RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy754
(610 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 421 bits (1085), Expect = e-141
Identities = 222/581 (38%), Positives = 303/581 (52%), Gaps = 62/581 (10%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAG---HYFNYLVDIPV-LNTNLILSPLN 98
EYD+II+GAG GC +ANRLSE P +LLLEAG + +++ + +P L L N
Sbjct: 5 EYDYIIIGAGSAGCVLANRLSEDPDVSVLLLEAGGPDYRWDFFIQMPAALAFPLQGKRYN 64
Query: 99 WGYKTEKEDCRACLGLKGQRCPWPSGKGVGGTSLINTMLYTRGNKRNYDDWAKL-GNYGW 157
W Y+TE E + +R P GK +GG+S IN M+Y RGN +YD+WA+L G GW
Sbjct: 65 WAYETEPEP-----HMNNRRMECPRGKVLGGSSSINGMVYIRGNAMDYDNWAELPGLEGW 119
Query: 158 SYNEVLPYFKKAERIQISELQNSSYHGTQGFIGVDY-TEYNTPMLDAFLQAGMEAGYPLV 216
SY + LPYFKKAE E Y G G + V P+ AF++AG++AGYP
Sbjct: 120 SYADCLPYFKKAETRDGGE---DDYRGGDGPLSVTRGKPGTNPLFQAFVEAGVQAGYPRT 176
Query: 217 -DYNGKTQTGFARAQATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTKKA 275
D NG Q GF T+ R S+A+ Y+DP KR NLT+ + +IL + K+A
Sbjct: 177 DDLNGYQQEGFGPMDRTVTNGRRWSAARAYLDPALKRPNLTIVTHALTDRILFEG--KRA 234
Query: 276 CGVLATIKGIDHKILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIPVIKNLR-VGE 334
GV G AR+EVILSAGA NSP+LL LSGIGP EHL +L IPV+ +L VGE
Sbjct: 235 VGVEYERGGGRETARARREVILSAGAINSPQLLQLSGIGPAEHLKELGIPVVHDLPGVGE 294
Query: 335 NLQEHLAMAGLTFLVNQPIGLLQDRLIKEMPKLFPQWYFEGKGKLTMLGC----EGLAYV 390
NLQ+HL + + + QP+ L PK+ +W F G G LG E ++
Sbjct: 295 NLQDHLEVY-IQYECKQPVSLYPALKWWNKPKIGAEWLFTGTG----LGASNHFEAGGFI 349
Query: 391 NTKYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNSVYSSVDRKDSWSIWPM 450
++ V D P+I++ F V++ DG ++ + G H + PM
Sbjct: 350 RSRAGV---DWPNIQYHFLPVAIRYDGSNAV-KGHGFQAH----------------VGPM 389
Query: 451 ILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSI-GST 509
SRG V LK + P P I N+ + +D + I++ E+ A G
Sbjct: 390 --RSPSRGSVKLKSADPRAHPSILFNYMSTEQDWREFRDAIRLTREIMAQPALDPYRGRE 447
Query: 510 LHKAPIPGCS-QYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGV 568
+ PG Q +D VR +H TCKMG D AVVDP+ +V+GV
Sbjct: 448 IS----PGADVQ----TDEEIDAFVREHAETAYHPSCTCKMGT--DPMAVVDPEGRVHGV 497
Query: 569 DNLRVVDASIIPVIPGGHTVAVVYMIAEKASDMIK-KTWLP 608
+ LRVVDASI+P I G+ A MIAEKA+D+I+ +T L
Sbjct: 498 EGLRVVDASIMPTITNGNLNAPTIMIAEKAADLIRGRTPLA 538
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 368 bits (947), Expect = e-121
Identities = 183/575 (31%), Positives = 287/575 (49%), Gaps = 51/575 (8%)
Query: 39 DLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAG-HYFNYLVDIPVLNTNLILSP- 96
++ +EYD++IVG+G G +A RLS+ +L+LEAG L+ +P L+ P
Sbjct: 3 EMKMEYDYVIVGSGSAGSVLAARLSDAGL-SVLVLEAGGPDRRPLIQMPAAYAFLMNGPR 61
Query: 97 LNWGYKTEKEDCRACLGLKGQRCPWPSGKGVGGTSLINTMLYTRGNKRNYDDWAKL-GNY 155
+WG++TE E L+G+ WP GK +GG+S IN M+Y RG+ ++D WA+ G
Sbjct: 62 YDWGFRTEPEP-----HLRGRELAWPRGKVLGGSSSINGMVYVRGHPEDFDAWAQESGAP 116
Query: 156 GWSYNEVLPYFKKAERIQISELQNSS-YHGTQGFIGVDYTEYNTPMLDAFLQAGMEAGYP 214
GW Y++VLPYFK+AE + Q+ +HG G + V P+ AF++AG + G+P
Sbjct: 117 GWPYDDVLPYFKRAEDLLGVGGQDLRTWHGGGGPLPVSPPRSPNPIARAFIEAGEQLGFP 176
Query: 215 LV-DYNGKTQTGFARAQATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTK 273
D NG Q GF T+ R S+A+ Y+ P KR NLT+ + V++IL++
Sbjct: 177 TTPDPNGADQEGFGPYCVTICNGRRWSAARAYLKPALKRPNLTLLTGARVRRILLEG--D 234
Query: 274 KACGVLATIK--GIDHKILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIP-VIKNL 330
+A GV I G +A +EV+L+AGA NSPKLL+LSGIGP +HL + I V +
Sbjct: 235 RAVGVEVEIGDGGTIETAVAAREVVLAAGAINSPKLLLLSGIGPADHLLEHGIDVVGRLP 294
Query: 331 RVGENLQEHLAMAGLTFLVNQPIGLLQDRLIKEMPKLFPQWYFEGKGKLTMLGCE-GLAY 389
VG+NLQ+HL + + F +P L ++ ++ G E G
Sbjct: 295 GVGQNLQDHLEI-YVAFEATEPTNDSVLSLFSKLGIGADRYLLTRDGPGATNHFEGGFVR 353
Query: 390 VNTKYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNSVYSSVDRKDSWSIWP 449
+ PD ++ F + LA + E G +++
Sbjct: 354 SGPAG-----EYPDGQYHFAPLPLAIR---AAGAEHG------------------FTLHV 387
Query: 450 MILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGST 509
+ P+SRG V L+ P P+I N+ + D + GI++ E+ A +
Sbjct: 388 GPMRPKSRGSVTLRSPDPDNRPVIDPNYLSAEGDRAIFRAGIRLTREIIGQPALDAR-RK 446
Query: 510 LHKAPIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGVD 569
AP P + +D ++R + +H GTC+MG ++ V DP L+V+G++
Sbjct: 447 AELAPGPRVT-----TDEDISAAIRFLARTAYHPMGTCRMG-SDPAAVVDDPYLRVHGLE 500
Query: 570 NLRVVDASIIPVIPGGHTVAVVYMIAEKASDMIKK 604
NLRVVDAS++P G + + +AE+A+D I
Sbjct: 501 NLRVVDASVMPTSTGVNPNLTIIALAERAADHILG 535
