RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9338
(130 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 = 126 bits (318), Expect = 2e-36
Identities = 49/97 (50%), Positives = 66/97 (68%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGD 92
LVGG G+V GA+ + VFEPG RHT + G+N+ANPTA++L S ML+H+ L+ + D
Sbjct: 237 LVGGPGLVPGANIGRDYAVFEPGVRHTGPDIAGQNIANPTALILSSVMMLNHLGLKEHAD 296
Query: 93 MIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
I+ AV + GK RTKDLGG +TT ++T AVI L
Sbjct: 297 RIQKAVLSTIAEGKNRTKDLGGTATTSDFTEAVIKRL 333
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 93.8 bits (234), Expect = 6e-24
Identities = 37/100 (37%), Positives = 51/100 (51%), Gaps = 3/100 (3%)
Query: 33 LVGGAGVVAGASWSPEC--VVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYY 90
L G G+ A+ E +FEP + + GK +ANP A +L + ML H+ +
Sbjct: 248 LTGSLGLAPSANLGDERGPALFEP-VHGSAPDIAGKGIANPIATILSAAMMLRHLGEKEA 306
Query: 91 GDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANLK 130
D I NAV +VL G +RT DLGG +TT E A+ L
Sbjct: 307 ADAIENAVEKVLAEGGIRTPDLGGNATTSEVGDAIAKALA 346
>gnl|CDD|215065 PLN00123, PLN00123, isocitrate dehydrogenase (NAD+).
Length = 360
Score = 90.7 bits (225), Expect = 1e-22
Identities = 46/100 (46%), Positives = 57/100 (57%), Gaps = 3/100 (3%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARH---TYSEAVGKNVANPTAMLLCSTKMLSHVNLQY 89
+ GG GV+ G + + VFE GA + V + ANP A+LL S ML H+
Sbjct: 260 IAGGTGVMPGGNVGADHAVFEQGASAGNVGNEKLVEQKKANPVALLLSSAMMLRHLQFPS 319
Query: 90 YGDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
+ D + AV RV+ GK RTKDLGG STTQE AVIANL
Sbjct: 320 FADRLETAVKRVIAEGKYRTKDLGGSSTTQEVVDAVIANL 359
>gnl|CDD|181606 PRK08997, PRK08997, isocitrate dehydrogenase; Provisional.
Length = 334
Score = 86.7 bits (215), Expect = 2e-21
Identities = 38/98 (38%), Positives = 60/98 (61%), Gaps = 3/98 (3%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYG 91
LVGG G+ GA+ + +FE A H + + GKN+ANPT+++L + +ML ++ +
Sbjct: 239 LVGGLGMAPGANIGRDAAIFE--AVHGSAPDIAGKNLANPTSVILAAIQMLEYLGMPDKA 296
Query: 92 DMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
+ IR A+ V++AG T+DLGG T ++T AVI L
Sbjct: 297 ERIRKAIVAVIEAGDRTTRDLGGTHGTTDFTQAVIDRL 334
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 84.5 bits (209), Expect = 2e-20
Identities = 40/99 (40%), Positives = 57/99 (57%), Gaps = 6/99 (6%)
Query: 37 AGVVAGASWSPECVVFEPG-----ARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYY 90
AG++ G +P C + E G A H + + GKN+ANPTA+LL + ML H+ L
Sbjct: 274 AGLIGGLGLTPSCNIGENGLALAEAVHGSAPDIAGKNLANPTALLLSAVMMLRHLKLNEQ 333
Query: 91 GDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
+ I NA+ + GK RT DLGG STT ++T A+ +L
Sbjct: 334 AEQIHNAILNTIAEGKYRTADLGGSSTTTDFTKAICDHL 372
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 67.3 bits (165), Expect = 3e-14
Identities = 37/98 (37%), Positives = 51/98 (52%), Gaps = 7/98 (7%)
Query: 33 LVGGAGVVAGASWSPECV-VFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSH-VNLQYY 90
L G G++ AS + +FEP + + GK ANP A +L + ML H + L+
Sbjct: 254 LTGSLGLLPSASLGADGFGLFEP-VHGSAPDIAGKGKANPIATILSAAMMLRHSLGLEDE 312
Query: 91 GDMIRNAVNRVLKAGKVRTKDLGG---QSTTQEYTYAV 125
D I AV +VL+AG RT DLGG +T E+ AV
Sbjct: 313 ADKIEAAVLKVLEAGI-RTGDLGGNATYVSTSEFGDAV 349
>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 = 66.7 bits (163), Expect = 5e-14
Identities = 30/96 (31%), Positives = 45/96 (46%), Gaps = 6/96 (6%)
Query: 33 LVGGAGVVAGASWSPECVVFEP--GARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYY 90
L G G+ A+ +FEP G+ + GK +ANPTA +L ML ++
Sbjct: 231 LAGSLGLAPSANIGDRKALFEPVHGSA---PDIAGKGIANPTAAILSVAMMLDYLGELEK 287
Query: 91 GDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVI 126
G ++ AV + GK T DLGG + T+E +
Sbjct: 288 GKLVWEAVEYYIIEGKK-TPDLGGTAKTKEVGDEIA 322
>gnl|CDD|184462 PRK14025, PRK14025, multifunctional 3-isopropylmalate
dehydrogenase/D-malate dehydrogenase; Provisional.
