RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020428
(326 letters)
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 285 bits (731), Expect = 1e-96
Identities = 102/247 (41%), Positives = 132/247 (53%), Gaps = 18/247 (7%)
Query: 6 KLVLAPMVRVGTLPFRLLAAQYGADITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTDS 65
KL+LAPMV V LPFRLL +YGAD+ Y E I LL+ R+ +
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLL------------ 48
Query: 66 VVFRTCHQERNHVVFQMGTSDAVRALTAAKMVC-KDVAAIDINMGCPKSFSVSGGMGAAL 124
T + E ++ Q+G SD AAK+V ID+NMGCP GG GAAL
Sbjct: 49 ----TRNPEERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAAL 104
Query: 125 LSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQD-TVELARRIEKTGVSALAVHGRKVAD 183
L PEL+ +I+ ++ + +PVT KIRL ++ T+ELA+ +E G SAL VHGR
Sbjct: 105 LKDPELVAEIVRAVREAVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQ 164
Query: 184 RPRDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASIFS 243
R PA W IA+I A+SIPVIANGD+F +D R G VM RGAL N +F
Sbjct: 165 RYSGPADWDYIAEIKEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFR 224
Query: 244 SQGKLHW 250
+L
Sbjct: 225 EIKELLE 231
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 195 bits (497), Expect = 3e-60
Identities = 92/248 (37%), Positives = 125/248 (50%), Gaps = 22/248 (8%)
Query: 1 MDYQNKLVLAPMVRVGTLPFRLLAAQYGA-DITYGEEIIDHKLLKCERRVNEYIGSTDFV 59
++ +N+++LAPM V LPFR LA + GA D+ Y E + LL ++ +
Sbjct: 7 IELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLL-DELEE 65
Query: 60 EKGTDSVVFRTCHQERNHVVFQMGTSDAVRALTAAKMVCKDVAA-IDINMGCPKSFSVSG 118
E V Q+G SD AAK+ + A ID+N GCP V G
Sbjct: 66 E---------------RPVAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKG 110
Query: 119 GMGAALLSKPELIHDILTMLKRNL-DVPVTCKIRLLKSSQD--TVELARRIEKTGVSALA 175
G GAALL PEL+ +I+ + + D+PVT KIRL D +E+AR +E G AL
Sbjct: 111 GAGAALLKNPELLAEIVKAMVEAVGDIPVTVKIRLGWDDDDILALEIARILEDAGADALT 170
Query: 176 VHGRKVADRPRDPAKWGEIADIVAALS-IPVIANGDVFEYDDFQRIKTAAGASSVMAARG 234
VHGR A PA W I ++ A+ IPVIANGD+ +D + + GA VM RG
Sbjct: 171 VHGRTRAQGYLGPADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRG 230
Query: 235 ALWNASIF 242
AL N +F
Sbjct: 231 ALGNPWLF 238
>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 = 182 bits (463), Expect = 2e-55
Identities = 96/283 (33%), Positives = 131/283 (46%), Gaps = 29/283 (10%)
Query: 8 VLAPMVRVGTLPFRLLAAQYGA-DITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTDSV 66
+LAPM V LPFR L +YGA D+ E + +
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMV----------TAKAQLRPEK--------Q 42
Query: 67 VFRTCHQERN--HVVFQMGTSDAVRALTAAKMVC-KDVAAIDINMGCPKSFSVSGGMGAA 123
+ + Q+G SD AAK+V IDINMGCP GG GAA
Sbjct: 43 RELMLPELEEPTPLAVQLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAA 102
Query: 124 LLSKPELIHDILTMLKRNLDVPVTCKIRLL--KSSQDTVELARRIEKTGVSALAVHGRKV 181
LL P+L+ I+ + + +D+PVT KIR+ +S ++ VE+ARR+E G AL VHGR
Sbjct: 103 LLRDPDLVAQIVKAVVKAVDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTR 162
Query: 182 ADRPRDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASI 241
A PA W I + A+SIPVIANGD+ + +D QR + GA VM RGAL N +
Sbjct: 163 AQNYEGPADWDAIKQVKQAVSIPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWL 222
Query: 242 FSSQGKLHWEDVKREYVRKSIFWENNVKSTKHTLKEMIMHYSS 284
F+ Q + E+ + E +H L + Y
Sbjct: 223 FAEQHTVKT----GEFDPRPPLAEEAEIVLEH-LSYLEEFYGE 260
>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 = 148 bits (376), Expect = 2e-42
Identities = 82/243 (33%), Positives = 114/243 (46%), Gaps = 21/243 (8%)
Query: 5 NKLVLAPMVRVGTLPFRLLAAQYGADITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTD 64
+++VLAPM V PFR L A+YGA +T E + ++ +
Sbjct: 8 SRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYD-----------------SQ 50
Query: 65 SVVFRTCHQER-NHVVFQMGTSDAVRALTAAKMVCKDVAA-IDINMGCPKSFSVSGGMGA 122
+ E + Q+ SD AAK+ + A IDINMGCP G G+
Sbjct: 51 RTMRLLDIAEDETPISVQLFGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGS 110
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRL--LKSSQDTVELARRIEKTGVSALAVHGRK 180
ALL P+LI I+ + +D+PVT KIR+ + + VE AR E G A+ +HGR
Sbjct: 111 ALLRDPDLIGKIVKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRT 170
Query: 181 VADRPRDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNAS 240
A A W IA + A+ IPVI NGD+F +D + + G VM RGAL N
Sbjct: 171 RAQGYSGEANWDIIARVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPW 230
Query: 241 IFS 243
