RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025866
(247 letters)
>gnl|CDD|216250 pfam01026, TatD_DNase, TatD related DNase. This family of proteins
are related to a large superfamily of metalloenzymes.
TatD, a member of this family has been shown
experimentally to be a DNase enzyme.
Length = 255
Score = 157 bits (399), Expect = 2e-47
Identities = 73/237 (30%), Positives = 99/237 (41%), Gaps = 55/237 (23%)
Query: 10 FVQERTPNWFSTLKEF--FEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKEL 67
E + L++ E A+GEIGLD E Q VFR+QLELAKEL
Sbjct: 65 EADEASEEVLEALEKLLLAEHPKVVAIGEIGLDYYYV-DESPKEAQEEVFRRQLELAKEL 123
Query: 68 KRPASIHCVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSM 127
P IH A DLLEI+K G V++H + GS E E+ LG Y S SG +
Sbjct: 124 DLPVVIHTRDAEEDLLEILKEAGAPGLRVVLHCFTGSLETAKEILDLGFYISISGIVTFK 183
Query: 128 KAQK-------VPSERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGS 180
A+K +P +R+L+ETDAP P P G
Sbjct: 184 NAKKLREVVAEIPLDRLLVETDAPYLAPV--------------------------PYRGK 217
Query: 181 ASDNQFHASKDSSTLPKETLNHPANIHNVLDYVASLLDMTKEELAELSYRNAIRLFS 237
N PA + V + +A L +++EE+A+++ NA RLF
Sbjct: 218 R-------------------NEPAYVPYVAEKLAELKGISEEEVAKITTENAKRLFG 255
>gnl|CDD|238635 cd01310, TatD_DNAse, TatD like proteins; E.coli TatD is a
cytoplasmic protein, shown to have magnesium dependent
DNase activity.
Length = 251
Score = 154 bits (391), Expect = 3e-46
Identities = 74/235 (31%), Positives = 96/235 (40%), Gaps = 55/235 (23%)
Query: 10 FVQERTPNWFSTLKEFFEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKR 69
E L+ A+GEIGLD + Q VFR QLELAKEL
Sbjct: 65 DADEHVDEDLDLLELLAANPKVVAIGEIGLDYYRDKSPREV--QKEVFRAQLELAKELNL 122
Query: 70 PASIHCVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMKA 129
P IH A D+LEI+K GP P + H + GSAE EL LG Y S SG + A
Sbjct: 123 PVVIHSRDAHEDVLEILKEYGP-PKRGVFHCFSGSAEEAKELLDLGFYISISGIVTFKNA 181
Query: 130 -------QKVPSERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSAS 182
+++P ER+LLETD+P P P G
Sbjct: 182 NELREVVKEIPLERLLLETDSPYLAPV--------------------------PFRGKR- 214
Query: 183 DNQFHASKDSSTLPKETLNHPANIHNVLDYVASLLDMTKEELAELSYRNAIRLFS 237
N PA + +V + +A L ++ EE+AE++ NA RLF
Sbjct: 215 ------------------NEPAYVKHVAEKIAELKGISVEEVAEVTTENAKRLFG 251
>gnl|CDD|223162 COG0084, TatD, Mg-dependent DNase [DNA replication, recombination,
and repair].
Length = 256
Score = 139 bits (352), Expect = 2e-40
Identities = 77/236 (32%), Positives = 101/236 (42%), Gaps = 55/236 (23%)
Query: 10 FVQERTPNWFSTLKEFFEITP-AAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELK 68
E + L++ E P A+GEIGLD +E D Q VF QLELAKEL
Sbjct: 67 DADEHSEEDLEELEQLAEHHPKVVAIGEIGLDY-YWDKEPDKERQEEVFEAQLELAKELN 125
Query: 69 RPASIHCVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMK 128
P IH A D LEI+K G P G ++H + GSAE +L LG Y S SG +
Sbjct: 126 LPVIIHTRDAHEDTLEILKEEGA-PVGGVLHCFSGSAEEARKLLDLGFYISISGIVTFKN 184
Query: 129 AQK-------VPSERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSA 181
A+K +P +R+LLETDAP P P G
Sbjct: 185 AEKLREVARELPLDRLLLETDAPYLAPV--------------------------PYRGKR 218
Query: 182 SDNQFHASKDSSTLPKETLNHPANIHNVLDYVASLLDMTKEELAELSYRNAIRLFS 237
N PA + +V + +A L ++ EE+AE++ NA RLF
Sbjct: 219 -------------------NEPAYVRHVAEKLAELKGISAEEVAEITTENAKRLFG 255
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST, starting
with a urease alpha subunit, finds a large superfamily
of proteins, including a number of different enzymes
that act as hydrolases at C-N bonds other than peptide
bonds (EC 3.5.-.-), many uncharacterized proteins, and
the members of this family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity [Unknown function, Enzymes of unknown
specificity].
