RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16199
(842 letters)
>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 = 332 bits (854), Expect = e-108
Identities = 127/200 (63%), Positives = 149/200 (74%), Gaps = 2/200 (1%)
Query: 565 ILIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNIS 624
ILIASIMC YNK+DW EL+K E+AGADALELN SCPHGM ERGMG A GQDPE+V I
Sbjct: 101 ILIASIMCEYNKEDWTELAKLVEEAGADALELNFSCPHGMPERGMGAAVGQDPELVEEIC 160
Query: 625 LWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVG 684
WVR +VKIP KLTPNIT+I +IA+AA EG ADGVSAINTV+ LM + DG P PA G
Sbjct: 161 RWVREAVKIPVIAKLTPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTP-PAPG 219
Query: 685 TKKLTTYGGVSGNATRPMGLKAVSSIAK-MFPNFPILGIGGIDSADVALQFIQAGAHAVQ 743
+ TTYGG SG A +P+ L+AVS IA+ P PI GIGGI+S + A +F+ GA VQ
Sbjct: 220 VEGKTTYGGYSGPAVKPIALRAVSQIARAPEPGLPISGIGGIESWEDAAEFLLLGASVVQ 279
Query: 744 ICSAVQNQDFTVVDDYITGL 763
+C+AV NQ FT+VDD TGL
Sbjct: 280 VCTAVMNQGFTIVDDMCTGL 299
Score = 151 bits (383), Expect = 1e-40
Identities = 58/87 (66%), Positives = 64/87 (73%), Gaps = 4/87 (4%)
Query: 347 DISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
D+SV CG+KFPNPFGLASAPPTT+ M+RRAFE GWG AVTKT L KD+VTNVSPRI
Sbjct: 1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLDKDIVTNVSPRIA 60
Query: 407 KGTTSRHLYGPEQGSFLNIELISEKTA 433
+ TS G Q F NIELISEK
Sbjct: 61 RLRTS----GRGQIGFNNIELISEKPL 83
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 227 bits (582), Expect = 1e-66
Identities = 91/207 (43%), Positives = 126/207 (60%), Gaps = 5/207 (2%)
Query: 564 SILIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNI 623
LIASIM N+++W E++ E+ GAD +ELN CPHGM ERGMG A GQ PE+V
Sbjct: 100 RALIASIMVECNEEEWKEIAPLVEETGADGIELNFGCPHGMSERGMGSAVGQVPELVEMY 159
Query: 624 SLWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADG-NPWPA 682
+ WV+ ++P VKLTPNIT+I + A+AA G AD VS INT++ + + D P P
Sbjct: 160 TRWVKRGSRLPVIVKLTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPI 219
Query: 683 VGTKKLTTYGGVSGNATRPMGLKAVSSIAK--MFPNFPILGIGGIDSADVALQFIQAGAH 740
V K +++GG G A +P+ L V+ IA+ PI GIGGI++ A +FI GA
Sbjct: 220 VNGK--SSHGGYCGPAVKPIALNMVAEIARDPETRGLPISGIGGIETWRDAAEFILLGAG 277
Query: 741 AVQICSAVQNQDFTVVDDYITGLQTLL 767
VQ+C+A F +V+D I+GL +
Sbjct: 278 TVQVCTAAMQYGFRIVEDMISGLSHYM 304
Score = 89.2 bits (222), Expect = 1e-18
Identities = 33/78 (42%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 490 SVKDVIGQAVQRVTNYTELDNKKQVVALINDDMCINCGKCYMACNDSGYQAITFHP-ETH 548
S++D++G AV VT++ +LD V A I+ D CI CG+CY+AC D+ +QAI + T
Sbjct: 311 SLEDMVGLAVPNVTDWEDLDLNYIVYARIDQDKCIGCGRCYIACEDTSHQAIEWDEDGTR 370
Query: 549 QAHV-TDECTGCTLCLSI 565
V +EC GC LC +
Sbjct: 371 TPEVIEEECVGCNLCAHV 388
Score = 84.2 bits (209), Expect = 4e-17
Identities = 42/88 (47%), Positives = 50/88 (56%), Gaps = 12/88 (13%)
Query: 347 DISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPR-- 404
D+S+ CG+K PNPF LASAPPT V RAFE GWG V KT L +V SPR
Sbjct: 3 DLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKT--LGPPIVNVSSPRFG 60
Query: 405 -IVKGTTSRHLYGPEQGSFLNIELISEK 431
+VK R G F NIELI+++
Sbjct: 61 ALVKE--DRRFIG-----FNNIELITDR 81
>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 = 193 bits (493), Expect = 9e-56
Identities = 81/201 (40%), Positives = 118/201 (58%), Gaps = 14/201 (6%)
Query: 565 ILIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNIS 624
LIAS+ + +K+D++EL++K E+AGA ALELNLSCP+ G R GQDPE V N+
Sbjct: 100 PLIASVGGS-SKEDYVELARKIERAGAKALELNLSCPNVGGGRQ----LGQDPEAVANLL 154
Query: 625 LWVRSSVKIPFFVKLTPNIT--NITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPA 682
V+++V IP VKL+P +I ++AKAA ADG++AINT+SG +
Sbjct: 155 KAVKAAVDIPLLVKLSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVDL------KT 208
Query: 683 VGTKKLTTYGGVSGNATRPMGLKAVSSIAKMFP-NFPILGIGGIDSADVALQFIQAGAHA 741
VG GG+SG RP+ L+ V+ +A + PI+G+GGIDS + L+ + AGA A
Sbjct: 209 VGPGPKRGTGGLSGAPIRPLALRWVARLAARLQLDIPIIGVGGIDSGEDVLEMLMAGASA 268
Query: 742 VQICSAVQNQDFTVVDDYITG 762
VQ+ +A+ V+
Sbjct: 269 VQVATALMWDGPDVIRKIKKE 289
Score = 69.7 bits (171), Expect = 7e-13
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 350 VEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIVKGT 409
V GLK NPFG+A+ P ++ RA G+G V KT +L N PR+ +
Sbjct: 1 VNFLGLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKTVTLHPR-PGNPLPRVARLP 59
Query: 410 TSRHLYGPEQGSFLNIELISEKT 432
PEQ LN +
Sbjct: 60 PEGE-SYPEQLGILNSFGLPNLG 81
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 181 bits (461), Expect = 3e-51
Identities = 74/184 (40%), Positives = 114/184 (61%), Gaps = 12/184 (6%)
Query: 566 LIASIMCTYNKDDWLELSKKTEKAG-ADALELNLSCPHGMGERGMGLACGQDPEMVRNIS 624
+IA++ ++++ E+++K KA DA+ELN+SCP+ G+A G DPE+ +
Sbjct: 94 IIANV-AGSTEEEYAEVAEKLSKAPNVDAIELNISCPNVKH---GGMAFGTDPELAYEVV 149
Query: 625 LWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVG 684
V+ VK+P VKLTPN+T+I +IAKAA E ADG+S INT+ G M++ P +
Sbjct: 150 KAVKEVVKVPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKG-MAIDIK-TRKPILA 207
Query: 685 TKKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQI 744
GG+SG A +P+ L+ V + + + PI+G+GGI SA+ A++FI AGA AVQ+
Sbjct: 208 NV----TGGLSGPAIKPIALRMVYQVYQAV-DIPIIGMGGISSAEDAIEFIMAGASAVQV 262
Query: 745 CSAV 748
+A
Sbjct: 263 GTAN 266
Score = 36.7 bits (86), Expect = 0.035
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 347 DISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
+SVE+ GLK NP AS R NG G VTK+ +L+ N +PRI
Sbjct: 1 RLSVELPGLKLKNPVMPASGTFGFGGEYARFYDLNGLGAIVTKSTTLEPRE-GNPTPRIA 59
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 184 bits (469), Expect = 1e-50
Identities = 103/290 (35%), Positives = 149/290 (51%), Gaps = 26/290 (8%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIG--KPNA 101
IP++RLP D V+ EVE + LGV+I + RDIT+++LR GY A+FIG G P
Sbjct: 183 IPEFRLPKDIVDREVERLLKLGVEIRTNTEVG-RDITLDELR-AGYDAVFIGTGAGLPRF 240
Query: 102 NVIPIFQGLTEEM-GFYTSKTFLPRVATSSKKGLCGGCKKESLPILKG-TVIVLGAGDTA 159
IP G E + G Y++ FL RV + G V+V+G G+TA
Sbjct: 241 LGIP---G--ENLGGVYSAVDFLTRVNQ----------AVADYDLPVGKRVVVIGGGNTA 285
Query: 160 FDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNKIA 219
D A +A R GA V +V+R+G + A EEV+ A EE EF +PV++ + ++
Sbjct: 286 MDAARTAKRLGAESVTIVYRRGREEMPASEEEVEHAKEEGVEFEWLAAPVEILGDEGRVT 345
Query: 220 GMQFNRTEQNEKGE----WVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYG 275
G++F R E E V E L A+ +I A G T +L ++L+++G
Sbjct: 346 GVEFVRMELGEPDASGRRRVPIEGSEFTLPADLVIKAIGQTPNPL-ILSTTPGLELNRWG 404
Query: 276 YPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEK 325
+ T TS+PGVF GGD + T V +V DGK AA IH+Y++
Sbjct: 405 TIIADDETGRTSLPGVFAGGDIVTGAATVVWAVGDGKDAAEAIHEYLEGA 454
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 181 bits (461), Expect = 3e-50
Identities = 88/206 (42%), Positives = 126/206 (61%), Gaps = 8/206 (3%)
Query: 565 ILIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNIS 624
ILIASIM YNKD W E+ ++ E+ G DALE+N SCPHGM ER MG A GQD +++ +
Sbjct: 115 ILIASIMEEYNKDAWEEIIERVEETGVDALEINFSCPHGMPERKMGAAVGQDCDLLEEVC 174
Query: 625 LWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADG-NPWPAV 683
W+ + +P + K+TPNIT+IT A+ A + +GV+AINT+ +M ++ D P P V
Sbjct: 175 GWINAKATVPVWAKMTPNITDITQPARVALKSGCEGVAAINTIMSVMGINLDTLRPEPCV 234
Query: 684 GTKKLTTYGGVSGNATRPMGLKAVSSIAKM----FP-NFPILGIGGIDSADVALQFIQAG 738
+ +T GG S A RP+ L V +IAKM FP + + GIGG+++ A +FI G
Sbjct: 235 --EGYSTPGGYSSKAVRPIALAKVMAIAKMMKSEFPEDRSLSGIGGVETGGDAAEFILLG 292
Query: 739 AHAVQICSAVQNQDFTVVDDYITGLQ 764
A VQ+C+ V + +V + LQ
Sbjct: 293 ADTVQVCTGVMMHGYPLVKNLCAELQ 318
Score = 82.2 bits (203), Expect = 1e-16
Identities = 35/86 (40%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 347 DISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
D+SV + GLK PNPF + S PP T ++++RAF+ GWG + KT SL V NV+PR
Sbjct: 10 DLSVTVNGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVIAKTVSLDASKVINVTPRYA 69
Query: 407 KGTTSRHL-YGPEQGSFLNIELISEK 431
+ + + NIELIS++
Sbjct: 70 RLRAGANGSAKGRVIGWQNIELISDR 95
>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 = 175 bits (445), Expect = 5e-49
Identities = 82/202 (40%), Positives = 123/202 (60%), Gaps = 12/202 (5%)
Query: 566 LIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISL 625
+IASI ++++E+++K AGADA+ELN+SCP+ +G G+A G DPE V I
Sbjct: 92 VIASIA-GSTVEEFVEVAEKLADAGADAIELNISCPN---VKGGGMAFGTDPEAVAEIVK 147
Query: 626 WVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVGT 685
V+ + +P VKLTPN+T+I +IA+AA E ADG++ INT+ G M++ + P +G
Sbjct: 148 AVKKATDVPVIVKLTPNVTDIVEIARAAEEAGADGLTLINTLKG-MAIDIETRK-PILGN 205
Query: 686 KKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQIC 745
GG+SG A +P+ L+ V + K PI+G+GGI S + AL+F+ AGA AVQ+
Sbjct: 206 V----TGGLSGPAIKPIALRMVYQVYKAV-EIPIIGVGGIASGEDALEFLMAGASAVQVG 260
Query: 746 SAVQNQDFTVVDDYITGLQTLL 767
+A D + I GL+ L
Sbjct: 261 TANF-VDPEAFKEIIEGLEAYL 281
Score = 37.1 bits (87), Expect = 0.025
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 349 SVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSL 393
SVE+ GL+ NP LAS + R A G VTK+ +L
Sbjct: 1 SVELAGLRLKNPVILASGTFGFGEELSRVADLGKLGAIVTKSITL 45
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 173 bits (440), Expect = 4e-48
Identities = 82/206 (39%), Positives = 123/206 (59%), Gaps = 13/206 (6%)
Query: 565 ILIASIMCTYNKDDWLELSKKTEKAG-ADALELNLSCPHGMGERGMGLACGQDPEMVRNI 623
+ I +++ W + ++ E+AG ADA+ELN+SCP+ G G A GQDPE++ +
Sbjct: 97 VNIGKNKGGPSEEAWADYARLLEEAGDADAIELNISCPNTPG----GRALGQDPELLEKL 152
Query: 624 SLWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTV-SGLMSLSADGNPWPA 682
V+++ K+P FVKL PNIT+I +IAKAA E ADG+ AINT SG+ P A
Sbjct: 153 LEAVKAATKVPVFVKLAPNITDIDEIAKAAEEAGADGLIAINTTKSGMKIDLETKKPVLA 212
Query: 683 VGTKKLTTYGGVSGNATRPMGLKAVSSIAKMF-PNFPILGIGGIDSADVALQFIQAGAHA 741
T GG+SG +P+ L+ V+ + K + PI+G+GGI++ + AL+FI AGA A
Sbjct: 213 NET------GGLSGPPLKPIALRVVAELYKRLGGDIPIIGVGGIETGEDALEFILAGASA 266
Query: 742 VQICSAVQNQDFTVVDDYITGLQTLL 767
VQ+ +A+ + +V + I GL L
Sbjct: 267 VQVGTALIYKGPGIVKEIIKGLARWL 292
Score = 58.8 bits (143), Expect = 3e-09
Identities = 27/78 (34%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 347 DISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
D+S EI GLKFPNP GLA+ + G+G VTKT + + N PR+
Sbjct: 1 DLSTEILGLKFPNPLGLAAGFDGKNGEELDALAALGFGAIVTKTVTPEP-QEGNPKPRLF 59
Query: 407 KGTTSRHLYGPEQGSFLN 424
R PE +N
Sbjct: 60 -----RL---PEDEGLIN 69
>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 = 154 bits (390), Expect = 1e-41
Identities = 81/185 (43%), Positives = 116/185 (62%), Gaps = 13/185 (7%)
Query: 566 LIASIMCTYNKDDWLELSKKTEKAG--ADALELNLSCPHGMGERGMGLACGQDPEMVRNI 623
LIAS+ + +++ E+++K EKA DA ELNLSCPH G G+A GQDPE+ ++
Sbjct: 93 LIASVY-GSSVEEFAEVAEKLEKAPPYVDAYELNLSCPHVKG---GGIAIGQDPELSADV 148
Query: 624 SLWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAV 683
V+ +P F KL+PN+T+IT+IAKAA E ADG++ INT+ G+ G P A
Sbjct: 149 VKAVKDKTDVPVFAKLSPNVTDITEIAKAAEEAGADGLTLINTLRGMKIDIKTGKPILA- 207
Query: 684 GTKKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQ 743
GG+SG A +P+ L+ V + KM + PI+G+GGI S + AL+F+ AGA AVQ
Sbjct: 208 -----NKTGGLSGPAIKPIALRMVYDVYKMV-DIPIIGVGGITSFEDALEFLMAGASAVQ 261
Query: 744 ICSAV 748
+ +AV
Sbjct: 262 VGTAV 266
Score = 37.8 bits (88), Expect = 0.017
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 348 ISVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
+ VE+ G++F NP LAS + +RR +G G VTK+ L+ +P IV
Sbjct: 1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIGLEPRP-GYRNPTIV 58
>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
Length = 464
Score = 143 bits (362), Expect = 2e-36
Identities = 97/295 (32%), Positives = 150/295 (50%), Gaps = 27/295 (9%)
Query: 44 IPQYRLPFDA-VNFEVELVKDLGVKIECERSLSTRDITIEKLRKD-GYTAIFIGIGKPNA 101
IP++RLP + V E+E +K LGVKIE + + +TI++L ++ G+ A+FIG G
Sbjct: 183 IPEFRLPKETVVKKEIENIKKLGVKIETNV-VVGKTVTIDELLEEEGFDAVFIGSGAG-- 239
Query: 102 NVIPIFQGLTEE--MGFYTSKTFLPRVATSSKKGLCGGCKKES-LPILKGT-VIVLGAGD 157
+P F G+ E G +++ FL RV L K E PI G V V+G G+
Sbjct: 240 --LPKFMGIPGENLNGVFSANEFLTRV------NLMKAYKPEYDTPIKVGKKVAVVGGGN 291
Query: 158 TAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDN- 216
A D A +ALR GA +V +V+R+ + A EEV A EE F +PV++ +N
Sbjct: 292 VAMDAARTALRLGA-EVHIVYRRSEEELPARVEEVHHAKEEGVIFDLLTNPVEILGDENG 350
Query: 217 KIAGMQFNRTEQNEKGEW-----VEDEEQRIKLKANYIISAFGSTLLDNDVL-EAIKPVK 270
+ GM+ + E E VE E L+ + +I + G++ N ++ K +K
Sbjct: 351 WVKGMKCIKMELGEPDASGRRRPVEIEGSEFVLEVDTVIMSLGTS--PNPLISSTTKGLK 408
Query: 271 LDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEK 325
++K G + T TS GVF GGD + T + ++ GK AA I +Y+ +K
Sbjct: 409 INKRGCIVADEETGLTSKEGVFAGGDAVTGAATVILAMGAGKKAAKAIDEYLSKK 463
>gnl|CDD|237200 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta;
Provisional.
