RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4398
(306 letters)
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 216 bits (552), Expect = 7e-70
Identities = 85/214 (39%), Positives = 116/214 (54%), Gaps = 18/214 (8%)
Query: 32 KIILAPMVRMNTLPFRLLALDYGADLVYSEELVDHKLVKTERKVNDLLNTIDFVDPLDGS 91
K+ILAPMV + LPFRLL YGADLVY+E + L++ RK LL
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLL------------ 48
Query: 92 VVFRTCPREKNKIILQIGTADPERALEAAKKV-EHDVAAIDINMGCPKQFSLTGGMGAAL 150
T E+ +I+Q+G +DPE EAAK V E ID+NMGCP GG GAAL
Sbjct: 49 ----TRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAAL 104
Query: 151 LSTPDIACNILTTLISNLSIPVSCKIRV-FHNEADTIALCKRLEACGIIAIGVHGRTKAE 209
L P++ I+ + + IPV+ KIR+ + +E +T+ L K LE G A+ VHGRT+ +
Sbjct: 105 LKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQ 164
Query: 210 RPRHRNRIEMIRTLTQHLKIPVIANGGSKEIVDY 243
R + I + + + IPVIANG + D
Sbjct: 165 RYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDA 198
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 162 bits (413), Expect = 3e-48
Identities = 71/209 (33%), Positives = 107/209 (51%), Gaps = 20/209 (9%)
Query: 34 ILAPMVRMNTLPFRLLALDYGA-DLVYSEELVDHKLVKTERKVNDLLNTIDFVDPLDGSV 92
+LAPM + LPFR L +YGA DLV +E + ++ E++ +L
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELML------------- 47
Query: 93 VFRTCPREKNKIILQIGTADPERALEAAKKV-EHDVAAIDINMGCPKQFSLTGGMGAALL 151
E + +Q+G +DP EAAK V + IDINMGCP + GG GAALL
Sbjct: 48 ---PELEEPTPLAVQLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALL 104
Query: 152 STPDIACNILTTLISNLSIPVSCKIRVF--HNEADTIALCKRLEACGIIAIGVHGRTKAE 209
PD+ I+ ++ + IPV+ KIR+ + + + + +R+E G A+ VHGRT+A+
Sbjct: 105 RDPDLVAQIVKAVVKAVDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTRAQ 164
Query: 210 RPRHRNRIEMIRTLTQHLKIPVIANGGSK 238
+ I+ + Q + IPVIANG
Sbjct: 165 NYEGPADWDAIKQVKQAVSIPVIANGDIT 193
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 155 bits (395), Expect = 2e-45
Identities = 80/242 (33%), Positives = 124/242 (51%), Gaps = 28/242 (11%)
Query: 23 NQANINYSNKIILAPMVRMNTLPFRLLALDYGA-DLVYSEELVDHKLVKTERKVNDLLNT 81
I N++ILAPM + LPFR LA + GA DL+Y+E + L+ +K LL+
Sbjct: 3 KIGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDE 62
Query: 82 IDFVDPLDGSVVFRTCPREKNKIILQIGTADPERALEAAKKV-EHDVAAIDINMGCPKQF 140
++ E+ + +Q+G +DPE EAAK E ID+N GCP
Sbjct: 63 LE----------------EERPVAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPK 106
Query: 141 SLTGGMGAALLSTPDIACNILTTLISNL-SIPVSCKIRVFHNEADTIA--LCKRLEACGI 197
+ GG GAALL P++ I+ ++ + IPV+ KIR+ ++ D +A + + LE G
Sbjct: 107 VVKGGAGAALLKNPELLAEIVKAMVEAVGDIPVTVKIRLGWDDDDILALEIARILEDAGA 166
Query: 198 IAIGVHGRTKAERPRHRNRIEMIRTLTQHLK-IPVIANGG------SKEIVDYGGVFSLN 250
A+ VHGRT+A+ + I+ L + + IPVIANG +KE+++Y G +
Sbjct: 167 DALTVHGRTRAQGYLGPADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVM 226
Query: 251 CA 252
Sbjct: 227 IG 228
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 132 bits (334), Expect = 2e-36
Identities = 72/218 (33%), Positives = 106/218 (48%), Gaps = 29/218 (13%)
Query: 26 NINYSNKIILAPMVRMNTLPFRLLALDYGADLVYSEELVDHKLVKTERKVNDLLNT---I 82
NI ++++LAPM + PFR L +YGA L E +V +E V D T +
Sbjct: 3 NIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCE------MVSSEAIVYDSQRTMRLL 56
Query: 83 DFVDPLDGSVVFRTCPREKNKIILQIGTADPERALEAAKKVEHDVAA-IDINMGCPKQFS 141
D + ++ I +Q+ +DP+ EAAK E A IDINMGCP
Sbjct: 57 DIAE-------------DETPISVQLFGSDPDTMAEAAKINEELGADIIDINMGCPVPKI 103
Query: 142 LTGGMGAALLSTPDIACNILTTLISNLSIPVSCKIRV----FHNEADTIALCKRLEACGI 197
G G+ALL PD+ I+ ++ + IPV+ KIR+ H A A + E G
Sbjct: 104 TKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAA--RIAEDAGA 161
Query: 198 IAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANG 235
