RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013796
(436 letters)
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 388 bits (1000), Expect = e-134
Identities = 140/315 (44%), Positives = 192/315 (60%), Gaps = 18/315 (5%)
Query: 61 MVARQYLPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAF 120
+ FSVAPMMDWTD H R RL+S+HA LYTEM+ II+ G+ +R LAF
Sbjct: 3 EKMSKLPSRRFSVAPMMDWTDRHCRYFHRLLSRHALLYTEMVTTGAIIH--GDRERLLAF 60
Query: 121 SPEQHPIVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPK 180
PE+HP+ LQ+GGS+ +LA+A +LA + YDEINLN GCPS +V +G FG LM +P+
Sbjct: 61 DPEEHPVALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQ-NGRFGACLMAEPE 119
Query: 181 FVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLN 240
V + + + ++PV+VK RIG+DD DSY LCDF+ V+ + FI+H+RKA L
Sbjct: 120 LVADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDFVDTVAE-AGCDTFIVHARKAWLK 178
Query: 241 GISPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK--GAHHVMVGRA 298
G+SP ENR IPPL Y+ Y L RDFP LT +NGGI T++E L+ G VM+GRA
Sbjct: 179 GLSPKENREIPPLDYDRVYRLKRDFPHLTIEINGGIKTLEEAKEHLQHVDG---VMIGRA 235
Query: 299 AYQNPWYTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGDAIL--GTYGNNRPHVRDVMKPL 356
AY NP+ L VD ++G P+ L+R +V+E Y + L G + + + +
Sbjct: 236 AYHNPYL-LAEVDRELFGEPAPPLSRSEVLEAMLPYIERHLAQGGR------LNHITRHM 288
Query: 357 LHFFHSEPGNGLFKR 371
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 = 3e-97
Identities = 138/326 (42%), Positives = 193/326 (59%), Gaps = 10/326 (3%)
Query: 71 FSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQ 130
FSVAPM+DWTD H+R RL+SKH LYTEM+ A+ II+ G+ L FSPE+ P+ LQ
Sbjct: 3 FSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIH--GDKKDILKFSPEESPVALQ 60
Query: 131 IGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIA 190
+GGS+ ++LAK ++A YDEINLN GCPS +V +G FG LM + V + + +
Sbjct: 61 LGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQ-NGNFGACLMGNADLVADCVKAMQ 119
Query: 191 ANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTI 250
N+PV+VK RIG+D DSY LCDF+ VS ++FI+H+RKA L+G+SP ENR I
Sbjct: 120 EAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKG-CQNFIVHARKAWLSGLSPKENREI 178
Query: 251 PPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNPWYTLGHV 310
PPL+YE Y L +DFP LT +NGGI +++ L VMVGR AY+NP Y L +V
Sbjct: 179 PPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHLSH-VDGVMVGREAYENP-YLLANV 236
Query: 311 DTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFK 370
D I+ LTR+++VE+ Y + Y + + + + LL F +PG ++
Sbjct: 237 DREIFNETDEILTRKEIVEQMLPY----IEEYLSQGLSLNHITRHLLGLFQGKPGAKQWR 292
Query: 371 RKADAAFQTCKTVKSFLEETIVAIPD 396
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 = 240 bits (615), Expect = 1e-77
Identities = 70/235 (29%), Positives = 117/235 (49%), Gaps = 16/235 (6%)
Query: 71 FSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQ 130
+APM+ TD +R L R +YTEM++A+ ++ R L +PE+ P+++Q
Sbjct: 2 LILAPMVGVTDLPFRLLCRRYG-ADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 131 IGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIA 190
+GGS+ + LA+A ++ D I+LN GCPSPKV G G +L+ DP+ V E + +
Sbjct: 61 LGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVT-KGGAGAALLKDPELVAEIVRAVR 119
Query: 191 ANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTI 250
+PV+VK R+G DD + + + + + +H R E R
Sbjct: 120 EAVPIPVTVKIRLGWDDEE---ETLELAKALED-AGASALTVHGRT--------REQRYS 167
Query: 251 PPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPW 304
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 = 225 bits (576), Expect = 1e-70
Identities = 92/325 (28%), Positives = 154/325 (47%), Gaps = 19/325 (5%)
Query: 67 LPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHP 126
L +APM TD +R LAR + + LYTEM++A+ +++ + L E+ P
Sbjct: 9 LRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDELEEERP 68
Query: 127 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAM 186
+ +Q+GGS+ + LA+A ++A D I+LNCGCPSPKV G G +L+ +P+ + E +
Sbjct: 69 VAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKGG-AGAALLKNPELLAEIV 127
Query: 187 S-VIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPA 245
++ A ++PV+VK R+G DD D L I ++ + +H R + PA
Sbjct: 128 KAMVEAVGDIPVTVKIRLGWDDDDI---LALEIARILEDAGADALTVHGRTRAQGYLGPA 184
Query: 246 ENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPW 304
+ ++Y L P + NG I ++++ L GA VM+GR A NPW