+F
Sbjct: 231 LFR 233
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 107 bits (268), Expect = 8e-27
Identities = 79/242 (32%), Positives = 114/242 (47%), Gaps = 21/242 (8%)
Query: 5 NKLVLAPMVRVGTLPFRLLAAQYGADITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTD 64
N+L+ APM + PFR L + GA +T V+E + S V + +D
Sbjct: 10 NRLIAAPMAGITDRPFRTLCYEMGAGLT----------------VSEMMSSNPQVWE-SD 52
Query: 65 SVVFRTCHQERNHV-VFQMGTSDAVRALTAAKM-VCKDVAAIDINMGCPKSFSVSGGMGA 122
R H + + Q+ SD AA++ V IDINMGCP G+
Sbjct: 53 KSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGS 112
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRL--LKSSQDTVELARRIEKTGVSALAVHGRK 180
ALL P+L+ ILT + +DVPVT KIR ++ VE+A+ E G+ AL +HGR
Sbjct: 113 ALLQYPDLVKSILTEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRT 172
Query: 181 VADRPRDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNAS 240
A A++ I + +SIPVIANGD+ + + + GA ++M R A
Sbjct: 173 RACLFNGEAEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPW 232
Query: 241 IF 242
IF
Sbjct: 233 IF 234
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 93.3 bits (232), Expect = 9e-22
Identities = 63/182 (34%), Positives = 96/182 (52%), Gaps = 13/182 (7%)
Query: 90 ALTAAKMVCKDVAAIDINMGCP-KSFSVSGGMGAALLSKPELIHDILTMLKRNL--DVPV 146
A AA+ V +D+N GCP K+ + SGG GA LL PELI+ ++ + +PV
Sbjct: 78 AENAARAVELGSWGVDLNCGCPSKTVNGSGG-GATLLKDPELIYQGAKAMREAVPAHLPV 136
Query: 147 TCKIRL-LKSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPA-KWGEIADIVAALSIP 204
T K+RL S + E+A +++ G + L VHGR D R W I +I L+IP
Sbjct: 137 TVKVRLGWDSGERKFEIADAVQQAGATELVVHGRTKEDGYRAEHINWQAIGEIRQRLTIP 196
Query: 205 VIANGDVFEYDDFQRIKTAAGASSVMAARGALW--NAS--IFSSQGKLHWEDVKR---EY 257
VIANG+++++ Q+ G +VM RGAL N S + ++ ++ W +V +Y
Sbjct: 197 VIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKY 256
Query: 258 VR 259
R
Sbjct: 257 TR 258
>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 = 61.8 bits (150), Expect = 8e-11
Identities = 32/112 (28%), Positives = 52/112 (46%), Gaps = 5/112 (4%)
Query: 74 ERNHVVFQMGTSDAVRALTAAKMVCK-DVAAIDINMGCPKSFSVSGGMGAALLSKPELIH 132
E + V Q+G SD AK+ K I++N+GCP +G GA L+ +L+
Sbjct: 53 EESPVALQLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVA 112
Query: 133 DILTMLKRNLDVPVTCKIRL----LKSSQDTVELARRIEKTGVSALAVHGRK 180
D + ++ +++PVT K R+ L S + + + G VH RK
Sbjct: 113 DCVKAMQEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARK 164
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 57.1 bits (139), Expect = 3e-09
Identities = 36/114 (31%), Positives = 54/114 (47%), Gaps = 17/114 (14%)
Query: 78 VVFQMGTSDAVRALTAAKMVCKDVAA------IDINMGCPKSFSVSGGM-GAALLSKPEL 130
V Q+G SD AAK+ A I++N+GCP S V G GA L+++PEL
Sbjct: 67 VALQLGGSDPADLAEAAKL-----AEDWGYDEINLNVGCP-SDRVQNGRFGACLMAEPEL 120
Query: 131 IHDILTMLKRNLDVPVTCKIRL----LKSSQDTVELARRIEKTGVSALAVHGRK 180
+ D + +K + +PVT K R+ S + + + + G VH RK
Sbjct: 121 VADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDFVDTVAEAGCDTFIVHARK 174
>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 = 51.2 bits (123), Expect = 1e-07
Identities = 52/147 (35%), Positives = 69/147 (46%), Gaps = 9/147 (6%)
Query: 90 ALTAAKMVCKDVAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCK 149
L AA +V K+ A ++IN C + V G G ALL PE + + + LK VPV+ K
Sbjct: 87 LLNAAALVAKNAAILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKE-TGVPVSVK 145
Query: 150 IRLLKSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVIANG 209
IR D ELAR IEK G + V A P + A +I DI L I I N
Sbjct: 146 IR-AGVDVDDEELARLIEKAGADIIHVD----AMDPGNHADLKKIRDISTELFI--IGNN 198
Query: 210 DVFEYDDFQRIKTAAGASSVMAARGAL 236
V + + + + GA V AR +L
Sbjct: 199 SVTTIESAKEM-FSYGADMVSVARASL 224
>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 = 48.5 bits (116), Expect = 2e-06
Identities = 39/160 (24%), Positives = 63/160 (39%), Gaps = 28/160 (17%)
Query: 101 VAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTV 160
A+++N+ CP + G G L PE + ++L +K +D+P+ K+ +D V
Sbjct: 125 AKALELNLSCP-----NVGGGRQLGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDLEDIV 179
Query: 161 ELARRIEKTGVSALAVHGR---KVADRPRDPAKWGEIA-------------DIVAALS-- 202
ELA+ E+ G L +V D VA L+
Sbjct: 180 ELAKAAERAGADGLTAINTISGRVVDLKTVGPGPKRGTGGLSGAPIRPLALRWVARLAAR 239
Query: 203 ----IPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWN 238
IP+I G + +D AGAS+V A +W+
Sbjct: 240 LQLDIPIIGVGGIDSGEDVLE-MLMAGASAVQVATALMWD 278
