RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2398
(433 letters)
>gnl|CDD|109787 pfam00743, FMO-like, Flavin-binding monooxygenase-like. This
family includes FMO proteins, cyclohexanone
mono-oxygenase and a number of different
mono-oxygenases.
Length = 532
Score = 180 bits (457), Expect = 4e-51
Identities = 117/440 (26%), Positives = 197/440 (44%), Gaps = 34/440 (7%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVW----NSQASCGRVYPSLHLISP 64
K+ +IG G G+ + E + +E D+GG+W + + +Y S+ S
Sbjct: 3 KVAVIGAGVSGLSSIKCCLEEGLEPTCFERSDDIGGLWRFTEHVEEGRASIYKSVVTNSS 62
Query: 65 KFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDI---- 120
K + D+P P++YP + ++S L+YLR +AK FD+ + F T V ++ + D
Sbjct: 63 KEMSCFSDFPFPEDYPNFMHNSKFLEYLRMFAKHFDLLKYIQFKTTVCSVTKRPDFSTSG 122
Query: 121 -WEV-ELSNGKKKK--YDFIAVCNGAQRVARYPNYS----GYFSGEILHSMDYKSPDQIR 172
WEV GK++ +D + VC G P S F G+ HS DYK P+ +
Sbjct: 123 QWEVVTEHEGKQESAVFDAVMVCTGHHTNPHLPLESFPGINKFKGQYFHSRDYKHPEGFQ 182
Query: 173 NKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRGYHYYPK-FIDGKPTPQWMLQ-----L 226
KRVLV+G GNSG DIAV+ S + +V+ STR G + G P + L
Sbjct: 183 GKRVLVIGLGNSGGDIAVELSRTAAQVFLSTRTGSWVLSRVSDWGYPWDMLLTTRFCSFL 242
Query: 227 GNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKPDHPLDAAHPIMNSQILYHIGHGDILPK 286
N ++ +Q+ K F+ +YGL P + A PI+N ++ I G + K
Sbjct: 243 RNILPTRISNWLMERQLNKR--FNHENYGL-SPKNGKLAKEPIVNDELPNRILCGAVKVK 299
Query: 287 DDIKNLNGNIVHFVDDTHIE-VDTIIYATGYNRHFPFIDKEKLEWKLGIPDLFIHIAPRN 345
+K F D T E +D +I+ATGY FPF+++ ++ + L+ ++ P N
Sbjct: 300 PSVKEFTETSAIFEDGTVEEDIDVVIFATGYTFSFPFLEESLVKVETNKISLYKYVFPPN 359
Query: 346 LD--NIFFFGFVNAAAGLGDGLRLQGQFIRSYIQAF--IRKSKGYLKFLNAKKNDNPDLG 401
L+ + G + + + LQ ++ + + S ++ + KK
Sbjct: 360 LEKPTLAIIGLIQPLGSIIPTVELQARWAVRVFKGLCKLPSSSKMMEEITEKKEKKIKR- 418
Query: 402 QDYFIDSHRHLWEVDFWKFI 421
F S + D+ ++
Sbjct: 419 ---FGFSQSSTIQTDYIAYM 435
>gnl|CDD|224983 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 145 bits (367), Expect = 5e-39
Identities = 89/346 (25%), Positives = 141/346 (40%), Gaps = 39/346 (11%)
Query: 5 NKNIKLCIIGGGPLGIGLGRELSEGNI-NYDLYEMESDLGGVWNSQASCGRVYPSLHLIS 63
+ + IIG G G+ L + + ++ ++E D+GG W YP L L S
Sbjct: 6 ATHTDVAIIGAGQSGLAAAYALKQAGVPDFVIFEKRDDVGGTWRYN-----RYPGLRLDS 60
Query: 64 PKFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNT--EVINLEQYEDIW 121
PK+ P P + + + DY++ Y +K+ + FNT EV + ++ W
Sbjct: 61 PKWLLGFPFLPFRW-DEAFAPFAEIKDYIKDYLEKYGLRFQIRFNTRVEVADWDEDTKRW 119
Query: 122 EVELSNGKKKKY--DFIAVCNGAQRVARYPNYSGY--FSGEILHSMDYKSPDQIRNKRVL 177
V S+G + DF+ V G P+++G F G ILHS D+ +P+ +R KRVL
Sbjct: 120 TVTTSDGGTGELTADFVVVATGHLSEPYIPDFAGLDEFKGRILHSADWPNPEDLRGKRVL 179
Query: 178 VVGAGNSGCDIAVDASHHSEKVYHSTRRGYHYYPKFIDGKPTP-----QWMLQLG----- 227
V+GAG S DIA + + V S R H PK + G+ + L G
Sbjct: 180 VIGAGASAVDIAPELAEVGASVTLSQRSPPHILPKPLLGEEVGGRLALRRALPAGWALRR 239
Query: 228 NKFSSKEETMAY--------IKQVFKLAG----FDGVDYGLK---KPDHPLDAAHPIMNS 272
+ A K+V L F +D G++ PD+ + +
Sbjct: 240 GRVLDALLPGAGYLPAFPAPDKRVEALLRAALRFLVLDAGVREDLGPDYAPGDGRLVPDG 299
Query: 273 QILYHIGHGDILPKDDIKNLNGNIVHFVDD-THIEVDTIIYATGYN 317
+ GD+ +I + +D E D II ATG +
Sbjct: 300 DLFEAGASGDVEVVTEIIDRFTEGGILLDSGREEEADVIITATGLD 345
>gnl|CDD|215116 PLN02172, PLN02172, flavin-containing monooxygenase FMO GS-OX.
Length = 461
Score = 96.1 bits (239), Expect = 1e-21
Identities = 87/343 (25%), Positives = 138/343 (40%), Gaps = 93/343 (27%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASC---------------GRVY 56
+IG G G+ REL ++E E +GG+W VY
Sbjct: 15 VIGAGAAGLVAARELRREGHTVVVFEREKQVGGLWVYTPKSESDPLSLDPTRSIVHSSVY 74
Query: 57 PSLHLISPKFNTQVPDYPM---PDNYPV----YPNHSMMLDYLRSYAKKFDVYNHSIFNT 109
SL P+ D+P D+ YP+H +L YL+ +A++F + F T
Sbjct: 75 ESLRTNLPRECMGYRDFPFVPRFDDESRDSRRYPSHREVLAYLQDFAREFKIEEMVRFET 134
Query: 110 EVINLEQYEDIWEVELSNG----KKKKYDFIAVCNG---AQRVARYPNYSGYFSGEILHS 162
EV+ +E + W V+ N K + +D + VCNG VA P + G+ +HS
Sbjct: 135 EVVRVEPVDGKWRVQSKNSGGFSKDEIFDAVVVCNGHYTEPNVAHIPGIKSW-PGKQIHS 193
Query: 163 MDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTR-RGYHYYPKFIDGKPTPQ 221
+Y+ PD +N+ V+V+G SG DI+ D + +++V+ ++R Y K P PQ
Sbjct: 194 HNYRVPDPFKNEVVVVIGNFASGADISRDIAKVAKEVHIASRASESDTYEKL----PVPQ 249
Query: 222 WMLQLGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKPDHPLDAAHPIMNSQILYHIGHG 281
L + ++ +D AH G
Sbjct: 250 NNLWMHSE---------------------------------IDTAHE-----------DG 265
Query: 282 DILPKDDIKNLNGNIVHFVDDTHIEVDTIIYATGYNRHFPFID 324
I+ K NG +V+ DTI++ TGY HFPF++
Sbjct: 266 SIVFK------NGKVVY--------ADTIVHCTGYKYHFPFLE 294
>gnl|CDD|234447 TIGR04046, MSMEG_0569_nitr, flavin-dependent oxidoreductase,
MSMEG_0569 family. Members of this protein family
belong to a conserved seven-gene biosynthetic cluster
found sparsely in Cyanobacteria, Proteobacteria, and
Actinobacteria. Distant homologies to characterized
proteins suggest that members are enzymes dependent on a
flavinoid cofactor.