A+ +HGRT+A+ ++I + Q ++IPVI NG
Sbjct: 162 QAVTLHGRTRAQGYSGEANWDIIARVKQAVRIPVIGNG 199
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 103 bits (259), Expect = 9e-26
Identities = 73/229 (31%), Positives = 111/229 (48%), Gaps = 25/229 (10%)
Query: 30 SNKIILAPMVRMNTLPFRLLALDYGADLVYSEELVDHKLVKTERKVNDLLNTIDFVDPLD 89
N++I APM + PFR L + GA L SE + + V K L + +P
Sbjct: 9 RNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSR--LRMVHIDEPGI 66
Query: 90 GSVVFRTCPREKNKIILQIGTADPERALEAAK-KVEHDVAAIDINMGCPKQFSLTGGMGA 148
+V QI +DP+ +AA+ VE IDINMGCP + G+
Sbjct: 67 RTV--------------QIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGS 112
Query: 149 ALLSTPDIACNILTTLISNLSIPVSCKIRV--FHNEADTIALCKRLEACGIIAIGVHGRT 206
ALL PD+ +ILT +++ + +PV+ KIR + + + + E CGI A+ +HGRT
Sbjct: 113 ALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRT 172
Query: 207 KAERPRHRNRIEMIRTLTQHLKIPVIANGG------SKEIVDYGGVFSL 249
+A + IR + Q + IPVIANG ++ ++DY G +L
Sbjct: 173 RACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADAL 221
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 61.4 bits (149), Expect = 8e-11
Identities = 68/231 (29%), Positives = 104/231 (45%), Gaps = 45/231 (19%)
Query: 32 KIILAPMVR-MNTLPFRLLALDYGADLVYSEELVDHKLVKTE--RKVNDLLNTIDFVDPL 88
+++LAPM +++L LL E+ D+ L TE R V+ LL F
Sbjct: 2 RVLLAPMEGVLDSLVRELLT-----------EVNDYDLCITEFLRVVDQLLPVKVF---- 46
Query: 89 DGSVVFRTCPREKNK--------IILQIGTADPERALE-AAKKVEHDVAAIDINMGCPKQ 139
R CP N + +Q+ P+ E AA+ VE +D+N GCP +
Sbjct: 47 -----HRLCPELHNASRTPSGTLVRIQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSK 101
Query: 140 FSLTGGMGAALLSTPDI----ACNILTTLISNLSIPVSCKIRV-FHNEADTIALCKRLEA 194
G GA LL P++ A + + ++L PV+ K+R+ + + + ++
Sbjct: 102 TVNGSGGGATLLKDPELIYQGAKAMREAVPAHL--PVTVKVRLGWDSGERKFEIADAVQQ 159
Query: 195 CGIIAIGVHGRTKAE--RPRHRNRIEMIRTLTQHLKIPVIANGGSKEIVDY 243
G + VHGRTK + R H N + I + Q L IPVIANG EI D+
Sbjct: 160 AGATELVVHGRTKEDGYRAEHIN-WQAIGEIRQRLTIPVIANG---EIWDW 206
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 59.5 bits (144), Expect = 4e-10
Identities = 38/150 (25%), Positives = 67/150 (44%), Gaps = 20/150 (13%)
Query: 31 NKIILAPMVRMNTLPFR-LLALDYGADLVYSEELVDHKLVKTERKVNDLLNTIDFVDPLD 89
+ +APM+ FR L L L+Y+E + ++ ++K D+L P
Sbjct: 1 GRFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKK--DILK----FSP-- 52
Query: 90 GSVVFRTCPREKNKIILQIGTADPERALEAAKKVEH-DVAAIDINMGCPKQFSLTGGMGA 148
E++ + LQ+G +DP + AK E I++N+GCP G GA
Sbjct: 53 ----------EESPVALQLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGA 102
Query: 149 ALLSTPDIACNILTTLISNLSIPVSCKIRV 178
L+ D+ + + + ++IPV+ K R+
Sbjct: 103 CLMGNADLVADCVKAMQEAVNIPVTVKHRI 132
>gnl|CDD|239204 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding
domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue.
Length = 289
Score = 42.7 bits (101), Expect = 1e-04
Identities = 33/156 (21%), Positives = 59/156 (37%), Gaps = 28/156 (17%)
Query: 104 IILQIGTADPERALEAAKKVEH-DVAAIDINMGCPKQFSLTGGMGAALLSTPDIACNILT 162
+I +G + E +E A+K+E A+++N+ CP GG G L P+ N+L
Sbjct: 101 LIASVGGSSKEDYVELARKIERAGAKALELNLSCPN----VGG-GRQLGQDPEAVANLLK 155
Query: 163 TLISNLSIPVSCKIRVFHNEADTIALCKRLEACGIIAIGVHGRTKAERPRHRNR------ 216
+ + + IP+ K+ + + D + L K E G + +
Sbjct: 156 AVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVDLKTVGPGPKR 215
Query: 217 --------------IEMIRTLTQHLK--IPVIANGG 236
+ + L L+ IP+I GG
Sbjct: 216 GTGGLSGAPIRPLALRWVARLAARLQLDIPIIGVGG 251
>gnl|CDD|239237 cd02911, arch_FMN, Archeal FMN-binding domain. This family of
archaeal proteins are part of the NAD(P)H-dependent
flavin oxidoreductase (oxidored) FMN-binding family that
reduce a range of alternative electron acceptors. Most
use FAD/FMN as a cofactor and NAD(P)H as electron donor.
