RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017176
(376 letters)
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 385 bits (992), Expect = e-134
Identities = 140/315 (44%), Positives = 192/315 (60%), Gaps = 18/315 (5%)
Query: 1 MVARQYLPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAF 60
+ FSVAPMMDWTD H R RL+S+HA LYTEM+ II+ G+ +R LAF
Sbjct: 3 EKMSKLPSRRFSVAPMMDWTDRHCRYFHRLLSRHALLYTEMVTTGAIIH--GDRERLLAF 60
Query: 61 SPEQHPIVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPK 120
PE+HP+ LQ+GGS+ +LA+A +LA + YDEINLN GCPS +V +G FG LM +P+
Sbjct: 61 DPEEHPVALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQ-NGRFGACLMAEPE 119
Query: 121 FVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLN 180
V + + + ++PV+VK RIG+DD DSY LCDF+ V+ + FI+H+RKA L
Sbjct: 120 LVADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDFVDTVAE-AGCDTFIVHARKAWLK 178
Query: 181 GISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK--GAHHVMVGRA 238
G+SP ENR IPPL Y+ Y L RDFP LT +NGGI T++E L+ G VM+GRA
Sbjct: 179 GLSPKENREIPPLDYDRVYRLKRDFPHLTIEINGGIKTLEEAKEHLQHVDG---VMIGRA 235
Query: 239 AYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGDAIL--GTYGNNRPHVRDVMKPL 296
AY NP+ L VD ++G P+ L+R +V+E Y + L G + + + +
Sbjct: 236 AYHNPYL-LAEVDRELFGEPAPPLSRSEVLEAMLPYIERHLAQGGR------LNHITRHM 288
Query: 297 LHFFHSEPGNGLFKR 311
L F PG ++R
Sbjct: 289 LGLFQGLPGARAWRR 303
>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 = 294 bits (753), Expect = 4e-98
Identities = 138/326 (42%), Positives = 193/326 (59%), Gaps = 10/326 (3%)
Query: 11 FSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQ 70
FSVAPM+DWTD H+R RL+SKH LYTEM+ A+ II+ G+ L FSPE+ P+ LQ
Sbjct: 3 FSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIH--GDKKDILKFSPEESPVALQ 60
Query: 71 IGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIA 130
+GGS+ ++LAK ++A YDEINLN GCPS +V +G FG LM + V + + +
Sbjct: 61 LGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQ-NGNFGACLMGNADLVADCVKAMQ 119
Query: 131 ANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTI 190
N+PV+VK RIG+D DSY LCDF+ VS ++FI+H+RKA L+G+SP ENR I
Sbjct: 120 EAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKG-CQNFIVHARKAWLSGLSPKENREI 178
Query: 191 PPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNPWYTLGHV 250
PPL+YE Y L +DFP LT +NGGI +++ L VMVGR AY+NP Y L +V
Sbjct: 179 PPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHLSH-VDGVMVGREAYENP-YLLANV 236
Query: 251 DTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFK 310
D I+ LTR+++VE+ Y + Y + + + + LL F +PG ++
Sbjct: 237 DREIFNETDEILTRKEIVEQMLPY----IEEYLSQGLSLNHITRHLLGLFQGKPGAKQWR 292
Query: 311 RKADAAFQTCKTVKSFLEETIVAIPD 336
R LE + +P+
Sbjct: 293 RYLSENAPKAGAGIEVLETALETVPE 318
>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 = 238 bits (611), Expect = 8e-78
Identities = 70/235 (29%), Positives = 117/235 (49%), Gaps = 16/235 (6%)
Query: 11 FSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQ 70
+APM+ TD +R L R +YTEM++A+ ++ R L +PE+ P+++Q
Sbjct: 2 LILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 71 IGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIA 130
+GGS+ + LA+A ++ D I+LN GCPSPKV G G +L+ DP+ V E + +
Sbjct: 61 LGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVT-KGGAGAALLKDPELVAEIVRAVR 119
Query: 131 ANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTI 190
+PV+VK R+G DD + + + + + +H R E R
Sbjct: 120 EAVPIPVTVKIRLGWDDEE---ETLELAKALED-AGASALTVHGRT--------REQRYS 167
Query: 191 PPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPW 244
P ++Y +++ + NG I ++++ L + G VM+GR A NPW
Sbjct: 168 GPADWDYIAE-IKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPW 221
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 223 bits (571), Expect = 1e-70
Identities = 92/325 (28%), Positives = 154/325 (47%), Gaps = 19/325 (5%)
Query: 7 LPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHP 66
L +APM TD +R LAR + + LYTEM++A+ +++ + L E+ P
Sbjct: 9 LRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDELEEERP 68
Query: 67 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAM 126