Length = 400
Score = 75.8 bits (187), Expect = 6e-15
Identities = 59/227 (25%), Positives = 99/227 (43%), Gaps = 28/227 (12%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFNTQVP 71
IIG G G+ + L + I++ + E + + W + + S L++P + ++P
Sbjct: 5 IIGAGQAGLSVSYYLKQAGIDHVVLEKHT-VAHSWRDER-----WDSFCLVTPNWQCRLP 58
Query: 72 DYPMPDNYPVYPNHSMM-----LDYLRSYAKKFD--VYNHSIFNTEVINLEQYE-DIWEV 123
+P P M + YL YA+ F+ V TEV +L ++ + V
Sbjct: 59 GHPYDGTDP----DGFMVKDEIVAYLDGYARSFNPPVREG----TEVTSLRKHGAGGFRV 110
Query: 124 ELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEI--LHSMDYKSPDQIRNKRVLVVGA 181
S G D + + G V P + ++ LHS +Y++PDQ+ + VLVVG+
Sbjct: 111 STSAGAFTA-DQVVIATGGYHVPVIPPLAERLPADVLQLHSSEYRNPDQLPDGAVLVVGS 169
Query: 182 GNSGCDIAVDASHHSEKVYHSTRRGYH-YYPKFIDGKPTPQWMLQLG 227
G SGC IA D KV+ + G +F G+ W+ +G
Sbjct: 170 GQSGCQIAEDLHLAGRKVHLAV--GSAPRCARFYRGRDVVDWLDDMG 214
>gnl|CDD|222355 pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide
oxidoreductase.
Length = 202
Score = 65.4 bits (160), Expect = 2e-12
Identities = 44/207 (21%), Positives = 84/207 (40%), Gaps = 21/207 (10%)
Query: 11 CIIGGGPLGIG-LGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISP-KFNT 68
++G G G+ L G+ + + + GG W + YP + L P F
Sbjct: 1 LVVGAGAAGMAFADHLLDLGDAPVIIVDRGAQPGGHWR------KWYPFVRLHQPSFFYG 54
Query: 69 ----------QVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYE 118
+ P D + + + YL A+++ + +T V +E+
Sbjct: 55 DFGMPDLNALSIDTSPKWDGKAELASGAEIAAYLEDLARRYGL--PIRLSTRVTAVERDG 112
Query: 119 DIWEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDYKSPDQIRNKRVLV 178
+ V L++G+ + D++ GA V + P + G + E +H +D ++ K V V
Sbjct: 113 GRFVVRLTDGETVRADYVVDATGAFSVPKPPGFPGADA-EGVHLVDVLERIDLKGKTVAV 171
Query: 179 VGAGNSGCDIAVDASHHSEKVYHSTRR 205
+G G++ D A++ + V TRR
Sbjct: 172 IGGGHTAIDAALNLLDLGKDVTWITRR 198
>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 = 45.4 bits (108), Expect = 3e-05
Identities = 42/200 (21%), Positives = 72/200 (36%), Gaps = 39/200 (19%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFNT 68
+ IIGGGP G+ L+ + L E E
Sbjct: 1 DVVIIGGGPAGLAAAIRLARLGLKVALIEREGGTCYNR---------------------G 39
Query: 69 QVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLE-QYEDIWEVELSN 127
+P + + ++ L K+F V + TEV++++ + + ++
Sbjct: 40 CLPKKLLLEVAEGLEL-AIGLALPEEVYKEFGV--EVLLGTEVVDIDRGEKTVVLKDVET 96
Query: 128 GKKKKYD--FIAVCNGAQRVARYPNYSGYFSGEILHSMDYKSPDQIRN-----KRVLVVG 180
G++ YD IA GA+ R P G E+ D+I KRV+VVG
Sbjct: 97 GREITYDKLIIAT--GAR--PRIPGIPGV---EVATLRGVIDSDEILELLELPKRVVVVG 149
Query: 181 AGNSGCDIAVDASHHSEKVY 200
G G ++A + ++V
Sbjct: 150 GGYIGLELAAALAKLGKEVT 169
>gnl|CDD|222125 pfam13434, K_oxygenase, L-lysine 6-monooxygenase (NADPH-requiring).
This is family of Rossmann fold oxidoreductases that
catalyzes the NADPH-dependent hydroxylation of lysine at
the N6 position, EC:1.14.13.59.
