RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy559
(376 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 = 454 bits (1169), Expect = e-161
Identities = 182/337 (54%), Positives = 234/337 (69%), Gaps = 20/337 (5%)
Query: 41 GGRNAVTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKSDSN-DDLEYAITSIRR 99
GG+ VT++PG GIGPE+ VK++FR A VP++FE + + P++D + + A+ SI+R
Sbjct: 1 GGKYTVTLIPGDGIGPEISGSVKKIFRAANVPIEFEEIDVSPQTDGKTEIPDEAVESIKR 60
Query: 100 NGVAIKGNIET----GSLDSLWTLKLCRLILR---------VIAMMILSVRCRQQGIDIV 146
N VA+KG +ET G SL + LR V + + R + +DIV
Sbjct: 61 NKVALKGPLETPIGKGGHRSL------NVALRKELDLYANVVHCKSLPGFKTRHEDVDIV 114
Query: 147 IVRQNTEGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANI 206
I+R+NTEGEY+ LEHESV GVVES+K+IT S R+++YAFEYA+K GRKKVT VHKANI
Sbjct: 115 IIRENTEGEYSGLEHESVPGVVESLKVITRDKSERIARYAFEYARKNGRKKVTAVHKANI 174
Query: 207 MKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVI 266
MK++DGLFL + R+VAKEYP+I MI+DNTCMQLVS P QFDVMVMPNLYG I SN+
Sbjct: 175 MKLADGLFLNVCREVAKEYPDITFESMIVDNTCMQLVSRPSQFDVMVMPNLYGNILSNLG 234
Query: 267 CGLIGGAGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKH 326
GL+GG GL+ G N G YAVFEPG R+TG IAG+NIANP A++ +SV ML HLG +H
Sbjct: 235 AGLVGGPGLVPGANIGRDYAVFEPGVRHTGPDIAGQNIANPTALILSSVMMLNHLGLKEH 294
Query: 327 ASIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNIIK 363
A I+ A+ TI E K T DLGGTAT+ D + +IK
Sbjct: 295 ADRIQKAVLSTIAEGKNRTKDLGGTATTSDFTEAVIK 331
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 309 bits (792), Expect = e-103
Identities = 156/336 (46%), Positives = 212/336 (63%), Gaps = 21/336 (6%)
Query: 41 GGRNAVTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKSDSNDDLEYAITSIRRN 100
G AVT++PG GIGP + V++V PV FE ++ D E + SIRRN
Sbjct: 28 GAPRAVTLIPGDGIGPLVTGAVEQVMEAMHAPVYFERYEV--HGDMKKVPEEVLESIRRN 85
Query: 101 GVAIKGNIET---GSLDSLWTLKLCRLILRVIAMMILSVRC--------RQQGIDIVIVR 149
V +KG + T G + SL ++L R L + A + V C R + +DIV++R
Sbjct: 86 KVCLKGGLATPVGGGVSSL-NVQL-RKELDLFASL---VNCFNLPGLPTRHENVDIVVIR 140
Query: 150 QNTEGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKI 209
+NTEGEY+ LEHE V GVVES+K+IT S R++KYAFEYA RKKVT VHKANIMK+
Sbjct: 141 ENTEGEYSGLEHEVVPGVVESLKVITKFCSERIAKYAFEYAYLNNRKKVTAVHKANIMKL 200
Query: 210 SDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGL 269
+DGLFLE R+VAK+YP I++N++I+DN CMQLVS P+QFDVMV PNLYG + +N G+
Sbjct: 201 ADGLFLESCREVAKKYPGIKYNEIIVDNCCMQLVSKPEQFDVMVTPNLYGNLVANTAAGI 260
Query: 270 IGGAGLISGKNYGDHYAVFEPGTR--NTGT-AIAGKNIANPIAMLNASVDMLEHLGHMKH 326
GG G++ G N G +AVFE G N G + + ANP+A+L +S ML HL
Sbjct: 261 AGGTGVMPGGNVGADHAVFEQGASAGNVGNEKLVEQKKANPVALLLSSAMMLRHLQFPSF 320
Query: 327 ASIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNII 362
A ++ A+++ I E K T DLGG++T+ +VV +I
Sbjct: 321 ADRLETAVKRVIAEGKYRTKDLGGSSTTQEVVDAVI 356
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 303 bits (777), Expect = e-101
Identities = 150/326 (46%), Positives = 204/326 (62%), Gaps = 11/326 (3%)
Query: 47 TMLPGGGIGPELMSYVKEVFRYAGVPVDFET----VQIDPKSDSNDDLEYAITSIRRNGV 102
T+ PG GIGPE+ VK+VF AGVP+++E +DP++ S E ++ S+RRN V
Sbjct: 45 TLFPGDGIGPEIAESVKQVFTAAGVPIEWEEHYVGTTVDPRTGSFLTWE-SLESVRRNKV 103
Query: 103 AIKGNIETGSLDSLWTLKLC-RLILRVIA-----MMILSVRCRQQGIDIVIVRQNTEGEY 156
+KG + T +L L R L + A + + R +D+V +R+NTEGEY
Sbjct: 104 GLKGPMATPIGKGHRSLNLTLRKELGLYANVRPCYSLPGYKTRYDDVDLVTIRENTEGEY 163
Query: 157 AMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDGLFLE 216
+ LEH+ V GVVES+KIIT S R+++YAF YAK GRK+V+ +HKANIMK +DGLFL+
Sbjct: 164 SGLEHQVVRGVVESLKIITRQASLRVAEYAFHYAKTHGRKRVSAIHKANIMKKTDGLFLK 223
Query: 217 ISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGAGLI 276
R+VA++YPEI + ++IIDN CM LV NP FDV+VMPNLYG I S++ GLIGG GL
Sbjct: 224 CCREVAEKYPEIVYEEVIIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLIGGLGLT 283
Query: 277 SGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIEK 336
N G++ + IAGKN+ANP A+L ++V ML HL + A I AI
Sbjct: 284 PSCNIGENGLALAEAVHGSAPDIAGKNLANPTALLLSAVMMLRHLKLNEQAEQIHNAILN 343
Query: 337 TINEDKIHTPDLGGTATSIDVVQNII 362
