RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11001
(81 letters)
>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 159 bits (404), Expect = 1e-48
Identities = 53/73 (72%), Positives = 59/73 (80%)
Query: 1 FTGRVCPAPCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGS 60
FTGRVCPAPCEGAC L IN VTIKNIE IID AFE+GW+KP+ P RTGKKVA+VGS
Sbjct: 92 FTGRVCPAPCEGACTLNINFGPVTIKNIERYIIDKAFEEGWVKPDPPVKRTGKKVAVVGS 151
Query: 61 GPSGLGAAHQLNK 73
GP+GL AA QL +
Sbjct: 152 GPAGLAAADQLAR 164
>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 = 136 bits (344), Expect = 4e-40
Identities = 50/73 (68%), Positives = 60/73 (82%)
Query: 1 FTGRVCPAPCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGS 60
FTGRVCPAPCEGAC LGI+E V IK+IE IID F++GW++P P+ RTGKKVA+VGS
Sbjct: 92 FTGRVCPAPCEGACTLGISEDPVGIKSIERIIIDKGFQEGWVQPRPPSKRTGKKVAVVGS 151
Query: 61 GPSGLGAAHQLNK 73
GP+GL AA QLN+
Sbjct: 152 GPAGLAAADQLNR 164
>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 = 109 bits (275), Expect = 4e-30
Identities = 43/76 (56%), Positives = 52/76 (68%), Gaps = 2/76 (2%)
Query: 1 FTGRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIV 58
TGRVCP CEGACVLGI E V I +E AI D A +GWI E+P RTGKKVA++
Sbjct: 70 ITGRVCPLGNLCEGACVLGIEELPVNIGALERAIGDKADREGWIPGELPGSRTGKKVAVI 129
Query: 59 GSGPSGLGAAHQLNKE 74
G+GP+GL AA L++
Sbjct: 130 GAGPAGLAAADDLSRA 145
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 94.1 bits (235), Expect = 2e-24
Identities = 36/72 (50%), Positives = 45/72 (62%), Gaps = 3/72 (4%)
Query: 2 TGRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVG 59
GRVCP CEGACV G V I +E I D A E GW+ + +TGKKVA++G
Sbjct: 89 CGRVCPQERLCEGACVRGKKGEPVAIGRLERYITDWAMETGWVLFKRAP-KTGKKVAVIG 147
Query: 60 SGPSGLGAAHQL 71
+GP+GL AAH+L
Sbjct: 148 AGPAGLTAAHRL 159
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 84.9 bits (211), Expect = 4e-21
Identities = 32/71 (45%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 3 GRVCPAPCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGSGP 62
GRVC PCE C G + AV I +E + D+A GW K P TGK+VA++G GP
Sbjct: 89 GRVCYHPCESGCNRGQVDDAVGINAVERFLGDYAIANGW-KFPAPAPDTGKRVAVIGGGP 147
Query: 63 SGLGAAHQLNK 73
+GL AA+ L +
Sbjct: 148 AGLSAAYHLRR 158
>gnl|CDD|130385 TIGR01318, gltD_gamma_fam, glutamate synthase small subunit family
protein, proteobacterial. This model represents one of
three built for the NADPH-dependent or NADH-dependent
glutamate synthase (EC 1.4.1.13 and 1.4.1.14,
respectively) small subunit and homologs. TIGR01317
describes the small subunit (or equivalent region from
longer forms) in eukaryotes, Gram-positive bacteria, and
some other lineages, both NADH and NADPH-dependent.
TIGR01316 describes a protein of similar length, from
Archaea and a number of bacterial lineages, that forms
glutamate synthase homotetramers without a large
subunit. This model describes both glutatate synthase
small subunit and closely related paralogs of unknown
function from a number of gamma and alpha subdivision
Proteobacteria, including E. coli.
Length = 467
Score = 79.1 bits (195), Expect = 4e-19
Identities = 37/82 (45%), Positives = 51/82 (62%), Gaps = 5/82 (6%)
Query: 2 TGRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIP-TLRTGKKVAIV 58
GRVCP CEGAC L AVTI N+E I D A GW +P++ + TGK+VA++
Sbjct: 89 CGRVCPQDRLCEGACTLNDEFGAVTIGNLERYITDTALAMGW-RPDLSHVVPTGKRVAVI 147
Query: 59 GSGPSGLGAAHQLNKEAGTELI 80
G+GP+GL A L + AG +++
Sbjct: 148 GAGPAGLACADILAR-AGVQVV 168
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 72.9 bits (179), Expect = 7e-17
Identities = 36/73 (49%), Positives = 46/73 (63%), Gaps = 4/73 (5%)
Query: 2 TGRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLR-TGKKVAIV 58
TGRVCP CEGAC L AVTI NIE I D A +GW +P++ + + K+VAI+
Sbjct: 275 TGRVCPQDRLCEGACTLRDEYGAVTIGNIERYISDQALAKGW-RPDLSQVTKSDKRVAII 333
Query: 59 GSGPSGLGAAHQL 71
G+GP+GL A L
Sbjct: 334 GAGPAGLACADVL 346
>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
Length = 464
Score = 68.5 bits (168), Expect = 2e-15
Identities = 35/74 (47%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 2 TGRVCP--APCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVG 59
GRVCP + CEG CVLGI V I +E + D A E G I + GKKVA++G
Sbjct: 89 CGRVCPQESQCEGKCVLGIKGEPVAIGKLERFVADWARENG-IDLSETEEKKGKKVAVIG 147
Query: 60 SGPSGLGAAHQLNK 73
SGP+GL A L K
Sbjct: 148 SGPAGLTCAGDLAK 161
Score = 25.4 bits (56), Expect = 4.1
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 43 KPEIPT-LRTGKKVAIVGSGPSGLGAA 68
KPE T ++ GKKVA+VG G + AA
Sbjct: 271 KPEYDTPIKVGKKVAVVGGGNVAMDAA 297
>gnl|CDD|139246 PRK12814, PRK12814, putative NADPH-dependent glutamate synthase
small subunit; Provisional.
Length = 652
Score = 62.1 bits (151), Expect = 4e-13
Identities = 35/74 (47%), Positives = 48/74 (64%), Gaps = 10/74 (13%)
Query: 3 GRVCPAPCEGACVL-GINEPAVTIKNIECAIIDHAFEQGWIKPE--IPTLR--TGKKVAI 57
GR+CPAPCE AC G++EP V+I CA+ +A ++ E IP +GKKVAI
Sbjct: 144 GRICPAPCEEACRRHGVDEP-VSI----CALKRYAADRDMESAERYIPERAPKSGKKVAI 198
Query: 58 VGSGPSGLGAAHQL 71
+G+GP+GL AA+ L
Sbjct: 199 IGAGPAGLTAAYYL 212
>gnl|CDD|237200 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta;
Provisional.
