RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7343
(487 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 = 298 bits (765), Expect = 1e-99
Identities = 107/233 (45%), Positives = 146/233 (62%), Gaps = 4/233 (1%)
Query: 150 RFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQ 209
+ ILAPMV ++LP+RLL RRYG+ L YT M+SA + + R +L PE+RPLI+Q
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 210 FCGNDSKNLTEAAKLAEP-HCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSLRQ 268
G+D + L EAAK+ E DGID+N+GCP +G GA L D L+ +V ++R+
Sbjct: 61 LGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVRE 120
Query: 269 AVQVPVSCKIRI-YQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAV 327
AV +PV+ KIR+ + D +T+E A+ LE AG L VHGRT +QR +G A W++I +
Sbjct: 121 AVPIPVTVKIRLGWDDEEETLELAKALEDAGASALTVHGRTREQR--YSGPADWDYIAEI 178
Query: 328 RKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALFTGQTRPAW 380
++A++IPVIANG+I L D CL QTGV GVM G L NP LF
Sbjct: 179 KEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
Score = 82.5 bits (205), Expect = 5e-18
Identities = 30/60 (50%), Positives = 41/60 (68%)
Query: 80 RFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQ 139
+ ILAPMV ++LP+RLL RRYG+ L YT M+SA + + R +L PE+RPLI+Q
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
>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 = 239 bits (613), Expect = 1e-75
Identities = 108/278 (38%), Positives = 146/278 (52%), Gaps = 22/278 (7%)
Query: 152 ILAPMVDASELPWRLLSRRYGSH-LCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQF 210
+LAPM ++LP+R L R YG+ L T MV+A + +K R+ +L E PL +Q
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQL 60
Query: 211 CGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSLRQA 269
G+D L EAAKL D IDIN+GCP RG GA L D L+ +V ++ +A
Sbjct: 61 GGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKA 120
Query: 270 VQVPVSCKIRIYQDVNK--TVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAV 327
V +PV+ KIRI D + VE AR +E AG Q L VHGRT Q G A W+ I V
Sbjct: 121 VDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTRAQNY--EGPADWDAIKQV 178
Query: 328 RKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALFTGQTR---------- 377
++A++IPVIANG+I D + CL+ TG GVM G L NP LF Q
Sbjct: 179 KQAVSIPVIANGDITDAEDAQRCLSYTGADGVMIGRGALGNPWLFAEQHTVKTGEFDPRP 238
Query: 378 PAWE---LASEYLDLVAQY---PVRLQYARGHVFNMCH 409
P E + E+L + ++ L++AR H+
Sbjct: 239 PLAEEAEIVLEHLSYLEEFYGEDKGLRHARKHLAWYLK 276
Score = 62.3 bits (152), Expect = 1e-10
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 82 ILAPMVDASELPWRLLSRRYGSH-LCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQ 139
+LAPM ++LP+R L R YG+ L T MV+A + +K R+ +L E PL +Q
Sbjct: 1 LLAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQ 59
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 222 bits (569), Expect = 6e-69
Identities = 115/327 (35%), Positives = 165/327 (50%), Gaps = 36/327 (11%)
Query: 142 IFPRLGSPRFILAPMVDASELPWRLLSRRYGS-HLCYTPMVSAHQFI-ADKKLRQEILMS 199
I R ILAPM ++LP+R L+R G+ L YT MVSA + KK +
Sbjct: 4 IGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDEL 63
Query: 200 TPEDRPLIIQFCGNDSKNLTEAAKLAEPHC-DGIDINIGCPQMVAKRGHYGAYLQDDWPL 258
E+RP+ +Q G+D + L EAAK+AE D ID+N GCP +G GA L + L
Sbjct: 64 -EEERPVAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKGGAGAALLKNPEL 122
Query: 259 LTNLVSSLRQAV-QVPVSCKIRI---YQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGM 314
L +V ++ +AV +PV+ KIR+ D+ +E AR+LE AG L VHGRT Q
Sbjct: 123 LAEIVKAMVEAVGDIPVTVKIRLGWDDDDIL-ALEIARILEDAGADALTVHGRTRAQGY- 180
Query: 315 NTGLASWEHITAVRKAL-TIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALF- 372
G A W++I +++A+ +IPVIANG+I+ L D + L TG GVM G L NP LF
Sbjct: 181 -LGPADWDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGNPWLFR 239
Query: 373 ------TGQTRPA-W----ELASEYLDLVAQYPVRLQYARGHVFNMCHHLL----TLPEN 417
TG+ P ++ E+L+L+ +Y Y + + + HL LP
Sbjct: 240 QIDYLETGELLPPTLAEVLDILREHLELLLEY-----YGKKGLRRLRKHLGYYLKGLPGA 294
Query: 418 SDVRLLVGKTNHIKDLRKAVDMLRERF 444
++R N +D + L F
Sbjct: 295 RELR---RALNKAEDGAEVRRALEAVF 318
Score = 61.6 bits (150), Expect = 2e-10
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 77 GSPRFILAPMVDASELPWRLLSRRYGS-HLCYTPMVSAHQFI-ADKKLRQEILMSTPEDR 134
R ILAPM ++LP+R L+R G+ L YT MVSA + KK + E+R
Sbjct: 9 LRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDEL-EEER 67
Query: 135 PLIIQ 139
P+ +Q
Sbjct: 68 PVAVQ 72
>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 = 171 bits (436), Expect = 1e-49
Identities = 110/317 (34%), Positives = 159/317 (50%), Gaps = 31/317 (9%)
Query: 150 RFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDRPLIIQ 209
R +LAPM ++ P+R L YG+ L MVS+ + D + +L ++ P+ +Q
Sbjct: 9 RVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQ 68
Query: 210 FCGNDSKNLTEAAKLAEPH-CDGIDINIGCP-QMVAKRGHYGAYLQDDWPLLTNLVSSLR 267
G+D + EAAK+ E D IDIN+GCP + K+G A L+D L+ +V ++
Sbjct: 69 LFGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDP-DLIGKIVKAVV 127
Query: 268 QAVQVPVSCKIRIYQDVNK--TVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHIT 325
AV +PV+ KIRI D VE AR+ E AG Q + +HGRT Q +G A+W+ I
Sbjct: 128 DAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQ--GYSGEANWDIIA 185
Query: 326 AVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALF--------TGQTR 377
V++A+ IPVI NG+I D +A L TG GVM G L NP LF TG+ +
Sbjct: 186 RVKQAVRIPVIGNGDIFSPEDAKAMLETTGCDGVMIGRGALGNPWLFRQIEQYLTTGKYK 245
Query: 378 PAWELAS------EYLDLVAQY---PVRLQYARGHVFNMCHHLLTLPENSDVRLLVGKTN 428
P A +L L+A Y L+ AR H+ +L P N+ +R + N
Sbjct: 246 PPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHI---AWYLKGFPGNAALRQTL---N 299
Query: 429 HIKDLRKAVDMLRERFI 445
H + V L + F
Sbjct: 300 HASS-FQEVKQLLDDFF 315
Score = 45.4 bits (108), Expect = 3e-05
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 75 QLGSPRFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILMSTPEDR 134
QL S R +LAPM ++ P+R L YG+ L MVS+ + D + +L ++
Sbjct: 5 QLKS-RVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDET 63
Query: 135 PLIIQ 139
P+ +Q
Sbjct: 64 PISVQ 68
>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 = 101 bits (253), Expect = 7e-24
Identities = 72/246 (29%), Positives = 119/246 (48%), Gaps = 27/246 (10%)
Query: 150 RFILAPMVDASELPWRLLSRRYGSH-LCYTPMVSAHQFIADKKLRQEILMSTPEDRPLII 208