TI E K T DLGG++T+ D + I
Sbjct: 344 TIAEGKYRTADLGGSSTTTDFTKAIC 369
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 288 bits (739), Expect = 2e-95
Identities = 137/342 (40%), Positives = 195/342 (57%), Gaps = 28/342 (8%)
Query: 46 VTMLPGGGIGPELMSYVKEVFRYAG-VPVDFETVQIDPKSDSNDD-----LEYAITSIRR 99
+ ++PG GIGPE+M+ +V A +DFE + + ++ D E + S+++
Sbjct: 6 IAVIPGDGIGPEVMAAALKVLEAAAEFGLDFEFEEAEVGGEAYDKHGEPLPEETLESLKK 65
Query: 100 NGVAIKGNIETGSLDSLW------TLKLCRLI-----LRVIAMMILSVRCR-QQGIDIVI 147
+ G + D L L L + + LR A + ++ +G+DIVI
Sbjct: 66 ADAILFGAVGGPKWDPLPRPERGLLLALRKELDLYANLRP-AKSLPGLKSPLVKGVDIVI 124
Query: 148 VRQNTEGEYAMLEHESVDG--VVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKAN 205
VR+NTEG Y E + G V K+IT S R++++AFE A+K GRKKVT+VHKAN
Sbjct: 125 VRENTEGLYFGEEGRILGGGEVAIDTKVITRKGSERIARFAFELARKRGRKKVTSVHKAN 184
Query: 206 IMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNV 265
++K+SDGL+ E+ +VAKEYP++E + M +D MQLV NP+QFDV+V NL+G I S+
Sbjct: 185 VLKLSDGLWREVVEEVAKEYPDVELDHMYVDAAAMQLVRNPEQFDVIVTSNLFGDILSDE 244
Query: 266 ICGLIGGAGLISGKNYGDH--YAVFEPGTRNTGTA--IAGKNIANPIAMLNASVDMLEHL 321
L G GL N GD A+FEP G+A IAGK IANPIA + ++ ML HL
Sbjct: 245 AAALTGSLGLAPSANLGDERGPALFEP---VHGSAPDIAGKGIANPIATILSAAMMLRHL 301
Query: 322 GHMKHASIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNIIK 363
G + A I+ A+EK + E I TPDLGG AT+ +V I K
Sbjct: 302 GEKEAADAIENAVEKVLAEGGIRTPDLGGNATTSEVGDAIAK 343
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 269 bits (690), Expect = 2e-88
Identities = 130/330 (39%), Positives = 189/330 (57%), Gaps = 12/330 (3%)
Query: 44 NAVTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKS-DSNDDL--EYAITSIRRN 100
+T++PG GIGP ++ ++ G ++E + + + +L + + I +N
Sbjct: 3 QTITVIPGDGIGPSIIDATLKILDKLGCDFEYEFADAGLTALEKHGELLPQRTLDLIEKN 62
Query: 101 GVAIKGNIET---GSLDSL-WTL-KLCRLILRV-IAMMILSVRCRQQGIDIVIVRQNTEG 154
+A+KG + T S+ TL K L V + + R IDI+ VR+NTEG
Sbjct: 63 KIALKGPLTTPVGEGFTSINVTLRKKFDLYANVRPVLSFPGTKARYDNIDIITVRENTEG 122
Query: 155 EYAMLEHE-SVDG-VVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDG 212
Y+ S DG E+ IIT + R+ ++A+E A+K GRKKVT VHKANIMK + G
Sbjct: 123 MYSGEGQTVSEDGETAEATSIITRKGAERIVRFAYELARKEGRKKVTAVHKANIMKSTSG 182
Query: 213 LFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGG 272
LFL+++R+VA YP+IE +MI+D TCMQLV NP+QFDV+V NL+G I S++ GL+GG
Sbjct: 183 LFLKVAREVALRYPDIEFEEMIVDATCMQLVMNPEQFDVIVTTNLFGDILSDLCAGLVGG 242
Query: 273 AGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKL 332
G+ G N G A+FE + IAGKN+ANP +++ A++ MLE+LG A I+
Sbjct: 243 LGMAPGANIGRDAAIFE-AVHGSAPDIAGKNLANPTSVILAAIQMLEYLGMPDKAERIRK 301
Query: 333 AIEKTINEDKIHTPDLGGTATSIDVVQNII 362
AI I T DLGGT + D Q +I
Sbjct: 302 AIVAVIEAGDRTTRDLGGTHGTTDFTQAVI 331
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 272 bits (698), Expect = 1e-87
Identities = 133/335 (39%), Positives = 183/335 (54%), Gaps = 43/335 (12%)
Query: 46 VTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPK----------SDSNDDLEYAIT 95
+T+ G GIGPE+M V ++ AG P++ ET++I K S S A
Sbjct: 7 ITVAYGDGIGPEIMEAVLKILEAAGAPLEIETIEIGEKVYKKGWTSGISPS------AWE 60
Query: 96 SIRRNGVAIKGNIET---GSLDSL-----WTLKL------CRLILRVIAMMILSVRCRQQ 141
SIRR V +K I T G SL TL L C V +
Sbjct: 61 SIRRTKVLLKAPITTPQGGGYKSLNVTLRKTLGLYANVRPCVSYHPF-------VETKHP 113
Query: 142 GIDIVIVRQNTEGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTV 201
+D+VI+R+N E YA +EH V + +K+I+ S ++ +YAFEYA+ GRKKVT +
Sbjct: 114 NLDVVIIRENEEDLYAGIEHRQTPDVYQCLKLISRPGSEKIIRYAFEYARANGRKKVTCL 173
Query: 202 HKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAI 261
K NIMK++DGLF ++ ++AKEYP+IE I+D +L +NP+ FDV+V PNLYG I
Sbjct: 174 TKDNIMKLTDGLFHKVFDEIAKEYPDIEAEHYIVDIGAARLATNPENFDVIVTPNLYGDI 233
Query: 262 TSNVICGLIGGAGLISGKNYGDHYAVFEPGTRNTGTA--IAGKNIANPIAMLNASVDMLE 319
S++ + G GL N G+ YA+FE G+A IAGKNIANP +LNA+V ML
Sbjct: 234 LSDIAAEISGSVGLAGSANIGEEYAMFEA---VHGSAPDIAGKNIANPSGLLNAAVMMLV 290
Query: 320 HLGHMKHASIIKLAIEKTINEDKIHTPDLGGTATS 354
H+G A +I+ A KT+ ED IHT D+ S
Sbjct: 291 HIGQFDIAELIENAWLKTL-EDGIHTADIYNEGVS 324