+ +Q+GGS+ + LA+A ++A D I+LNCGCPSPKV G G +L+ +P+ + E +
Sbjct: 69 VAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKGG-AGAALLKNPELLAEIV 127
Query: 127 S-VIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPA 185
++ A ++PV+VK R+G DD D L I ++ + +H R + PA
Sbjct: 128 KAMVEAVGDIPVTVKIRLGWDDDDI---LALEIARILEDAGADALTVHGRTRAQGYLGPA 184
Query: 186 ENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPW 244
+ ++Y L P + NG I ++++ L GA VM+GR A NPW
Sbjct: 185 D--------WDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGNPW 236
Query: 245 YTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEP 304
L + T +V++ + + + +L YG +R + K L ++ P
Sbjct: 237 --LFRQIDYLETGELLPPTLAEVLDILREHLELLLEYYGKK--GLRRLRKHLGYYLKGLP 292
Query: 305 GNGLFKRKADAAFQTCKTVKSFLEE 329
G +R + V+ LE
Sbjct: 293 GARELRRAL-NKAEDGAEVRRALEA 316
>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 = 188 bits (480), Expect = 3e-57
Identities = 78/311 (25%), Positives = 127/311 (40%), Gaps = 20/311 (6%)
Query: 12 SVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQH--PIVL 69
+APM TD +R L R + TEM+ A+ + R L + P+ +
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLR--PEKQRELMLPELEEPTPLAV 58
Query: 70 QIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVI 129
Q+GGS+ LA+A +L D I++N GCP+ KV G G +L+ DP V + + +
Sbjct: 59 QLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGG-AGAALLRDPDLVAQIVKAV 117
Query: 130 AANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRT 189
++PV+VK RIG D +S+ + +V +H R + A+N
Sbjct: 118 VKAVDIPVTVKIRIGWD--ESHENAVEIARRVEDAGAQ-ALTVHGR-------TRAQNYE 167
Query: 190 IPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPWYTLG 248
P ++ + + + NG I ++ L GA VM+GR A NPW
Sbjct: 168 G-PADWDAIKQVKQAVS-IPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWL-FA 224
Query: 249 HVDTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGL 308
T G + E + + YG ++ +R K L + PG
Sbjct: 225 EQHTVKTGEFDPRPPLAEEAEIVLEHLSYLEEFYGEDK-GLRHARKHLAWYLKGFPGAAE 283
Query: 309 FKRKADAAFQT 319
+R+ + F
Sbjct: 284 LRRELNDVFDP 294
>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 = 126 bits (318), Expect = 2e-33
Identities = 81/325 (24%), Positives = 141/325 (43%), Gaps = 21/325 (6%)
Query: 14 APMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQIGG 73
APM TD+ +R L EM+++E I+Y R L + ++ PI +Q+ G
Sbjct: 13 APMAGVTDSPFRRLVAEYGA-GLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFG 71
Query: 74 SNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANT 133
S+ D +A+A ++ D I++N GCP PK+ G G +L+ DP +G+ + +
Sbjct: 72 SDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGA-GSALLRDPDLIGKIVKAVVDAV 130
Query: 134 NVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKA--LLNGISPAENRTIP 191
++PV+VK RIG DD N +++ + + +H R +G A I
Sbjct: 131 DIPVTVKIRIGWDD-AHIN--AVEAARIAEDAGAQAVTLHGRTRAQGYSG--EANWDIIA 185
Query: 192 PLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAAL-RKGAHHVMVGRAAYQNPWYTLGHV 250
+K +R P + NG I + ++ A L G VM+GR A NPW
Sbjct: 186 RVK-----QAVR-IPVIG---NGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIE 236
Query: 251 DTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFK 310
G T + ++ + + YG ++ +R K + + PGN +
Sbjct: 237 QYLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESK-GLRIARKHIAWYLKGFPGNAALR 295
Query: 311 RKADAAFQTCKTVKSFLEETIVAIP 335
+ + A + + VK L++ +
Sbjct: 296 QTLNHA-SSFQEVKQLLDDFFETVG 319
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 63.5 bits (154), Expect = 4e-11
Identities = 61/241 (25%), Positives = 101/241 (41%), Gaps = 19/241 (7%)
Query: 7 LPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHP 66
L APM TD +RTL + +EM+++ +++ + E
Sbjct: 8 LRNRLIAAPMAGITDRPFRTLCYEMGA-GLTVSEMMSSNPQVWESDKSRLRMVHIDEPGI 66
Query: 67 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAM 126
+QI GS+ +A A + I++N GCP+ KV G +L+ P V +
Sbjct: 67 RTVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKV-NRKLAGSALLQYPDLVKSIL 125
Query: 127 SVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIH--SRKALLNGISP 184
+ + +VPV++K R G ++ C I +++ + IH +R L NG