Length = 752
Score = 62.1 bits (151), Expect = 5e-13
Identities = 32/77 (41%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 2 TGRVCP--APCEGACVLGI-NEPAVTIKNIECAIIDHAFEQGWIKPEIPTL--RTGKKVA 56
GRVCP CE C+ G E AV I +E + D+ E G +P + + GKKVA
Sbjct: 378 CGRVCPQEKQCESKCIHGKMGEEAVAIGYLERFVADYERESG--NISVPEVAEKNGKKVA 435
Query: 57 IVGSGPSGLGAAHQLNK 73
++GSGP+GL A L K
Sbjct: 436 VIGSGPAGLSFAGDLAK 452
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 57.3 bits (138), Expect = 2e-11
Identities = 35/80 (43%), Positives = 49/80 (61%), Gaps = 5/80 (6%)
Query: 3 GRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGK-KVAIVG 59
GRVCP CEGAC L + AV+I N+E I D A GW +P++ + KVA++G
Sbjct: 259 GRVCPQDRLCEGACTLKDHSGAVSIGNLERYITDTALAMGW-RPDVSKVVPRSEKVAVIG 317
Query: 60 SGPSGLGAAHQLNKEAGTEL 79
+GP+GLG A L + AG ++
Sbjct: 318 AGPAGLGCADILAR-AGVQV 336
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 56.7 bits (137), Expect = 4e-11
Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 3 GRVCPAPCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIK-PEIPTLRTGKKVAIVGSG 61
GRVC CE C +G + I+ ++ I+D+ + + + + + KKVAIVGSG
Sbjct: 233 GRVCTHKCETVCSIGHRGEPIAIRWLKRYIVDNVPVEKYSEILDDEPEKKNKKVAIVGSG 292
Query: 62 PSGLGAAHQLNK 73
P+GL AA+ L
Sbjct: 293 PAGLSAAYFLAT 304
>gnl|CDD|130383 TIGR01316, gltA, glutamate synthase (NADPH), homotetrameric. This
protein is homologous to the small subunit of NADPH and
NADH forms of glutamate synthase as found in eukaryotes
and some bacteria. This protein is found in numerous
species having no homolog of the glutamate synthase
large subunit. The prototype of the family, from
Pyrococcus sp. KOD1, was shown to be active as a
homotetramer and to require NADPH [Amino acid
biosynthesis, Glutamate family].
Length = 449
Score = 55.3 bits (133), Expect = 1e-10
Identities = 28/78 (35%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 2 TGRVCPAP--CEGACVLGINEP----AVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKV 55
GRVCP CEG C +G V+I +E + D + G T KKV
Sbjct: 77 CGRVCPQERQCEGQCTVGKMFKDVGKPVSIGALERFVADWERQHGIETEPEKAPSTHKKV 136
Query: 56 AIVGSGPSGLGAAHQLNK 73
A++G+GP+GL A +L K
Sbjct: 137 AVIGAGPAGLACASELAK 154
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 47.3 bits (113), Expect = 7e-08
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 2 TGRVCPAPCEGACVLGINEPAVTIKNIECAIIDHA---FEQGWIKPEIPTLRTGKKVAIV 58
TG +C C+ C + AV I+ ++ ++ ++Q W KP + + KKVA++
Sbjct: 488 TGHICDHQCQYNCTRLDYDEAVNIRELKKVALEKGWDEYKQRWHKP--AGIGSRKKVAVI 545
Query: 59 GSGPSGLGAAHQLNKE 74
G+GP+GL AA+ L +
Sbjct: 546 GAGPAGLAAAYFLARA 561
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 44.5 bits (105), Expect = 6e-07
Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 3 GRVCP--APCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGS 60
GRVCP CE C++ +V I +E + D+A + P + KVAI GS
Sbjct: 381 GRVCPQETQCEAQCIIAKKHESVGIGRLERFVGDNARAKPVKPPRFS--KKLGKVAICGS 438
Query: 61 GPSGLGAAHQLNK 73
GP+GL AA L K
Sbjct: 439 GPAGLAAAADLVK 451
>gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit.
Members of this protein family are YgfK, predicted to be
one subunit of a three-subunit, molybdopterin-containing
selenate reductase. This enzyme is found, typically, in
genomic regions associated with xanthine dehydrogenase
homologs predicted to belong to the selenium-dependent
molybdenum hydroxylases (SDMH). Therefore, the selenate
reductase is suggested to play a role in furnishing
selenide for SelD, the selenophosphate synthase.
Length = 1012
Score = 40.5 bits (95), Expect = 1e-05
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 2 TGRVCPAPCEGACVLGINEPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGK-KVAIVGS 60
TG +C C+ C + +V I+ ++ + +++ + P ++ KVA++G+
Sbjct: 486 TGTICDHQCQYKCTRLDYDESVNIREMKKVAAEKGYDEYKTRWHKPQGKSSAHKVAVIGA 545
Query: 61 GPSGLGAAHQLNKE 74
GP+GL A + L +
Sbjct: 546 GPAGLSAGYFLARA 559
>gnl|CDD|237197 PRK12770, PRK12770, putative glutamate synthase subunit beta;
Provisional.
Length = 352
Score = 39.6 bits (93), Expect = 3e-05
Identities = 14/19 (73%), Positives = 17/19 (89%)
Query: 50 RTGKKVAIVGSGPSGLGAA 68
TGKKVAI+G+GP+GL AA
Sbjct: 16 PTGKKVAIIGAGPAGLAAA 34
Score = 25.3 bits (56), Expect = 4.3
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 35 HAFEQGWI-KPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKE 74
A + G++ ++P + GKKV +VG+G + + AA +
Sbjct: 155 RAAKLGYLPWEKVPPVE-GKKVVVVGAGLTAVDAALEAVLL 194
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 36.2 bits (84), Expect = 5e-04
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKEAGT 77
K+AI+G G +GL AA++L K
Sbjct: 1 MKIAIIGGGIAGLSAAYRLQKAGPD 25
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 36.0 bits (84), Expect = 6e-04
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 54 KVAIVGSGPSGLGAAHQLNK 73
K+AIVG G +GL AA++L K
Sbjct: 1 KIAIVGGGIAGLAAAYRLAK 20
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 35.3 bits (82), Expect = 0.001
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 17 GINEPAVTIKNIECAI-----IDHAFEQGWIKPEIPTLRTGKKVAIVGSGPSGL------ 65
G E A +K +E A+ + AFE+ + + L T + IVG GP+G+
Sbjct: 118 GAAEYAFGLKTLEDALRLRRHLLEAFEKASQEEDDRALLT---IVIVGGGPTGVELAGEL 174
Query: 66 -GAAHQLNKEAGTELIK 81
H+L K+ + +
Sbjct: 175 AERLHRLLKKFRVDPSE 191
Score = 25.3 bits (56), Expect = 4.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 53 KKVAIVGSGPSGLGAAHQL 71
K++ I+G G GL AA +L
Sbjct: 4 KRIVILGGGFGGLSAAKRL 22
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 35.2 bits (81), Expect = 0.001
Identities = 26/88 (29%), Positives = 34/88 (38%), Gaps = 23/88 (26%)
Query: 2 TGRVCPAP--CEGACVLGINEPAVTIKNIECAIIDHAFEQG-------------WIKPEI 46
TGRVCP C+G C + + I +E + H W
Sbjct: 249 TGRVCPQELQCQGVCTH--TKRPIEIGQLEWYLPQHEKLVNPNANERFAGRISPWAAAVK 306
Query: 47 PTLRTGKKVAIVGSGPSGLGAAHQLNKE 74
P +A+VGSGPSGL A+ L E
Sbjct: 307 P------PIAVVGSGPSGLINAYLLAVE 328
>gnl|CDD|224983 COG2072, TrkA, Predicted flavoprotein involved in K+ transport
[Inorganic ion transport and metabolism].