Sbjct: 185 D--------WDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGNPW 236
Query: 305 YTLGHVDTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEP 364
L + T +V++ + + + +L YG +R + K L ++ P
Sbjct: 237 --LFRQIDYLETGELLPPTLAEVLDILREHLELLLEYYGKK--GLRRLRKHLGYYLKGLP 292
Query: 365 GNGLFKRKADAAFQTCKTVKSFLEE 389
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 = 190 bits (486), Expect = 2e-57
Identities = 78/311 (25%), Positives = 127/311 (40%), Gaps = 20/311 (6%)
Query: 72 SVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQH--PIVL 129
+APM TD +R L R + TEM+ A+ + R L + P+ +
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLR--PEKQRELMLPELEEPTPLAV 58
Query: 130 QIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVI 189
Q+GGS+ LA+A +L D I++N GCP+ KV G G +L+ DP V + + +
Sbjct: 59 QLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGG-AGAALLRDPDLVAQIVKAV 117
Query: 190 AANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRT 249
++PV+VK RIG D +S+ + +V +H R + A+N
Sbjct: 118 VKAVDIPVTVKIRIGWD--ESHENAVEIARRVEDAGAQ-ALTVHGR-------TRAQNYE 167
Query: 250 IPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRK-GAHHVMVGRAAYQNPWYTLG 308
P ++ + + + NG I ++ L GA VM+GR A NPW
Sbjct: 168 G-PADWDAIKQVKQAVS-IPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWL-FA 224
Query: 309 HVDTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGL 368
T G + E + + YG ++ +R K L + PG
Sbjct: 225 EQHTVKTGEFDPRPPLAEEAEIVLEHLSYLEEFYGEDK-GLRHARKHLAWYLKGFPGAAE 283
Query: 369 FKRKADAAFQT 379
+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 = 127 bits (321), Expect = 2e-33
Identities = 81/325 (24%), Positives = 141/325 (43%), Gaps = 21/325 (6%)
Query: 74 APMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQIGG 133
APM TD+ +R L EM+++E I+Y R L + ++ PI +Q+ G
Sbjct: 13 APMAGVTDSPFRRLVAEYGA-GLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFG 71
Query: 134 SNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANT 193
S+ D +A+A ++ D I++N GCP PK+ G G +L+ DP +G+ + +
Sbjct: 72 SDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGA-GSALLRDPDLIGKIVKAVVDAV 130
Query: 194 NVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKA--LLNGISPAENRTIP 251
++PV+VK RIG DD N +++ + + +H R +G A I
Sbjct: 131 DIPVTVKIRIGWDD-AHIN--AVEAARIAEDAGAQAVTLHGRTRAQGYSG--EANWDIIA 185
Query: 252 PLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAAL-RKGAHHVMVGRAAYQNPWYTLGHV 310
+K +R P + NG I + ++ A L G VM+GR A NPW
Sbjct: 186 RVK-----QAVR-IPVIG---NGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIE 236
Query: 311 DTAIYGAPSSGLTRRQVVEKYQIYGDAILGTYGNNRPHVRDVMKPLLHFFHSEPGNGLFK 370
G T + ++ + + YG ++ +R K + + PGN +
Sbjct: 237 QYLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESK-GLRIARKHIAWYLKGFPGNAALR 295
Query: 371 RKADAAFQTCKTVKSFLEETIVAIP 395
+ + A + + VK L++ +
Sbjct: 296 QTLNHA-SSFQEVKQLLDDFFETVG 319
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 63.8 bits (155), Expect = 3e-11
Identities = 61/241 (25%), Positives = 101/241 (41%), Gaps = 19/241 (7%)
Query: 67 LPPWFSVAPMMDWTDNHYRTLARLISKHAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHP 126
L APM TD +RTL + +EM+++ +++ + E
Sbjct: 8 LRNRLIAAPMAGITDRPFRTLCYEMGA-GLTVSEMMSSNPQVWESDKSRLRMVHIDEPGI 66
Query: 127 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAM 186
+QI GS+ +A A + I++N GCP+ KV G +L+ P V +
Sbjct: 67 RTVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKV-NRKLAGSALLQYPDLVKSIL 125
Query: 187 SVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIH--SRKALLNGISP 244
+ + +VPV++K R G ++ C I +++ + IH +R L NG
Sbjct: 126 TEVVNAVDVPVTLKIRTGWAPE---HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG--E 180
Query: 245 AENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALR-KGAHHVMVGRAAYQNP 303
AE +I +K + ++ NG I + A L GA +M+GRAA P
Sbjct: 181 AEYDSIRAVKQKVSIPVIA---------NGDITDPLKARAVLDYTGADALMIGRAAQGRP 231
Query: 304 W 304
W
Sbjct: 232 W 232
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 50.2 bits (120), Expect = 8e-07
Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 9/83 (10%)
Query: 137 DNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFV---GEAMSVIAANT 193
+N A+A EL ++ D LNCGCPS V G G G +L+ DP+ + +AM A
Sbjct: 79 ENAARAVELG-SWGVD---LNCGCPSKTVNGSGG-GATLLKDPELIYQGAKAMRE-AVPA 132
Query: 194 NVPVSVKCRIGVDDHDSYNQLCD 216
++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 = 46.8 bits (112), Expect = 1e-05