RF +APM+D ++ +R R H L YT M++A I K ++IL +PE+ P+ +
Sbjct: 2 RFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDK--KDILKFSPEESPVAL 59
Query: 209 QFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSLR 267
Q G+D +L + AK+AE D I++N+GCP + G++GA L + L+ + V +++
Sbjct: 60 QLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAMQ 119
Query: 268 QAVQVPVSCKIRI-------YQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGM----NT 316
+AV +PV+ K RI Y+ + ++ ++ GCQ VH R G+ N
Sbjct: 120 EAVNIPVTVKHRIGIDPLDSYEFL---CDFVEIVSGKGCQNFIVHARKAWLSGLSPKENR 176
Query: 317 GLASWEHITAVR-----KALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPAL 371
+ + + LTI + NG I+ ++ L+ V GVM NP L
Sbjct: 177 EIPPLRYERVYQLKKDFPHLTIEI--NGGIKNSEQIKQHLSH--VDGVMVGREAYENPYL 232
Query: 372 FTGQTR 377
R
Sbjct: 233 LANVDR 238
Score = 41.0 bits (96), Expect = 8e-04
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 80 RFILAPMVDASELPWRLLSRRYGSH-LCYTPMVSAHQFIADKKLRQEILMSTPEDRPLII 138
RF +APM+D ++ +R R H L YT M++A I K ++IL +PE+ P+ +
Sbjct: 2 RFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDK--KDILKFSPEESPVAL 59
Query: 139 Q 139
Q
Sbjct: 60 Q 60
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 100 bits (251), Expect = 1e-23
Identities = 80/248 (32%), Positives = 121/248 (48%), Gaps = 19/248 (7%)
Query: 150 RFILAPMVDASELPWRLLSRRYGSHLCYTPMVSAH-QFIADKKLRQEILMSTPEDRPLI- 207
R I APM ++ P+R L G+ L + M+S++ Q K R ++ D P I
Sbjct: 11 RLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVHI---DEPGIR 67
Query: 208 -IQFCGNDSKNLTEAAKL-AEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSS 265
+Q G+D K + +AA++ E IDIN+GCP R G+ L L+ ++++
Sbjct: 68 TVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTE 127
Query: 266 LRQAVQVPVSCKIRI--YQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEH 323
+ AV VPV+ KIR + VE A++ E G Q L +HGRT + + G A ++
Sbjct: 128 VVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRT--RACLFNGEAEYDS 185
Query: 324 ITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPALF--------TGQ 375
I AV++ ++IPVIANG+I A L TG +M P +F TG+
Sbjct: 186 IRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGE 245
Query: 376 TRPAWELA 383
P LA
Sbjct: 246 LLPPLPLA 253
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 93.7 bits (233), Expect = 3e-21
Identities = 63/176 (35%), Positives = 87/176 (49%), Gaps = 5/176 (2%)
Query: 200 TPEDRPLIIQFCGNDSKNLTE-AAKLAEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPL 258
TP + IQ G + L E AA+ E G+D+N GCP GA L D L
Sbjct: 59 TPSGTLVRIQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPEL 118
Query: 259 LTNLVSSLRQAV--QVPVSCKIRIYQDV-NKTVEYARMLERAGCQLLAVHGRTVDQRGMN 315
+ ++R+AV +PV+ K+R+ D + E A +++AG L VHGRT + G
Sbjct: 119 IYQGAKAMREAVPAHLPVTVKVRLGWDSGERKFEIADAVQQAGATELVVHGRTKED-GYR 177
Query: 316 TGLASWEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPAL 371
+W+ I +R+ LTIPVIANG I + C+A TG VM G L P L
Sbjct: 178 AEHINWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNIPNL 233
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 91.3 bits (228), Expect = 3e-20
Identities = 63/177 (35%), Positives = 90/177 (50%), Gaps = 30/177 (16%)
Query: 148 SPRFILAPMVDASELPW---------RLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILM 198
S RF +APM+D W RLLSR L YT MV+ I + R +L
Sbjct: 10 SRRFSVAPMMD-----WTDRHCRYFHRLLSRHA---LLYTEMVTTGAIIHGDRER--LLA 59
Query: 199 STPEDRPLIIQFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWP 257
PE+ P+ +Q G+D +L EAAKLAE D I++N+GCP + G +GA L +
Sbjct: 60 FDPEEHPVALQLGGSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACLMAEPE 119
Query: 258 LLTNLVSSLRQAVQVPVSCKIRI-------YQDVNKTVEYARMLERAGCQLLAVHGR 307
L+ + V +++ AV +PV+ K RI Y+ + V+ + E AGC VH R
Sbjct: 120 LVADCVKAMKDAVSIPVTVKHRIGIDDQDSYEFLCDFVD--TVAE-AGCDTFIVHAR 173
Score = 33.6 bits (78), Expect = 0.20
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 19/71 (26%)
Query: 78 SPRFILAPMVDASELPW---------RLLSRRYGSHLCYTPMVSAHQFIADKKLRQEILM 128
S RF +APM+D W RLLSR L YT MV+ I + R +L
Sbjct: 10 SRRFSVAPMMD-----WTDRHCRYFHRLLSRHA---LLYTEMVTTGAIIHGDRER--LLA 59
Query: 129 STPEDRPLIIQ 139
PE+ P+ +Q
Sbjct: 60 FDPEEHPVALQ 70
>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 = 60.1 bits (146), Expect = 5e-10
Identities = 49/209 (23%), Positives = 78/209 (37%), Gaps = 37/209 (17%)
Query: 190 KKLRQEILMSTPE-DRPLIIQFCGNDSKNLTEAAK---LAEPHCDGIDINIGCPQMVAKR 245
+ +E+ E PLI G+ + E A+ A P+ D ++N+ CP +
Sbjct: 76 EAFLEELKPVREEFPTPLIASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKG-- 133
Query: 246 GHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLAVH 305
G + D L ++V +++ VPV K+ +V E A+ E AG L
Sbjct: 134 --GGIAIGQDPELSADVVKAVKDKTDVPVFAKLS--PNVTDITEIAKAAEEAGADGL-TL 188
Query: 306 GRTVDQRGMNTGLASWEHITA---------------------VRKALTIPVIANGNIQCL 344
T+ RGM + + + I A V K + IP+I G I
Sbjct: 189 INTL--RGMKIDIKTGKPILANKTGGLSGPAIKPIALRMVYDVYKMVDIPIIGVGGITSF 246
Query: 345 AD-VEACLAQTGVAGVMTAEGNLYNPALF 372
D +E +A G + V Y F
Sbjct: 247 EDALEFLMA--GASAVQVGTAVYYRGFAF 273
>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 = 56.6 bits (137), Expect = 7e-09
Identities = 49/192 (25%), Positives = 78/192 (40%), Gaps = 28/192 (14%)
Query: 203 DRPLIIQFCGNDSKNLTEAAKLAEP-HCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTN 261
+PLI G+ ++ E A+ E +++N+ CP + R D + N
Sbjct: 98 GQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCPNVGGGRQLG-----QDPEAVAN 152
Query: 262 LVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLA----VHGRTVDQRGMNTG 317
L+ +++ AV +P+ K+ Y D+ VE A+ ERAG L + GR VD + + G
Sbjct: 153 LLKAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVDLKTVGPG 212
Query: 318 LAS----------------WEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMT 361
W A R L IP+I G I DV L G + V
Sbjct: 213 PKRGTGGLSGAPIRPLALRWVARLAARLQLDIPIIGVGGIDSGEDVLEML-MAGASAVQV 271
Query: 362 AEGNLYN-PALF 372
A +++ P +
Sbjct: 272 ATALMWDGPDVI 283
>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 = 56.4 bits (137), Expect = 1e-08
Identities = 34/128 (26%), Positives = 51/128 (39%), Gaps = 14/128 (10%)
Query: 258 LLTNLVSSLRQAV--QVPVSCKIRIYQDVNK------TVEYARMLERAGCQLLAVHGRTV 309
L +V+++R+AV PV ++ V +E A+ LE AG L V G +
Sbjct: 193 FLLEIVAAVREAVGPDFPVGVRLSADDFVPGGLTLEEAIEIAKALEEAGVDALHVSGGSY 252