Length = 752
Score = 139 bits (351), Expect = 8e-34
Identities = 89/293 (30%), Positives = 145/293 (49%), Gaps = 25/293 (8%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP++RLP V+ E+E +K LGVK E + + + ITIE+L ++G+ IFI G
Sbjct: 474 IPEFRLPKKIVDVEIENLKKLGVKFETD-VIVGKTITIEELEEEGFKGIFIASGAG---- 528
Query: 104 IPIFQGLTEE--MGFYTSKTFLPRVATSSKKGLCGGCKKES-LPILKG-TVIVLGAGDTA 159
+P F + E G +S +L RV L +S PI G V V+G G+TA
Sbjct: 529 LPNFMNIPGENSNGVMSSNEYLTRV------NLMDAASPDSDTPIKFGKKVAVVGGGNTA 582
Query: 160 FDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQV------DV 213
D A +A R GA +V +V+R+ + A EEV+ A EE EFL +P++ V
Sbjct: 583 MDSARTAKRLGAERVTIVYRRSEEEMPARLEEVKHAKEEGIEFLTLHNPIEYLADEKGWV 642
Query: 214 KDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDNDVL-EAIKPVKLD 272
K + M+ + + + V + + +I + G + N ++ +I ++L+
Sbjct: 643 KQVVLQKMELGEPDASGRRRPVAIPGSTFTVDVDLVIVSVGVS--PNPLVPSSIPGLELN 700
Query: 273 KYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEK 325
+ G V+ +S+PG++ GGD T + ++ DGK AA I +Y+ K
Sbjct: 701 RKGTIVVDEEMQ-SSIPGIYAGGDIVRGGATVILAMGDGKRAAAAIDEYLSSK 752
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 134 bits (340), Expect = 5e-33
Identities = 83/283 (29%), Positives = 140/283 (49%), Gaps = 25/283 (8%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP YRLP + ++ E++ + DLGV++ + DIT+E+L + + A+F+ IG
Sbjct: 180 IPAYRLPREVLDAEIQRILDLGVEVRLGVRVGE-DITLEQLEGE-FDAVFVAIGAQLGKR 237
Query: 104 IPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTVIVLGAGDTAFDCA 163
+PI + G + FL V P L V+V+G G+TA D A
Sbjct: 238 LPIPGE--DAAGVLDAVDFLRAVGE------------GEPPFLGKRVVVIGGGNTAMDAA 283
Query: 164 TSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNKIAGMQF 223
+A R GA +V +V+R+ ++ A EE++ A E E +PV+++ +N G++
Sbjct: 284 RTARRLGAEEVTIVYRRTREDMPAHDEEIEEALREGVEINWLRTPVEIEGDENGATGLRV 343
Query: 224 NRTEQNEKGE--W---VEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPE 278
E+ E E V EE+ + +A+ ++ A G +D+ LE++ V++ + G +
Sbjct: 344 ITVEKMELDEDGRPSPVTGEEETL--EADLVVLAIGQD-IDSAGLESVPGVEVGR-GVVQ 399
Query: 279 VNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKY 321
V+ M T PGVF GGD T ++ GK AA +I +
Sbjct: 400 VDPNFMMTGRPGVFAGGDMVPGPRTVTTAIGHGKKAARNIDAF 442
Score = 36.0 bits (84), Expect = 0.084
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 522 MCINCGKCYMACNDSGYQAITFHPETHQAHVT-DECTGCTLC 562
C C CY AC AI + H D+CTGC +C
Sbjct: 511 NCFECDNCYGACPQ---DAIIKLGPGRRYHFDYDKCTGCHIC 549
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 135 bits (343), Expect = 1e-32
Identities = 83/294 (28%), Positives = 135/294 (45%), Gaps = 31/294 (10%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIE--CERSLSTRDITIEKLRKDGYTAIFIGIGKPNA 101
IPQ+R+P + + ++E VK GVK E C D+T+E+L+ +GY + + IG
Sbjct: 582 IPQFRIPAELIQHDIEFVKAHGVKFEFGCS-----PDLTVEQLKNEGYDYVVVAIGADKN 636
Query: 102 NVIPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTVIVLGAGDTAFD 161
+ + G + FL K K +L + K V+V+G G+TA D
Sbjct: 637 GGLKLEGG---NQNVIKALPFLEEY----KN------KGTALKLGK-HVVVVGGGNTAMD 682
Query: 162 CATSALRC-GANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNKIAG 220
A +ALR G KV VV+R+ + A EE + A E+ EF ++P D D +
Sbjct: 683 AARAALRVPGVEKVTVVYRRTKQEMPAWREEYEEALEDGVEFKELLNPESFD-ADGTLTC 741
Query: 221 MQFNRTEQNEKGEW-VEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPEV 279
E +E G + + + L+A+ +I+A G +D ++L+A + LDK G+P V
Sbjct: 742 RVMKLGEPDESGRRRPVETGETVTLEADTVITAIGEQ-VDTELLKANG-IPLDKKGWPVV 799
Query: 280 NYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEKNNLTVPDK 333
+ TS+ V+ GD T V ++ D + AA I + +
Sbjct: 800 D-ANGETSLTNVYMIGDVQRGPSTIVAAIADARRAA----DAILSREGIRSHQN 848
>gnl|CDD|223567 COG0493, GltD, NADPH-dependent glutamate synthase beta chain and
related oxidoreductases [Amino acid transport and
metabolism / General function prediction only].
Length = 457
Score = 129 bits (327), Expect = 6e-32
Identities = 91/294 (30%), Positives = 137/294 (46%), Gaps = 26/294 (8%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIEC--ERSLSTRDITIEKLRKDGYTAIFIGIGKPNA 101
IP ++LP D ++ +EL++ GV+ + RDIT+E+L K+ Y A+F+ G
Sbjct: 166 IPDFKLPKDILDRRLELLERSGVEFKLNVRVG---RDITLEELLKE-YDAVFLATGAGKP 221
Query: 102 NVIPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKG-TVIVLGAGDTAF 160
+ I + G + FL R+ K + G ++ P KG V+V+G GDTA
Sbjct: 222 RPLDIP--GEDAKGVAFALDFLTRL----NKEVLGDFAEDRTPPAKGKRVVVIGGGDTAM 275
Query: 161 DCATSALRCGANKVLVVFRKGCTN------IRAVPEEVQLAWEEKCEFLPFMSPVQVDVK 214
DCA +ALR GA V +R+ + A EV+ A EE E LPF+ P
Sbjct: 276 DCAGTALRLGAKSVTCFYREDRDDETNEWPTWAAQLEVRSAGEEGVERLPFVQPKAFIGN 335
Query: 215 DN-KIAGMQFNRTEQNE------KGEWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIK 267
+ ++ G++F R E E + V A+ +I A G D L
Sbjct: 336 EGGRVTGVKFGRVEPGEYVDGWGRRGPVGVIGTEKTDAADTVILAIGFEGDATDGLLLEF 395
Query: 268 PVKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKY 321
+KLDK G +V+ TS+PGVF GGD + V ++ +G+ AA I K
Sbjct: 396 GLKLDKRGRIKVDENLQQTSIPGVFAGGDAVRGAALVVWAIAEGREAAKAIDKE 449
>gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit.
Members of this protein family are YgfK, predicted to be
one subunit of a three-subunit, molybdopterin-containing
selenate reductase. This enzyme is found, typically, in
genomic regions associated with xanthine dehydrogenase
homologs predicted to belong to the selenium-dependent
molybdenum hydroxylases (SDMH). Therefore, the selenate
reductase is suggested to play a role in furnishing
selenide for SelD, the selenophosphate synthase.
Length = 1012
Score = 132 bits (335), Expect = 1e-31
Identities = 87/308 (28%), Positives = 144/308 (46%), Gaps = 30/308 (9%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP++R+ +++ ++ELVK GV+ + S D+T+ +L+ GY + + IG
Sbjct: 580 IPEFRISAESIQKDIELVKFHGVEFKYGCS---PDLTVAELKNQGYKYVILAIGAWKHGP 636
Query: 104 IPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTVIVLGAGDTAFDCA 163
+ + G + S FL + K+G P+ K V+V+G G+TA D A
Sbjct: 637 LRLEGGGERVLK---SLEFL----RAFKEG------PTINPLGK-HVVVVGGGNTAMDAA 682
Query: 164 TSALRC-GANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNKIAGMQ 222
+ALR G KV VV+R+ + A EE++ A E+ +F +SP + D +
Sbjct: 683 RAALRVPGVEKVTVVYRRTKRYMPASREELEEALEDGVDFKELLSPESFE--DGTLTCEV 740
Query: 223 FNRTEQNEKGEW--VEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPEVN 280
E + G V E + L A+ +I+A G + D D+L+ + LD+YG+P VN
Sbjct: 741 MKLGEPDASGRRRPVGTGET-VDLPADTVIAAVGEQV-DTDLLQKNG-IPLDEYGWPVVN 797
Query: 281 YTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEKNNLTVPDKPCLPKFM 340
T T++ VF GD T VE++ DG+ AA I + L D +
Sbjct: 798 QATGETNITNVFVIGDANRGPATIVEAIADGRKAA----NAILSREGLN-SDVDKVFPIN 852
Query: 341 SHIDLVDI 348
+ L ++
Sbjct: 853 EEVRLAEV 860
>gnl|CDD|130383 TIGR01316, gltA, glutamate synthase (NADPH), homotetrameric. This
protein is homologous to the small subunit of NADPH and
NADH forms of glutamate synthase as found in eukaryotes
and some bacteria. This protein is found in numerous
species having no homolog of the glutamate synthase
large subunit. The prototype of the family, from
Pyrococcus sp. KOD1, was shown to be active as a
homotetramer and to require NADPH [Amino acid
biosynthesis, Glutamate family].
Length = 449
Score = 122 bits (308), Expect = 1e-29
Identities = 90/291 (30%), Positives = 141/291 (48%), Gaps = 29/291 (9%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIG--KPNA 101
IP++RLP + V E++ +K LGV L + T+E+L Y A+FIG G P
Sbjct: 176 IPEFRLPKEIVVTEIKTLKKLGVTFRMNF-LVGKTATLEELFSQ-YDAVFIGTGAGLPKL 233
Query: 102 NVIPIFQGLTEEM-GFYTSKTFLPRVATSSKKGLCGGCKKESLPILKG-TVIVLGAGDTA 159
IP EE+ G Y++ FL R P+ G +V+V+G G+TA
Sbjct: 234 MNIP-----GEELCGVYSANDFLTRANLMKAYEF----PHADTPVYAGKSVVVIGGGNTA 284
Query: 160 FDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDN-KI 218
D A +ALR GA +V ++R+ ++ A EE+ A EE +F PV++ + +
Sbjct: 285 VDSARTALRLGA-EVHCLYRRTREDMTARVEEIAHAEEEGVKFHFLCQPVEIIGDEEGNV 343
Query: 219 AGMQFNRT---EQNEKGEWVE----DEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKL 271
++F + EQ + GE D E KL+A+ +I A G N ++ +K
Sbjct: 344 RAVKFRKMDCQEQIDSGERRFLPCGDAE--CKLEADAVIVAIG--NGSNPIMAETTRLKT 399
Query: 272 DKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYI 322
+ G V+ TS+PGVF GGD + T + ++ GK AA I++Y+
Sbjct: 400 SERGTIVVDEDQR-TSIPGVFAGGDIILGAATVIRAMGQGKRAAKSINEYL 449
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 115 bits (289), Expect = 3e-28
Identities = 70/196 (35%), Positives = 103/196 (52%), Gaps = 16/196 (8%)
Query: 577 DDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRSSVKIPFF 636
+D++E+++K AD LELN+SCP+ G R A DPE+ + V+ K+P
Sbjct: 106 EDYVEVARKIG-PFADYLELNVSCPNTPGLR----ALQTDPELAAILLKVVKEVSKVPVL 160
Query: 637 VKLTPNITNITDIAKAAYEGKADGVSAIN----TVSGLMSLSADGNPWPAVGTKKLTTYG 692
VKL P++T+I I A DG++ IN TV G+ +P A GT G
Sbjct: 161 VKLAPDLTDIVIIDIADVAAGEDGLTGINATNTTVRGMRIDLKTESPILANGT------G 214
Query: 693 GVSGNATRPMGLKAVSSIAKMF-PNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQ 751
G+SG A +P+ LK + + + P PI+G+GGI + + AL+ I AGA AVQI +A+
Sbjct: 215 GLSGPAIKPIALKVIRELYQRVGPEIPIIGVGGIFTGEDALEKILAGASAVQIGTALIFG 274
Query: 752 DFTVVDDYITGLQTLL 767
+ I L LL
Sbjct: 275 GPFIFPKIIDELPELL 290
Score = 34.6 bits (80), Expect = 0.19
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 349 SVEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRIV 406
+V+I GLKF NP GLAS ++ +G K+ + + N +PR+
Sbjct: 3 AVKIPGLKFKNPIGLASGFDKFGEEALKWLALGKFGAIEIKSVTPEPQP-GNPTPRVF 59
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 117 bits (294), Expect = 8e-27
Identities = 98/300 (32%), Positives = 153/300 (51%), Gaps = 37/300 (12%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKD-GYTAIFIGIGKPNAN 102
IP +RLP D ++ EV+ + D+GVKIE + + + T+ +L D G+ A+F+G+G
Sbjct: 473 IPSFRLPRDIIDREVQRLVDIGVKIETNKVIG-KTFTVPQLMNDKGFDAVFLGVGAG--- 528
Query: 103 VIPIFQGLTEEMG--FYTSKTFLPRVATSSKKGLCGGCKKESL--PILKG-TVIVLGAGD 157
P F G+ E Y++ FL RV L GG K L PI G +V+V+GAG+
Sbjct: 529 -APTFLGIPGEFAGQVYSANEFLTRV------NLMGGDKFPFLDTPISLGKSVVVIGAGN 581
Query: 158 TAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDV-KDN 216
TA DC A R GA V V+R+ A EE++ A EE +F SPV++ V +
Sbjct: 582 TAMDCLRVAKRLGAPTVRCVYRRSEAEAPARIEEIRHAKEEGIDFFFLHSPVEIYVDAEG 641
Query: 217 KIAGMQFNRTEQNEKGEWVEDEEQR---------IKLKANYIISAFGSTLLDNDVLEAIK 267
+ GM + E+ E GE DE+ R L+ + +I A G T + + ++
Sbjct: 642 SVRGM---KVEEMELGE--PDEKGRRKPMPTGEFKDLECDTVIYALG-TKANPIITQSTP 695
Query: 268 PVKLDKYGYPEVN----YTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQ 323
+ L+K+G + +T +T++PGVF GGD T + ++ G+ AA I Y++
Sbjct: 696 GLALNKWGNIAADDGKLESTQSTNLPGVFAGGDIVTGGATVILAMGAGRRAARSIATYLR 755
>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 114 bits (288), Expect = 9e-27
Identities = 80/307 (26%), Positives = 126/307 (41%), Gaps = 44/307 (14%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP ++L + ++ +EL++ G++ + +DIT E+L + Y A+F+G G
Sbjct: 186 IPDFKLEKEVIDRRIELMEAEGIEFRTNVEVG-KDITAEELLAE-YDAVFLGTGAYKPRD 243
Query: 104 IPI----FQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKG-TVIVLGAGDT 158
+ I G+ M F T R G + E KG V+V+G GDT
Sbjct: 244 LGIPGRDLDGVHFAMDFLIQNT---RR--------VLGDETEPFISAKGKHVVVIGGGDT 292
Query: 159 AFDCATSALRCGANKVLVVFRKGCTNIRAVP----------------EEVQLAWEEKCEF 202
DC +A+R GA V +I +P EV A EE E
Sbjct: 293 GMDCVGTAIRQGAKSV-TQR-----DIMPMPPSRRNKNNPWPYWPMKLEVSNAHEEGVER 346
Query: 203 LPFMSPVQVDVKDNKIAGMQFNRTEQNEKG-EWVEDEEQRIKLKANYIISAFGSTLLDND 261
+ + + ++ K+ G++ RTE E E VE E + A+ ++ A G T +
Sbjct: 347 EFNVQTKEFEGENGKVTGVKVVRTELGEGDFEPVEGSEFVL--PADLVLLAMGFTGPEAG 404
Query: 262 VLEAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKY 321
+L V+LD+ G TS P VF GD V ++ +G+ AA I Y
Sbjct: 405 LLAQFG-VELDERGRVAAPDNAYQTSNPKVFAAGDMRRGQSLVVWAIAEGRQAARAIDAY 463
Query: 322 IQEKNNL 328
+ L
Sbjct: 464 LMGSTAL 470
>gnl|CDD|139246 PRK12814, PRK12814, putative NADPH-dependent glutamate synthase
small subunit; Provisional.