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 236 bits (604), Expect = 2e-75
Identities = 117/338 (34%), Positives = 179/338 (52%), Gaps = 29/338 (8%)
Query: 46 VTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKSDSNDDL---------EYAITS 96
+ ++ G GIG E++ V G+P +F +++ D++ E I +
Sbjct: 4 ICVIEGDGIGKEVVPAALHVLEATGLPFEFV------YAEAGDEVFEKTGKALPEETIEA 57
Query: 97 IRRNGVAIKGNIETGSLDSLWTLKLCRLILRVIAMM-----ILSVRCRQQGIDIVIVRQN 151
+ + G + D + L R IL A + V+C ID VIVR+N
Sbjct: 58 AKEADAVLFGAAGETAADVIVKL---RRILDTYANVRPVKSYKGVKCLYPDIDYVIVREN 114
Query: 152 TEGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKK----FGRKKVTTVHKANIM 207
TEG Y +E E DGV + ++IT S R+ ++AFE AK+ KVT HKAN++
Sbjct: 115 TEGLYKGIEAEIADGVTVATRVITRKASERIFRFAFEMAKRRKKMGKEGKVTCAHKANVL 174
Query: 208 KISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVIC 267
K +DGLF + +VAKEYP+I+ D +D M +++ P+ FDV+V NL+G I S+
Sbjct: 175 KKTDGLFKKTFYEVAKEYPDIKAEDYYVDAMNMYIITRPQTFDVVVTSNLFGDILSDGAA 234
Query: 268 GLIGGAGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHA 327
GL+GG GL N GD Y +FEP + IAGK IANP A + +V ML HLG + A
Sbjct: 235 GLVGGLGLAPSANIGDKYGLFEP-VHGSAPDIAGKGIANPTATILTAVLMLRHLGENEEA 293
Query: 328 SIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNIIKLV 365
++ A+E+ + + TPDLGG +++++ + + K V
Sbjct: 294 DKVEKALEEVLAL-GLTTPDLGGNLSTMEMAEEVAKRV 330
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 221 bits (565), Expect = 2e-69
Identities = 110/339 (32%), Positives = 158/339 (46%), Gaps = 33/339 (9%)
Query: 46 VTMLPGGGIGPELMSYVKEVFRYA----GVPVDFETVQIDPKS-DSNDDL--EYAITSIR 98
+ +LPG GIGPE+ +V + A + +FE + D E + + +
Sbjct: 2 IAVLPGDGIGPEVTEAALKVLKAALEKAPLEFEFEEGLAGGAAIDETGTPLPEETLEACK 61
Query: 99 RNGVAIKGNIET-----------GSLDSLW-TLKLCRLILRVIAMMILSVRC-----RQQ 141
+ + G + L +L L L + V L +
Sbjct: 62 KADAVLLGAVGGPKWNPGGVRPENGLLALRKELGLFANLRPVKVFPSLGDASPLKREVVE 121
Query: 142 GIDIVIVRQNTEGEYAMLEHESVDGV-----VESMKIITAANSYRLSKYAFEYAKKFGRK 196
G+DIVIVR+ T G Y + K+ + R+++ AFE A+K GRK
Sbjct: 122 GVDIVIVRELTGGIYFGIPKGIKGSGNGEEGAVDTKLYSRDEIERIARVAFELARKRGRK 181
Query: 197 KVTTVHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPN 256
KVT+V KAN++K S + EYP++E M++DN MQLV NPKQFDV+V N
Sbjct: 182 KVTSVDKANVLKSSRLWRKIVEEVAKAEYPDVELEHMLVDNAAMQLVKNPKQFDVIVTEN 241
Query: 257 LYGAITSNVICGLIGGAGLISGKNYG-DHYAVFEPGTRNTGTAIAGKNIANPIAMLNASV 315
L+G I S+ L G GL+ + G D + +FEP + IAGK ANPIA + ++
Sbjct: 242 LFGDILSDEASMLTGSLGLLPSASLGADGFGLFEP-VHGSAPDIAGKGKANPIATILSAA 300
Query: 316 DMLEH-LGHMKHASIIKLAIEKTINEDKIHTPDLGGTAT 353
ML H LG A I+ A+ K + E I T DLGG AT
Sbjct: 301 MMLRHSLGLEDEADKIEAAVLKVL-EAGIRTGDLGGNAT 338
>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 = 221 bits (565), Expect = 5e-68
Identities = 127/322 (39%), Positives = 178/322 (55%), Gaps = 17/322 (5%)
Query: 46 VTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKSDSNDDLEYAIT-----SIRRN 100
+T+ G GIGPE+M V + + A P+D ET++I K I+ SIRR
Sbjct: 3 ITVAYGDGIGPEIMEAVLLILKEAEAPIDIETIEIGEKV-YKKGWPSGISPSSWESIRRT 61
Query: 101 GVAIKGNIET---GSLDSL-----WTLKLCRLILRVIAMMILSVRCRQQGIDIVIVRQNT 152
V +K I T G SL TL L I ++ + + ++IVIVR+N
Sbjct: 62 KVLLKAPITTPQGGGHKSLNVTLRKTLGLYANIRPCVSYHPF-IETKSPNLNIVIVRENE 120
Query: 153 EGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDG 212
E Y +E+ E K+IT + S ++ +YAFEYA+K RKKVT + K NIMK++DG
Sbjct: 121 EDLYTGIEYRQTPDTYECTKLITRSGSEKICRYAFEYARKHNRKKVTCLTKDNIMKMTDG 180
Query: 213 LFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGG 272
+F +I K+A EYP+IE I+D +L +NP+ FDV+V PNLYG I S+V + G
Sbjct: 181 IFHKIFDKIAAEYPDIESEHYIVDIGMARLATNPENFDVIVTPNLYGDILSDVAAEISGS 240
Query: 273 AGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKL 332
GL N G+ YA+FE + IAG+NIANP +LNA++ ML H+G A +I
Sbjct: 241 VGLAGSANIGEEYAMFE-AVHGSAPDIAGQNIANPSGLLNAAIQMLVHIGQSDIAQLIYN 299
Query: 333 AIEKTINEDKIHTPDLGGTATS 354
A KT+ ED +HT D+ TS
Sbjct: 300 AWLKTL-EDGVHTADIYNEKTS 320
>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 = 216 bits (551), Expect = 1e-67
Identities = 116/336 (34%), Positives = 174/336 (51%), Gaps = 33/336 (9%)