Length = 330
Score = 65.9 bits (161), Expect = 8e-14
Identities = 33/97 (34%), Positives = 47/97 (48%), Gaps = 2/97 (2%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGD 92
LVGG G+ A+ + +FEP + + GK +ANPTA +L + ML H+ D
Sbjct: 236 LVGGLGLAPSANIGDKYGLFEP-VHGSAPDIAGKGIANPTATILTAVLMLRHLGENEEAD 294
Query: 93 MIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
+ A+ VL G T DLGG +T E V +
Sbjct: 295 KVEKALEEVLALGLT-TPDLGGNLSTMEMAEEVAKRV 330
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 60.1 bits (147), Expect = 9e-12
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 65 GKNVANPTAMLLCSTKMLSH-VNLQYYGDMIRNAVNRVLKAGKVRTKDL---GGQSTTQE 120
GK +ANP A +L + ML + + L+ D I AV +VL G RT D+ GG+ +T E
Sbjct: 288 GKGIANPIATILSAAMMLRYSLGLEEAADAIEAAVEKVLAQG-YRTADIAEGGGKVSTSE 346
Query: 121 YTYAVIANLK 130
A++A L
Sbjct: 347 MGDAILAALA 356
>gnl|CDD|181281 PRK08194, PRK08194, tartrate dehydrogenase; Provisional.
Length = 352
Score = 59.3 bits (144), Expect = 2e-11
Identities = 28/101 (27%), Positives = 51/101 (50%), Gaps = 5/101 (4%)
Query: 33 LVGGAGVVAGASWSPEC---VVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQY 89
++G G+ A+ + +FEP + + GK +ANP + + ML H +
Sbjct: 252 IMGSIGIAPAANINVNGKYPSMFEP-VHGSAPDIAGKGIANPIGQIWTAKLMLDHFGEEE 310
Query: 90 YGDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANLK 130
G + + + V + G ++T D+GG++TT E T +I+ LK
Sbjct: 311 LGSHLLDVIEDVTEDG-IKTPDIGGRATTDEVTDEIISRLK 350
>gnl|CDD|223612 COG0538, Icd, Isocitrate dehydrogenases [Energy production and
conversion].