Length = 335
Score = 44.0 bits (105), Expect = 8e-05
Identities = 45/260 (17%), Positives = 90/260 (34%), Gaps = 54/260 (20%)
Query: 90 DYLRSYAKKFDVYNHSIFNTEVINLE--QYEDIWEVELSN-GKKKKYDFIAVCNGAQRVA 146
DYL+ A + + + F EV +E + V + G ++ Y + G
Sbjct: 99 DYLQWAASQLE---NVRFGAEVEEVEPDDSGFLLRVHTRDTGTEQTYLARNLVLGTGTTP 155
Query: 147 RYP-NYSGYFSGEILHSMDYKS--PDQIRNKRVLVVGAGNSGCDIAVDA---SHHSEKVY 200
P + HS +Y P + KR+ VVG G S +I +D + +
Sbjct: 156 YIPECAKPLPGERVFHSSEYLLRKPRLLAGKRITVVGGGQSAAEIFLDLLRRQPGYQLTW 215
Query: 201 HSTRRGY-----------HYYPKFIDG-----KPTPQWMLQLGNKFSSKEETMAYIKQVF 244
+ R + ++ P+++D + +L+ + K I++++
Sbjct: 216 VTRRPNFFPLDDSPFTNEYFSPEYVDYFYALPEEKRDRLLREQKLTNYKGIDPDLIEEIY 275
Query: 245 ------KLAGFDGVDYGLKKPDHPLDAAHPIMNSQILYHIGHGDILPKDDIKNLNGNIVH 298
K+ G L P+ + AA + L ++N
Sbjct: 276 RRLYQQKVLG--DPRVRL-LPNREVQAAEATGDGYQL------------TLRNGEQG--- 317
Query: 299 FVDDTHIEVDTIIYATGYNR 318
++ ++ D ++ ATGY
Sbjct: 318 --EEETLDADAVVLATGYRY 335
>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 = 43.3 bits (103), Expect = 1e-04
Identities = 48/204 (23%), Positives = 75/204 (36%), Gaps = 39/204 (19%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPS-LHLISPKFN 67
+ IIG GP G+ E + ++Y + E G + NS YP+ + S
Sbjct: 1 DVIIIGAGPCGLACAIEAQKAGLSYLIIEK----GNLVNSI----YRYPTNMTFFSTSER 52
Query: 68 TQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSN 127
++ P P P + L+Y R A++F +N+ YE++ +V
Sbjct: 53 LEIGGIPFISENP-KPTRNEALEYYRRVAERFK-----------LNIRLYEEVLKV---- 96
Query: 128 GKKKKYDFIAVCNGAQRVARY----------PNYSGYFSGEILH--SMDYKSPDQIRNKR 175
KK F A+ PN GE L S YK ++
Sbjct: 97 -KKTDGGFEVTTEKGTYQAKNVIVATGYYDIPNLLN-VPGEDLPKVSHYYKEAHPYFGQK 154
Query: 176 VLVVGAGNSGCDIAVDASHHSEKV 199
V+VVG NS D A++ +V
Sbjct: 155 VVVVGGSNSAVDAALELYRKGAEV 178
>gnl|CDD|223566 COG0492, TrxB, Thioredoxin reductase [Posttranslational
modification, protein turnover, chaperones].
Length = 305
Score = 42.7 bits (101), Expect = 2e-04
Identities = 48/201 (23%), Positives = 75/201 (37%), Gaps = 38/201 (18%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFNTQVP 71
IIGGGP G+ + + L + GG T V
Sbjct: 8 IIGGGPAGLTAAIYAARAGLKVVLILEGGEPGG------------------QLTKTTDVE 49
Query: 72 DYPMPDNYPVYPNHSM---MLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNG 128
NYP +P + +++ ++ A+KF V I EV +E ++V+ G
Sbjct: 50 ------NYPGFPGGILGPELMEQMKEQAEKFGV---EIVEDEVEKVELEGGPFKVKTDKG 100
Query: 129 K-KKKYDFIAVCNGAQRVARYPNYSGY--FSGEILHSMDYKSPDQIRNKRVLVVGAGNSG 185
+ K IA GA AR G F G+ + + K V+V+G G+S
Sbjct: 101 TYEAKAVIIAT--GA--GARKLGVPGEEEFEGKGVSYCATCDGF-FKGKDVVVIGGGDSA 155
Query: 186 CDIAVDASHHSEKVYHSTRRG 206
+ A+ S ++KV RR
Sbjct: 156 VEEALYLSKIAKKVTLVHRRD 176
>gnl|CDD|237197 PRK12770, PRK12770, putative glutamate synthase subunit beta;
Provisional.
Length = 352
Score = 41.9 bits (99), Expect = 4e-04
Identities = 33/117 (28%), Positives = 50/117 (42%), Gaps = 34/117 (29%)
Query: 107 FNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGA--QRVARYP--NYSGYFSG-EILH 161
F +++LE EL KKYD + + G R P + G +S E L
Sbjct: 105 FVERIVSLE--------EL----VKKYDAVLIATGTWKSRKLGIPGEDLPGVYSALEYLF 152
Query: 162 S--------MDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHS-----EKVYHSTRR 205
+ ++ + K+V+VVGAG + AVDA+ + EKVY + RR
Sbjct: 153 RIRAAKLGYLPWEKVPPVEGKKVVVVGAGLT----AVDAALEAVLLGAEKVYLAYRR 205
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 40.8 bits (96), Expect = 0.001
Identities = 46/240 (19%), Positives = 77/240 (32%), Gaps = 51/240 (21%)
Query: 9 KLCIIGGGPLGIGLGREL-----SEGNINYDLYEMESDLG-GVWNSQASCGRVYPSLHLI 62
K+ IIGGG GI + L G I ++E + G G+ S HL+
Sbjct: 3 KVAIIGGGFSGIYMAAHLLKSPRPSGLI--SIFEPRPNFGQGIAYSTEE------PEHLL 54
Query: 63 ---SPKFNTQVPDYP-------------------MPDNYPVYPNHSMMLDYLRSYAKKF- 99
+ + + PD P + + YP + +YLR
Sbjct: 55 NVPAARMSAFAPDIPQDFVRWLQKQLQRYRDPEDINHDGQAYPPRRLFGEYLREQLAALL 114
Query: 100 -----DVYNHSIFNTEVINLEQYED--IWEVELSNGKKKKYDFI--AVCNGAQRVARYPN 150
E ++ Q + + V ++G + D I A + A
Sbjct: 115 ARGRQTRVRTI--REEATSVRQDTNAGGYLVTTADGPSEIADIIVLATGHSAPPADPAAR 172
Query: 151 YSGYFSGEILHSMDYKSPDQIR-NKRVLVVGAGNSGCDI--AVDASHHSEKVYHSTRRGY 207
I + D + + RVL+VG+G + D + H + +RRG
Sbjct: 173 DLKGSPRLIADPYPANALDGVDADDRVLIVGSGLTSIDQVLVLRRRGHKGPITAISRRGL 232
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 37.2 bits (87), Expect = 0.005
Identities = 32/161 (19%), Positives = 52/161 (32%), Gaps = 40/161 (24%)
Query: 11 CIIGGGPLGIG----LGRELSEGNINYDLYE-MESDLGGVWNSQASCGRVYPSLHLI--- 62
IIG GP G+ L R + ++ +++ GGVW + P L+
Sbjct: 1 AIIGAGPRGLSVLERLLRRAPDRPLDITVFDPSPPGAGGVWRTDQ------PPQLLLNTP 54
Query: 63 ----------SPKFN----TQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFD-------- 100
P F Q + D P +YLR +
Sbjct: 55 AAQMSLFPDDPPSFLEWLEAQGEEEAGLDPDDFPPRALFG-EYLRWRFSELLARAPAGVT 113
Query: 101 VYNHSIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNG 141
V H EV++L + V L++G + D + + G
Sbjct: 114 VRVH---RAEVVDLRPRGGGYTVTLADGATLRADAVVLATG 151
>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 = 38.0 bits (89), Expect = 0.006
Identities = 48/209 (22%), Positives = 75/209 (35%), Gaps = 49/209 (23%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFNT 68
+ IIG GP G+ + N+ L E + GG
Sbjct: 1 DVIIIGAGPAGLTAAIYAARANLKPLLIE-GGEPGG------------------------ 35
Query: 69 QVPDYPMPDNYPVYPN----HSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVE 124
Q+ +NYP +P +M ++ A KF I EVI +++ ++V
Sbjct: 36 QLTTTTEVENYPGFPEGISGPELMEK-MKEQAVKFGA---EIIYEEVIKVDKSGRPFKVY 91
Query: 125 LSNGKKKKYDFIAVCNGAQRVARYPNYSG--YFSGE------ILHSMDYKSPDQIRNKRV 176
+GK+ + + GA AR G F G +K NK V
Sbjct: 92 TGDGKEYTAKAVIIATGAS--ARKLGIPGEDEFWGRGVSYCATCDGPFFK------NKEV 143
Query: 177 LVVGAGNSGCDIAVDASHHSEKVYHSTRR 205
VVG G+S + A+ + ++KV RR
Sbjct: 144 AVVGGGDSAIEEALYLTRIAKKVTLVHRR 172
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 34.4 bits (80), Expect = 0.008
Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 15/81 (18%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFNTQVP 71
I+G G G+ L++ + + E +GG S+ G +
Sbjct: 1 IVGAGLSGLVAAYLLAKRGKDVLVLEKRDRIGGNAYSERDPGYRH--------------- 45
Query: 72 DYPMPDNYPVYPNHSMMLDYL 92
DY + YPN +LD L
Sbjct: 46 DYGAHIFHTSYPNVRELLDEL 66
>gnl|CDD|237200 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta;
Provisional.
