RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2343
(396 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 = 173 bits (441), Expect = 4e-49
Identities = 110/408 (26%), Positives = 184/408 (45%), Gaps = 34/408 (8%)
Query: 4 DLGGVW----NSQASCGRVYPSLHLISPKFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYA 59
D+GG+W + + +Y S+ S K + D+P P++YP + ++S L+YLR +A
Sbjct: 35 DIGGLWRFTEHVEEGRASIYKSVVTNSSKEMSCFSDFPFPEDYPNFMHNSKFLEYLRMFA 94
Query: 60 KKFDVYNHSIFNTEVINLEQYEDI-----WEV-ELSNGKKKK--YDFIAVCNGAQRVARY 111
K FD+ + F T V ++ + D WEV GK++ +D + VC G
Sbjct: 95 KHFDLLKYIQFKTTVCSVTKRPDFSTSGQWEVVTEHEGKQESAVFDAVMVCTGHHTNPHL 154
Query: 112 PNYS----GYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTR 167
P S F G+ HS DYK P+ + KRVLV+G GNSG DIAV+ S + +V+ STR
Sbjct: 155 PLESFPGINKFKGQYFHSRDYKHPEGFQGKRVLVIGLGNSGGDIAVELSRTAAQVFLSTR 214
Query: 168 RGYHYYPK-FIDGKPTPQWMLQ-----LGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKK 221
G + G P + L N ++ +Q+ K F+ +YGL
Sbjct: 215 TGSWVLSRVSDWGYPWDMLLTTRFCSFLRNILPTRISNWLMERQLNKR--FNHENYGL-S 271
Query: 222 PDHPLDAAHPIMNSQILYHIGHGDILPKDDIKNLNGNIVHFVDDTHIE-VDTIIYATGYN 280
P + A PI+N ++ I G + K +K F D T E +D +I+ATGY
Sbjct: 272 PKNGKLAKEPIVNDELPNRILCGAVKVKPSVKEFTETSAIFEDGTVEEDIDVVIFATGYT 331
Query: 281 RHFPFIDKEKLEWKLGIPDLFIHIAPRNLD--NIFFFGFVNAAAGLGDGLRLQGQFIRSY 338
FPF+++ ++ + L+ ++ P NL+ + G + + + LQ ++
Sbjct: 332 FSFPFLEESLVKVETNKISLYKYVFPPNLEKPTLAIIGLIQPLGSIIPTVELQARWAVRV 391
Query: 339 IQAF--IRKSKGYLKFLNAKKNDNPDLGQDYFIDSHRHLWEVDFWKFI 384
+ + S ++ + KK F S + D+ ++
Sbjct: 392 FKGLCKLPSSSKMMEEITEKKEKKIKR----FGFSQSSTIQTDYIAYM 435
>gnl|CDD|224983 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 119 bits (301), Expect = 5e-30
Identities = 82/312 (26%), Positives = 125/312 (40%), Gaps = 38/312 (12%)
Query: 1 MESDLGGVWNSQASCGRVYPSLHLISPKFNTQVPDYPMPDNYPVYPNHSMMLDYLRSYAK 60
D+GG W YP L L SPK+ P P + + + DY++ Y +
Sbjct: 40 KRDDVGGTWRYN-----RYPGLRLDSPKWLLGFPFLPFRW-DEAFAPFAEIKDYIKDYLE 93
Query: 61 KFDVYNHSIFNT--EVINLEQYEDIWEVELSNGKKKKY--DFIAVCNGAQRVARYPNYSG 116
K+ + FNT EV + ++ W V S+G + DF+ V G P+++G
Sbjct: 94 KYGLRFQIRFNTRVEVADWDEDTKRWTVTTSDGGTGELTADFVVVATGHLSEPYIPDFAG 153
Query: 117 Y--FSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRGYHYYP 174
F G ILHS D+ +P+ +R KRVLV+GAG S DIA + + V S R H P
Sbjct: 154 LDEFKGRILHSADWPNPEDLRGKRVLVIGAGASAVDIAPELAEVGASVTLSQRSPPHILP 213
Query: 175 KFIDGKPTP-----QWMLQLG-----NKFSSKEETMAY--------IKQVFKLAG----F 212
K + G+ + L G + A K+V L F
Sbjct: 214 KPLLGEEVGGRLALRRALPAGWALRRGRVLDALLPGAGYLPAFPAPDKRVEALLRAALRF 273
Query: 213 DGVDYGLK---KPDHPLDAAHPIMNSQILYHIGHGDILPKDDIKNLNGNIVHFVDD-THI 268
+D G++ PD+ + + + GD+ +I + +D
Sbjct: 274 LVLDAGVREDLGPDYAPGDGRLVPDGDLFEAGASGDVEVVTEIIDRFTEGGILLDSGREE 333
Query: 269 EVDTIIYATGYN 280
E D II ATG +
Sbjct: 334 EADVIITATGLD 345
>gnl|CDD|215116 PLN02172, PLN02172, flavin-containing monooxygenase FMO GS-OX.