Sbjct: 126 TEVVNAVDVPVTLKIRTGWAPE---HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG--E 180
Query: 185 AENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALR-KGAHHVMVGRAAYQNP 243
AE +I +K + ++ NG I + A L GA +M+GRAA P
Sbjct: 181 AEYDSIRAVKQKVSIPVIA---------NGDITDPLKARAVLDYTGADALMIGRAAQGRP 231
Query: 244 W 244
W
Sbjct: 232 W 232
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 49.4 bits (118), Expect = 1e-06
Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 9/83 (10%)
Query: 77 DNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFV---GEAMSVIAANT 133
+N A+A EL ++ D LNCGCPS V G G G +L+ DP+ + +AM A
Sbjct: 79 ENAARAVELG-SWGVD---LNCGCPSKTVNGSGG-GATLLKDPELIYQGAKAMRE-AVPA 132
Query: 134 NVPVSVKCRIGVDDHDSYNQLCD 156
++PV+VK R+G D + ++ D
Sbjct: 133 HLPVTVKVRLGWDSGERKFEIAD 155
>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 = 46.0 bits (110), Expect = 1e-05
Identities = 50/189 (26%), Positives = 80/189 (42%), Gaps = 23/189 (12%)
Query: 66 PIVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEA 125
P++ I GS ++ + E D I LN CP+ K G++ DP+ V E
Sbjct: 91 PVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNVK-----GGGMAFGTDPEAVAEI 145
Query: 126 MSVIAANTNVPVSVKCRIGVDDHDSYNQLC-----DFIYKVSSLSPTRHFI-IHSRKALL 179
+ + T+VPV VK V D + D + +++L I I +RK +L
Sbjct: 146 VKAVKKATDVPVIVKLTPNVTDIVEIARAAEEAGADGLTLINTLKGMA--IDIETRKPIL 203
Query: 180 N----GIS-PAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVM 234
G+S PA I P+ Y + + ++ GGI + ++ L GA V
Sbjct: 204 GNVTGGLSGPA----IKPIALRMVYQVYKAV-EIPIIGVGGIASGEDALEFLMAGASAVQ 258
Query: 235 VGRAAYQNP 243
VG A + +P
Sbjct: 259 VGTANFVDP 267
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 43.6 bits (104), Expect = 8e-05
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 66 PIVLQIGGSNLDNLAK-ATELANAYNYDEINLNCGCPSPKVAGHGC--FGVSLMLDPKFV 122
PI+ + GS + A+ A +L+ A N D I LN CP+ HG FG DP+
Sbjct: 93 PIIANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN---VKHGGMAFGT----DPELA 145
Query: 123 GEAMSVIAANTNVPVSVKCRIGVDD 147
E + + VPV VK V D
Sbjct: 146 YEVVKAVKEVVKVPVIVKLTPNVTD 170
>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 = 43.2 bits (102), Expect = 1e-04
Identities = 48/189 (25%), Positives = 78/189 (41%), Gaps = 21/189 (11%)
Query: 66 PIVLQIGGSNLDNLAKATE-LANAYNY-DEINLNCGCPSPKVAGHGCFGVSLMLDPKFVG 123
P++ + GS+++ A+ E L A Y D LN CP K G +++ DP+
Sbjct: 92 PLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKGGG-----IAIGQDPELSA 146
Query: 124 EAMSVIAANTNVPVSVKCRIGVDDHDSYNQLC-----DFIYKVSSLSPTRHFIIHSRKAL 178
+ + + T+VPV K V D + D + +++L + I + L
Sbjct: 147 DVVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMKIDIKTGKPIL 206
Query: 179 LN---GIS-PAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVM 234
N G+S PA I P+ Y + + D+ GGI + ++ L GA V
Sbjct: 207 ANKTGGLSGPA----IKPIALRMVYDVYKMV-DIPIIGVGGITSFEDALEFLMAGASAVQ 261
Query: 235 VGRAAYQNP 243
VG A Y
Sbjct: 262 VGTAVYYRG 270
>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 = 39.2 bits (92), Expect = 0.002
Identities = 41/167 (24%), Positives = 63/167 (37%), Gaps = 24/167 (14%)
Query: 73 GSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAAN 132
S+L+ L A L + +N C P++ G G +L+ DP+ + E + +
Sbjct: 81 SSSLEPLLNAAALVAKNA-AILEINAHCRQPEMVEAGA-GEALLKDPERLSEFIKALKE- 137
Query: 133 TNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPP 192
T VPVSVK R GVD +L I K + IIH + P
Sbjct: 138 TGVPVSVKIRAGVD--VDDEELARLIEKAGAD------IIHV-------------DAMDP 176
Query: 193 LKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAA 239
+ + +L N + T++ GA V V RA+
Sbjct: 177 GNHADLKKIRDISTELFIIGNNSVTTIESAKEMFSYGADMVSVARAS 223
>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 = 38.1 bits (89), Expect = 0.005
Identities = 49/196 (25%), Positives = 79/196 (40%), Gaps = 30/196 (15%)
Query: 66 PIVLQIGGSNLDN---LAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFV 122
P++ +GGS+ ++ LA+ E A A E+NL+C P V G G L DP+ V
Sbjct: 100 PLIASVGGSSKEDYVELARKIERAGAK-ALELNLSC----PNVGG----GRQLGQDPEAV 150
Query: 123 GEAMSVIAANTNVPVSVKCRIGVDDHD------SYNQL-CDFIYKVSSLSPTRHFI---- 171