>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 = 44.9 bits (106), Expect = 2e-05
Identities = 39/166 (23%), Positives = 64/166 (38%), Gaps = 8/166 (4%)
Query: 73 QERNHVVFQMGTSDAVRALTAAKMVCKDVAAIDINMGCPKSFSVSGGMGAALLSKPELIH 132
+ R V + D A + + I+IN C + G+G LL EL+
Sbjct: 65 ESRALVSVNVRFVDLEEAYDVLLTIAEHADIIEINAHCRQPEITEIGIGQELLKNKELLK 124
Query: 133 DILTMLKRNLDVPVTCKIRLLKSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAKWG 192
+ LT +K L+ P+ KIR D + A + G + V A P P
Sbjct: 125 EFLTKMKE-LNKPIFVKIRGNCIPLDELIDALNLVDDGFDGIHVD----AMYPGKPYADM 179
Query: 193 EIADIVAAL--SIPVIANGDVFEYDDFQRIKTAAGASSVMAARGAL 236
++ I++ +I N + + + + + AGA V AR L
Sbjct: 180 DLLKILSEEFNDKIIIGNNSIDDIESAKEM-LKAGADFVSVARAIL 224
>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 = 44.8 bits (107), Expect = 2e-05
Identities = 46/163 (28%), Positives = 69/163 (42%), Gaps = 33/163 (20%)
Query: 90 ALTAAKMVCKDVAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCK 149
A K+ AI++N+ CP +V GG G A + PE + +I+ +K+ DVPV K
Sbjct: 105 VEVAEKLADAGADAIELNISCP---NVKGG-GMAFGTDPEAVAEIVKAVKKATDVPVIVK 160
Query: 150 IRLLKSSQDTVELARRIEKTGVSAL----AVHGRKVADRPRDPA---KWG---------- 192
L + D VE+AR E+ G L + G + R P G
Sbjct: 161 --LTPNVTDIVEIARAAEEAGADGLTLINTLKGMAIDIETRKPILGNVTGGLSGPAIKPI 218
Query: 193 ---EIADIVAALSIPVIANGDVFEYDD---FQRIKTAAGASSV 229
+ + A+ IP+I G + +D F AGAS+V
Sbjct: 219 ALRMVYQVYKAVEIPIIGVGGIASGEDALEF----LMAGASAV 257
>gnl|CDD|239201 cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN
binding domain. OYE was the first flavin-dependent
enzyme identified, however its true physiological role
remains elusive to this day. Each monomer of OYE
contains FMN as a non-covalently bound cofactor, uses
NADPH as a reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 327
Score = 42.6 bits (101), Expect = 2e-04
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 8/88 (9%)
Query: 157 QDTVELARRIEKTGVSALAV----HGRKVADRPRDPAKWGEIADIVA----ALSIPVIAN 208
++ +E+A+ +E+ GV AL V + P G ++ A+ IPVIA
Sbjct: 228 EEAIEIAKALEEAGVDALHVSGGSYESPPPIIPPPYVPEGYFLELAEKIKKAVKIPVIAV 287
Query: 209 GDVFEYDDFQRIKTAAGASSVMAARGAL 236
G + + + + I A V R L
Sbjct: 288 GGIRDPEVAEEILAEGKADLVALGRALL 315
>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 = 41.6 bits (98), Expect = 3e-04
Identities = 44/164 (26%), Positives = 68/164 (41%), Gaps = 27/164 (16%)
Query: 99 KDVAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQD 158
V A ++N+ CP V GG G A+ PEL D++ +K DVPV K L + D
Sbjct: 117 PYVDAYELNLSCP---HVKGG-GIAIGQDPELSADVVKAVKDKTDVPVFAK--LSPNVTD 170
Query: 159 TVELARRIEKTGVSAL----AVHGRKV---ADRPRDPAKWGEIA-------------DIV 198
E+A+ E+ G L + G K+ +P K G ++ D+
Sbjct: 171 ITEIAKAAEEAGADGLTLINTLRGMKIDIKTGKPILANKTGGLSGPAIKPIALRMVYDVY 230
Query: 199 AALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASIF 242
+ IP+I G + ++D AGAS+V + F
Sbjct: 231 KMVDIPIIGVGGITSFEDALEF-LMAGASAVQVGTAVYYRGFAF 273
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 41.4 bits (98), Expect = 4e-04
Identities = 42/157 (26%), Positives = 64/157 (40%), Gaps = 33/157 (21%)
Query: 98 CKDVAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQ 157
D AI++N+ CP + GG AL PEL+ +L +K VPV K+ +
Sbjct: 121 AGDADAIELNISCP---NTPGGR--ALGQDPELLEKLLEAVKAATKVPVFVKLA--PNIT 173
Query: 158 DTVELARRIEKTGVSAL-AVHGRKVADRPRDPAKWGEIADIVAALS-------------- 202
D E+A+ E+ G L A++ K + K +A+ LS
Sbjct: 174 DIDEIAKAAEEAGADGLIAINTTKSGMKIDLETKKPVLANETGGLSGPPLKPIALRVVAE 233
Query: 203 --------IPVIANGDVFEYDD-FQRIKTAAGASSVM 230
IP+I G + +D + I AGAS+V
Sbjct: 234 LYKRLGGDIPIIGVGGIETGEDALEFI--LAGASAVQ 268
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 39.4 bits (93), Expect = 0.002
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 101 VAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTV 160
V AI++N+ CP +V G G A + PEL ++++ +K + VPV K L + D V
Sbjct: 119 VDAIELNISCP---NVKHG-GMAFGTDPELAYEVVKAVKEVVKVPVIVK--LTPNVTDIV 172
Query: 161 ELARRIEKTGVSAL 174
E+A+ E+ G L
Sbjct: 173 EIAKAAEEAGADGL 186
>gnl|CDD|132195 TIGR03151, enACPred_II, putative enoyl-[acyl-carrier-protein]
reductase II. This oxidoreductase of the 2-nitropropane
dioxygenase family (pfam03060) is commonly found in
apparent operons with genes involved in fatty acid
biosynthesis. Furthermore, this genomic context
generally includes the fabG 3-oxoacyl-[ACP] reductase
and lacks the fabI enoyl-[ACP] reductase.