Length = 461
Score = 81.4 bits (201), Expect = 9e-17
Identities = 75/285 (26%), Positives = 120/285 (42%), Gaps = 78/285 (27%)
Query: 18 VYPSLHLISPKFNTQVPDYPM---PDNYPV----YPNHSMMLDYLRSYAKKFDVYNHSIF 70
VY SL P+ D+P D+ YP+H +L YL+ +A++F + F
Sbjct: 73 VYESLRTNLPRECMGYRDFPFVPRFDDESRDSRRYPSHREVLAYLQDFAREFKIEEMVRF 132
Query: 71 NTEVINLEQYEDIWEVELSNG----KKKKYDFIAVCNG---AQRVARYPNYSGYFSGEIL 123
TEV+ +E + W V+ N K + +D + VCNG VA P + G+ +
Sbjct: 133 ETEVVRVEPVDGKWRVQSKNSGGFSKDEIFDAVVVCNGHYTEPNVAHIPGIKSW-PGKQI 191
Query: 124 HSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTR-RGYHYYPKFIDGKPT 182
HS +Y+ PD +N+ V+V+G SG DI+ D + +++V+ ++R Y K P
Sbjct: 192 HSHNYRVPDPFKNEVVVVIGNFASGADISRDIAKVAKEVHIASRASESDTYEKL----PV 247
Query: 183 PQWMLQLGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKPDHPLDAAHPIMNSQILYHIG 242
PQ L + ++ +D AH
Sbjct: 248 PQNNLWMHSE---------------------------------IDTAHE----------- 263
Query: 243 HGDILPKDDIKNLNGNIVHFVDDTHIEVDTIIYATGYNRHFPFID 287
G I+ K NG +V+ DTI++ TGY HFPF++
Sbjct: 264 DGSIVFK------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 = 68.1 bits (167), Expect = 1e-12
Identities = 49/178 (27%), Positives = 79/178 (44%), Gaps = 22/178 (12%)
Query: 24 LISPKFNTQVPDYPMPDNYPVYPNHSMM-----LDYLRSYAKKFD--VYNHSIFNTEVIN 76
L++P + ++P +P P M + YL YA+ F+ V TEV +
Sbjct: 48 LVTPNWQCRLPGHPYDGTDP----DGFMVKDEIVAYLDGYARSFNPPVREG----TEVTS 99
Query: 77 LEQYE-DIWEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEI--LHSMDYKSPDQ 133
L ++ + V S G D + + G V P + ++ LHS +Y++PDQ
Sbjct: 100 LRKHGAGGFRVSTSAGAFTA-DQVVIATGGYHVPVIPPLAERLPADVLQLHSSEYRNPDQ 158
Query: 134 IRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRGYH-YYPKFIDGKPTPQWMLQLG 190
+ + VLVVG+G SGC IA D KV+ + G +F G+ W+ +G
Sbjct: 159 LPDGAVLVVGSGQSGCQIAEDLHLAGRKVHLAV--GSAPRCARFYRGRDVVDWLDDMG 214
>gnl|CDD|222355 pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide
oxidoreductase.
Length = 202
Score = 55.0 bits (133), Expect = 7e-09
Identities = 39/174 (22%), Positives = 72/174 (41%), Gaps = 20/174 (11%)
Query: 6 GGVWNSQASCGRVYPSLHLISP-KFNT----------QVPDYPMPDNYPVYPNHSMMLDY 54
GG W + YP + L P F + P D + + + Y
Sbjct: 34 GGHWR------KWYPFVRLHQPSFFYGDFGMPDLNALSIDTSPKWDGKAELASGAEIAAY 87
Query: 55 LRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVARYPNY 114
L A+++ + +T V +E+ + V L++G+ + D++ GA V + P +
Sbjct: 88 LEDLARRYGL--PIRLSTRVTAVERDGGRFVVRLTDGETVRADYVVDATGAFSVPKPPGF 145
Query: 115 SGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRR 168
G + E +H +D ++ K V V+G G++ D A++ + V TRR
Sbjct: 146 PGADA-EGVHLVDVLERIDLKGKTVAVIGGGHTAIDAALNLLDLGKDVTWITRR 198
>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 = 43.3 bits (103), Expect = 1e-04
Identities = 45/260 (17%), Positives = 90/260 (34%), Gaps = 54/260 (20%)
Query: 53 DYLRSYAKKFDVYNHSIFNTEVINLE--QYEDIWEVELSN-GKKKKYDFIAVCNGAQRVA 109
DYL+ A + + + F EV +E + V + G ++ Y + G
Sbjct: 99 DYLQWAASQLE---NVRFGAEVEEVEPDDSGFLLRVHTRDTGTEQTYLARNLVLGTGTTP 155
Query: 110 RYP-NYSGYFSGEILHSMDYKS--PDQIRNKRVLVVGAGNSGCDIAVDA---SHHSEKVY 163
P + HS +Y P + KR+ VVG G S +I +D + +
Sbjct: 156 YIPECAKPLPGERVFHSSEYLLRKPRLLAGKRITVVGGGQSAAEIFLDLLRRQPGYQLTW 215
Query: 164 HSTRRGY-----------HYYPKFIDG-----KPTPQWMLQLGNKFSSKEETMAYIKQVF 207
+ R + ++ P+++D + +L+ + K I++++
Sbjct: 216 VTRRPNFFPLDDSPFTNEYFSPEYVDYFYALPEEKRDRLLREQKLTNYKGIDPDLIEEIY 275
Query: 208 ------KLAGFDGVDYGLKKPDHPLDAAHPIMNSQILYHIGHGDILPKDDIKNLNGNIVH 261
K+ G L P+ + AA + L ++N
Sbjct: 276 RRLYQQKVLG--DPRVRL-LPNREVQAAEATGDGYQL------------TLRNGEQG--- 317
Query: 262 FVDDTHIEVDTIIYATGYNR 281
++ ++ D ++ ATGY
Sbjct: 318 --EEETLDADAVVLATGYRY 335
>gnl|CDD|237197 PRK12770, PRK12770, putative glutamate synthase subunit beta;
Provisional.