Query: 46 VTMLPGGGIGPELMSYVKEV-------FRYAGVPVDFETVQIDPKSDSNDDLEYAITSIR 98
V ++PG GIGPE++ + + E ++ + D LE IR
Sbjct: 1 VAVIPGDGIGPEVIEAAIRILNKLGLEIEFIEFEAGDEALKKYGSALPEDTLE----EIR 56
Query: 99 RNGVAIKGNIETGSLDSLWTLKLCRLILRVIAMMILSVRCRQ------------QGIDIV 146
+ + G + T + ++ I+ + + L R G DIV
Sbjct: 57 KADAILFGAVTTPANPGYKSV-----IVTLRKELDLYANVRPAKSLPGIPDLYPNGKDIV 111
Query: 147 IVRQNTEGEYAMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANI 206
IVR+NTEG YA E D ++++IT S R++++AF AK+ RK VT VHKAN+
Sbjct: 112 IVRENTEGLYAGFEFGFSDRA-IAIRVITREGSERIARFAFNLAKERNRK-VTCVHKANV 169
Query: 207 MKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVI 266
+K +DGLF E+ R++AK Y +E+ DM +D+ M LV +P +FDV+V N++G I S++
Sbjct: 170 LKGTDGLFREVCREIAKRYG-VEYRDMYVDSAAMNLVKDPWRFDVIVTTNMFGDILSDLA 228
Query: 267 CGLIGGAGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKH 326
L G GL N GD A+FEP + IAGK IANP A + + ML++LG ++
Sbjct: 229 SALAGSLGLAPSANIGDRKALFEP-VHGSAPDIAGKGIANPTAAILSVAMMLDYLGELEK 287
Query: 327 ASIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNII 362
++ A+E I E K TPDLGGTA + +V I
Sbjct: 288 GKLVWEAVEYYIIEGKK-TPDLGGTAKTKEVGDEIA 322
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 158 bits (403), Expect = 3e-45
Identities = 90/226 (39%), Positives = 131/226 (57%), Gaps = 20/226 (8%)
Query: 141 QGIDIVIVRQNTEGEY-----AMLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGR 195
G+DI+IVR+ T G Y + ++M + T R+++ AFE A+K R
Sbjct: 126 AGLDILIVRELTGGIYFGEPRGREGLGGEERAFDTM-VYTREEIERIARVAFELARK-RR 183
Query: 196 KKVTTVHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMP 255
KKVT+V KAN+++ S L+ E+ +VAKEYP++E + M +DN MQLV NPKQFDV+V
Sbjct: 184 KKVTSVDKANVLE-SSRLWREVVTEVAKEYPDVELSHMYVDNAAMQLVRNPKQFDVIVTE 242
Query: 256 NLYGAITSNVICGLIGGAGLISGKNYGDH-YAVFEPGTRNTGTA--IAGKNIANPIAM-L 311
NL+G I S+ L G G++ + G+ ++EP G+A IAGK IANPIA L
Sbjct: 243 NLFGDILSDEAAMLTGSLGMLPSASLGESGPGLYEPI---HGSAPDIAGKGIANPIATIL 299
Query: 312 NASVDMLEH-LGHMKHASIIKLAIEKTINEDKIHTPDL--GGTATS 354
+A++ ML + LG + A I+ A+EK + T D+ GG S
Sbjct: 300 SAAM-MLRYSLGLEEAADAIEAAVEKVL-AQGYRTADIAEGGGKVS 343
Score = 29.3 bits (67), Expect = 3.3
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 46 VTMLPGGGIGPELMSYVKEV 65
+ +LPG GIGPE+M+ +V
Sbjct: 5 IAVLPGDGIGPEVMAEAVKV 24
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 147 bits (374), Expect = 1e-40
Identities = 99/313 (31%), Positives = 140/313 (44%), Gaps = 65/313 (20%)
Query: 93 AITSIRRNGVAIKGNIET---GSLDSL-WTLKLCRLILRVIAMMILSVRC---------R 139
+ +I++ GVAIKG + T SL TL R IL + VR R
Sbjct: 78 TLEAIKKYGVAIKGPLTTPVGKGWRSLNVTL---RQILDLYVF-RRPVRYFPGVPSPVKR 133
Query: 140 QQGIDIVIVRQNTEGEYAMLE--------------------HESVD-----GVVESMKII 174
+ +D+VI R+NTE YA +E + + G+ +K I
Sbjct: 134 PEKVDMVIFRENTEDIYAGIEWKAGSPEALKLIFFLEDEMGVKKIRFPEDSGIG--IKPI 191
Query: 175 TAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYPEIEH---- 230
+ S RL + A EYA + RK VT VHK NIMK ++G F + +VA+E +
Sbjct: 192 SKEGSIRLVRAAIEYAIENKRKSVTLVHKGNIMKFTEGAFKDWGYEVAEEEEFGDEVVTG 251
Query: 231 ---------------NDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGAGL 275
D I D+ Q++ P ++DV+ NL G S+ + +GG GL
Sbjct: 252 KEKFELKGPKGKIVYKDRIADDMLQQILLRPGEYDVIATKNLNGDYISDALAAQVGGLGL 311
Query: 276 ISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIE 335
G N GD A FE T T AGK+ NPIA + + ML H G ++ A +I+ A+E
Sbjct: 312 APGANIGDGTAEFEA-THGTAPKYAGKDSTNPIASILSGTMMLRHRGWLEAADLIEKAVE 370
Query: 336 KTINEDKIHTPDL 348
TI E T DL
Sbjct: 371 DTI-ESGKVTYDL 382
>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 = 145 bits (367), Expect = 3e-40
Identities = 90/269 (33%), Positives = 136/269 (50%), Gaps = 21/269 (7%)
Query: 115 SLW--TLKLCRLILRVIAM---MILS------VRCRQQGIDIVIVRQNTEGEYAMLE--- 160
SLW LK+ R + + +L C D V+VR+N+EGEY+ +
Sbjct: 87 SLWGLLLKIRREFDQYANVRPAKLLPGVTSPLRNCGPGDFDFVVVRENSEGEYSGVGGRI 146
Query: 161 HESVDG-VVESMKIITAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDGLFLEISR 219
H D V I T R+ ++AFE A+K RK +T+ K+N ++ S + E+
Sbjct: 147 HRGTDEEVATQNAIFTRKGVERIMRFAFELAQK-RRKHLTSATKSNGIRHSMPFWDEVFA 205