Length = 407
Score = 57.7 bits (140), Expect = 8e-11
Identities = 36/105 (34%), Positives = 48/105 (45%), Gaps = 9/105 (8%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGD 92
VGG G+ GA+ FE T + GK+ NP A +L T ML H D
Sbjct: 305 QVGGLGLAPGANIGDGTAEFEA-THGTAPKYAGKDSTNPIASILSGTMMLRHRGWLEAAD 363
Query: 93 MIRNAVNRVLKAGKVRTKDLGGQS-------TTQEYTYAVIANLK 130
+I AV +++GKV T DL +T E+ A+I NLK
Sbjct: 364 LIEKAVEDTIESGKV-TYDLARLMGGAKRYLSTSEFADAIIENLK 407
>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 = 56.0 bits (135), Expect = 3e-10
Identities = 36/100 (36%), Positives = 53/100 (53%), Gaps = 5/100 (5%)
Query: 33 LVGGAGVVAGASWSPE---CVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQY 89
L+G GV A+ +PE +FEP + + GK +ANP + + ML H+ +
Sbjct: 255 LMGSLGVAPSANINPEGKFPSMFEP-VHGSAPDIAGKGIANPIGAIWTAAMMLEHLGEKE 313
Query: 90 YGDMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAVIANL 129
G I +A+ RV AG + T D+GG++TT E T AV L
Sbjct: 314 AGAKIMDAIERVTAAG-ILTPDVGGKATTSEVTEAVCNAL 352
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 51.4 bits (124), Expect = 1e-08
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 10/104 (9%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYG 91
+ G G+ A+ E +FE A H + + GKN+ANP+ +L + ML H+
Sbjct: 241 ISGSVGLAGSANIGEEYAMFE--AVHGSAPDIAGKNIANPSGLLNAAVMMLVHIGQFDIA 298
Query: 92 DMIRNAVNRVLKAGKVRTKDLGGQST------TQEYTYAVIANL 129
++I NA + L+ G + T D+ + T+E+ AVI NL
Sbjct: 299 ELIENAWLKTLEDG-IHTADIYNEGVSKKKVGTKEFAEAVIENL 341
>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 = 49.1 bits (117), Expect = 7e-08
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 6/102 (5%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGD 92
VGG G+ GA+ E +FE T + G++ NP +++L ML H+ + D
Sbjct: 316 QVGGIGIAPGANIGDEIGIFEA-THGTAPKYAGQDKVNPGSIILSGEMMLEHMGWKEAAD 374
Query: 93 MIRNAVNRVLKAGKV-----RTKDLGGQSTTQEYTYAVIANL 129
+I+ A+ + + + V R D + E+ A+I N+
Sbjct: 375 LIKKAMEKAIASKIVTYDFARLMDGAKEVKCSEFAEAIIENM 416
>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 = 48.6 bits (116), Expect = 1e-07
Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 2/94 (2%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSH-VNLQYYG 91
+ G G++ AS + + + GK +ANP A +L + +L + NL+
Sbjct: 250 ITGSLGMLPSASLGSDGFGLFEPVHGSAPDIAGKGIANPIAQILSAAMLLRYSFNLEEAA 309
Query: 92 DMIRNAVNRVLKAGKVRTKDLGGQSTTQEYTYAV 125
D I AV +VL G RT DLG +TT T +
Sbjct: 310 DAIEAAVKKVLAEGY-RTPDLGSSATTAVGTAEM 342
>gnl|CDD|235803 PRK06451, PRK06451, isocitrate dehydrogenase; Validated.
Length = 412
Score = 46.0 bits (109), Expect = 9e-07
Identities = 35/104 (33%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYG 91
LVG G++ GA+ +FE A H T + GKNVANPT ++ ML +
Sbjct: 309 LVGNIGMLGGANIGDTGGMFE--AIHGTAPKYAGKNVANPTGIIKGGELMLRFMGWDKAA 366
Query: 92 DMIRNAVNRVLKAGKVRTKDLG-----GQSTTQEYTYAVIANLK 130
D+I A+ +K KV T+DL +T EYT +I+ +
Sbjct: 367 DLIDKAIMESIKQKKV-TQDLARFMGVRALSTTEYTDELISIID 409
>gnl|CDD|180792 PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed.
Length = 409
Score = 44.7 bits (106), Expect = 3e-06
Identities = 26/102 (25%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 34 VGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGD 92
VGG G+ GA+ + +FE A H T + G + NP +++L + ML H+ D
Sbjct: 310 VGGIGIAPGANINDGHAIFE--ATHGTAPKYAGLDKVNPGSVILSAEMMLRHMGWTEAAD 367
Query: 93 MIRNAVNRVLKAGKV-----RTKDLGGQSTTQEYTYAVIANL 129
+I ++ + + + V R + + E+ A+I N+
Sbjct: 368 LIIKSMEKTIASKTVTYDFARLMEGATEVKCSEFGDALIKNM 409
>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 = 42.4 bits (100), Expect = 2e-05
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 65 GKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKAGKVRTKDLGGQST------T 118
G+N+ANP+ +L + +ML H+ +I NA + L+ G V T D+ + T T
Sbjct: 268 GQNIANPSGLLNAAIQMLVHIGQSDIAQLIYNAWLKTLEDG-VHTADIYNEKTSKQKVGT 326
Query: 119 QEYTYAVIANL 129
+E+ AV ANL
Sbjct: 327 KEFAEAVTANL 337
>gnl|CDD|180944 PRK07362, PRK07362, isocitrate dehydrogenase; Validated.