Length = 443
Score = 35.1 bits (81), Expect = 0.001
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 47 PTLRTGKKVAIVGSGPSGLGAAHQLNKE 74
+ T VAI+G+G SGL AA+ L +
Sbjct: 3 VGVATHTDVAIIGAGQSGLAAAYALKQA 30
Score = 26.3 bits (58), Expect = 2.0
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGT 77
GK+V ++G+G S + A +L + +
Sbjct: 174 RGKRVLVIGAGASAVDIAPELAEVGAS 200
>gnl|CDD|235241 PRK04176, PRK04176, ribulose-1,5-biphosphate synthetase;
Provisional.
Length = 257
Score = 34.4 bits (80), Expect = 0.002
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
VAIVG+GPSGL AA+ L K
Sbjct: 28 VAIVGAGPSGLTAAYYLAKA 47
>gnl|CDD|178144 PLN02529, PLN02529, lysine-specific histone demethylase 1.
Length = 738
Score = 32.9 bits (75), Expect = 0.008
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 44 PEIPTLRTGKKVAIVGSGPSGLGAAHQL 71
IP T V IVG+G +GL AA QL
Sbjct: 152 SPIPEEGTEGSVIIVGAGLAGLAAARQL 179
>gnl|CDD|235967 PRK07208, PRK07208, hypothetical protein; Provisional.
Length = 479
Score = 32.9 bits (76), Expect = 0.008
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKE 74
K V I+G+GP+GL AA++L K
Sbjct: 5 KSVVIIGAGPAGLTAAYELLKR 26
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 30.9 bits (71), Expect = 0.012
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 57 IVGSGPSGLGAAHQLNKE 74
IVG+G SGL AA+ L K
Sbjct: 1 IVGAGLSGLVAAYLLAKR 18
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 32.5 bits (74), Expect = 0.012
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNKE 74
KK+ +VG+GP+GL AA L ++
Sbjct: 693 RKKIIVVGAGPAGLTAARHLQRQ 715
>gnl|CDD|236198 PRK08243, PRK08243, 4-hydroxybenzoate 3-monooxygenase; Validated.
Length = 392
Score = 32.5 bits (75), Expect = 0.012
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQLNKEAGTE 78
+RT +VAI+G+GP+GL L+ AG +
Sbjct: 1 MRT--QVAIIGAGPAGLLLGQLLHL-AGID 27
>gnl|CDD|178578 PLN03000, PLN03000, amine oxidase.
Length = 881
Score = 32.3 bits (73), Expect = 0.013
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 42 IKPEIPTLRTGKKVAIVGSGPSGLGAAHQL 71
IK + P + V IVG+G SGL AA QL
Sbjct: 174 IKDKFPAQSSKSSVVIVGAGLSGLAAARQL 203
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 31.4 bits (72), Expect = 0.018
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 56 AIVGSGPSGLGAAHQL 71
AI+G+GP GL +L
Sbjct: 1 AIIGAGPRGLSVLERL 16
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 32.0 bits (73), Expect = 0.018
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 55 VAIVGSGPSGLGAAHQLNKEAG 76
V IVG+GP+G AA +L +AG
Sbjct: 6 VVIVGAGPAGSSAARRL-AKAG 26
>gnl|CDD|224550 COG1635, THI4, Ribulose 1,5-bisphosphate synthetase, converts
PRPP to RuBP, flavoprotein [Carbohydrate transport
and metabolism].
Length = 262
Score = 31.5 bits (72), Expect = 0.023
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
V IVG+GPSGL AA+ L K
Sbjct: 33 VIIVGAGPSGLTAAYYLAKA 52
>gnl|CDD|215314 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 31.5 bits (72), Expect = 0.025
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
K VA+VG+G SGL AA+ L + G ++
Sbjct: 12 SKDVAVVGAGVSGLAAAYALASKHGVNVL 40
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 31.4 bits (72), Expect = 0.027
Identities = 13/21 (61%), Positives = 18/21 (85%)
Query: 53 KKVAIVGSGPSGLGAAHQLNK 73
KKVAI+G G +GL AA++L+K
Sbjct: 1 KKVAIIGGGITGLSAAYRLHK 21
>gnl|CDD|236223 PRK08294, PRK08294, phenol 2-monooxygenase; Provisional.
Length = 634
Score = 30.7 bits (70), Expect = 0.045
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 55 VAIVGSGPSGLGAAHQL 71
V IVG GP+GL A QL
Sbjct: 35 VLIVGCGPAGLTLAAQL 51
>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 = 30.6 bits (70), Expect = 0.047
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 46 IPTLRTGKKVAIVGSGPSG 64
P L GK++ +VG G S
Sbjct: 179 KPRLLAGKRITVVGGGQSA 197
>gnl|CDD|145231 pfam01946, Thi4, Thi4 family. This family includes a putative
thiamine biosynthetic enzyme.
Length = 229
Score = 30.5 bits (69), Expect = 0.049
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
V IVG+GPSGL AA+ L K+
Sbjct: 20 VVIVGAGPSGLTAAYYLAKK 39
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 30.4 bits (69), Expect = 0.052
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 53 KKVAIVGSGPSGLGAAHQL 71
KVAI+G G SG+ A L
Sbjct: 2 FKVAIIGGGFSGIYMAAHL 20
>gnl|CDD|225915 COG3380, COG3380, Predicted NAD/FAD-dependent oxidoreductase
[General function prediction only].