+ + A ++P+ VK D D + + D + ++++S R
Sbjct: 151 ANLLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTISG-RVVDLKTV 209
Query: 172 IHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLN--GGINTVDEVNAALRKG 229
K G+S A R PL + L L + GGI++ ++V L G
Sbjct: 210 GPGPKRGTGGLSGAPIR---PLALRWVARLAARLQ-LDIPIIGVGGIDSGEDVLEMLMAG 265
Query: 230 AHHVMVGRAAYQNPWY 245
A V V A +
Sbjct: 266 ASAVQVATALMWDGPD 281
>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 = 37.4 bits (88), Expect = 0.007
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 210 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
T+ GGI ++++ LR GA V + AA +NP
Sbjct: 74 LTVGGGIRSLEDARRLLRAGADKVSINSAAVENP 107
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 37.0 bits (87), Expect = 0.009
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 210 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
T+ GGI +V++ LR GA V + AA NP
Sbjct: 77 LTVGGGIRSVEDARRLLRAGADKVSINSAAVANP 110
>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 = 36.3 bits (85), Expect = 0.013
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
+ + GGI ++++ L GA V++G AA +NP
Sbjct: 73 FIPVQVGGGIRSLEDAERLLSAGADKVIIGTAAVKNP 109
>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 = 35.6 bits (82), Expect = 0.027
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 84 ELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRI 143
L A + D I +N C P++ G G L+ + + + E ++ + N P+ VK R
Sbjct: 86 LLTIAEHADIIEINAHCRQPEITEIGI-GQELLKNKELLKEFLTKM-KELNKPIFVKIRG 143
Query: 144 GV 145
Sbjct: 144 NC 145
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 35.4 bits (82), Expect = 0.041
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 112 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 144
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 59 GVARMADPKMIEEIMDAVS----IPVMAKVRIG 87
>gnl|CDD|233108 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
subunit. [Amino acid biosynthesis, Histidine family].
Length = 254
Score = 35.0 bits (81), Expect = 0.048
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
+ T+ GGI ++++V+ LR GA V + AA +NP
Sbjct: 74 FIPLTVGGGIKSIEDVDKLLRAGADKVSINTAAVKNP 110
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
Length = 293
Score = 35.1 bits (82), Expect = 0.049
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 112 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 144
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 56 GVARMADPKMIEEIMDAVS----IPVMAKARIG 84
>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 = 34.6 bits (80), Expect = 0.058
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 210 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
T+ GGI ++++ L GA V + AA +NP
Sbjct: 77 LTVGGGIRSLEDAKKLLSLGADKVSINTAALENP 110
>gnl|CDD|129443 TIGR00343, TIGR00343, pyridoxal 5'-phosphate synthase, synthase
subunit Pdx1. This protein had been believed to be a
singlet oxygen resistance protein. Subsequent work
showed that it is a protein of pyridoxine (vitamin B6)
biosynthesis, and that pyridoxine quenches the highly
toxic singlet form of oxygen produced by light in the
presence of certain chemicals [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 287
Score = 34.0 bits (78), Expect = 0.098
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 112 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 144
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 49 GVARMSDPKMIKEIMDAVS----IPVMAKVRIG 77
>gnl|CDD|240078 cd04727, pdxS, PdxS is a subunit of the pyridoxal 5'-phosphate
(PLP) synthase, an important enzyme in deoxyxylulose
5-phosphate (DXP)-independent pathway for de novo
biosynthesis of PLP, present in some eubacteria, in
archaea, fungi, plants, plasmodia, and some metazoa.
Together with PdxT, PdxS forms the PLP synthase, a
heteromeric glutamine amidotransferase (GATase), whereby
PdxT produces ammonia from glutamine and PdxS combines
ammonia with five- and three-carbon phosphosugars to
form PLP. PLP is the biologically active form of vitamin
B6, an essential cofactor in many biochemical processes.
