RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12309
(152 letters)
>gnl|CDD|240417 PTZ00435, PTZ00435, isocitrate dehydrogenase; Provisional.
Length = 413
Score = 285 bits (731), Expect = 5e-97
Identities = 99/126 (78%), Positives = 114/126 (90%)
Query: 14 FGKPTYNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLI 73
F + + AL +K PLYLSTKNTILKKYDG FKDIFQE+Y++ YK++FE+A +WYEHRLI
Sbjct: 193 FARSCFQYALDRKMPLYLSTKNTILKKYDGRFKDIFQEIYDEEYKAKFEKAGLWYEHRLI 252
Query: 74 DDMVAQALKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
DDMVAQA+K GGFVWACKNYDGDVQSDIVAQGYGSLGLMTS+L+CPDGKT+E+EAAHGT
Sbjct: 253 DDMVAQAIKSEGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSVLVCPDGKTVEAEAAHGT 312
Query: 134 VTRHYR 139
VTRHYR
Sbjct: 313 VTRHYR 318
>gnl|CDD|236226 PRK08299, PRK08299, isocitrate dehydrogenase; Validated.
Length = 402
Score = 270 bits (694), Expect = 2e-91
Identities = 95/126 (75%), Positives = 108/126 (85%)
Query: 14 FGKPTYNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLI 73
F + ++N L +K+P+YLSTKNTILK YDG FKDIFQEVYE +K +FE A I YEHRLI
Sbjct: 190 FARASFNYGLDRKYPVYLSTKNTILKAYDGRFKDIFQEVYEAEFKEKFEAAGITYEHRLI 249
Query: 74 DDMVAQALKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
DDMVA ALK GG+VWACKNYDGDVQSD VAQG+GSLGLMTS+LM PDGKT+E+EAAHGT
Sbjct: 250 DDMVASALKWEGGYVWACKNYDGDVQSDTVAQGFGSLGLMTSVLMTPDGKTVEAEAAHGT 309
Query: 134 VTRHYR 139
VTRHYR
Sbjct: 310 VTRHYR 315
>gnl|CDD|177720 PLN00103, PLN00103, isocitrate dehydrogenase (NADP+); Provisional.
Length = 410
Score = 257 bits (657), Expect = 6e-86
Identities = 102/132 (77%), Positives = 114/132 (86%)
Query: 8 ESTFWIFGKPTYNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIW 67
+ + F + + N A QKKWPLYLSTKNTILKKYDG FKDIFQEVYE +KS+FE A IW
Sbjct: 188 DESIRAFAEASMNTAYQKKWPLYLSTKNTILKKYDGRFKDIFQEVYEAQWKSKFEAAGIW 247
Query: 68 YEHRLIDDMVAQALKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIES 127
YEHRLIDDMVA ALK GG+VWACKNYDGDVQSD +AQG+GSLGLMTS+L+CPDGKTIE+
Sbjct: 248 YEHRLIDDMVAYALKSEGGYVWACKNYDGDVQSDFLAQGFGSLGLMTSVLVCPDGKTIEA 307
Query: 128 EAAHGTVTRHYR 139
EAAHGTVTRHYR
Sbjct: 308 EAAHGTVTRHYR 319
>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 = 255 bits (652), Expect = 3e-85
Identities = 103/126 (81%), Positives = 113/126 (89%)
Query: 14 FGKPTYNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLI 73
F ++ +AL+KKWPLYLSTKNTILKKYDG FKDIFQEVYE YKS+FE IWYEHRLI
Sbjct: 191 FAHSSFQLALEKKWPLYLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEALGIWYEHRLI 250
Query: 74 DDMVAQALKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
DDMVAQALK GGF+WACKNYDGDVQSDIVAQG+GSLGLMTS+L+CPDGKT E+EAAHGT
Sbjct: 251 DDMVAQALKSEGGFIWACKNYDGDVQSDIVAQGFGSLGLMTSVLICPDGKTFEAEAAHGT 310
Query: 134 VTRHYR 139
VTRHYR
Sbjct: 311 VTRHYR 316
>gnl|CDD|178617 PLN03065, PLN03065, isocitrate dehydrogenase (NADP+); Provisional.