Some contain 4Fe-4S cluster to transfer electron from
FAD to FMN. The specific function of this group is
unknown.
Length = 233
Score = 42.3 bits (100), Expect = 1e-04
Identities = 39/140 (27%), Positives = 59/140 (42%), Gaps = 14/140 (10%)
Query: 111 ADPERALEAAKKVEHDVAAIDINMGCPKQFSLTGGMGAALLSTPDIACNILTTLISNLSI 170
+ E L AA V + A ++IN C + + G G ALL P+ + + +
Sbjct: 82 SSLEPLLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKA-LKETGV 140
Query: 171 PVSCKIRVFHNEADTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIP 230
PVS KIR + D L + +E G I V A P + ++ IR ++ L I
Sbjct: 141 PVSVKIRAGV-DVDDEELARLIEKAGADIIHV----DAMDPGNHADLKKIRDISTELFI- 194
Query: 231 VIANGG------SKEIVDYG 244
I N +KE+ YG
Sbjct: 195 -IGNNSVTTIESAKEMFSYG 213
>gnl|CDD|239201 cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN
binding domain. OYE was the first flavin-dependent
enzyme identified, however its true physiological role
remains elusive to this day. Each monomer of OYE
contains FMN as a non-covalently bound cofactor, uses
NADPH as a reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 327
Score = 42.2 bits (100), Expect = 2e-04
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 14/81 (17%)
Query: 170 IPVSCKIRVFH------NEADTIALCKRLEACGIIAIGVHGRTKAERPRHRNR------- 216
PV ++ + I + K LE G+ A+ V G + P
Sbjct: 209 FPVGVRLSADDFVPGGLTLEEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEGY 268
Query: 217 -IEMIRTLTQHLKIPVIANGG 236
+E+ + + +KIPVIA GG
Sbjct: 269 FLELAEKIKKAVKIPVIAVGG 289
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 40.9 bits (97), Expect = 5e-04
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 11/80 (13%)
Query: 104 IILQIGTADPERALEAAKKVE---HDVAAIDINMGCPK---QFSLTGGMGAALLSTPDIA 157
+ LQ+G +DP EAAK E +D I++N+GCP Q G GA L++ P++
Sbjct: 67 VALQLGGSDPADLAEAAKLAEDWGYD--EINLNVGCPSDRVQ---NGRFGACLMAEPELV 121
Query: 158 CNILTTLISNLSIPVSCKIR 177
+ + + +SIPV+ K R
Sbjct: 122 ADCVKAMKDAVSIPVTVKHR 141
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 38.5 bits (90), Expect = 0.003
Identities = 45/194 (23%), Positives = 72/194 (37%), Gaps = 36/194 (18%)
Query: 73 RKVNDLLNTIDFVDPLDGSVVFRTCPREKNK-----IILQIGTADPERALEAAKKVEHDV 127
R +LN + +P +V+ R K IIL + E +E A+K+
Sbjct: 60 RLPEGVLNAMGLNNPGLDAVLEELLKRRKEYPRPLGIILSKAGSTVEDYVEVARKIGPFA 119
Query: 128 AAIDINMGCPKQFSLTGGMGAALLSTPDIACNILTTLISNLSIPVSCKI--RVFHNEADT 185
+++N+ CP T G AL + P++A +L + +PV K+ +
Sbjct: 120 DYLELNVSCPN----TPG-LRALQTDPELAAILLKVVKEVSKVPVLVKLAPDLTDIVIID 174
Query: 186 IALCKRLEACGIIAIGVHGRT--------KAERPRHRNR-------------IEMIRTLT 224
IA G+ I T K E P N +++IR L
Sbjct: 175 IAD-VAAGEDGLTGINATNTTVRGMRIDLKTESPILANGTGGLSGPAIKPIALKVIRELY 233
Query: 225 QHLK--IPVIANGG 236
Q + IP+I GG
Sbjct: 234 QRVGPEIPIIGVGG 247
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 38.2 bits (89), Expect = 0.003
Identities = 35/156 (22%), Positives = 64/156 (41%), Gaps = 29/156 (18%)
Query: 104 IILQIGTADPERALEAAKKVEHD---VAAIDINMGCPKQFSLTGGMGAALLSTPDIACNI 160
+I + + E E A+K+E V A ++N+ CP G G A+ P+++ ++
Sbjct: 93 LIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPH----VKGGGIAIGQDPELSADV 148
Query: 161 LTTLISNLSIPVSCKIRVFHNEADTIALCKRLE---ACGIIAI----GVHGRTKAERPRH 213
+ + +PV K+ N D + K E A G+ I G+ K +P
Sbjct: 149 VKAVKDKTDVPVFAKLS--PNVTDITEIAKAAEEAGADGLTLINTLRGMKIDIKTGKPIL 206
Query: 214 RNR-------------IEMIRTLTQHLKIPVIANGG 236
N+ + M+ + + + IP+I GG
Sbjct: 207 ANKTGGLSGPAIKPIALRMVYDVYKMVDIPIIGVGG 242
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA targets.