Length = 752
Score = 36.6 bits (85), Expect = 0.023
Identities = 47/216 (21%), Positives = 80/216 (37%), Gaps = 54/216 (25%)
Query: 5 NKNIKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISP 64
K+ +IG GP G+ +L++ YD+ V+ +LH I
Sbjct: 429 KNGKKVAVIGSGPAGLSFAGDLAK--RGYDVT------------------VFEALHEIGG 468
Query: 65 KFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVE 124
+P++ +P V ++ L+ KF + V E++
Sbjct: 469 VLKYGIPEFRLPKKI-VDVE----IENLKKLGVKF------ETDVIVGKTITIEEL---- 513
Query: 125 LSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHS---------MDYKSPDQ----I 171
+++ + I + +GA + + N G S ++ S MD SPD
Sbjct: 514 ----EEEGFKGIFIASGAG-LPNFMNIPGENSNGVMSSNEYLTRVNLMDAASPDSDTPIK 568
Query: 172 RNKRVLVVGAGNSGCDIAVDASH-HSEKVYHSTRRG 206
K+V VVG GN+ D A A +E+V RR
Sbjct: 569 FGKKVAVVGGGNTAMDSARTAKRLGAERVTIVYRRS 604
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 36.5 bits (85), Expect = 0.026
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 8 IKLCIIGGGPLGIGLGRELSE--GNINYDLYEMESDLGGV 45
+K+ IIGGG G+ L + ++ L+E + +GG+
Sbjct: 1 MKIAIIGGGIAGLSAAYRLQKAGPDVEVTLFEADDRVGGL 40
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 36.0 bits (84), Expect = 0.032
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGG 44
K+ I+GGG G+ L++ ++E + LGG
Sbjct: 1 KIAIVGGGIAGLAAAYRLAKRGHEVTVFEADDQLGG 36
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 35.7 bits (83), Expect = 0.042
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 105 SIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ 143
FNTE+ +LE+ + W++ +NG+ + + NGAQ
Sbjct: 151 LHFNTEITSLERDGEGWQLLDANGEVIAASVVVLANGAQ 189
>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
Length = 464
Score = 35.0 bits (81), Expect = 0.064
Identities = 47/218 (21%), Positives = 81/218 (37%), Gaps = 55/218 (25%)
Query: 4 KNKNIKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLIS 63
+ K K+ +IG GP G+ +L++ + ++E + GGV VY
Sbjct: 137 EKKGKKVAVIGSGPAGLTCAGDLAKMGYDVTIFEALHEPGGVL--------VY------- 181
Query: 64 PKFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNT----EVINLEQYED 119
+P++ +P V ++ ++ K + N + T E++ E ++
Sbjct: 182 -----GIPEFRLPKETVVKKE----IENIKKLGVKIET-NVVVGKTVTIDELLEEEGFDA 231
Query: 120 IWEVELSNGKKKKYDFIAVCNGAQRVARYP--NYSGYFSG-EIL--------HSMDYKSP 168
+ FI G + P N +G FS E L + +Y +P
Sbjct: 232 V--------------FIGSGAGLPKFMGIPGENLNGVFSANEFLTRVNLMKAYKPEYDTP 277
Query: 169 DQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 206
K+V VVG GN D A A +V+ RR
Sbjct: 278 -IKVGKKVAVVGGGNVAMDAARTALRLGAEVHIVYRRS 314
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 35.0 bits (81), Expect = 0.099
Identities = 40/216 (18%), Positives = 78/216 (36%), Gaps = 60/216 (27%)
Query: 4 KNKNIKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLIS 63
K+ +IG GP G+ L+ ++E E + GGV ++I
Sbjct: 536 IGSRKKVAVIGAGPAGLAAAYFLARAGHPVTVFEREENAGGVVK------------NII- 582
Query: 64 PKFNTQVPDYPMPDNYPVYPNHSMM---LDYLRSYAKKFDVYNHSIFNTEVINLEQYEDI 120
P + +P ++ +++++++ KF + S + V L
Sbjct: 583 -------PQFRIPA--------ELIQHDIEFVKAHGVKF-EFGCSP-DLTVEQL------ 619
Query: 121 WEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY-----KSPDQIR-NK 174
K + YD++ V GA + G + ++ ++ + ++ K
Sbjct: 620 --------KNEGYDYVVVAIGADKNGGLKLEGG--NQNVIKALPFLEEYKNKGTALKLGK 669
Query: 175 RVLVVGAGNSGCDIA-----VDASHHSEKVYHSTRR 205
V+VVG GN+ D A V VY T++
Sbjct: 670 HVVVVGGGNTAMDAARAALRVPGVEKVTVVYRRTKQ 705
>gnl|CDD|234119 TIGR03140, AhpF, alkyl hydroperoxide reductase subunit F. This
enzyme is the partner of the peroxiredoxin (alkyl
hydroperoxide reductase) AhpC which contains the
peroxide-reactive cysteine. AhpF contains the reductant
(NAD(P)H) binding domain (pfam00070) and presumably acts
to resolve the disulfide which forms after oxidation of
the active site cysteine in AphC. This proteins contains
two paired conserved cysteine motifs, CxxCP and CxHCDGP
[Cellular processes, Detoxification, Cellular processes,
Adaptations to atypical conditions].