Length = 474
Score = 37.8 bits (88), Expect = 7e-04
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 33 LVGGAGVVAGASWSPECVVFEPGARH-TYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYG 91
+VGG G+ GA+ +FE A H T + G + NP +++L ML ++ Q
Sbjct: 373 IVGGLGMAPGANIGDNAAIFE--ATHGTAPKHAGLDRINPGSVILSGVMMLEYLGWQEAA 430
Query: 92 DMIRNAVNRVLKAGKVRTKDL 112
D+I ++ + +V T DL
Sbjct: 431 DLITKGLSAAIANKQV-TYDL 450
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 36.1 bits (84), Expect = 0.003
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 33 LVGGAGVVAGASWSPECV---VFEP--GARHTYSEAVGKNVANPTAMLLCSTKMLSHVNL 87
+ GG G+ A + +P +FEP G+ + G+ +A+PTA +L +L H+
Sbjct: 252 VTGGIGLAASGNINPTGTNPSMFEPVHGSAPDIA---GQGIADPTAAILSVALLLDHLGE 308
Query: 88 QYYGDMIRNAVNRVLKAGKVRTKDLGGQSTTQ 119
+ I AV L + G+ST +
Sbjct: 309 EDAAARIEAAVEADL-----AERGKMGRSTAE 335
>gnl|CDD|182165 PRK09954, PRK09954, putative kinase; Provisional.
Length = 362
Score = 35.7 bits (82), Expect = 0.003
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 54 PGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNR--VLKAGKVRTKD 111
PG H + VG+N+A+ A+L +LS + +YG+ + R V +G +R
Sbjct: 85 PGTIHCSAGGVGRNIAHNLALLGRDVHLLSAIGDDFYGETLLEETRRAGVNVSGCIR--- 141
Query: 112 LGGQSTTQEYTYAVIANLK 130
L GQST+ TY IAN +
Sbjct: 142 LHGQSTS---TYLAIANRQ 157
>gnl|CDD|218901 pfam06110, DUF953, Eukaryotic protein of unknown function
(DUF953). This family consists of several hypothetical
eukaryotic proteins of unknown function.
Length = 119
Score = 28.6 bits (64), Expect = 0.59
Identities = 15/46 (32%), Positives = 19/46 (41%)
Query: 18 PSVKSKQNNIWLDLRLVGGAGVVAGASWSPECVVFEPGARHTYSEA 63
+VK +N L G+ G SW P+CV EP R A
Sbjct: 10 KAVKESENGSKPIFALFTGSKDTTGESWCPDCVRAEPVIREALKHA 55
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 28.4 bits (64), Expect = 0.95
Identities = 22/51 (43%), Positives = 25/51 (49%), Gaps = 22/51 (43%)
Query: 14 QLSAPSVKSKQNNIWLDLR----LVGGA---GVVAGASWSPECVVFEPGAR 57
QL+ P+ LR LVGG GVVAGAS+ E VF GAR
Sbjct: 21 QLTRPT-----------LRGRPVLVGGLGGRGVVAGASY--EARVF--GAR 56
>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase. Most species with a
member of this family belong to the high GC
Gram-positive bacteria, and these also have the IMP
dehydrogenase described by TIGRFAMs equivalog model
TIGR01302 [Unknown function, General].
Length = 369
Score = 27.9 bits (62), Expect = 1.7
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 13/75 (17%)
Query: 6 LDLKEDSKQLSAPSVKSKQNN--IWLDLRLVGGAGVVAGASWSPECVVFEPGARHTYSEA 63
L+LKE +L P + N+ L L G AGV+ G PG +T
Sbjct: 178 LNLKEFIGELDVPVIAGGVNDYTTALHLMRTGAAGVIVG-----------PGGANTTRLV 226
Query: 64 VGKNVANPTAMLLCS 78
+G V TA+ +
Sbjct: 227 LGIEVPMATAIADVA 241
>gnl|CDD|177640 PHA03412, PHA03412, putative methyltransferase; Provisional.