Length = 352
Score = 42.7 bits (101), Expect = 2e-04
Identities = 33/117 (28%), Positives = 50/117 (42%), Gaps = 34/117 (29%)
Query: 70 FNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGA--QRVARYP--NYSGYFSG-EILH 124
F +++LE EL KKYD + + G R P + G +S E L
Sbjct: 105 FVERIVSLE--------EL----VKKYDAVLIATGTWKSRKLGIPGEDLPGVYSALEYLF 152
Query: 125 S--------MDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHS-----EKVYHSTRR 168
+ ++ + K+V+VVGAG + AVDA+ + EKVY + RR
Sbjct: 153 RIRAAKLGYLPWEKVPPVEGKKVVVVGAGLT----AVDAALEAVLLGAEKVYLAYRR 205
>gnl|CDD|223566 COG0492, TrxB, Thioredoxin reductase [Posttranslational
modification, protein turnover, chaperones].
Length = 305
Score = 41.9 bits (99), Expect = 3e-04
Identities = 36/136 (26%), Positives = 60/136 (44%), Gaps = 14/136 (10%)
Query: 40 DNYPVYPNHSM---MLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNGK-KKK 95
+NYP +P + +++ ++ A+KF V I EV +E ++V+ G + K
Sbjct: 49 ENYPGFPGGILGPELMEQMKEQAEKFGV---EIVEDEVEKVELEGGPFKVKTDKGTYEAK 105
Query: 96 YDFIAVCNGAQRVARYPNYSGY--FSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAV 153
IA GA AR G F G+ + + K V+V+G G+S + A+
Sbjct: 106 AVIIAT--GA--GARKLGVPGEEEFEGKGVSYCATCDGF-FKGKDVVVIGGGDSAVEEAL 160
Query: 154 DASHHSEKVYHSTRRG 169
S ++KV RR
Sbjct: 161 YLSKIAKKVTLVHRRD 176
>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 = 39.3 bits (92), Expect = 0.002
Identities = 31/142 (21%), Positives = 57/142 (40%), Gaps = 18/142 (12%)
Query: 30 NTQVPDYPMPDNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLE-QYEDIWEVEL 88
+P + + ++ L K+F V + TEV++++ + + ++
Sbjct: 38 RGCLPKKLLLEVAEGLEL-AIGLALPEEVYKEFGV--EVLLGTEVVDIDRGEKTVVLKDV 94
Query: 89 SNGKKKKYD--FIAVCNGAQRVARYPNYSGYFSGEILHSMDYKSPDQIRN-----KRVLV 141
G++ YD IA GA+ R P G E+ D+I KRV+V
Sbjct: 95 ETGREITYDKLIIAT--GAR--PRIPGIPGV---EVATLRGVIDSDEILELLELPKRVVV 147
Query: 142 VGAGNSGCDIAVDASHHSEKVY 163
VG G G ++A + ++V
Sbjct: 148 VGGGYIGLELAAALAKLGKEVT 169
>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 = 36.8 bits (86), Expect = 0.013
Identities = 36/141 (25%), Positives = 57/141 (40%), Gaps = 24/141 (17%)
Query: 40 DNYPVYPN----HSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNGKKKK 95
+NYP +P +M ++ A KF I EVI +++ ++V +GK+
Sbjct: 44 ENYPGFPEGISGPELMEK-MKEQAVKFGA---EIIYEEVIKVDKSGRPFKVYTGDGKEYT 99
Query: 96 YDFIAVCNGAQRVARYPNYSG--YFSGE------ILHSMDYKSPDQIRNKRVLVVGAGNS 147
+ + GA AR G F G +K NK V VVG G+S
Sbjct: 100 AKAVIIATGAS--ARKLGIPGEDEFWGRGVSYCATCDGPFFK------NKEVAVVGGGDS 151
Query: 148 GCDIAVDASHHSEKVYHSTRR 168
+ A+ + ++KV RR
Sbjct: 152 AIEEALYLTRIAKKVTLVHRR 172
>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 = 36.0 bits (84), Expect = 0.025
Identities = 26/111 (23%), Positives = 39/111 (35%), Gaps = 18/111 (16%)
Query: 64 VYNHSIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVARY----------PN 113
Y + +N+ YE++ +V KK F A+ PN