Length = 515
Score = 33.9 bits (78), Expect = 0.17
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 31/106 (29%)
Query: 102 YNHSIF-NTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ-R--------------V 145
Y + N +E + + V L +G+ K + V GA+ R V
Sbjct: 280 YPIDLMENQRAKKIETEDGLIVVTLESGEVLKAKSVIVATGARWRKLGVPGEKEYIGKGV 339
Query: 146 ARYPNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVD 191
A P+ G F +K K V V+G GNSG + A+D
Sbjct: 340 AYCPHCDGPF---------FK------GKDVAVIGGGNSGIEAAID 370
>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 = 33.8 bits (78), Expect = 0.19
Identities = 40/202 (19%), Positives = 70/202 (34%), Gaps = 61/202 (30%)
Query: 8 IKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLHLISPKFN 67
K+ +IG GP G+ +LS + ++E + GG L L
Sbjct: 124 KKVAVIGAGPAGLAAADDLSRAGHDVTVFERVALDGG--------------LLLYG---- 165
Query: 68 TQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEV---INLEQYEDIWEVE 124
+PD+ +P + L+ L +F + N V I LE+
Sbjct: 166 --IPDFKLPKD-----ILDRRLELLERSGVEFKL------NVRVGRDITLEEL------- 205
Query: 125 LSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY--------------KSPDQ 170
K+YD + + GA + G + + ++D+
Sbjct: 206 -----LKEYDAVFLATGAGKPRPLD-IPGEDAKGVAFALDFLTRLNKEVLGDFAEDRTPP 259
Query: 171 IRNKRVLVVGAGNSGCDIAVDA 192
+ KRV+V+G G++ D A A
Sbjct: 260 AKGKRVVVIGGGDTAMDCAGTA 281
>gnl|CDD|224070 COG1148, HdrA, Heterodisulfide reductase, subunit A and related
polyferredoxins [Energy production and conversion].
Length = 622
Score = 33.6 bits (77), Expect = 0.23
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYP----SLHLISPKFN 67
+IGGG GI EL++ L E E +GG A + +P S+ +++PK
Sbjct: 129 VIGGGVAGITAALELADMGFKVYLVEKEPSIGG---RMAKLNKTFPTNDCSICILAPKMV 185
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 33.2 bits (76), Expect = 0.27
Identities = 43/204 (21%), Positives = 73/204 (35%), Gaps = 61/204 (29%)
Query: 1 MKYKNKNIKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSLH 60
+ + KN K+ I+G GP G+ L+ +YE S GGV
Sbjct: 277 DEPEKKNKKVAIVGSGPAGLSAAYFLATMGYEVTVYESLSKPGGV--------------- 321
Query: 61 LISPKFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEV---INLEQY 117
+P Y +PD LD ++ + V H NT V I LE+
Sbjct: 322 -----MRYGIPSYRLPDE---------ALDKDIAFIEALGVKIHL--NTRVGKDIPLEEL 365
Query: 118 EDIWEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDYKSPDQIRN---- 173
++K+D + + G + R G +++ ++ +IR+
Sbjct: 366 ------------REKHDAVFLSTGFT-LGRSTRIPGTDHPDVIQALPLL--REIRDYLRG 410
Query: 174 --------KRVLVVGAGNSGCDIA 189
+ ++V+G GN DIA
Sbjct: 411 EGPKPKIPRSLVVIGGGNVAMDIA 434
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 33.0 bits (75), Expect = 0.32
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGG 44
+ ++G GP+G+ ++ L E LGG
Sbjct: 138 DVVVVGAGPIGLEAAEAAAKRGKKVTLIEAADRLGG 173
>gnl|CDD|131408 TIGR02355, moeB, molybdopterin synthase sulfurylase MoeB. This
model describes the molybdopterin biosynthesis protein
MoeB in E. coli and related species. The enzyme
covalently modifies the molybdopterin synthase MoaD by
sulfurylation. This enzyme is closely related to ThiF, a
thiamine biosynthesis enzyme that modifies ThiS by an
analogous adenylation. Both MoeB and ThiF belong to the
HesA/MoeB/ThiF family (pfam00899) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 240
Score = 32.1 bits (73), Expect = 0.42
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 159 ILHSMDYKSPDQIRNKRVLVVGAGNSGC 186
IL D+ + ++ RVL+VG G GC
Sbjct: 10 ILRGFDFDGQEALKASRVLIVGLGGLGC 37
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 32.4 bits (74), Expect = 0.59
Identities = 24/117 (20%), Positives = 37/117 (31%), Gaps = 24/117 (20%)
Query: 284 LPKDDIKNL---NGNIVHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLEWKLGIPDLFIH 340
+PK +G ++H T + ++ G R + K LF
Sbjct: 435 MPKWTRIAAVFRDGQLIHPQGSTRLREGDVLCVIGSERDLRALGK-----------LFSS 483
Query: 341 IAPRNLDNIFFFGF----------VNAAAGLGDGLRLQGQFIRSYIQAFIRKSKGYL 387
P LD FF F V A GLGDG + Q + + + +
Sbjct: 484 APPVALDARFFGDFILEPSAKAADVALAYGLGDGYADKAQTLGELVTQLLGGAPVLG 540
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 31.8 bits (73), Expect = 0.67
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 174 KRVLVVGAGNSGCDIAVDASHHSEKV 199
+RVLVVG G G ++A+D + V
Sbjct: 142 QRVLVVGGGLIGTELAMDLCRAGKAV 167
>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 = 32.1 bits (73), Expect = 0.69
Identities = 44/201 (21%), Positives = 69/201 (34%), Gaps = 49/201 (24%)
Query: 10 LCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYP-SLHLISPKFNT 68
L IIGGGP G+ G + G D +E D G + S YP L+ P+
Sbjct: 7 LIIIGGGPAGLSAG--IYAGRAKLDTLIIEKDDFGGQITITSEVVNYPGILNTTGPELMQ 64
Query: 69 QVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNG 128
+ +R A+ F V EV++++ DI ++ + G
Sbjct: 65 E----------------------MRQQAQDFGV---KFLQAEVLDVDFDGDIKTIKTARG 99
Query: 129 KKKKYDFIAVCNGAQRVARYPN----------YSGYFSGEILHSMDYKSPDQIRNKRVLV 178
K + + R +P Y GE MD V V
Sbjct: 100 DYKTLAVLIATGASPRKLGFPGEEEFTGRGVAYCATCDGEFFTGMD-----------VFV 148
Query: 179 VGAGNSGCDIAVDASHHSEKV 199
+G G + + AV + ++ KV
Sbjct: 149 IGGGFAAAEEAVFLTRYASKV 169
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 30.2 bits (69), Expect = 0.79
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 11 CIIGGGPLGIGLGRELSEGNINY 33
IIG G +G L EL EG +
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDV 24
>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
reductase subunit; Provisional.