Query: 220 KVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGAGLISGK 279
+VA EYP++E + ID + V P+ FDV+V NL+G I S++ L+G G+
Sbjct: 206 EVAAEYPDVEWDSYHIDALAARFVLKPETFDVIVASNLFGDILSDLGAALMGSLGVAPSA 265
Query: 280 NY---GDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIEK 336
N G ++FEP + IAGK IANPI + + MLEHLG + + I AIE+
Sbjct: 266 NINPEGKFPSMFEP-VHGSAPDIAGKGIANPIGAIWTAAMMLEHLGEKEAGAKIMDAIER 324
Query: 337 TINEDKIHTPDLGGTATSIDVVQNIIKLV 365
I TPD+GG AT+ +V + + +
Sbjct: 325 VTA-AGILTPDVGGKATTSEVTEAVCNAL 352
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 141 bits (358), Expect = 6e-39
Identities = 83/230 (36%), Positives = 126/230 (54%), Gaps = 9/230 (3%)
Query: 144 DIVIVRQNTEGEYAMLE---HESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKVTT 200
D+++VR+N+EGEY+ + H D + + T + R +YAFE A K RK VT+
Sbjct: 125 DLLVVRENSEGEYSEVGGRIHRGEDEIAIQNAVFTRKGTERAMRYAFELAAK-RRKHVTS 183
Query: 201 VHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGA 260
K+N + S + E+ ++V K+YPEIE + ID V+ P++FDV+V NL+G
Sbjct: 184 ATKSNGIVHSMPFWDEVFQEVGKDYPEIETDSQHIDALAAFFVTRPEEFDVIVASNLFGD 243
Query: 261 ITSNV---ICGLIGGAGLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDM 317
I +++ I G IG A + G + ++FEP + IAGK IANPI + + M
Sbjct: 244 ILTDIGAAIMGSIGIAPAANINVNGKYPSMFEP-VHGSAPDIAGKGIANPIGQIWTAKLM 302
Query: 318 LEHLGHMKHASIIKLAIEKTINEDKIHTPDLGGTATSIDVVQNIIKLVQT 367
L+H G + S + IE ED I TPD+GG AT+ +V II ++
Sbjct: 303 LDHFGEEELGSHLLDVIEDVT-EDGIKTPDIGGRATTDEVTDEIISRLKK 351
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 139 bits (352), Expect = 5e-38
Identities = 70/208 (33%), Positives = 114/208 (54%), Gaps = 12/208 (5%)
Query: 143 IDIVIVRQNTEGEYA----MLEHESVDGVVESMKIITAANSYRLSKYAFEYAKKFGRKKV 198
ID V+VR+ TEG Y L + V + + TA R+ + AFE A+K RK +
Sbjct: 122 IDFVVVREGTEGPYTGNGGALRVGTPHEVATEVSVNTAFGVERVVRDAFERAQKRPRKHL 181
Query: 199 TTVHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLY 258
T VHK N++ + L+ +VA EYP++ + +D + +V++P +FDV+V NL+
Sbjct: 182 TLVHKTNVLTFAGDLWQRTVDEVAAEYPDVTVDYQHVDAATIFMVTDPSRFDVIVTDNLF 241
Query: 259 GAITSNVICGLIGGAGLISGKNY---GDHYAVFEPGTRNTGTA--IAGKNIANPIAMLNA 313
G I +++ + GG GL + N G + ++FEP G+A IAG+ IA+P A + +
Sbjct: 242 GDIITDLAAAVTGGIGLAASGNINPTGTNPSMFEP---VHGSAPDIAGQGIADPTAAILS 298
Query: 314 SVDMLEHLGHMKHASIIKLAIEKTINED 341
+L+HLG A+ I+ A+E + E
Sbjct: 299 VALLLDHLGEEDAAARIEAAVEADLAER 326
>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 = 129 bits (326), Expect = 2e-34
Identities = 105/353 (29%), Positives = 167/353 (47%), Gaps = 65/353 (18%)
Query: 46 VTMLPGGGIGPELMSYVKEV-------------FRYA----------GVPVDFETVQIDP 82
+ +LPG GIGPE+M+ +V F G P+ ET++
Sbjct: 2 IAVLPGDGIGPEVMAQALKVLKAVAERFGLKFEFEEHLIGGAAIDATGQPLPEETLKGCK 61
Query: 83 KSD----------------SNDDLEYAITSIRRNGVAIKGNIETGSL-DSLWTLKLCRLI 125
++D + E + +R+ + + N+ + L L L
Sbjct: 62 EADAVLLGAVGGPKWDNLPRDQRPEQGLLKLRK-SLDLFANLRPAKVFPGL--EDLSPLK 118
Query: 126 LRVIAMMILSVRCRQQGIDIVIVRQNTEGEY-AMLEHESVDGVVESMKIITAANSYRLSK 184
+ +G+D V+VR+ T G Y + +G ++ T R+++
Sbjct: 119 PEIA-----------KGVDFVVVRELTGGIYFGEPKGREGEGEAWDTEVYTVPEIERIAR 167
Query: 185 YAFEYAKKFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVS 244
AFE A+K RKKVT+V KAN+++ S L+ + ++AKEYP++E IDN MQLV
Sbjct: 168 VAFEMARK-RRKKVTSVDKANVLESSR-LWRKTVEEIAKEYPDVELEHQYIDNAAMQLVK 225
Query: 245 NPKQFDVMVMPNLYGAITSNVICGLIGGAGLI-SGKNYGDHYAVFEPGTRNTGTA--IAG 301
+P QFDV+V NL+G I S+ + G G++ S D + +FEP G+A IAG
Sbjct: 226 SPTQFDVVVTSNLFGDILSDEASVITGSLGMLPSASLGSDGFGLFEP---VHGSAPDIAG 282
Query: 302 KNIANPIAMLNASVDMLEH-LGHMKHASIIKLAIEKTINEDKIHTPDLGGTAT 353
K IANPIA + ++ +L + + A I+ A++K + E TPDLG +AT
Sbjct: 283 KGIANPIAQILSAAMLLRYSFNLEEAADAIEAAVKKVLAEGY-RTPDLGSSAT 334
>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 = 122 bits (308), Expect = 2e-31
Identities = 90/310 (29%), Positives = 138/310 (44%), Gaps = 69/310 (22%)
Query: 94 ITSIRRNGVAIKGNIET---GSLDSLWTLKLCRLILRVIAMMILSVR-CR---------- 139
+ +I+ VAIKG + T G + SL + LR + + +R R
Sbjct: 89 LDAIKEYRVAIKGPLTTPVGGGIRSL------NVALRQELDLYVCLRPVRYYKGVPSPVK 142
Query: 140 -QQGIDIVIVRQNTEGEYAMLEHESVDGVVESMKIITAAN-------------------- 178