Length = 331
Score = 30.5 bits (69), Expect = 0.058
Identities = 14/24 (58%), Positives = 19/24 (79%), Gaps = 1/24 (4%)
Query: 55 VAIVGSGPSGLGAAHQLNKEAGTE 78
+AIVG+G +GL AA+ L +EAG E
Sbjct: 4 IAIVGAGIAGLAAAYAL-REAGRE 26
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 30.5 bits (69), Expect = 0.060
Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKEAGTELI 80
+VAI G+G +GL AA++L +AG ++
Sbjct: 1 MRVAIAGAGLAGLAAAYEL-ADAGYDVT 27
>gnl|CDD|235874 PRK06847, PRK06847, hypothetical protein; Provisional.
Length = 375
Score = 30.2 bits (69), Expect = 0.065
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKE 74
KKV IVG G GL AA L +
Sbjct: 5 KKVLIVGGGIGGLSAAIALRRA 26
>gnl|CDD|235727 PRK06183, mhpA, 3-(3-hydroxyphenyl)propionate hydroxylase;
Validated.
Length = 500
Score = 30.3 bits (69), Expect = 0.070
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 55 VAIVGSGPSGLGAAHQL 71
V IVG+GP GL A+ L
Sbjct: 13 VVIVGAGPVGLTLANLL 29
>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 = 29.8 bits (67), Expect = 0.084
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
V IVG+GPSGL AA+ L K
Sbjct: 24 VIIVGAGPSGLTAAYYLAKN 43
>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 = 30.0 bits (68), Expect = 0.099
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 55 VAIVGSGPSGLGAAHQL 71
V IVG GP+GL A L
Sbjct: 4 VLIVGGGPAGLMLALLL 20
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and
related FAD-dependent oxidoreductases [Coenzyme
metabolism / Energy production and conversion].
Length = 387
Score = 29.7 bits (67), Expect = 0.10
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEAG 76
VAIVG+GP+GL A L AG
Sbjct: 4 DVAIVGAGPAGLALALAL-ARAG 25
>gnl|CDD|223566 COG0492, TrxB, Thioredoxin reductase [Posttranslational
modification, protein turnover, chaperones].
Length = 305
Score = 29.6 bits (67), Expect = 0.11
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 54 KVAIVGSGPSGLGAA 68
V I+G GP+GL AA
Sbjct: 5 DVIIIGGGPAGLTAA 19
>gnl|CDD|176242 cd08282, PFDH_like, Pseudomonas putida aldehyde-dismutating
formaldehyde dehydrogenase (PFDH). Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Unlike typical FDH, Pseudomonas putida
aldehyde-dismutating FDH (PFDH) is
glutathione-independent. PFDH converts 2 molecules of
aldehydes to corresponding carboxylic acid and alcohol.
MDH family uses NAD(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like the zinc-dependent alcohol dehydrogenases (ADH) of
the medium chain alcohol dehydrogenase/reductase family
(MDR), these tetrameric FDHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains
and a structural zinc in a lobe of the catalytic domain.
Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in
FDH is a tightly bound redox cofactor (similar to
nicotinamide proteins). The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of an beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 375
Score = 29.5 bits (67), Expect = 0.13
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 37 FEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAH 69
F GW E+ ++ G VA+ G+GP GL AA+
Sbjct: 162 FPTGWHGLELAGVQPGDTVAVFGAGPVGLMAAY 194
>gnl|CDD|215116 PLN02172, PLN02172, flavin-containing monooxygenase FMO GS-OX.
Length = 461
Score = 29.4 bits (66), Expect = 0.14
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGT 77
+ VA++G+G +GL AA +L +E T
Sbjct: 9 NSQHVAVIGAGAAGLVAARELRREGHT 35
>gnl|CDD|225459 COG2907, COG2907, Predicted NAD/FAD-binding protein [General
function prediction only].
Length = 447
Score = 29.4 bits (66), Expect = 0.15
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEA 75
K+A++GSG SGL AA L++
Sbjct: 10 KIAVIGSGISGLSAAWLLSRRH 31
>gnl|CDD|176184 cd05281, TDH, Threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via NAD(H)-
dependent oxidation. THD is a member of the
zinc-requiring, medium chain NAD(H)-dependent alcohol
dehydrogenase family (MDR). MDRs have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The N-terminal region typically
has an all-beta catalytic domain. These proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria) and have 2 tightly bound
zinc atoms per subunit. Sorbitol and aldose reductase
are NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose.
Length = 341
Score = 29.1 bits (66), Expect = 0.17
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
+GK V I G GP GL A + K AG L+
Sbjct: 163 SGKSVLITGCGPIGLMAI-AVAKAAGASLV 191
>gnl|CDD|213540 TIGR00562, proto_IX_ox, protoporphyrinogen oxidase. This enzyme
oxidizes protoporphyrinogen IX to protoporphyrin IX, a
precursor of heme and chlorophyll. Bacillus subtilis
HemY also has coproporphyrinogen III to coproporphyrin
III oxidase activity in a heterologous expression
system, although the role for this activity in vivo is
unclear. This protein is a flavoprotein and has a
beta-alpha-beta dinucleotide binding motif near the
amino end [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 462
Score = 29.0 bits (65), Expect = 0.19
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKE---AGTELI 80
K V I+G G SGL AA+ L KE EL
Sbjct: 3 KHVVIIGGGISGLCAAYYLEKEIPELPVELT 33
>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 = 29.0 bits (65), Expect = 0.22
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEAGTELI 80
+VAI+G+GPSGL L+K AG + +
Sbjct: 4 QVAIIGAGPSGLLLGQLLHK-AGIDNV 29
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase
[Cell envelope biogenesis, outer membrane].
Length = 448
Score = 28.8 bits (65), Expect = 0.24
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKE 74
GKKV ++G G SGL AA L K
Sbjct: 6 QGKKVLVLGLGKSGLAAARFLLKL 29
>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 = 28.9 bits (65), Expect = 0.25
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 51 TGKKVAIVGSGPSGLGAA 68
GK VA++G G SG+ AA
Sbjct: 351 KGKDVAVIGGGNSGIEAA 368
>gnl|CDD|178082 PLN02463, PLN02463, lycopene beta cyclase.
Length = 447
Score = 28.5 bits (64), Expect = 0.26
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 45 EIPTLRTGKK----VAIVGSGPSGLGAAHQLNKE 74
E+P K + +VG GP+GL A Q+++
Sbjct: 17 ELPRFDPSKSRVVDLVVVGGGPAGLAVAQQVSEA 50
>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 = 28.4 bits (64), Expect = 0.28
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 54 KVAIVGSGPSGLGAA 68
V I+G+GP+GL AA
Sbjct: 1 DVIIIGAGPAGLTAA 15
>gnl|CDD|222355 pfam13738, Pyr_redox_3, Pyridine nucleotide-disulphide
oxidoreductase.