Length = 252
Score = 116 bits (294), Expect = 6e-32
Identities = 66/234 (28%), Positives = 96/234 (41%), Gaps = 55/234 (23%)
Query: 11 VQERTPNWFSTLKEFFEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKRP 70
V + T L+ A+GE GLD Q VFR QL+LA+EL P
Sbjct: 66 VDDDTKEDIKELERLAAHPKVVAIGETGLDYYKADEYKRR--QEEVFRAQLQLAEELNLP 123
Query: 71 ASIHCVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQ 130
IH A D+L+I++ P G ++H + G AE+ +L LG Y S SG + A+
Sbjct: 124 VIIHARDAEEDVLDILREEKP-KVGGVLHCFTGDAELAKKLLDLGFYISISGIVTFKNAK 182
Query: 131 -------KVPSERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSASD 183
K+P ER+L+ETD+P +L P K
Sbjct: 183 SLREVVRKIPLERLLVETDSP-----------YLA------PVPYRGKR----------- 214
Query: 184 NQFHASKDSSTLPKETLNHPANIHNVLDYVASLLDMTKEELAELSYRNAIRLFS 237
N PA + ++ +A + M EELA+++ +NA RLF
Sbjct: 215 -----------------NEPAFVRYTVEAIAEIKGMDVEELAQITTKNAKRLFG 251
>gnl|CDD|236767 PRK10812, PRK10812, putative DNAse; Provisional.
Length = 265
Score = 63.2 bits (154), Expect = 6e-12
Identities = 60/240 (25%), Positives = 98/240 (40%), Gaps = 62/240 (25%)
Query: 19 FSTLKEFFEITPAAAVGEIGLD----KGSKGREIDFMDQVGVFRQQLELAKELKRPASIH 74
L+ A+GE GLD +K R Q FR +++ +EL +P +H
Sbjct: 77 VEELRRLAAEEGVVAMGETGLDYYYTPETKVR------QQESFRHHIQIGRELNKPVIVH 130
Query: 75 CVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQK--- 131
A D L I++ G ++H + E +L LG Y SFSG + A++
Sbjct: 131 TRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRD 190
Query: 132 ----VPSERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSASDNQFH 187
VP +R+L+ETD+P P +P H
Sbjct: 191 AARYVPLDRLLVETDSPYLAP---------------VP---------------------H 214
Query: 188 ASKDSSTLPKETLNHPANIHNVLDYVASLLDMTKEELAELSYRNAIRLFSYEGSKILTEK 247
K+ N PA + +V +Y+A L ++ EELA+++ N RLF + S++ + +
Sbjct: 215 RGKE---------NQPAMVRDVAEYMAVLKGVSVEELAQVTTDNFARLFHIDASRLQSIR 265
>gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional.
Length = 258
Score = 55.4 bits (134), Expect = 3e-09
Identities = 44/134 (32%), Positives = 63/134 (47%), Gaps = 28/134 (20%)
Query: 33 AVGEIGLD---KGSKGREIDFMDQVGVFRQQLELAKELKRPASIHCVRA---FGDLLEIM 86
A+GE GLD S E Q F QL +A EL P +HC A F LLE
Sbjct: 88 AIGECGLDFNRNFSTPEE-----QERAFVAQLAIAAELNMPVFMHCRDAHERFMALLE-- 140
Query: 87 KSVGPFPD---GVIIHSYLGSAEMVPELSKLGAYFSFSGFL------MSMKA--QKVPSE 135
P+ D G ++H + G+ E + G Y +G++ + ++ +P+E
Sbjct: 141 ----PWLDKLPGAVLHCFTGTREEMQACLARGLYIGITGWVCDERRGLELRELLPLIPAE 196
Query: 136 RILLETDAPDALPK 149
R+LLETDAP LP+
Sbjct: 197 RLLLETDAPYLLPR 210
>gnl|CDD|224024 COG1099, COG1099, Predicted metal-dependent hydrolases with the
TIM-barrel fold [General function prediction only].