Length = 652
Score = 112 bits (281), Expect = 2e-25
Identities = 78/286 (27%), Positives = 135/286 (47%), Gaps = 22/286 (7%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP++RLP ++ ++ ++ +G + RDIT+E+L+K+ + A+ + +G A+
Sbjct: 236 IPRFRLPESVIDADIAPLRAMGAEFRFNTVFG-RDITLEELQKE-FDAVLLAVGAQKASK 293
Query: 104 IPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTVIVLGAGDTAFDCA 163
+ I G E G + FL VA + V+V+G G+TA D A
Sbjct: 294 MGI-PG-EELPGVISGIDFLRNVALGTA------------LHPGKKVVVIGGGNTAIDAA 339
Query: 164 TSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNKIA---- 219
+ALR GA V +++R+ + A E++ A E +PV ++ + +
Sbjct: 340 RTALRLGAESVTILYRRTREEMPANRAEIEEALAEGVSLRELAAPVSIERSEGGLELTAI 399
Query: 220 GMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPEV 279
MQ +++ + V E L+A+ +ISA G + D + EA + + G +V
Sbjct: 400 KMQQGEPDESGRRRPVPVEGSEFTLQADTVISAIGQQV-DPPIAEA-AGIGTSRNGTVKV 457
Query: 280 NYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEK 325
+ T+ TSV GVF GGD +D + +V GK AA I ++ K
Sbjct: 458 DPETLQTSVAGVFAGGDCVTGADIAINAVEQGKRAAHAIDLFLNGK 503
>gnl|CDD|130385 TIGR01318, gltD_gamma_fam, glutamate synthase small subunit family
protein, proteobacterial. This model represents one of
three built for the NADPH-dependent or NADH-dependent
glutamate synthase (EC 1.4.1.13 and 1.4.1.14,
respectively) small subunit and homologs. TIGR01317
describes the small subunit (or equivalent region from
longer forms) in eukaryotes, Gram-positive bacteria, and
some other lineages, both NADH and NADPH-dependent.
TIGR01316 describes a protein of similar length, from
Archaea and a number of bacterial lineages, that forms
glutamate synthase homotetramers without a large
subunit. This model describes both glutatate synthase
small subunit and closely related paralogs of unknown
function from a number of gamma and alpha subdivision
Proteobacteria, including E. coli.
Length = 467
Score = 102 bits (255), Expect = 9e-23
Identities = 85/297 (28%), Positives = 136/297 (45%), Gaps = 33/297 (11%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGV--KIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNA 101
IP ++L ++ E+ +G+ + CE RDI+++ L +D Y A+F+G+G +
Sbjct: 184 IPSFKLDKAVLSRRREIFTAMGIEFHLNCEVG---RDISLDDLLED-YDAVFLGVGTYRS 239
Query: 102 NVIPIFQGLTEE--MGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGT---VIVLGAG 156
+ GL E G + FL ++ + L G + P++ V+VLG G
Sbjct: 240 ----MRGGLPGEDAPGVLQALPFL----IANTRQLMGLPESPEEPLIDVEGKRVVVLGGG 291
Query: 157 DTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDV-KD 215
DTA DC +A+R GA V +R+ N+ EV A EE EFL + PV ++ +D
Sbjct: 292 DTAMDCVRTAIRLGAASVTCAYRRDEANMPGSRREVANAREEGVEFLFNVQPVYIECDED 351
Query: 216 NKIAGMQFNRTEQNEKG-------EWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKP 268
++ G+ RT E V E L A+ +I AFG L
Sbjct: 352 GRVTGVGLVRTALGEPDADGRRRPVPVAGSEF--VLPADVVIMAFGFQPHAMPWLAG-HG 408
Query: 269 VKLDKYGY---PEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYI 322
+ LD +G +V+Y T+ P +F GGD +D V +V +G+ AA I ++
Sbjct: 409 ITLDSWGRIITGDVSYLPYQTTNPKIFAGGDAVRGADLVVTAVAEGRQAAQGILDWL 465
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 96.0 bits (239), Expect = 2e-20
Identities = 78/310 (25%), Positives = 142/310 (45%), Gaps = 59/310 (19%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIG--KPNA 101
IP YRLP +A++ ++ ++ LGVKI + +DI +E+LR+ + A+F+ G +
Sbjct: 326 IPSYRLPDEALDKDIAFIEALGVKIHLNTRVG-KDIPLEELRE-KHDAVFLSTGFTLGRS 383
Query: 102 NVIP------IFQGLT--EEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTVIVL 153
IP + Q L E+ Y L G K +P +++V+
Sbjct: 384 TRIPGTDHPDVIQALPLLREIRDY----------------LRGEGPKPKIP---RSLVVI 424
Query: 154 GAGDTAFDCATSALRC-----GANKVLVVFRKGC-TNIRAVPEEVQLAWEEKCEFLPFMS 207
G G+ A D A S R G V V + + A EE++ EE P
Sbjct: 425 GGGNVAMDIARSMARLQKMEYGEVNVKVTSLERTFEEMPADMEEIEEGLEEGVVIYPGWG 484
Query: 208 PVQVDVKDNKIAGMQFNRTEQ--NEKGEWVE--DEEQRIKLKANYIISAFGS----TLLD 259
P++V ++++K+ G++F + + +E+G + DE +I ++A+ ++ A G + L
Sbjct: 485 PMEVVIENDKVKGVKFKKCVEVFDEEGRFNPKFDESDQIIVEADMVVEAIGQAPDYSYLP 544
Query: 260 NDVLEAIK----PVKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAA 315
++ ++ + ++YG TS+P +F GGD + D + V DG AA
Sbjct: 545 EELKSKLEFVRGRILTNEYG---------QTSIPWLFAGGDIVHGPD-IIHGVADGYWAA 594
Query: 316 WHIHKYIQEK 325
I Y++++
Sbjct: 595 EGIDMYLRKQ 604
>gnl|CDD|240089 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2.
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, their cellular
location and their natural electron acceptor used to
reoxidize the flavin group. Members of class 1 are
cytosolic enzymes and multimers, while class 2 enzymes
are membrane associated, monomeric and use respiratory
quinones as their physiological electron acceptors.
Length = 327
Score = 89.9 bits (224), Expect = 2e-19
Identities = 48/165 (29%), Positives = 79/165 (47%), Gaps = 22/165 (13%)
Query: 591 ADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRS-----SVKIPFFVKLTPNITN 645
AD L +N+S P+ G R + Q E +R + V+ K+P VK+ P++++
Sbjct: 161 ADYLVVNVSSPNTPGLRDL-----QGKEALRELLTAVKEERNKLGKKVPLLVKIAPDLSD 215
Query: 646 --ITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVGTKKLTTYGGVSGNATRPMG 703
+ DIA A E DG+ A NT ++S G + GG+SG +
Sbjct: 216 EELEDIADVALEHGVDGIIATNT-----TISRPGLL----RSPLANETGGLSGAPLKERS 266
Query: 704 LKAVSSIAKMFPN-FPILGIGGIDSADVALQFIQAGAHAVQICSA 747
+ + + K+ PI+G+GGI S + A + I+AGA VQ+ +
Sbjct: 267 TEVLRELYKLTGGKIPIIGVGGISSGEDAYEKIRAGASLVQLYTG 311
Score = 35.9 bits (84), Expect = 0.065
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 349 SVEICGLKFPNPFGLA 364
VE+ GL FPNP GLA
Sbjct: 40 EVEVFGLTFPNPVGLA 55
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 92.6 bits (230), Expect = 4e-19
Identities = 86/291 (29%), Positives = 140/291 (48%), Gaps = 33/291 (11%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP++RLP ++ VE +K LG + + + + T+E L+ G+ IF+G G
Sbjct: 349 IPEFRLPNQLIDDVVEKIKLLGGRF-VKNFVVGKTATLEDLKAAGFWKIFVGTGAG---- 403
Query: 104 IPIFQGLTEE--MGFYTSKTFLPRVATSSKKGLCGGCKKE---SLPILKG-TVIVLGAGD 157
+P F + E +G ++ FL RV L G + LP +KG V V+G G+
Sbjct: 404 LPTFMNVPGEHLLGVMSANEFLTRV------NLMRGLDDDYETPLPEVKGKEVFVIGGGN 457
Query: 158 TAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDVKDNK 217
TA D A +A R G N V +V+R+ + + A EE+ A EE +P + + D+
Sbjct: 458 TAMDAARTAKRLGGN-VTIVYRRTKSEMPARVEELHHALEEGINLAVLRAPREF-IGDDH 515
Query: 218 IAGMQFNRTEQNEKGEWVEDEEQR---------IKLKANYIISAFGSTLLDNDVLEAIKP 268
+ + NE GE D+ R ++ + +I A G+T N +++ +P
Sbjct: 516 THFVTHALLDVNELGE--PDKSGRRSPKPTGEIERVPVDLVIMALGNT--ANPIMKDAEP 571
Query: 269 -VKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHI 318
+K +K+G EV + TS+ GV+ GGD A T + + DG+ AA I
Sbjct: 572 GLKTNKWGTIEVEKGSQRTSIKGVYSGGDAARGGSTAIRAAGDGQAAAKEI 622
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 86.3 bits (214), Expect = 2e-17
Identities = 81/304 (26%), Positives = 132/304 (43%), Gaps = 63/304 (20%)
Query: 40 DSSEIPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGK- 98
D S + + R F A+ E EL ++G +DI++E L +D Y A+F+G+G
Sbjct: 376 DKSLLARRREIFSAMGIEFELNCEVG-----------KDISLESLLED-YDAVFVGVGTY 423
Query: 99 -------PNANVIPIFQGL------TEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPI 145
PN + ++ L T+++ P + T+
Sbjct: 424 RSMKAGLPNEDAPGVYDALPFLIANTKQVMGLEELPEEPFINTAGLN------------- 470
Query: 146 LKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPF 205
V+VLG GDTA DC +ALR GA+ V +R+ N+ +EV+ A EE F
Sbjct: 471 ----VVVLGGGDTAMDCVRTALRHGASNVTCAYRRDEANMPGSKKEVKNAREEGANFEFN 526
Query: 206 MSPVQVDVKDN-KIAGMQFNRTEQNEKGEWVEDEEQRIK----------LKANYIISAFG 254
+ PV +++ + + G++F RT E D + R + + A+ +I AFG
Sbjct: 527 VQPVALELNEQGHVCGIRFLRTRLGEP-----DAQGRRRPVPIPGSEFVMPADAVIMAFG 581
Query: 255 STLLDNDVLEAIKPVKLDKYGY---PEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDG 311
LE+ V +DK+G + TS P +F GGD +D V ++ +G
Sbjct: 582 FNPHGMPWLES-HGVTVDKWGRIIADVESQYRYQTSNPKIFAGGDAVRGADLVVTAMAEG 640
Query: 312 KTAA 315
+ AA
Sbjct: 641 RHAA 644
>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 79.1 bits (196), Expect = 1e-15
Identities = 55/172 (31%), Positives = 81/172 (47%), Gaps = 36/172 (20%)
Query: 591 ADALELNLSCPHGMGERGMGLACGQDPE-------MVRNISLWVRSSVKIPFFVKLTPNI 643
AD +N+S P+ G R + Q E ++ + V P VK+ P++
Sbjct: 170 ADYFTVNISSPNTPGLRDL-----QYGEALDELLAALKEAQAELHGYV--PLLVKIAPDL 222
Query: 644 TN--ITDIAKAAYEGKADGVSAINTVSGLMSLSADG--NPWPAVGTKKLTTYGGVSGNAT 699
++ + DIA A E DGV A NT +LS DG A GG+SG
Sbjct: 223 SDEELDDIADLALEHGIDGVIATNT-----TLSRDGLKGLPNADEA------GGLSG--- 268
Query: 700 RPMGLKA---VSSIAK-MFPNFPILGIGGIDSADVALQFIQAGAHAVQICSA 747
RP+ ++ + + K + PI+G+GGIDSA+ A + I+AGA VQI S
Sbjct: 269 RPLFERSTEVIRRLYKELGGRLPIIGVGGIDSAEDAYEKIRAGASLVQIYSG 320
Score = 35.1 bits (82), Expect = 0.13
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 349 SVEICGLKFPNPFGLA 364
V + GL FPNP GLA
Sbjct: 50 PVTVMGLTFPNPVGLA 65
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 80.5 bits (198), Expect = 1e-15
Identities = 79/296 (26%), Positives = 129/296 (43%), Gaps = 25/296 (8%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP ++L ++ E+ +G+ + RDIT L + Y A+FIG+G
Sbjct: 353 IPPFKLDKTVLSQRREIFTAMGIDFHLNCEIG-RDITFSDLTSE-YDAVFIGVGTYGM-- 408
Query: 104 IPIFQGLTEE--MGFYTSKTFLPRVATSSKKGLCGGCKKESLPI--LKG-TVIVLGAGDT 158
+ L E G + FL T+ + L G + E P+ ++G V+VLG GDT
Sbjct: 409 --MRADLPHEDAPGVIQALPFL----TAHTRQLMGLPESEEYPLTDVEGKRVVVLGGGDT 462
Query: 159 AFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPVQVDV-KDNK 217
DC +++R A V +R+ ++ +EV A EE EF + P + +D +
Sbjct: 463 TMDCLRTSIRLNAASVTCAYRRDEVSMPGSRKEVVNAREEGVEFQFNVQPQYIACDEDGR 522
Query: 218 IAGMQFNRTEQNEKGEWVEDEEQRI-----KLKANYIISAFGSTLLDNDVLEAIKPVKLD 272
+ + RT E G + + +L A+ +I AFG L+ +KLD
Sbjct: 523 LTAVGLIRTAMGEPGPDGRRRPRPVAGSEFELPADVLIMAFGFQAHAMPWLQGSG-IKLD 581
Query: 273 KYGY---PEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEK 325
K+G +V Y T + VF GGD + +D V ++ G+ AA + K
Sbjct: 582 KWGLIQTGDVGYLPTQTHLKKVFAGGDAVHGADLVVTAMAAGRQAARDMLTLFDTK 637
>gnl|CDD|237197 PRK12770, PRK12770, putative glutamate synthase subunit beta;
Provisional.