Length = 241
Score = 27.3 bits (60), Expect = 2.2
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 58 HTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVLKAGKVRTKDLGGQST 117
HTY + +GK + P A + + + + + + I N GK++T D G+ T
Sbjct: 86 HTYYK-LGKRIV-PEATWINADALTTEFD-TLFDMAISNP-----PFGKIKTSDFKGKYT 137
Query: 118 TQEYTYAVI 126
E+ Y VI
Sbjct: 138 GAEFEYKVI 146
>gnl|CDD|239250 cd02952, TRP14_like, Human TRX-related protein 14 (TRP14)-like
family; composed of proteins similar to TRP14, a 14kD
cytosolic protein that shows disulfide reductase
activity in vitro with a different substrate
specificity compared with another human cytosolic
protein, TRX1. TRP14 catalyzes the reduction of small
disulfide-containing peptides but does not reduce
disulfides of ribonucleotide reductase, peroxiredoxin
and methionine sulfoxide reductase, which are TRX1
substrates. TRP14 also plays a role in tumor necrosis
factor (TNF)-alpha signaling pathways, distinct from
that of TRX1. Its depletion promoted TNF-alpha induced
activation of c-Jun N-terminal kinase and
mitogen-activated protein kinases.
Length = 119
Score = 26.9 bits (60), Expect = 2.3
Identities = 11/28 (39%), Positives = 12/28 (42%)
Query: 42 GASWSPECVVFEPGARHTYSEAVGKNVA 69
G SW P+CV EP R A V
Sbjct: 36 GQSWCPDCVKAEPVVREALKAAPEDCVF 63
>gnl|CDD|152623 pfam12188, STAT2_C, Signal transducer and activator of
transcription 2 C terminal. This domain family is
found in eukaryotes, and is approximately 60 amino
acids in length. The family is found in association
with pfam02865, pfam00017, pfam01017, pfam02864. There
is a conserved DLP sequence motif. STATs are involved
in transcriptional regulation and are the only
regulators known to be modulated by tyrosine
phosphorylation. STAT2 forms a trimeric complex with
STAT1 and IRF-9 (Interferon Regulatory Factor 9), on
activation of the cell by interferon, which is called
ISGF3 (Interferon-stimulated gene factor 3). The C
terminal domain of STAT2 contains a nuclear export
signal (NES) which allows export of STAT2 into the
cytoplasm along with any complexed molecules.
Length = 56
Score = 25.6 bits (56), Expect = 2.4
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 4 SELDLKEDSKQLSAPSVKSKQNNIWLDLRLVGGAGVVAGASWSPECVVFEP 54
E DL D +QL+ ++ +NNI ++ + G ++AG + E V P
Sbjct: 5 PEPDLPHDLQQLNTEEMEIFRNNINIEEIMPNGDPLLAGQNTVDEAYVSCP 55
>gnl|CDD|238916 cd01941, YeiC_kinase_like, YeiC-like sugar kinase. Found in
eukaryotes and bacteria, YeiC-like kinase is part of the
ribokinase/pfkB sugar kinase superfamily. Its
oligomerization state is unknown at this time.
Length = 288
Score = 27.3 bits (61), Expect = 2.7
Identities = 30/90 (33%), Positives = 38/90 (42%), Gaps = 14/90 (15%)
Query: 40 VAGASWSPECVVFEPGARHTYSEAVGKNVANPTAMLLCSTKMLSHVNLQYYGDMIRNAVN 99
V G S +P V PG VG+N+A A L S +LS V G+ I
Sbjct: 21 VPGTS-NPGHVKQSPGG-------VGRNIAENLARLGVSVALLSAVGDDSEGESILEESE 72
Query: 100 RVLKAG-KVRTKDLGGQSTTQEYTYAVIAN 128
KAG VR G+ST YT A++
Sbjct: 73 ---KAGLNVRGIVFEGRSTAS-YT-AILDK 97
>gnl|CDD|234109 TIGR03105, gln_synth_III, glutamine synthetase, type III. This
family consists of the type III isozyme of glutamine
synthetase, originally described in Rhizobium meliloti,
where types I and II also occur.