+ +D+VI R+NTE YA +E +G E+ K+I
Sbjct: 143 HPEKVDMVIFRENTEDIYAGIEWA--EGSEEAKKLIRFLQNELGVKKIRFPEDSGIGIKP 200
Query: 179 -----SYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDGLFLEISRKVA-KEY------- 225
+ RL + A EYA + RK VT VHK NIMK ++G F + ++A KE+
Sbjct: 201 ISEEGTKRLVRAAIEYAIENDRKSVTLVHKGNIMKFTEGAFRDWGYELAKKEFGAECITW 260
Query: 226 ------------PEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGA 273
EI D I D Q+++ P ++DV+ NL G S+ + +GG
Sbjct: 261 GLWDKYKNPNPGKEIVIKDRIADAFLQQILTRPDEYDVIATMNLNGDYISDALAAQVGGI 320
Query: 274 GLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLA 333
G+ G N GD +FE T T AG++ NP +++ + MLEH+G + A +IK A
Sbjct: 321 GIAPGANIGDEIGIFEA-THGTAPKYAGQDKVNPGSIILSGEMMLEHMGWKEAADLIKKA 379
Query: 334 IEKTINEDKI 343
+EK I +
Sbjct: 380 MEKAIASKIV 389
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 112 bits (282), Expect = 8e-28
Identities = 75/247 (30%), Positives = 120/247 (48%), Gaps = 43/247 (17%)
Query: 143 IDIVIVRQNTEGEYAMLEH--------------------ESVDGVVESMKIITAANSYRL 182
ID++I R+NT+ Y +E+ E D +K+I+ + R+
Sbjct: 142 IDLIIFRENTDDLYRGIEYPYDSEEAKKIRDFLRKELGVEVEDDTGIGIKLISKFKTQRI 201
Query: 183 SKYAFEYAKKFGRKKVTTVHKANIMKISDGLFLEISRKVA-KEYPE-------------- 227
++ A +YA RKKVT +HK N+MK ++G F E + +VA KE+ +
Sbjct: 202 ARMAIKYAIDHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEFRDYVVTEEEVTKNYNG 261
Query: 228 ------IEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGAGLISGKNY 281
+ ND I DN Q++ P ++D+++ PN+ G S+ L+G G++ G N
Sbjct: 262 VPPSGKVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISDAAGALVGNIGMLGGANI 321
Query: 282 GDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIEKTINED 341
GD +FE T AGKN+ANP ++ ML +G K A +I AI ++I +
Sbjct: 322 GDTGGMFE-AIHGTAPKYAGKNVANPTGIIKGGELMLRFMGWDKAADLIDKAIMESIKQK 380
Query: 342 KIHTPDL 348
K+ T DL
Sbjct: 381 KV-TQDL 386
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 110 bits (275), Expect = 6e-27
Identities = 99/334 (29%), Positives = 167/334 (50%), Gaps = 42/334 (12%)
Query: 43 RNAVTMLPGGGIGPELMSYVKEVFRYAG----VPVDFETVQIDPKSDSNDDL------EY 92
R + +LPG GIGPE++S K V + AG + DF+ + P + DL E
Sbjct: 46 RYNIALLPGDGIGPEVISVAKNVLQKAGSLEGLEFDFQEM---PVGGAALDLVGVPLPEE 102
Query: 93 AITSIRRNGVAIKGNI-------ETGSLDSLWTLKLCRLILRVIAMMILSVRCRQ----- 140
T+ +++ + G I L L R L+V A + + Q
Sbjct: 103 TFTAAKQSDAILLGAIGGYKWDKNEKHLRPEMALFYLRRDLKVFANLRPATVLPQLVDAS 162
Query: 141 -------QGIDIVIVRQNTEGEY-----AMLEHESVDGVVESMKIITAANSYRLSKYAFE 188
+G+D++IVR+ T G Y + +E+ + V S +I A R+++ AFE
Sbjct: 163 TLKKEVAEGVDMMIVRELTGGIYFGEPRGITINENGEEVGVSTEIYAAHEIDRIARVAFE 222
Query: 189 YAKKFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYPEIEHNDMIIDNTCMQLVSNPKQ 248
A+K R K+ +V KAN++ S L+ + +A EYP++E + M +DN MQL+ +PKQ
Sbjct: 223 TARK-RRGKLCSVDKANVLDASI-LWRKRVTALASEYPDVELSHMYVDNAAMQLIRDPKQ 280
Query: 249 FDVMVMPNLYGAITSNVICGLIGGAGLISGKNYGDH-YAVFEPGTRNTGTAIAGKNIANP 307
FD +V N++G I S+ + G G++ + G+ +FEP + IAG++ ANP
Sbjct: 281 FDTIVTNNIFGDILSDEASMITGSIGMLPSASLGESGPGLFEP-IHGSAPDIAGQDKANP 339
Query: 308 IAMLNASVDMLEH-LGHMKHASIIKLAIEKTINE 340
+A + ++ +L++ LG K A I+ A+ +N+
Sbjct: 340 LATILSAAMLLKYGLGEEKAAKRIEDAVVDALNK 373
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 105 bits (264), Expect = 3e-25
Identities = 72/250 (28%), Positives = 113/250 (45%), Gaps = 48/250 (19%)
Query: 139 RQQGIDIVIVRQNTEGEYAMLEHESVDGVVESMKII------------------------ 174
R + D+VI R+N+E YA +E ++ G E+ K+I
Sbjct: 136 RPEDTDMVIFRENSEDIYAGIEWKA--GSAEAKKVIKFLQEEMGVKKIRFPETSGIGIKP 193
Query: 175 -TAANSYRLSKYAFEYAKKFGRKKVTTVHKANIMKISDGLF----LEISR---------- 219
+ + RL + A EYA RK VT VHK NIMK ++G F +++
Sbjct: 194 VSEEGTERLVRAAIEYAIDNDRKSVTLVHKGNIMKFTEGAFKDWGYQLAEEEFGDELIDG 253
Query: 220 ------KVAKEYPEIEHNDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGA 273
K + EI D I D Q++ P ++DV+ NL G S+ + +GG
Sbjct: 254 GPWDKIKNPETGKEIIVKDSIADAFLQQILLRPAEYDVIATMNLNGDYISDALAAQVGGI 313
Query: 274 GLISGKNYGDHYAVFEPGTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLA 333
G+ G N D +A+FE T T AG + NP +++ ++ ML H+G + A +I +