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 350 bits (899), Expect = e-114
Identities = 208/568 (36%), Positives = 284/568 (50%), Gaps = 50/568 (8%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAG---HYFNYLVDIPV-LNTNLILSPLNWG 100
D+II+G G G +A RLSE +L+LEAG + ++ L+ +P L NW
Sbjct: 1 DYIIIGGGSAGSVLAGRLSEDVSNSVLVLEAGGSDYPWDLLIQMPAALAYPAGNKRYNWI 60
Query: 101 YKTEKEDCRACLGLKGQRCPWPSGKGVGGTSLINTMLYTRGNKRNYDDWAK-LGNYGWSY 159
Y+TE E + +R GK +GG+S IN M+Y RGN +Y+ WAK G W Y
Sbjct: 61 YETEPEP-----HMNNRRVGHARGKVLGGSSSINGMIYQRGNPMDYEKWAKPEGMESWDY 115
Query: 160 NEVLPYFKKAERIQISELQNSSYHGTQGFIGVDYTEYNTPMLDAFLQAGMEAGYPLV-DY 218
+ LPY+K+ E E Y G G I V + P+ AF++AG+EAGY D
Sbjct: 116 ADCLPYYKRLETTFGGE---KPYRGHDGPIKVRRGPADNPLFQAFIEAGVEAGYNKTPDV 172
Query: 219 NGKTQTGFARAQATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTKKACGV 278
NG Q GF +T+H R S+A+ Y+ P KR NL V+ +FV KI + +A GV
Sbjct: 173 NGFRQEGFGPMDSTVHNGRRVSAARAYLHPAMKRPNLEVQTRAFVTKINFE--GNRATGV 230
Query: 279 LATIKGIDHKILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIPVIKNLR-VGENLQ 337
G A KEVILSAGA NSP+LL LSGIG EHL +L I +L VGENLQ
Sbjct: 231 EFKKGGRKEHTEANKEVILSAGAINSPQLLQLSGIGDAEHLRELGIEPRIHLPGVGENLQ 290
Query: 338 EHLAMAGLTFLVNQPIGLLQDRLIKEMPKLFPQWYFEGKGKLTMLGCEGLAYVNTKYNVF 397
+HL + + QP+ L + P + QW F KG EG +V + +V
Sbjct: 291 DHLEVY-VQHACKQPVSLYPSLNWLKQPFIGAQWLFGRKGAGASNHFEGGGFVRSNDDV- 348
Query: 398 PDDLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNSVYSSVDRKDSWSIWPMILYPRSR 457
D P+I++ F V++ DG + + G H + PM Y SR
Sbjct: 349 --DYPNIQYHFLPVAIRYDGTKAPK-AHGFQVH----------------VGPM--YSNSR 387
Query: 458 GKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGSTLHKAP--I 515
G V +K P P I N+ + D E I++ E+ K KA ++
Sbjct: 388 GHVKIKSKDPFEKPEIVFNYMSHEEDWREFREAIRVTREILKQKALD-----PYRGGEIS 442
Query: 516 PGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGVDNLRVVD 575
PG T + RH T L H CGTCKMGP D +VVDP+ +V+G++ LRVVD
Sbjct: 443 PGPEVQT--DEEIDEFVRRHGETAL-HPCGTCKMGPASDEMSVVDPETRVHGMEGLRVVD 499
Query: 576 ASIIPVIPGGHTVAVVYMIAEKASDMIK 603
ASI+P I G+ A V M+ EKA+D+I+
Sbjct: 500 ASIMPRITNGNLNAPVIMMGEKAADIIR 527
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 211 bits (538), Expect = 2e-61
Identities = 162/576 (28%), Positives = 241/576 (41%), Gaps = 109/576 (18%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYFNYLVDIPVLNTNLIL------SPLN 98
D ++VG G GC VA RLSE P + +LEAG + +P T+ + SP+
Sbjct: 2 DVLVVGGGSAGCVVAARLSEDPSCTVTVLEAGPGYRDPSRLPAQLTDGLRLPIGPASPVV 61
Query: 99 WGYKTEKEDCRACLGLKGQRCPWPSGKGVGGTSLINTMLYTRGNKRNYDDWAKLGNYGWS 158
W Y E D + G+ +GG+ +N + R ++D W G WS
Sbjct: 62 WRYGVELTD------GPRRASAIVRGRVLGGSGAVNGGYFCRALPADFDAWPIPG---WS 112
Query: 159 YNEVLPYFKKAERIQISELQ-NSSYHGTQGFIGVDYTEYNTPMLDAFLQAGMEAGYP-LV 216
+++VLP+F+ E +L + HGT G I V T + AF+ A + AG+ +
Sbjct: 113 WDDVLPHFRAIET----DLDFDGPLHGTAGPIPVRRTAELDGISAAFVAAALGAGFGWIA 168
Query: 217 DYNGKT---QTGFARAQATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTK 273
D NG TG + R S+A Y+ P KR NLTV+ + V +IL
Sbjct: 169 DLNGSGPDAPTGVGAVPLNVDGGRRVSTAVAYLLPALKRPNLTVEADTRVVRILFS--GT 226
Query: 274 KACGVLATIKGIDHKILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIPVIKNLRVG 333
+A GV + + L V+L AGA S LL+LSGIGP E L
Sbjct: 227 RAVGVEV-LGDGGPRTLRADRVVLCAGAVESAHLLLLSGIGPAEQLRA------------ 273
Query: 334 ENLQEHLAMAGLTFLVNQPIGL-LQDRLIKEMPKLFPQWYFEGKGKLTMLGCEGLAYVNT 392
AG+ +++ P+G D P+W L Y
Sbjct: 274 ---------AGIAVVLDLPVGSDFVDH---------PEW--------------VLPYRWR 301
Query: 393 KYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNSVYSSVDRKDSWSIWPMI- 451
+ PD P +E + + +R Y + ++++ S P +
Sbjct: 302 PTHDRPDTSPVLETVLNT------ADIEIRP--------YTAGFTAL-VPGSPRDDPHLG 346
Query: 452 ---LYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGS 508
+ P SRG++ L + P PP I + + D + G +A EL
Sbjct: 347 VALMRPHSRGRIRLASADPADPPRIEHRYDSSAADRAALRAGAALAHELLG--------- 397
Query: 509 TLHKAPIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGV 568
P +A W + R T+Q H CG+C+MG R D AVVD + +V GV
Sbjct: 398 --SPELGPLLEPAVREGEASWVLA-RLATSQ--HLCGSCRMGGRDDPGAVVDARCRVRGV 452
Query: 569 DNLRVVDASIIPVIP--GGHTVAVVYMIAEKASDMI 602
+ L VVD SI+PVIP G H AV M+AE+A++ +
Sbjct: 453 EGLWVVDGSILPVIPSRGPHATAV--MVAERAAEFL 486
>gnl|CDD|218493 pfam05199, GMC_oxred_C, GMC oxidoreductase. This domain found
associated with pfam00732.