Length = 202
Score = 28.4 bits (64), Expect = 0.28
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 56 AIVGSGPSGLGAAHQLNKEAGTELI 80
+VG+G +G+ A L +I
Sbjct: 1 LVVGAGAAGMAFADHLLDLGDAPVI 25
Score = 25.3 bits (56), Expect = 3.9
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 47 PTLRTGKKVAIVGSGPSGLGAA 68
GK VA++G G + + AA
Sbjct: 161 RIDLKGKTVAVIGGGHTAIDAA 182
>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 = 28.5 bits (64), Expect = 0.31
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 54 KVAIVGSGPSGLGAAHQL 71
V I+G GP+GL AA +L
Sbjct: 1 DVVIIGGGPAGLAAAIRL 18
Score = 25.8 bits (57), Expect = 2.3
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 52 GKKVAIVGSGPSGL---GAAHQLNKE 74
K+V +VG G GL A +L KE
Sbjct: 142 PKRVVVVGGGYIGLELAAALAKLGKE 167
>gnl|CDD|238939 cd01981, Pchlide_reductase_B, Pchlide_reductase_B: B protein of the
NB protein complex of Protochlorophyllide
(Pchlide)_reductase. Pchlide reductase catalyzes the
reductive formation of chlorophyllide (chlide) from
protochlorophyllide (pchlide) during biosynthesis of
chlorophylls and bacteriochlorophylls. This group
contains both the light-independent Pchlide reductase
(DPOR) and light-dependent Pchlide reductase (LPOR).
Angiosperms contain only LPOR, cyanobacteria, algae and
gymnosperms contain both DPOR and LPOR, primitive
anoxygenic photosynthetic bacteria contain only DPOR. NB
is structurally similar to the FeMo protein of
nitrogenase, forming an N2B2 heterotetramer. N and B are
homologous to the FeMo alpha and beta subunits
respectively. Also in common with nitrogenase in vitro
DPOR activity requires ATP hydrolysis and dithoionite or
ferredoxin as electron donor. The NB protein complex may
serve as a catalytic site for Pchlide reduction similar
to MoFe for nitrogen reduction.
Length = 430
Score = 28.1 bits (63), Expect = 0.35
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
TGK+ + G A L +E G ++
Sbjct: 300 TGKRAFVFGDATHVAAATRILAREMGFRVV 329
>gnl|CDD|182134 PRK09897, PRK09897, hypothetical protein; Provisional.
Length = 534
Score = 28.2 bits (63), Expect = 0.36
Identities = 9/13 (69%), Positives = 13/13 (100%)
Query: 53 KKVAIVGSGPSGL 65
KK+AIVG+GP+G+
Sbjct: 2 KKIAIVGAGPTGI 14
>gnl|CDD|224154 COG1233, COG1233, Phytoene dehydrogenase and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 487
Score = 28.2 bits (63), Expect = 0.37
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 51 TGKKVAIVGSGPSGLGAAHQL 71
V ++G+G +GL AA L
Sbjct: 2 PMYDVVVIGAGLNGLAAAALL 22
>gnl|CDD|240658 cd12181, ceo_syn, N(5)-(carboxyethyl)ornithine synthase.
N(5)-(carboxyethyl)ornithine synthase (ceo_syn)
catalyzes the NADP-dependent conversion of
N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine +
pyruvate. Ornithine plays a key role in the urea cycle,
which in mammals is used in arginine biosynthesis, and
is a precursor in polyamine synthesis. ceo_syn is
related to the NAD-dependent L-alanine dehydrogenases.
Like formate dehydrogenase and related enzymes, ceo_syn
is comprised of 2 domains connected by a long alpha
helical stretch, each resembling a Rossmann fold
NAD-binding domain. The NAD-binding domain is inserted
within the linear sequence of the more divergent
catalytic domain. These ceo_syn proteins have a
partially conserved NAD-binding motif and active site
residues that are characteristic of related enzymes such
as Saccharopine Dehydrogenase.
Length = 295
Score = 28.0 bits (63), Expect = 0.41
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 29 ECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNK 73
A++ HA + I P KVA++G G + GA L
Sbjct: 137 YAAVL-HALQLYGITP-----YRQTKVAVLGFGNTARGAIRALKL 175
>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 = 28.0 bits (63), Expect = 0.46
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 54 KVAIVGSGPSGLGAAHQL 71
V ++G G GL A++L
Sbjct: 1 DVVVIGGGIVGLSTAYEL 18
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 28.0 bits (63), Expect = 0.46
Identities = 12/25 (48%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 47 PTLRTGKKVAIVGSGPSGLGAAHQL 71
T T V IVG GP GL A L
Sbjct: 4 NTSET--PVLIVGGGPVGLALALDL 26
>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
This group is related to formaldehyde dehydrogenase
(FDH), which is a member of the zinc-dependent/medium
chain alcohol dehydrogenase family. This family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. Another member is identified
as a dihydroxyacetone reductase. Like the zinc-dependent
alcohol dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), tetrameric FDHs
have a catalytic zinc that resides between the catalytic
and NAD(H)binding domains and a structural zinc in a
lobe of the catalytic domain. Unlike ADH, where
NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly
bound redox cofactor (similar to nicotinamide proteins).
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 28.0 bits (63), Expect = 0.47
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 49 LRTGKKVAIVGSGPSGLGA 67
++ G VAIVG+GP GL A
Sbjct: 164 VKPGDTVAIVGAGPVGLAA 182
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 27.6 bits (62), Expect = 0.57
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 52 GKKVAIVGSGPSGLGAAHQLN-KEAGTELI 80
GKKVAI+G G G A LN +++G +I
Sbjct: 18 GKKVAIIGYGSQGH--AQALNLRDSGLNVI 45
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 27.6 bits (61), Expect = 0.63
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKE 74
V I+G G GL AA+ L +
Sbjct: 5 MDVVIIGGGIVGLSAAYYLAER 26
>gnl|CDD|215457 PLN02852, PLN02852, ferredoxin-NADP+ reductase.
Length = 491
Score = 27.7 bits (62), Expect = 0.64
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
V +VGSGP+G A +L K
Sbjct: 29 VCVVGSGPAGFYTADKLLKA 48
>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 = 27.4 bits (61), Expect = 0.71
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 55 VAIVGSGPSGLGAAHQLNKEAGTELI 80
VA++G GPSG AA L + AG E I
Sbjct: 3 VAVIGGGPSGATAAETLAR-AGIETI 27
>gnl|CDD|235373 PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase;
Provisional.
Length = 461
Score = 27.4 bits (62), Expect = 0.73
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 57 IVGSGPSGLGAAHQLNK 73
++GSGP+G GAA Q K
Sbjct: 10 VIGSGPAGEGAAMQAAK 26
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 27.2 bits (61), Expect = 0.77
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 28 IEC-AIIDHAFEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
+E AI HA + + G V +VG+GP GLG Q+ K G +I
Sbjct: 142 VEPLAIGAHAVRRAGVTA-------GDTVLVVGAGPIGLGVI-QVAKARGARVI 187
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
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 subdomain 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.