Exemplified by Staufen, which is involved in
localisation of at least five different mRNAs in the
early Drosophila embryo. Also by interferon-induced
protein kinase in humans, which is part of the cellular
response to dsRNA.
Length = 66
Score = 35.0 bits (81), Expect = 0.004
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 264 PKTILYAHCKYKRFEVPKYETVQ----YEKLFRSLVTVNGKQYTS 304
PK++L C+ K + P + + F VTVNGK+Y +
Sbjct: 1 PKSLLQELCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKYGT 45
>gnl|CDD|240091 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 296
Score = 37.1 bits (87), Expect = 0.007
Identities = 34/155 (21%), Positives = 62/155 (40%), Gaps = 27/155 (17%)
Query: 103 KIILQIGTADPERALEAAKKVE-HDVAAIDINMGCPKQFSLTGGMGAALLSTPDIACNIL 161
+I I + E +E A+K+ AI++N+ CP G G A + P+ I+
Sbjct: 91 PVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPN----VKGGGMAFGTDPEAVAEIV 146
Query: 162 TTLISNLSIPVSCKIRVFHNEADTIALCKRLE---ACGIIAI----GVHGRTKAERPRHR 214
+ +PV K+ N D + + + E A G+ I G+ + +P
Sbjct: 147 KAVKKATDVPVIVKLTP--NVTDIVEIARAAEEAGADGLTLINTLKGMAIDIETRKPILG 204
Query: 215 NR-------------IEMIRTLTQHLKIPVIANGG 236
N + M+ + + ++IP+I GG
Sbjct: 205 NVTGGLSGPAIKPIALRMVYQVYKAVEIPIIGVGG 239
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 34.4 bits (80), Expect = 0.054
Identities = 37/156 (23%), Positives = 64/156 (41%), Gaps = 28/156 (17%)
Query: 103 KIILQIGTADPERALEAAKKVE--HDVAAIDINMGCPKQFSLTGGMGAALLSTPDIACNI 160
II + + E E A+K+ +V AI++N+ CP G A + P++A +
Sbjct: 93 PIIANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN----VKHGGMAFGTDPELAYEV 148
Query: 161 LTTLISNLSIPVSCKIRVFHNEADTIALCKRLE---ACGIIAI----GVHGRTKAERPRH 213
+ + + +PV K+ N D + + K E A G+ I G+ K +P
Sbjct: 149 VKAVKEVVKVPVIVKLTP--NVTDIVEIAKAAEEAGADGLSLINTLKGMAIDIKTRKPIL 206
Query: 214 RNR-------------IEMIRTLTQHLKIPVIANGG 236
N + M+ + Q + IP+I GG
Sbjct: 207 ANVTGGLSGPAIKPIALRMVYQVYQAVDIPIIGMGG 242
>gnl|CDD|240082 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). Imidazole glycerol phosphate synthase
(IGPS) catalyzes the fifth step of histidine
biosynthesis, the formation of the imidazole ring. IGPS
converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria.
Length = 243
Score = 32.8 bits (76), Expect = 0.17
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 217 IEMIRTLTQHLKIPVIANGG 236
+E+IR ++ + IPVIA+GG
Sbjct: 182 LELIRAVSSAVNIPVIASGG 201
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases
H1, and dsRNA dependent adenosine deaminases.
Length = 68
Score = 30.3 bits (69), Expect = 0.19
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 264 PKTILYAHCKYKRFEVPKYETVQ-----YEKLFRSLVTVNGKQY 302
PK++L + + +P+YE V+ + F VTV GK
Sbjct: 2 PKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKIT 45
>gnl|CDD|132611 TIGR03572, WbuZ, glycosyl amidation-associated protein WbuZ. This
clade of sequences is highly similar to the HisF
protein, but generally represents the second HisF
homolog in the genome where the other is an authentic
HisF observed in the context of a complete histidine
biosynthesis operon. The similarity between these WbuZ
sequences and true HisFs is such that often the closest
match by BLAST of a WbuZ is a HisF. Only by making a
multiple sequence alignment is the homology relationship
among the WbuZ sequences made apparent. WbuZ genes are
invariably observed in the presence of a homolog of the
HisH protein (designated WbuY) and a proposed N-acetyl
sugar amidotransferase designated in WbuX in E. coli ,
IfnA in P. aeriginosa and PseA in C. jejuni. Similarly,
this trio of genes is invariably found in the context of
saccharide biosynthesis loci. It has been shown that the
WbuYZ homologs are not essential components of the
activity expressed by WbuX, leading to the proposal that
these to proteins provide ammonium ions to the
amidotransferase when these are in low concentration.
WbuY (like HisH) is proposed to act as a glutaminase to
release ammonium. In histidine biosynthesis this is also
dispensible in the presence of exogenous ammonium ion.
HisH and HisF form a complex such that the ammonium ion
is passed directly to HisF where it is used in an
amidation reaction causing a subsequent cleavage and
cyclization. In the case of WbuYZ, the ammonium ion
would be passed from WbuY to WbuZ. WbuZ, being
non-essential and so similar to HisF that a sugar
substrate is unlikely, would function instead as a
amoonium channel to the WbuX protein which does the
enzymatic work.