Length = 307
Score = 36.3 bits (84), Expect = 0.015
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 159 TVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVIANG 209
+V LA+R+EK G A+ G + + + +V A+SIPVIA G
Sbjct: 118 SVALAKRMEKAGADAVIAEGMESGGHIGELTTMALVPQVVDAVSIPVIAAG 168
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 35.7 bits (83), Expect = 0.019
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 12/81 (14%)
Query: 154 KSSQDTVELARRIEKTGVSALA-----VHGRKVADRPRDPAKWGEIADIVAALSIPVIAN 208
K+ VE A+R E+ G ++ V G +P + ++V ++ IPVIA+
Sbjct: 146 KTGYTPVEAAKRFEELGAGSILFTNVDVEGLLEGVNT-EP-----VKELVDSVDIPVIAS 199
Query: 209 GDVFEYDDFQRIKTAAGASSV 229
G V DD + +K AGA+ V
Sbjct: 200 GGVTTLDDLRALKE-AGAAGV 219
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 35.7 bits (83), Expect = 0.024
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 103 AIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVEL 162
A+++N CP GMGAA+ PEL+ +I ++ + +PV K L + D E+
Sbjct: 129 ALELNFSCPHGMP-ERGMGAAVGQDPELVEEICRWVREAVKIPVIAK--LTPNITDIREI 185
Query: 163 ARRIEKTGVSALA 175
AR ++ G ++
Sbjct: 186 ARAAKEGGADGVS 198
>gnl|CDD|239242 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs.
Length = 336
Score = 35.2 bits (82), Expect = 0.034
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 157 QDTVELARRIEKTGV------SALAVHGRKVADRPRDPAKWGEIADIV-AALSIPVIANG 209
+D+VELA+ +++ GV S +K+ P P A+ + IPVIA G
Sbjct: 241 EDSVELAKALKELGVDLIDVSSGGNSPAQKI---PVGPGYQVPFAERIRQEAGIPVIAVG 297
Query: 210 DVFEYDDFQRIKTAAGASSVMAARGALWN 238
+ + + + I + A V R L N
Sbjct: 298 LITDPEQAEAILESGRADLVALGRELLRN 326
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 34.1 bits (79), Expect = 0.066
Identities = 30/107 (28%), Positives = 48/107 (44%), Gaps = 18/107 (16%)
Query: 158 DTVELARRIEKTGVSALAVHGRKVADRPRDPAKWG----EIADIVAALSIPVIANGDVFE 213
D VE A+ +E+ G + + RD K G + A++IPVIA+G +
Sbjct: 156 DAVEWAKEVEELGAGEILLTSMD-----RDGTKAGYDLELTRAVREAVNIPVIASGGAGK 210
Query: 214 YDDFQRIKTAAGASSVMAARGALWNASIFSSQGKLHWEDVKREYVRK 260
+ F T A + +A ASIF G++ +VK EY+ +
Sbjct: 211 PEHFVEAFTEGKADAALA-------ASIF-HFGEITIGEVK-EYLAE 248
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 33.8 bits (78), Expect = 0.10
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 94 AKMVCKDVAA--IDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCK 149
A +V ++ A I++N GCP S GMG+A+ PEL+ +KR +PV K
Sbjct: 119 APLV-EETGADGIELNFGCPHGMS-ERGMGSAVGQVPELVEMYTRWVKRGSRLPVIVK 174
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 33.5 bits (78), Expect = 0.11
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 197 IVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASIF 242
+ A+++PVIA+G + F T GA + +A ASIF
Sbjct: 192 VSDAVNVPVIASGGAGNLEHFVEAFTEGGADAALA-------ASIF 230
>gnl|CDD|240082 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). Imidazole glycerol phosphate synthase
(IGPS) catalyzes the fifth step of histidine
biosynthesis, the formation of the imidazole ring. IGPS
converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria.
Length = 243
Score = 32.4 bits (75), Expect = 0.22
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 194 IADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASIF 242
I + +A++IPVIA+G + + F GA + +A ASIF
Sbjct: 185 IRAVSSAVNIPVIASGGAGKPEHFVEAFEEGGADAALA-------ASIF 226
>gnl|CDD|238317 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
synthase)/TenI. TMP synthase catalyzes an important step
in the thiamine biosynthesis pathway, the substitution
of the pyrophosphate of 2-methyl-4-amino-5-
hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-
(beta-hydroxyethyl) thiazole phosphate to yield thiamine
phosphate. TenI is a enzymatically inactive regulatory
protein involved in the regulation of several
extracellular enzymes. This superfamily also contains
other enzymatically inactive proteins with unknown
functions.
Length = 196
Score = 32.1 bits (74), Expect = 0.24
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 14/89 (15%)
Query: 159 TVELARRIEKTGVSALAVHG-------RKVADRPRDPAKWGEIADIVAALSIPVIANGDV 211
++E A R E+ G + G + A P + +I + IPV+A G +
Sbjct: 104 SLEEALRAEELGADYVGF-GPVFPTPTKPGAGPPLGLEL---LREIAELVEIPVVAIGGI 159
Query: 212 FEYDDFQRIKTAAGASSVMAARGALWNAS 240
++ + AAGA V A A+ A
Sbjct: 160 TP-ENAAEVL-AAGADGV-AVISAITGAD 185
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 32.6 bits (75), Expect = 0.24
Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 15/87 (17%)
Query: 155 SSQDTVELARRIEKTGVSAL--AVHGRKVADRPRDPAKWG----EIADIVAALSIPVIAN 208
+ ++ VELA+ +E+ G+ G + G A I A+ IPVIA
Sbjct: 235 TIEEAVELAKALEEAGLVDYIHVSEGGYERGGTITVSGPGYQVEFAARIKKAVRIPVIAV 294
Query: 209 GDVFEYDDFQRIKTAAGASSVMAARGA 235
G I A ++A+ A
Sbjct: 295 G---------GINDPEQAEEILASGRA 312
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 32.0 bits (74), Expect = 0.34
Identities = 25/79 (31%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 155 SSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAKWG----EIADIVAALSIPVIANGD 210
S +LA+R E GV A+ D RD G ++ AA+ IPVIA+G
Sbjct: 144 SGVTAEDLAKRFEDAGVKAIIY-----TDISRDGTLSGPNVEATRELAAAVPIPVIASGG 198
Query: 211 VFEYDDFQRIKTAAGASSV 229
V DD + +K V
Sbjct: 199 VSSLDDIKALKGLGAVEGV 217