Length = 435
Score = 27.3 bits (61), Expect = 2.8
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 15 LSAPSVKSKQNNIWLDLRLVGGAGVVAGASWSPECVVF 52
+ AP+V S + RL +GA+W+P + +
Sbjct: 282 VLAPTVNSYK-------RLNAP-RTTSGATWAPNFISY 311
>gnl|CDD|184989 PRK15029, PRK15029, arginine decarboxylase; Provisional.
Length = 755
Score = 26.7 bits (59), Expect = 3.8
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 51 VFEPGARHTYSEAVGKNVANPTAMLLCST 79
VF GA ++S VG + +N T M C T
Sbjct: 217 VF--GADRSWSVVVGTSGSNRTIMQACMT 243
>gnl|CDD|225500 COG2949, SanA, Uncharacterized membrane protein [Function unknown].
Length = 235
Score = 26.6 bits (59), Expect = 4.1
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 69 ANPTAMLLCSTKMLSHVNL-QYYGDMIRNAVNRVLKAGKVRTKDLGGQSTTQEY 121
A ++L ++K L+ +YY I A+ + KAGKV L G + T Y
Sbjct: 56 ARQVGVVLGTSKYLAKGPPNRYYTYRIDAAIA-LYKAGKVNYLLLSGDNATVSY 108
>gnl|CDD|216018 pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B. This family
of proteins contains a transmembrane region.
Length = 711
Score = 26.0 bits (58), Expect = 6.4
Identities = 8/34 (23%), Positives = 17/34 (50%)
Query: 69 ANPTAMLLCSTKMLSHVNLQYYGDMIRNAVNRVL 102
+ ++ +T + LQ+ D +R +NR+L
Sbjct: 378 SATGGNVIETTSSIEFAQLQFAYDHLRAHINRML 411
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 25.5 bits (56), Expect = 7.1
Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 17/105 (16%)
Query: 32 RLVGGAGVVAGASWSPECVVFEPGARHTYSEAVGK------NVANPTAMLLCSTKMLSHV 85
RL GG G + A + G + N + ML K+L
Sbjct: 6 RLFGGGGPRQASGQPGMMRGAATQAAGA-AGGGGSFFANLASPMNLSGMLNNVQKVLGVA 64
Query: 86 N-----LQYYGDMIRNA-----VNRVLKAGKVRTKDLGGQSTTQE 120
+Q YG ++RN + R L + ++ +ST +
Sbjct: 65 QQVGPMVQQYGPLVRNLPAMWKIFRELSSSDDEEEETEEESTDET 109
>gnl|CDD|217190 pfam02698, DUF218, DUF218 domain. This large family of proteins
contains several highly conserved charged amino acids,
suggesting this may be an enzymatic domain (Bateman A
pers. obs). The family includes SanA, which is involved
in Vancomycin resistance. This protein may be involved
in murein synthesis.
Length = 148
Score = 25.3 bits (56), Expect = 7.9
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 46 SPECVVFEPGARHTYSEAV 64
E ++ EP +R+TY A
Sbjct: 62 PAEAILLEPQSRNTYENAR 80
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein
TraB; Provisional.
Length = 475
Score = 25.9 bits (57), Expect = 8.7
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 20 VKSKQNNIWLDLRLVGGAGVVAGASW 45
VK KQ +WL + +VG A + GA +
Sbjct: 8 VKRKQY-LWLGIVVVGAAAAIGGALY 32
>gnl|CDD|222442 pfam13899, Thioredoxin_7, Thioredoxin-like. Thioredoxins are
small enzymes that participate in redox reactions, via
the reversible oxidation of an active centre disulfide
bond.
Length = 81
Score = 24.6 bits (54), Expect = 9.6
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 39 VVAGASWSPECVVFE 53
V GA W P C +
Sbjct: 22 VDFGADWCPTCQALD 36
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
0.315 0.130 0.376
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,253,971
Number of extensions: 517428
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 44
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)