Length = 232
Score = 32.6 bits (75), Expect = 0.20
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 217 IEMIRTLTQHLKIPVIANGG 236
+E+I+T++ + IPVIA GG
Sbjct: 186 LELIKTVSDAVSIPVIALGG 205
>gnl|CDD|239435 cd03319, L-Ala-DL-Glu_epimerase, L-Ala-D/L-Glu epimerase catalyzes
the epimerization of L-Ala-D/L-Glu and other dipeptides.
The genomic context and the substrate specificity of
characterized members of this family from E.coli and
B.subtilis indicates a possible role in the metabolism
of the murein peptide of peptidoglycan, of which
L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a
member of the enolase-superfamily, which is
characterized by the presence of an enolate anion
intermediate which is generated by abstraction of the
alpha-proton of the carboxylate substrate by an active
site residue and is stabilized by coordination to the
essential Mg2+ ion.
Length = 316
Score = 31.8 bits (73), Expect = 0.36
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 12/64 (18%)
Query: 174 CKIRVFHNEA----DTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKI 229
++RV N+ + + L + L G+ I E+P + + L +
Sbjct: 178 ARLRVDANQGWTPEEAVELLRELAELGVELI--------EQPVPAGDDDGLAYLRDKSPL 229
Query: 230 PVIA 233
P++A
Sbjct: 230 PIMA 233
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 31.9 bits (73), Expect = 0.40
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 118 EAAKKVEHDVA-AIDINMGCPKQFSLTGGMGAALLSTPDIACNILTTLISNLSIPVSCKI 176
E AK VE A A+++N CP GMGAA+ P++ I + + IPV K+
Sbjct: 117 ELAKLVEEAGADALELNFSCPHGMP-ERGMGAAVGQDPELVEEICRWVREAVKIPVIAKL 175
>gnl|CDD|237520 PRK13813, PRK13813, orotidine 5'-phosphate decarboxylase;
Provisional.
Length = 215
Score = 31.5 bits (72), Expect = 0.43
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 101 KNKIILQIGTADPERALEAAKKVEHDVAAIDIN 133
++IIL + D ERAL+ A++++ V AI +
Sbjct: 3 DSRIILALDVTDRERALKIAEELDDYVDAIKVG 35
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 31.8 bits (73), Expect = 0.44
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 183 ADTIALCKRLEACGIIAI--GVHGRTKAERPRH----RNRIEMIRTLTQHLKIPVIANGG 236
+ + L K LE G++ G + ++E + + ++IPVIA GG
Sbjct: 237 EEAVELAKALEEAGLVDYIHVSEGGYERGGTITVSGPGYQVEFAARIKKAVRIPVIAVGG 296
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 31.1 bits (71), Expect = 0.62
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 217 IEMIRTLTQHLKIPVIANGG---SKEIVD 242
+E++++ LKIP+IA GG +IV+
Sbjct: 185 LELLKSFRNALKIPLIALGGAGSLDDIVE 213
>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
receiver domain and a methylesterase domain [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 350
Score = 31.1 bits (71), Expect = 0.64
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 108 IGTA-DPERALEAAKKVEHDVAAIDINMG 135
+GTA + A++ KK++ DV +D+ M
Sbjct: 30 VGTARNGREAIDKVKKLKPDVITLDVEMP 58
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 31.0 bits (71), Expect = 0.70
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 217 IEMIRTLTQHLKIPVIANGGSKEIVDYGGVFSLNCA 252
+E+ R + + + IPVIA+GG+ + + F+ A
Sbjct: 188 LELTRAVREAVNIPVIASGGAGKPEHFVEAFTEGKA 223
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 30.7 bits (70), Expect = 0.85
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 256 NHYPVEKLPKTILYAHCKYKRFEVPKYETVQYE-----KLFRSLVTVNGKQY 302
+ K PKT L + + +P+Y V+ E K F V V GK+
Sbjct: 155 DAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKEL 206
>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase;
Provisional.
Length = 354
Score = 30.5 bits (70), Expect = 1.0
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 108 IGTA-DPERALEAAKKVEHDVAAIDINM 134
+GTA D A E KK+ DV +D+ M
Sbjct: 32 VGTAPDGLEAREKIKKLNPDVITLDVEM 59
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 30.4 bits (70), Expect = 1.1
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 217 IEMIRTLTQHLKIPVIANGG 236
+E+ R ++ + +PVIA+GG
Sbjct: 186 LELTRAVSDAVNVPVIASGG 205
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 29.9 bits (68), Expect = 1.3
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 184 DTIALCKRLEACGIIAIG--VHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANGG 236
T+ G IG + G T+ E+++ L + L IPVIA G
Sbjct: 131 STLEEALNAAKLGFDIIGTTLSGYTEETAKTEDPDFELLKELRKALGIPVIAEGR 185
>gnl|CDD|216225 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins
involved in steps 4 and 6 of the histidine biosynthesis
pathway are contained in this family. Histidine is
formed by several complex and distinct biochemical
reactions catalyzed by eight enzymes. The enzymes in
this Pfam entry are called His6 and His7 in eukaryotes
and HisA and HisF in prokaryotes. The structure of HisA
is known to be a TIM barrel fold. In some archaeal HisA
proteins the TIM barrel is composed of two tandem
repeats of a half barrel . This family belong to the
common phosphate binding site TIM barrel family.