Sbjct: 74 EYYRRVAERFKLNIRLYEEVLKV-----KKTDGGFEVTTEKGTYQAKNVIVATGYYDIPN 128
Query: 114 YSGYFSGEILH--SMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKV 162
GE L S YK ++V+VVG NS D A++ +V
Sbjct: 129 LLN-VPGEDLPKVSHYYKEAHPYFGQKVVVVGGSNSAVDAALELYRKGAEV 178
>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 = 35.3 bits (82), Expect = 0.042
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 68 SIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ 106
FNTE+ +LE+ + W++ +NG+ + + NGAQ
Sbjct: 151 LHFNTEITSLERDGEGWQLLDANGEVIAASVVVLANGAQ 189
>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 = 34.3 bits (79), Expect = 0.12
Identities = 27/106 (25%), Positives = 40/106 (37%), Gaps = 31/106 (29%)
Query: 65 YNHSIF-NTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ-R--------------V 108
Y + N +E + + V L +G+ K + V GA+ R V
Sbjct: 280 YPIDLMENQRAKKIETEDGLIVVTLESGEVLKAKSVIVATGARWRKLGVPGEKEYIGKGV 339
Query: 109 ARYPNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVD 154
A P+ G F +K K V V+G GNSG + A+D
Sbjct: 340 AYCPHCDGPF---------FK------GKDVAVIGGGNSGIEAAID 370
>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 = 0.34
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 122 ILHSMDYKSPDQIRNKRVLVVGAGNSGC 149
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 = 0.44
Identities = 24/117 (20%), Positives = 37/117 (31%), Gaps = 24/117 (20%)
Query: 247 LPKDDIKNL---NGNIVHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLEWKLGIPDLFIH 303
+PK +G ++H T + ++ G R + K LF
Sbjct: 435 MPKWTRIAAVFRDGQLIHPQGSTRLREGDVLCVIGSERDLRALGK-----------LFSS 483
Query: 304 IAPRNLDNIFFFGF----------VNAAAGLGDGLRLQGQFIRSYIQAFIRKSKGYL 350
P LD FF F V A GLGDG + Q + + + +
Sbjct: 484 APPVALDARFFGDFILEPSAKAADVALAYGLGDGYADKAQTLGELVTQLLGGAPVLG 540
>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 = 29.5 bits (67), Expect = 0.60
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 138 RVLVVGAGNSGCDIAVDASHHSEKVY 163
RV+VVG G G + A + KV
Sbjct: 1 RVVVVGGGYIGLEFASALAKLGSKVT 26
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 31.8 bits (73), Expect = 0.61
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 137 KRVLVVGAGNSGCDIAVDASHHSEKV 162
+RVLVVG G G ++A+D + V
Sbjct: 142 QRVLVVGGGLIGTELAMDLCRAGKAV 167
>gnl|CDD|237200 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta;
Provisional.
Length = 752
Score = 32.0 bits (73), Expect = 0.67
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 92 KKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHS---------MDYKSPDQ----IRNKR 138
+++ + I + +GA + + N G S ++ S MD SPD K+
Sbjct: 514 EEEGFKGIFIASGAG-LPNFMNIPGENSNGVMSSNEYLTRVNLMDAASPDSDTPIKFGKK 572
Query: 139 VLVVGAGNSGCDIAVDASH-HSEKVYHSTRRG 169
V VVG GN+ D A A +E+V RR
Sbjct: 573 VAVVGGGNTAMDSARTAKRLGAERVTIVYRRS 604
>gnl|CDD|170080 PRK09754, PRK09754, phenylpropionate dioxygenase ferredoxin
reductase subunit; Provisional.