Identities = 50/189 (26%), Positives = 80/189 (42%), Gaps = 23/189 (12%)
Query: 126 PIVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEA 185
P++ I GS ++ + E D I LN CP+ K G++ DP+ V E
Sbjct: 91 PVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNVK-----GGGMAFGTDPEAVAEI 145
Query: 186 MSVIAANTNVPVSVKCRIGVDDHDSYNQLC-----DFIYKVSSLSPTRHFI-IHSRKALL 239
+ + T+VPV VK V D + D + +++L I I +RK +L
Sbjct: 146 VKAVKKATDVPVIVKLTPNVTDIVEIARAAEEAGADGLTLINTLKGMA--IDIETRKPIL 203
Query: 240 N----GIS-PAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVM 294
G+S PA I P+ Y + + ++ GGI + ++ L GA V
Sbjct: 204 GNVTGGLSGPA----IKPIALRMVYQVYKAV-EIPIIGVGGIASGEDALEFLMAGASAVQ 258
Query: 295 VGRAAYQNP 303
VG A + +P
Sbjct: 259 VGTANFVDP 267
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 44.0 bits (105), Expect = 8e-05
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 126 PIVLQIGGSNLDNLAK-ATELANAYNYDEINLNCGCPSPKVAGHGC--FGVSLMLDPKFV 182
PI+ + GS + A+ A +L+ A N D I LN CP+ HG FG DP+
Sbjct: 93 PIIANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN---VKHGGMAFGT----DPELA 145
Query: 183 GEAMSVIAANTNVPVSVKCRIGVDD 207
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 = 43.6 bits (103), Expect = 1e-04
Identities = 48/189 (25%), Positives = 78/189 (41%), Gaps = 21/189 (11%)
Query: 126 PIVLQIGGSNLDNLAKATE-LANAYNY-DEINLNCGCPSPKVAGHGCFGVSLMLDPKFVG 183
P++ + GS+++ A+ E L A Y D LN CP K G +++ DP+
Sbjct: 92 PLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKGGG-----IAIGQDPELSA 146
Query: 184 EAMSVIAANTNVPVSVKCRIGVDDHDSYNQLC-----DFIYKVSSLSPTRHFIIHSRKAL 238
+ + + T+VPV K V D + D + +++L + I + L
Sbjct: 147 DVVKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMKIDIKTGKPIL 206
Query: 239 LN---GIS-PAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVM 294
N G+S PA I P+ Y + + D+ GGI + ++ L GA V
Sbjct: 207 ANKTGGLSGPA----IKPIALRMVYDVYKMV-DIPIIGVGGITSFEDALEFLMAGASAVQ 261
Query: 295 VGRAAYQNP 303
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: 133 GSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAAN 192
S+L+ L A L + +N C P++ G G +L+ DP+ + E + +
Sbjct: 81 SSSLEPLLNAAALVAKNA-AILEINAHCRQPEMVEAGA-GEALLKDPERLSEFIKALKE- 137
Query: 193 TNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPP 252
T VPVSVK R GVD +L I K + IIH + P
Sbjct: 138 TGVPVSVKIRAGVD--VDDEELARLIEKAGAD------IIHV-------------DAMDP 176
Query: 253 LKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAA 299
+ + +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 = 38.5 bits (90), Expect = 0.004
Identities = 49/196 (25%), Positives = 79/196 (40%), Gaps = 30/196 (15%)
Query: 126 PIVLQIGGSNLDN---LAKATELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFV 182
P++ +GGS+ ++ LA+ E A A E+NL+C P V G G L DP+ V
Sbjct: 100 PLIASVGGSSKEDYVELARKIERAGAK-ALELNLSC----PNVGG----GRQLGQDPEAV 150
Query: 183 GEAMSVIAANTNVPVSVKCRIGVDDHD------SYNQL-CDFIYKVSSLSPTRHFI---- 231
+ + A ++P+ VK D D + + D + ++++S R
Sbjct: 151 ANLLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTISG-RVVDLKTV 209
Query: 232 IHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTFTLN--GGINTVDEVNAALRKG 289
K G+S A R PL + L L + GGI++ ++V L G
Sbjct: 210 GPGPKRGTGGLSGAPIR---PLALRWVARLAARLQ-LDIPIIGVGGIDSGEDVLEMLMAG 265
Query: 290 AHHVMVGRAAYQNPWY 305
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: 270 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 37.4 bits (88), Expect = 0.009
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 270 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 36.7 bits (86), Expect = 0.013
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
+ + 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 = 35.3 bits (81), Expect = 0.038
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 144 ELANAYNYDEINLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRI 203
L A + D I +N C P++ G G L+ + + + E ++ + N P+ VK R
Sbjct: 86 LLTIAEHADIIEINAHCRQPEITEIGI-GQELLKNKELLKEFLTKM-KELNKPIFVKIRG 143
Query: 204 GV 205
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: 172 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 204
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 = 0.047
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
+ 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 = 0.048