PdxS subunits form two hexameric rings.
Length = 283
Score = 33.8 bits (78), Expect = 0.11
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 112 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 144
GV+ M DPK + E M ++ +PV K RIG
Sbjct: 47 GVARMADPKMIKEIMDAVS----IPVMAKVRIG 75
>gnl|CDD|201920 pfam01680, SOR_SNZ, SOR/SNZ family. Members of this family are
enzymes involved in a new pathway of
pyridoxine/pyridoxal 5-phosphate biosynthesis. This
family was formerly known as UPF0019.
Length = 197
Score = 33.2 bits (76), Expect = 0.13
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 112 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 144
GV+ M DPK + E M+ ++ +PV K RIG
Sbjct: 42 GVARMSDPKMIKEIMNAVS----IPVMAKVRIG 70
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 33.3 bits (77), Expect = 0.14
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 210 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
T+ GGI +V++ LR GA V + AA ++P
Sbjct: 77 LTVGGGIRSVEDARKLLRAGADKVSINSAAVKDP 110
>gnl|CDD|232779 TIGR00007, TIGR00007, phosphoribosylformimino-5-aminoimidazole
carboxamide ribotide isomerase. This protein family
consists of HisA,
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase, the enzyme catalyzing the fourth
step in histidine biosynthesis. It is closely related to
the enzyme HisF for the sixth step. Examples of this
enzyme in Actinobacteria have been found to be
bifunctional, also possessing phosphoribosylanthranilate
isomerase activity ; the trusted cutoff here has now
been raised to 275.0 to exclude the bifunctional group,
now represented by model TIGR01919. HisA from
Lactococcus lactis was reported to be inactive
(MEDLINE:93322317) [Amino acid biosynthesis, Histidine
family].
Length = 230
Score = 32.9 bits (76), Expect = 0.19
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 202 LRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 242
L ++ +GG++++D++ A + G + V+VG+A Y+
Sbjct: 184 LVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIVGKALYEG 224
Score = 31.4 bits (72), Expect = 0.52
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
GGI ++++V L G V++G AA +NP
Sbjct: 79 GGIRSLEDVEKLLDLGVDRVIIGTAAVENP 108
>gnl|CDD|237589 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
Length = 241
Score = 32.2 bits (74), Expect = 0.36
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP-W 244
D+ L+GGI + + AAL G V +G AA +NP W
Sbjct: 75 DVKVELSGGIRDDESLEAALATGCARVNIGTAALENPEW 113
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 31.8 bits (73), Expect = 0.39
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
GGI ++++V A L G V++G AA +NP
Sbjct: 82 GGIRSLEDVEALLDAGVARVIIGTAAVKNP 111
>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 = 31.4 bits (72), Expect = 0.73
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 181 GISPAENRTIPPLKYEYYY-----ALLRDFPDLTFTLNGGINTVDEVNAALRKG-AHHVM 234
G + IPP Y ++ + GGI + L +G A V
Sbjct: 250 GSYESPPPIIPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVA 309
Query: 235 VGRAAYQNP 243
+GRA +P
Sbjct: 310 LGRALLADP 318
>gnl|CDD|176126 cd08435, PBP2_GbpR, The C-terminal substrate binding domain of
galactose-binding protein regulator contains the type 2
periplasmic binding fold. Galactose-binding protein
regulator (GbpR), a member of the LysR family of
bacterial transcriptional regulators, regulates the
expression of chromosomal virulence gene chvE. The
chvE gene is involved in the uptake of specific sugars,
in chemotaxis to these sugars, and in the VirA-VirG
two-component signal transduction system. In the
presence of an inducing sugar such as L-arabinose,
D-fucose, or D-galactose, GbpR activates chvE
expression, while in the absence of an inducing sugar,
GbpR represses expression. The topology of this
substrate-binding domain is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 201
Score = 30.7 bits (70), Expect = 0.89
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 200 ALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAA 239
LL P LT + G T DE+ LR G + +GR A
Sbjct: 21 RLLARHPRLTVRVVEG--TSDELLEGLRAGELDLAIGRLA 58
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 29.8 bits (68), Expect = 1.1
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 240
DLT L + TV+EVNAAL++ A + G Y
Sbjct: 87 DLTVELEKPV-TVEEVNAALKEAAEGALKGILGY 119
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 292
Score = 30.7 bits (70), Expect = 1.2
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 210 FTLNGGINTVDEVNAALRKGAHHVM 234
+TL G+ +V+ ++ A++ GA+H M
Sbjct: 203 YTLYEGVGSVEAIDTAMKLGANHPM 227
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 30.3 bits (69), Expect = 1.5
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 212 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
L GGI + ++ + L G V++G AA +NP
Sbjct: 81 LGGGIRSAEDAASLLDLGVDRVILGTAAVENP 112
>gnl|CDD|239206 cd02812, PcrB_like, PcrB_like proteins. One member of this family,
a protein from Archaeoglobus fulgidus, has been
characterized as a (S)-3-O-geranylgeranylglyceryl
phosphate synthase (AfGGGPS). AfGGGPS catalyzes the
formation of an ether linkage between
sn-glycerol-1-phosphate (G1P) and geranylgeranyl
diphosphate (GGPP), the committed step in archaeal lipid
biosynthesis. Therefore, it has been proposed that
PcrB-like proteins are either prenyltransferases or are
involved in lipoteichoic acid biosynthesis although the
exact function is still unknown.