Length = 311
Score = 27.2 bits (61), Expect = 0.77
Identities = 14/35 (40%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 33 IDHAFEQG-WIKPEIPTLRT--GKKVAIVGSGPSG 64
D G W +PE R GK V IVG G G
Sbjct: 120 ADRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIG 154
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and
conversion].
Length = 562
Score = 27.3 bits (61), Expect = 0.82
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEAG 76
V ++G G +GL AA + EAG
Sbjct: 8 DVVVIGGGGAGLRAAIEA-AEAG 29
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 27.1 bits (61), Expect = 0.84
Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
GK VA+ G G SGL A L G E+I
Sbjct: 9 GKTVAVFGLGGSGLATARAL-VAGGAEVI 36
>gnl|CDD|237942 PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F;
Provisional.
Length = 517
Score = 27.0 bits (61), Expect = 0.97
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 52 GKKVAIVGSGPSGLGAA 68
GK+VA++G G SG+ AA
Sbjct: 351 GKRVAVIGGGNSGVEAA 367
>gnl|CDD|224549 COG1634, COG1634, Uncharacterized Rossmann fold enzyme [General
function prediction only].
Length = 232
Score = 27.0 bits (60), Expect = 0.97
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 42 IKPEIPTLRTGKKVAIVGSGPSG 64
+ E+ L G++VA+VG+GPS
Sbjct: 42 AEAELLELIEGREVAVVGAGPSL 64
>gnl|CDD|234436 TIGR03997, mycofact_OYE_2, mycofactocin system FadH/OYE family
oxidoreductase 2. The yeast protein called old yellow
enzyme and FadH from Escherichia coli (2,4-dienoyl CoA
reductase) are enzymes with 4Fe-4S, FMN, and FAD
prosthetic groups, and interact with NADPH as well as
substrate. Members of this related protein family occur
in the vicinity of the putative mycofactocin
biosynthesis operon in a number of Actinobacteria such
as Frankia sp. and Rhodococcus sp., in Pelotomaculum
thermopropionicum SI (Firmicutes), and in Geobacter
uraniireducens Rf4 (Deltaproteobacteria). The function
of this oxidoreductase is unknown.
Length = 645
Score = 27.0 bits (60), Expect = 0.97
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 53 KKVAIVGSGPSGLGAA 68
K+V +VG GP+GL AA
Sbjct: 380 KRVLVVGGGPAGLEAA 395
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 27.1 bits (61), Expect = 0.98
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 54 KVAIVGSGPSGLGAA 68
V +VG+GP GL A
Sbjct: 25 PVVVVGAGPVGLALA 39
>gnl|CDD|225953 COG3419, PilY1, Tfp pilus assembly protein, tip-associated adhesin
PilY1 [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 1036
Score = 27.1 bits (60), Expect = 1.0
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 12 GACVLGINEPAVTIKNIECAIIDH---AFEQGWIKPEIPTLRTGKKVAIVGSGPS 63
G L + +P + N+ + KP I L G ++G+G +
Sbjct: 661 GLYALDVTDPDFSNSNLLWENNSNDDPDLGYTMGKPRIVPLHDGSWAVLLGNGYN 715
>gnl|CDD|177713 PLN00093, PLN00093, geranylgeranyl diphosphate reductase;
Provisional.
Length = 450
Score = 27.0 bits (60), Expect = 1.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 54 KVAIVGSGPSGLGAAHQLNKE 74
+VA++G GP+G AA L K
Sbjct: 41 RVAVIGGGPAGACAAETLAKG 61
>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
Length = 569
Score = 27.1 bits (60), Expect = 1.0
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 38 EQGWIKPEIPTLRTGK-KVAIVGSGPSGLGAAHQL 71
+G PE + K KVAI+G+G +G+ A +L
Sbjct: 60 PKGLFPPEPEAYKGPKLKVAIIGAGLAGMSTAVEL 94
>gnl|CDD|224152 COG1231, COG1231, Monoamine oxidase [Amino acid transport and
metabolism].
Length = 450
Score = 27.0 bits (60), Expect = 1.1
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNK 73
V IVG+G +GL AA++L K
Sbjct: 7 TADVIIVGAGLAGLSAAYELKK 28
>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 = 26.7 bits (59), Expect = 1.2
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 52 GKKVAIVGSGPSGL 65
KKVA++G+G SGL
Sbjct: 1 AKKVAVIGAGVSGL 14
Score = 24.8 bits (54), Expect = 6.8
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 45 EIPTLRTGKKVAIVGSGPSGLGAAHQLNKEA 75
+ P GK+V ++G G SG A +L++ A
Sbjct: 176 KHPEGFQGKRVLVIGLGNSGGDIAVELSRTA 206
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 26.5 bits (59), Expect = 1.2
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
L+ G V ++G+G GL AA QL K AG +I
Sbjct: 132 LKPGDTVLVLGAGGVGLLAA-QLAKAAGARVI 162
>gnl|CDD|221798 pfam12831, FAD_oxidored, FAD dependent oxidoreductase. This
family of proteins contains FAD dependent
oxidoreductases and related proteins.
Length = 415
Score = 26.8 bits (60), Expect = 1.3
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 55 VAIVGSGPSGLGAA 68
V +VG GP+G+ AA
Sbjct: 2 VVVVGGGPAGVAAA 15
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 26.6 bits (59), Expect = 1.3
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 50 RTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
R G V +VG+GP GL A L K G ++
Sbjct: 167 RPGGTVVVVGAGPIGLLAI-ALAKLLGASVV 196
>gnl|CDD|235905 PRK06996, PRK06996, hypothetical protein; Provisional.
Length = 398
Score = 26.6 bits (59), Expect = 1.3
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 55 VAIVGSGPSGLGAAHQLNKEAGT 77
+AIVG+GP GL A L + + T
Sbjct: 14 IAIVGAGPVGLALAGWLARRSAT 36
>gnl|CDD|169028 PRK07588, PRK07588, hypothetical protein; Provisional.
Length = 391
Score = 26.6 bits (59), Expect = 1.3
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 53 KKVAIVGSGPSGLGAAHQLNK 73
KVAI G+G +G A+ L +
Sbjct: 1 MKVAISGAGIAGPTLAYWLRR 21
>gnl|CDD|213220 cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of
iron-sulfur clusters transporter, subfamily C. ATM1 is
an ABC transporter that is expressed in the
mitochondria. Although the specific function of ATM1 is
unknown, its disruption results in the accumulation of
excess mitochondrial iron, loss of mitochondrial
cytochromes, oxidative damage to mitochondrial DNA, and
decreased levels of cytosolic heme proteins. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 236
Score = 26.4 bits (59), Expect = 1.3
Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 48 TLRTGKKVAIVGSGPSGLG 66
T+ GKKVAIV GPSG G
Sbjct: 23 TIPAGKKVAIV--GPSGSG 39
>gnl|CDD|131779 TIGR02732, zeta_caro_desat, 9,9'-di-cis-zeta-carotene desaturase.