Length = 230
Score = 29.8 bits (68), Expect = 1.5
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 217 IEMIRTLTQHLKIPVIANGG 236
+E+ R L + + IPVIA+GG
Sbjct: 181 LELTRELAEAVNIPVIASGG 200
>gnl|CDD|201648 pfam01188, MR_MLE, Mandelate racemase / muconate lactonizing
enzyme, C-terminal domain. C-terminal domain is TIM
barrel fold, dehydratase-like domain. Manganese is
associated with this domain.
Length = 69
Score = 27.8 bits (63), Expect = 1.6
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 181 NEADTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIA 233
+ I L + LE G++ I E P + +E + L + IP+ A
Sbjct: 24 TPEEAIRLARALEPYGLLWI--------EEPLPPDDLEGLAELRRATPIPIAA 68
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.9 bits (68), Expect = 1.9
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 47 RLLALDYGADLVYSEELVDH 66
R L ++GA+LVYSE LV+H
Sbjct: 785 RRLKENHGAELVYSEALVEH 804
>gnl|CDD|233635 TIGR01915, npdG, NADPH-dependent F420 reductase. This model
represents a subset of a parent family described by
pfam03807. Unlike the parent family, members of this
family are found only in species with evidence of
coenzyme F420. All members of this family are believed
to act as NADPH-dependent F420 reductase [Energy
metabolism, Electron transport].
Length = 219
Score = 29.0 bits (65), Expect = 2.4
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 102 NKIILQIGTADPERALEAAKKVE 124
NKII IG+ D E+A EAA K
Sbjct: 25 NKII--IGSRDLEKAEEAAAKAL 45
>gnl|CDD|238317 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
synthase)/TenI. TMP synthase catalyzes an important step
in the thiamine biosynthesis pathway, the substitution
of the pyrophosphate of 2-methyl-4-amino-5-
hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-
(beta-hydroxyethyl) thiazole phosphate to yield thiamine
phosphate. TenI is a enzymatically inactive regulatory
protein involved in the regulation of several
extracellular enzymes. This superfamily also contains
other enzymatically inactive proteins with unknown
functions.
Length = 196
Score = 28.6 bits (65), Expect = 2.8
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 185 TIALCKRLEACGI--IAIG-VHG-RTKAERPRHRNRIEMIRTLTQHLKIPVIANGGSKE 239
++ R E G + G V TK +E++R + + ++IPV+A GG
Sbjct: 104 SLEEALRAEELGADYVGFGPVFPTPTKPGAGPPLG-LELLREIAELVEIPVVAIGGITP 161
>gnl|CDD|130398 TIGR01331, bisphos_cysQ, 3'(2'),5'-bisphosphate nucleotidase,
bacterial. Sulfate is incorporated into
3-phosphoadenylylsulfate, PAPS, for utilization in
pathways such as methionine biosynthesis. Transfer of
sulfate from PAPS to an acceptor leaves adenosine
3'-5'-bisphosphate, APS. This model describes a form
found in bacteria of the enzyme 3'(2'),5'-bisphosphate
nucleotidase, which removes the 3'-phosphate from APS to
regenerate AMP and help drive the cycle [Central
intermediary metabolism, Sulfur metabolism].
Length = 249
Score = 29.0 bits (65), Expect = 2.9
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 24/77 (31%)
Query: 206 TKAERPRHRNRIEMIRTLTQHLKIPVIAN----------------------GGSKEIVDY 243
T+A+R HR +E +R LT IPV++ G+KE ++
Sbjct: 36 TEADRAAHRFILEGLRALTP--DIPVLSEEDASIPLTPRQTWQRFWLVDPLDGTKEFINR 93
Query: 244 GGVFSLNCAFLRNHYPV 260
G F++N A + + PV
Sbjct: 94 NGDFTVNIALVEHGVPV 110
>gnl|CDD|217379 pfam03125, Sre, C. elegans Sre G protein-coupled chemoreceptor.
Caenorhabditis elegans Sre proteins are candidate
chemosensory receptors. There are four main recognised
groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre
(this family), Sra pfam02117 and Srb pfam02175 comprise
the Sra group. All of the above receptors are thought to
be G protein-coupled seven transmembrane domain
proteins. The existence of several different
chemosensory receptors underlies the fact that in spite
of having only 20-30 chemosensory neurones, C. elegans
detects hundreds of different chemicals, with the
ability to discern individual chemicals among
combinations.
Length = 363
Score = 29.2 bits (66), Expect = 3.1
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 149 ALLSTPDIACNILTTLISNLSIPVSCKIRVFH 180
LLS ++ IL I +S+ V KIR+FH
Sbjct: 26 LLLSIFELLFYILCAYIVFVSLYVILKIRLFH 57
>gnl|CDD|235682 PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
Length = 553
Score = 29.1 bits (66), Expect = 3.2
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 142 LTGGMGAALLSTPDIACNILTTLISNLSIPVSCKIRVFHN 181
L M AL + IA I++ LIS+L+IP I + H
Sbjct: 448 LHAAMAFALFISLGIA-KIMSDLISSLNIPAETVIGIIHV 486
>gnl|CDD|205943 pfam13770, DUF4169, Domain of unknown function (DUF4169).