Length = 396
Score = 31.4 bits (71), Expect = 0.86
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 119 DIWEVELSNGKKKKYDFIAVCNGAQRVARYP--NYSGYFSGEILHSMDYKSPDQI--RNK 174
D E+ L+NG+ +D + + GA P + G + H+ D ++ +
Sbjct: 87 DTRELVLTNGESWHWDQLFIATGA-AARPLPLLDALGERCFTLRHAGDAARLREVLQPER 145
Query: 175 RVLVVGAGNSGCDIAVDASHHSEKV 199
V++VGAG G ++A A+ KV
Sbjct: 146 SVVIVGAGTIGLELAASATQRRCKV 170
>gnl|CDD|215691 pfam00070, Pyr_redox, 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 = 82
Score = 29.1 bits (66), Expect = 0.86
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 175 RVLVVGAGNSGCDIAVDASHHSEKVY 200
RV+VVG G G + A + KV
Sbjct: 1 RVVVVGGGYIGLEFASALAKLGSKVT 26
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 31.3 bits (72), Expect = 0.98
Identities = 35/117 (29%), Positives = 48/117 (41%), Gaps = 36/117 (30%)
Query: 92 LRSYAKKFDVYNHSIFNTE-VINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ-R----- 144
L + K++DV I N + LE + EVEL+NG K + + GA+ R
Sbjct: 272 LEEHVKEYDV---DIMNLQRASKLEPAAGLIEVELANGAVLKAKTVILATGARWRNMNVP 328
Query: 145 ---------VARYPNYSG-YFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVD 191
VA P+ G F G KRV V+G GNSG + A+D
Sbjct: 329 GEDEYRNKGVAYCPHCDGPLFKG----------------KRVAVIGGGNSGVEAAID 369
>gnl|CDD|182343 PRK10262, PRK10262, thioredoxin reductase; Provisional.
Length = 321
Score = 31.2 bits (70), Expect = 1.1
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 29/143 (20%)
Query: 77 DNYPVYPNH---SMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSN------ 127
+N+P PN ++++ + +A KF+ TE+I ++ I +V+L N
Sbjct: 51 ENWPGDPNDLTGPLLMERMHEHATKFE--------TEII----FDHINKVDLQNRPFRLT 98
Query: 128 GKKKKY--DFIAVCNGAQRVARY---PNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAG 182
G +Y D + + GA ARY P+ F G + + RN++V V+G G
Sbjct: 99 GDSGEYTCDALIIATGAS--ARYLGLPSEEA-FKGRGVSACATCDGFFYRNQKVAVIGGG 155
Query: 183 NSGCDIAVDASHHSEKVYHSTRR 205
N+ + A+ S+ + +V+ RR
Sbjct: 156 NTAVEEALYLSNIASEVHLIHRR 178
>gnl|CDD|235528 PRK05600, PRK05600, thiamine biosynthesis protein ThiF; Validated.
Length = 370
Score = 31.0 bits (70), Expect = 1.1
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 143 QRVARYPNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGC 186
+R AR G+ + +++ N RVLV+GAG GC
Sbjct: 20 RRTARQLALPGF---------GIEQQERLHNARVLVIGAGGLGC 54
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.1 bits (71), Expect = 1.2
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 6/23 (26%)
Query: 163 MDYKSPDQIRNKRVLVVGAGNSG 185
M+ K K+VLVVGAG SG
Sbjct: 1 MELK------GKKVLVVGAGVSG 17
>gnl|CDD|226160 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 520
Score = 31.3 bits (71), Expect = 1.2
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 172 RNKRVLVVGAGNSGCDIAVD 191
+ KRV V+G GNSG + A+D
Sbjct: 353 KGKRVAVIGGGNSGVEAAID 372
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 29.3 bits (67), Expect = 1.3
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 11/32 (34%)
Query: 170 QIRNKRVLVVGAGN-----------SGCDIAV 190
++ KRVLVVG G +G + V
Sbjct: 4 DLKGKRVLVVGGGEVALRKIRALLEAGAKVTV 35
>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 = 31.0 bits (70), Expect = 1.3
Identities = 33/148 (22%), Positives = 57/148 (38%), Gaps = 28/148 (18%)
Query: 111 VINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY----- 165
V N E DI EL K+++D + + GA + P G I ++M++
Sbjct: 211 VTNTEIGVDISADEL----KEQFDAVVLAGGATKPRDLP-IPGRELKGIHYAMEFLPSAT 265
Query: 166 --------KSPDQIR--NKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRGYHYYPKFID 215
K I+ K+V+V+G G++G D + H H + PK +
Sbjct: 266 KALLGKDFKDIIFIKAKGKKVVVIGGGDTGADCVGTSLRHGAASVHQ----FEIMPKPPE 321
Query: 216 GK----PTPQWMLQLGNKFSSKEETMAY 239
+ P P+W ++ +E Y
Sbjct: 322 ARAKDNPWPEWPRVYRVDYAHEEAAAHY 349
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 31.0 bits (71), Expect = 1.5
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 107 FNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ 143
F EV LE+ +D W+++ + G + + NG
Sbjct: 426 FGHEVARLEREDDGWQLDFAGGTLASAPVVVLANGHD 462
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 30.8 bits (69), Expect = 1.5
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGV 45
K+ +IG GP G+G L+ + D+++ ++GG+
Sbjct: 312 KVAVIGAGPAGLGCADILARAGVQVDVFDRHPEIGGM 348
>gnl|CDD|226017 COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 436
Score = 30.7 bits (70), Expect = 1.6
Identities = 25/131 (19%), Positives = 49/131 (37%), Gaps = 28/131 (21%)
Query: 89 LDYLRSYAKKFDVYNHSIFNTEVINLEQY--------------EDIWEVELSNGKKKKYD 134
L+YL + + ++ N+ F+ Y E++ ++ +G
Sbjct: 75 LNYLHEHGRLYEFLNYETFHIPRREYNDYCQWAASQLPSLRFGEEVTDISSLDGDAVVRL 134
Query: 135 FIAVCNGAQRVARY------------PNYSGYFSGEILHSMDYKS--PDQIRNKRVLVVG 180
F+ NG AR P + + HS +Y P+ ++ + V V+G
Sbjct: 135 FVVTANGTVYRARNLVLGVGTQPYIPPCFRSLIGERVFHSSEYLERHPELLQKRSVTVIG 194
Query: 181 AGNSGCDIAVD 191
+G S +I +D
Sbjct: 195 SGQSAAEIFLD 205
>gnl|CDD|226839 COG4408, COG4408, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 431
Score = 30.5 bits (69), Expect = 1.7
Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 174 KRVLVVGAGNSGCDIAVDASHHSEK----VYHSTRRGYHYYPKFIDGKPTPQWMLQLGNK 229
VL++G G +AVD S H + + R TPQ LQ +
Sbjct: 5 LPVLLLGTGPVAIQLAVDLSAHGDARLGLYNRPSTRSERLKQAL---ALTPQLYLQGQGE 61
Query: 230 FSSKEETMAYIKQVFK 245
+ E I K
Sbjct: 62 AHRQLEGSVTIDCYIK 77
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family
includes various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 30.0 bits (68), Expect = 1.8
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGVWNSQASCGRVYPSL 59
+ +IGGG +G+ EL+ ++ L E DL S + G ++P L
Sbjct: 1 DVVVIGGGIVGLSTAYELARRGLSVTLLERG-DLAS-GASGRNAGLLHPGL 49
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 30.6 bits (70), Expect = 1.9
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 106 IFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVAR 147
T V +++ D +E+ LSNG + + D + V +
Sbjct: 237 HKGTPVTKIDKSGDGYEIVLSNGGEIEADAVIVAVPHPVLPS 278
>gnl|CDD|218389 pfam05025, RbsD_FucU, RbsD / FucU transport protein family. The
Escherichia coli high-affinity ribose-transport system
consists of six proteins encoded by the rbs operon
(rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). Of the six
components, RbsD is the only one whose function is
unknown although it is thought that it somehow plays a
critical role in PtsG-mediated ribose transport. This
family also includes FucU a protein from the fucose
biosynthesis operon that is presumably also involved in
fucose transport by similarity to RbsD.