Length = 139
Score = 166 bits (423), Expect = 5e-49
Identities = 52/145 (35%), Positives = 71/145 (48%), Gaps = 6/145 (4%)
Query: 454 PRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAFQSIGSTLHKA 513
PRSRG+V L S PL P+I N+ +D DL + +++A + L
Sbjct: 1 PRSRGRVTLSSSDPLGLPVIDPNYLSDPADLAALRAALRLARRILAAA-----LVELTPG 55
Query: 514 PIPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSSAVVDPQLKVYGVDNLRV 573
P+ SD +R H GTC+MG VVDP L+V+GVDNLRV
Sbjct: 56 PVEVVPGAAEASDDEILEYIRAAAVTSWHPMGTCRMGAD-PDDGVVDPDLRVHGVDNLRV 114
Query: 574 VDASIIPVIPGGHTVAVVYMIAEKA 598
VDAS+ P P G+ +Y +AE+A
Sbjct: 115 VDASVFPSSPSGNPTLTIYALAERA 139
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 160 bits (406), Expect = 2e-45
Identities = 74/234 (31%), Positives = 104/234 (44%), Gaps = 39/234 (16%)
Query: 116 GQRCPWPSGKGVGGTSLINTMLYTRGNKRNYDDWAKL-GNYGWSYNEVLPYFKKAERIQI 174
G+R P+G VGG S +N R D+WA G GW Y++ LPY K E
Sbjct: 16 GRRMILPAGSTVGGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE---- 71
Query: 175 SELQNSSYHGTQGFIGVDYT-EYNTPMLDAFLQAGMEAGYPLV----DYNGKTQTGFARA 229
G +GV +P+ A L+A E GYP+ + NG GF
Sbjct: 72 ------------GPLGVTTKGIEESPLNQALLKAAEELGYPVEAVPRNSNGCHYCGFCGL 119
Query: 230 QATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTKKACGVLATIK--GIDH 287
+ S+A+ ++ P +R NL + + +KI+I +A GV A GI
Sbjct: 120 GCPTGAKQ--STARTWLRPALER-NLRILTGAKAEKIIILGRGGRAVGVEARDGGGGIKR 176
Query: 288 KILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIPVIKNLRVGENLQEHLA 341
I A KEV+++AGA N+P LL+ SG+G H VG+NLQ H
Sbjct: 177 LITAAKEVVVAAGALNTPPLLLRSGLGKNPH------------PVGKNLQLHPV 218
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 79.1 bits (195), Expect = 2e-15
Identities = 83/318 (26%), Positives = 128/318 (40%), Gaps = 74/318 (23%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYFNYLVDIPVLNTNLILSPLNWGYKT 103
YD+I+VG G GC +A LS+ ++ +LLLE G +P N N+
Sbjct: 56 YDYIVVGGGTAGCPLAATLSQ--NFSVLLLERG-------GVPFGNANVSFL-------- 98
Query: 104 EKEDCRACLGLKGQRCP---WPSGKGV--------GGTSLINTMLYTRGNKRNYDDWAKL 152
E+ L + S GV GG + IN Y+R + R
Sbjct: 99 --ENFHIGLADTSPTSASQAFISTDGVINARARVLGGGTCINAGFYSRASTRFIQK---- 152
Query: 153 GNYGWSYNEVLPYFKKAERIQISELQNSSYHGTQGFIGVDY---TEYNTPMLDAFLQAGM 209
GW ++L N SY + I V + + + D+ L+ G+
Sbjct: 153 --AGWD----------------AKLVNESYPWVERQI-VHWPKVAPWQAALRDSLLEVGV 193
Query: 210 EAGYPLVDYNGKTQTGF--ARAQATLHKRS-RRSSAKDYIDPIKKRCNLTVKDSSFVKKI 266
+NG T + T+ RR +A + + L V + V+KI
Sbjct: 194 SP------FNGFTYDHVYGTKVGGTIFDEFGRRHTAAELLAAGNPN-KLRVLLHATVQKI 246
Query: 267 LIDPVTK--KACGVLATIK--GIDHKILARK---EVILSAGAFNSPKLLMLSGIGPQEHL 319
+ D K +A GV+ + L+ E+ILSAGA SP++L+LSGIGP++ L
Sbjct: 247 VFDTSGKRPRATGVIFKDENGNQHQAFLSNNKGSEIILSAGAIGSPQMLLLSGIGPKKEL 306
Query: 320 NDLNIPVI-KNLRVGENL 336
IPV+ N VG+ +
Sbjct: 307 KKHKIPVVLHNEHVGKGM 324
Score = 59.0 bits (143), Expect = 4e-09
Identities = 46/158 (29%), Positives = 65/158 (41%), Gaps = 24/158 (15%)
Query: 451 ILYPRSRGKVLLKDSHPLTPPLIHANFFNDTRDLDVIVEGIKMAIELSKTKAF----QSI 506
I P S G + L +++ P + N+F +DL V GI+ ++ KT F Q
Sbjct: 421 IAGPISTGHLSLINTNVDDNPSVTFNYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCD 480
Query: 507 GSTLHKAP----------IPGCSQYTFGSDAYWGCSVRHITTQLHHQCGTCKMGPRWDSS 556
T+ K IP + T + + C IT +H G C +G
Sbjct: 481 KQTMEKVLNMSVKANINLIPKHTNDTKSLEQF--CKDTVITIWHYH--GGCHVG------ 530
Query: 557 AVVDPQLKVYGVDNLRVVDASIIPVIPGGHTVAVVYMI 594
VVD KV GV LRV+D S PG + A V M+
Sbjct: 531 KVVDQNYKVLGVSRLRVIDGSTFDESPGTNPQATVMMM 568
>gnl|CDD|233671 TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase,
UbiH/UbiF/VisC/COQ6 family. This model represents a
family of FAD-dependent hydroxylases (monooxygenases)
which are all believed to act in the aerobic ubiquinone
biosynthesis pathway. A separate set of hydroxylases,
as yet undiscovered, are believed to be active under
anaerobic conditions. In E. coli three enzyme
activities have been described, UbiB (which acts first
at position 6, see TIGR01982), UbiH (which acts at
position 4,) and UbiF (which acts at position 5,). UbiH
and UbiF are similar to one another and form the basis
of this subfamily. Interestingly, E. coli contains
another hydroxylase gene, called visC, that is highly
similar to UbiF, adjacent to UbiH and, when mutated,
results in a phenotype similar to that of UbiH (which
has also been named visB). Several other species appear
to have three homologs in this family, although they
assort themselves differently on phylogenetic trees
(e.g. Xylella and Mesorhizobium) making it difficult to
ascribe a specific activity to each one. Eukaryotes
appear to have only a single homolog in this subfamily
(COQ6,) which complements UbiH, but also possess a
non-orthologous gene, COQ7 which complements UbiF
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 387