Length = 396
Score = 31.4 bits (71), Expect = 0.74
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 82 DIWEVELSNGKKKKYDFIAVCNGAQRVARYP--NYSGYFSGEILHSMDYKSPDQI--RNK 137
D E+ L+NG+ +D + + GA P + G + H+ D ++ +
Sbjct: 87 DTRELVLTNGESWHWDQLFIATGA-AARPLPLLDALGERCFTLRHAGDAARLREVLQPER 145
Query: 138 RVLVVGAGNSGCDIAVDASHHSEKV 162
V++VGAG G ++A A+ KV
Sbjct: 146 SVVIVGAGTIGLELAASATQRRCKV 170
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 31.7 bits (73), Expect = 0.77
Identities = 35/117 (29%), Positives = 48/117 (41%), Gaps = 36/117 (30%)
Query: 55 LRSYAKKFDVYNHSIFNTE-VINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ-R----- 107
L + K++DV I N + LE + EVEL+NG K + + GA+ R
Sbjct: 272 LEEHVKEYDV---DIMNLQRASKLEPAAGLIEVELANGAVLKAKTVILATGARWRNMNVP 328
Query: 108 ---------VARYPNYSG-YFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVD 154
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 = 31.6 bits (71), Expect = 0.77
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 29/143 (20%)
Query: 40 DNYPVYPNH---SMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSN------ 90
+N+P PN ++++ + +A KF+ TE+I ++ I +V+L N
Sbjct: 51 ENWPGDPNDLTGPLLMERMHEHATKFE--------TEII----FDHINKVDLQNRPFRLT 98
Query: 91 GKKKKY--DFIAVCNGAQRVARY---PNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAG 145
G +Y D + + GA ARY P+ F G + + RN++V V+G G
Sbjct: 99 GDSGEYTCDALIIATGAS--ARYLGLPSEEA-FKGRGVSACATCDGFFYRNQKVAVIGGG 155
Query: 146 NSGCDIAVDASHHSEKVYHSTRR 168
N+ + A+ S+ + +V+ RR
Sbjct: 156 NTAVEEALYLSNIASEVHLIHRR 178
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 31.1 bits (71), Expect = 0.99
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 6/23 (26%)
Query: 126 MDYKSPDQIRNKRVLVVGAGNSG 148
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 = 1.0
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 135 RNKRVLVVGAGNSGCDIAVD 154
+ KRV V+G GNSG + A+D
Sbjct: 353 KGKRVAVIGGGNSGVEAAID 372
>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 = 1.1
Identities = 33/148 (22%), Positives = 57/148 (38%), Gaps = 28/148 (18%)
Query: 74 VINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY----- 128
V N E DI EL K+++D + + GA + P G I ++M++
Sbjct: 211 VTNTEIGVDISADEL----KEQFDAVVLAGGATKPRDLP-IPGRELKGIHYAMEFLPSAT 265
Query: 129 --------KSPDQIR--NKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRGYHYYPKFID 178
K I+ K+V+V+G G++G D + H H + PK +
Sbjct: 266 KALLGKDFKDIIFIKAKGKKVVVIGGGDTGADCVGTSLRHGAASVHQ----FEIMPKPPE 321
Query: 179 GK----PTPQWMLQLGNKFSSKEETMAY 202
+ P P+W ++ +E Y
Sbjct: 322 ARAKDNPWPEWPRVYRVDYAHEEAAAHY 349
>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: 106 QRVARYPNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGC 149
+R AR G+ + +++ N RVLV+GAG GC
Sbjct: 20 RRTARQLALPGF---------GIEQQERLHNARVLVIGAGGLGC 54
>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 = 1.2
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 11/32 (34%)
Query: 133 QIRNKRVLVVGAGN-----------SGCDIAV 153
++ KRVLVVG G +G + V
Sbjct: 4 DLKGKRVLVVGGGEVALRKIRALLEAGAKVTV 35
>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 = 30.6 bits (70), Expect = 1.5
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 70 FNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQ 106
F EV LE+ +D W+++ + G + + NG
Sbjct: 426 FGHEVARLEREDDGWQLDFAGGTLASAPVVVLANGHD 462
>gnl|CDD|226017 COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 436
Score = 30.4 bits (69), Expect = 1.8
Identities = 25/131 (19%), Positives = 49/131 (37%), Gaps = 28/131 (21%)
Query: 52 LDYLRSYAKKFDVYNHSIFNTEVINLEQY--------------EDIWEVELSNGKKKKYD 97
L+YL + + ++ N+ F+ Y E++ ++ +G
Sbjct: 75 LNYLHEHGRLYEFLNYETFHIPRREYNDYCQWAASQLPSLRFGEEVTDISSLDGDAVVRL 134
Query: 98 FIAVCNGAQRVARY------------PNYSGYFSGEILHSMDYKS--PDQIRNKRVLVVG 143
F+ NG AR P + + HS +Y P+ ++ + V V+G
Sbjct: 135 FVVTANGTVYRARNLVLGVGTQPYIPPCFRSLIGERVFHSSEYLERHPELLQKRSVTVIG 194
Query: 144 AGNSGCDIAVD 154
+G S +I +D
Sbjct: 195 SGQSAAEIFLD 205
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 30.6 bits (70), Expect = 1.8
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 69 IFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNGAQRVAR 110
T V +++ D +E+ LSNG + + D + V +
Sbjct: 237 HKGTPVTKIDKSGDGYEIVLSNGGEIEADAVIVAVPHPVLPS 278
>gnl|CDD|226839 COG4408, COG4408, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 431
Score = 30.5 bits (69), Expect = 1.8
Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 137 KRVLVVGAGNSGCDIAVDASHHSEK----VYHSTRRGYHYYPKFIDGKPTPQWMLQLGNK 192