Query: 310 DQRGMNTG------LASWEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTAE 363
+ E ++KA+ IPVIA G I+ E LA+ V
Sbjct: 253 ESPPPIIPPPYVPEGYFLELAEKIKKAVKIPVIAVGGIRDPEVAEEILAEGKADLVALGR 312
Query: 364 GNLYNPAL 371
L +P L
Sbjct: 313 ALLADPDL 320
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 49.4 bits (119), Expect = 2e-06
Identities = 58/199 (29%), Positives = 87/199 (43%), Gaps = 45/199 (22%)
Query: 203 DRPLIIQFCGNDSKNLTEAAKLAE--PHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLT 260
D P+I G+ + E A+ P+ D I++NI CP K H G D L
Sbjct: 91 DTPIIANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPN--VK--HGGMAFGTDPELAY 146
Query: 261 NLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQ-LLAVHGRTVDQRGM----N 315
+V ++++ V+VPV K+ V VE A+ E AG L ++ T+ +GM
Sbjct: 147 EVVKAVKEVVKVPVIVKLTPN--VTDIVEIAKAAEEAGADGLSLIN--TL--KGMAIDIK 200
Query: 316 TG---LASWEHIT-----------AVR------KALTIPVIANGNIQCLAD-VEACLA-Q 353
T LA ++T A+R +A+ IP+I G I D +E +A
Sbjct: 201 TRKPILA---NVTGGLSGPAIKPIALRMVYQVYQAVDIPIIGMGGISSAEDAIEFIMAGA 257
Query: 354 TGVAGVMTAEGNLYNPALF 372
+ V V TA N Y+P F
Sbjct: 258 SAVQ-VGTA--NFYDPYAF 273
>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 = 51/171 (29%), Positives = 69/171 (40%), Gaps = 27/171 (15%)
Query: 221 AAKLAEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRI 280
A KLA+ D I++NI CP G D + +V ++++A VPV K+
Sbjct: 108 AEKLADAGADAIELNISCPN----VKGGGMAFGTDPEAVAEIVKAVKKATDVPVIVKLT- 162
Query: 281 YQDVNKTVEYARMLERAGCQLL----AVHGRTVDQR------GMNTGLAS--WEHITAVR 328
+V VE AR E AG L + G +D G TG S A+R
Sbjct: 163 -PNVTDIVEIARAAEEAGADGLTLINTLKGMAIDIETRKPILGNVTGGLSGPAIKPIALR 221
Query: 329 ------KALTIPVIANGNIQCLADV-EACLAQTGVAGVMTAEGNLYNPALF 372
KA+ IP+I G I D E +A V TA N +P F
Sbjct: 222 MVYQVYKAVEIPIIGVGGIASGEDALEFLMAGASAVQVGTA--NFVDPEAF 270
>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 = 45.0 bits (107), Expect = 3e-05
Identities = 32/121 (26%), Positives = 50/121 (41%), Gaps = 18/121 (14%)
Query: 257 PLLTNLVSSL--RQAVQVPVSCK-------IRIYQDVNKT------VEYARMLERAGCQL 301
P L + Q V V + K ++Y D + VE+AR E+ G
Sbjct: 110 PDLIEEAARRFGSQCVVVSIDVKKELDGSDYKVYSDNGRRATGRDPVEWAREAEQLGAGE 169
Query: 302 LAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMT 361
+ ++ ++D+ G G E I V A++IPVIA G L D+ + G + V
Sbjct: 170 ILLN--SIDRDGTMKGY-DLELIKTVSDAVSIPVIALGGAGSLDDLVEVALEAGASAVAA 226
Query: 362 A 362
A
Sbjct: 227 A 227
>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 = 44.6 bits (106), Expect = 6e-05
Identities = 30/99 (30%), Positives = 50/99 (50%), Gaps = 5/99 (5%)
Query: 203 DRPLIIQ-FCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLT 260
D+ LI C + ++ TE AKL E D +++N CP + +RG GA + D L+
Sbjct: 99 DKILIASIMCEYNKEDWTELAKLVEEAGADALELNFSCPHGMPERG-MGAAVGQDPELVE 157
Query: 261 NLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGC 299
+ +R+AV++PV K+ ++ E AR + G
Sbjct: 158 EICRWVREAVKIPVIAKLT--PNITDIREIARAAKEGGA 194
>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 = 44.0 bits (105), Expect = 6e-05
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 288 VEYARMLERAGCQLLAVHGRT-VDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLAD 346
E A+ E G + + T + + G +G ++E + A IPVIA+G + L D
Sbjct: 149 EELAKRFEELGVKAIIY---TDISRDGTLSG-PNFELYKELAAATGIPVIASGGVSSLDD 204
Query: 347 VEACLAQTGVAGV 359
++A L + GVAGV
Sbjct: 205 IKA-LKELGVAGV 216
Score = 30.9 bits (71), Expect = 1.0
Identities = 27/73 (36%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 288 VEYARMLERAGCQLLAVHGRTVDQRGMNTGLAS-WEHITAVRKALTIPVIANGNIQCLAD 346
VE A+ E AG + L V VD G G E I + KA+ IPV G I+ L D
Sbjct: 32 VEVAKKWEEAGAKWLHV----VDLDGAKGGEPVNLELIEEIVKAVGIPVQVGGGIRSLED 87
Query: 347 VEACLAQTGVAGV 359
+E L GV
Sbjct: 88 IERLLD----LGV 96
>gnl|CDD|223184 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 44.1 bits (105), Expect = 7e-05
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 288 VEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADV 347
E A+ LE G + + D G +G + + + + +A+ IPVIA+G + L D+
Sbjct: 150 EELAKRLEEVGLAHILYTDISRD--GTLSGP-NVDLVKELAEAVDIPVIASGGVSSLDDI 206
Query: 348 EACLAQTGVAGV 359
+A +GV GV
Sbjct: 207 KALKELSGVEGV 218
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 43.4 bits (103), Expect = 1e-04
Identities = 48/208 (23%), Positives = 76/208 (36%), Gaps = 58/208 (27%)
Query: 190 KKLRQEILMSTPEDRPLIIQFCGNDSKNLTEAAKLAEPHCDGIDIN---IGCPQMV---A 243
+ L E M PL G K L +A K+ + + IN + P ++ A
Sbjct: 67 ENLASECFM------PLCY---GGGIKTLEQAKKIFSLGVEKVSINTAALEDPDLITEAA 117
Query: 244 KRGHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIR------IYQDVNKT-------VEY 290
+R +G Q+V V + K +Y N T +E
Sbjct: 118 ER--FG-----------------SQSVVVSIDVKKNLGGKFDVYTH-NGTKKLKKDPLEL 157
Query: 291 ARMLERAG-CQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADVEA 349
A+ E G ++L ++D+ G G E + + R AL IP+IA G L D+
Sbjct: 158 AKEYEALGAGEILL---NSIDRDGTMKGY-DLELLKSFRNALKIPLIALGGAGSLDDIVE 213
Query: 350 CLAQTGVAGVMTAEGNLYNPALFTGQTR 377
+ G A G+L+ F G +
Sbjct: 214 AILNLGADAA--AAGSLFV---FKGVYK 236
>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 = 42.8 bits (102), Expect = 2e-04
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 287 TVEYARMLERAGCQ--LLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCL 344
VE+A+ +E G LL ++D+ G G E I AV A+ IPVIA+G
Sbjct: 151 AVEWAKEVEELGAGEILLT----SMDRDGTKKGYDL-ELIRAVSSAVNIPVIASGGAGKP 205
Query: 345 ADVEACLAQTGVAGVMTA 362
+ G + A
Sbjct: 206 EHFVEAFEEGGADAALAA 223
>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 = 42.5 bits (101), Expect = 2e-04
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 286 KTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLA 345
VE+A+ LE G + + +D+ G +G E + +A+ IPVIA+G + L
Sbjct: 149 DAVEWAKKLEELGAGEILLT--DIDRDGTLSGPD-LELTRELAEAVNIPVIASGGVGSLE 205
Query: 346 DVEACLAQTGVAGVMTA 362
D++ L GV GV+
Sbjct: 206 DLKE-LFSEGVDGVIAG 221
Score = 31.3 bits (72), Expect = 0.79
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 15/70 (21%)
Query: 288 VEYARMLERAGCQLLAVHGRTVD------QRGMNTGLASWEHITAVRKALTIPVIANGNI 341
VE A+ E G L VD R +N + I + + + IPV G I
Sbjct: 32 VELAKRYEEEGADELHF----VDLDAAKEGRPVNL-----DLIEEIAEEVFIPVQVGGGI 82
Query: 342 QCLADVEACL 351
+ L D E L
Sbjct: 83 RSLEDAERLL 92
>gnl|CDD|179108 PRK00748, PRK00748,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Validated.