Length = 483
Score = 254 bits (651), Expect = 3e-84
Identities = 95/126 (75%), Positives = 112/126 (88%)
Query: 14 FGKPTYNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLI 73
F + + +ALQKKWPLYLSTKNTILKKYDG FKDIFQEVYE+ +K +FE+ IWYEHRLI
Sbjct: 261 FAESSMAMALQKKWPLYLSTKNTILKKYDGRFKDIFQEVYEEQWKQKFEEHSIWYEHRLI 320
Query: 74 DDMVAQALKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
DDMVA A+K GG+VWACKNYDGDVQSD++AQG+GSLGLMTS+L+ DGKT+E+EAAHGT
Sbjct: 321 DDMVAYAVKSEGGYVWACKNYDGDVQSDLLAQGFGSLGLMTSVLLSSDGKTLEAEAAHGT 380
Query: 134 VTRHYR 139
VTRH+R
Sbjct: 381 VTRHFR 386
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 172 bits (438), Expect = 4e-53
Identities = 47/136 (34%), Positives = 63/136 (46%), Gaps = 18/136 (13%)
Query: 25 KKWPLYLSTKNTILKKYDGHFKDIFQEVYEKN--------YKSQFEQA----KIWYEHRL 72
K+ + L K I+K +G FKD EV E+ K +FE KI Y+ R+
Sbjct: 211 KRKSVTLVHKGNIMKFTEGAFKDWGYEVAEEEEFGDEVVTGKEKFELKGPKGKIVYKDRI 270
Query: 73 IDDMVAQALKGNGGF-VWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAH 131
DDM+ Q L G + V A KN +GD SD +A G LGL + T E EA H
Sbjct: 271 ADDMLQQILLRPGEYDVIATKNLNGDYISDALAAQVGGLGLAPGANI--GDGTAEFEATH 328
Query: 132 GTVTRHYRFLGINDIN 147
GT ++ G + N
Sbjct: 329 GTAPKYA---GKDSTN 341
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 120 bits (304), Expect = 9e-34
Identities = 32/118 (27%), Positives = 51/118 (43%), Gaps = 10/118 (8%)
Query: 22 ALQK-KWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQA 80
A ++ + + K +LK ++ I +EV + Y + EH L+D+ Q
Sbjct: 175 ARKRGRKKVTSVDKANVLKSSRL-WRKIVEEVAKAEYP------DVELEHMLVDNAAMQL 227
Query: 81 LKGNGGF-VWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGTVTRH 137
+K F V +N GD+ SD + GSLGL+ S + DG E HG+
Sbjct: 228 VKNPKQFDVIVTENLFGDILSDEASMLTGSLGLLPSASLGADG-FGLFEPVHGSAPDI 284
>gnl|CDD|177715 PLN00096, PLN00096, isocitrate dehydrogenase (NADP+); Provisional.
Length = 393
Score = 59.3 bits (143), Expect = 5e-11
Identities = 43/115 (37%), Positives = 64/115 (55%), Gaps = 10/115 (8%)
Query: 30 YLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYE-----HRLIDDMVAQALK-G 83
Y+ TK T+ K + F +I ++V+++ +KS+F + H L D + +
Sbjct: 197 YVVTKKTVFK-WQEPFWEIMKKVFDEEFKSKFVDKGVMKSGDELVHLLSDAATMKLVVWT 255
Query: 84 NGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPD--GKTI-ESEAAHGTVT 135
+GGF A NYDGDV +D +AQ + S G +TS L+ D G I E EA+HGTVT
Sbjct: 256 DGGFGMAAHNYDGDVLTDELAQVHKSPGFITSNLVGVDENGTLIKEFEASHGTVT 310
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 45.6 bits (108), Expect = 2e-06
Identities = 35/101 (34%), Positives = 48/101 (47%), Gaps = 9/101 (8%)
Query: 34 KNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWACK 92
K I+KK DG F +EV EK +I YE +ID+ +K F V
Sbjct: 210 KANIMKKTDGLFLKCCREVAEKY-------PEIVYEEVIIDNCCMMLVKNPALFDVLVMP 262
Query: 93 NYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
N GD+ SD+ A G LGL S + +G + +EA HG+
Sbjct: 263 NLYGDIISDLCAGLIGGLGLTPSCNIGENGLAL-AEAVHGS 302
>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 = 44.4 bits (105), Expect = 6e-06
Identities = 32/102 (31%), Positives = 47/102 (46%), Gaps = 10/102 (9%)
Query: 33 TKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWAC 91
TK+ I+K DG F IF ++ E I EH ++D +A+ F V
Sbjct: 170 TKDNIMKMTDGIFHKIFDKIAA-------EYPDIESEHYIVDIGMARLATNPENFDVIVT 222
Query: 92 KNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
N GD+ SD+ A+ GS+GL S + + EA HG+
Sbjct: 223 PNLYGDILSDVAAEISGSVGLAGSANIGEEYAMF--EAVHGS 262
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 44.1 bits (105), Expect = 7e-06
Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 8/101 (7%)
Query: 33 TKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWAC 91
K +LK DG ++++ +EV + E + +H +D Q ++ F V
Sbjct: 181 HKANVLKLSDGLWREVVEEVAK-------EYPDVELDHMYVDAAAMQLVRNPEQFDVIVT 233
Query: 92 KNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHG 132
N GD+ SD A GSLGL S + + E HG
Sbjct: 234 SNLFGDILSDEAAALTGSLGLAPSANLGDERGPALFEPVHG 274
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 42.6 bits (101), Expect = 2e-05
Identities = 29/81 (35%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 33 TKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWAC 91
TK+ I+K DG F +F E+ K Y E EH ++D A+ F V
Sbjct: 174 TKDNIMKLTDGLFHKVFDEI-AKEY-PDIEA-----EHYIVDIGAARLATNPENFDVIVT 226
Query: 92 KNYDGDVQSDIVAQGYGSLGL 112
N GD+ SDI A+ GS+GL
Sbjct: 227 PNLYGDILSDIAAEISGSVGL 247
>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 = 41.7 bits (98), Expect = 5e-05
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 9/98 (9%)
Query: 19 YNVALQKKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVA 78
+N+A ++ + K +LK DG F+++ +E+ K Y ++ +D
Sbjct: 151 FNLAKERNRKVTCVHKANVLKGTDGLFREVCREI-AKRYGVEYRDM-------YVDSAAM 202
Query: 79 QALKGNGGF-VWACKNYDGDVQSDIVAQGYGSLGLMTS 115
+K F V N GD+ SD+ + GSLGL S
Sbjct: 203 NLVKDPWRFDVIVTTNMFGDILSDLASALAGSLGLAPS 240
>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 = 37.0 bits (86), Expect = 0.002
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 69 EHRLIDDMVAQALKGNGGF-VWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIES 127
EH+ ID+ Q +K F V N GD+ SD + GSLG++ S + DG +
Sbjct: 212 EHQYIDNAAMQLVKSPTQFDVVVTSNLFGDILSDEASVITGSLGMLPSASLGSDGFGLF- 270
Query: 128 EAAHGT 133
E HG+
Sbjct: 271 EPVHGS 276
>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 = 34.7 bits (80), Expect = 0.011
Identities = 26/101 (25%), Positives = 41/101 (40%), Gaps = 9/101 (8%)
Query: 34 KNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWACK 92
K I+K DG F ++ +EV K Y I +E ++D+ Q + F V
Sbjct: 171 KANIMKLADGLFLNVCREV-AKEYP------DITFESMIVDNTCMQLVSRPSQFDVMVMP 223
Query: 93 NYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIESEAAHGT 133
N G++ S++ A G GL+ + D E T
Sbjct: 224 NLYGNILSNLGAGLVGGPGLVPGANIGRDYAVFE-PGVRHT 263
>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 = 33.7 bits (77), Expect = 0.024
Identities = 33/133 (24%), Positives = 57/133 (42%), Gaps = 29/133 (21%)
Query: 34 KNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHR--------LIDDMVAQA----- 80
K I+K +G F+D E+ +K + ++ +W +++ +I D +A A
Sbjct: 230 KGNIMKFTEGAFRDWGYELAKKEFGAECITWGLWDKYKNPNPGKEIVIKDRIADAFLQQI 289
Query: 81 -LKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDGKTIES-----EAAHGTV 134
+ + V A N +GD SD +A G +G + P G I EA HGT
Sbjct: 290 LTRPDEYDVIATMNLNGDYISDALAAQVGGIG------IAP-GANIGDEIGIFEATHGTA 342
Query: 135 TRHYRFLGINDIN 147
++ G + +N
Sbjct: 343 PKY---AGQDKVN 352
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 33.6 bits (77), Expect = 0.028
Identities = 30/83 (36%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 34 KNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQALKGNGGF-VWACK 92
K +LKK DG FK F EV K Y I E +D M + F V
Sbjct: 170 KANVLKKTDGLFKKTFYEV-AKEYPD------IKAEDYYVDAMNMYIITRPQTFDVVVTS 222
Query: 93 NYDGDVQSDIVAQGYGSLGLMTS 115
N GD+ SD A G LGL S
Sbjct: 223 NLFGDILSDGAAGLVGGLGLAPS 245
>gnl|CDD|140318 PTZ00297, PTZ00297, pantothenate kinase; Provisional.