Length = 352
Score = 76.6 bits (189), Expect = 7e-15
Identities = 81/315 (25%), Positives = 141/315 (44%), Gaps = 56/315 (17%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGV------KIECERSL--------STRDITIEKLRKDGY 89
IP++R+P + V V+ +++ GV K+ C L R +++E+L K Y
Sbjct: 61 IPEFRIPIERVREGVKELEEAGVVFHTRTKVCCGEPLHEEEGDEFVERIVSLEELVKK-Y 119
Query: 90 TAIFIGIG--KPNANVIPIFQGLTEEM-GFYTSKTFLPRVATSSKKGLCGGCKKESLPIL 146
A+ I G K IP E++ G Y++ +L R+ ++K G E +P +
Sbjct: 120 DAVLIATGTWKSRKLGIP-----GEDLPGVYSALEYLFRI-RAAKLGYL---PWEKVPPV 170
Query: 147 KG-TVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPF 205
+G V+V+GAG TA D A A+ GA KV + +R+ A E++ EFL
Sbjct: 171 EGKKVVVVGAGLTAVDAALEAVLLGAEKVYLAYRRTINEAPAGKYEIERLIARGVEFLEL 230
Query: 206 MSPVQVDVKDNKIAGMQFNRTEQNEKGEW-------VEDEEQRIKLKANYIISAFGSTLL 258
++PV++ + + ++ G++ + E E + E L+A+ ++ A G
Sbjct: 231 VTPVRI-IGEGRVEGVELAKMRLGEPDESGRPRPVPIPGSE--FVLEADTVVFAIG---- 283
Query: 259 DNDVLEAIKP--------VKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVND 310
E P ++L++ G V+ M TS GVF GD +++
Sbjct: 284 -----EIPTPPFAKECLGIELNRKGEIVVDEKHM-TSREGVFAAGDVVTGPSKIGKAIKS 337
Query: 311 GKTAAWHIHKYIQEK 325
G AA IH+++ K
Sbjct: 338 GLRAAQSIHEWLDLK 352
>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 = 75.0 bits (185), Expect = 2e-14
Identities = 61/248 (24%), Positives = 97/248 (39%), Gaps = 78/248 (31%)
Query: 563 LSI-LIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDP---- 617
+SI +IAS+ + W++ +++ E+AGADALELN+ A DP
Sbjct: 98 VSIPVIASLNG-VSAGGWVDYARQIEEAGADALELNI------------YALPTDPDISG 144
Query: 618 --------EMVRNISLWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAIN---- 665
+++R V+S+V IP VKL+P + + +AK ADG+ N
Sbjct: 145 AEVEQRYLDILRA----VKSAVTIPVAVKLSPFFSALAHMAKQLDAAGADGLVLFNRFYQ 200
Query: 666 ---------TVSGL-MSLSAD-GNP--WPAVGTKKLTTYGGVSGNATRPMGLKAVSSIAK 712
V L +S A+ P W A+ G V L A
Sbjct: 201 PDIDLETLEVVPNLLLSSPAEIRLPLRWIAI------LSGRV------KASLAAS----- 243
Query: 713 MFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQDFTVVDDYITGLQTLL----Y 768
GG+ A+ ++++ AGA V SA+ + + GL+ + Y
Sbjct: 244 ----------GGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEAWMEEHGY 293
Query: 769 LKSTQLKG 776
QL+G
Sbjct: 294 ESVQQLRG 301
>gnl|CDD|240092 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A
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 = 294
Score = 74.3 bits (183), Expect = 2e-14
Identities = 50/188 (26%), Positives = 81/188 (43%), Gaps = 20/188 (10%)
Query: 586 TEKAGADALELNLSCPH--GMGERGMGLACGQDPEMVRNISLWVRSSVKIPFFVKLTPNI 643
+K A+ELNLSCP+ G + ++ V+++ IP VK P
Sbjct: 115 HQKQFPLAMELNLSCPNVPGKPPPA---YDFDA--TLEYLT-AVKAAYSIPVGVKTPP-Y 167
Query: 644 TNIT--DIAKAAYEGKADGVS---AINTV-SGLMSLSADGNPWPAVGTKKLTTYGGVSGN 697
T+ D A A +S A NT+ +GL+ L + V K T +GG++G
Sbjct: 168 TDPAQFDTLAEALNAFACPISFITATNTLGNGLV-LDPERE---TVVLKPKTGFGGLAGA 223
Query: 698 ATRPMGLKAVSSIAKM-FPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQDFTVV 756
P+ L V + ++ I+G+GG+ A + AGA AVQ+ +A+ + V
Sbjct: 224 YLHPLALGNVRTFRRLLPSEIQIIGVGGVLDGRGAFRMRLAGASAVQVGTALGKEGPKVF 283
Query: 757 DDYITGLQ 764
L+
Sbjct: 284 ARIEKELE 291
>gnl|CDD|233243 TIGR01036, pyrD_sub2, dihydroorotate dehydrogenase, subfamily 2.
This model describes enzyme protein dihydroorotate
dehydrogenase exclusively for subfamily 2. It includes
members from bacteria, yeast, plants etc. The
subfamilies 1 and 2 share extensive homology,
particularly toward the C-terminus. This subfamily has a
longer N-terminal region [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 336
Score = 73.3 bits (180), Expect = 7e-14
Identities = 53/182 (29%), Positives = 85/182 (46%), Gaps = 25/182 (13%)
Query: 576 KDDWLELSKKTEKAG--ADALELNLSCPHGMGERGMGLACGQDP--EMVRNISLWVRSSV 631
KDD+L K A + +N+S P+ G R + D ++N +++
Sbjct: 153 KDDYLAC---LRKIYPYAGYIVVNISSPNTPGLRDLQYGEALDDLLTAIKNEQNDLQAHH 209
Query: 632 KIPFFVKLTPNIT--NITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVGTKKLT 689
+P VK+ P+++ ++ IA + DGV A NT ++S G K
Sbjct: 210 HVPIAVKIAPDLSESDLIQIADSLVRHGIDGVIATNT-----TVSRSL----VQGPKNCD 260
Query: 690 TYGGVSGNATRPMGLKAVSSIAKMFPNF----PILGIGGIDSADVALQFIQAGAHAVQIC 745
GG+SG +P+ LK+ I +++ PI+G+GGIDSA A + I AGA +QI
Sbjct: 261 QTGGLSG---KPLQLKSTEIIRRLYLELNGRLPIIGVGGIDSAQDAREKIAAGASLLQIY 317
Query: 746 SA 747
S
Sbjct: 318 SG 319
Score = 30.1 bits (68), Expect = 5.0
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 350 VEICGLKFPNPFGLASAPPTTASSMVRRAFENGWGFAVTKTFSLQKDMVTNVSPRI 405
V + GL FPNP GLA+ + G+G+ T + + N PR+
Sbjct: 48 VTVLGLTFPNPLGLAAGFDKDG-EAIDALGAMGFGYLEIGTVT-PRPQPGNPKPRL 101
>gnl|CDD|236051 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
Length = 334
Score = 72.6 bits (179), Expect = 1e-13
Identities = 64/277 (23%), Positives = 106/277 (38%), Gaps = 83/277 (29%)
Query: 539 QAITFHPETHQAHV-----TDECTGCTLCLSI-LIASIMCTYNKDDWLELSKKTEKAGAD 592
+A+ + PE + +V + + I +IAS+ + W++ +++ E+AGAD
Sbjct: 71 EALDYFPEPAKFYVGPEEYLELIRRAKEAVDIPVIASLNG-SSAGGWVDYARQIEQAGAD 129
Query: 593 ALELNLSCPHGMGERGMGLACGQDPEM------------VRNISLWVRSSVKIPFFVKLT 640
ALELN+ DP++ +R V+S+V IP VKL+
Sbjct: 130 ALELNIYYLPT------------DPDISGAEVEQRYLDILRA----VKSAVSIPVAVKLS 173
Query: 641 PNITNITDIAKAAYEGKADGVSAIN-------------TVSGL-MSLSADG-NP--WPAV 683
P +N+ ++AK ADG+ N V GL +S A+ P W A+
Sbjct: 174 PYFSNLANMAKRLDAAGADGLVLFNRFYQPDIDLETLEVVPGLVLSTPAELRLPLRWIAI 233
Query: 684 GTKKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQ 743
G V L A G+ A+ ++ + AGA V
Sbjct: 234 ------LSGRV------GADLAAT---------------TGVHDAEDVIKMLLAGADVVM 266
Query: 744 ICSAVQNQDFTVVDDYITGLQTLL----YLKSTQLKG 776
I SA+ + + GL+ + Y Q +G
Sbjct: 267 IASALLRHGPDYIGTILRGLEDWMERHGYESLQQFRG 303
>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 = 61.1 bits (148), Expect = 2e-10
Identities = 37/183 (20%), Positives = 59/183 (32%), Gaps = 42/183 (22%)
Query: 565 ILIASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNIS 624
L + + AGAD +E++ + + E D E++R
Sbjct: 59 PLGVQLAINDAAAAVDIAAAAARAAGADGVEIHGAVGYLARE---------DLELIR--- 106
Query: 625 LWVRSSV-KIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAV 683
+R +V + VKL+P A AA E D V
Sbjct: 107 -ELREAVPDVKVVVKLSPTGE---LAAAAAEEAGVDEV---------------------- 140
Query: 684 GTKKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQ 743
L GG G + +AK P++ GGI+ + A + + GA V
Sbjct: 141 ---GLGNGGGGGGGRDAVPIADLLLILAKRGSKVPVIAGGGINDPEDAAEALALGADGVI 197
Query: 744 ICS 746
+ S
Sbjct: 198 VGS 200
>gnl|CDD|223566 COG0492, TrxB, Thioredoxin reductase [Posttranslational
modification, protein turnover, chaperones].
Length = 305
Score = 58.1 bits (141), Expect = 5e-09
Identities = 48/179 (26%), Positives = 82/179 (45%), Gaps = 22/179 (12%)
Query: 150 VIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFMSPV 209
V+V+G GD+A + A + A KV +V R+ RA V+ +K + ++
Sbjct: 146 VVVIGGGDSAVEEALYLSK-IAKKVTLVHRRDE--FRAEEILVERL--KKNVKIEVLTNT 200
Query: 210 QVD-VKDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKP 268
V + + + G+ +N KGE E L + + A G L + ++L+ +
Sbjct: 201 VVKEILGDDVEGVVL----KNVKGEEKE-------LPVDGVFIAIGH-LPNTELLKGL-- 246
Query: 269 VKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVE-SVNDGKTAAWHIHKYIQEKN 326
LD+ GY V+ M TSVPG+F GD A+ + + + DG AA +Y++
Sbjct: 247 GVLDENGYIVVD-EEMETSVPGIFAAGDVADKNGRQIATAAGDGAIAALSAERYLESLA 304
>gnl|CDD|233345 TIGR01292, TRX_reduct, thioredoxin-disulfide reductase. This model
describes thioredoxin-disulfide reductase, a member of
the pyridine nucleotide-disulphide oxidoreductases
(pfam00070) [Energy metabolism, Electron transport].
Length = 299
Score = 55.7 bits (135), Expect = 3e-08
Identities = 53/182 (29%), Positives = 81/182 (44%), Gaps = 21/182 (11%)
Query: 144 PILKG-TVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWE-EKCE 201
P K V V+G GD+A + A L A KV +V R+ RA + + K E
Sbjct: 136 PFFKNKEVAVVGGGDSAIEEALY-LTRIAKKVTLVHRR--DKFRAEKILLDRLKKNPKIE 192
Query: 202 FLPFMSPVQVDVKDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDND 261
FL + ++ V DNK+ G++ T E+ E L+ + + A G +
Sbjct: 193 FLWNSTVKEI-VGDNKVEGVKIKNTVTGEEEE----------LEVDGVFIAIGHEPN-TE 240
Query: 262 VLEAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGD-TANLSDTTVESVNDGKTAAWHIHK 320
+L+ + ++LD+ GY + M TSVPGVF GD V + DG AA +
Sbjct: 241 LLKGL--LELDENGYIVTD-EGMRTSVPGVFAAGDVRDKGYRQAVTAAGDGCIAALSAER 297
Query: 321 YI 322
Y+
Sbjct: 298 YL 299
>gnl|CDD|225433 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfB [Energy production and conversion].
Length = 198
Score = 54.0 bits (130), Expect = 4e-08
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 486 ETILSVKDVIGQAVQRVTNYTELDNKKQVVALINDDMCINCGKCYMAC-NDSGYQAITFH 544
I + +++G + + ++VALI++ CI C KC AC D AI
Sbjct: 80 AVIRKIAELLGVEPPPADGSEHGEEQARMVALIDEANCIGCTKCIQACPVD----AIVGA 135
Query: 545 PETHQAHVTDECTGCTLCL 563
+ + D CTGC LC+
Sbjct: 136 TKAMHTVIADLCTGCDLCV 154
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 53.9 bits (130), Expect = 1e-07
Identities = 37/155 (23%), Positives = 65/155 (41%), Gaps = 14/155 (9%)
Query: 142 SLPILKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCE 201
L L V+V+G G + A + + G +V R + +E+ A EK E
Sbjct: 137 ELLELPKRVVVVGGGYIGLELAAALAKLGKEVTVVERRDRL--LARADDEISAALLEKLE 194
Query: 202 FLPFMSPVQVDVKDNKIAGMQFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDND 261
L + + + + K V+ + +L A+ ++ A G + +
Sbjct: 195 KL--------LLGVTVLLVVVVVVKVGDGKVVEVKLGD-GEELDADVVLVAIGRR-PNTE 244
Query: 262 VLEAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGD 296
+LE V+LD+ GY V+ + TSVPG++ GD
Sbjct: 245 LLEQA-GVELDERGYIVVD-EYLRTSVPGIYAAGD 277
>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 51
Score = 48.1 bits (114), Expect = 2e-07
Identities = 14/48 (29%), Positives = 18/48 (37%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCLSI 565
I+ D CI CG+C AC D C GC C+ +
Sbjct: 2 IDPDKCIGCGRCVAACPARVGAGAIRDEGGAVEIDPDRCIGCGACVEV 49
Score = 28.1 bits (62), Expect = 2.4
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 518 INDDMCINCGKCYMAC 533
I+ D CI CG C C
Sbjct: 35 IDPDRCIGCGACVEVC 50
>gnl|CDD|162300 TIGR01317, GOGAT_sm_gam, glutamate synthases, NADH/NADPH, small
subunit. This model represents one of three built for
the NADPH-dependent or NADH-dependent glutamate synthase
(EC 1.4.1.13 and 1.4.1.14, respectively) small subunit
or homologous region. TIGR01316 describes a family in
several archaeal and deeply branched bacterial lineages
of a homotetrameric form for which there is no large
subunit. Another model describes glutamate synthase
small subunit from gamma and some alpha subdivision
Proteobacteria plus paralogs of unknown function. This
model describes the small subunit, or homologous region
of longer forms proteins, of eukaryotes, Gram-positive
bacteria, cyanobacteria, and some other lineages. All
members with known function participate in NADH or
NADPH-dependent reactions to interconvert between
glutamine plus 2-oxoglutarate and two molecules of
glutamate.
Length = 485
Score = 53.7 bits (129), Expect = 3e-07
Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 50/311 (16%)
Query: 44 IPQYRLPFDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANV 103
IP +L V+ ++L+ G+ + DI+ ++L++ + A+ + G
Sbjct: 186 IPNMKLDKAIVDRRIDLLSAEGIDFVTNTEIG-VDISADELKEQ-FDAVVLAGGATKPRD 243
Query: 104 IPI----FQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPI-LKGT-VIVLGAGD 157
+PI +G+ M F S T K L G K+ + I KG V+V+G GD
Sbjct: 244 LPIPGRELKGIHYAMEFLPSAT----------KALLGKDFKDIIFIKAKGKKVVVIGGGD 293
Query: 158 TAFDCATSALRCGANKVL----------------------VVFRKGCTNIRAVPEEVQLA 195
T DC ++LR GA V V+R + EE
Sbjct: 294 TGADCVGTSLRHGAASVHQFEIMPKPPEARAKDNPWPEWPRVYR-----VDYAHEEAAAH 348
Query: 196 WEEKCEFLPFMSPVQVDVKDNKIAGMQFNRTE--QNEKGEW--VEDEEQRIKLKANYIIS 251
+ ++ + + K+ ++ R E +++ G+W VE +A+ ++
Sbjct: 349 YGRDPREYSILTKEFIGDDEGKVTALRTVRVEWKKSQDGKWQFVEIPGSEEVFEADLVLL 408
Query: 252 AFGSTLLDNDVLEAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGDTANLSDTTVESVNDG 311
A G + +L+ VK + G Y +TS+PGVF GD V ++N+G
Sbjct: 409 AMGFVGPEQILLDDFG-VKKTRRGNISAGYDDYSTSIPGVFAAGDCRRGQSLIVWAINEG 467
Query: 312 KTAAWHIHKYI 322
+ AA + +Y+
Sbjct: 468 RKAAAAVDRYL 478
>gnl|CDD|235347 PRK05113, PRK05113, electron transport complex protein RnfB;
Provisional.
Length = 191
Score = 48.8 bits (117), Expect = 2e-06
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 486 ETILSVKDVIGQAVQRVTNYTELDNKKQVVALINDDMCINCGKCYMACNDSGYQAITFHP 545
T+L + +++G Q + + + VA I++D CI C KC AC AI
Sbjct: 79 ATMLKLAELLGVEPQPLDGEAQEATPARKVAFIDEDNCIGCTKCIQACP---VDAIV--G 133
Query: 546 ETHQAH--VTDECTGCTLCL 563
T H ++D CTGC LC+
Sbjct: 134 ATKAMHTVISDLCTGCDLCV 153
>gnl|CDD|233648 TIGR01944, rnfB, electron transport complex, RnfABCDGE type, B
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the B subunit [Energy
metabolism, Electron transport].