Length = 138
Score = 29.4 bits (67), Expect = 2.1
Identities = 7/21 (33%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 267 HPIMNSQILYHI---GHGDIL 284
P++N ++L + GHGD +
Sbjct: 4 TPLLNPELLAVLAAMGHGDEI 24
>gnl|CDD|215369 PLN02685, PLN02685, iron superoxide dismutase.
Length = 299
Score = 30.0 bits (67), Expect = 2.3
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 18/99 (18%)
Query: 221 QWMLQLGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKPDHPLDAAHPIMNSQIL-YHIG 279
QW + + +++ I A F+ LK P +PLDA P M+ + L YH G
Sbjct: 26 QWKGK--RRTCTRKAVSGVI-----TAKFE-----LKPPPYPLDALEPHMSRETLEYHWG 73
Query: 280 HGDILPKDDIKNLNGNIVHFVDDTHIEVDTIIYATGYNR 318
+ + NLN IV D + ++ ++ T YN+
Sbjct: 74 KHH---RAYVDNLNKQIVGTELDG-MSLEDVVLIT-YNK 107
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 30.3 bits (69), Expect = 2.5
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 10 LCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGGV 45
+ +IG GP G ++ + L E LGG
Sbjct: 7 VVVIGAGPAGYVAAIRAAQLGLKVALVEKGERLGGT 42
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 29.7 bits (67), Expect = 2.5
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 83 PNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWE---VELSNGKKKKYDFIAVC 139
++ + L S + D Y H F TE+ Q E I + ELS G+ ++ IA C
Sbjct: 72 ADYEGTVRDLLS-SITKDFYTHPYFKTEIAKPLQIEQILDREVPELSGGELQRVA-IAAC 129
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 29.8 bits (68), Expect = 2.6
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 168 PDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 206
++ K VL+VG G+ G +IA A +V R G
Sbjct: 129 VRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSG 167
>gnl|CDD|235967 PRK07208, PRK07208, hypothetical protein; Provisional.
Length = 479
Score = 29.9 bits (68), Expect = 2.6
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 12 IIGGGPLGIGLGRELSEGNINYDLYEMESDLGGV 45
IIG GP G+ EL + + E + +GG+
Sbjct: 9 IIGAGPAGLTAAYELLKRGYPVTVLEADPVVGGI 42
>gnl|CDD|166263 PLN02622, PLN02622, iron superoxide dismutase.
Length = 261
Score = 29.6 bits (66), Expect = 2.8
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 10/46 (21%)
Query: 254 YGLKKPDHPLDAAHPIMNSQIL------YHIGHGD----ILPKDDI 289
YGLK P +PLDA P M+ + L +H G+ + L KDDI
Sbjct: 48 YGLKTPPYPLDALEPYMSRRTLEVHWGEHHRGYVEGLNKQLAKDDI 93
>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
Length = 569
Score = 30.2 bits (68), Expect = 2.8
Identities = 15/43 (34%), Positives = 21/43 (48%)
Query: 2 KYKNKNIKLCIIGGGPLGIGLGRELSEGNINYDLYEMESDLGG 44
YK +K+ IIG G G+ EL + D+YE +GG
Sbjct: 70 AYKGPKLKVAIIGAGLAGMSTAVELLDQGHEVDIYESRPFIGG 112
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 30.2 bits (68), Expect = 2.9
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 164 DYKSP-DQIRNKRVLVVGAGNSGCDIAVDASH---HSEKVYHSTR 204
DY++P +++ K V V+G GN+ D A A + VY T+
Sbjct: 437 DYETPLPEVKGKEVFVIGGGNTAMDAARTAKRLGGNVTIVYRRTK 481
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.7 bits (67), Expect = 3.0
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 294 GNIVHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLE 329
G + +D+ H V + + Y F+DKE+LE
Sbjct: 108 GTLEEIIDENHAIVSSSVGPEYYVNILSFVDKEQLE 143
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 29.9 bits (68), Expect = 3.1
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 282 DILPKDDIKNLNGNIVHFVD-DTHIEVDTIIYATG 315
++L + + + V D + I DT+++A G
Sbjct: 225 EVLLGTPVTEVTPDGVTLKDGEEEIPADTVVWAAG 259
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 29.8 bits (68), Expect = 3.3
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 10/33 (30%)
Query: 174 KRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 206
KRV V+G G +G A YH R G
Sbjct: 138 KRVAVIGGGPAGLSAA----------YHLRRMG 160
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 29.7 bits (68), Expect = 3.3
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 170 QIRNKRVLVVGAGNSGCDIA 189
+ ++R++ +GAG++GC IA
Sbjct: 292 PLSDQRIVFLGAGSAGCGIA 311
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 29.5 bits (67), Expect = 3.9
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 11 CIIGGGPLGIGLGRELSEGNINYD--LYEMESDLG 43
IIGGG +G ELSE + L E E +
Sbjct: 7 VIIGGGIMGAATAYELSEYEPDLSVALLEKEDGVA 41
Score = 28.4 bits (64), Expect = 7.6
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 90 DYLRSYAKKFDVYNHSI-FNTEVINLEQYED-IWEVELSNGKKK-KYDFIAVCNG--AQR 144
+ R+ A++ + NTEV +E+ D ++ + SNG++ + F+ G A
Sbjct: 154 ELTRALAEEAQANGVELRLNTEVTGIEKQSDGVFVLNTSNGEETLEAKFVINAAGLYADP 213
Query: 145 VAR 147
+A+
Sbjct: 214 LAQ 216
>gnl|CDD|215257 PLN02464, PLN02464, glycerol-3-phosphate dehydrogenase.
