RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3672
(178 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 = 115 bits (290), Expect = 1e-31
Identities = 51/102 (50%), Positives = 58/102 (56%), Gaps = 22/102 (21%)
Query: 31 RFSYVQDLLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRD 90
R+++ + RKKVTAVHKANIMKL DGLFLN C+E+AK YP T MI
Sbjct: 152 RYAFEYARKNGRKKVTAVHKANIMKLADGLFLNVCREVAKEYPDITFESMI--------- 202
Query: 91 INVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNIFD 132
V N Q+VS P QFDVMVMPNLYGNI
Sbjct: 203 -------------VDNTCMQLVSRPSQFDVMVMPNLYGNILS 231
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 104 bits (262), Expect = 2e-27
Identities = 48/92 (52%), Positives = 55/92 (59%), Gaps = 22/92 (23%)
Query: 39 LSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTI 98
L+NRKKVTAVHKANIMKL DGLFL SC+E+AK YP ++I
Sbjct: 183 LNNRKKVTAVHKANIMKLADGLFLESCREVAKKYPGIKYNEII----------------- 225
Query: 99 RRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
V N Q+VS P QFDVMV PNLYGN+
Sbjct: 226 -----VDNCCMQLVSKPEQFDVMVTPNLYGNL 252
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 88.0 bits (219), Expect = 3e-21
Identities = 35/90 (38%), Positives = 45/90 (50%), Gaps = 22/90 (24%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRR 100
RKKVT+VHKAN++KL DGL+ +E+AK YP M
Sbjct: 173 GRKKVTSVHKANVLKLSDGLWREVVEEVAKEYPDVELDHMY------------------- 213
Query: 101 IITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
V Q+V NP QFDV+V NL+G+I
Sbjct: 214 ---VDAAAMQLVRNPEQFDVIVTSNLFGDI 240
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 85.2 bits (211), Expect = 4e-20
Identities = 41/100 (41%), Positives = 49/100 (49%), Gaps = 22/100 (22%)
Query: 31 RFSYVQDLLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRD 90
RF+Y RKKVTAVHKANIMK GLFL +E+A YP +MI
Sbjct: 154 RFAYELARKEGRKKVTAVHKANIMKSTSGLFLKVAREVALRYPDIEFEEMI--------- 204
Query: 91 INVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
V Q+V NP QFDV+V NL+G+I
Sbjct: 205 -------------VDATCMQLVMNPEQFDVIVTTNLFGDI 231
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 83.4 bits (206), Expect = 2e-19
Identities = 39/99 (39%), Positives = 52/99 (52%), Gaps = 24/99 (24%)
Query: 32 FSYVQDLLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDI 91
F Y + RK+V+A+HKANIMK DGLFL C+E+A+ YP ++I
Sbjct: 194 FHYAK--THGRKRVSAIHKANIMKKTDGLFLKCCREVAEKYPEIVYEEVI---------- 241
Query: 92 NVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+ N +V NP FDV+VMPNLYG+I
Sbjct: 242 ------------IDNCCMMLVKNPALFDVLVMPNLYGDI 268
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 77.2 bits (191), Expect = 5e-17
Identities = 35/90 (38%), Positives = 44/90 (48%), Gaps = 22/90 (24%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRR 100
RKKVT + K NIMKL DGLF E+AK YP DI +
Sbjct: 166 GRKKVTCLTKDNIMKLTDGLFHKVFDEIAKEYP----------------DIEAEHY---- 205
Query: 101 IITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
I+ ++ +NP FDV+V PNLYG+I
Sbjct: 206 IVD--IGAARLATNPENFDVIVTPNLYGDI 233
>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 = 67.1 bits (164), Expect = 1e-13
Identities = 38/120 (31%), Positives = 54/120 (45%), Gaps = 28/120 (23%)
Query: 13 SVCDKVSLRY--EETIDPCPRFSYVQDLLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAK 70
C K+ R E+ F Y + NRKKVT + K NIMK+ DG+F ++A