Length = 165
Score = 47.1 bits (112), Expect = 4e-06
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 486 ETILSVKDVIGQAVQRVTNYTELDNKKQ-VVALINDDMCINCGKCYMACNDSGYQAITFH 544
IL++ +++G + + +VALI++D CI C KC AC AI
Sbjct: 77 AVILALAELLGVEPIPQPLDADAGTIQPPMVALIDEDNCIGCTKCIQACP---VDAIVGA 133
Query: 545 PETHQAHVTDECTGCTLCL 563
+ + DECTGC LC+
Sbjct: 134 AKAMHTVIADECTGCDLCV 152
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 48.4 bits (116), Expect = 8e-06
Identities = 50/201 (24%), Positives = 88/201 (43%), Gaps = 13/201 (6%)
Query: 575 NKDDWLELSKKTEKAG-ADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRSSVKI 633
+ ++ + KK + + +ELNLSCP+ G+ + D E I V +
Sbjct: 103 SPEETHTILKKIQASDFNGLVELNLSCPNVPGKPQIAY----DFETTEQILEEVFTYFTK 158
Query: 634 PFFVKLTP--NITNITDIAKAAYEGKADGVSAINTV-SGLMSLSADGNPWPAVGTKKLTT 690
P VKL P +I + A + V+ IN++ +GL+ D V K
Sbjct: 159 PLGVKLPPYFDIVHFDQAAAIFNKFPLAFVNCINSIGNGLVIDPED----ETVVIKPKNG 214
Query: 691 YGGVSGNATRPMGLKAVSSIAKMF-PNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQ 749
+GG+ G+ +P L V + + P+ I+G GG+ + A + I GA VQ+ +A+
Sbjct: 215 FGGIGGDYIKPTALANVRAFYQRLNPSIQIIGTGGVKTGRDAFEHILCGASMVQVGTALH 274
Query: 750 NQDFTVVDDYITGLQTLLYLK 770
+ V + L+ ++ K
Sbjct: 275 KEGPAVFERLTKELKAIMAEK 295
>gnl|CDD|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion].
Length = 68
Score = 43.2 bits (102), Expect = 2e-05
Identities = 13/45 (28%), Positives = 16/45 (35%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
I+ D CI CG C C + +EC C LC
Sbjct: 5 IDYDKCIGCGICVEVCPAGVFDLGEDEGGKPVVARPEECIDCGLC 49
Score = 29.7 bits (67), Expect = 0.88
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 506 TELDNKKQVVALINDDMCINCGKCYMACNDSGYQAITFHPETH 548
E + K VV + CI+CG C +AC AI
Sbjct: 28 GEDEGGKPVV--ARPEECIDCGLCELACPV---GAIKVDILRP 65
>gnl|CDD|221801 pfam12838, Fer4_7, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 48
Score = 41.8 bits (98), Expect = 3e-05
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 523 CINCGKCYMACNDSGYQAITFHPETHQA----HVTDECTGCTLCLS 564
CI CG C AC Y AIT E + D+CTGC C++
Sbjct: 1 CIGCGACVRACP---YGAITLDEEGGKKGTVEIDPDKCTGCGACVA 43
Score = 31.0 bits (70), Expect = 0.20
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 511 KKQVVALINDDMCINCGKCYMAC 533
K+ I+ D C CG C C
Sbjct: 23 GKKGTVEIDPDKCTGCGACVAVC 45
>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
Length = 409
Score = 47.0 bits (112), Expect = 3e-05
Identities = 46/168 (27%), Positives = 76/168 (45%), Gaps = 23/168 (13%)
Query: 591 ADALELNLSCPHGMGERGM-GLACGQD-PEMV---RNISLWVRSSVKIPFFVKLTPNIT- 644
AD L +N+S P+ G R + G +D + V R+ W P VK+ P+++
Sbjct: 217 ADYLVINVSSPNTPGLRKLQGRKQLKDLLKKVLAARDEMQWGEEG-PPPLLVKIAPDLSK 275
Query: 645 -NITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVGTKKLTTYGGVSGNATRPMG 703
++ DIA A DG+ NT P +G GG+SG +P+
Sbjct: 276 EDLEDIAAVALALGIDGLIISNTTIS--------RPDSVLGHPHADEAGGLSG---KPLF 324
Query: 704 LKAVSSIAKMFP----NFPILGIGGIDSADVALQFIQAGAHAVQICSA 747
+ + +M+ P++G GG+ S + A + I+AGA VQ+ +A
Sbjct: 325 DLSTEVLREMYRLTRGKIPLVGCGGVSSGEDAYKKIRAGASLVQLYTA 372
Score = 31.6 bits (72), Expect = 1.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 348 ISVEICGLKFPNPFGLA 364
+ VE+ G F NP GLA
Sbjct: 74 LGVEVWGRTFSNPIGLA 90
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 44.8 bits (107), Expect = 1e-04
Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 225 RTEQNEKGEWVEDEEQRIKLKANYIISAFGST-LLDNDVLEAIKPVKLDKYGYPEVNYTT 283
+EK E +E + ++A+Y++ A G D LE ++LD+ G P V+ T
Sbjct: 236 EKSGDEKVEELEKGGKTETIEADYVLVATGRRPNTDGLGLENTG-IELDERGRPVVDEHT 294
Query: 284 MATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHIHKYIQEKNNLTV 330
TSVPG++ GD E+ ++G+ AA + +
Sbjct: 295 Q-TSVPGIYAAGDVNGKPPLLHEAADEGRIAAENAAGDVAGGVRYHP 340
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 44.5 bits (106), Expect = 2e-04
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 4/94 (4%)
Query: 227 EQNEKGEWVEDE-EQRIKLKANYIISAFGSTL-LDNDVLEAIKPVKLDKYGYPEVNYTTM 284
E+ + G V E + ++A+ ++ A G D LE V+LD G+ +V+ M
Sbjct: 241 EKKDDGVLVTLEDGEGGTIEADAVLVAIGRKPNTDGLGLENAG-VELDDRGFIKVDDQ-M 298
Query: 285 ATSVPGVFCGGDTANLSDTTVESVNDGKTAAWHI 318
T+VPG++ GD ++ +G+ AA +I
Sbjct: 299 TTNVPGIYAIGDVIGGPMLAHVAMAEGRIAAENI 332
>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 = 42.9 bits (102), Expect = 2e-04
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 697 NATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQD 752
A P+GL+ + IA++ P++ IGGI + A + + AGA V + SA+ D
Sbjct: 132 GAGPPLGLELLREIAELV-EIPVVAIGGITPENAA-EVLAAGADGVAVISAITGAD 185
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 43.1 bits (102), Expect = 4e-04
Identities = 42/187 (22%), Positives = 70/187 (37%), Gaps = 44/187 (23%)
Query: 578 DWL-ELSKKTEKAGADALELNLSCP------HGMGERGMGLACGQDPEMVRNISLWVRSS 630
+ L E +K E+ GAD ++LN CP G G + ++PE++ I + +
Sbjct: 79 ELLAEAAKIAEELGADIIDLNCGCPSPKVVKGGAGAALL-----KNPELLAEIVKAMVEA 133
Query: 631 V-KIPFFVKL----TPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVGT 685
V IP VK+ + +IA+ + G A+ TV G
Sbjct: 134 VGDIPVTVKIRLGWDDDDILALEIARILEDA---GADAL-TVHG---------------- 173
Query: 686 KKLTTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQA-GAHAVQI 744
T G G A + + + P+ P++ G I S + A + ++ GA V I
Sbjct: 174 --RTRAQGYLGPAD----WDYIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMI 227
Query: 745 CSAVQNQ 751
Sbjct: 228 GRGALGN 234
>gnl|CDD|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1
[Energy production and conversion].
Length = 203
Score = 41.7 bits (98), Expect = 5e-04
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 517 LINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGC 559
L++ D+CI CG C AC Y A F+P+ V D+CT C
Sbjct: 96 LVDKDLCIGCGYCIAACP---YGAPQFNPDK---GVVDKCTFC 132
Score = 28.9 bits (65), Expect = 9.3
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 506 TELDNKKQVVALINDDMCINCGKCYMACND 535
D ++ +I+ CI C C +AC +
Sbjct: 3 QARDMMERYAFVIDSSRCIGCKACVVACKE 32
>gnl|CDD|234590 PRK00043, thiE, thiamine-phosphate pyrophosphorylase; Reviewed.
Length = 212
Score = 41.7 bits (99), Expect = 5e-04
Identities = 29/101 (28%), Positives = 41/101 (40%), Gaps = 28/101 (27%)
Query: 650 AKAAYEGKAD--GVSAINTVSGLMSLSADGNPWPAVGTKKLTTYGGVSGNATRPMGLKAV 707
A AA AD GV I +P TKK +A P GL+ +
Sbjct: 117 AAAALAAGADYVGVGPI---------------FPTP-TKK---------DAKAPQGLEGL 151
Query: 708 SSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAV 748
I + PI+ IGGI + + ++AGA V + SA+
Sbjct: 152 REIRAAVGDIPIVAIGGITPENAP-EVLEAGADGVAVVSAI 191
>gnl|CDD|235903 PRK06991, PRK06991, ferredoxin; Provisional.
Length = 270
Score = 41.7 bits (98), Expect = 0.001
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 515 VALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCL 563
VA+I++ +CI C C AC AI P+ + D CTGC LC+
Sbjct: 79 VAVIDEQLCIGCTLCMQACP---VDAIVGAPKQMHTVLADLCTGCDLCV 124
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 42.2 bits (100), Expect = 0.001
Identities = 32/130 (24%), Positives = 54/130 (41%), Gaps = 17/130 (13%)
Query: 226 TEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPEVNYTTMA 285
TE G ++D E+ I A+ ++ A G + +L+ + ++ D+ G VN T
Sbjct: 233 TEVTPDGVTLKDGEEEIP--ADTVVWAAGVR--ASPLLKDLSGLETDRRGRLVVNPTLQV 288
Query: 286 TSVPGVFCGGDTANLSD------TTVESVNDGKTAAWHIHKYIQEKNNLTVPDKPCLPKF 339
P +F GD A + D T + G+ AA +I ++ K P KP K+
Sbjct: 289 PGHPDIFAAGDCAAVIDPRPVPPTAQAAHQQGEYAAKNIKARLKGK-----PLKP--FKY 341
Query: 340 MSHIDLVDIS 349
L +
Sbjct: 342 KDKGTLASLG 351
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 41.2 bits (97), Expect = 0.002
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 9/58 (15%)
Query: 515 VALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCLSILIASIMC 572
+ I+ + CI CGKC C + AI P D C GC C SI+C
Sbjct: 63 IPEIDPEKCIRCGKCAEVCR---FGAIVVLPGGKPVLNPDLCEGCGAC------SIVC 111
>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 = 40.4 bits (95), Expect = 0.003
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 571 MCTYNKDDWLELSKKTEKAGADALELNLSCP-HGMGERGMGLACGQDPEMVRNISLWVRS 629
+ + D E +K E+ GAD +++N+ CP + ++G G A +DP+++ I V
Sbjct: 69 LFGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKIVKAVVD 128
Query: 630 SVKIPFFVKL----TPNITNITDIAKAAYEGKADGVSAINTVSG 669
+V IP VK+ N + A+ A + G A+ T+ G
Sbjct: 129 AVDIPVTVKIRIGWDDAHINAVEAARIA---EDAGAQAV-TLHG 168
>gnl|CDD|233094 TIGR00693, thiE, thiamine-phosphate pyrophosphorylase. This model
represents the thiamine-phosphate pyrophosphorylase,
ThiE, of a number of bacteria, and N-terminal domains of
bifunctional thiamine proteins of Saccharomyces
cerevisiae and Schizosaccharomyces pombe, in which the
C-terminal domain corresponds to the bacterial
hydroxyethylthiazole kinase (EC 2.7.1.50), ThiM. This
model includes ThiE from Bacillus subtilis but excludes
its paralog, the regulatory protein TenI , and neighbors
of TenI [Biosynthesis of cofactors, prosthetic groups,
and carriers, Thiamine].
Length = 196
Score = 39.5 bits (93), Expect = 0.003
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 697 NATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAV 748
+ P G++ + IA + PI+ IGGI + A + + AGA V + SA+
Sbjct: 133 DPAPPAGVELLREIAATSIDIPIVAIGGITLENAA-EVLAAGADGVAVVSAI 183
>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 = 40.2 bits (95), Expect = 0.003
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 577 DDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISL--WVRSSVKIP 634
++ +E++K E+AG DA L++S G E + + L ++ +VKIP
Sbjct: 228 EEAIEIAKALEEAGVDA--LHVSG--GSYESPPPIIPPPYVPEGYFLELAEKIKKAVKIP 283
Query: 635 FFVKLTPNITNITDIAKAAYEGKADGVS 662
I + + EGKAD V+
Sbjct: 284 VIA--VGGIRDPEVAEEILAEGKADLVA 309
>gnl|CDD|205098 pfam12837, Fer4_6, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 24
Score = 35.3 bits (82), Expect = 0.004
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 515 VALINDDMCINCGKCYMACNDSGYQAI 541
V I+ D CI CG+C C AI
Sbjct: 1 VVEIDPDKCIGCGRCVAVCP---EGAI 24
>gnl|CDD|132187 TIGR03143, AhpF_homolog, putative alkyl hydroperoxide reductase F
subunit. This family of thioredoxin reductase homologs
is found adjacent to alkylhydroperoxide reductase C
subunit predominantly in cases where there is only one C
subunit in the genome and that genome is lacking the F
subunit partner (also a thioredcxin reductase homolog)
that is usually found (TIGR03140).
Length = 555
Score = 40.1 bits (94), Expect = 0.004
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 269 VKLDKYGYPEVNYTTMATSVPGVFCGGD--TANLSDTTVESVNDGKTAAWHIHKYIQEK 325
V+LDK GY N M T+VPGV+ GD L V +V DG AA +Y++E
Sbjct: 255 VELDKRGYIPTN-EDMETNVPGVYAAGDLRPKELRQ-VVTAVADGAIAATSAERYVKEL 311
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 38.9 bits (91), Expect = 0.011
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDE-CTGCTLCLSI 565
++++ C CG C SG +I P +A + C GC C+ +
Sbjct: 574 VDEEKCTGCGDCI---VLSGCPSIEPDPTFKKARIDPSSCNGCGSCVEV 619
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 37.1 bits (87), Expect = 0.015
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 703 GLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAV-----QICSAVQNQDF 753
G + ++ FP + GG+ + A +++ AG AV AV D+
Sbjct: 130 GPAYIKALKGPFPQVRFMPTGGVSLDNAA-EWLAAGVVAVGGGSLLPKDAVAAGDW 184
>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 = 36.4 bits (85), Expect = 0.023
Identities = 18/49 (36%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 700 RPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAV 748
P+GL+ + +IA+ N P++ IGGI +V + ++AGA V + SA+
Sbjct: 134 PPLGLEGLRAIAEAV-NIPVVAIGGITPENVP-EVLEAGADGVAVVSAI 180
>gnl|CDD|215671 pfam00037, Fer4, 4Fe-4S binding domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich.
Length = 24
Score = 33.0 bits (76), Expect = 0.024
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 518 INDDMCINCGKCYMAC 533
I+++ CI CG C C
Sbjct: 3 IDEEKCIGCGACVEVC 18
>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 = 37.3 bits (87), Expect = 0.026
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 575 NKDDWLELSKKTEKAGADALELNLSCP-HGMGERGMGLACGQDPEMVRNISLWVRSSVKI 633
+ E +K GAD +++N+ CP + G G A +DP++V I V +V I
Sbjct: 64 DPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKAVDI 123
Query: 634 PFFVK 638
P VK
Sbjct: 124 PVTVK 128
>gnl|CDD|234122 TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S
protein. Members of this protein family are the Fe-S
protein, NrfC, of a cytochrome c nitrite reductase
system for which the pentaheme cytochrome c protein,
NrfB (family TIGR03146) is an unambiguous marker.
Members of this protein family show similarity to other
ferredoxin-like proteins, including a subunit of a
polysulfide reductase [Energy metabolism, Electron
transport].
Length = 225
Score = 36.7 bits (85), Expect = 0.027
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGC 559
++ D+C+ C C AC Y+ HP T A D+C C
Sbjct: 122 VHKDLCVGCQYCIAACP---YRVRFIHPVTKSA---DKCNFC 157
>gnl|CDD|181550 PRK08764, PRK08764, ferredoxin; Provisional.
