, Down-regulated in metastasis. These eukaryotic
proteins include DRIM (Down-Regulated In Metastasis),
which is differentially expressed in metastatic and
non-metastatic human breast carcinoma cells. It is
believed to be involved in processing of non-coding RNA.
Length = 140
Score = 26.8 bits (60), Expect = 9.8
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 306 NPTALLLSAVMMLRHLDLNTHADV-IQKAALDTI 338
NP AL + + L L + D +QK ALD I
Sbjct: 8 NPKALYKADELYELLLTLLSSRDPEVQKLALDCI 41
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
0.317 0.134 0.396
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,195,458
Number of extensions: 1752249
Number of successful extensions: 1469
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1398
Number of HSP's successfully gapped: 63
Length of query: 364
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 266
Effective length of database: 6,590,910
Effective search space: 1753182060
Effective search space used: 1753182060
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 (21.6 bits)
S2: 60 (26.8 bits)