Sbjct: 136 YECTKLITRSGSEKICRYA--FEYAR--KHNRKKVTCLTKDNIMKMTDGIFHKIFDKIAA 191
Query: 71 LYPVWTNRKMITGFIWTTRDINVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
YP DI + I+ + ++ +NP FDV+V PNLYG+I
Sbjct: 192 EYP----------------DIESEHY----IVDI--GMARLATNPENFDVIVTPNLYGDI 229
>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 = 61.7 bits (150), Expect = 9e-12
Identities = 28/92 (30%), Positives = 41/92 (44%), Gaps = 23/92 (25%)
Query: 39 LSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTI 98
+KVT VHKAN++K DGLF C+E+AK Y V +
Sbjct: 155 KERNRKVTCVHKANVLKGTDGLFREVCREIAKRYGVEYRDMYVDSAAM------------ 202
Query: 99 RRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+V +P +FDV+V N++G+I
Sbjct: 203 -----------NLVKDPWRFDVIVTTNMFGDI 223
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 61.1 bits (149), Expect = 1e-11
Identities = 28/91 (30%), Positives = 38/91 (41%), Gaps = 24/91 (26%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYP-VWTNRKMITGFIWTTRDINVFIWTIR 99
RKKVT+V KAN++K + YP V ++ D
Sbjct: 179 GRKKVTSVDKANVLKSSRLWRKIVEEVAKAEYPDVELEHMLV--------D--------- 221
Query: 100 RIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
N Q+V NP QFDV+V NL+G+I
Sbjct: 222 ------NAAMQLVKNPKQFDVIVTENLFGDI 246
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 60.1 bits (146), Expect = 3e-11
Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 26/102 (25%)
Query: 32 FSYVQD--LLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYP-VWTNRKMITGFIWTT 88
F + + KVT HKAN++K DGLF + E+AK YP + +
Sbjct: 150 FEMAKRRKKMGKEGKVTCAHKANVLKKTDGLFKKTFYEVAKEYPDIKAEDYYVDA----- 204
Query: 89 RDINVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+N++ I++ P FDV+V NL+G+I
Sbjct: 205 --MNMY----------------IITRPQTFDVVVTSNLFGDI 228
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 48.6 bits (117), Expect = 3e-07
Identities = 31/89 (34%), Positives = 44/89 (49%), Gaps = 23/89 (25%)
Query: 42 RKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRRI 101
RKKVT+V KAN+++ L+ E+AK YP D+ +
Sbjct: 183 RKKVTSVDKANVLE-SSRLWREVVTEVAKEYP----------------DVEL------SH 219
Query: 102 ITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+ V N Q+V NP QFDV+V NL+G+I
Sbjct: 220 MYVDNAAMQLVRNPKQFDVIVTENLFGDI 248
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 47.3 bits (113), Expect = 9e-07
Identities = 29/95 (30%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTT-RDINVFIWTIR 99
RK VT VHK NIMK +G F + E+A+ +++TG + I
Sbjct: 211 KRKSVTLVHKGNIMKFTEGAFKDWGYEVAEEEEF--GDEVVTGKEKFELKGPKGKIVYKD 268
Query: 100 RIITVFNWTRQIVSNPHQFDVMVMPNLYGNIFDVM 134
RI + +QI+ P ++DV+ NL G D +
Sbjct: 269 RIAD--DMLQQILLRPGEYDVIATKNLNG---DYI 298
>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 = 47.1 bits (112), Expect = 1e-06
Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIW-------TTRDINV 93
+RK VT VHK NIMK +G F + E+AK + IT +W ++I +
Sbjct: 221 DRKSVTLVHKGNIMKFTEGAFRDWGYELAKKE---FGAECITWGLWDKYKNPNPGKEIVI 277
Query: 94 FIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGN 129
RI F +QI++ P ++DV+ NL G+
Sbjct: 278 ----KDRIADAF--LQQILTRPDEYDVIATMNLNGD 307
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 44.8 bits (106), Expect = 6e-06
Identities = 32/121 (26%), Positives = 54/121 (44%), Gaps = 18/121 (14%)