Length = 55
Score = 26.3 bits (59), Expect = 3.6
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 203 HGRTKAERPRHRNRIEMI-RTLTQH 226
GRTKAE+ + R E R L H
Sbjct: 29 FGRTKAEKALDKARAEKAKRLLDGH 53
>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family.
Members of this protein family include YggS from
Escherichia coli and YBL036C, an uncharacterized
pyridoxal protein of Saccharomyces cerevisiae [Unknown
function, Enzymes of unknown specificity].
Length = 229
Score = 28.3 bits (63), Expect = 4.2
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 2/44 (4%)
Query: 182 EADTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQ 225
A I K L+ G++ IG + + + N M Q
Sbjct: 146 LAIQIEELKHLKLRGLMTIGAPTDSHED--QEENFRFMKLLFWQ 187
>gnl|CDD|129819 TIGR00736, nifR3_rel_arch, TIM-barrel protein, putative. Members
of this family show a distant relationship by PSI-BLAST
to alpha/beta (TIM) barrel enzymes such as
dihydroorotate dehydrogenase and glycolate oxidase. At
least two closely related but well-separable families
among the bacteria, the nifR3/yhdG family and the yjbN
family, share a more distant relationship to this family
of shorter, exclusively archaeal proteins [Unknown
function, General].
Length = 231
Score = 28.3 bits (63), Expect = 4.5
Identities = 25/92 (27%), Positives = 35/92 (38%), Gaps = 5/92 (5%)
Query: 115 RALEAAKKVEHDVAA----IDINMGCPKQFSLTGGMGAALLSTPDIACNILTTLISNLSI 170
LE A V +A I+IN C + G+G LL ++ LT + L+
Sbjct: 77 VDLEEAYDVLLTIAEHADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTK-MKELNK 135
Query: 171 PVSCKIRVFHNEADTIALCKRLEACGIIAIGV 202
P+ KIR D + L G I V
Sbjct: 136 PIFVKIRGNCIPLDELIDALNLVDDGFDGIHV 167
>gnl|CDD|225252 COG2377, COG2377, Predicted molecular chaperone distantly related
to HSP70-fold metalloproteases [Posttranslational
modification, protein turnover, chaperones].
Length = 371
Score = 28.4 bits (64), Expect = 4.9
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 191 RLEACGIIAIGVHGRTKAERP----RHRNRI---EMIRTLTQHLKIPVIANGGSKEIVDY 243
L I AIG HG+T RP ++ +I LT I V+ + +++
Sbjct: 87 GLLPRDIRAIGCHGQTVLHRPPGHAPDTVQLGDGPLIAELTG---ITVVGDFRRRDMA-A 142
Query: 244 GG 245
GG
Sbjct: 143 GG 144
>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
Provisional.
Length = 267
Score = 28.2 bits (63), Expect = 5.2
Identities = 9/35 (25%), Positives = 19/35 (54%)
Query: 142 LTGGMGAALLSTPDIACNILTTLISNLSIPVSCKI 176
+ G GA +L P++ + ++L ++PV C+
Sbjct: 135 VQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRA 169
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 28.1 bits (64), Expect = 5.2
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 217 IEMIRTLTQHLKIPVIANGGSKEIVD 242
+E R L + IPVIA+GG + D
Sbjct: 179 VEATRELAAAVPIPVIASGGVSSLDD 204
>gnl|CDD|239242 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs.
Length = 336
Score = 28.2 bits (64), Expect = 5.6
Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 183 ADTIALCKRLEACGIIAI-----GVHGRTKAERPRHRN-RIEMIRTLTQHLKIPVIANGG 236
D++ L K L+ G+ I G K P ++ + Q IPVIA G
Sbjct: 241 EDSVELAKALKELGVDLIDVSSGGNSPAQKI--PVGPGYQVPFAERIRQEAGIPVIAVGL 298
>gnl|CDD|107256 cd01543, PBP1_XylR, Ligand-binding domain of DNA transcription
repressor specific for xylose (XylR). Ligand-binding
domain of DNA transcription repressor specific for
xylose (XylR), a member of the LacI-GalR family of
bacterial transcription regulators. The ligand-binding
domain of XylR is structurally homologous to the
periplasmic sugar-binding domain of ABC-type
transporters and both domains contain the type I
periplasmic binding protein-like fold. The LacI-GalR
family repressors are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the type I periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcription
repressor undergoes a conformational change upon ligand
binding which in turn changes the DNA binding affinity
of the repressor.