Length = 627
Score = 29.7 bits (67), Expect = 3.9
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 176 VLVVGAGNSGCDIAVDA 192
VLVVG G +G +A+DA
Sbjct: 74 VLVVGGGATGAGVALDA 90
>gnl|CDD|233382 TIGR01372, soxA, sarcosine oxidase, alpha subunit family,
heterotetrameric form. This model describes the alpha
subunit of a family of known and putative
heterotetrameric sarcosine oxidases. Five operons of
such oxidases are found in Mesorhizobium loti and three
in Agrobacterium tumefaciens, a high enough copy number
to suggest that not all members are share the same
function. The model is designated as subfamily rather
than equivalog for this reason.Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine to
glycine. The reaction converts tetrahydrofolate to
5,10-methylene-tetrahydrofolate. The enzyme is known in
monomeric and heterotetrameric (alpha,beta,gamma,delta)
forms [Energy metabolism, Amino acids and amines].
Length = 985
Score = 29.7 bits (67), Expect = 4.2
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 176 VLVVGAGNSGCDIAVDASHHSEKVYHSTRR-----GYHYYPKFIDGKPTPQW 222
VLVVGAG +G A+ A+ +V + + IDGKP W
Sbjct: 166 VLVVGAGPAGLAAALAAARAGARVILVDEQPEAGGSLLSEAETIDGKPAADW 217
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 28.7 bits (65), Expect = 4.9
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 159 ILHSMDYKSPDQIRNKRVLVVGAGNSGC 186
IL D+ ++++ RVLVVG G GC
Sbjct: 18 ILRGFDFDGQEKLKAARVLVVGLGGLGC 45
>gnl|CDD|216530 pfam01494, FAD_binding_3, FAD binding domain. This domain is
involved in FAD binding in a number of enzymes.
Length = 349
Score = 28.8 bits (65), Expect = 5.2
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 11 CIIGGGPLGIGLGRELSE 28
I+GGGP G+ L L+
Sbjct: 5 LIVGGGPAGLMLALLLAR 22
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 28.9 bits (65), Expect = 5.3
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 166 KSPDQIRNKRVLVVGAGNSGCDI--AVDASHHSEKV 199
++ KRV V G G GC I AV +E V
Sbjct: 163 HQAGDLQGKRVFVSGVGPIGCLIVAAVKTLGAAEIV 198
>gnl|CDD|185416 PTZ00052, PTZ00052, thioredoxin reductase; Provisional.
Length = 499
Score = 29.0 bits (65), Expect = 6.2
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 283 ILPKDDIKNLNGNI-VHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLE-WKLGIPDLFIH 340
++P + I+ ++ I V F D T DT++YATG P I L + +
Sbjct: 243 VVPIN-IEKMDDKIKVLFSDGTTELFDTVLYATGRK---PDIKGLNLNAIGVHVNKSNKI 298
Query: 341 IAPR---NLDNIFFFGFV 355
IAP N+ NIF G V
Sbjct: 299 IAPNDCTNIPNIFAVGDV 316
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 29.0 bits (66), Expect = 6.2
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 21/77 (27%)
Query: 130 KKKYD--FIAVCNGAQRVARYPNYSGYFSGE----ILHSMDY-KSPDQ-------IRNKR 175
+ YD FI G R P GE + ++D+ +Q KR
Sbjct: 223 RAGYDAVFIGTGAGLPRFLGIP-------GENLGGVYSAVDFLTRVNQAVADYDLPVGKR 275
Query: 176 VLVVGAGNSGCDIAVDA 192
V+V+G GN+ D A A
Sbjct: 276 VVVIGGGNTAMDAARTA 292
>gnl|CDD|131413 TIGR02360, pbenz_hydroxyl, 4-hydroxybenzoate 3-monooxygenase.
Members of this family are the enzyme 4-hydroxybenzoate
3-monooxygenase, also called p-hydroxybenzoate
hydroxylase. It converts 4-hydroxybenzoate + NADPH +
molecular oxygen to protocatechuate + NADPH + water. It
contains monooxygenase (pfam01360) and FAD binding
(pfam01494) domains. Pathways that contain this enzyme
include the protocatechuate 4,5-degradation pathway
[Energy metabolism, Other].
Length = 390
Score = 28.6 bits (64), Expect = 6.9
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNINYDLYEMES 40
++ IIG GP G+ LG+ L + I+ + E +S
Sbjct: 4 QVAIIGAGPSGLLLGQLLHKAGIDNVILERQS 35
>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 = 28.4 bits (64), Expect = 8.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 171 IRNKRVLVVGAGNSGCDIA 189
++ K+VLV+GAG G A
Sbjct: 176 LKGKKVLVIGAGEMGELAA 194
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 28.0 bits (63), Expect = 8.1
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 9 KLCIIGGGPLGIGLGRELSEGNIN 32
K+ IIG G +G + RELSE N
Sbjct: 2 KIIIIGAGRVGRSVARELSEEGHN 25
>gnl|CDD|132171 TIGR03127, RuMP_HxlB, 6-phospho 3-hexuloisomerase. Members of this
protein family are 6-phospho 3-hexuloisomerase (PHI), or
the PHI domain of a fusion protein. This enzyme is part
of the ribulose monophosphate (RuMP) pathway, which in
one direction removes the toxic metabolite formaldehyde
by assimilation into fructose-6-phosphate. In the other
direction, in species lacking a complete pentose
phosphate pathway, the RuMP pathway yields
ribulose-5-phosphate, necessary for nucleotide
biosynthesis, at the cost of also yielding formaldehyde.
These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin.
Length = 179
Score = 27.7 bits (62), Expect = 9.2
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 8/38 (21%)
Query: 156 SGEILHSMDYKSPDQ--------IRNKRVLVVGAGNSG 185
EI ++ I+ KR+ V GAG SG
Sbjct: 5 LDEISQVASRIDEEELDKLADKIIKAKRIFVAGAGRSG 42
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 28.5 bits (64), Expect = 9.4
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 170 QIRNKRVLVVGAGNSGCDIAVDASHHSEKV 199
I V+V+G G +G A++A+ KV
Sbjct: 3 TIHEFDVVVIGGGGAGLRAAIEAAEAGLKV 32
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 28.3 bits (63), Expect = 9.5
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 149 PNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYH-STRRGY 207
P +G+ + +H M I+ K V + G GN A A+ KV S GY
Sbjct: 204 PEATGFGALYFVHQMLETKGIDIKGKTVAISGFGNVAWGAATKATELGAKVVTISGPDGY 263
Query: 208 HYYPKFIDGKPTPQWMLQLGN 228
Y P I G+ +ML+L
Sbjct: 264 IYDPDGISGEKI-DYMLELRA 283
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.141 0.444
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,355,705
Number of extensions: 2336241
Number of successful extensions: 2647
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2626
Number of HSP's successfully gapped: 100
Length of query: 433
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 333
Effective length of database: 6,502,202
Effective search space: 2165233266
Effective search space used: 2165233266
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.9 bits)