Score = 41.8 bits (99), Expect = 8e-04
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAG 76
D +IVG GP G +A L+ K+ L+EA
Sbjct: 1 DIVIVGGGPVGLALALALARSGGLKVALIEAT 32
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 40.3 bits (95), Expect = 0.003
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEI-PHWKILLLE 74
+YD +I+G G G A LSE P + LLE
Sbjct: 3 DYDVVIIGGGIMGAATAYELSEYEPDLSVALLE 35
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 35.9 bits (84), Expect = 0.004
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 48 IVGAGPGGCTVANRLSEIPHWKILLLEAGHYF 79
IVGAG G A L++ +L+LE
Sbjct: 1 IVGAGLSGLVAAYLLAKR-GKDVLVLEKRDRI 31
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 38.6 bits (90), Expect = 0.009
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYFNYLVDIPVLNTNLI 93
EYD +IVGAGP G + A RL++ +L+LE G +
Sbjct: 3 EYDVVIVGAGPAGSSAARRLAKA-GLDVLVLEKGSEPGA----KPCCGGGL 48
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 38.3 bits (90), Expect = 0.010
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYF 79
EYD +++GAGP G A R +++ K+ L+E G
Sbjct: 4 EYDVVVIGAGPAGYVAAIRAAQL-GLKVALVEKGERL 39
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and
related FAD-dependent oxidoreductases [Coenzyme
metabolism / Energy production and conversion].
Length = 387
Score = 37.8 bits (88), Expect = 0.015
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
D IVGAGP G +A L+ + LLE
Sbjct: 3 LDVAIVGAGPAGLALALALARAGL-DVTLLER 33
>gnl|CDD|233693 TIGR02032, GG-red-SF, geranylgeranyl reductase family. This
model represents a subfamily which includes
geranylgeranyl reductases involved in chlorophyll and
bacteriochlorophyll biosynthesis as well as other
related enzymes which may also act on geranylgeranyl
groups or related substrates [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 295
Score = 37.3 bits (87), Expect = 0.017
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
YD ++VGAGP G + A RL++ ++LLLE
Sbjct: 1 YDVVVVGAGPAGASAAYRLADKGL-RVLLLE 30
>gnl|CDD|224534 COG1619, LdcA, Uncharacterized proteins, homologs of microcin C7
resistance protein MccF [Defense mechanisms].
Length = 313
Score = 36.5 bits (85), Expect = 0.034
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 7/60 (11%)
Query: 274 KACGVLATIKGIDHKILARKEVILSAGAFNSPKLLMLSGIGPQEHLNDLNIPVIKNLRVG 333
K G+L + GI IL R S L + ++ LNIPVI L G
Sbjct: 230 KLAGILEKVSGI---ILGRFTKCTPNEYDPSYTLEEVL----RDLALSLNIPVIYGLDFG 282
>gnl|CDD|233669 TIGR01984, UbiH, 2-polyprenyl-6-methoxyphenol 4-hydroxylase.
This model represents the FAD-dependent monoxygenase
responsible for the second hydroxylation step in the
aerobic ubiquinone bioynthetic pathway. The scope of
this model is limited to the proteobacteria. This
family is closely related to the UbiF hydroxylase which
catalyzes the final hydroxylation step. The enzyme has
also been named VisB due to a mutant VISible light
sensitive phenotype [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 382
Score = 36.5 bits (85), Expect = 0.037
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
D IIVG G G ++A LS + KI L+EA
Sbjct: 1 DVIIVGGGLVGLSLALALSRLGKIKIALIEA 31
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 36.7 bits (86), Expect = 0.038
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 42 LEYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHY 78
+YD I++GAGP G A R +++ K+ L+E G
Sbjct: 2 EKYDVIVIGAGPAGYVAARRAAKLGK-KVALIEKGPL 37
>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 = 34.6 bits (80), Expect = 0.11
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAGH 77
D +++G G G + A L+ + LLE G
Sbjct: 1 DVVVIGGGIVGLSTAYELAR-RGLSVTLLERGD 32
>gnl|CDD|218770 pfam05834, Lycopene_cycl, Lycopene cyclase protein. This family
consists of lycopene beta and epsilon cyclase proteins.
Carotenoids with cyclic end groups are essential
components of the photosynthetic membranes in all
plants, algae, and cyanobacteria. These lipid-soluble
compounds protect against photo-oxidation, harvest
light for photosynthesis, and dissipate excess light
energy absorbed by the antenna pigments. The
cyclisation of lycopene (psi, psi-carotene) is a key
branch point in the pathway of carotenoid biosynthesis.
Two types of cyclic end groups are found in higher
plant carotenoids: the beta and epsilon rings.
Carotenoids with two beta rings are ubiquitous, and
those with one beta and one epsilon ring are common;
however, carotenoids with two epsilon rings are rare.
Length = 374
Score = 35.0 bits (81), Expect = 0.11
Identities = 15/33 (45%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 45 DFIIVGAGPGGCTVANRLSEI-PHWKILLLEAG 76
D +IVGAG G +A RL + P ++LL++AG
Sbjct: 1 DLVIVGAGLAGLLLALRLRQARPGLRVLLIDAG 33
>gnl|CDD|235905 PRK06996, PRK06996, hypothetical protein; Provisional.