VL++G G +AVD S H + + R TPQ LQ +
Sbjct: 5 LPVLLLGTGPVAIQLAVDLSAHGDARLGLYNRPSTRSERLKQAL---ALTPQLYLQGQGE 61
Query: 193 FSSKEETMAYIKQVFK 208
+ E I K
Sbjct: 62 AHRQLEGSVTIDCYIK 77
>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 = 1.9
Identities = 7/21 (33%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 230 HPIMNSQILYHI---GHGDIL 247
P++N ++L + GHGD +
Sbjct: 4 TPLLNPELLAVLAAMGHGDEI 24
>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 = 2.1
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 46 PNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWE---VELSNGKKKKYDFIAVC 102
++ + L S + D Y H F TE+ Q E I + ELS G+ ++ IA C
Sbjct: 72 ADYEGTVRDLLS-SITKDFYTHPYFKTEIAKPLQIEQILDREVPELSGGELQRVA-IAAC 129
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 30.3 bits (69), Expect = 2.1
Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 13/88 (14%)
Query: 92 KKKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY-----KSPDQIR-NKRVLVVGAG 145
K + YD++ V GA + G + ++ ++ + ++ K V+VVG G
Sbjct: 620 KNEGYDYVVVAIGADKNGGLKLEGG--NQNVIKALPFLEEYKNKGTALKLGKHVVVVGGG 677
Query: 146 NSGCDIA-----VDASHHSEKVYHSTRR 168
N+ D A V VY T++
Sbjct: 678 NTAMDAARAALRVPGVEKVTVVYRRTKQ 705
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 30.1 bits (68), Expect = 2.1
Identities = 26/141 (18%), Positives = 45/141 (31%), Gaps = 15/141 (10%)
Query: 43 PVYPNHSMMLDYLRSYAKKF------DVYNHSIFNTEVINLEQYED--IWEVELSNGKKK 94
YP + +YLR E ++ Q + + V ++G +
Sbjct: 94 QAYPPRRLFGEYLREQLAALLARGRQTRVRTI--REEATSVRQDTNAGGYLVTTADGPSE 151
Query: 95 KYDFI--AVCNGAQRVARYPNYSGYFSGEILHSMDYKSPDQIR-NKRVLVVGAGNSGCDI 151
D I A + A I + D + + RVL+VG+G + D
Sbjct: 152 IADIIVLATGHSAPPADPAARDLKGSPRLIADPYPANALDGVDADDRVLIVGSGLTSIDQ 211
Query: 152 --AVDASHHSEKVYHSTRRGY 170
+ H + +RRG
Sbjct: 212 VLVLRRRGHKGPITAISRRGL 232
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 29.1 bits (66), Expect = 2.3
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 11/60 (18%)
Query: 53 DYLRSYAKKFD--------VYNHSIFNTEVINLEQYEDIWEVELSNGKKKKYDFIAVCNG 104
+YLR + V H EV++L + V L++G + D + + G
Sbjct: 95 EYLRWRFSELLARAPAGVTVRVH---RAEVVDLRPRGGGYTVTLADGATLRADAVVLATG 151
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.7 bits (67), Expect = 2.5
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 257 GNIVHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLE 292
G + +D+ H V + + Y F+DKE+LE
Sbjct: 108 GTLEEIIDENHAIVSSSVGPEYYVNILSFVDKEQLE 143
>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 = 2.5
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 131 PDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 169
++ K VL+VG G+ G +IA A +V R G
Sbjct: 129 VRELAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSG 167
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 30.2 bits (68), Expect = 2.5
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 127 DYKSP-DQIRNKRVLVVGAGNSGCDIAVDASH---HSEKVYHSTR 167
DY++P +++ K V V+G GN+ D A A + VY T+
Sbjct: 437 DYETPLPEVKGKEVFVIGGGNTAMDAARTAKRLGGNVTIVYRRTK 481
>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 = 30.0 bits (68), Expect = 2.5
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 15/77 (19%)
Query: 93 KKKYDFIAVCNGAQRVARYPNYSGYFSGEILHSMDY--------------KSPDQIRNKR 138
K+YD + + GA + G + + ++D+ + KR
Sbjct: 206 LKEYDAVFLATGAGKPRPLD-IPGEDAKGVAFALDFLTRLNKEVLGDFAEDRTPPAKGKR 264
Query: 139 VLVVGAGNSGCDIAVDA 155
V+V+G G++ D A A
Sbjct: 265 VVVIGGGDTAMDCAGTA 281
>gnl|CDD|215369 PLN02685, PLN02685, iron superoxide dismutase.
Length = 299
Score = 29.6 bits (66), Expect = 2.6
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 18/99 (18%)
Query: 184 QWMLQLGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKPDHPLDAAHPIMNSQIL-YHIG 242
QW + + +++ I A F+ LK P +PLDA P M+ + L YH G
Sbjct: 26 QWKGK--RRTCTRKAVSGVI-----TAKFE-----LKPPPYPLDALEPHMSRETLEYHWG 73
Query: 243 HGDILPKDDIKNLNGNIVHFVDDTHIEVDTIIYATGYNR 281
+ + NLN IV D + ++ ++ T YN+
Sbjct: 74 KHH---RAYVDNLNKQIVGTELDG-MSLEDVVLIT-YNK 107
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 29.9 bits (68), Expect = 2.7
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 245 DILPKDDIKNLNGNIVHFVD-DTHIEVDTIIYATG 278
++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 = 2.7
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 10/33 (30%)
Query: 137 KRVLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 169
KRV V+G G +G A YH R G
Sbjct: 138 KRVAVIGGGPAGLSAA----------YHLRRMG 160
>gnl|CDD|166263 PLN02622, PLN02622, iron superoxide dismutase.