Length = 219
Score = 29.9 bits (68), Expect = 1.7
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
GGI + ++ GA ++VG ++P
Sbjct: 182 GGIRSGEQAKEMAEAGADTIVVGNIVEEDP 211
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 29.5 bits (67), Expect = 2.4
Identities = 26/104 (25%), Positives = 41/104 (39%), Gaps = 19/104 (18%)
Query: 54 LDRFLAFSPEQHPIVLQIGGSN--------LDNLAKATELANAYNYDEINLNCGCPSPKV 105
L+ E PI + IG + D E +A E+N++C P
Sbjct: 82 LEELKLAKYEGKPIGVNIGKNKGGPSEEAWADYARLLEEAGDAD-AIELNISC----PNT 136
Query: 106 AGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHD 149
G G +L DP+ + + + + A T VPV VK + + D
Sbjct: 137 PG----GRALGQDPELLEKLLEAVKAATKVPVFVK--LAPNITD 174
>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 = 29.1 bits (66), Expect = 2.7
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 179 LNGISPAENRTIPPLKYEYYYALLRDF---PDLTFTLNGGINTVDEVNAALRKGAHHVMV 235
L+G + +T P + LL++ + G IN+ ++ AL GA V+V
Sbjct: 151 LSGYTEETAKTEDPD-----FELLKELRKALGIPVIAEGRINSPEQAAKALELGADAVVV 205
Query: 236 GRA 238
G A
Sbjct: 206 GSA 208
>gnl|CDD|130974 TIGR01919, hisA-trpF,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide
isomerase/N-(5'phosphoribosyl)anthranilate isomerase.
This model represents a bifunctional protein posessing
both hisA
(1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase) and trpF
(N-(5'phosphoribosyl)anthranilate isomerase) activities.
Thus, it is involved in both the histidine and
tryptophan biosynthetic pathways. Enzymes with this
property have been described only in the Actinobacteria
(High-GC gram-positive). The enzyme is closely related
to the monofunctional HisA proteins (TIGR00007) and in
Actinobacteria, the classical monofunctional TrpF is
generally absent.
Length = 243
Score = 29.2 bits (65), Expect = 3.2
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 212 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNPWYT 246
L+GG + AAL G V G AA +NPW+
Sbjct: 79 LSGGRRDDSSLRAALTGGRARVNGGTAALENPWWA 113
>gnl|CDD|222800 PHA00458, PHA00458, single-stranded DNA-binding protein.
Length = 233
Score = 29.0 bits (65), Expect = 3.8
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 277 AILGTYGNNRPHVRDVMKPL------LHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEET 330
A L Y N P V+ KPL + FF + G FK K A+++ KT ++ +
Sbjct: 69 AALEEYEANPPKVQRGKKPLKPYEGDMPFFDNGDGTVTFKFKCYASYKDKKTGEN--KPI 126
Query: 331 IVAIPDS 337
++ + DS
Sbjct: 127 VLRVVDS 133
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 29.1 bits (66), Expect = 3.8
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 240
DLT L + TV+E+NAAL+ + + G Y
Sbjct: 243 DLTVELEKEV-TVEEINAALKAASEIGLKGILGY 275
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 28.6 bits (65), Expect = 4.0
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRA 238
G INT ++ AL GAH V+VG A
Sbjct: 180 GRINTPEQAKKALELGAHAVVVGGA 204
>gnl|CDD|167709 PRK04128, PRK04128,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 228
Score = 29.0 bits (65), Expect = 4.0
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 242
D F GG+++ ++V G V++G+A Y+
Sbjct: 182 DEEFIYAGGVSSAEDVKKLAEIGFSGVIIGKALYEG 217
>gnl|CDD|145928 pfam03040, CemA, CemA family. Members of this family are probable
integral membrane proteins. Their molecular function is
unknown. CemA proteins are found in the inner envelope
membrane of chloroplasts but not in the thylakoid
membrane. A cyanobacterial member of this family has
been implicated in CO2 transport, but is probably not a
CO2 transporter itself. They are predicted to be
haem-binding however this has not been proven
experimentally.