Length = 233
Score = 40.8 bits (97), Expect = 7e-04
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 288 VEYARMLERAGCQLLAVHGRT-VDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLAD 346
+ A+ E AG + + T + + G +G + E + A+ IPVIA+G + L D
Sbjct: 149 EDLAKRFEDAGVKAIIY---TDISRDGTLSG-PNVEATRELAAAVPIPVIASGGVSSLDD 204
Query: 347 VEACLAQTGVAGVMT 361
++A V GV+
Sbjct: 205 IKALKGLGAVEGVIV 219
Score = 32.3 bits (75), Expect = 0.44
Identities = 26/78 (33%), Positives = 35/78 (44%), Gaps = 16/78 (20%)
Query: 288 VEYARMLERAGCQLLAVHGRTVD------QRGMNTGLASWEHITAVRKALTIPVIANGNI 341
V A+ E G + L + VD + +N E I A+ KA+ IPV G I
Sbjct: 33 VAQAKAWEDQGAKWLHL----VDLDGAKAGKPVNL-----ELIEAIVKAVDIPVQVGGGI 83
Query: 342 QCLADVEACLAQTGVAGV 359
+ L VEA L GV+ V
Sbjct: 84 RSLETVEALLD-AGVSRV 100
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 40.7 bits (96), Expect = 0.001
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 287 TVEYARMLERAG-CQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLA 345
VE A+ E G +L + VD G+ G+ + E + + ++ IPVIA+G + L
Sbjct: 151 PVEAAKRFEELGAGSILFTN---VDVEGLLEGVNT-EPVKELVDSVDIPVIASGGVTTLD 206
Query: 346 DVEACLAQTGVAGV 359
D+ A L + G AGV
Sbjct: 207 DLRA-LKEAGAAGV 219
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 39.5 bits (93), Expect = 0.002
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 11/95 (11%)
Query: 190 KKLRQEILMSTPEDRPLIIQFCGN-DSKNLTEAAKLAE-----PHCDGIDINIGCPQMVA 243
+E+ ++ E +P+ + N + A A D I++NI CP
Sbjct: 79 DAFLEELKLAKYEGKPIGVNIGKNKGGPSEEAWADYARLLEEAGDADAIELNISCPNTPG 138
Query: 244 KRGHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKI 278
R L D LL L+ +++ A +VPV K+
Sbjct: 139 GRA-----LGQDPELLEKLLEAVKAATKVPVFVKL 168
>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 = 37.8 bits (89), Expect = 0.006
Identities = 27/80 (33%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 287 TVEYARMLERAGCQLLAV-------HGRTVDQRGMNTGLASWEHITAVRKALTIPVIANG 339
+VE AR E AG L H T D + ++ + VR A+ IPVIA G
Sbjct: 111 SVEEARKAEAAGADALVAQGAEAGGHRGTFD-------IGTFALVPEVRDAVDIPVIAAG 163
Query: 340 NIQCLADVEACLAQTGVAGV 359
I + A LA G GV
Sbjct: 164 GIADGRGIAAALAL-GADGV 182
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 37.5 bits (88), Expect = 0.009
Identities = 31/117 (26%), Positives = 47/117 (40%), Gaps = 22/117 (18%)
Query: 286 KTVEYARMLER--AGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIAN---GN 340
VE+A+ +E AG LL ++D+ G G E AVR+A+ IPVIA+ G
Sbjct: 156 DAVEWAKEVEELGAGEILLT----SMDRDGTKAGY-DLELTRAVREAVNIPVIASGGAGK 210
Query: 341 IQCLADVEACLAQTGVAGVMTAEGNLYNPALFTGQTRPAWELASEYLDLVAQYPVRL 397
+ + + + A ++F E+ EYL VRL
Sbjct: 211 PEHFVEA---FTEGKADAALAA-------SIFHFGEITIGEV-KEYLA-EQGIEVRL 255
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 37.3 bits (87), Expect = 0.013
Identities = 42/187 (22%), Positives = 67/187 (35%), Gaps = 32/187 (17%)
Query: 201 PEDRPLIIQFCGNDSKNLTEAAKLAEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLT 260
P +I+ G+ ++ E A+ P D +++N+ CP R LQ D L
Sbjct: 91 PRPLGIILSKAGSTVEDYVEVARKIGPFADYLELNVSCPNTPGLRA-----LQTDPELAA 145
Query: 261 NLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAG-CQLLAVHGRTVDQRGMNTGLA 319
L+ +++ +VPV K+ D+ V AG L ++ RGM L
Sbjct: 146 ILLKVVKEVSKVPVLVKLA--PDLTDIVIIDIADVAAGEDGLTGINATNTTVRGMRIDLK 203
Query: 320 SWEHITA---------------------VRKAL--TIPVIANGNIQCLADV-EACLAQTG 355
+ I A + + + IP+I G I D E LA
Sbjct: 204 TESPILANGTGGLSGPAIKPIALKVIRELYQRVGPEIPIIGVGGIFTGEDALEKILAGAS 263
Query: 356 VAGVMTA 362
+ TA
Sbjct: 264 AVQIGTA 270
>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 = 37.5 bits (88), Expect = 0.013
Identities = 27/94 (28%), Positives = 36/94 (38%), Gaps = 12/94 (12%)
Query: 283 DVNKTVEYARMLERAGCQLLAVH--GRTVDQR-----GMNTGLASWEHITAVRKALTIPV 335
D+ +VE A+ L+ G L+ V G + Q+ G A +R+ IPV
Sbjct: 239 DLEDSVELAKALKELGVDLIDVSSGGNSPAQKIPVGPGYQVPFAE-----RIRQEAGIPV 293
Query: 336 IANGNIQCLADVEACLAQTGVAGVMTAEGNLYNP 369
IA G I EA L V L NP
Sbjct: 294 IAVGLITDPEQAEAILESGRADLVALGRELLRNP 327
>gnl|CDD|234737 PRK00366, ispG, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Reviewed.
Length = 360
Score = 36.6 bits (86), Expect = 0.027
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 20/75 (26%)
Query: 283 DVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAV---RKALTIPVIA-- 337
DV TV + L RAGC+++ V V E A+ +K L +P++A
Sbjct: 40 DVEATVAQIKRLARAGCEIVRV---AVP---------DMEAAAALPEIKKQLPVPLVADI 87
Query: 338 --NGNIQCLADVEAC 350
+ + LA EA
Sbjct: 88 HFDYRL-ALAAAEAG 101
>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 = 35.3 bits (82), Expect = 0.042
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 288 VEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADV 347
E A+ LE G L + + + G +G ++E + KA+ +PVIA+G + + D+
Sbjct: 148 EELAKRLEELG--LEGIIYTDISRDGTLSGP-NFELTKELVKAVNVPVIASGGVSSIDDL 204
Query: 348 EACLAQTGVAGV 359
A L + GV GV
Sbjct: 205 IA-LKKLGVYGV 215
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 35.7 bits (83), Expect = 0.044
Identities = 28/112 (25%), Positives = 43/112 (38%), Gaps = 13/112 (11%)
Query: 258 LLTNLVSSLRQAV--QVPVSCKI-------RIYQDVNKTVEYARMLERAG--CQLLAVHG 306
L +V ++R+AV PV ++ + + VE A+ LE AG + G
Sbjct: 201 FLLEVVDAVREAVGADFPVGVRLSPDDFFDGGGLTIEEAVELAKALEEAGLVDYIHVSEG 260
Query: 307 RTVDQRGMNTGLASW--EHITAVRKALTIPVIANGNIQCLADVEACLAQTGV 356
+ + E ++KA+ IPVIA G I E LA
Sbjct: 261 GYERGGTITVSGPGYQVEFAARIKKAVRIPVIAVGGINDPEQAEEILASGRA 312
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 35.1 bits (82), Expect = 0.065
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 9/73 (12%)
Query: 291 ARMLERA---GCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADV 347
+L RA G + L + TVD + L +W+ + +R P+I G I D
Sbjct: 132 EDLLRRAEAAGYKALVL---TVDTPVLGRRL-TWDDLAWLRSQWKGPLILKG-ILTPEDA 186
Query: 348 EACLAQTGVAGVM 360
G G++
Sbjct: 187 LRA-VDAGADGIV 198
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 35.1 bits (82), Expect = 0.071
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 15/77 (19%)
Query: 292 RMLERA---GCQLLAVHGRTVD-----QRGMNTGLASWEHITAVRKALTIPVIANGNIQC 343
+LERA G + L + TVD R L +W+ + +R P++ G I
Sbjct: 127 DLLERAEAAGYKALVL---TVDTPVLGNR--ERDLRTWDDLAWLRDQWKGPLVVKG-ILS 180
Query: 344 LADVEACLAQTGVAGVM 360
D + + GV G++
Sbjct: 181 PEDAKRA-VEAGVDGIV 196
>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 = 34.5 bits (80), Expect = 0.073
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 287 TVEYARMLERAGCQLL--AVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCL 344
T+E A + G ++ + G T + T +E + +RKAL IPVIA G I
Sbjct: 132 TLEEALNAAKLGFDIIGTTLSGYTEETA--KTEDPDFELLKELRKALGIPVIAEGRINSP 189
Query: 345 ADVEACLA 352
L
Sbjct: 190 EQAAKALE 197
>gnl|CDD|234996 PRK02083, PRK02083, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 253
Score = 34.3 bits (80), Expect = 0.11
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 19/84 (22%)
Query: 287 TVEYARMLERAGCQ--LLAVHGRTV-DQRGMNTG--LASWEHITAVRKALTIPVIANG-- 339
VE+A+ +E G LL T D+ G G L E AV A+ +PVIA+G
Sbjct: 155 AVEWAKEVEELGAGEILL-----TSMDRDGTKNGYDL---ELTRAVSDAVNVPVIASGGA 206
Query: 340 -NIQCLADVEACLAQTGVAGVMTA 362
N++ + + G + A
Sbjct: 207 GNLEHFVEA---FTEGGADAALAA 227
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 34.0 bits (79), Expect = 0.12
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 5/75 (6%)
Query: 287 TVEYARMLERAGCQLLA--VHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCL 344
T+E ++ G + + G T ++ + + + KA+ PVIA G I
Sbjct: 128 TLEEGLAAQKLGFDFIGTTLSGYT-EETKKPEE-PDFALLKELLKAVGCPVIAEGRINTP 185
Query: 345 ADVEACLAQTGVAGV 359
+ L G V
Sbjct: 186 EQAKKALE-LGAHAV 199
>gnl|CDD|217120 pfam02581, TMP-TENI, Thiamine monophosphate synthase/TENI.