Length = 1452
Score = 31.7 bits (72), Expect = 0.14
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 36 TILKKYDGHFKDIFQEVYEKNYKSQFEQAKIWYEHRLIDDMVAQAL 81
T L D + + QEVY + F Q ++ ++ L+D++ A+
Sbjct: 35 TFLASVDAYDVVLLQEVYAASVLPYFLQKQLCFQKMLVDELKARGF 80
>gnl|CDD|215505 PLN02935, PLN02935, Bifunctional NADH kinase/NAD(+) kinase.
Length = 508
Score = 29.0 bits (65), Expect = 1.1
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 81 LKGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMT 114
L G+G +WA + G V +V GSLG MT
Sbjct: 269 LGGDGTVLWAASMFKGPVPP-VVPFSMGSLGFMT 301
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 28.5 bits (64), Expect = 1.3
Identities = 27/91 (29%), Positives = 39/91 (42%), Gaps = 19/91 (20%)
Query: 67 WYEHRLIDDMVAQAL------KGNGGFVWACKNYDGDVQSDIVAQGYGSLGLMTSILMCP 120
W E L+DD +A ++ + + A N +GD SD A G LG M P
Sbjct: 328 WKEKVLVDDRIADSIFQQIQTRPQEYSILATLNLNGDYISDAAAAIVGGLG------MAP 381
Query: 121 DGKTIES----EAAHGTVTRHYRFLGINDIN 147
++ EA HGT +H G++ IN
Sbjct: 382 GANIGDNAAIFEATHGTAPKH---AGLDRIN 409
>gnl|CDD|185547 PTZ00304, PTZ00304, NADH dehydrogenase [ubiquinone] flavoprotein
1; Provisional.
Length = 461
Score = 28.6 bits (64), Expect = 1.4
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 14/72 (19%)
Query: 29 LYLSTKNTILKKYDGHFKD---IFQEVYEKN--YKSQFEQAKIWYEHR---------LID 74
+L ++L + G KD IF +Y Y + WY + +ID
Sbjct: 6 GFLRLTASLLVRVHGGLKDQDRIFTNLYRDFDTYIDGALKRGDWYRTKDILLKGHDWIID 65
Query: 75 DMVAQALKGNGG 86
++ L+G GG
Sbjct: 66 EIKKSGLRGRGG 77
>gnl|CDD|225987 COG3456, COG3456, Predicted component of the type VI protein
secretion system, contains a FHA domain [Intracellular
trafficking, secretion, and vesicular transport;
Signal transduction mechanisms].
Length = 430
Score = 28.2 bits (63), Expect = 1.6
Identities = 5/39 (12%), Positives = 16/39 (41%)
Query: 25 KKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQ 63
+ W +Y + + + F+ +F + + Y+ +
Sbjct: 388 QAWDMYQFYYRELASEAESGFEKLFGADFAQAYEEHDRE 426
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 27.5 bits (61), Expect = 3.1
Identities = 29/135 (21%), Positives = 52/135 (38%), Gaps = 18/135 (13%)
Query: 19 YNVALQ-KKWPLYLSTKNTILKKYDGHFKDIFQEV--------------YEKNYKSQFEQ 63
A+ K+ + + K ++K +G F++ EV KNY
Sbjct: 206 IKYAIDHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEFRDYVVTEEEVTKNYNGVPPS 265
Query: 64 AKIWYEHRLIDDMVAQALKGNGGF-VWACKNYDGDVQSDIVAQGYGSLGLMTSILMCPDG 122
K+ R+ D+M Q + + + N +GD SD G++G++ + G
Sbjct: 266 GKVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISDAAGALVGNIGMLGGANIGDTG 325
Query: 123 KTIESEAAHGTVTRH 137
EA HGT ++
Sbjct: 326 GMF--EAIHGTAPKY 338
>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein.
Members of this protein family are FHA
(forkhead-associated) domain-containing proteins that
are part of type VI secretion loci in a considerable
number of bacteria, most of which are known pathogens.
Species include Pseudomonas aeruginosa PAO1, Aeromonas
hydrophila, Yersinia pestis, Burkholderia mallei, etc
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 396
Score = 27.3 bits (61), Expect = 3.1
Identities = 7/37 (18%), Positives = 15/37 (40%)
Query: 25 KKWPLYLSTKNTILKKYDGHFKDIFQEVYEKNYKSQF 61
W +YL + + F+ +F E + + Y+
Sbjct: 359 WAWDMYLRYYRELRSDREQGFERLFGEDFAQAYEEAL 395
>gnl|CDD|219787 pfam08306, Glyco_hydro_98M, Glycosyl hydrolase family 98. This
domain is the putative catalytic domain of glycosyl
hydrolase family 98 proteins.