Length = 135
Score = 35.7 bits (82), Expect = 0.028
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 515 VALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCL 563
VA I + CI C KC AC AI + + CTGC LC+
Sbjct: 79 VAWIVEADCIGCTKCIQACP---VDAIVGGAKHMHTVIAPLCTGCELCV 124
>gnl|CDD|221963 pfam13183, Fer4_8, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 54
Score = 33.4 bits (76), Expect = 0.037
Identities = 12/45 (26%), Positives = 12/45 (26%), Gaps = 4/45 (8%)
Query: 521 DMCINCGKCYMAC---NDSGYQAITFHPETHQAHVTDECTGCTLC 562
CI CG C C G A CT C C
Sbjct: 3 SKCIRCGACRAVCPVYRALGR-FSGDPRGGALAAELWSCTSCGAC 46
>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3. See
PMID:20395274 for descriptions of different groups.
Length = 462
Score = 37.2 bits (87), Expect = 0.037
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 516 ALINDDMCINCGKCYMAC 533
A+I+ D CI+CG C +AC
Sbjct: 183 AVIDYDKCISCGACMVAC 200
Score = 31.8 bits (73), Expect = 1.5
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 516 ALINDDMCINCGKCYMACNDSGYQAI 541
A I+ + CI CGKC AC Y AI
Sbjct: 137 AYIDQEKCIECGKCKKACP---YNAI 159
>gnl|CDD|224068 COG1145, NapF, Ferredoxin [Energy production and conversion].
Length = 99
Score = 34.5 bits (78), Expect = 0.039
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHV-TDECTGCTLCLSI 565
I+ + CI CG C C + I + + D C C CL +
Sbjct: 26 IDAEKCIGCGLCVKVCPTGAIELIEEGLLLPEVVIDPDLCVLCGACLKV 74
Score = 28.3 bits (62), Expect = 4.7
Identities = 10/53 (18%), Positives = 17/53 (32%), Gaps = 3/53 (5%)
Query: 507 ELDNKKQVVALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGC 559
+ +I+ D+C+ CG C C A++ E A
Sbjct: 49 IEEGLLLPEVVIDPDLCVLCGACLKVCP---VDALSIAEELVNAGEAKLRERE 98
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the E3
component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to have
distinct functions (ferric leghemoglobin reductase and
NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 36.9 bits (86), Expect = 0.042
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 227 EQNEKGEWVEDEEQRI-KLKANYIISAFGSTL-LDNDVLEAIKPVKLDKYGYPEVNYTTM 284
E+N+ E++ L ++ A G + LE + V+LD+ G V+ M
Sbjct: 238 EKNDDQVTYENKGGETETLTGEKVLVAVGRKPNTEGLGLEKLG-VELDERGRIVVD-EYM 295
Query: 285 ATSVPGVFCGGD 296
T+VPG++ GD
Sbjct: 296 RTNVPGIYAIGD 307
>gnl|CDD|234064 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of
this family are homodimeric ferredoxins from nitrogen
fixation regions of many nitrogen-fixing bacteria. As
characterized in Rhodobacter capsulatus, these proteins
are homodimeric, with two 4Fe-4S clusters bound per
monomer. Although nif-specific, this protein family is
not usiveral, as other nitrogenase systems may
substitute flavodoxins, or different types of ferredoxin
[Central intermediary metabolism, Nitrogen fixation].
Length = 91
Score = 33.9 bits (78), Expect = 0.050
Identities = 16/69 (23%), Positives = 22/69 (31%), Gaps = 22/69 (31%)
Query: 513 QVVALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDE----------------- 555
Q V I+ + CI CG+CY C G +T + +
Sbjct: 13 QFVTSIDQEKCIGCGRCYKVC---GRDVLTLKGINEEGELVASDDDDDEIERKVMVVANP 69
Query: 556 --CTGCTLC 562
C GC C
Sbjct: 70 GNCIGCGAC 78
>gnl|CDD|224067 COG1144, COG1144, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, delta subunit
[Energy production and conversion].
Length = 91
Score = 33.9 bits (78), Expect = 0.051
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
+++D CINC C++ C + D C GC +C
Sbjct: 32 VDEDKCINCKLCWLYCPEPAILEEEG--GYKVRIDYDYCKGCGIC 74
>gnl|CDD|221966 pfam13187, Fer4_9, 4Fe-4S dicluster domain.
Length = 44
Score = 32.6 bits (74), Expect = 0.053
Identities = 11/40 (27%), Positives = 12/40 (30%), Gaps = 6/40 (15%)
Query: 523 CINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
CI CG C C V +C GC C
Sbjct: 2 CIGCGACVKVCPAGVIMRDNGGK------VVVKCIGCGAC 35
>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 = 35.9 bits (84), Expect = 0.057
Identities = 32/89 (35%), Positives = 44/89 (49%), Gaps = 16/89 (17%)
Query: 587 EKAGADALELNLSCP-----HGMGERGMGLACGQDPEMVRNISLWVRSSVKIPFFVK--- 638
E+ GAD ++LN+ CP G G G A +DPE+V I VR +V IP VK
Sbjct: 77 EELGADGIDLNMGCPSPKVTKG----GAGAALLKDPELVAEIVRAVREAVPIPVTVKIRL 132
Query: 639 LTPNITNITDIAKAAYEGKADGVSAINTV 667
+ ++AKA + G SA+ TV
Sbjct: 133 GWDDEEETLELAKALEDA---GASAL-TV 157
Score = 30.2 bits (69), Expect = 4.2
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 20/91 (21%)
Query: 575 NKDDWLELSKKTEKAGADALELNLSCPHG--MGERGMGLACGQDPEMVRNISLWVRSSVK 632
++++ LEL+K E AGA AL + HG +R G A D + + I + +V
Sbjct: 136 DEEETLELAKALEDAGASALTV-----HGRTREQRYSGPA---DWDYIAEI----KEAVS 183
Query: 633 IPFFVKLTPN--ITNITDIAKAAYEGKADGV 661
IP N I ++ D + + DGV
Sbjct: 184 IPVIA----NGDIFSLEDALRCLEQTGVDGV 210
>gnl|CDD|236596 PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta;
Reviewed.
Length = 133
Score = 34.3 bits (79), Expect = 0.078
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 519 NDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCLSI 565
N+++CINC C++ C D+ AI + + C GC +C+ +
Sbjct: 57 NNEICINCFNCWVYCPDA---AILSRDKKLKGVDYSHCKGCGVCVEV 100
>gnl|CDD|205077 pfam12797, Fer4_2, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 22
Score = 30.9 bits (70), Expect = 0.13
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 517 LINDDMCINCGKCYMAC 533
LI++D CI CG C AC
Sbjct: 4 LIDEDKCIGCGACVSAC 20
>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated.
Length = 280
Score = 34.9 bits (81), Expect = 0.14
Identities = 25/72 (34%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 523 CINCGKCYMACNDSGYQAITFHPETHQAHVTDE-CTGCTLCLSILIASIMCTYNKDDWLE 581
CI CGKC AC AIT E + A + E CT C C+ + NK
Sbjct: 215 CIGCGKCVKACPA---GAITM--ENNLAVIDQEKCTSCGKCVEKCPTKAIRILNKPP--- 266
Query: 582 LSKKTEKAGADA 593
K+ +KA A+A
Sbjct: 267 KVKEPKKAAAEA 278
>gnl|CDD|234170 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase,
alpha subunit. Indolepyruvate ferredoxin oxidoreductase
(IOR) is an alpha 2/beta 2 tetramer related to ketoacid
oxidoreductases for pyruvate (1.2.7.1, POR),
2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate
(1.2.7.7, VOR). These multi-subunit enzymes typically
are found in anaerobes and are inactiviated by oxygen.
IOR in Pyrococcus acts in fermentation of all three
aromatic amino acids, following removal of the amino
group by transamination. In Methanococcus maripaludis,
by contrast, IOR acts in the opposite direction, in
pathways of amino acid biosynthesis from phenylacetate,
indoleacetate, and p-hydroxyphenylacetate. In M.
maripaludis and many other species, iorA and iorB are
found next to an apparent phenylacetate-CoA ligase.
Length = 595
Score = 35.1 bits (81), Expect = 0.15
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 518 INDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCLSI 565
++ D CI C KC + G AI PE +A + CTGC +C I
Sbjct: 547 VDQDKCIGCKKC---IKELGCPAI--EPEDKEAVIDPLCTGCGVCAQI 589
>gnl|CDD|188533 TIGR04018, Bthiol_YpdA, putative bacillithiol system
oxidoreductase, YpdA family. Members of this protein
family, including YpdA from Bacillus subtilis, are
apparent oxidoreductases present only in species with an
active bacillithiol system. They have been suggested
actually to be thiol disulfide oxidoreductases (TDOR),
although the evidence is incomplete [Unknown function,
Enzymes of unknown specificity].
Length = 316
Score = 34.8 bits (81), Expect = 0.16
Identities = 44/170 (25%), Positives = 71/170 (41%), Gaps = 29/170 (17%)
Query: 140 KESLPILKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEK 199
KE+ P V+V+G ++A D A R GA +V +V R V V+ W
Sbjct: 145 KEAHPYFGQKVVVVGGSNSAVDAALELYRKGA-EVTMVHRGD-----EVSSSVK-YW--- 194
Query: 200 CEFLP-FMSPVQVDVKDNKIAGMQFNR--TEQNEKGEWVEDEEQRI-KLKANYIISAFGS 255
P + +K+ I FN E E +E + + + +++ + G
Sbjct: 195 --VRPDIEN----RIKEGSIK-AYFNSRVKEITEDSVTLETPDGEVHTIPNDFVFALTGY 247
Query: 256 TLLDNDVLEAIKPVKLDK-YGYPEVNYTTMATSVPGVF-----CGGDTAN 299
D + LE++ V+LD+ G P N TM T+VPG++ G N
Sbjct: 248 R-PDFEFLESLG-VELDEDTGIPVYNPETMETNVPGLYLAGVIAAGMDTN 295
>gnl|CDD|222205 pfam13534, Fer4_17, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 61
Score = 31.3 bits (71), Expect = 0.22
Identities = 15/53 (28%), Positives = 16/53 (30%), Gaps = 15/53 (28%)
Query: 523 CINCGKCYMACNDSGYQAITFHP------------ETHQA-HVTDECTGCTLC 562
CI CG C C Y P E A D C+ C LC
Sbjct: 2 CIQCGYCVPVC--PSYLLNGDEPKKLMRAAYNGDLEELLANEAADSCSECGLC 52
>gnl|CDD|235237 PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like
protein; Reviewed.
Length = 232
Score = 34.0 bits (79), Expect = 0.25
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 691 YGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAV 742
YGG +G+ P + V ++ K P++ GGI S + A + + AGA +
Sbjct: 162 YGGGAGDPVPP---EMVKAVKKALDITPLIYGGGIRSPEQARELMAAGADTI 210
>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 = 34.0 bits (78), Expect = 0.26
Identities = 41/181 (22%), Positives = 69/181 (38%), Gaps = 33/181 (18%)
Query: 567 IASIMCTYNKDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLAC--GQDPEMVRNIS 624
+A + + +D + +K EK G D + LN+ CP + G AC G ++V +
Sbjct: 57 VALQLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACLMGN-ADLVADCV 115
Query: 625 LWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVG 684
++ +V IP VK I +YE + VSG G
Sbjct: 116 KAMQEAVNIPVTVK-----HRIGIDPLDSYE---FLCDFVEIVSGK-------------G 154
Query: 685 TKKLTTYG------GVSGNATR---PMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFI 735
+ + G+S R P+ + V + K FP+ I GGI +++ Q +
Sbjct: 155 CQNFIVHARKAWLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGIKNSEQIKQHL 214
Query: 736 Q 736
Sbjct: 215 S 215
>gnl|CDD|131996 TIGR02951, DMSO_dmsB, DMSO reductase, iron-sulfur subunit. This
family consists of the iron-sulfur subunit, or chain B,
of an enzyme called the anaerobic dimethyl sulfoxide
reductase. Chains A and B are catalytic, while chain C
is a membrane anchor.
Length = 161
Score = 33.2 bits (76), Expect = 0.26
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 517 LINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGC 559
L++ D CI C C AC Y A + P+ +C GC
Sbjct: 91 LVDQDKCIGCRYCVWACP---YGAPQYDPQQGVMG---KCDGC 127
>gnl|CDD|235779 PRK06327, PRK06327, dihydrolipoamide dehydrogenase; Validated.
Length = 475
Score = 34.1 bits (79), Expect = 0.30
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 220 GMQFNRTEQNEKG---EWVEDEEQRIKLKANYIISAFGSTL-LDNDVLEAIKPVKLDKYG 275
G++ + KG + + + + L+ + +I + G D LEA+ +KLD+ G
Sbjct: 244 GVKIGEIKTGGKGVSVAYTDADGEAQTLEVDKLIVSIGRVPNTDGLGLEAVG-LKLDERG 302
Query: 276 YPEVNYTTMATSVPGVFCGGD 296
+ V+ T+VP V+ GD
Sbjct: 303 FIPVD-DHCRTNVPNVYAIGD 322
>gnl|CDD|131234 TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoreductase, delta
subunit, pyruvate/2-ketoisovalerate family. A number of
anaerobic and microaerophilic species lack pyruvate
dehydrogenase and have instead a four subunit,
oxygen-sensitive pyruvate oxidoreductase, with either
ferredoxins or flavodoxins used as the acceptor. Several
related four-subunit enzymes may exist in the same
species. This model describes a subfamily of delta
subunits, representing mostly pyruvate,
2-ketoisovalerate, and 2-oxoglutarate specific enzymes.
The delta subunit is the smallest and resembles
ferredoxins.
Length = 78
Score = 31.1 bits (71), Expect = 0.39
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 17/52 (32%)
Query: 518 INDDMCINCGKCYMACNDS-------GYQAITFHPETHQAHVTDECTGCTLC 562
++ + CI C C++ C + G+ I + D C GC +C
Sbjct: 22 VDKEKCIKCKNCWLYCPEGAIQEDEGGFVGIDY----------DYCKGCGIC 63
>gnl|CDD|170017 PRK09624, porD, pyuvate ferredoxin oxidoreductase subunit delta;
Reviewed.
Length = 105
Score = 31.5 bits (71), Expect = 0.41
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 519 NDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
N D C+ C CY+ C + AI E + D C GC +C
Sbjct: 49 NRDKCVRCYLCYIYCPEP---AIYLDEEGYPVFDYDYCKGCGIC 89
>gnl|CDD|183490 PRK12385, PRK12385, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 244
Score = 33.1 bits (76), Expect = 0.41
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 522 MCINCGKCYMAC 533
CINCG CY AC
Sbjct: 148 GCINCGLCYAAC 159
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 33.0 bits (76), Expect = 0.48
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 13/88 (14%)
Query: 576 KDDWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRSSVKIPF 635
K D LEL+K+ E GA + LN + G G D E++++ R+++KIP
Sbjct: 151 KKDPLELAKEYEALGAGEILLN-----SIDRDGTM--KGYDLELLKSF----RNALKIP- 198
Query: 636 FVKLTPNITNITDIAKAAYEGKADGVSA 663
+ ++ DI +A AD +A
Sbjct: 199 -LIALGGAGSLDDIVEAILNLGADAAAA 225
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 33.0 bits (76), Expect = 0.49
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 701 PMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAV 748
P+GL+ + I + N P++ IGGI+ +V + ++AGA V + SA+
Sbjct: 144 PLGLEGLREI-RELVNIPVVAIGGINLENVP-EVLEAGADGVAVVSAI 189
>gnl|CDD|222081 pfam13370, Fer4_13, 4Fe-4S single cluster domain.
Length = 58
Score = 29.9 bits (68), Expect = 0.50
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 9/51 (17%)
Query: 518 INDDMCINCGKCYMAC------NDSGYQAITFH---PETHQAHVTDECTGC 559
++ D CI CG C +D G ++ PE +A + C
Sbjct: 1 VDRDTCIGCGLCREIAPDVFAYDDDGGASVVLDQPVPEEEEAAALEALDSC 51
>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma. This
model represents that clade of F420-dependent
hydrogenases (FRH) beta subunits found exclusively and
universally in methanogenic archaea. This protein
contains two 4Fe-4S cluster binding domains (pfam00037)
and scores above the trusted cutoff to model pfam01058
for the "NADH ubiquinone oxidoreductase, 20 Kd subunit"
family.
