RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9334
(65 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 = 95.5 bits (238), Expect = 8e-26
Identities = 34/50 (68%), Positives = 38/50 (76%)
Query: 15 AKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
AK YP I FE MIVDN MQ+VS P QFDVMVMPNLYGNI+ NL + + G
Sbjct: 190 AKEYPDITFESMIVDNTCMQLVSRPSQFDVMVMPNLYGNILSNLGAGLVG 239
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 84.1 bits (208), Expect = 2e-21
Identities = 32/53 (60%), Positives = 41/53 (77%)
Query: 12 QTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
+ +AK YP I++ ++IVDNC MQ+VS P QFDVMV PNLYGN+V N A+ I G
Sbjct: 210 REVAKKYPGIKYNEIIVDNCCMQLVSKPEQFDVMVTPNLYGNLVANTAAGIAG 262
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 81.8 bits (203), Expect = 1e-20
Identities = 24/52 (46%), Positives = 36/52 (69%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+AK YP ++ + M VD MQ+V NP QFDV+V NL+G+I+ + A+ + GS
Sbjct: 200 VAKEYPDVELDHMYVDAAAMQLVRNPEQFDVIVTSNLFGDILSDEAAALTGS 251
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 75.3 bits (186), Expect = 5e-18
Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 15 AKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
AK YP I+ E IVD ++ +NP FDV+V PNLYG+I+ ++A++I GS
Sbjct: 194 AKEYPDIEAEHYIVDIGAARLATNPENFDVIVTPNLYGDILSDIAAEISGS 244
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 74.9 bits (184), Expect = 5e-18
Identities = 26/51 (50%), Positives = 40/51 (78%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
+A+ YP+I +E++I+DNC M +V NP FDV+VMPNLYG+I+ +L + + G
Sbjct: 228 VAEKYPEIVYEEVIIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLIG 278
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 74.8 bits (184), Expect = 5e-18
Identities = 26/50 (52%), Positives = 36/50 (72%)
Query: 15 AKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
A YP I+FE+MIVD MQ+V NP QFDV+V NL+G+I+ +L + + G
Sbjct: 192 ALRYPDIEFEEMIVDATCMQLVMNPEQFDVIVTTNLFGDILSDLCAGLVG 241
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 72.8 bits (180), Expect = 2e-17
Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+AK YP ++ M VDN MQ+V NP QFDV+V NL+G+I+ + A+ + GS
Sbjct: 208 VAKEYPDVELSHMYVDNAAMQLVRNPKQFDVIVTENLFGDILSDEAAMLTGS 259
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 71.2 bits (175), Expect = 1e-16
Identities = 25/48 (52%), Positives = 35/48 (72%)
Query: 18 YPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
YP ++ E M+VDN MQ+V NP QFDV+V NL+G+I+ + AS + GS
Sbjct: 210 YPDVELEHMLVDNAAMQLVKNPKQFDVIVTENLFGDILSDEASMLTGS 257
>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 = 65.9 bits (161), Expect = 8e-15
Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+AK YP ++ E +DN MQ+V +P QFDV+V NL+G+I+ + AS I GS
Sbjct: 202 IAKEYPDVELEHQYIDNAAMQLVKSPTQFDVVVTSNLFGDILSDEASVITGS 253
>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 = 62.1 bits (151), Expect = 3e-13
Identities = 24/54 (44%), Positives = 36/54 (66%)
Query: 12 QTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+A YP I+ E IVD ++ +NP FDV+V PNLYG+I+ ++A++I GS
Sbjct: 187 DKIAAEYPDIESEHYIVDIGMARLATNPENFDVIVTPNLYGDILSDVAAEISGS 240
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 54.7 bits (131), Expect = 9e-11
Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+A YP ++ M VDN MQ++ +P QFD +V N++G+I+ + AS I GS
Sbjct: 253 LASEYPDVELSHMYVDNAAMQLIRDPKQFDTIVTNNIFGDILSDEASMITGS 304
>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 = 51.7 bits (124), Expect = 9e-10
Identities = 21/52 (40%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 14 MAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+AK Y +++ M VD+ M +V +P +FDV+V N++G+I+ +LAS + GS
Sbjct: 184 IAKRYG-VEYRDMYVDSAAMNLVKDPWRFDVIVTTNMFGDILSDLASALAGS 234
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 51.9 bits (125), Expect = 9e-10
Identities = 19/53 (35%), Positives = 34/53 (64%)
Query: 12 QTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
+A YP + + VD T+ +V++P +FDV+V NL+G+I+ +LA+ + G
Sbjct: 202 DEVAAEYPDVTVDYQHVDAATIFMVTDPSRFDVIVTDNLFGDIITDLAAAVTG 254
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 50.5 bits (121), Expect = 2e-09
Identities = 21/50 (42%), Positives = 31/50 (62%)
Query: 15 AKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
AK YP I+ E VD M I++ P FDV+V NL+G+I+ + A+ + G
Sbjct: 189 AKEYPDIKAEDYYVDAMNMYIITRPQTFDVVVTSNLFGDILSDGAAGLVG 238
>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 = 49.1 bits (117), Expect = 9e-09
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 12 QTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
+A YP ++++ +D + V P FDV+V NL+G+I+ +L + + GS
Sbjct: 205 AEVAAEYPDVEWDSYHIDALAARFVLKPETFDVIVASNLFGDILSDLGAALMGS 258
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 45.5 bits (108), Expect = 1e-07
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 12 QTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
Q + K YP+I+ + +D V+ P +FDV+V NL+G+I+ ++ + I GS
Sbjct: 202 QEVGKDYPEIETDSQHIDALAAFFVTRPEEFDVIVASNLFGDILTDIGAAIMGS 255
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 38.0 bits (89), Expect = 6e-05