Length = 265
Score = 27.9 bits (63), Expect = 6.2
Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 17/79 (21%)
Query: 173 SCKIRVFHNEADT---IALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKI 229
++ + K + GIIA R + EM L Q L I
Sbjct: 27 HGPWSIYLEPRGLQEPLRWLKDWQGDGIIA------------RIDDP-EMAEAL-QKLGI 72
Query: 230 PVIANGGSKEIVDYGGVFS 248
PV+ GS+E V +
Sbjct: 73 PVVDVSGSREKPGIPRVTT 91
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 27.7 bits (62), Expect = 6.6
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 67 KLVKTERKVNDLLNTIDFVDPLDGSVVFRTCPREKNKIILQIGTADPERALEAAKKVE 124
+L + ++++ L D V P G +V+ TC + I + L+ VE
Sbjct: 188 QLAELQKEL--LKAAWDLVKP-GGVLVYSTCSVLPEENEAVI-----KYFLQKRPDVE 237
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 27.8 bits (63), Expect = 6.9
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 12/85 (14%)
Query: 183 ADTIALCKRLEACGI----IAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANGGSK 238
D + + + L+ G+ + G + + + IR L ++K+ + K
Sbjct: 19 EDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDDWEVLRAIRKLVPNVKLQALVRNREK 78
Query: 239 EI-------VDYGGVF-SLNCAFLR 255
I VD +F S + R
Sbjct: 79 GIERALEAGVDEVRIFDSASETHSR 103
>gnl|CDD|233587 TIGR01821, 5aminolev_synth, 5-aminolevulinic acid synthase. This
model represents 5-aminolevulinic acid synthase, an
enzyme for one of two routes to the heme precursor
5-aminolevulinate. The protein is a pyridoxal
phosphate-dependent enzyme related to
2-amino-3-ketobutyrate CoA tranferase and
8-amino-7-oxononanoate synthase. This enzyme appears
restricted to the alpha Proteobacteria and mitochondrial
derivatives [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 402
Score = 27.8 bits (62), Expect = 7.2
Identities = 13/51 (25%), Positives = 24/51 (47%)
Query: 185 TIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQHLKIPVIANG 235
T +L + A +I ++ R H+ ++ ++ L + L IPVI N
Sbjct: 276 TTSLPPAIAAGATASIRHLKESQDLRRAHQENVKRLKNLLEALGIPVIPNP 326
>gnl|CDD|224980 COG2069, CdhD, CO dehydrogenase/acetyl-CoA synthase delta subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 403
Score = 27.9 bits (62), Expect = 7.5
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 20/102 (19%)
Query: 53 YGAD-----LVYSEELVDHKLVKTERK-VNDLLNTID--FV-----DPLDGSVVFRTCPR 99
+GAD L+ ++ + K K + D+L +D + +P V
Sbjct: 163 FGADMVTIHLISTDPKIKDTPAKEAAKTLEDVLQAVDVPIIIGGSGNPEKDPEVLEKAAE 222
Query: 100 --EKNKIILQIGT--ADPERALEAAKKVEHDV---AAIDINM 134
E + +L D ER EAA K +H V +D+NM
Sbjct: 223 VAEGERCLLASANLDLDYERIAEAALKYDHVVLSWTQMDVNM 264
>gnl|CDD|227284 COG4948, COG4948, L-alanine-DL-glutamate epimerase and related
enzymes of enolase superfamily [Cell envelope
biogenesis, outer membrane / General function prediction
only].
Length = 372
Score = 27.7 bits (62), Expect = 8.1
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 170 IPVSCKIRVFHNEA----DTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQ 225
+ ++ V N + I L + LE G+ I E P + +E +R L
Sbjct: 185 VGDDVRLMVDANGGWTLEEAIRLARALEEYGLEWI--------EEPLPPDDLEGLRELRA 236
Query: 226 HLKIPVIA 233
P+ A
Sbjct: 237 ATSTPIAA 244
>gnl|CDD|113257 pfam04481, DUF561, Protein of unknown function (DUF561). Protein
of unknown function found in a cyanobacterium, and the
chloroplasts of algae.
Length = 243
Score = 27.4 bits (61), Expect = 9.6
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 11/63 (17%)
Query: 184 DTIALCKRLEACGIIAIGVHGRTKAERPRHRNRIEMIRTLTQ----------HLKIPVIA 233
+ I L K+LE+ GI I G+ + ++ ++I H+++PVI
Sbjct: 133 EQINLAKQLESLGIDLIQTEGKITSI-SKNHCVNDLIEKSASTLASTYEISKHVQLPVIC 191
Query: 234 NGG 236
G
Sbjct: 192 ASG 194
>gnl|CDD|238327 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a
hexameric molecular chaperone complex, found in both
eukaryotes and archaea, that binds and stabilizes newly
synthesized polypeptides allowing them to fold
correctly. The complex contains two alpha and four beta
subunits, the two subunits being evolutionarily related.
In archaea, there is usually only one gene for each
subunit while in eukaryotes there two or more paralogous
genes encoding each subunit adding heterogeneity to the
structure of the hexamer. The structure of the complex
consists of a double beta barrel assembly with six
protruding coiled-coils.
Length = 129
Score = 26.4 bits (59), Expect = 9.9
Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 15/69 (21%)
Query: 67 KLVKTERKVNDLLNTIDFVD----------PLDGSVVFRTCPREKNKIILQIGT---ADP 113
+L + + T++ + PL V + ++ +K+++ +GT
Sbjct: 24 RLNEAIAEYEQAKETLETLKKADEGKETLVPLGAGVFVKAKVKDTDKVLVDLGTGYYV-- 81
Query: 114 ERALEAAKK 122
E+ LE A +
Sbjct: 82 EKDLEEAIE 90
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
0.323 0.139 0.405
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,685,638
Number of extensions: 1534615
Number of successful extensions: 1631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1593
Number of HSP's successfully gapped: 77
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.3 bits)