Thiamine monophosphate synthase (TMP) (EC:2.5.1.3)
catalyzes 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. This Pfam family
also includes the regulatory protein TENI.
Length = 180
Score = 33.3 bits (77), Expect = 0.13
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 321 WEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGV 359
E + A+ +A+ IPV+A G I +V + + G GV
Sbjct: 138 LEGLRAIAEAVNIPVVAIGGI-TPENVPE-VLEAGADGV 174
>gnl|CDD|236051 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
Length = 334
Score = 34.1 bits (79), Expect = 0.13
Identities = 27/112 (24%), Positives = 48/112 (42%), Gaps = 21/112 (18%)
Query: 261 NLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAG-----CQLLAVH------GRTV 309
L+ ++AV +PV + V+YAR +E+AG + + G V
Sbjct: 91 ELIRRAKEAVDIPVIASLNGSSA-GGWVDYARQIEQAGADALELNIYYLPTDPDISGAEV 149
Query: 310 DQRGMNTGLASWEHITAVRKALTIPVIA--NGNIQCLADVEACLAQTGVAGV 359
+QR ++ + AV+ A++IPV + LA++ L G G+
Sbjct: 150 EQRYLDI-------LRAVKSAVSIPVAVKLSPYFSNLANMAKRLDAAGADGL 194
>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 = 34.1 bits (79), Expect = 0.14
Identities = 28/115 (24%), Positives = 46/115 (40%), Gaps = 27/115 (23%)
Query: 261 NLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAG-----CQLLAVH------GRTV 309
L+ ++AV +PV + V+YAR +E AG + A+ G V
Sbjct: 89 ELIRRAKRAVSIPVIASLNGVSA-GGWVDYARQIEEAGADALELNIYALPTDPDISGAEV 147
Query: 310 DQRGMNTGLASWEHITAVRKALTIPVIAN-----GNIQCLADVEACLAQTGVAGV 359
+QR + + + AV+ A+TIPV + +A L G G+
Sbjct: 148 EQRYL-------DILRAVKSAVTIPVAVKLSPFFSALAHMAKQ---LDAAGADGL 192
>gnl|CDD|119340 cd00377, ICL_PEPM, Members of the ICL/PEPM enzyme family catalyze
either P-C or C-C bond formation/cleavage. Known members
are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate
hydrolase (PPH), carboxyPEP mutase (CPEP mutase),
oxaloacetate hydrolase (OAH), isocitrate lyase (ICL),
and 2-methylisocitrate lyase (MICL). Isocitrate lyase
(ICL) catalyzes the conversion of isocitrate to
succinate and glyoxylate, the first committed step in
the glyoxylate pathway. This carbon-conserving pathway
is present in most prokaryotes, lower eukaryotes and
plants, but has not been observed in vertebrates. PEP
mutase (PEPM) turns phosphoenolpyruvate (PEP) into
phosphonopyruvate (P-pyr), an important intermediate in
the formation of organophosphonates, which function as
antibiotics or play a role in pathogenesis or signaling.
P-pyr can be hydrolyzed by phosphonopyruvate hydrolase
(PPH) to from pyruvate and phosphate. Oxaloacetate
acetylhydrolase (OAH) catalyzes the hydrolytic cleavage
of oxaloacetate to form acetate and oxalate, an
important pathway to produce oxalate in filamentous
fungi. 2-methylisocitrate lyase (MICL) cleaves
2-methylisocitrate to pyruvate and succinate, part of
the methylcitrate cycle for the alpha-oxidation of
propionate.
Length = 243
Score = 33.2 bits (77), Expect = 0.19
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 291 ARMLERAGCQLLAVHGRTV-DQRGM-NTGLASW----EHITAVRKALTIPVIAN-----G 339
AR+ ERAG + + G V G+ + GL + + + +A+ +PVIA+ G
Sbjct: 22 ARLAERAGFKAIYTSGAGVAASLGLPDGGLLTLDEVLAAVRRIARAVDLPVIADADTGYG 81
Query: 340 NIQCLADVEACLAQTGVAGVM 360
N +A L + G AG+
Sbjct: 82 NALNVARTVRELEEAGAAGIH 102
>gnl|CDD|233052 TIGR00612, ispG_gcpE, 1-hydroxy-2-methyl-2-(E)-butenyl
4-diphosphate synthase. This protein of previously
unknown biochemical function has now been identified as
an enzyme of the non-mevalonate pathway of IPP
biosynthesis. Chlamydial members of the family have a
long insert. The family is largely restricted to
Bacteria, where it is widely but not universally
distributed. No homology can be detected between the
GcpE family and other proteins [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 346
Score = 33.6 bits (77), Expect = 0.23
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 11/91 (12%)
Query: 283 DVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQ 342
DV+ TV R LE AGC+++ V TV + S E + +++ +P++A+ +
Sbjct: 32 DVDATVAQIRRLEEAGCEIVRV---TVPDK------ESAEALEEIKEGSNVPLVADIHFA 82
Query: 343 CLADVEACLAQTGVAGVMTAEGNLYNPALFT 373
A GVA V GN+
Sbjct: 83 YSYAALAM--AKGVAKVRINPGNIGFEERVR 111
>gnl|CDD|236322 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 368
Score = 33.2 bits (77), Expect = 0.27
Identities = 22/86 (25%), Positives = 30/86 (34%), Gaps = 25/86 (29%)
Query: 286 KTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHIT---------AVRKALTIPVI 336
+ E A + AG L + G V S EH++ L +PVI
Sbjct: 142 RAQELAPTVVEAGVDLFVIQGTVV----------SAEHVSKEGEPLNLKEFIYELDVPVI 191
Query: 337 ANGNIQCLADVEAC--LAQTGVAGVM 360
G C L +TG AGV+
Sbjct: 192 VGG---C-VTYTTALHLMRTGAAGVL 213
>gnl|CDD|223891 COG0821, gcpE, 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate
synthase [Lipid metabolism].
Length = 361
Score = 33.0 bits (76), Expect = 0.29
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 9/55 (16%)
Query: 283 DVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIA 337
DV TV + LERAGC ++ V TV + + E + +++ L +P++A
Sbjct: 34 DVEATVAQIKALERAGCDIVRV---TVP------DMEAAEALKEIKQRLNVPLVA 79
>gnl|CDD|240074 cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase (HisA) and
the cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). The 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. The 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 = 233
Score = 32.6 bits (75), Expect = 0.33
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 308 TVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGVMTA 362
+D+ G G E + + IPVIA G ++ + D+E L + G +G + A
Sbjct: 166 DIDRVGSGQGP-DLELLERLAARADIPVIAAGGVRSVEDLEL-LKKLGASGALVA 218
>gnl|CDD|225311 COG2513, PrpB, PEP phosphonomutase and related enzymes
[Carbohydrate transport and metabolism].