Sbjct: 314 GIAPGANINDGHAIFE-ATHGTAPKYAGLDKVNPGSVILSAEMMLRHMGWTEAADLIIKS 372
Query: 334 IEKTINEDKI 343
+EKTI +
Sbjct: 373 MEKTIASKTV 382
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 64.0 bits (156), Expect = 4e-11
Identities = 37/118 (31%), Positives = 63/118 (53%), Gaps = 2/118 (1%)
Query: 231 NDMIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGAGLISGKNYGDHYAVFEP 290
+D I D+ Q+ + P+++ ++ NL G S+ ++GG G+ G N GD+ A+FE
Sbjct: 335 DDRIADSIFQQIQTRPQEYSILATLNLNGDYISDAAAAIVGGLGMAPGANIGDNAAIFE- 393
Query: 291 GTRNTGTAIAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIEKTINEDKIHTPDL 348
T T AG + NP +++ + V MLE+LG + A +I + I ++ T DL
Sbjct: 394 ATHGTAPKHAGLDRINPGSVILSGVMMLEYLGWQEAADLITKGLSAAIANKQV-TYDL 450
Score = 55.1 bits (133), Expect = 3e-08
Identities = 46/166 (27%), Positives = 70/166 (42%), Gaps = 51/166 (30%)
Query: 94 ITSIRRNGVAIKGNIET---GSLDSLWTLKLCRLILRVIAMMILSVR-CR---------- 139
+ +IR GVAIKG + T G + SL + LR I + VR CR
Sbjct: 91 LEAIREYGVAIKGPLTTPIGGGIRSL------NVALRQIFDLYSCVRPCRYYAGTPSPHK 144
Query: 140 -QQGIDIVIVRQNTEGEYAMLEHESVDGVVESM--------------------------- 171
+ +D+++ R+NTE Y +E E+ D + + +
Sbjct: 145 NPEKLDVIVYRENTEDIYMGIEWEAGDEIGDKLIKHLNEEVIPASPELGKRQIPLGSGIG 204
Query: 172 -KIITAANSYRLSKYAFEYAKKFGRKK--VTTVHKANIMKISDGLF 214
K ++ S R + A E+A + K VT VHK NIMK ++G F
Sbjct: 205 IKPVSKTGSQRHIRRAIEHALRLPGDKRHVTLVHKGNIMKYTEGAF 250
>gnl|CDD|181402 PRK08363, PRK08363, alanine aminotransferase; Validated.
Length = 398
Score = 32.1 bits (73), Expect = 0.54
Identities = 22/66 (33%), Positives = 30/66 (45%)
Query: 55 GPELMSYVKEVFRYAGVPVDFETVQIDPKSDSNDDLEYAITSIRRNGVAIKGNIETGSLD 114
GP Y V Y GVPV++ T++ + DD+ IT + I N TG+L
Sbjct: 124 GPSYPPYTGLVKFYGGVPVEYRTIEEEGWQPDIDDIRKKITEKTKAIAVINPNNPTGALY 183
Query: 115 SLWTLK 120
TLK
Sbjct: 184 EKKTLK 189
>gnl|CDD|224906 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 332
Score = 31.5 bits (72), Expect = 0.70
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 296 GTA--IAGKNIANPIAMLNA 313
GTA IAGK IA+P +++ A
Sbjct: 299 GTAFDIAGKGIADPGSLIAA 318
>gnl|CDD|224844 COG1933, COG1933, Archaeal DNA polymerase II, large subunit [DNA
replication, recombination, and repair].
Length = 253
Score = 30.9 bits (70), Expect = 0.93
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 192 KFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYP 226
G K V TV K I K +L ++ + EY
Sbjct: 188 ICGGKIVLTVSKGAIEK-----YLGTAKMLVTEYK 217
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 31.4 bits (72), Expect = 0.95
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 5/35 (14%)
Query: 192 KFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYP 226
K G + TVHK ++ K +LE+S+K+A+EY
Sbjct: 1058 KCGGNLILTVHKGSVEK-----YLEVSKKLAEEYG 1087
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150 residue
intein. The other subunit, DP1, has sequence similarity
to the eukaryotic DNA polymerase delta small subunit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 1095
Score = 31.4 bits (71), Expect = 1.1
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 192 KFGRKKVTTVHKANIMKISDGLFLEISRKVAKEYP 226
K G TV K ++MK +LE+S+ +A+ Y
Sbjct: 1033 KCGNNLTLTVSKGSVMK-----YLELSKFLAENYN 1062
>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 = 29.8 bits (68), Expect = 2.2
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 296 GTA--IAGKNIANPIAMLNA 313
GTA IAGK A+P +++ A
Sbjct: 293 GTAFDIAGKGKADPGSLIAA 312
>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 = 29.6 bits (67), Expect = 2.6
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 296 GTA--IAGKNIANPIAMLNA 313
GTA IAGK A+P +++ A
Sbjct: 275 GTAFDIAGKGKADPGSLIAA 294
>gnl|CDD|234696 PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Reviewed.
Length = 332
Score = 29.4 bits (67), Expect = 3.5
Identities = 9/20 (45%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 296 GTA--IAGKNIANPIAMLNA 313
GTA +AGK IA+ + + A
Sbjct: 300 GTALDLAGKGIADVGSFITA 319
>gnl|CDD|223484 COG0407, HemE, Uroporphyrinogen-III decarboxylase [Coenzyme
metabolism].