Length = 230
Score = 28.6 bits (65), Expect = 4.3
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 54 LDRFLAFSPEQHPIVLQIGGSNLDNLAKATELANAYNYDEIN 95
LD + SP L+I KA ELA YN + I
Sbjct: 70 LDELIKESPPTSLQELRIEIHK-----KAIELAKIYNEESIQ 106
>gnl|CDD|237105 PRK12457, PRK12457, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 281
Score = 28.6 bits (64), Expect = 5.1
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGR 237
DL F L GGIN ++ ++ L +V V R
Sbjct: 14 DLPFVLFGGINVLESLDFTLDVCGEYVEVTR 44
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably acts
to resolve the disulfide which forms after oxidation of
the active site cysteine in AphC. This proteins contains
two paired conserved cysteine motifs, CxxCP and CxHCDGP
[Cellular processes, Detoxification, Cellular processes,
Adaptations to atypical conditions].
Length = 515
Score = 28.9 bits (65), Expect = 5.2
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 116 MLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFII 172
MLD + + S +A+ N V + H+ +L + + +++SLS
Sbjct: 1 MLDQSLLAQLKSYLASLEN---PVTLVLSAGSHEKSKELLELLDEIASLSDKISLTQ 54
>gnl|CDD|240086 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 4. 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.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 353
Score = 28.7 bits (65), Expect = 5.6
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
G INT D+ AL GA V +GR +P
Sbjct: 291 GSINTPDDALEALETGADLVAIGRGLLVDP 320
>gnl|CDD|239784 cd04251, AAK_NAGK-UC, AAK_NAGK-UC: N-Acetyl-L-glutamate kinase -
uncharacterized (NAGK-UC). This domain is similar to
Escherichia coli and Pseudomonas aeruginosa NAGKs which
catalyze the phosphorylation of the gamma-COOH group of
N-acetyl-L-glutamate (NAG) by ATP in the second step of
microbial arginine biosynthesis. These uncharacterized
domain sequences are found in some bacteria (Deinococci
and Chloroflexi) and archea and belong to the Amino Acid
Kinase Superfamily (AAK).
Length = 257
Score = 28.5 bits (64), Expect = 5.6
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 67 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGC----FGVSLMLDPKFV 122
IV++IGGS + +L K D+I N G V G G + L ++PKFV
Sbjct: 1 IVVKIGGSVVSDLDK--------VIDDIA-NFGERLIVVHGGGNYVNEYLKRLGVEPKFV 51
>gnl|CDD|235237 PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like
protein; Reviewed.
Length = 232
Score = 28.2 bits (64), Expect = 5.8
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
GGI + ++ + GA ++VG ++P
Sbjct: 191 GGIRSPEQARELMAAGADTIVVGNIIEEDP 220
>gnl|CDD|188481 TIGR03966, actino_HemFlav, heme/flavin dehydrogenase, mycofactocin
system. Members of this protein family possess an
N-terminal heme-binding domain and C-terminal
flavodehydrogenase domain, and share homology to yeast
flavocytochrome b2, to E. coli L-lactate dehydrogenase
[cytochrome], to (S)-mandelate dehydrogenase, etc. This
enzyme appears only in the context of the mycofactocin
system. Interestingly, it is absent from the four
species detected so far with mycofactocin but without an
F420 biosynthesis system.
Length = 385
Score = 28.6 bits (64), Expect = 6.3
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 212 LNGGINTVDEVNAALRKGAHHVMVGRA 238
L+GGI +V AL GA VM+GRA
Sbjct: 307 LDGGIRRGSDVVKALALGARAVMIGRA 333
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 7.0
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 199 YALLRDFPDLTF---TLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 243
Y L+ + F GGI T+++ G V + AA ++P
Sbjct: 63 YELIENLASECFMPLCYGGGIKTLEQAKKIFSLGVEKVSINTAALEDP 110
>gnl|CDD|240083 cd04732, HisA, HisA. Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase catalyzes
the fourth step in histidine biosynthesis, an
isomerisation of the aminoaldose moiety of ProFAR to the
aminoketose of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene.