>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 333
Score = 31.9 bits (73), Expect = 0.42
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 7/92 (7%)
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVELARR-IEKTGVSALAVHGRKV 181
A L PE + + + P+ I + + E A+ I+ ALA+H +
Sbjct: 93 AALKDPETADTFEVVREEAPNGPLIANIGAPQLVEGGPEEAQEAIDMIEADALAIHLNVL 152
Query: 182 ADRP-----RDPAKWGE-IADIVAALSIPVIA 207
+ R+ W E IA+I + LS+PVI
Sbjct: 153 QELVQPEGDRNFKGWLEKIAEICSQLSVPVIV 184
>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 = 31.3 bits (72), Expect = 0.49
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 10/84 (11%)
Query: 154 KSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAKWG----EIADIVAALSIPVIANG 209
++ D VE A+++E+ G + + D RD G ++ A++IPVIA+G
Sbjct: 145 ETGIDAVEWAKKLEELGAGEILLT-----DIDRDGTLSGPDLELTRELAEAVNIPVIASG 199
Query: 210 DVFEYDDFQRIKTAAGASSVMAAR 233
V +D + + + G V+A
Sbjct: 200 GVGSLEDLKELFS-EGVDGVIAGS 222
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 31.3 bits (72), Expect = 0.53
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 159 TVELARRIEKTGVSAL------AVHGRKVADRPRDPAKWGEIADIVAALSIPVIANG 209
T +L R E G AL V G R RD W ++A + P++ G
Sbjct: 125 TEDLLERAEAAGYKALVLTVDTPVLGN----RERDLRTWDDLAWLRDQWKGPLVVKG 177
>gnl|CDD|188639 cd00952, CHBPH_aldolase, Trans-o-hydroxybenzylidenepyruvate
hydratase-aldolase (HBPHA) and
trans-2'-carboxybenzalpyruvate hydratase-aldolase
(CBPHA). Trans-o-hydroxybenzylidenepyruvate
hydratase-aldolase (HBPHA) and
trans-2'-carboxybenzalpyruvate hydratase-aldolase
(CBPHA). HBPHA catalyzes HBP to salicyaldehyde and
pyruvate. This reaction is part of the degradative
pathways for naphthalene and naphthalenesulfonates by
bacteria. CBPHA is homologous to HBPHA and catalyzes the
cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate
during the degradation of phenanthrene. They are member
of the DHDPS family of Schiff-base-dependent class I
aldolases.
Length = 309
Score = 31.3 bits (71), Expect = 0.57
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 143 DVPVTCKIRLLKSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAK---WGEIADIVA 199
VPV L +++DT+ R + G + GR + + ++A+ V
Sbjct: 77 RVPVFVGATTL-NTRDTIARTRALLDLGADGTML-GRPMWLPLDVDTAVQFYRDVAEAVP 134
Query: 200 ALSIPVIANGDVFEYD 215
++I + AN + F++D
Sbjct: 135 EMAIAIYANPEAFKFD 150
>gnl|CDD|240081 cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the
nitroalkane oxidizing enzyme families, catalyzes
oxidative denitrification of nitroalkanes to their
corresponding carbonyl compounds and nitrites. NDP is a
member of the NAD(P)H-dependent flavin oxidoreductase
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.
Length = 236
Score = 31.3 bits (72), Expect = 0.57
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 159 TVELARRIEKTGVSALAV-------HGRKVADRPRDPAKWGEIADIVAALSIPVIANG 209
+VE AR+ E G AL H + ++ A+ IPVIA G
Sbjct: 111 SVEEARKAEAAGADALVAQGAEAGGHRGTFDIGTFAL-----VPEVRDAVDIPVIAAG 163
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 31.0 bits (71), Expect = 0.60
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 154 KSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPA----KWGEIADIVAALSIPVIANG 209
S + ELA+R+E+ G++ + D RD + ++ A+ IPVIA+G
Sbjct: 144 DSGVELEELAKRLEEVGLAHILYT-----DISRDGTLSGPNVDLVKELAEAVDIPVIASG 198
Query: 210 DVFEYDDFQRIKTAAGASSV 229
V DD + +K +G V
Sbjct: 199 GVSSLDDIKALKELSGVEGV 218
>gnl|CDD|218322 pfam04909, Amidohydro_2, Amidohydrolase. These proteins are
amidohydrolases that are related to pfam01979.
Length = 272
Score = 31.0 bits (70), Expect = 0.76
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 159 TVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPV 205
EL RR+ + G + ++ DP I + +A L +PV
Sbjct: 87 AAELERRLAELGFRGVRLNPHPGGGPLLDPRLDDPIFEALAELGLPV 133
>gnl|CDD|181086 PRK07695, PRK07695, transcriptional regulator TenI; Provisional.
Length = 201
Score = 30.4 bits (69), Expect = 0.91
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 193 EIADIVAALSIPVIANGDVFEYDDFQRIKTAAGAS--SVMAARGALWNASIFSSQGKLHW 250
E++DI ALSIPVIA G + ++ + + AAG S +VM+ IFSS
Sbjct: 140 ELSDIARALSIPVIAIGGITP-ENTRDVL-AAGVSGIAVMSG--------IFSSANPYSK 189
Query: 251 EDVKREYVRK 260
E ++K
Sbjct: 190 AKRYAESIKK 199
>gnl|CDD|236203 PRK08255, PRK08255, salicylyl-CoA 5-hydroxylase; Reviewed.
Length = 765
Score = 31.1 bits (71), Expect = 0.91
Identities = 26/100 (26%), Positives = 34/100 (34%), Gaps = 28/100 (28%)
Query: 157 QDTVELARRIEKTGVSAL------------AVHGR----KVADRPRDPAKWGEIADIVAA 200
D VE+AR + G + V+GR ADR R+ A
Sbjct: 638 DDAVEIARAFKAAGADLIDVSSGQVSKDEKPVYGRMYQTPFADRIRNEA----------- 686
Query: 201 LSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNAS 240
I IA G + E D I A A AR L + +
Sbjct: 687 -GIATIAVGAISEADHVNSIIAAGRADLCALARPHLADPA 725
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 30.3 bits (69), Expect = 1.4
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 21 RLLAAQYGADITYGEEIIDHKLLKC 45
R L +GA++ Y E +++H + +C
Sbjct: 785 RRLKENHGAELVYSEALVEHIVARC 809
>gnl|CDD|239205 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl
diphosphate isomerase type 2 (IDI-2) FMN-binding domain.
Two types of IDIs have been characterized at present.