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 15 AKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIV-DNLASDIKG 64
KI ++ I D+ QI+ P ++DV+ NL G+ + D LA+ + G
Sbjct: 258 KGPKGKIVYKDRIADDMLQQILLRPGEYDVIATKNLNGDYISDALAAQVGG 308
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 34.8 bits (80), Expect = 9e-04
Identities = 13/46 (28%), Positives = 26/46 (56%)
Query: 20 KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKGS 65
K+ I DN QI+ P ++D+++ PN+ G+ + + A + G+
Sbjct: 267 KVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISDAAGALVGN 312
>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 = 34.4 bits (79), Expect = 0.001
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 3 CRFGYPNLGQTMAKLYPKIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGN-IVDNLASD 61
++ PN G+ +I + I D QI++ P ++DV+ NL G+ I D LA+
Sbjct: 264 DKYKNPNPGK-------EIVIKDRIADAFLQQILTRPDEYDVIATMNLNGDYISDALAAQ 316
Query: 62 IKG 64
+ G
Sbjct: 317 VGG 319
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 28.1 bits (63), Expect = 0.21
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 20 KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGN-IVDNLASDIKG 64
+I + I D QI+ P ++DV+ NL G+ I D LA+ + G
Sbjct: 267 EIIVKDSIADAFLQQILLRPAEYDVIATMNLNGDYISDALAAQVGG 312
>gnl|CDD|213629 TIGR01489, DKMTPPase-SF, 2,3-diketo-5-methylthio-1-phosphopentane
phosphatase. This phosphatase is a member of the IB
subfamily (TIGR01488) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. With
the exception of OMNI|NTL01BS01361 from B. subtilis and
GP|15024582 from Clostridium acetabutylicum, the members
of this group are all eukaryotic, spanning metazoa,
plants and fungi. The B. subtilus gene (YkrX, renamed
MtnX) is part of an operon for the conversion of
methylthioribose (MTR) to methionine. It works with the
enolase MtnW, a RuBisCO homolog. The combination of MtnW
and MtnX achieves the same overall reaction as the
enolase-phosphatase MtnC. The function of MtnX was shown
by Ashida, et al. (2003) to be
2,3-diketo-5-methylthio-1-phosphopentane phosphatase,
rather than 2,3-diketo-5-methylthio-1-phosphopentane
phosphatase as proposed earlier. See the Genome Property
for methionine salvage for more details. In eukaryotes,
methionine salvage from methylthioadenosine also occurs.
It seems reasonable that members of this family in
eukaryotes fulfill a similar role as in Bacillus. A more
specific, equivalog-level model is TIGR03333. Note that
a member of this family from S. cerevisiae is annotated
as a "probable membrane protein" due to a predicted
transmembrane helix. The region in question contains the
second of the three conserved HAD superfamily catalytic
motifs and thus, considering the fold of the HAD
catalytic domain, is unlikely to be a transmembrane
region in fact [Central intermediary metabolism, Other].
Length = 188
Score = 25.9 bits (57), Expect = 1.3
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 23 FEQMIVDNCTMQIVSNPHQFD 43
E + + ++I SNP FD
Sbjct: 106 LEGIGEKDVFIEIYSNPASFD 126
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 24.7 bits (54), Expect = 4.5
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 20 KIQFEQMIVDNCTMQIVSNPHQFDVMVMPNLYGNIVDNLASDIKG 64
K+ + I D+ QI + P ++ ++ NL G+ + + A+ I G
Sbjct: 331 KVLVDDRIADSIFQQIQTRPQEYSILATLNLNGDYISDAAAAIVG 375
>gnl|CDD|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2),
C-terminal domain. PolD2 (DNA polymerase delta, subunit
2) is an auxiliary subunit of the eukaryotic DNA
polymerase delta (PolD) complex thought to play a
regulatory role and to serve as a scaffold for PolD
assembly by interacting simultaneously with all of the
other three subunits. PolD2 is catalytically inactive
and lacks the active site residues required for
phosphoesterase activity in other members of this
superfamily. PolD2 is also involved in the recruitment
of several proteins regulating DNA metabolism, including
p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists
of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3),
and p12(PolD4). PolD is one of three major replicases
in eukaryotes. PolD also plays an essential role in
translesion DNA synthesis, homologous recombination, and
DNA repair. Within the PolD complex, PolD2 tightly
associates with PolD3. PolD2 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but share a conserved domain with
an active site consisting of two metal ions (usually
manganese, iron, or zinc) coordinated with octahedral
geometry by a cage of histidine, aspartate, and
asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 24.1 bits (53), Expect = 5.0
Identities = 5/13 (38%), Positives = 11/13 (84%)
Query: 32 TMQIVSNPHQFDV 44
T+ +V+NP++F +
Sbjct: 129 TLNLVTNPYEFSI 141
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
0.324 0.139 0.428
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,131,002
Number of extensions: 210736
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 179
Number of HSP's successfully gapped: 25
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)