Length = 289
Score = 32.6 bits (75), Expect = 0.37
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 291 ARMLERAGCQLLAVHGRTV-DQRGM-NTGLASWEHITAVRKALT----IPVIAN-----G 339
A + ERAG + L + G V G+ + G+ + + + A + +T +PV+ + G
Sbjct: 31 ALLAERAGFKALYLSGAGVAASLGLPDLGITTLDEVLADARRITDAVDLPVLVDIDTGFG 90
Query: 340 NIQCLADVEACLAQTGVAGV 359
+A L Q G AG+
Sbjct: 91 EALNVARTVRELEQAGAAGI 110
>gnl|CDD|239238 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.
FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a
respiratory enzyme located in the intermembrane space of
fungal mitochondria which catalyzes the oxidation of
L-lactate to pyruvate. FCB2 also participates in a short
electron-transport chain involving cytochrome c and
cytochrome oxidase which ultimately directs the reducing
equivalents gained from L-lactate oxidation to oxygen,
yielding one molecule of ATP for every L-lactate
molecule consumed. FCB2 is composed of 2 domains: a
C-terminal flavin-binding domain, which includes the
active site for lacate oxidation, and an N-terminal
b2-cytochrome domain, required for efficient cytochrome
c reduction. FCB2 is a homotetramer and contains two
noncovalently bound cofactors, FMN and heme per subunit.
Length = 344
Score = 32.2 bits (74), Expect = 0.56
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 320 SWEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGV 359
+W+ I +RK +P++ G +Q + D A+ GV G+
Sbjct: 201 TWDDIKWLRKHTKLPIVLKG-VQTVEDAVLA-AEYGVDGI 238
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 31.8 bits (73), Expect = 0.81
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 203 DRPLIIQFCG-NDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLT 260
DR LI + + E A L E DGI++N GCP +++RG A Q P L
Sbjct: 99 DRALIASIMVECNEEEWKEIAPLVEETGADGIELNFGCPHGMSERGMGSAVGQV--PELV 156
Query: 261 NLVSS-LRQAVQVPVSCK 277
+ + +++ ++PV K
Sbjct: 157 EMYTRWVKRGSRLPVIVK 174
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 31.9 bits (73), Expect = 0.81
Identities = 28/112 (25%), Positives = 49/112 (43%), Gaps = 16/112 (14%)
Query: 261 NLVSSLRQA------VQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLAVHGRTVDQRGM 314
NL ++++ A VQ +S + VE A+ L G + + D G+
Sbjct: 126 NLKTAIKAAKKHGAHVQGTISYTTSPVHTLEYYVELAKELLEMGVDSICIK----DMAGL 181
Query: 315 NTGLASWEHITAVRKALTIPVI----ANGNIQCLADVEACLAQTGVAGVMTA 362
T ++E + A++K L +PV A + + ++A A GV G+ TA
Sbjct: 182 LTPYEAYELVKAIKKELPVPVELHTHATSGMAEMTYLKAVEA--GVDGIDTA 231
>gnl|CDD|218143 pfam04551, GcpE, GcpE protein. In a variety of organisms,
including plants and several eubacteria, isoprenoids are
synthesised by the mevalonate-independent
2-C-methyl-D-erythritol 4-phosphate (MEP) pathway.
Although different enzymes of this pathway have been
described, the terminal biosynthetic steps of the MEP
pathway have not been fully elucidated. GcpE gene of
Escherichia coli is involved in this pathway.
Length = 345
Score = 31.7 bits (73), Expect = 0.91
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 283 DVNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIA 337
DV TV + LE AGC ++ V V + + E + ++K IP++A
Sbjct: 29 DVEATVAQIKRLEEAGCDIVRV---AVP------DMEAAEALKEIKKQSPIPLVA 74
>gnl|CDD|237589 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
Length = 241
Score = 30.7 bits (70), Expect = 1.5
Identities = 27/83 (32%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 294 LERAGCQLLAVHGRTVDQ--RGMNTGLASWEHITAVRKALTIPVIANGNIQCLADVEACL 351
L+ AGC V T D G N L + V PV+A+G + L D+ A L
Sbjct: 155 LDSAGCSRYVVTDVTKDGTLTGPNLEL-----LREVCARTDAPVVASGGVSSLDDLRA-L 208
Query: 352 AQTGVAGVMTAEGNLYNPALFTG 374
A+ GV EG + AL+ G
Sbjct: 209 AELVPLGV---EGAIVGKALYAG 228
>gnl|CDD|197263 cd09166, PLDc_PPK1_C1_unchar, Catalytic C-terminal domain, first
repeat, of uncharacterized prokaryotic polyphosphate
kinases. Catalytic C-terminal domain, first repeat (C1
domain), of a group of uncharacterized prokaryotic
polyphosphate kinases (Poly P kinase 1 or PPK1, EC
2.7.4.1). Inorganic polyphosphate (Poly P) plays an
important role in bacterial stress responses and
stationary-phase survival. PPK1 is the key enzyme
responsible for the synthesis of Poly P in bacteria. It
can catalyze the reversible conversion of the
terminal-phosphate of ATP to Poly P. Therefore, PPK1 is
essential for bacterial motility, quorum sensing,
biofilm formation, and the production of virulence
factors and may serve as an attractive antimicrobial
drug target. Dimerization is crucial for the enzymatic
activity of PPK1. Each PPK1 monomer includes four
structural domains, the N-terminal (N) domain, the head
(H) domain, and two closely related C-terminal (C1 and
C2) domains. The N domain provides the upper binding
interface for the adenine ring of the ATP. The H domain
is involved in dimerization, while both the C1 and C2
domains contain residues crucial for catalytic activity.
The intersection of the N, C1, and C2 domains forms a
structural tunnel in which the PPK catalytic reactions
are carried out. In spite of the lack of sequence
homology, the C1 and C2 domains of PPK1 are structurally
similar to the two repetitive catalytic domains of
phospholipase D (PLD). Moreover, some residues in the
HKD motif (H-x-K-x(4)-D, where x represents any amino
acid residue) of the PLD superfamily are spatially
conserved in the active site of PPK1. It is possible
that the bacterial PPK1 family and the PLD family have a
common ancestor and diverged early in evolution.
Length = 162
Score = 30.0 bits (68), Expect = 1.8
Identities = 27/117 (23%), Positives = 47/117 (40%), Gaps = 23/117 (19%)
Query: 187 IADKKLRQEILMSTP-EDRPLIIQFCGNDSKNLTEAAKLAEPHCDGIDINIGCPQMVAKR 245
I + ++++L+S P E + L EAA+ +P I I + +AK+
Sbjct: 2 IFKQVRQKDVLLSYPYESMDPFLNL-------LKEAAE--DPEVISIKITL---YRLAKQ 49
Query: 246 GHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLL 302
YL + + V V ++R D +E+A LE AGC ++
Sbjct: 50 SRLVEYL----------IEAAENGKDVTVLMELRARFDEENNIEWAERLEEAGCTVI 96
>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 = 29.8 bits (68), Expect = 2.0
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 322 EHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGV 359
E + + + + IPV+A G I + LA G GV
Sbjct: 140 ELLREIAELVEIPVVAIGGI-TPENAAEVLA-AGADGV 175
>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 = 30.3 bits (68), Expect = 2.0
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 3/78 (3%)
Query: 228 HCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKT 287
H D I+IN C Q G L + LL ++ +++ + P+ KIR
Sbjct: 92 HADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTKMKELNK-PIFVKIRGNCIPLDE 150
Query: 288 VEYARMLERAGCQLLAVH 305
+ A L G +H
Sbjct: 151 LIDALNLVDDGF--DGIH 166
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 30.6 bits (69), Expect = 2.2
Identities = 30/116 (25%), Positives = 53/116 (45%), Gaps = 10/116 (8%)
Query: 190 KKLRQEILMSTPEDRPLIIQFCGNDSKNLTEA--AKLAEPHCDGIDINIGCPQMVAKRGH 247
K+L++E DR LI +K+ E ++ E D ++IN CP + +R
Sbjct: 105 KQLKEEY-----PDRILIASIMEEYNKDAWEEIIERVEETGVDALEINFSCPHGMPER-K 158
Query: 248 YGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYARMLERAGCQLLA 303
GA + D LL + + VPV K+ ++ + AR+ ++GC+ +A
Sbjct: 159 MGAAVGQDCDLLEEVCGWINAKATVPVWAKMT--PNITDITQPARVALKSGCEGVA 212
>gnl|CDD|234436 TIGR03997, mycofact_OYE_2, mycofactocin system FadH/OYE family
oxidoreductase 2. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp., in Pelotomaculum
thermopropionicum SI (Firmicutes), and in Geobacter
uraniireducens Rf4 (Deltaproteobacteria). The function
of this oxidoreductase is unknown.