Length = 261
Score = 29.6 bits (66), Expect = 2.7
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 10/46 (21%)
Query: 217 YGLKKPDHPLDAAHPIMNSQIL------YHIGHGD----ILPKDDI 252
YGLK P +PLDA P M+ + L +H G+ + L KDDI
Sbjct: 48 YGLKTPPYPLDALEPYMSRRTLEVHWGEHHRGYVEGLNKQLAKDDI 93
>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
Length = 464
Score = 30.0 bits (68), Expect = 2.8
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 14/91 (15%)
Query: 92 KKKKYD--FIAVCNGAQRVARYP--NYSGYFSG-EIL--------HSMDYKSPDQIRNKR 138
+++ +D FI G + P N +G FS E L + +Y +P K+
Sbjct: 225 EEEGFDAVFIGSGAGLPKFMGIPGENLNGVFSANEFLTRVNLMKAYKPEYDTP-IKVGKK 283
Query: 139 VLVVGAGNSGCDIAVDASHHSEKVYHSTRRG 169
V VVG GN D A A +V+ RR
Sbjct: 284 VAVVGGGNVAMDAARTALRLGAEVHIVYRRS 314
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 29.7 bits (68), Expect = 2.9
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 133 QIRNKRVLVVGAGNSGCDIA 152
+ ++R++ +GAG++GC IA
Sbjct: 292 PLSDQRIVFLGAGSAGCGIA 311
>gnl|CDD|215257 PLN02464, PLN02464, glycerol-3-phosphate dehydrogenase.
Length = 627
Score = 29.4 bits (66), Expect = 3.8
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 139 VLVVGAGNSGCDIAVDA 155
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 = 29.3 bits (66), Expect = 4.0
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 5/52 (9%)
Query: 139 VLVVGAGNSGCDIAVDASHHSEKVYHSTRR-----GYHYYPKFIDGKPTPQW 185
VLVVGAG +G A+ A+ +V + + IDGKP W
Sbjct: 166 VLVVGAGPAGLAAALAAARAGARVILVDEQPEAGGSLLSEAETIDGKPAADW 217
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 29.0 bits (66), Expect = 4.2
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 122 ILHSMDYKSPDQIRNKRVLVVGAGNSGC 149
IL D+ ++++ RVLVVG G GC
Sbjct: 18 ILRGFDFDGQEKLKAARVLVVGLGGLGC 45
>gnl|CDD|185416 PTZ00052, PTZ00052, thioredoxin reductase; Provisional.
Length = 499
Score = 29.0 bits (65), Expect = 4.6
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 246 ILPKDDIKNLNGNI-VHFVDDTHIEVDTIIYATGYNRHFPFIDKEKLE-WKLGIPDLFIH 303
++P + I+ ++ I V F D T DT++YATG P I L + +
Sbjct: 243 VVPIN-IEKMDDKIKVLFSDGTTELFDTVLYATGRK---PDIKGLNLNAIGVHVNKSNKI 298
Query: 304 IAPR---NLDNIFFFGFV 318
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 = 4.6
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 21/77 (27%)
Query: 93 KKKYD--FIAVCNGAQRVARYPNYSGYFSGE----ILHSMDY-KSPDQ-------IRNKR 138
+ YD FI G R P GE + ++D+ +Q KR
Sbjct: 223 RAGYDAVFIGTGAGLPRFLGIP-------GENLGGVYSAVDFLTRVNQAVADYDLPVGKR 275
Query: 139 VLVVGAGNSGCDIAVDA 155
V+V+G GN+ D A A
Sbjct: 276 VVVIGGGNTAMDAARTA 292
>gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional.