Length = 315
Score = 27.2 bits (60), Expect = 4.0
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 7/68 (10%)
Query: 8 ESTFWIFGKPTYNVALQKKWP-LYLSTKNTILKKY-----DGHFKDIFQEVYEKNYKSQF 61
E F KP + A+QK W KNT + ++ + + +
Sbjct: 172 EKAFGENRKPAFFEAVQKYWKNFIFMEKNTPNAGGNDAGTESIMLGLWLSGFAGQWGIRM 231
Query: 62 EQAKIWYE 69
+ K WYE
Sbjct: 232 DTWK-WYE 238
>gnl|CDD|222518 pfam14062, DUF4253, Domain of unknown function (DUF4253). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
110 amino acids in length.
Length = 110
Score = 26.0 bits (58), Expect = 4.4
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 97 DVQSDIVAQGYGSLGLMTSILM 118
DIV QG G++ + L+
Sbjct: 79 AFCPDIVDQGTGTIEALAEALL 100
>gnl|CDD|215380 PLN02710, PLN02710, farnesyltranstransferase subunit beta.
Length = 439
Score = 26.7 bits (59), Expect = 5.4
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 72 LIDDMVAQALKGNGGFVWACKNYDGDVQSDIVAQ---GYGSLGLMTSILM 118
L++ + + +KG G ++ +C+ Y+G + + A+ GY GL IL+
Sbjct: 184 LLNILDDELVKGVGDYILSCQTYEGGIGGEPGAEAHGGYTFCGLAAMILI 233
>gnl|CDD|233139 TIGR00814, stp, serine transporter. The Hydroxy/Aromatic Amino
Acid Permease (HAAAP) Family- serine/threonine subfamily
(TC 2.A.42.2) The HAAAP family includes well
characterized aromatic amino acid:H+ symport permeases
and hydroxy amino acid permeases. This subfamily is
specific for hydroxy amino acid transporters and
includes the serine permease, SdaC, of E. coli, and the
threonine permease, TdcC, of E. coli.//added GO terms,
none avaialbelf or ser/thr specifically [SS 2/6/05]
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 397
Score = 26.5 bits (59), Expect = 6.6
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 28 PLYLSTKNTILKKYDGHFKDIFQEVY 53
P+Y K LKKY G ++F V
Sbjct: 369 PMYAIYKVPALKKYRGRISNVFVTVI 394
>gnl|CDD|224086 COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and
metabolism].
Length = 598
Score = 26.5 bits (59), Expect = 6.8
Identities = 8/55 (14%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 30 YLSTKNTILKKYDGHFKDIFQEVYEKNYKSQFEQAKI--WYEHRLIDDMVAQALK 82
Y +NT+ + K + +NY + A + + ++D+++ +
Sbjct: 218 YEKHRNTLAALLNTLVKVLAFLARARNYDDVIDSALLRNEVDREVVDNLIESVKE 272
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other enzymes)
catalyzes NADP-dependent sterol C-4 demethylation, as
part of steroid biosynthesis. 3-keto reductase is a
classical SDR, with a well conserved canonical active
site tetrad and fairly well conserved characteristic
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 290
Score = 26.2 bits (58), Expect = 7.9
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 26 KWPLYLSTKNTILKKYDGHFKDIFQEVYEKN 56
P Y +L + D +D EV++ N
Sbjct: 121 TNPTYKIQAEGLLSQGDKATEDGLGEVFQTN 151
>gnl|CDD|151200 pfam10707, YrbL-PhoP_reg, PhoP regulatory network protein YrbL.
This is a family of proteins that are activated by PhoP.
PhoP protein controls the expression of a large number
of genes that mediate adaptation to low Mg2+
environments and/or virulence in several bacterial
species. YbrL is proposed to be acting in a loop
activity with PhoP and PrmA analogous to the
multicomponent loop in Salmonella where the
PhoP-dependent PmrD protein activates the regulatory
protein PmrA, and the activated PmrA then represses
transcription from the PmrD promoter which harbours
binding sites for both the PhoP and PmrA proteins.
Expression of YrbL is induced in low Mg2+ in a
PhoP-dependent fashion and repressed by Fe3+ in a
PmrA-dependent manner.
Length = 199
Score = 25.7 bits (57), Expect = 9.6
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 94 YDGDVQSDIVAQGYGSLGLMTSILMCPDG---KTIESEAAHGTVT 135
Y G V++D G LGL+T + DG T+E +G +T
Sbjct: 82 YYGFVETD---LG---LGLVTERIRDADGNISPTLEDLLKNGGLT 120
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
0.320 0.136 0.425
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,751,908
Number of extensions: 682333
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 613
Number of HSP's successfully gapped: 40
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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: 55 (24.9 bits)