Length = 645
Score = 30.4 bits (69), Expect = 2.4
Identities = 27/122 (22%), Positives = 44/122 (36%), Gaps = 35/122 (28%)
Query: 202 EDRPLIIQFCGND----SKNLTEAAKLAEPHCDG-----IDINIGC---------PQMVA 243
DR L ++ CG++ L +A ++A I+ +IG M
Sbjct: 208 PDRALGVRLCGDELVPGGLTLADAVEIARLLEALGLVDYINTSIGVATYTLHLVEASMHV 267
Query: 244 KRGHYGAYLQDDWPLLTNLVSSLRQAVQVPVSCKIRIYQDVNKTVEYA-RMLERAGCQLL 302
G Y A+L +++R+AV +PV RI A R L L+
Sbjct: 268 PPG-YAAFLA----------AAIREAVDLPVFAVGRI-----NDPAQAERALAEGQADLV 311
Query: 303 AV 304
+
Sbjct: 312 GM 313
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 29.5 bits (67), Expect = 2.7
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 321 WEHITAVRKALTIPVIANGNIQCLADVEACLAQTGVAGV 359
E + +R+ + IPV+A G I L +V + + G GV
Sbjct: 147 LEGLREIRELVNIPVVAIGGIN-LENVPE-VLEAGADGV 183
>gnl|CDD|235479 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase;
Provisional.
Length = 326
Score = 29.5 bits (67), Expect = 3.4
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 287 TVEYARMLERAGCQLLAVH---GR---TVDQRGMNTGLASWEHITAVR---KALTIPVIA 337
T E R LE AG V G+ T + G TG W+ + A+R KA P+IA
Sbjct: 150 TPEAVRELENAGADATKVGIGPGKVCITKIKTGFGTG--GWQ-LAALRWCAKAARKPIIA 206
Query: 338 NGNI 341
+G I
Sbjct: 207 DGGI 210
>gnl|CDD|235912 PRK07028, PRK07028, bifunctional hexulose-6-phosphate
synthase/ribonuclease regulator; Validated.
Length = 430
Score = 30.0 bits (68), Expect = 3.4
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 284 VNKTVEYARMLERAGCQLLAVH-GRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQ 342
V V+ A LE G + VH G +DQ+ M G E + V + ++IP+ G +
Sbjct: 117 VPDPVKRAVELEELGVDYINVHVG--IDQQ-M-LGKDPLELLKEVSEEVSIPIAVAGGLD 172
Query: 343 CLADVEACLAQTGVAGVMTAEGNLYNPALFTGQTR 377
A+ A G A ++ GN+ A T R
Sbjct: 173 --AETAAKAVAAG-ADIVIVGGNIIKSADVTEAAR 204
>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase. Most species with a
member of this family belong to the high GC
Gram-positive bacteria, and these also have the IMP
dehydrogenase described by TIGRFAMs equivalog model
TIGR01302 [Unknown function, General].
Length = 369
Score = 29.8 bits (67), Expect = 3.4
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 287 TVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPVIANGNIQCLAD 346
E A ++ +AG LL + G V ++T + + L +PVIA G + D
Sbjct: 144 AREIAPIVVKAGADLLVIQGTLVSAEHVSTSGEPLNLKEFIGE-LDVPVIAGG----VND 198
Query: 347 VEACL--AQTGVAGVMTAEG 364
L +TG AGV+ G
Sbjct: 199 YTTALHLMRTGAAGVIVGPG 218
>gnl|CDD|217344 pfam03060, NMO, Nitronate monooxygenase. Nitronate monooxygenase
(NMO), formerly referred to as 2-nitropropane
dioxygenase (NPD) (EC:1.13.11.32), is an FMN-dependent
enzyme that uses molecular oxygen to oxidize (anionic)
alkyl nitronates and, in the case of the enzyme from
Neurospora crassa, (neutral) nitroalkanes to the
corresponding carbonyl compounds and nitrite. Previously
classified as 2-nitropropane dioxygenase, but it is now
recognized that this was the result of the slow
ionization of nitroalkanes to their nitronate (anionic)
forms. The enzymes from the fungus Neurospora crassa and
the yeast Williopsis saturnus var. mrakii (formerly
classified as Hansenula mrakii) contain non-covalently
bound FMN as the cofactor. Active towards linear alkyl
nitronates of lengths between 2 and 6 carbon atoms and,
with lower activity, towards propyl-2-nitronate. The
enzyme from N. crassa can also utilize neutral
nitroalkanes, but with lower activity. One atom of
oxygen is incorporated into the carbonyl group of the
aldehyde product. The reaction appears to involve the
formation of an enzyme-bound nitronate radical and an
a-peroxynitroethane species, which then decomposes,
either in the active site of the enzyme or after
release, to acetaldehyde and nitrite.
Length = 329
Score = 29.7 bits (67), Expect = 3.7
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 7/84 (8%)
Query: 287 TVEYARMLERAGCQLLAVHGRTVD-QRGMNTGLASWEHITAVRKALTIPVIANGNIQCLA 345
+ + AR E AG + G G G+ ++ + V A+ IPVIA G I
Sbjct: 146 SAKEARKAEAAGADAVVAQGPEAGGHIGTFVGVTTFLLVPTVVDAVDIPVIAAGGIADGR 205
Query: 346 DVEACLA------QTGVAGVMTAE 363
+ A LA Q G + T E
Sbjct: 206 GIAAALALGAEGVQIGTRFLATKE 229
>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 = 29.7 bits (67), Expect = 3.7
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 284 VNKTVEYARMLERAGCQLLAVHGRTVDQRGMNTG-LASWEHITAVRKALTIPVIANGNI 341
V +V A+ +E+AG + G + G + G L + + V A++IPVIA G I
Sbjct: 115 VVASVALAKRMEKAGADAVIAEGM---ESGGHIGELTTMALVPQVVDAVSIPVIAAGGI 170
>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 = 29.4 bits (67), Expect = 3.7
Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 18/102 (17%)
Query: 291 ARMLERAGCQLLAVHGRTV-DQRGM-NTGLASWE----HITAVRKALTIPVIA---NGNI 341
AR+ E AG + LA V G + L + + + +A+ +PV +G
Sbjct: 22 ARIAEAAGFKALATSSAAVAASLGYPDGELLPLDELLAAVRRIARAVDLPVSVDLESGYG 81
Query: 342 QCLADVEAC---LAQTGVAGV------MTAEGNLYNPALFTG 374
+V L + G G+ G LY+ F
Sbjct: 82 DSPENVAETVRRLIEAGAVGINIEDSTGGGGGGLYDIEEFAA 123
>gnl|CDD|216067 pfam00696, AA_kinase, Amino acid kinase family. This family
includes kinases that phosphorylate a variety of amino
acid substrates, as well as uridylate kinase and
carbamate kinase. This family includes: Aspartokinase
EC:2.7.2.4, Acetylglutamate kinase EC:2.7.2.8, Glutamate
5-kinase EC:2.7.2.11, Uridylate kinase EC:2.7.4.-,
Carbamate kinase EC:2.7.2.2.