The long known IDI-1 is only dependent on divalent
metals for activity, whereas IDI-2 requires a metal, FMN
and NADPH. IDI-2 catalyzes the interconversion of
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP) in the mevalonate pathway.
Length = 326
Score = 30.2 bits (69), Expect = 1.5
Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 19/62 (30%)
Query: 159 TVELARR-IEKTGVSALAVH-----------GRKVADRPRDPAKWGE-IADIVAALSIPV 205
VE ARR +E ALA+H G DR D W E I ++V ALS+PV
Sbjct: 128 GVEEARRAVEMIEADALAIHLNPLQEAVQPEG----DR--DFRGWLERIEELVKALSVPV 181
Query: 206 IA 207
I
Sbjct: 182 IV 183
>gnl|CDD|212495 cd09807, retinol-DH_like_SDR_c, retinol dehydrogenases
(retinol-DHs), classical (c) SDRs. Classical SDR-like
subgroup containing retinol-DHs and related proteins.
Retinol is processed by a medium chain alcohol
dehydrogenase followed by retinol-DHs. Proteins in this
subfamily share the glycine-rich NAD-binding motif of
the classical SDRs, have a partial match to the
canonical active site tetrad, but lack the typical
active site Ser. This subgroup includes the human
proteins: retinol dehydrogenase -12, -13 ,and -14. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 274
Score = 29.7 bits (67), Expect = 1.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 159 TVELARRIEKTGVSALAVH 177
T ELARR++ TGV+ A+H
Sbjct: 173 TRELARRLQGTGVTVNALH 191
>gnl|CDD|235465 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase;
Provisional.
Length = 352
Score = 29.7 bits (68), Expect = 2.1
Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 19/98 (19%)
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVELARR-IEKTGVSALAVH---- 177
A L PEL + K D + + ++ VE A+R +E AL +H
Sbjct: 100 AALKDPELADSFSVVRKVAPDGLLFANLGAVQLYGYGVEEAQRAVEMIEADALQIHLNPL 159
Query: 178 -------GRKVADRPRDPAKWGE-IADIVAALSIPVIA 207
G DR D W + IA+IV+AL +PVI
Sbjct: 160 QELVQPEG----DR--DFRGWLDNIAEIVSALPVPVIV 191
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 29.6 bits (67), Expect = 2.2
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 101 VAAIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKI 150
+++N+ CP + G AL + PEL +L ++K VPV K+
Sbjct: 119 ADYLELNVSCP---NTPGL--RALQTDPELAAILLKVVKEVSKVPVLVKL 163
>gnl|CDD|237805 PRK14726, PRK14726, bifunctional preprotein translocase subunit
SecD/SecF; Provisional.
Length = 855
Score = 29.3 bits (66), Expect = 3.0
Identities = 16/59 (27%), Positives = 25/59 (42%)
Query: 153 LKSSQDTVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVIANGDV 211
L+ + + A R + L +G+ V R DPA+ D + L+ PV A G
Sbjct: 71 LEETVANIRNALRDAGIRYTGLTGNGQTVQVRITDPAQTQAAVDALKPLTAPVSAGGLG 129
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 29.2 bits (66), Expect = 3.1
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 159 TVELARRIEKTGVSALAVHGRKVAD--------RPRDPAKWGEIADIVAALSIPVIA 207
E AR E+ G A+ R AD R DP I +I+ A+SIPV+A
Sbjct: 29 NAEQARIAEEAGAVAVMALERVPADIRAAGGVARMADPKM---IEEIMDAVSIPVMA 82
>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 = 28.8 bits (65), Expect = 3.4
Identities = 17/36 (47%), Positives = 21/36 (58%)
Query: 197 IVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAA 232
+ A+SIPVIA G DD + AGAS+V AA
Sbjct: 192 VSDAVSIPVIALGGAGSLDDLVEVALEAGASAVAAA 227
>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 = 29.1 bits (66), Expect = 3.5
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 9/87 (10%)
Query: 158 DTVELARRIEKTGVSALAVHGRKVAD-RPRDPAKWGEIADIVA---ALSIPVIANGDVFE 213
DT+ L ++ G+ L + R I ++V A +P+IA G +
Sbjct: 236 DTLALVDKLADKGLDYLHISLWDFDRKSRRGRDDNQTIMELVKERIAGRLPLIAVGSINT 295
Query: 214 YDDFQRIKTA--AGASSVMAARGALWN 238
DD A GA V RG L +
Sbjct: 296 PDD---ALEALETGADLVAIGRGLLVD 319
>gnl|CDD|107256 cd01543, PBP1_XylR, Ligand-binding domain of DNA transcription
repressor specific for xylose (XylR). Ligand-binding
domain of DNA transcription repressor specific for
xylose (XylR), a member of the LacI-GalR family of
bacterial transcription regulators. The ligand-binding
domain of XylR is structurally homologous to the
periplasmic sugar-binding domain of ABC-type
transporters and both domains contain the type I
periplasmic binding protein-like fold. The LacI-GalR
family repressors are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the type I periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcription
repressor undergoes a conformational change upon ligand
binding which in turn changes the DNA binding affinity
of the repressor.
Length = 265
Score = 28.3 bits (64), Expect = 4.5
Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 11/61 (18%)
Query: 184 RPRDPAKWG-----------EIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAA 232
R W E+A+ + L IPV+ E R+ T A MAA
Sbjct: 42 PLRWLKDWQGDGIIARIDDPEMAEALQKLGIPVVDVSGSREKPGIPRVTTDNAAIGRMAA 101
Query: 233 R 233
Sbjct: 102 E 102
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 28.6 bits (65), Expect = 4.6
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 6/41 (14%)
Query: 194 IADIVAALS---IPVIANGDV-FEYDDFQRIKTAAGASSVM 230
IAD A IPVIA+G + + D + + AAGAS+VM
Sbjct: 320 IADAAEAAKKYGIPVIADGGIRYSGDIAKAL--AAGASAVM 358
>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 = 28.3 bits (64), Expect = 4.8
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 17/81 (20%)
Query: 138 LKRNLDVPVTCKIRLLKSSQDT--VELARRIEKTGVSALAVHGRKVADRPRDPAKWGE-- 193
KR + +PV I L V+ AR+IE+ G AL ++ + P DP G
Sbjct: 94 AKRAVSIPV---IASLNGVSAGGWVDYARQIEEAGADALELNIYAL---PTDPDISGAEV 147
Query: 194 -------IADIVAALSIPVIA 207
+ + +A++IPV
Sbjct: 148 EQRYLDILRAVKSAVTIPVAV 168
>gnl|CDD|222337 pfam13714, PEP_mutase, Phosphoenolpyruvate phosphomutase. This
domain includes the enzyme Phosphoenolpyruvate
phosphomutase (EC:5.4.2.9). The PEP mutase from
Streptomyces viridochromogenes has been characterized as
catalyzing the formation of a carbon-phosphorus bond by
converting phosphoenolpyruvate (PEP) to
phosphonopyruvate (P-Pyr). This enzyme has a TIM barrel
fold.