Query: 31 RFSYVQDLLSNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRD 90
R + + RKKVT +HK N+MK +G F E+A K ++ T +
Sbjct: 203 RMAIKYAIDHKRKKVTIMHKGNVMKYTEGAFREWAYEVAL--------KEFRDYVVTEEE 254
Query: 91 INVFIWTI---RRIIT----VFNWTRQIVSNPHQFDVMVMPNLYGN-IFDVMVMPNLYGN 142
+ + ++I N +QI+ P ++D+++ PN+ G+ I D L GN
Sbjct: 255 VTKNYNGVPPSGKVIINDRIADNMFQQIIIRPDEYDIILAPNVNGDYISD--AAGALVGN 312
Query: 143 I 143
I
Sbjct: 313 I 313
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 43.4 bits (103), Expect = 2e-05
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 22/89 (24%)
Query: 42 RKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRRI 101
RK +T VHK N++ L+ + E+A YP D+ V +
Sbjct: 178 RKHLTLVHKTNVLTFAGDLWQRTVDEVAAEYP----------------DVTVDYQHV-DA 220
Query: 102 ITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
T+F +V++P +FDV+V NL+G+I
Sbjct: 221 ATIF-----MVTDPSRFDVIVTDNLFGDI 244
>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 = 42.0 bits (99), Expect = 7e-05
Identities = 28/89 (31%), Positives = 42/89 (47%), Gaps = 23/89 (25%)
Query: 42 RKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRRI 101
RKKVT+V KAN+++ L+ + +E+AK YP
Sbjct: 177 RKKVTSVDKANVLESSR-LWRKTVEEIAKEYPDVELEHQY-------------------- 215
Query: 102 ITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+ N Q+V +P QFDV+V NL+G+I
Sbjct: 216 --IDNAAMQLVKSPTQFDVVVTSNLFGDI 242
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 41.2 bits (97), Expect = 1e-04
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 20/98 (20%)
Query: 41 NRKKVTAVHKANIMKLGDGLFLNSCKEMA-KLYPVWTNRKMITGFIW-------TTRDIN 92
+RK VT VHK NIMK +G F + ++A + + ++I G W T ++I
Sbjct: 214 DRKSVTLVHKGNIMKFTEGAFKDWGYQLAEEEF----GDELIDGGPWDKIKNPETGKEI- 268
Query: 93 VFIWTIRRIIT-VFNWTRQIVSNPHQFDVMVMPNLYGN 129
++ I F +QI+ P ++DV+ NL G+
Sbjct: 269 ----IVKDSIADAF--LQQILLRPAEYDVIATMNLNGD 300
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 35.5 bits (82), Expect = 0.008
Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 33/105 (31%)
Query: 31 RFSYVQDLLSNRKK-VTAVHKAN----IMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFI 85
R+++ +L + R+K VT+ K+N M D +F +E+ K YP
Sbjct: 168 RYAF--ELAAKRRKHVTSATKSNGIVHSMPFWDEVF----QEVGKDYP------------ 209
Query: 86 WTTRDINVFIWTIRRIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+I I + F V+ P +FDV+V NL+G+I
Sbjct: 210 ----EIETDSQHIDALAAFF------VTRPEEFDVIVASNLFGDI 244
>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 = 34.4 bits (79), Expect = 0.018
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 22/91 (24%)
Query: 40 SNRKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIR 99
RK +T+ K+N ++ + E+A YP W + I+
Sbjct: 179 KRRKHLTSATKSNGIRHSMPFWDEVFAEVAAEYP---------DVEWDSYHID------- 222
Query: 100 RIITVFNWTRQIVSNPHQFDVMVMPNLYGNI 130
+ V P FDV+V NL+G+I
Sbjct: 223 -ALAAR-----FVLKPETFDVIVASNLFGDI 247
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 34.3 bits (79), Expect = 0.023
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 38 LLSNRKKVTAVHKANIMKLGDGLFLNSCKEMA 69
L +++ VT VHK NIMK +G F + E+A
Sbjct: 227 LPGDKRHVTLVHKGNIMKYTEGAFRDWGYELA 258
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 30.8 bits (69), Expect = 0.35
Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 23/90 (25%)
Query: 42 RKKVTAVHKANIMKLGDGLFLNSCKEMAKLYPVWTNRKMITGFIWTTRDINVFIWTIRRI 101