Length = 398
Score = 35.0 bits (81), Expect = 0.12
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 43 EYDFIIVGAGPGGCTVAN---RLSEIPHWKILLLEA 75
++D IVGAGP G +A R S I L++A
Sbjct: 11 DFDIAIVGAGPVGLALAGWLARRSATRALSIALIDA 46
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 34.9 bits (81), Expect = 0.12
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 21/85 (24%)
Query: 10 VNEFDYAVKSYIEDG------IFEQLEYKSSNKDQDLLLEYDFIIVGAGPGG----CTVA 59
E+ + +K+ +ED + E E S +D LL +IVG GP G +A
Sbjct: 119 AAEYAFGLKT-LEDALRLRRHLLEAFEKASQEEDDRALL--TIVIVGGGPTGVELAGELA 175
Query: 60 NRLSEI--------PHWKILLLEAG 76
RL + +++L+EAG
Sbjct: 176 ERLHRLLKKFRVDPSELRVILVEAG 200
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 34.4 bits (80), Expect = 0.18
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGH 77
YD I++GAG G +A R + + K+ L+E G
Sbjct: 6 YDAIVIGAGQAGPPLAARAAGL-GMKVALIERGL 38
>gnl|CDD|224550 COG1635, THI4, Ribulose 1,5-bisphosphate synthetase, converts
PRPP to RuBP, flavoprotein [Carbohydrate transport
and metabolism].
Length = 262
Score = 33.8 bits (78), Expect = 0.19
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 36 KDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYF 79
+D LE D IIVGAGP G T A L++ K+ + E F
Sbjct: 23 EDLLDYLESDVIIVGAGPSGLTAAYYLAK-AGLKVAIFERKLSF 65
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 31.3 bits (71), Expect = 0.19
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 14/54 (25%)
Query: 373 FEGKGKLTMLGCEGLAYVNTKYNVFPDDLPDIEFIFTAVSLASDGGVSLRQEMG 426
FE GK C+G A+V D +IEF A+ G +LR E G
Sbjct: 33 FEDSGK-----CKGFAFV---------DFEEIEFATNALKGKHLNGRALRVEYG 72
>gnl|CDD|145231 pfam01946, Thi4, Thi4 family. This family includes a putative
thiamine biosynthetic enzyme.
Length = 229
Score = 33.6 bits (77), Expect = 0.20
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 32 KSSNKDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLEA-----------GHYFN 80
+ +D E D +IVGAGP G T A L++ K+ ++E G F+
Sbjct: 6 ERYFEDLLDYAESDVVIVGAGPSGLTAAYYLAK-KGLKVAIIERSLSPGGGAWGGGMLFS 64
Query: 81 YLV 83
+V
Sbjct: 65 AMV 67
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 34.1 bits (78), Expect = 0.20
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEAGH 77
+ D +I+G G G + A L+E + +LEAG
Sbjct: 4 KMDVVIIGGGIVGLSAAYYLAER-GADVTVLEAGE 37
>gnl|CDD|232908 TIGR00292, TIGR00292, thiazole biosynthesis enzyme. This enzyme
is involved in the biosynthesis of the thiamine
precursor thiazole, and is repressed by thiamine. This
family includes c-thi1, a Citrus gene induced during
natural and ethylene induced fruit maturation and is
highly homologous to plant and yeast thi genes involved
in thiamine biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Thiamine].
Length = 254
Score = 33.7 bits (77), Expect = 0.21
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 32 KSSNKDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLE-----------AGHYFN 80
+ +D E D IIVGAGP G T A L++ K+ +LE G F+
Sbjct: 10 ERYFEDLLDYAESDVIIVGAGPSGLTAAYYLAK-NGLKVCVLERSLAFGGGSWGGGMLFS 68
Query: 81 YLV 83
+V
Sbjct: 69 KIV 71
>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 = 33.5 bits (77), Expect = 0.24
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYFNYLV 83
D +I+G GP G A RL+ K+ L+E Y
Sbjct: 1 DVVIIGGGPAGLAAAIRLAR-LGLKVALIEREGGTCYNR 38
>gnl|CDD|178082 PLN02463, PLN02463, lycopene beta cyclase.
Length = 447
Score = 33.9 bits (78), Expect = 0.24
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 27 EQLEYKSSNKDQDLLLEYDFIIVGAGPGGCTVANRLSE 64
E L+++ D D ++VG GP G VA ++SE
Sbjct: 12 ENLDFELPRFDPSKSRVVDLVVVGGGPAGLAVAQQVSE 49
>gnl|CDD|240384 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
Length = 567
Score = 34.1 bits (78), Expect = 0.24
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 20 YIEDGIFEQLEYKSSNKDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
+ + I +L +K + + D YD IIVG G +A LS+ K+L+LE
Sbjct: 14 LLLNRILSRLRFKPARTNYD----YDVIIVGGSIAGPVLAKALSKQGR-KVLMLE 63
>gnl|CDD|233672 TIGR01989, COQ6, ubiquinone biosynthesis monooxygenase COQ6.
This model represents the monooxygenase responsible for
the 4-hydroxylateion of the phenol ring in the aerobic
biosynthesis of ubiquinone.
Length = 437
Score = 34.0 bits (78), Expect = 0.26
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHW---KILLLEAG 76
+D +IVG GP G +A L P K+LLL+A
Sbjct: 1 FDVVIVGGGPVGLALAAALGNNPLTKDLKVLLLDAV 36
>gnl|CDD|178267 PLN02661, PLN02661, Putative thiazole synthesis.
Length = 357
Score = 33.6 bits (77), Expect = 0.30
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 36 KDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
D + D +IVGAG G + A LS+ P+ K+ ++E
Sbjct: 85 TDMITYADTDVVIVGAGSAGLSCAYELSKNPNVKVAIIE 123
>gnl|CDD|130850 TIGR01790, carotene-cycl, lycopene cyclase family protein. This
family includes lycopene beta and epsilion cyclases
(which form beta and delta carotene, respectively) from
bacteria and plants as well as the plant
capsanthin/capsorubin and neoxanthin cyclases which
appear to have evolved from the plant lycopene
cyclases. The plant lycopene epsilon cyclases also
transform neurosporene to alpha zeacarotene.
Length = 388
Score = 33.2 bits (76), Expect = 0.35
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAG 76
D ++G GP G +A L+ P ++ L+E
Sbjct: 1 DLAVIGGGPAGLAIALELAR-PGLRVQLIEPH 31
>gnl|CDD|130849 TIGR01789, lycopene_cycl, lycopene cyclase. This model
represents a family of bacterial lycopene cyclases
catalyzing the transformation of lycopene to carotene.
These enzymes are found in a limited spectrum of alpha
and gamma proteobacteria as well as Flavobacterium.