Length = 234
Score = 27.8 bits (63), Expect = 7.9
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 214 GGINTVDEVNAALRKGAHHVMVGRAAYQN 242
GG++++D++ A G V+VG+A Y+
Sbjct: 197 GGVSSLDDIKALKELGVAGVIVGKALYEG 225
>gnl|CDD|233453 TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type
I. This model represents glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), the enzyme responsible for the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in glycolysis
and gluconeogenesis. Forms exist which utilize NAD (EC
1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In
some species, NAD- and NADP- utilizing forms exist,
generally being responsible for reactions in the
anabolic and catabolic directions respectively. Two PFAM
models cover the two functional domains of this protein;
pfam00044 represents the N-terminal NAD(P)-binding
domain and pfam02800 represents the C-terminal catalytic
domain. An additional form of gap gene is found in gamma
proteobacteria and is responsible for the conversion of
erythrose-4-phosphate (E4P) to 4-phospho-erythronate in
the biosynthesis of pyridoxine. This pathway of
pyridoxine biosynthesis appears to be limited, however,
to a relatively small number of bacterial species
although it is prevalent among the gamma-proteobacteria.
This enzyme is described by TIGR001532. These sequences
generally score between trusted and noise to this GAPDH
model due to the close evolutionary relationship. There
exists the possiblity that some forms of GAPDH may be
bifunctional and act on E4P in species which make
pyridoxine and via hydroxythreonine and lack a separate
E4PDH enzyme (for instance, the GAPDH from Bacillus
stearothermophilus has been shown to posess a limited
E4PD activity as well as a robust GAPDH activity). There
are a great number of sequences in the databases which
score between trusted and noise to this model, nearly
all of them due to fragmentary sequences. It seems that
study of this gene has been carried out in many species
utilizing PCR probes which exclude the extreme ends of
the consenses used to define this model. The noise level
is set relative not to E4PD, but the next closest
outliers, the class II GAPDH's (found in archaea,
TIGR01546) and aspartate semialdehyde dehydrogenase
(ASADH, TIGR01296) both of which have highest-scoring
hits around -225 to the prior model [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 326
Score = 28.0 bits (63), Expect = 8.3
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 207 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 240
DL L + TV+EVNAAL++ A + G Y
Sbjct: 242 DLVVNLEKDV-TVEEVNAALKEAAEGELKGVLGY 274
>gnl|CDD|218322 pfam04909, Amidohydro_2, Amidohydrolase. These proteins are
amidohydrolases that are related to pfam01979.
Length = 272
Score = 27.9 bits (62), Expect = 8.5
Identities = 26/177 (14%), Positives = 45/177 (25%), Gaps = 16/177 (9%)
Query: 34 HAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQIGGSNLDNLAKATELANAYNYDE 93
H + ++ ++G R SPE + ++ G + N
Sbjct: 6 HLPGGSIPDPRLPLMDRRGYDPRD--ASPEDYLVLGAALG--VARAVIVAASCRGANNRV 61
Query: 94 INLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQ 153
+ P V G + E +A V + G
Sbjct: 62 LAEALKRPGRFVGG---AALPPPDPEDAAAELERRLAELGFRGVRLNPHPGGGPLLDPRL 118
Query: 154 LCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTF 210
++ L +H+ G + + PL L R FPDL
Sbjct: 119 DDPIFEALAELG--LPVDLHT----GFGDAGEDLDAAQPL---LLSGLARRFPDLKI 166
>gnl|CDD|225555 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase
[Carbohydrate transport and metabolism].
Length = 229
Score = 27.6 bits (62), Expect = 8.9
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 199 YALLRDFPDLTFTL--NGGINTVDEVNAALRKGAHHVMVGRA 238
+ L++ D + G NT ++ A+ GA V+VG A
Sbjct: 170 FQLVKQLSDAGCRVIAEGRYNTPEQAKKAIEIGADAVVVGSA 211
>gnl|CDD|240090 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. 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.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive.
Length = 325
Score = 28.0 bits (63), Expect = 8.9
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 183 SPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 242
SPAE R PL++ A+L + +GG++ ++V L GA VM A ++
Sbjct: 218 SPAEIRL--PLRW---IAILSGRVKASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRH 272
>gnl|CDD|222325 pfam13700, DUF4158, Domain of unknown function (DUF4158). The
exact function of this domain is not clear, but it
frequently occurs as an N-terminal region of transposase
3 or IS3 family of insertion elements.
Length = 166
Score = 27.5 bits (62), Expect = 9.5
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 16 MMDWTDNHYRTLARLISKHAWLYTE--MLAAETIIY 49
++ YR L + + AW + L E I Y
Sbjct: 109 YRPFSSKDYRELIEWLLELAWTTDKPIYLFDELIEY 144
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
0.321 0.137 0.424
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,934,820
Number of extensions: 1962037
Number of successful extensions: 1782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1742
Number of HSP's successfully gapped: 70
Length of query: 376
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 278
Effective length of database: 6,590,910
Effective search space: 1832272980
Effective search space used: 1832272980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.7 bits)