Length = 343
Score = 28.9 bits (65), Expect = 4.8
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 129 KSPDQIRNKRVLVVGAGNSGCDI--AVDASHHSEKV 162
++ KRV V G G GC I AV +E V
Sbjct: 163 HQAGDLQGKRVFVSGVGPIGCLIVAAVKTLGAAEIV 198
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 28.8 bits (65), Expect = 5.5
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 53 DYLRSYAKKFDVYNHSI-FNTEVINLEQYED-IWEVELSNGKKK-KYDFIAVCNG--AQR 107
+ R+ A++ + NTEV +E+ D ++ + SNG++ + F+ G A
Sbjct: 154 ELTRALAEEAQANGVELRLNTEVTGIEKQSDGVFVLNTSNGEETLEAKFVINAAGLYADP 213
Query: 108 VAR 110
+A+
Sbjct: 214 LAQ 216
>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 = 6.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 134 IRNKRVLVVGAGNSGCDIA 152
++ K+VLV+GAG G A
Sbjct: 176 LKGKKVLVIGAGEMGELAA 194
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 28.6 bits (64), Expect = 6.8
Identities = 41/157 (26%), Positives = 61/157 (38%), Gaps = 19/157 (12%)
Query: 112 PNYSGYFSGEILHSMDYKSPDQIRNKRVLVVGAGNSGCDIAVDASHHSEKVYH-STRRGY 170
P +G+ + +H M I+ K V + G GN A A+ KV S GY
Sbjct: 204 PEATGFGALYFVHQMLETKGIDIKGKTVAISGFGNVAWGAATKATELGAKVVTISGPDGY 263
Query: 171 HYYPKFIDGKPTPQWMLQLGNKFSSKEETMAYIKQVFKLAGFDGVDYGLKKP-DHPLDAA 229
Y P I G+ +ML+L S + +A + F + F + KKP + +D A
Sbjct: 264 IYDPDGISGEKI-DYMLELRA---SGNDIVAPYAEKFPGSTF----FAGKKPWEQKVDIA 315
Query: 230 HPIMNSQILYHIGHGDILPKDDIKNLNGNIVHFVDDT 266
P L +G +D L N V V +
Sbjct: 316 LPCATQNEL----NG-----EDADKLIKNGVLCVAEV 343
>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 = 7.5
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 8/38 (21%)
Query: 119 SGEILHSMDYKSPDQ--------IRNKRVLVVGAGNSG 148
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 = 8.0
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 133 QIRNKRVLVVGAGNSGCDIAVDASHHSEKV 162
I V+V+G G +G A++A+ KV
Sbjct: 3 TIHEFDVVVIGGGGAGLRAAIEAAEAGLKV 32
>gnl|CDD|172756 PRK14268, PRK14268, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 258
Score = 28.0 bits (62), Expect = 8.8
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 87 ELSNGKKKKYDFIAVCNGAQRVARYPNYSGYF-SGEIL 123
+L KK Y + V + Q+ AR +Y+G+F GE++
Sbjct: 195 DLIMNLKKDYTIVIVTHNMQQAARISDYTGFFLMGELI 232
>gnl|CDD|222956 PHA02992, PHA02992, hypothetical protein; Provisional.
Length = 728
Score = 28.1 bits (63), Expect = 8.9
Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 16/75 (21%)
Query: 40 DNYPVYPNHSMMLDYLRSYAKKFDVYNHSIFNTEVINLEQYEDIWEVELSNGKKKKYDFI 99
D Y Y +L + VY + F+ I+L +Y D+ + EL
Sbjct: 250 DQYIPYAEE-----FLVDRKEDLGVYANIFFDDVAIDLTKY-DLTKTELEI--------- 294
Query: 100 AVCNGAQRVARYPNY 114
+C R Y +Y
Sbjct: 295 -ICKYIDRYEIYIDY 308
>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed.
Length = 581
Score = 28.1 bits (63), Expect = 9.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 139 VLVVGAGNSGCDIAVDASHHSEKV 162
VLV+G+G +G AV A+ H KV
Sbjct: 15 VLVIGSGAAGLSAAVTAAWHGLKV 38
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 27.9 bits (63), Expect = 9.2
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 12/83 (14%)
Query: 223 DHPLDAAHPIMNSQILYHIGHGDILPKDDIK----NLNGNIVHFV----DDTHIEVDTII 274
D L P ++ ++ + G + + K + V + IE D ++
Sbjct: 206 DRILPGEDPEISKELTKQLEKGGVKILLNTKVTAVEKKDDGVLVTLEDGEGGTIEADAVL 265
Query: 275 YATGYNRHFPFIDKEKLEWKLGI 297
A G R P D LE G+
Sbjct: 266 VAIG--RK-PNTDGLGLE-NAGV 284
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 28.2 bits (63), Expect = 9.4
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 132 DQIRNKRVLVVGAGNSG 148
+IR K VL+VGAG G
Sbjct: 20 RKIREKHVLIVGAGALG 36
>gnl|CDD|223651 COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 532
Score = 28.0 bits (63), Expect = 9.6
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 10/32 (31%)
Query: 139 VLVVGAGNSGCDIAVDASHHSEKVYHSTRRGY 170
V+V+G G +G IA DA+ RG
Sbjct: 15 VIVIGGGITGAGIARDAA----------GRGL 36
>gnl|CDD|235701 PRK06116, PRK06116, glutathione reductase; Validated.
Length = 450
Score = 27.8 bits (63), Expect = 10.0
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 248 PKDDIKNLNGNI-VHFVDDTHIEVDTIIYATG 278
PK KN +G++ + D + VD +I+A G
Sbjct: 231 PKAVEKNADGSLTLTLEDGETLTVDCLIWAIG 262
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
0.322 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: 21,376,401
Number of extensions: 2135517
Number of successful extensions: 2296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2285
Number of HSP's successfully gapped: 83
Length of query: 396
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 297
Effective length of database: 6,546,556
Effective search space: 1944327132
Effective search space used: 1944327132
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.9 bits)