Carotene 7,8-desaturase, also called zeta-carotene
desaturase, catalyzes multiple steps in the pathway
from geranylgeranyl-PP to all-trans-lycopene in plants
and cyanobacteria. A similar enzyme and pathway is
found in the green sulfur bacterium Chlorobium tepidum.
Length = 474
Score = 26.7 bits (59), Expect = 1.3
Identities = 14/26 (53%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEAGTEL 79
KVAIVG+G +GL A +L +AG E+
Sbjct: 1 KVAIVGAGLAGLSTAVEL-VDAGHEV 25
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 26.7 bits (60), Expect = 1.4
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 48 TLRTGKKVAIVGSGPSGLGAAHQLN 72
TL G+++A+V GPSG G LN
Sbjct: 372 TLPAGQRIALV--GPSGAGKTSLLN 394
>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 = 26.5 bits (59), Expect = 1.4
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
GKKV ++G+G G AA L + E+
Sbjct: 177 KGKKVLVIGAGEMGELAAKHLAAKGVAEIT 206
>gnl|CDD|224992 COG2081, COG2081, Predicted flavoproteins [General function
prediction only].
Length = 408
Score = 26.4 bits (59), Expect = 1.4
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 54 KVAIVGSGPSGLGAAHQLNK 73
V I+G GP+GL AA K
Sbjct: 5 DVIIIGGGPAGLMAAISAAK 24
>gnl|CDD|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 447
Score = 26.3 bits (59), Expect = 1.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNK 73
KKV ++G SG AA L+K
Sbjct: 5 NKKVLVLGLAKSGYAAAKLLHK 26
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 26.4 bits (58), Expect = 1.4
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQL 71
K V +VG+GP GL AA
Sbjct: 133 AEPPKDVVVVGAGPIGLEAAEAA 155
>gnl|CDD|131083 TIGR02028, ChlP, geranylgeranyl reductase. This model represents
the reductase which acts reduces the geranylgeranyl
group to the phytyl group in the side chain of
chlorophyll. It is unclear whether the enzyme has a
preference for acting before or after the attachment of
the side chain to chlorophyllide a by chlorophyll
synthase. This clade is restricted to plants and
cyanobacteria to separate it from the homologues which
act in the biosynthesis of bacteriochlorophyll
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 398
Score = 26.4 bits (58), Expect = 1.5
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 54 KVAIVGSGPSGLGAAHQLNKEAGTELI 80
+VA+VG GP+G AA L AG +
Sbjct: 2 RVAVVGGGPAGASAAETLAS-AGIQTF 27
>gnl|CDD|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 26.4 bits (59), Expect = 1.5
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 53 KKVAIVGSGPSGLGAAHQLNK 73
V ++G G +GL AA K
Sbjct: 1 YDVIVIGGGAAGLMAAISAAK 21
>gnl|CDD|215308 PLN02568, PLN02568, polyamine oxidase.
Length = 539
Score = 26.3 bits (58), Expect = 1.5
Identities = 8/18 (44%), Positives = 15/18 (83%)
Query: 54 KVAIVGSGPSGLGAAHQL 71
++ I+G+G +GL AA++L
Sbjct: 7 RIVIIGAGMAGLTAANKL 24
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 26.6 bits (59), Expect = 1.6
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 31 AIIDHAFEQGWIKPEIPTLRTGK---KVAIVGSGPSGLGAAHQLNKEAGTELIK 81
+ A+E I+ G KV I+G+G GLGAA K L+
Sbjct: 138 GVQLGAYELARIQGGRMGGAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVY 191
>gnl|CDD|187600 cd05341, 3beta-17beta-HSD_like_SDR_c, 3beta17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs. This subgroup
includes members identified as 3beta17beta
hydroxysteroid dehydrogenase, 20beta hydroxysteroid
dehydrogenase, and R-alcohol dehydrogenase. These
proteins exhibit the canonical active site tetrad and
glycine rich NAD(P)-binding motif of the classical
SDRs. 17beta-dehydrogenases are a group of isozymes
that catalyze activation and inactivation of estrogen
and androgens, and include members of the SDR family.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 247
Score = 26.2 bits (58), Expect = 1.6
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 54 KVAIVGSGPSGLGAAH 69
KVAIV G GLG AH
Sbjct: 6 KVAIVTGGARGLGLAH 21
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 26.5 bits (59), Expect = 1.7
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 2/19 (10%)
Query: 48 TLRTGKKVAIVGSGPSGLG 66
TL G+KVAI+ G SG G
Sbjct: 360 TLAQGEKVAIL--GRSGSG 376
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino
acids valine and isoleucine.
Length = 165
Score = 26.0 bits (58), Expect = 1.7
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 52 GKKVAIVGSGPSGLGAAHQLN-KEAGTELI 80
GKK+A++G G G AH LN +++G +I
Sbjct: 4 GKKIAVIGYGSQGH--AHALNLRDSGVNVI 31
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 26.1 bits (58), Expect = 1.8
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 46 IPTLRTGKKVAIVGSGPSGLGAAHQLNKEAG 76
+P TGK+V I+G+G + A L EAG
Sbjct: 120 LPVDVTGKRVLILGAGGAARAVAFAL-AEAG 149
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 26.0 bits (58), Expect = 1.9
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 53 KKVAIVGSGPSGLGAAHQLNK--EAGTELI 80
++V IVG+G G A +L + E G ++
Sbjct: 129 RRVLIVGAGELGRRLAERLARNPELGYRVV 158
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of
Shikimate dehydrogenase. Shikimate dehydrogenase (DH)
is an amino acid DH family member. Shikimate pathway
links metabolism of carbohydrates to de novo
biosynthesis of aromatic amino acids, quinones and
folate. It is essential in plants, bacteria, and fungi
but absent in mammals, thus making enzymes involved in
this pathway ideal targets for broad spectrum
antibiotics and herbicides. Shikimate DH catalyzes the
reduction of 3-hydroshikimate to shikimate using the
cofactor NADH. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily
and include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 26.1 bits (58), Expect = 1.9
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGTEL 79
GKKV I+G+G + A+ L + ++
Sbjct: 18 KGKKVLILGAGGAARAVAYALAELGAAKI 46
>gnl|CDD|226160 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 520
Score = 26.3 bits (58), Expect = 2.0
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 52 GKKVAIVGSGPSGLGAA 68
GK+VA++G G SG+ AA
Sbjct: 354 GKRVAVIGGGNSGVEAA 370
>gnl|CDD|233137 TIGR00811, sit, silicon transporter. Marine diatoms such as
Cylindrotheca fusiformis encode at least six silicon
transport protein homologues which exhibit similar size
and topology. One characterized member of the family
(Sit1) functions in the energy-dependent uptake of
either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by
a Na+ symport mechanism. The system is found in marine
diatoms which make their "glass houses" out of silicon
[Transport and binding proteins, Other].