Length = 230
Score = 28.9 bits (65), Expect = 5.1
Identities = 18/104 (17%), Positives = 30/104 (28%), Gaps = 28/104 (26%)
Query: 289 EYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALT---IPVIA-------N 338
+ ER G + +A+ G+ A+++ L +PVI
Sbjct: 81 IVVSLGERLGARAVALLL---SDGGLPAVRLDLVDTEAIKELLEAGVVPVITGFGGENDT 137
Query: 339 GNIQCLA---------------DVEACLAQTGVAGVMTAEGNLY 367
G L + + T V GV TA+
Sbjct: 138 GETTTLGRGSSDTLAALLAEALGADKLIILTDVDGVYTADPRKN 181
>gnl|CDD|163677 cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related
proteins, catalytic TIM barrel domain. FrbC (NifV) of
Streptomyces rubellomurinus catalyzes the condensation
of acetyl-CoA and alpha-ketoglutarate to form
homocitrate and CoA, a reaction similar to one catalyzed
by homocitrate synthase. The gene encoding FrbC is one
of several genes required for the biosynthesis of
FR900098, a potent antimalarial antibiotic. This
protein is also required for assembly of the nitrogenase
MoFe complex but its exact role is unknown. This
family also includes the NifV proteins of Heliobacterium
chlorum and Gluconacetobacter diazotrophicus, which
appear to be orthologous to FrbC. This family belongs
to the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 259
Score = 28.6 bits (65), Expect = 6.4
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 288 VEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEHITAVRKALTIPV 335
+E+A + + AG L R D G+ ++E I +R A +P+
Sbjct: 142 IEFAEVAQEAGADRL----RFADTVGILDPFTTYELIRRLRAATDLPL 185
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 28.1 bits (63), Expect = 7.3
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 396 RLQYARGHVFNMCHHLLTLPENSDVRLLVG 425
R+QY + LLTL E RL G
Sbjct: 44 RVQYTLAKIRKAARELLTLDEKDPKRLFEG 73
>gnl|CDD|224981 COG2070, COG2070, Dioxygenases related to 2-nitropropane
dioxygenase [General function prediction only].
Length = 336
Score = 28.8 bits (65), Expect = 7.4
Identities = 27/91 (29%), Positives = 34/91 (37%), Gaps = 15/91 (16%)
Query: 287 TVEYARMLERAGCQLLAVHGRTVDQRGMNTGLASWEH-----ITAVRKALT-IPVIANGN 340
TV A ERAG + G G + G E + V A+ IPVIA G
Sbjct: 136 TVREALKAERAGADAVIAQGAEA---GGHRGGVDLEVSTFALVPEVVDAVDGIPVIAAGG 192
Query: 341 IQCLADVEACLA------QTGVAGVMTAEGN 365
I + A LA Q G + T E +
Sbjct: 193 IADGRGIAAALALGADGVQMGTRFLATKEAD 223
>gnl|CDD|223953 COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid
metabolism].
Length = 613
Score = 28.8 bits (65), Expect = 7.6
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 11 VLCYLSLHWVFGLVTSMELHRHSPV--AHPPNP 41
VL +L L +F L + V +P
Sbjct: 236 VLSFLPLAHIFERAFEGGLALYGGVTVLFKEDP 268
>gnl|CDD|178595 PLN03024, PLN03024, Putative EG45-like domain containing protein 1;
Provisional.
Length = 125
Score = 27.3 bits (60), Expect = 8.3
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 38 PPNPIPQECHSPAARCKGTNVVPKDCHSSTARS-DAWTQLGSP 79
P N +P C + K + P C S+ S +A+ Q+ +P
Sbjct: 72 PRNAVPHPCTGKSVTVKIVDHCPSGCASTLDLSREAFAQIANP 114
>gnl|CDD|167581 PRK03670, PRK03670, competence damage-inducible protein A;
Provisional.
Length = 252
Score = 28.2 bits (63), Expect = 8.3
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 116 FIADKKLRQEILMSTPEDRPLIIQRTIFPRLGSPRFI----LAPMVDASEL 162
+I K + +L P + ++++ + PRLG +F+ LA + D S+L
Sbjct: 146 YIEHKGTKIFVLPGMPREMKAMLEKEVLPRLGERKFVQKKFLAEITDESKL 196
>gnl|CDD|222464 pfam13941, MutL, MutL protein. This small family includes,
GlmL/MutL from Clostridium tetanomorphum and Clostridium
cochlearium. GlmL is located between the genes for the
two subunits, epsilon (GlmE) and sigma (GlmS), of the
coenzyme-B12-dependent glutamate mutase (methylaspartate
mutase), the first enzyme in a pathway of glutamate
fermentation. Members shows significant sequence
similarity to the hydantoinase branch of the
hydantoinase/oxoprolinase family.
Length = 457
Score = 28.7 bits (65), Expect = 8.6
Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 331 LTIPVIANGNIQCLADVEACLAQTGVAGVMTAEGNLYNPAL 371
L IPVI GN +V L G + N+ P L
Sbjct: 154 LDIPVIYAGNKAAQDEVAEILGDAGKPLTIVE--NVR-PTL 191
>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 = 28.4 bits (64), Expect = 9.6
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 288 VEYARMLERAGCQLLAV----HGRTVDQRGMNTGLASWEHITA-VRKALTIPVIANGNIQ 342
V A+ LE AG +L H V + ++ TA +++A+ IPVIA+ I
Sbjct: 227 VALAKALEAAGADILNTGIGWHEARVPTIATSVPRGAFAWATAKLKRAVDIPVIASNRIN 286
Query: 343 CLADVEACLAQ 353
E LA
Sbjct: 287 TPEVAERLLAD 297
>gnl|CDD|240085 cd04734, OYE_like_3_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 3. 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. One
member of this subgroup, the Sinorhizobium meliloti
stachydrine utilization protein stcD, has been idenified
as a putative N-methylproline demethylase.
Length = 343
Score = 28.3 bits (64), Expect = 9.6
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 313 GMNTGLASWEHITA-VRKALTIPVIANGNIQCLADVEACLAQ 353
M + + A +++A+ +PV G I+ A+ E LA
Sbjct: 265 SMGMPPGPFLPLAARIKQAVDLPVFHAGRIRDPAEAEQALAA 306
>gnl|CDD|197262 cd09165, PLDc_PaPPK1_C1_like, Catalytic C-terminal domain, first
repeat, of Pseudomonas aeruginosa polyphosphate kinase 1
and similar proteins. Catalytic C-terminal domain,
first repeat (C1 domain), of polyphosphate kinase (Poly
P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas
aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1),
and other similar proteins. Inorganic polyphosphate
(Poly P) plays an important role in bacterial stress
responses and stationary-phase survival. PaPPK1 is the
key enzyme responsible for the synthesis of Poly P in
Pseudomonas aeruginosa. It can catalyze the reversible
conversion of the terminal-phosphate of ATP to Poly P.
PaPPK1 shows high sequence homolog to Escherichia coli
polyphosphate kinase (EcPPK), which contains four
structural domains per chain: the N-terminal (N) domain,
the head (H) domain, and two closely related C-terminal
(C1 and C2) domains. The N domain provides the upper
binding interface for the adenine ring of the ATP. The H
domain is involved in dimerization, while both the C1
and C2 domains contain residues crucial for catalytic
activity. The intersection of the N, C1, and C2 domains
forms a structural tunnel in which the PPK catalytic
reactions are carried out. The polyphosphate kinase from
Dictyostelium discoideum (DdPPK1) shares similar
structural features with EcPPK1 in the ATP-binding
pocket and poly P tunnel, but has a unique N-terminal
extension that may be responsible for its enzymatic
activity, cellular localization, and physiological
functions. In spite of the lack of sequence homology,
the C1 and C2 domains of the family members are
structurally similar to the two repetitive catalytic
domains of phospholipase D (PLD). Moreover, some
residues in the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) of the PLD
superfamily are spatially conserved in the active site
of PPK1. It is possible that the bacterial PPK1 family
and the PLD family have a common ancestor and diverged
early in evolution. In some bacteria, such as
Pseudomonas aeruginosa, a second enzyme, PPK2, which is
involved in the alternative pathway of polyphosphate
synthesis, has been found. It can catalyze the synthesis
of poly P from GTP or ATP, with a preference for Mn2+
over Mg2+. PPK2 shows no sequence similarity to PPK1 and
belongs to a different superfamily.
Length = 164
Score = 27.5 bits (62), Expect = 9.8
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 14/59 (23%)
Query: 262 LVSSLRQA------VQVPVSCKIRIYQDVNKTVEYARMLERAGCQL------LAVHGRT 308
+V +L +A V V V K R ++ N + +AR LE AGC + L H +
Sbjct: 52 IVDALIEAAENGKQVTVLVELKARFDEENN--IHWARKLEEAGCHVVYGLVGLKTHAKL 108
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.136 0.434
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,170,196
Number of extensions: 2452694
Number of successful extensions: 2226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2178
Number of HSP's successfully gapped: 92
Length of query: 487
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 386
Effective length of database: 6,457,848
Effective search space: 2492729328
Effective search space used: 2492729328
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 (22.0 bits)
S2: 61 (27.2 bits)