Length = 254
Score = 52.4 bits (126), Expect = 3e-08
Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 29/150 (19%)
Query: 22 LKEFFEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKRPASIHCVR---- 77
L+E A+GEIGL++ + ++ VFR+QLELA+EL P +H R
Sbjct: 88 LEELLSNEDVVAIGEIGLEEATD-------EEKEVFREQLELARELDVPVIVHTPRRNKK 140
Query: 78 -AFGDLLEIMKSVGPFPDGVII-HSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQKV--- 132
A +L+I+ G P V+I H + E V E+ Y + + ++
Sbjct: 141 EATSKILDILIESGLKPSLVVIDHV---NEETVDEVLDEEFYVGLTVQPGKLTVEEAVEI 197
Query: 133 ----PSERILLETDA------PDALPKAEL 152
+ERI+L +DA P A+P+ L
Sbjct: 198 VREYGAERIILNSDAGSAASDPLAVPRTAL 227
>gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional.
Length = 258
Score = 49.2 bits (117), Expect = 5e-07
Identities = 55/211 (26%), Positives = 75/211 (35%), Gaps = 55/211 (26%)
Query: 33 AVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKRPASIHCVRAFGDLLEIMKSVGPF 92
AVGEIGLD G + F Q + +QL+LAK P +H R L +K
Sbjct: 94 AVGEIGLDL--FGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKR-HDL 150
Query: 93 PDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQK-------VPSERILLETDAPD 145
P ++H + GS + +LG G + +A K +P +LLETDAPD
Sbjct: 151 PRTGVVHGFSGSLQQAERFVQLGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPD 210
Query: 146 ALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSASDNQFHASKDSSTLPKETLNHPAN 205
+P LN G P N P
Sbjct: 211 -MP---LNGF---QGQP--------------------------------------NRPEQ 225
Query: 206 IHNVLDYVASLLDMTKEELAELSYRNAIRLF 236
V D + L +E+AE+ N LF
Sbjct: 226 AARVFDVLCELRPEPADEIAEVLLNNTYTLF 256
>gnl|CDD|238617 cd01292, metallo-dependent_hydrolases, Superfamily of
metallo-dependent hydrolases (also called amidohydrolase
superfamily) is a large group of proteins that show
conservation in their 3-dimensional fold (TIM barrel)
and in details of their active site. The vast majority
of the members have a conserved metal binding site,
involving four histidines and one aspartic acid residue.
In the common reaction mechanism, the metal ion (or
ions) deprotonate a water molecule for a nucleophilic
attack on the substrate. The family includes urease
alpha, adenosine deaminase, phosphotriesterase
dihydroorotases, allantoinases, hydantoinases, AMP-,
adenine and cytosine deaminases, imidazolonepropionase,
aryldialkylphosphatase, chlorohydrolases,
formylmethanofuran dehydrogenases and others.
Length = 275
Score = 33.1 bits (75), Expect = 0.089
Identities = 21/107 (19%), Positives = 35/107 (32%), Gaps = 6/107 (5%)
Query: 47 EIDFMDQVGVFRQQLELAKELKRPASIHC---VRAFGDLLEIMKSVGPFPDGVIIHSYLG 103
R+ LE A++L P IH L +++ + VI H
Sbjct: 125 YTATGLSDESLRRVLEEARKLGLPVVIHAGELPDPTRALEDLVALLRLGGRVVIGHVSHL 184
Query: 104 SAEMVPELSKLGAYFSFSG---FLMSMKAQKVPSERILLETDAPDAL 147
E++ L + G +L+ + + R LLE L
Sbjct: 185 DPELLELLKEAGVSLEVCPLSNYLLGRDGEGAEALRRLLELGIRVTL 231
>gnl|CDD|179417 PRK02382, PRK02382, dihydroorotase; Provisional.