Length = 228
Score = 32.5 bits (74), Expect = 0.66
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 518 INDDMCINCGKCYMAC 533
+N D CI CG CY+ C
Sbjct: 200 VNRDRCIKCGACYVQC 215
Score = 30.6 bits (69), Expect = 2.7
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 517 LINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
++N +C+ CG C AC + P ++ D C C C
Sbjct: 170 VVNQGLCMGCGTCAAACPTRAIEMEDGRPNVNR----DRCIKCGAC 211
>gnl|CDD|222168 pfam13484, Fer4_16, 4Fe-4S double cluster binding domain.
Length = 67
Score = 29.8 bits (67), Expect = 0.71
Identities = 14/75 (18%), Positives = 22/75 (29%), Gaps = 31/75 (41%)
Query: 523 CINCGKCYMACNDSGYQAIT----------------------FHPETHQAHVTDECTGCT 560
C CGKC AC AI+ + + + + GC
Sbjct: 2 CGTCGKCADAC---PTGAISGEDEPTWDARRCISYNTIGKKGWIIDELKCLLGGRIYGCG 58
Query: 561 LCLSILIASIMCTYN 575
+C + C +N
Sbjct: 59 ICQEV------CPFN 67
>gnl|CDD|223185 COG0107, HisF, Imidazoleglycerol-phosphate synthase [Amino acid
transport and metabolism].
Length = 256
Score = 32.5 bits (75), Expect = 0.71
Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 13/86 (15%)
Query: 578 DWLELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRSSVKIPFFV 637
D +E +K+ E+ GA + L M G G D E+ R VR +V IP V
Sbjct: 156 DAVEWAKEVEELGAGEILLT-----SMDRDGT--KAGYDLELTRA----VREAVNIP--V 202
Query: 638 KLTPNITNITDIAKAAYEGKADGVSA 663
+ +A EGKAD A
Sbjct: 203 IASGGAGKPEHFVEAFTEGKADAALA 228
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 33.1 bits (75), Expect = 0.88
Identities = 38/122 (31%), Positives = 55/122 (45%), Gaps = 14/122 (11%)
Query: 42 SEIPQ-YRLP---FDAVNFEVELVKDLGVKIECERSLSTRDI---TIEKLRKDGYTAIFI 94
SEI Q YRL D + EV ++K + K+E T + +I+KL D
Sbjct: 2656 SEIQQVYRLQGVRIDNKHLEV-ILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMS 2714
Query: 95 GIGKPNANVIPIFQGLT----EEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPILKGTV 150
GK A+ +PI QG+T E F ++ +F ++ CG K + L LK V
Sbjct: 2715 NSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCG--KSDPLSGLKENV 2772
Query: 151 IV 152
IV
Sbjct: 2773 IV 2774
>gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA
protein. Members of this protein family are BoxA, the A
component of the BoxAB benzoyl-CoA oxygenase/reductase.
This oxygen-requiring enzyme acts in an aerobic pathway
of benzoate catabolism via coenzyme A ligation. BoxA is
a homodimeric iron-sulphur-flavoprotein and acts as an
NADPH-dependent reductase for BoxB [Energy metabolism,
Other].
Length = 411
Score = 32.5 bits (74), Expect = 0.97
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 517 LINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLCLS 564
LI+ ++CI C C C AIT H + + D C GC C+S
Sbjct: 6 LIDPEICIRCNTCEETCP---IDAIT-HDDRNYVVKADVCNGCMACVS 49
>gnl|CDD|200976 pfam00072, Response_reg, Response regulator receiver domain. This
domain receives the signal from the sensor partner in
bacterial two-component systems. It is usually found
N-terminal to a DNA binding effector domain.
Length = 111
Score = 30.2 bits (69), Expect = 1.2
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 703 GLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAH 740
GL+ + I + P P++ + + A++ ++AGA+
Sbjct: 57 GLELLRRIRRRPPTTPVIVLTAHGDEEDAVEALKAGAN 94
>gnl|CDD|148675 pfam07213, DAP10, DAP10 membrane protein. This family consists of
several mammalian DAP10 membrane proteins. In activated
mouse natural killer (NK) cells, the NKG2D receptor
associates with two intracellular adaptors, DAP10 and
DAP12, which trigger phosphatidyl inositol 3 kinase
(PI3K) and Syk family protein tyrosine kinases,
respectively. It has been suggested that the DAP10-PI3K
pathway is sufficient to initiate NKG2D-mediated killing
of target cells.
Length = 79
Score = 29.5 bits (66), Expect = 1.3
Identities = 24/70 (34%), Positives = 29/70 (41%), Gaps = 15/70 (21%)
Query: 122 FLPRVATSSKKGLCGGCKKESLPILKGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKG 181
LP A + G C GC SLP+L G V A D S L G VVF
Sbjct: 12 LLPVAAAQTTPGSCSGCGPLSLPLLAGLV--------AADAVMSLLIVG-----VVFV-- 56
Query: 182 CTNIRAVPEE 191
C +R+ P +
Sbjct: 57 CARLRSRPAQ 66
>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2,) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 31.9 bits (73), Expect = 1.3
Identities = 11/47 (23%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 517 LINDDMCINCGKCYMACNDSGYQAI-TFHPETHQAHVTDECTGCTLC 562
L ++ C+ CGKC C + ++CT C C
Sbjct: 44 LFKENRCLGCGKCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKC 90
>gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit
gamma/delta; Provisional.
Length = 312
Score = 31.9 bits (72), Expect = 1.3
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 15/90 (16%)
Query: 343 IDLVDISVEICGLKFPN-PFGLASAPPTTASSM--VRRAFENGWGFAVTKTFSLQKDMV- 398
+D + I+ + L PN P A + S+ +R AFE G AV + F+ K+
Sbjct: 120 LDAIGIARKHLKLDVPNGPLAGAFSKVMGFPSLESIRTAFETQLGKAVEENFAATKEAYE 179
Query: 399 -----------TNVSPRIVKGTTSRHLYGP 417
+ P+ + TTS L GP
Sbjct: 180 VAVVIPPEKVDASAKPKGIISTTSAFLTGP 209
>gnl|CDD|233700 TIGR02053, MerA, mercuric reductase. This model represents the
mercuric reductase found in the mer operon for the
detoxification of mercury compounds. MerA is a
FAD-containing flavoprotein which reduces Hg(II) to
Hg(0) utilizing NADPH [Cellular processes,
Detoxification].
Length = 463
Score = 32.0 bits (73), Expect = 1.4
Identities = 47/213 (22%), Positives = 81/213 (38%), Gaps = 40/213 (18%)
Query: 88 GYTAIFIGIG-KPNANVIPIFQGLTEEMGFYTSKTFLPRVATSSKKGLCGGCKKESLPIL 146
G I G +P IP GL +E G+ TS+ L + +P
Sbjct: 128 GAKRFLIATGARPAIPPIP---GL-KEAGYLTSEEAL---------------ALDRIP-- 166
Query: 147 KGTVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCEFLPFM 206
++ V+G G + A + R G+ +V ++ R +L E+ E +
Sbjct: 167 -ESLAVIGGGAIGVELAQAFARLGS-EVTILQRSD-----------RLLPREEPEISAAV 213
Query: 207 SPVQVDVKDNKIAGMQFNRTEQNEKGEWVEDEEQRIK--LKANYIISAFGST-LLDNDVL 263
+ + Q G+ + E+ + ++A+ ++ A G D L
Sbjct: 214 EEALAEEGIEVVTSAQVKAVSVRGGGKIITVEKPGGQGEVEADELLVATGRRPNTDGLGL 273
Query: 264 EAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGD 296
E VKLD+ G V+ T+ TS PG++ GD
Sbjct: 274 EKAG-VKLDERGGILVD-ETLRTSNPGIYAAGD 304
>gnl|CDD|234157 TIGR03287, methan_mark_16, putative methanogenesis marker 16
metalloprotein. Members of this protein family, to
date, are found in a completed prokaryotic genome if and
only if the species is one of the archaeal methanogens.
The exact function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
This protein is a predicted to bind FeS clusters, based
on the presence of two copies of the Fer4 domain
(pfam00037), with each copy having four Cys residues
invariant across all members [Energy metabolism,
Methanogenesis].
Length = 391
Score = 31.7 bits (72), Expect = 1.5
Identities = 24/107 (22%), Positives = 35/107 (32%), Gaps = 27/107 (25%)
Query: 461 NLKKLNSDGVSLQNGLPKRQINTPVETILSVKDVIGQAVQRVTNYTELDNKKQVVALIND 520
NLK L+SD L V D+ + Y ++ + V N
Sbjct: 260 NLKVLDSDIP------------------LPVVDISDRTPIAEITYADVWDNTDVRPKYNP 301
Query: 521 DMCINCGKCYM--ACNDSGYQAITFHPETHQAHVTDECTGCTLCLSI 565
+ C NC C + AC + T++C GC C I
Sbjct: 302 ERCENCDPCLVEEACP-------VPAIKKDGTLNTEDCFGCGYCAEI 341
>gnl|CDD|205080 pfam12800, Fer4_4, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 17
Score = 27.8 bits (62), Expect = 1.5
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 521 DMCINCGKCYMAC 533
+ CI CG C AC
Sbjct: 2 EKCIGCGACVDAC 14
>gnl|CDD|214968 smart01004, ALAD, Delta-aminolevulinic acid dehydratase. This
entry represents porphobilinogen (PBG) synthase (PBGS,
or 5-aminoaevulinic acid dehydratase, or ALAD, ), which
functions during the second stage of tetrapyrrole
biosynthesis. This enzyme catalyses a Knorr-type
condensation reaction between two molecules of ALA to
generate porphobilinogen, the pyrrolic building block
used in later steps. The structure of the enzyme is
based on a TIM barrel topology made up of eight
identical subunits, where each subunit binds to a metal
ion that is essential for activity, usually zinc (in
yeast, mammals and certain bacteria) or magnesium (in
plants and other bacteria). A lysine has been
implicated in the catalytic mechanism. The lack of PBGS
enzyme causes a rare porphyric disorder known as ALAD
porphyria, which appears to involve conformational
changes in the enzyme.
Length = 321
Score = 31.6 bits (73), Expect = 1.8
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 26 KDLPDIERPVAALPDSSEIPQYRLPFDAVNFEVELVKDLGVK 67
+ D + P+ ++P YRL D + E E +LG+
Sbjct: 36 TEGEDEKEPIPSMPG-----VYRLSVDLLVEEAEEAVELGIP 72
>gnl|CDD|110106 pfam01081, Aldolase, KDPG and KHG aldolase. This family includes
the following members: 4-hydroxy-2-oxoglutarate aldolase
(KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate
aldolase (KDPG-aldolase).
Length = 196
Score = 30.9 bits (70), Expect = 2.0
Identities = 37/167 (22%), Positives = 63/167 (37%), Gaps = 33/167 (19%)
Query: 575 NKDDWLELSKKTEKAGADALELNLSCPHG-------MGER-GMGLACGQ--DPEMVRNIS 624
+K+D L L++ G LE+ L P R + G + + + +
Sbjct: 18 DKEDALPLAEALAAGGIRVLEVTLRTPCALDAIRLLRKNRPDALVGAGTVLNAQQLAEAA 77
Query: 625 LWVRSSVKIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWPAVG 684
F V +P +T D+ K A + K + ++T S +M L D +G
Sbjct: 78 -----EAGAQFVV--SPGLT--ADLLKHAVDVKIPLIPGVSTPSEIM-LGLD------LG 121
Query: 685 TKKLTTY-GGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADV 730
+ + SG G+ A+ ++A FP GGI A+V
Sbjct: 122 LTRFKFFPAEASG------GVPAIKALAGPFPQVRFCPTGGIHPANV 162
>gnl|CDD|237344 PRK13306, ulaD, 3-keto-L-gulonate-6-phosphate decarboxylase;
Provisional.
Length = 216
Score = 31.1 bits (71), Expect = 2.0
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 703 GLKAVSSIAKMFPNFPILGIGGIDSAD----VALQFIQAGAHAVQ-ICSA---VQNQDFT 754
G+KAV + ++P+ I+ I AD +A +AGA V IC+A
Sbjct: 43 GMKAVRVLRALYPDKIIVADTKI--ADAGKILAKMAFEAGADWVTVICAAHIPTIKAALK 100
Query: 755 VVDDYITGLQTLLY 768
V ++ +Q LY
Sbjct: 101 VAKEFNGEIQIELY 114
>gnl|CDD|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit
delta; Reviewed.
Length = 105
Score = 29.5 bits (66), Expect = 2.1
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 515 VALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCTLC 562
+ ++++ C+ C C+ C + AI + + A D C GC +C
Sbjct: 45 MPVVDESKCVKCYICWKFCPEP---AIYIKEDGYVAIDYDYCKGCGIC 89
>gnl|CDD|236534 PRK09476, napG, quinol dehydrogenase periplasmic component;
Provisional.
Length = 254
Score = 30.7 bits (70), Expect = 2.6
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 25/79 (31%)
Query: 504 NYTELDNKKQVVA-LINDDMCIN-----CGKCYMAC-------------ND-SGYQAITF 543
++D+ + +A L++ + C+N C CY C N+ +G A F
Sbjct: 119 ELVDIDDARMGLAVLVDQENCLNFQGLRCDVCYRVCPLIDKAITLELERNERTGKHAF-F 177
Query: 544 HPETHQAHVTDECTGCTLC 562
P H +D CTGC C
Sbjct: 178 LPTVH----SDACTGCGKC 192
>gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional.
Length = 244
Score = 30.6 bits (69), Expect = 2.7
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 511 KKQVVALINDDMCINCGKCYMACNDSGYQAITFHPETHQAHVTDECTGCT 560
++ + ++++ C+ C C AC Y A + ET A D+CT C
Sbjct: 120 REDGIVVVDNKRCVGCAYCVQACP---YDARFINHETQTA---DKCTFCV 163
>gnl|CDD|236023 PRK07474, PRK07474, sulfur oxidation protein SoxY; Provisional.
Length = 154
Score = 30.0 bits (68), Expect = 2.7
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 675 ADGNPWPAVGTKKLTTYGGVSGNATRPMGL---KAVSSIAKM 713
ADGNP P V T G + +TR + L + V +IA+M
Sbjct: 93 ADGNPQPGVATFHFGPAAGRAEASTR-IRLAQTQNVIAIAEM 133
>gnl|CDD|236450 PRK09283, PRK09283, delta-aminolevulinic acid dehydratase;
Validated.
Length = 323
Score = 30.8 bits (71), Expect = 3.1
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 30 DIERPVAALPDSSEIPQYRLPFDAVNFEVELVKDLGVK 67
+ + ++P YRL D + E E +LG+
Sbjct: 42 NEREEIPSMPG-----VYRLSIDLLVKEAEEAVELGIP 74
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 30.9 bits (71), Expect = 3.2
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 704 LKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQI 744
L V I +P+ I+ G + +A+ A I+AGA AV++
Sbjct: 257 LDRVREIKAKYPDVQIIA-GNVATAEAARALIEAGADAVKV 296
>gnl|CDD|223555 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
protein subunit [Energy production and conversion].
Length = 234
Score = 30.3 bits (69), Expect = 3.3
Identities = 7/13 (53%), Positives = 7/13 (53%)
Query: 522 MCINCGKCYMACN 534
CI CG C AC
Sbjct: 143 ECILCGCCTAACP 155
>gnl|CDD|233564 TIGR01768, GGGP-family, geranylgeranylglyceryl phosphate synthase
family protein. This model represents a family of
sequences including geranylgeranylglyceryl phosphate
synthase which catalyzes the first committed step in the
synthesis of ether-linked membrane lipids in archaea.
The clade of bacterial sequences may have the same
function or a closely related function. This model
supercedes TIGR00265, which has been retired.
Length = 223
Score = 30.1 bits (68), Expect = 3.4
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 691 YGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQN 750
G + P + V+ + K+ + GGI S + A + +AGA + + ++
Sbjct: 157 AGSGAPEPVPP---ELVAEVKKVLDKARLFVGGGIRSVEKAREMAEAGADTIVTGNVIEE 213
Query: 751 QD 752
Sbjct: 214 DV 215
>gnl|CDD|130536 TIGR01470, cysG_Nterm, siroheme synthase, N-terminal domain. This
model represents a subfamily of CysG N-terminal
region-related sequences. All sequences in the seed
alignment for this model are N-terminal regions of known
or predicted siroheme synthases. The C-terminal region
of each is uroporphyrin-III C-methyltransferase (EC
2.1.1.107), which catalyzes the first step committed to
the biosynthesis of either siroheme or cobalamin
(vitamin B12) rather than protoheme (heme). The region
represented by this model completes the process of
oxidation and iron insertion to yield siroheme. Siroheme
is a cofactor for nitrite and sulfite reductases, so
siroheme synthase is CysG of cysteine biosynthesis in
some organisms [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 205
Score = 30.1 bits (68), Expect = 3.4
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 143 LPI---LKG-TVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEE 198
LP+ L+G V+V+G GD A A L+ GA ++ V+ + + + + E+ + W
Sbjct: 1 LPVFANLEGRAVLVVGGGDVALRKARLLLKAGA-QLRVIAEELESELTLLAEQGGITWLA 59
Query: 199 KC 200
+C
Sbjct: 60 RC 61
>gnl|CDD|188556 TIGR04041, activase_YjjW, glycine radical enzyme activase, YjjW
family. Members of this family are radical SAM enzymes,
designated YjjW in E. coli, that are paired with and
appear to activate a glycyl radical enzyme of unknown
function, designated YjjI. This activase and its target
are found in Clostridial species as well as E. coli and
cousins. Members of this family may be misannotated as
pyruvate formate lyase activating enzyme [Protein fate,
Protein modification and repair].