Length = 352
Score = 29.1 bits (66), Expect = 4.1
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 14/84 (16%)
Query: 26 FVMPKLKEVYTKAKYGGRNAVTMLPGGGIGPELMSYVKEVFRYAGVPVDFETVQIDPKSD 85
FV+P +K + + K + G G L K F GV V
Sbjct: 224 FVLPYMKRIVREVKEVKGGVPVIHFCKGAGHLLEDMAKTGFDVLGVD---WRV------- 273
Query: 86 SNDDLEYAITSIRRNGVAIKGNIE 109
DL+ A + VA++GN++
Sbjct: 274 ---DLKEA-KKRLGDKVALQGNLD 293
>gnl|CDD|151314 pfam10865, DUF2703, Domain of unknown function (DUF2703). This
family of protein has no known function, but it may be
distantly related to the thioredoxin fold. It contains
the CXXC motif that is characteristic of thioredoxins.
Length = 120
Score = 27.7 bits (62), Expect = 4.2
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 52 GGIGPELMSYV---KEVFRYAGVPVDFETVQIDPKSDSNDDLEYAITSIRRNGVAI 104
GG G L + V +E G+ V E ++DP+ + LE I NG +
Sbjct: 19 GGTGEALEAAVNELREALEPLGIEVVLEETELDPEEFARAPLES--NRIWINGRPL 72
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of Di19
is unknown.
Length = 209
Score = 28.1 bits (63), Expect = 5.4
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 302 KNIANPIAMLNASVDMLEHLGHMKHASIIKL 332
KN P+ DM+ H+ ++H + K+
Sbjct: 61 KNGVCPVCADRVGKDMVAHI-TVQHGHLFKM 90
>gnl|CDD|235066 PRK02746, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 345
Score = 28.7 bits (65), Expect = 5.4
Identities = 17/42 (40%), Positives = 18/42 (42%), Gaps = 18/42 (42%)
Query: 296 GTA--IAGKNIANPIAMLNASVDMLEHLGHMKHASIIKLAIE 335
GTA IAGK IA P +M A IKLA E
Sbjct: 313 GTAFDIAGKGIARPQSMKAA----------------IKLAWE 338
>gnl|CDD|99779 cd06182, CYPOR_like, NADPH cytochrome p450 reductase (CYPOR) serves
as an electron donor in several oxygenase systems and is
a component of nitric oxide synthases and methionine
synthase reductases. CYPOR transfers two electrons from
NADPH to the heme of cytochrome p450 via FAD and FMN.
CYPOR has a C-terminal ferredoxin reducatase (FNR)- like
FAD and NAD binding module, an FMN-binding domain, and
an additional conecting domain (inserted within the FAD
binding region) that orients the FNR and FMN binding
domains. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria and participate in a wide
variety of redox metabolic pathways. The C-terminal
domain contains most of the NADP(H) binding residues and
the N-terminal domain interacts non-covalently with the
isoalloxazine rings of the flavin molecule which lies
largely in a large gap betweed the two domains.
Ferredoxin-NADP+ reductase first accepts one electron
from reduced ferredoxin to form a flavin semiquinone
intermediate. The enzyme then accepts a second electron
to form FADH2, which then transfers two electrons and a
proton to NADP+ to form NADPH.
Length = 267
Score = 28.5 bits (64), Expect = 5.8
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 15/75 (20%)
Query: 5 MCSNFLAASKVYDKQSVR---TMAFVMPKLKEVYTKAKYGGRNAVTML-PGGGIGPELMS 60
+CSNFLA ++ K +V +F +PK + M+ PG GI P
Sbjct: 84 VCSNFLAGLQLGAKVTVFIRPAPSFRLPKDPTT----------PIIMVGPGTGIAP-FRG 132
Query: 61 YVKEVFRYAGVPVDF 75
+++E
Sbjct: 133 FLQERAALRANGKAR 147
>gnl|CDD|149775 pfam08822, DUF1804, Protein of unknown function (DUF1804). This
family of bacterial protein is uncharacterized.
Length = 165
Score = 27.7 bits (62), Expect = 7.8
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 312 NASVDMLEHLGHMKHASIIKL------AIEKTINEDKIHTPDLGGTATSIDVVQNIIKLV 365
A++D L+ + + KL + KT+ K P+ AT+++V+Q + V
Sbjct: 80 QATMDELQEDEDLPPSDKAKLLASLADSFSKTVAASKRVLPETSKLATALEVLQRLADFV 139
Query: 366 QTNDLRH 372
Q +H
Sbjct: 140 QERYPQH 146
>gnl|CDD|217862 pfam04051, TRAPP, Transport protein particle (TRAPP) component.
TRAPP plays a key role in the targeting and/or fusion of
ER-to-Golgi transport vesicles with their acceptor
compartment. TRAPP is a large multimeric protein that
contains at least 10 subunits. This family contains many
TRAPP family proteins. The Bet3 subunit is one of the
better characterized TRAPP proteins and has a dimeric
structure with hydrophobic channels. The channel
entrances are located on a putative membrane-interacting
surface that is distinctively flat, wide and decorated
with positively charged residues. Bet3 is proposed to
localise TRAPP to the Golgi.
Length = 148
Score = 27.1 bits (61), Expect = 8.6
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 233 MIIDNTCMQLVSNPKQFDVMVMPNLYGAITSNVICGLIGGA 273
++IDN QF V + P+ G N +CG+I GA
Sbjct: 83 VLIDNDNP-----LSQF-VELPPDYSGLNYLNFLCGIIRGA 117
>gnl|CDD|235402 PRK05312, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 27.9 bits (63), Expect = 9.7
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 296 GTA--IAGKNIANPIAMLNA 313
GTA IAGK IA P +++ A
Sbjct: 305 GTAFDIAGKGIARPDSLIAA 324
>gnl|CDD|182391 PRK10341, PRK10341, DNA-binding transcriptional activator TdcA;
Provisional.
Length = 312
Score = 27.9 bits (62), Expect = 10.0
Identities = 12/36 (33%), Positives = 25/36 (69%)
Query: 94 ITSIRRNGVAIKGNIETGSLDSLWTLKLCRLILRVI 129
+T+++RNG++I+ ++T S+ +++ L L L VI
Sbjct: 211 LTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVI 246
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
0.319 0.135 0.384
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,886,687
Number of extensions: 1855748
Number of successful extensions: 1839
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1773
Number of HSP's successfully gapped: 59
Length of query: 376
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 278
Effective length of database: 6,590,910
Effective search space: 1832272980
Effective search space used: 1832272980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)