Length = 443
Score = 32.7 bits (75), Expect = 0.15
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 15 TPNWFSTLKEFFEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKRPASIH 74
T NW L+ +E A+GEI + + G ID F + L A L A++H
Sbjct: 127 TGNW-DPLESLWER-GVFALGEIFMADSTGGMGIDEEL----FEEALAEAARLGVLATVH 180
>gnl|CDD|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin
upstream promoter transcription factors, a member of the
nuclear receptor family. The ligand binding domain of
chicken ovalbumin upstream promoter transcription
factors (COUP-TFs): COUP-TFs are orphan members of the
steroid/thyroid hormone receptor superfamily. They are
expressed in many tissues and are involved in the
regulation of several important biological processes,
such as neurogenesis, organogenesis, cell fate
determination, and metabolic homeostasis. In mammals two
isoforms named COUP-TFI and COUP-TFII have been
identified. Both genes show an exceptional homology and
overlapping expression patterns, suggesting that they
may serve redundant functions. Although COUP-TF was
originally characterized as a transcriptional activator
of the chicken ovalbumin gene, COUP-TFs are generally
considered to be repressors of transcription for other
nuclear hormone receptors, such as retinoic acid
receptor (RAR), thyroid hormone receptor (TR), vitamin D
receptor (VDR), peroxisome proliferator activated
receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4).
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
COUP-TFs have a central well cons erved DNA binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD).
Length = 236
Score = 32.0 bits (73), Expect = 0.23
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 26 FEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELK-RPASIHCVRA 78
+ P A + S R + FMD + +F++Q+E K L A C++A
Sbjct: 87 LHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKA 140
>gnl|CDD|130381 TIGR01314, gntK_FGGY, gluconate kinase, FGGY type. Gluconate is
derived from glucose in two steps. This model describes
one form of gluconate kinase, belonging to the FGGY
family of carbohydrate kinases. Gluconate kinase
phosphoryates gluconate for entry into the
Entner-Douderoff pathway [Energy metabolism, Sugars].
Length = 505
Score = 29.9 bits (67), Expect = 1.4
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 76 VRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMK 128
+ + L EI V P DG++ H YL E P L A SF G S K
Sbjct: 321 IDPYDVLTEIAARVSPGADGLLFHPYLA-GERAP-LWNANARGSFFGLTYSHK 371
>gnl|CDD|193466 pfam12993, DUF3877, Domain of unknown function, E. rectale Gene
description (DUF3877). Based on Eubacterium rectale
gene EUBREC_0237. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 175
Score = 27.6 bits (62), Expect = 4.6
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 215 SLLDMTKEELAELSYR-NAIRLF 236
+L+D+ KEE A+L YR IRL+
Sbjct: 7 NLIDVIKEEQAKLGYRKETIRLY 29
>gnl|CDD|168162 PRK05665, PRK05665, amidotransferase; Provisional.
Length = 240
Score = 27.9 bits (62), Expect = 4.9
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 202 HPANIHNVLDYVASLLDMTKEELAELSYRNAI 233
HP +H DY +LLD+ +E L E Y +
Sbjct: 185 HPEFVH---DYSRALLDLRQEHLGEEVYSKGV 213
>gnl|CDD|239454 cd03338, TCP1_delta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, delta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 515
Score = 27.6 bits (62), Expect = 7.7
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 53 QVGVFRQQLELAKELKRPASIHCVRAFGDLLEI 85
++ + Q E A+ L +CVRAF D LE+
Sbjct: 406 EIEIALQLSEWARTLTG-VEQYCVRAFADALEV 437
>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
kD subunit (chain G) [Energy production and conversion].