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 172 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 204
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 = 0.073
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 270 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 34.4 bits (79), Expect = 0.10
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 172 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 204
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 = 34.1 bits (79), Expect = 0.11
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 172 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 204
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 = 33.6 bits (77), Expect = 0.13
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 172 GVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIG 204
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 = 33.7 bits (78), Expect = 0.14
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 270 FTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 33.3 bits (77), Expect = 0.19
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 262 LRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 302
L ++ +GG++++D++ A + G + V+VG+A Y+
Sbjct: 184 LVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIVGKALYEG 224
Score = 31.8 bits (73), Expect = 0.51
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
GGI ++++V L G V++G AA +NP
Sbjct: 79 GGIRSLEDVEKLLDLGVDRVIIGTAAVENP 108
>gnl|CDD|237589 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
Length = 241
Score = 32.6 bits (75), Expect = 0.30
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP-W 304
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 = 32.2 bits (74), Expect = 0.37
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 31.8 bits (73), Expect = 0.70
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 6/69 (8%)
Query: 241 GISPAENRTIPPLKYEYYY-----ALLRDFPDLTFTLNGGINTVDEVNAALRKG-AHHVM 294
G + IPP Y ++ + GGI + L +G A V
Sbjct: 250 GSYESPPPIIPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVA 309
Query: 295 VGRAAYQNP 303
+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 = 31.1 bits (71), Expect = 0.80
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 260 ALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAA 299
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 = 30.2 bits (69), Expect = 1.3
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 300
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 = 1.3
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 270 FTLNGGINTVDEVNAALRKGAHHVM 294
+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: 272 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
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 = 30.3 bits (69), Expect = 1.7
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
GGI + ++ GA ++VG ++P
Sbjct: 182 GGIRSGEQAKEMAEAGADTIVVGNIVEEDP 211
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 29.9 bits (68), Expect = 2.4
Identities = 26/104 (25%), Positives = 41/104 (39%), Gaps = 19/104 (18%)
Query: 114 LDRFLAFSPEQHPIVLQIGGSN--------LDNLAKATELANAYNYDEINLNCGCPSPKV 165
L+ E PI + IG + D E +A E+N++C P
Sbjct: 82 LEELKLAKYEGKPIGVNIGKNKGGPSEEAWADYARLLEEAGDAD-AIELNISC----PNT 136
Query: 166 AGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHD 209
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 = 29.5 bits (67), Expect = 2.4
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 239 LNGISPAENRTIPPLKYEYYYALLRDF---PDLTFTLNGGINTVDEVNAALRKGAHHVMV 295
L+G + +T P + LL++ + G IN+ ++ AL GA V+V
Sbjct: 151 LSGYTEETAKTEDPD-----FELLKELRKALGIPVIAEGRINSPEQAAKALELGADAVVV 205
Query: 296 GRA 298
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 = 29.6 bits (66), Expect = 2.8
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 272 LNGGINTVDEVNAALRKGAHHVMVGRAAYQNPWYT 306
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 = 29.4 bits (66), Expect = 3.6
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 337 AILGTYGNNRPHVRDVMKPL------LHFFHSEPGNGLFKRKADAAFQTCKTVKSFLEET 390
A L Y N P V+ KPL + FF + G FK K A+++ KT ++ +
Sbjct: 69 AALEEYEANPPKVQRGKKPLKPYEGDMPFFDNGDGTVTFKFKCYASYKDKKTGEN--KPI 126
Query: 391 IVAIPDS 397
++ + DS
Sbjct: 127 VLRVVDS 133
>gnl|CDD|218322 pfam04909, Amidohydro_2, Amidohydrolase. These proteins are
amidohydrolases that are related to pfam01979.