Length = 276
Score = 30.3 bits (69), Expect = 3.5
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 10/46 (21%)
Query: 521 DMCINCGKCYMACNDSGYQAITFHPETHQAHVT---DECTGCTLCL 563
+ C +CG C C A++ V + C GC C+
Sbjct: 41 NHCDHCGDCVAGCP---AGALSLVDGK----VVWDKERCIGCDTCI 79
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 30.5 bits (70), Expect = 3.8
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 26 KDLPDIERPVAALPDSSEIPQYRLPFDAVNFEVELVKDLGVK 67
+ D + P+ ++P YRL D + EVE +LG+
Sbjct: 36 TEGEDEKEPIPSMPG-----VYRLSVDLLVKEVEEAVELGIP 72
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 30.9 bits (70), Expect = 4.0
Identities = 15/69 (21%), Positives = 19/69 (27%), Gaps = 25/69 (36%)
Query: 521 DMCINCGKCYMACNDSGYQAITFHPE------------------------THQAHVTDEC 556
D CI C +C C + + E Q D C
Sbjct: 683 DNCIQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISPLD-C 741
Query: 557 TGCTLCLSI 565
TGC C+ I
Sbjct: 742 TGCGNCVDI 750
>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 = 30.2 bits (69), Expect = 4.0
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 704 LKAVSSIAKMFPNFPI-LGIGGIDSADVALQFIQAGAHAVQICS-AVQNQDF 753
L + I + P+ +G GGI S + + + G V I + AV+N D
Sbjct: 61 LPVIKKIVRET-GVPVQVG-GGIRSLEDVEKLLDLGVDRVIIGTAAVENPDL 110
>gnl|CDD|179586 PRK03512, PRK03512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 211
Score = 30.0 bits (68), Expect = 4.0
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 701 PMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQDFTVVDDYI 760
P GL ++ + ++P + IGGI S + A + G ++ + SA+ T D+
Sbjct: 143 PQGLAQLARHVERLADYPTVAIGGI-SLERAPAVLATGVGSIAVVSAI-----TQAADWR 196
Query: 761 TGLQTLLYL 769
LL L
Sbjct: 197 AATAQLLEL 205
>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 = 30.2 bits (69), Expect = 4.1
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 704 LKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQI 744
++ + I K +PN ++ G + +A+ A I AGA V++
Sbjct: 123 IEMIKFIKKKYPNVDVIA-GNVVTAEAARDLIDAGADGVKV 162
>gnl|CDD|235701 PRK06116, PRK06116, glutathione reductase; Validated.
Length = 450
Score = 30.5 bits (70), Expect = 4.1
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 258 LDNDVLEAIKPVKLDKYGYPEVN-YTTMATSVPGVFCGGD 296
D LE VKL++ GY V+ Y T+VPG++ GD
Sbjct: 267 TDGLGLENAG-VKLNEKGYIIVDEY--QNTNVPGIYAVGD 303
>gnl|CDD|220775 pfam10479, FSA_C, Fragile site-associated protein C-terminus. This
is the conserved C-terminal half of the protein KIAA1109
which is the fragile site-associated protein FSA.
Genome-wide-association studies showed this protein to
linked to the susceptibility to coeliac disease. The
protein may also be associated with polycystic kidney
disease.
Length = 615
Score = 30.7 bits (69), Expect = 4.2
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 51 FDAVNFEVELVKDLGVKIECERSLSTRDITIEKLRKDGYTAIFIGIGKPNANVIPIFQ 108
F N E++ V + E E + +I + R G ++ N N IF
Sbjct: 373 FAKKNSEIDAVDRFPI-SENENEAKSPTSSISRFRGSGSSSAKEKGQATNHNREVIFA 429
>gnl|CDD|236535 PRK09477, napH, quinol dehydrogenase membrane component;
Provisional.
Length = 271
Score = 30.3 bits (69), Expect = 4.2
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 512 KQVVALINDDMCINCGKCYMACND 535
KQ + + CI CG+C C++
Sbjct: 233 KQSPSQVTSGDCITCGRCIDVCSE 256
>gnl|CDD|188634 cd00945, Aldolase_Class_I, Class I aldolases. Class I aldolases.
The class I aldolases use an active-site lysine which
stabilizes a reaction intermediates via Schiff base
formation, and have TIM beta/alpha barrel fold. The
members of this family include
2-keto-3-deoxy-6-phosphogluconate (KDPG) and
2-keto-4-hydroxyglutarate (KHG) aldolases,
transaldolase, dihydrodipicolinate synthase sub-family,
Type I 3-dehydroquinate dehydratase, DeoC and DhnA
proteins, and metal-independent
fructose-1,6-bisphosphate aldolase. Although
structurally similar, the class II aldolases use a
different mechanism and are believed to have an
independent evolutionary origin.
Length = 201
Score = 30.0 bits (68), Expect = 4.3
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 689 TTYGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAV 742
T+ G G AT +K + + GGI + + AL I+AGA +
Sbjct: 148 TSTGFGGGGAT-VEDVKLMKEAVG--GRVGVKAAGGIKTLEDALAAIEAGADGI 198
>gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta
subunit. Dissimilatory sulfite reductase catalyzes the
six-electron reduction of sulfite to sulfide, as the
terminal reaction in dissimilatory sulfate reduction. It
remains unclear however, whether trithionate and
thiosulfate serve as intermediate compounds to sulfide,
or as end products of sulfite reduction. Sulfite
reductase is a multisubunit enzyme composed of dimers of
either alpha/beta or alpha/beta/gamma subunits, each
containing a siroheme and iron sulfur cluster prosthetic
center. Found in sulfate-reducing bacteria, these genes
are commonly located in an unidirectional gene cluster.
This model describes the beta subunit of sulfite
reductase [Central intermediary metabolism, Sulfur
metabolism].
Length = 341
Score = 30.2 bits (68), Expect = 4.8
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 509 DNKKQVVALINDDMCINCGKCYMAC 533
+ K ++ + CI CG CY C
Sbjct: 202 RDGKNKSLEVDVEKCIYCGNCYTMC 226
>gnl|CDD|226117 COG3589, COG3589, Uncharacterized conserved protein [Function
unknown].
Length = 360
Score = 30.0 bits (68), Expect = 4.8
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 62 KDLGVKIECERSLSTRDIT-IEKLRKDGYTAIFIGIGKPNANVIPIFQGLTE 112
+ LG I RS +DI I+++ K G+ IF + P + F E
Sbjct: 2 RMLGFSIFPNRSPKEKDIAYIDRMHKYGFKRIFTSLLIPEEDAELYFHRFKE 53
>gnl|CDD|117908 pfam09366, DUF1997, Protein of unknown function (DUF1997). This
family of proteins are functionally uncharacterized.
Length = 170
Score = 29.5 bits (67), Expect = 4.9
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 14 DIEMSTAKVCLSKDLPDIERPVAALPDSSEIPQ-----YRL---PFDAVNFEVELVKDLG 65
D+ + L++ L +R +AL D ++ + YRL PF FEVE V L
Sbjct: 8 DLPLPAPAEPLAEYLRQPQRVFSALLDPMKVERLGDGRYRLTVRPFGFFGFEVEPVVVLR 67
Query: 66 V 66
V
Sbjct: 68 V 68
>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
pfam02906. This family represents a division among
families that belong to pfam02906, which also includes
proteins such as nuclear prelamin A recognition factor
in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 30.0 bits (68), Expect = 5.4
Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 12/60 (20%)
Query: 518 INDDM--CINCGKCYMACNDSG----YQAITFHPETHQAHVTD------ECTGCTLCLSI 565
I DM CI CG+C AC + + +T A C GC C +
Sbjct: 2 IVRDMSKCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLV 61
>gnl|CDD|216975 pfam02326, YMF19, Plant ATP synthase F0. This family corresponds
to subunit 8 (YMF19) of the F0 complex of plant and
algae mitochondrial F-ATPases (EC:3.6.1.34).
Length = 84
Score = 27.7 bits (62), Expect = 5.5
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 434 FIFFFLF------QAIPNFGEYKKIRENLITELNLKKLNSDGVSLQN 474
+FFF F +P K+R+ L++ L KL + L
Sbjct: 16 CLFFFTFYIFLLNFILPKISRILKLRKKLLSSLISSKLGKEQSLLGV 62
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 30.3 bits (69), Expect = 5.5
Identities = 9/31 (29%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 503 TNYTELDNKKQVVALINDDMCINCGKCYMAC 533
T ++ K+ ++ ++++ CI+CGKC C
Sbjct: 595 TGAIRIEEGKRKIS-VDEEKCIHCGKCTEVC 624
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 30.1 bits (68), Expect = 6.0
Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 10/54 (18%)
Query: 519 NDDMCINCGKCYMACND-SGYQAITFHPETHQAHVT---------DECTGCTLC 562
+ + CI CG+C AC + +A+T V C C C
Sbjct: 147 DPNQCILCGRCVEACQEVQVNEALTIDWRGEDPRVIWDNDVPINESSCVSCGAC 200
>gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This is
a bacterial family of proteins with unknown function.
Length = 452
Score = 30.0 bits (67), Expect = 6.5
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 632 KIPFFVKLTPNITNITDIAKAAYEGKADGVSAINTVSGLMSLSADGNPWP-AVGTKKLTT 690
K F+ + NI ++ DIA G G+ +IN + +S GNP+ A K
Sbjct: 140 KTEVFISYSHNIGDMMDIASWKRAGGNSGMQSINGKDIAIFVSCGGNPFFFAENNKDNPI 199
Query: 691 YG 692
YG
Sbjct: 200 YG 201
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 29.8 bits (68), Expect = 6.7
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 269 VKLDKYGYPEVNYTTMATSVPGVFCGGD 296
V+ D GY +V+ + T+ PG++ GD
Sbjct: 283 VETDARGYIKVD-DQLRTTNPGIYAAGD 309
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 29.8 bits (68), Expect = 6.7
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 18/85 (21%)
Query: 580 LELSKKTEKAGADALELNLSCP-HGMGERGMGLACGQDPEMVRNISLWVRSSVKIPFFVK 638
+L ++ E AG AL L + P G ER + + + + W+R K P VK
Sbjct: 126 EDLLERAEAAGYKALVLTVDTPVLGNRERDL-----RTWDDLA----WLRDQWKGPLVVK 176
Query: 639 --LTPNITNITDIAKAAYEGKADGV 661
L+P + AK A E DG+
Sbjct: 177 GILSP------EDAKRAVEAGVDGI 195
>gnl|CDD|236054 PRK07573, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 640
Score = 29.8 bits (68), Expect = 6.9
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 11/36 (30%)
Query: 276 YPEVNYTTMA---------TSVPGVFCGGDTANLSD 302
YP V+YT M +++PG+F G+ AN SD
Sbjct: 399 YPAVHYT-MGGLWVDYNLMSTIPGLFVIGE-ANFSD 432
>gnl|CDD|185377 PRK15480, PRK15480, glucose-1-phosphate thymidylyltransferase RfbA;
Provisional.
Length = 292
Score = 29.3 bits (65), Expect = 7.7
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 222 QFNRTEQNEKGEWVEDEEQRIKLKANYIISAFGSTLLDNDVLEAIKPVKLDKYGYPEV 279
++ E ++ G + EE+ ++ K+NY ++ G DNDV+E K +K G E+
Sbjct: 145 RYGVVEFDQNGTAISLEEKPLQPKSNYAVT--GLYFYDNDVVEMAKNLKPSARGELEI 200
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 29.6 bits (67), Expect = 8.0
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 17/71 (23%)
Query: 275 GYPEVNYTTMATSVPGVFCGGDTA-------------NLSDTTVESVNDGKTAAWHIHKY 321
G N + T +PG+F G+ A +L D V G+ A +Y
Sbjct: 356 GGIPTNTGRVETKIPGLFAAGEAAGVSHHGANRLGGNSLLDLVVF----GRIAGEAAAEY 411
Query: 322 IQEKNNLTVPD 332
+EK+
Sbjct: 412 AKEKSGSPPAS 422
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 29.1 bits (66), Expect = 8.1
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 703 GLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQICSAVQNQDFTVVDDY 759
G + ++A FP GG+ + A ++ AG AV + S + +D D+
Sbjct: 140 GPAMLKALAGPFPQVRFCPTGGVSLDNAA-DYLAAGVVAVGLGSWLVPKDLIAAGDW 195
>gnl|CDD|224560 COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel
fold [General function prediction only].
Length = 240
Score = 29.2 bits (66), Expect = 8.1
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 691 YGGVSGNATRPMGLKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAV 742
G +G+ + V S + I+G GGI S + A + +AGA +
Sbjct: 172 AGSGAGDPVPVEMVSRVLSDTPL-----IVG-GGIRSPEQAREMAEAGADTI 217
>gnl|CDD|146748 pfam04276, DUF443, Protein of unknown function (DUF443). Family of
uncharacterized proteins.
Length = 197
Score = 29.1 bits (66), Expect = 8.2
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 422 FLNIELISEKTAFIFFFLFQAIPNFGEYKKIRENLITELNLKKLNSDGVS 471
+ I+L+S + F FL IP +Y KI + I LN+ K N +
Sbjct: 13 YYIIDLVSTWWKYFFPFLNWLIPK--KYYKISKEEIENLNIVKPNKNNSF 60
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 29.2 bits (66), Expect = 8.4
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 143 LPILKG-TVIVLGAGDTAFDCATSALRCGANKVLVVFRKGCTNIRAVPEEVQLAWEEKCE 201
LKG V+V+GAG+ A G ++ + R T RA +LA E
Sbjct: 173 FGNLKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANR---TYERA----EELAKELGGN 225
Query: 202 FLPF 205
+P
Sbjct: 226 AVPL 229
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 29.1 bits (66), Expect = 8.7
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 689 TTYGGVSGNATRPMG-----LKAVSSIAKMFPNFPILGIGGIDSADVALQFIQAGAHAVQ 743
TT G + + LK + P++ G I+S + A + ++ GA AV
Sbjct: 149 TTLSGYTEETAKTEDPDFELLKELRKALG----IPVIAEGRINSPEQAAKALELGADAVV 204
Query: 744 ICSAV 748
+ SA+
Sbjct: 205 VGSAI 209
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 28.4 bits (64), Expect = 9.6
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 140 KESLPILKG-TVIVLGAGDTAFDCATSALRCGANKVLVVFR 179
+E+ LKG V++LGAG A A + GA K+++V R
Sbjct: 11 EEAGIELKGKKVLILGAGGAARAVAYALAELGAAKIVIVNR 51
>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 = 29.0 bits (66), Expect = 9.7
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 22/90 (24%)
Query: 576 KDDWL--ELSKKTEKAGADALELNLSCPHGMGERGMGLACGQDPEMVRNISLWVRSSVKI 633
+D + +L ++ E AG AL L + P +G R + + W+RS K
Sbjct: 126 RDREITEDLLRRAEAAGYKALVLTVDTP-VLGRR-------LTWDDLA----WLRSQWKG 173
Query: 634 PFFVK--LTPNITNITDIAKAAYEGKADGV 661
P +K LTP + A A + ADG+
Sbjct: 174 PLILKGILTP------EDALRAVDAGADGI 197
>gnl|CDD|180579 PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed.
Length = 471
Score = 29.2 bits (66), Expect = 9.9
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 249 IISAFGSTLLDNDVLEAIKPVKLDKYGYPEVNYTTMATSVPGVFCGGD 296
++ A G + V++D+ G+ V+ T+VP +F GD
Sbjct: 266 VLVAVGRVPNGKLLDAEKAGVEVDERGFIRVD-KQCRTNVPHIFAIGD 312
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
0.317 0.135 0.400
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 42,026,802
Number of extensions: 4099653
Number of successful extensions: 4168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4025
Number of HSP's successfully gapped: 202
Length of query: 842
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 737
Effective length of database: 6,280,432
Effective search space: 4628678384
Effective search space used: 4628678384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (27.7 bits)