Length = 693
Score = 27.3 bits (61), Expect = 8.3
Identities = 28/177 (15%), Positives = 57/177 (32%), Gaps = 31/177 (17%)
Query: 15 TPNW-FSTLKEFFEITPAAAVGEIGLDKGSKGREIDFMDQVGVFRQQLELAKELKRPASI 73
W ++ L A + E+ L + + ++ + + + LA K+ A +
Sbjct: 403 VAEWLYALLLSILLGAGIALLDELALGAEAATAAVKKAERELIEKGKGALAGA-KKAAIL 461
Query: 74 HCVRAFGDLLEIMKSVGPFPDGVIIHSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQKVP 133
D L ++ GV++H A + + +P
Sbjct: 462 ALAEKLADELGAAEARWN---GVVLHE---------------AASRVNA----LGLGFLP 499
Query: 134 SERILLETDAPDALPKAELNSLFLVDGDPSLPQELSAKEEHSPNVGSASDNQFHASK 190
DA L A+ N+L L+ D E +EH+ V + + ++
Sbjct: 500 GLSGE---DAALMLGPADANALLLLGIDE----EADEADEHAKFVVYSDHHGDAGAE 549
>gnl|CDD|215261 PLN02470, PLN02470, acetolactate synthase.
Length = 585
Score = 27.4 bits (61), Expect = 8.4
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 99 HSYLGSAEMVPELSKLGAYFSFSGFLMSMKAQKVPSERILLETDAPDALPK 149
H+YLG + E+ F FL + K+P+ R+ ++D +A+ K
Sbjct: 500 HTYLGDPDAEAEI--------FPDFLKFAEGCKIPAARVTRKSDLREAIQK 542
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 27.5 bits (61), Expect = 9.3
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 7/46 (15%)
Query: 196 PKETLNHP--ANIHN---VLDYVASLLDMTKEELAELSYRNAIRLF 236
PK L HP N+ + +LDY++S L+ EEL E+S N +R
Sbjct: 898 PKNDLGHPLCNNLRDGHWMLDYISSRLNSYSEELGEVS--NWLRAR 941
>gnl|CDD|233719 TIGR02090, LEU1_arch, isopropylmalate/citramalate/homocitrate
synthases. Methanogenic archaea contain three closely
related homologs of the 2-isopropylmalate synthases
(LeuA) represented by TIGR00973. Two of these in
Methanococcus janaschii (MJ1392 - CimA ; MJ0503 - AksA )
have been characterized as catalyzing alternative
reactions leaving the third (MJ1195) as the presumptive
LeuA enzyme. CimA is citramalate (2-methylmalate)
synthase which condenses acetyl-CoA with pyruvate. This
enzyme is believed to be involved in the biosynthesis of
isoleucine in methanogens and possibly other species
lacking threonine dehydratase. AksA is a homocitrate
synthase which also produces (homo)2-citrate and
(homo)3-citrate in the biosynthesis of Coenzyme B which
is restricted solely to methanogenic archaea.
Methanogens, then should and aparrently do contain all
three of these enzymes. Unfortunately, phylogenetic
trees do not resolve into three unambiguous clades,
making assignment of function to particular genes
problematic. Other archaea which lack a threonine
dehydratase (mainly Euryarchaeota) should contain both a
CimA and a LeuA gene. This is true of, for example,
archaeoglobus fulgidis, but not for the Pyrococci which
have none in this clade, but one in TIGR00973 and one in
TIGRT00977 which may fulfill these roles. Other species
which have only one hit to this model and lack threonine
dehydratase are very likely LeuA enzymes.
Length = 363
Score = 27.1 bits (60), Expect = 9.8
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 48 IDFMDQVGVFRQQL------ELAKELKRPASIHCVRAFG 80
I+ D VGV Q +L + +K P S+HC FG
Sbjct: 158 INIADTVGVLTPQKMEELIKKLKENVKLPISVHCHNDFG 196
>gnl|CDD|181507 PRK08626, PRK08626, fumarate reductase flavoprotein subunit;
Provisional.
Length = 657
Score = 27.2 bits (61), Expect = 9.9
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 9/40 (22%)
Query: 51 MDQVGVFRQQLELAKELKRPASIHCVRAFGDLLEIMKSVG 90
M++VG+FR EL K V+ +LLE K++G
Sbjct: 476 MEKVGIFRNGPELEK---------AVKELQELLERSKNIG 506
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
0.317 0.134 0.387
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,715,942
Number of extensions: 1208212
Number of successful extensions: 1082
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1065
Number of HSP's successfully gapped: 37
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
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 (21.7 bits)
S2: 58 (26.1 bits)