Length = 370
Score = 32.9 bits (75), Expect = 0.51
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 45 DFIIVGAGPGGCTVANRLSEI-PHWKILLLEAG 76
D IIVG G G +A RL P ++I ++EAG
Sbjct: 1 DCIIVGGGLAGGLIALRLQRARPDFRIRVIEAG 33
>gnl|CDD|235241 PRK04176, PRK04176, ribulose-1,5-biphosphate synthetase;
Provisional.
Length = 257
Score = 32.5 bits (75), Expect = 0.58
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 42 LEYDFIIVGAGPGGCTVANRLSE 64
LE D IVGAGP G T A L++
Sbjct: 24 LEVDVAIVGAGPSGLTAAYYLAK 46
>gnl|CDD|223636 COG0562, Glf, UDP-galactopyranose mutase [Cell envelope
biogenesis, outer membrane].
Length = 374
Score = 32.3 bits (74), Expect = 0.74
Identities = 10/32 (31%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
+D++IVGAG G +A +++ ++L++E
Sbjct: 2 FDYLIVGAGLSGAVIAEVAAQLGK-RVLIVEK 32
>gnl|CDD|183292 PRK11728, PRK11728, hydroxyglutarate oxidase; Provisional.
Length = 393
Score = 32.1 bits (74), Expect = 0.79
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 44 YDFIIVGAGPGGCTVANRLSE-IPHWKILLLE 74
YDF+I+G G G + A +L E P +I +LE
Sbjct: 3 YDFVIIGGGIVGLSTAMQLQERYPGARIAVLE 34
>gnl|CDD|236223 PRK08294, PRK08294, phenol 2-monooxygenase; Provisional.
Length = 634
Score = 31.9 bits (73), Expect = 1.2
Identities = 16/32 (50%), Positives = 20/32 (62%)
Query: 35 NKDQDLLLEYDFIIVGAGPGGCTVANRLSEIP 66
N+ DL E D +IVG GP G T+A +LS P
Sbjct: 24 NRPADLPDEVDVLIVGCGPAGLTLAAQLSAFP 55
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 31.4 bits (71), Expect = 1.6
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 8/66 (12%)
Query: 46 FIIVGAGPGGCTVANRL-SEIPHWKILLLEAG---HY----FNYLVDIPVLNTNLILSPL 97
+IVG G G + A L + +I L+ Y + V + + + P
Sbjct: 1 IVIVGGGAAGLSAATTLRRLLLAAEITLIGREPKYSYYRCPLSLYVGGGIASLEDLRYPP 60
Query: 98 NWGYKT 103
+ T
Sbjct: 61 RFNRAT 66
>gnl|CDD|240421 PTZ00445, PTZ00445, p36-lilke protein; Provisional.
Length = 219
Score = 30.8 bits (70), Expect = 1.6
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 5 SLSINVNEFDYAVKSYIEDGIFEQLEYKSS-NKDQDLLLE---------YDFIIVGAGPG 54
+ +F A K YIE G+F+ L S +K DLL E +D ++ G
Sbjct: 1 MPTSAQKKFHDAFKEYIESGLFDHLNPHESADKFVDLLNECGIKVIASDFDLTMITKHSG 60
Query: 55 G 55
G
Sbjct: 61 G 61
>gnl|CDD|222355 pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide
oxidoreductase.
Length = 202
Score = 30.7 bits (70), Expect = 1.7
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 47 IIVGAGPGGCTVANRLSEIPHWKILLLEAGH 77
++VGAG G A+ L ++ +++++ G
Sbjct: 1 LVVGAGAAGMAFADHLLDLGDAPVIIVDRGA 31
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 30.6 bits (70), Expect = 2.3
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 272 TKKACGVLATIKGIDHKILARKEVILSAGAF 302
+ GV A G I ARK V+L+AG F
Sbjct: 208 DGRVVGVEARRYGETVAIRARKGVVLAAGGF 238
>gnl|CDD|178530 PLN02942, PLN02942, dihydropyrimidinase.
Length = 486
Score = 30.6 bits (69), Expect = 2.4
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 557 AVVDPQLKVYGVDNLRVVDASIIPVIPGG---HT-VAVVYMIAEKASD 600
V P LKV D++RV+DA+ V+PGG HT +A+ +M E D
Sbjct: 33 VAVAPNLKV--PDDVRVIDATGKFVMPGGIDPHTHLAMPFMGTETIDD 78
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family
includes members that bind FAD. This family includes
the flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 30.7 bits (70), Expect = 2.5
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPHWKILLLEAGHYFN 80
D +++G+G G A +E K+ ++E G F
Sbjct: 1 DVVVIGSGLAGLAAALEAAEAGL-KVAVVEKGQPFG 35
>gnl|CDD|217220 pfam02771, Acyl-CoA_dh_N, Acyl-CoA dehydrogenase, N-terminal
domain. The N-terminal domain of Acyl-CoA dehydrogenase
is an all-alpha domain.
Length = 113
Score = 29.0 bits (66), Expect = 2.6
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 574 VDASIIPVIPGGHTVAVVYMIAEKASDMIKKTWLP 608
DAS+ + H+ V I ++ K+ +LP
Sbjct: 74 ADASV-GLALSVHSSLVAPPILRFGTEEQKEKYLP 107
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and
conversion].
Length = 562
Score = 30.8 bits (70), Expect = 2.6
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 42 LEYDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
E+D +++G G G A +E K+ LL
Sbjct: 5 HEFDVVVIGGGGAGLRAAIEAAEAGL-KVALLS 36
>gnl|CDD|225307 COG2509, COG2509, Uncharacterized FAD-dependent dehydrogenases
[General function prediction only].
Length = 486
Score = 30.4 bits (69), Expect = 3.0
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 32 KSSNKDQD--LLLEYDFIIVGAGPGGCTVANRLSE----IPHWKILLLEAGH 77
+ DQ+ + D +IVGAGP G A LS +P KI +++ G
Sbjct: 5 LPIDHDQEALMNAALDVVIVGAGPAGLFAAYELSGDARKVPILKIYVVDVGL 56
>gnl|CDD|223566 COG0492, TrxB, Thioredoxin reductase [Posttranslational
modification, protein turnover, chaperones].
Length = 305
Score = 30.3 bits (69), Expect = 3.1
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 44 YDFIIVGAGPGGCTVA 59
YD II+G GP G T A
Sbjct: 4 YDVIIIGGGPAGLTAA 19
>gnl|CDD|217064 pfam02487, CLN3, CLN3 protein. This is a family of proteins from
the CLN3 gene. A missense mutation of glutamic acid (E)
to lysine (K) at position 295 in the human protein has
been implicated in Juvenile neuronal ceroid
lipofuscinosis (Batten disease).