Length = 238
Score = 28.3 bits (64), Expect = 4.9
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 158 DTVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVI 206
+ +E AR + G + V G K DP EIA + AA+ +P+
Sbjct: 156 EAIERARAYAEAGADGIFVPGLK------DPD---EIAALAAAVPLPLN 195
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 27.9 bits (62), Expect = 5.1
Identities = 40/234 (17%), Positives = 64/234 (27%), Gaps = 41/234 (17%)
Query: 7 LVLAPMVRVG---TLPFRLLAAQYGADITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGT 63
++LA + + AA+ GAD II
Sbjct: 1 VILALLAGGPSGDPVELAKAAAEAGADA-----IIVGTRSSDPEEAETDD---------- 45
Query: 64 DSVVFRTCHQERNHVVFQ-MGTSDAVRALTAAKMVCKDVA-AIDINMGCPKSFSVSGGMG 121
V+ + + Q A AA A ++I+
Sbjct: 46 KEVLKEVAAETDLPLGVQLAINDAAAAVDIAAAAARAAGADGVEIHGAVGYLARED---- 101
Query: 122 AALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVELARRIEKTGVSALAVHGRKV 181
ELI ++ + DV V K+ S A E+ GV + +
Sbjct: 102 ------LELIRELR---EAVPDVKVVVKL-----SPTGELAAAAAEEAGVDEVGLGNGGG 147
Query: 182 A--DRPRDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAAR 233
R P + +PVIA G + + +D A GA V+
Sbjct: 148 GGGGRDAVPIADLLLILAKRGSKVPVIAGGGINDPEDAAEAL-ALGADGVIVGS 200
>gnl|CDD|238223 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine
monophosphate dehydrogenase. IMPDH catalyzes the
NAD-dependent oxidation of inosine 5'-monophosphate
(IMP) to xanthosine 5' monophosphate (XMP). It is a
rate-limiting step in the de novo synthesis of the
guanine nucleotides. There is often a CBS domain
inserted in the middle of this domain, which is proposed
to play a regulatory role. IMPDH is a key enzyme in the
regulation of cell proliferation and differentiation. It
has been identified as an attractive target for
developing chemotherapeutic agents.
Length = 325
Score = 28.3 bits (64), Expect = 5.2
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 20/48 (41%)
Query: 194 IADIVAA---LSIPVIANGDVFEYDDFQRIKT--------AAGASSVM 230
+AD+ AA +PVIA+G I+T AAGA +VM
Sbjct: 186 VADVAAAARDYGVPVIADGG---------IRTSGDIVKALAAGADAVM 224
>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 = 28.4 bits (64), Expect = 5.3
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 159 TVELARRIEKTGVSALAVHGRKVAD--------RPRDPAKWGEIADIVAALSIPVIA 207
E AR E+ G A+ R AD R DP I +I+ A+SIPV+A
Sbjct: 17 NAEQARIAEEAGAVAVMALERVPADIRAAGGVARMADPKM---IKEIMDAVSIPVMA 70
>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 = 27.8 bits (62), Expect = 6.2
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 159 TVELARRIEKTGVSALAVHGRKVAD--------RPRDPAKWGEIADIVAALSIPVIA 207
E AR E+ G A+ R AD R DP I +I+ A+SIPV+A
Sbjct: 12 NAEQARIAEEAGAVAVMALERVPADIRAAGGVARMSDPKM---IKEIMNAVSIPVMA 65
>gnl|CDD|239240 cd02930, DCR_FMN, 2,4-dienoyl-CoA reductase (DCR) FMN-binding
domain. DCR in E. coli is an iron-sulfur flavoenzyme
which contains FMN, FAD, and a 4Fe-4S cluster. It is
also a monomer, unlike that of its eukaryotic
counterparts which form homotetramers and lack the
flavin and iron-sulfur cofactors. Metabolism of
unsaturated fatty acids requires auxiliary enzymes in
addition to those used in b-oxidation. After a given
number of cycles through the b-oxidation pathway, those
unsaturated fatty acyl-CoAs with double bonds at
even-numbered carbon positions contain 2-trans, 4-cis
double bonds that can not be modified by enoyl-CoA
hydratase. DCR utilizes NADPH to remove the C4-C5 double
bond. DCR can catalyze the reduction of both natural
fatty acids with cis double bonds, as well as substrates
containing trans double bonds. The reaction is initiated
by hybrid transfer from NADPH to FAD, which in turn
transfers electrons, one at a time, to FMN via the
4Fe-4S cluster. The fully reduced FMN provides a hydrid
ion to the C5 atom of substrate, and Tyr and His are
proposed to form a catalytic dyad that protonates the C4
atom of the substrate and completes the reaction.
Length = 353
Score = 28.0 bits (63), Expect = 6.5
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 21/87 (24%)
Query: 155 SSQD-TVELARRIEKTGVSALAV----HGRKV----ADRPRDPAKWGEIADIV-AALSIP 204
S+ + V LA+ +E G L H +V PR + + A+ IP
Sbjct: 221 STWEEVVALAKALEAAGADILNTGIGWHEARVPTIATSVPR--GAFAWATAKLKRAVDIP 278
Query: 205 VIANGDVFEYDDFQRIKTAAGASSVMA 231
VIA+ RI T A ++A
Sbjct: 279 VIAS---------NRINTPEVAERLLA 296
>gnl|CDD|193521 cd05643, M28_like_7, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They typically have
co-catalytic zinc ions; each zinc ion is tetrahedrally
co-ordinated, with three amino acid ligands plus
activated water; one aspartate residue binds both metal
ions. This protein subfamily conserves some of the
metal-coordinating residues of the typically
co-catalytic M28 family which might suggest binding of a
single metal ion.