R K+ +V KAN++ D L W RK +T D+ +
Sbjct: 228 RGKLCSVDKANVL---DASIL------------W--RKRVTALASEYPDVEL------SH 264
Query: 102 ITVFNWTRQIVSNPHQFDVMVMPNLYGNIF 131
+ V N Q++ +P QFD +V N++G+I
Sbjct: 265 MYVDNAAMQLIRDPKQFDTIVTNNIFGDIL 294
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 28.1 bits (62), Expect = 3.6
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 5 LLDRLRQLSVCDKVSLRYEETIDPCPRFSYVQDLLSNRKKVTAVHKANIMKLGDGL--FL 62
+ + QL ++ YE +DP L NR K + + IMKL + +
Sbjct: 226 ITSKEAQLESSREIVKSYENELDP----------LKNRLKEIEHNLSKIMKLDNEIKALK 275
Query: 63 NSCKEMAKL 71
+ K+M K
Sbjct: 276 SRKKQMEKD 284
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 27.6 bits (62), Expect = 3.8
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 1 LFLYLLDRLRQLSVCDKVSLRYEETIDPCPRFSYVQDLLSNR--KKVTA 47
LFL LL++L +L + V+L+ + S + +LL KK+
Sbjct: 161 LFLQLLNKLERLPL---VTLQQLRRLSD-HLKSDIAELLDENILKKMMH 205
>gnl|CDD|151784 pfam11343, DUF3145, Protein of unknown function (DUF3145). This
family of proteins with unknown function appear to be
restricted to Actinobacteria.
Length = 158
Score = 26.9 bits (60), Expect = 4.4
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 20 LRYEETIDPCP-----RFSYVQDL 38
LR+E T DP P R+S+ DL
Sbjct: 67 LRFEVTEDPSPGADGGRWSHTPDL 90
>gnl|CDD|239777 cd04244, AAK_AK-LysC-like, AAK_AK-LysC-like: Amino Acid Kinase
Superfamily (AAK), AK-LysC-like; this CD includes the
N-terminal catalytic aspartokinase (AK) domain of the
lysine-sensitive AK isoenzyme found in higher plants.
The lysine-sensitive AK isoenzyme is a monofunctional
protein. It is involved in the overall regulation of the
aspartate pathway and can be synergistically inhibited
by S-adenosylmethionine. Also included in this CD is an
uncharacterized LysC-like AK found in Euryarchaeota and
some bacteria. AK catalyzes the conversion of aspartate
and ATP to aspartylphosphate and ADP.
Length = 298
Score = 27.0 bits (60), Expect = 5.7
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 69 AKLYPVWTNRKM--ITGFIWTTRD 90
+L P+ + K+ +TGFI T D
Sbjct: 175 KRLLPMLEDGKIPVVTGFIGATED 198
>gnl|CDD|177904 PLN02263, PLN02263, serine decarboxylase.
Length = 470
Score = 27.1 bits (60), Expect = 6.2
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 128 GNIFDVMVMPNLYGNIVDNLASDSVISRT-----GSCQQSC 163
GNI V+VMP++ +D + V R+ G Q C
Sbjct: 414 GNIAHVVVMPSVTIEKLDYFLKELVEKRSTWYPDGKVQPPC 454
>gnl|CDD|203115 pfam04896, AmoC, Ammonia monooxygenase/methane monooxygenase,
subunit C. Ammonia monooxygenase plays a key role in
the nitrogen cycle and degrades a wide range of
hydrocarbons and halogenated hydrocarbons. This family
represents the AmoC subunit. It also includes the
particulate methane monooxygenase subunit PmoC from
methanotrophic bacteria.
Length = 241
Score = 26.2 bits (58), Expect = 8.9
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 83 GFIWTTRDINVFIWT----IRRIITVFNW 107
G++W TRD N+ +RR + W
Sbjct: 68 GWLWKTRDRNLAALAPREELRRYFYLLMW 96
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
0.328 0.139 0.440
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,935,164
Number of extensions: 799802
Number of successful extensions: 744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 43
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.4 bits)