Length = 409
Score = 30.2 bits (68), Expect = 3.4
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 8/59 (13%)
Query: 373 FEGKGKLTMLGCEGLAYVNTKYNVFPDDLPDI-EFIFTAVSLASDGGVSLRQEMGITDH 430
FEG +LG G +YVNT +N+ + PD+ EF A S++ GV+L + + H
Sbjct: 351 FEG-----LLG--GASYVNTFHNIHKEVDPDVREFAMGAASISDSLGVNLAALLALPLH 402
>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed.
Length = 581
Score = 30.5 bits (69), Expect = 3.4
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 15/127 (11%)
Query: 274 KACGVLATIKGIDHKILARKEVILSAGAF--NSPKLLMLSGIGPQEHLNDLNIPVIKN-- 329
+ G + G +I ARK V+L+AG F + + L P H + L++P N
Sbjct: 249 RVAGAVVETPGGLQEIRARKGVVLAAGGFPHDPARRAALFPRAPTGHEH-LSLPPPGNSG 307
Query: 330 --LRVGENLQEHLAMAGLTFLVNQPIGLLQDRLIKEM---PKLFPQWYFEGKGKLTMLGC 384
LR+GE+ A + + P+ L+ FP GK L +
Sbjct: 308 DGLRLGES-----AGGVVATDLASPVAWAPVSLVPHADGSVGHFPHIIERGKPGLIGVLA 362
Query: 385 EGLAYVN 391
G +VN
Sbjct: 363 NGKRFVN 369
>gnl|CDD|235798 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
Length = 462
Score = 30.1 bits (69), Expect = 3.6
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 43 EYDFIIVGAGPGGCTVANRLSE 64
EYD I++GAGPGG A R ++
Sbjct: 4 EYDVIVIGAGPGGYVAAIRAAQ 25
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 30.1 bits (69), Expect = 3.7
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 48 IVGAGPGGCTVANRL 62
++GAGP G T A+RL
Sbjct: 145 VIGAGPAGLTAAHRL 159
>gnl|CDD|233689 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model
represents a group of geranylgeranyl reductases
specific for the biosyntheses of bacteriochlorophyll
and chlorophyll. It is unclear whether the processes of
isoprenoid ligation to the chlorin ring and reduction
of the geranylgeranyl chain to a phytyl chain are
necessarily ordered the same way in all species (see
introduction to ) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 388
Score = 30.1 bits (68), Expect = 3.7
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILL 72
YD ++G GP G T A L+ ILL
Sbjct: 1 YDVAVIGGGPSGATAAETLARAGIETILL 29
>gnl|CDD|130488 TIGR01421, gluta_reduc_1, glutathione-disulfide reductase,
animal/bacterial. The tripeptide glutathione is an
important reductant, e.g., for maintaining the cellular
thiol/disulfide status and for protecting against
reactive oxygen species such as hydrogen peroxide.
Glutathione-disulfide reductase regenerates reduced
glutathione from oxidized glutathione (glutathione
disulfide) + NADPH. This model represents one of two
closely related subfamilies of glutathione-disulfide
reductase. Both are closely related to trypanothione
reductase, and separate models are built so each of the
three can describe proteins with conserved function.
This model describes glutathione-disulfide reductases
of animals, yeast, and a number of animal-resident
bacteria [Energy metabolism, Electron transport].
Length = 450
Score = 30.2 bits (68), Expect = 3.7
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
YD++++G G GG A R +E K LL+EA
Sbjct: 2 HYDYLVIGGGSGGIASARRAAEHGA-KALLVEA 33
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the
E3 component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to
have distinct functions (ferric leghemoglobin reductase
and NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 29.9 bits (68), Expect = 3.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 43 EYDFIIVGAGPGGCTVANRL 62
YD I++G GPGG A R
Sbjct: 1 AYDVIVIGGGPGGYVAAIRA 20
>gnl|CDD|232791 TIGR00031, UDP-GALP_mutase, UDP-galactopyranose mutase. This
enzyme is involved in the conversion of UDP-GALP into
UDP-GALF through a 2-keto intermediate. It contains FAD
as a cofactor. The gene is known as glf, ceoA, and
rfbD. It is known experimentally in E. coli,
Mycobacterium tuberculosis, and Klebsiella pneumoniae
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 377
Score = 30.1 bits (68), Expect = 4.0
Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
+D+IIVGAG G +AN L+++ ++L++E
Sbjct: 2 FDYIIVGAGLSGIVLANILAQLNK-RVLVVE 31
>gnl|CDD|185420 PTZ00058, PTZ00058, glutathione reductase; Provisional.
Length = 561
Score = 30.0 bits (67), Expect = 4.1
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 31 YKSSNKDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
+ + YD I++G G GG A R + K+ L+E
Sbjct: 40 HLKKKPR----MVYDLIVIGGGSGGMAAARRAARNK-AKVALVE 78
>gnl|CDD|215362 PLN02676, PLN02676, polyamine oxidase.
Length = 487
Score = 30.1 bits (68), Expect = 4.2
Identities = 16/29 (55%), Positives = 18/29 (62%)
Query: 47 IIVGAGPGGCTVANRLSEIPHWKILLLEA 75
IIVGAG G + A LSE IL+LEA
Sbjct: 30 IIVGAGMSGISAAKTLSEAGIEDILILEA 58
>gnl|CDD|235584 PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 395
Score = 29.8 bits (68), Expect = 4.6
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPH--WKILLLEA 75
D IIVG G G T+A LS + H + L+EA
Sbjct: 4 MDVIIVGGGMAGATLALALSRLSHGGLPVALIEA 37
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 28.7 bits (65), Expect = 4.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 48 IVGAGPGGCTVANRLSE 64
I+GAGP G +V RL
Sbjct: 2 IIGAGPRGLSVLERLLR 18
>gnl|CDD|236001 PRK07364, PRK07364, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 415
Score = 29.6 bits (67), Expect = 5.0
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 33 SSNKDQDLLLEYDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
S L YD IVG G G T+A L + +I L+EA
Sbjct: 8 SPTLPSTRSLTYDVAIVGGGIVGLTLAAALKD-SGLRIALIEA 49
>gnl|CDD|179162 PRK00910, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase;
Provisional.