Length = 272
Score = 29.5 bits (66), Expect = 3.7
Identities = 26/177 (14%), Positives = 45/177 (25%), Gaps = 16/177 (9%)
Query: 94 HAWLYTEMLAAETIIYQQGNLDRFLAFSPEQHPIVLQIGGSNLDNLAKATELANAYNYDE 153
H + ++ ++G R SPE + ++ G + N
Sbjct: 6 HLPGGSIPDPRLPLMDRRGYDPRD--ASPEDYLVLGAALG--VARAVIVAASCRGANNRV 61
Query: 154 INLNCGCPSPKVAGHGCFGVSLMLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQ 213
+ P V G + E +A V + G
Sbjct: 62 LAEALKRPGRFVGG---AALPPPDPEDAAAELERRLAELGFRGVRLNPHPGGGPLLDPRL 118
Query: 214 LCDFIYKVSSLSPTRHFIIHSRKALLNGISPAENRTIPPLKYEYYYALLRDFPDLTF 270
++ L +H+ G + + PL L R FPDL
Sbjct: 119 DDPIFEALAELG--LPVDLHT----GFGDAGEDLDAAQPL---LLSGLARRFPDLKI 166
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 29.0 bits (66), Expect = 3.9
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRA 298
G INT ++ AL GAH V+VG A
Sbjct: 180 GRINTPEQAKKALELGAHAVVVGGA 204
>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 = 4.3
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 300
DLT L + TV+E+NAAL+ + + G Y
Sbjct: 243 DLTVELEKEV-TVEEINAALKAASEIGLKGILGY 275
>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 = 4.5
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 302
D F GG+++ ++V G V++G+A Y+
Sbjct: 182 DEEFIYAGGVSSAEDVKKLAEIGFSGVIIGKALYEG 217
>gnl|CDD|236869 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 29.1 bits (66), Expect = 4.9
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 7/45 (15%)
Query: 53 IILHTKAEMVARQYLPPWFSVAPMMDWTDNHYRTLARLISKHAWL 97
II +A+ V + P+ D +H + L + A L
Sbjct: 75 IIQRARAKYVTER-------GPPLRDRILSHTDLMGSLATPFAPL 112
>gnl|CDD|235237 PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like
protein; Reviewed.
Length = 232
Score = 28.6 bits (65), Expect = 5.6
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
GGI + ++ + GA ++VG ++P
Sbjct: 191 GGIRSPEQARELMAAGADTIVVGNIIEEDP 220
>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 = 5.8
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 127 IVLQIGGSNLDNLAKATELANAYNYDEINLNCGCPSPKVAGHGC----FGVSLMLDPKFV 182
IV++IGGS + +L K D+I N G V G G + L ++PKFV
Sbjct: 1 IVVKIGGSVVSDLDK--------VIDDIA-NFGERLIVVHGGGNYVNEYLKRLGVEPKFV 51
>gnl|CDD|237105 PRK12457, PRK12457, 2-dehydro-3-deoxyphosphooctonate aldolase;
Provisional.