Length = 288
Score = 28.1 bits (63), Expect = 6.5
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 32 TYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTDSVVF 68
+Y +E++ KL N G + E G+D +F
Sbjct: 181 SYLDELLYDKLENVALPEN-RYGRKEPYEGGSDHDIF 216
>gnl|CDD|184335 PRK13802, PRK13802, bifunctional indole-3-glycerol phosphate
synthase/tryptophan synthase subunit beta; Provisional.
Length = 695
Score = 28.5 bits (63), Expect = 6.5
Identities = 35/114 (30%), Positives = 51/114 (44%), Gaps = 18/114 (15%)
Query: 138 LKRNLDVPVTCKIRLLKSSQ-------DTVELARRIEKTGVSALAV--HGRKVADRPRDP 188
LKR +PV +I+ S+ D LAR E+ G SA++V GR+ D
Sbjct: 44 LKRADGIPVIAEIKRASPSKGHLSDIPDPAALAREYEQGGASAISVLTEGRRFLGSLDDF 103
Query: 189 AKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAA-GASSVMAARGALWNASI 241
K + AA+ IPV+ F D+Q + A GA V+ AL +A +
Sbjct: 104 DK------VRAAVHIPVLRKD--FIVTDYQIWEARAHGADLVLLIVAALDDAQL 149
>gnl|CDD|183711 PRK12738, kbaY, tagatose-bisphosphate aldolase; Reviewed.
Length = 286
Score = 27.7 bits (61), Expect = 7.6
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 158 DTVELARRIEKTGVSALAV-----HGRKVADRPRDPAKWGEIADIVAALSIPVIANGDVF 212
D E R +E TGV +LAV HG + P+ + +A+I + +P++ +G
Sbjct: 156 DPQEAKRFVELTGVDSLAVAIGTAHGL-YSKTPK--IDFQRLAEIREVVDVPLVLHGASD 212
Query: 213 EYDDFQRIKTAAGASSVMAA 232
D+F R G + V A
Sbjct: 213 VPDEFVRRTIELGVTKVNVA 232
>gnl|CDD|180098 PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed.
Length = 127
Score = 27.0 bits (61), Expect = 7.7
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 204 PVIANGDVFEYDDFQRIKTAAGA---SSVM-AARGALWNASI--FS--SQGKLH 249
PV+A G+ FEY ++T +G M G + I F LH
Sbjct: 74 PVLAPGESFEYTSGAVLETPSGTMQGHYQMVDEDGERFEVPIPPFRLAVPRTLH 127
>gnl|CDD|236579 PRK09585, anmK, anhydro-N-acetylmuramic acid kinase; Reviewed.
Length = 365
Score = 27.8 bits (63), Expect = 8.0
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 165 RIEKTGVSALAVHGRKVADRPRDPAKW--GEIADIVAALSIPVIAN 208
+ + A+ HG+ V RP + G+ A I I V+A+
Sbjct: 85 GLSPEDIDAIGSHGQTVRHRPGEGFTLQIGDGALIAELTGITVVAD 130
>gnl|CDD|218067 pfam04402, SIMPL, Protein of unknown function (DUF541). Members of
this family have so far been found in bacteria and mouse
SwissProt or TrEMBL entries. However possible family
members have also been identified in translated rat
(Genbank:AW144450) and human (Genbank:AI478629) ESTs. A
mouse family member has been named SIMPL (signalling
molecule that associates with mouse pelle-like kinase).
SIMPL appears to facilitate and/or regulate complex
formation between IRAK/mPLK (IL-1 receptor-associated
kinase) and IKK (inhibitor of kappa-B kinase) containing
complexes, and thus regulate NF-kappa-B activity.
Separate experiments demonstrate that a mouse family
member (named LaXp180) binds the Listeria monocytogenes
surface protein ActA, which is a virulence factor that
induces actin polymerisation. It may also bind stathmin,
a protein involved in signal transduction and in the
regulation of microtubule dynamics. In bacteria its
function is unknown, but it is thought to be located in
the periplasm or outer membrane.
Length = 210
Score = 27.7 bits (62), Expect = 8.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 186 RDPAKWGEIADIVAALSIPVIANGDV-FEYDDFQRIKTAAGASSVMAAR 233
RD K GE+ D + A ++ + F D +K A A +V AR
Sbjct: 91 RDLEKLGELLDALVAAGANNVSISGIEFSLSDEAELKDEALAEAVKDAR 139
>gnl|CDD|177430 PHA02605, 54, baseplate subunit; Provisional.
Length = 305
Score = 27.9 bits (62), Expect = 8.4
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 60 EKGTDSVVFRTCHQERNHVVFQMGTSDAVRALTAAKMVCKDV-AAIDIN----MGCPKSF 114
E + FR + N+ Q + +T + + DV A I +N G P +
Sbjct: 154 EYDPLVLSFRMDSEASNYRAMQDWVNAVQDPVTGLRALPDDVEADIQVNLHNRDGLPHTV 213
Query: 115 SVSGGMGAALLSKPELIHD 133
+ G +S PEL ++
Sbjct: 214 VMFNGCIPVSVSSPELSYE 232
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 27.8 bits (63), Expect = 9.5
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 157 QDTVELARRIEKTGVSALAVHG 178
++ E+A + G SALA+HG
Sbjct: 253 KECQEVADALNAQGFSALALHG 274
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
0.319 0.134 0.387
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,724,409
Number of extensions: 1617365
Number of successful extensions: 1775
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1734
Number of HSP's successfully gapped: 91
Length of query: 326
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 229
Effective length of database: 6,635,264
Effective search space: 1519475456
Effective search space used: 1519475456
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: 59 (26.4 bits)