Length = 218
Score = 29.2 bits (65), Expect = 5.1
Identities = 19/66 (28%), Positives = 29/66 (43%)
Query: 215 LVDYNGKTQTGFARAQATLHKRSRRSSAKDYIDPIKKRCNLTVKDSSFVKKILIDPVTKK 274
+V+ N QT F + H + SA+D + IK N K + + P+ +
Sbjct: 85 VVNNNSANQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRAR 144
Query: 275 ACGVLA 280
A GVLA
Sbjct: 145 AGGVLA 150
>gnl|CDD|224983 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 29.3 bits (66), Expect = 6.2
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 11/47 (23%)
Query: 44 YDFIIVGAGPGGCTVANRLSE--IPHWKILLLEAG-------HYFNY 81
D I+GAG G A L + +P ++ E Y Y
Sbjct: 9 TDVAIIGAGQSGLAAAYALKQAGVP--DFVIFEKRDDVGGTWRYNRY 53
>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 = 29.0 bits (66), Expect = 6.6
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 44 YDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
YD I +G GP ++A L EIP + L E
Sbjct: 3 YDLIGIGIGPFNLSLAALLEEIPELRALFFER 34
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 28.8 bits (65), Expect = 6.8
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 45 DFIIVGAGPGGCTVANRLSEIPH 67
II+GAG G +VA LSE H
Sbjct: 2 KIIIIGAGRVGRSVARELSEEGH 24
>gnl|CDD|183139 PRK11445, PRK11445, putative oxidoreductase; Provisional.
Length = 351
Score = 29.3 bits (66), Expect = 7.3
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLE 74
YD I+G GP G +A L+ K++ ++
Sbjct: 1 HYDVAIIGLGPAGSALARLLAG--KMKVIAID 30
>gnl|CDD|128502 smart00206, NTR, Tissue inhibitor of metalloproteinase family.
Form complexes with metalloproteinases, such as
collagenases, and irreversibly inactivate them.
Length = 172
Score = 28.2 bits (63), Expect = 7.8
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 398 PDDLPDIEFIFTAVSLASDGGVSLR----QEMGITDHLYN 433
D L DI FI+T S S G L +E I L +
Sbjct: 50 FDKLGDIRFIYTPAS-ESLCGYKLESQNKEEYLIAGRLED 88
>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 = 7.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 43 EYDFIIVGAGPGGCTVANRLSE 64
E D +IVG GP G +A L+
Sbjct: 1 ETDVLIVGGGPAGLMLALLLAR 22
>gnl|CDD|183983 PRK13339, PRK13339, malate:quinone oxidoreductase; Reviewed.
Length = 497
Score = 28.9 bits (65), Expect = 8.4
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 45 DFIIVGAGPGGCTVANRLSEI-PHWKILLLE 74
D ++VGAG T L E+ P W I ++E
Sbjct: 8 DVVLVGAGILSTTFGVLLKELDPDWNIEVVE 38
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 28.8 bits (65), Expect = 8.8
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 46 FIIVGAGPGGCTVANRLSE-IPHWKILLLEAG 76
I+G G G + A RL + P ++ L EA
Sbjct: 3 IAIIGGGIAGLSAAYRLQKAGPDVEVTLFEAD 34
>gnl|CDD|180409 PRK06115, PRK06115, dihydrolipoamide dehydrogenase; Reviewed.
Length = 466
Score = 29.0 bits (65), Expect = 8.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 43 EYDFIIVGAGPGGCTVANR 61
YD +I+G GPGG A R
Sbjct: 3 SYDVVIIGGGPGGYNAAIR 21
>gnl|CDD|233412 TIGR01438, TGR, thioredoxin and glutathione reductase
selenoprotein. This homodimeric, FAD-containing member
of the pyridine nucleotide disulfide oxidoreductase
family contains a C-terminal motif Cys-SeCys-Gly, where
SeCys is selenocysteine encoded by TGA (in some
sequence reports interpreted as a stop codon). In some
members of this subfamily, Cys-SeCys-Gly is replaced by
Cys-Cys-Gly. The reach of the selenium atom at the
C-term arm of the protein is proposed to allow broad
substrate specificity.
Length = 484
Score = 29.0 bits (65), Expect = 9.4
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 43 EYDFIIVGAGPGGCTVANRLSEIPHWKILLLEA 75
+YD I++G G GG A + K++LL+
Sbjct: 2 DYDLIVIGGGSGGLAAAKEAAAYGA-KVMLLDF 33
>gnl|CDD|143651 cd07935, RHD-n_NFkB1, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa B1 (NF-kappa
B1). Proteins containing the Rel homology domain (RHD)
are metazoan transcription factors. The RHD is composed
of two structural sub-domains; this model characterizes
the N-terminal RHD sub-domain of the NF-kappa B1 family
of transcription factors, a class I member of the
NF-kappa B family. In class I NF-kappa Bs, the RHD
domain co-occurs with C-terminal ankyrin repeats.
NF-kappa B1 is commonly referred to as p105 or p50
(proteolytically processed form). NF-kappa B proteins
are part of a protein complex that acts as a
transcription factor, which is responsible for
regulating a host of cellular responses to a variety of
stimuli. This complex tightly regulates the expression
of a large number of genes, and is involved in processes
such as adaptive and innate immunity, stress response,
inflammation, cell adhesion, proliferation and
apoptosis. The cytosolic NF-kappa B complex is activated
via phosphorylation of the ankyrin-repeat containing
inhibitory protein I-kappa B, which dissociates from the
complex and exposes the nuclear localization signal of
the heterodimer (NF-kappa B and REL). NF-kappa B1 is
involved in the canonical NF-kappa B signaling pathway
which is activated by many agonists and is essential in
immune and inflammatory responses, as well as cell
survival. p105 is involved in its own specific NF-kappa
B signaling pathway which is also implicated in immune
and inflammatory responses. p105 may also act as an
I-kappa B due to its C-terminal ankyrin repeats. It is
also involved in mitogen-activated protein kinase (MAPK)
signaling as its degradation leads to the activation of
TPL-2, a MAPK kinase kinase which activates ERK
pathways.
Length = 202
Score = 28.3 bits (63), Expect = 9.4
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 400 DLPDIEFIFTAVSLASDGGVSLRQEMGITDHLYNS 434
DL + +FTA S GG + R E ++D +Y+S
Sbjct: 167 DLSVVRLMFTAFLPDSTGGFTRRLEPVVSDAIYDS 201
>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 575
Score = 28.9 bits (65), Expect = 9.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 41 LLEYDFIIVGAGPGGCTVA 59
+LE+D +IVG G GC A
Sbjct: 1 MLEHDVVIVGGGLAGCRAA 19
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.422
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,342,925
Number of extensions: 3085076
Number of successful extensions: 2699
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2658
Number of HSP's successfully gapped: 91
Length of query: 610
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 507
Effective length of database: 6,369,140
Effective search space: 3229153980
Effective search space used: 3229153980
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: 62 (27.8 bits)