Length = 281
Score = 28.6 bits (64), Expect = 5.8
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGR 297
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 = 6.1
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 176 MLDPKFVGEAMSVIAANTNVPVSVKCRIGVDDHDSYNQLCDFIYKVSSLSPTRHFII 232
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 = 6.3
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
G INT D+ AL GA V +GR +P
Sbjct: 291 GSINTPDDALEALETGADLVAIGRGLLVDP 320
>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: 272 LNGGINTVDEVNAALRKGAHHVMVGRA 298
L+GGI +V AL GA VM+GRA
Sbjct: 307 LDGGIRRGSDVVKALALGARAVMIGRA 333
>gnl|CDD|218990 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA).
This family consists of several Ribosomal protein L11
methyltransferase (EC:2.1.1.-) sequences.
Length = 294
Score = 28.4 bits (64), Expect = 6.8
Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 4/29 (13%)
Query: 54 ILHTKAEMVARQYLPPWFSVAPMM---DW 79
IL +A+ VA Y F + + +W
Sbjct: 259 ILEEQADDVAEAY-SQGFELITVEEREEW 286
>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 = 28.3 bits (64), Expect = 7.1
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 114 LDRFLAFSPEQHPIVLQIGGSNLDNLAKATELANAYNYDEIN 155
LD + SP L+I KA ELA YN + I
Sbjct: 70 LDELIKESPPTSLQELRIEIHK-----KAIELAKIYNEESIQ 106
>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 = 28.2 bits (64), Expect = 8.0
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 274 GGINTVDEVNAALRKGAHHVMVGRAAYQN 302
GG++++D++ A G V+VG+A Y+
Sbjct: 197 GGVSSLDDIKALKELGVAGVIVGKALYEG 225
>gnl|CDD|227584 COG5259, RSC8, RSC chromatin remodeling complex subunit RSC8
[Chromatin structure and dynamics / Transcription].
Length = 531
Score = 28.7 bits (64), Expect = 8.1
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 8 FAGSSLISSFTPFDSVLLKKHRRFSVNSFFKNSNNPRSLSTCTQNIILHTKAEMVARQYL 67
F G S + + K +R F +NS+ N N +++ C +N+ A + ++L
Sbjct: 78 FNGRSPSKTPEVY-----KDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAAIVRVHRFL 132
Query: 68 PPW 70
W
Sbjct: 133 EKW 135
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 8.8
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 259 YALLRDFPDLTF---TLNGGINTVDEVNAALRKGAHHVMVGRAAYQNP 303
Y L+ + F GGI T+++ G V + AA ++P
Sbjct: 63 YELIENLASECFMPLCYGGGIKTLEQAKKIFSLGVEKVSINTAALEDP 110
>gnl|CDD|225555 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase
[Carbohydrate transport and metabolism].
Length = 229
Score = 28.0 bits (63), Expect = 9.2
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 259 YALLRDFPDLTFTL--NGGINTVDEVNAALRKGAHHVMVGRA 298
+ 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 = 9.2
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 243 SPAENRTIPPLKYEYYYALLRDFPDLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAYQN 302
SPAE R PL++ A+L + +GG++ ++V L GA VM A ++
Sbjct: 218 SPAEIRL--PLRW---IAILSGRVKASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRH 272
>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 = 9.8
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 267 DLTFTLNGGINTVDEVNAALRKGAHHVMVGRAAY 300
DL L + TV+EVNAAL++ A + G Y
Sbjct: 242 DLVVNLEKDV-TVEEVNAALKEAAEGELKGVLGY 274
>gnl|CDD|237236 PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
Length = 340
Score = 28.1 bits (63), Expect = 9.8
Identities = 7/46 (15%), Positives = 11/46 (23%), Gaps = 11/46 (23%)
Query: 275 GINTVDEVNAALRKGAHHVMVGRAAYQNPWYTLGHVDTAIYGAPSS 320
G+ + +N L + A PW I
Sbjct: 303 GVANITRLNEVLERTAT-----------PWKDKYGGKDGIEVNDLP 337
>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 = 9.9
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 76 MMDWTDNHYRTLARLISKHAWLYTE--MLAAETIIY 109
++ 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 0.136 0.417
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: 22,822,108
Number of extensions: 2246302
Number of successful extensions: 1991
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1951
Number of HSP's successfully gapped: 72
Length of query: 436
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 336
Effective length of database: 6,502,202
Effective search space: 2184739872
Effective search space used: 2184739872
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 (21.9 bits)
S2: 60 (26.7 bits)