Length = 545
Score = 26.1 bits (57), Expect = 2.0
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 1 FTGRVCPAPCEGACVLGINE 20
FT +C AP EGA VLG+ E
Sbjct: 112 FTINLCGAPLEGAEVLGLPE 131
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 26.1 bits (58), Expect = 2.2
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNK 73
GKKV +VG+G SGL A L K
Sbjct: 4 KGKKVLVVGAGVSGLALAKFLKK 26
>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 = 26.2 bits (58), Expect = 2.2
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 55 VAIVGSGPSGLGAA 68
V +VG+GP+GL AA
Sbjct: 166 VLVVGAGPAGLAAA 179
>gnl|CDD|234025 TIGR02819, fdhA_non_GSH, formaldehyde dehydrogenase,
glutathione-independent. Members of this family
represent a distinct clade within the larger family of
zinc-dependent dehydrogenases of medium chain alcohols,
a family that also includes the so-called
glutathione-dependent formaldehyde dehydrogenase.
Members of this protein family have a tightly bound NAD
that can act as a true cofactor, rather than a
cosubstrate in dehydrogenase reactions, in dismutase
reactions for some aldehydes. The name given to this
family, however, is formaldehyde dehydrogenase,
glutathione-independent [Central intermediary
metabolism, One-carbon metabolism].
Length = 393
Score = 26.0 bits (57), Expect = 2.2
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 51 TGKKVAIVGSGPSGLGAAH 69
G V I G+GP GL AA
Sbjct: 185 PGSTVYIAGAGPVGLAAAA 203
>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 = 26.1 bits (58), Expect = 2.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
V ++GSG +GL AA + +
Sbjct: 2 VVVIGSGLAGLAAALEAAEA 21
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 25.9 bits (58), Expect = 2.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 55 VAIVGSGPSGLGAAHQLNK 73
V ++G+GP+G AA + K
Sbjct: 6 VIVIGAGPAGYVAARRAAK 24
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 25.8 bits (58), Expect = 2.4
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 2/19 (10%)
Query: 48 TLRTGKKVAIVGSGPSGLG 66
T++ G+KVAIV GPSG G
Sbjct: 24 TIKPGEKVAIV--GPSGSG 40
>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 = 25.7 bits (57), Expect = 2.5
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 55 VAIVGSGPSGLGAAHQL 71
+ IVG+G +GL A +L
Sbjct: 2 LVIVGAGLAGLLLALRL 18
>gnl|CDD|235491 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 25.8 bits (58), Expect = 2.7
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 3/30 (10%)
Query: 52 GKKVAIVGSGPSGLGAAHQLN-KEAGTELI 80
GKKVAI+G G G AH LN +++G +++
Sbjct: 17 GKKVAIIGYGSQ--GHAHALNLRDSGVDVV 44
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 25.7 bits (57), Expect = 2.8
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 35 HAFEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
HA I G V ++G+G GL A Q K G + +
Sbjct: 150 HAVRLAGITL-------GDTVVVIGAGTIGLLAI-QWLKILGAKRV 187
>gnl|CDD|180814 PRK07057, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 591
Score = 25.6 bits (56), Expect = 2.9
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 42 IKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKEAG 76
IK +P + V IVG+G SG+ A+ QL AG
Sbjct: 4 IKTSLPRRKF--DVVIVGAGGSGMRASLQL-ARAG 35
>gnl|CDD|178267 PLN02661, PLN02661, Putative thiazole synthesis.
Length = 357
Score = 25.6 bits (56), Expect = 2.9
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 55 VAIVGSGPSGLGAAHQLNK 73
V IVG+G +GL A++L+K
Sbjct: 95 VVIVGAGSAGLSCAYELSK 113
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1
and is thought to have a role in resistance to
oxidative stress. Interestingly, subfamily B is more
closely related to the carboxyl-terminal component of
subfamily C than the two halves of ABCC molecules are
with one another.
Length = 238
Score = 25.6 bits (57), Expect = 3.1
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 9/31 (29%)
Query: 43 KPEIP-------TLRTGKKVAIVGSGPSGLG 66
+P++P T+ GK VA+V G SG G
Sbjct: 13 RPDVPILKGLSLTIPPGKTVALV--GSSGCG 41
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 25.4 bits (56), Expect = 3.2
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 48 TLRTGKKVAIVGSGPSGLG 66
T+R G+ VA+V GPSG G
Sbjct: 362 TVRPGETVALV--GPSGAG 378
>gnl|CDD|176218 cd08256, Zn_ADH2, Alcohol dehydrogenases of the MDR family. This
group has the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenases of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 350
Score = 25.4 bits (56), Expect = 3.2
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 20 EPAVTIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGSGPSGLG 66
E A+ I+ + CA+ HA ++ IK V + G+GP GLG
Sbjct: 152 EDAILIEPLACAL--HAVDRANIK-------FDDVVVLAGAGPLGLG 189
>gnl|CDD|236439 PRK09267, PRK09267, flavodoxin FldA; Validated.
Length = 169
Score = 25.2 bits (56), Expect = 3.2
Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 44 PEIPTLR-TGKKVAIVGSG 61
PE+ + +GKKVA+ G G
Sbjct: 71 PELEEIDFSGKKVALFGLG 89
>gnl|CDD|213265 cd03298, ABC_ThiQ_thiamine_transporter, ATP-binding cassette
domain of the thiamine transport system. Part of the
binding-protein-dependent transport system tbpA-thiPQ
for thiamine and TPP. Probably responsible for the
translocation of thiamine across the membrane. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 211
Score = 25.5 bits (56), Expect = 3.3
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 48 TLRTGKKVAIVGSGPSGLGAAHQLNKEAGTEL 79
T G+ AIVG PSG G + LN AG E
Sbjct: 20 TFAQGEITAIVG--PSGSGKSTLLNLIAGFET 49
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 25.7 bits (57), Expect = 3.3
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 36 AFEQGWIKPEIPTLR---TGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
A E+ + + GKKVAI G G L A L E G E++
Sbjct: 260 ARERARLLDALADYHEYLGGKKVAIFGDGDLLLALARFL-LELGMEVV 306
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 25.4 bits (56), Expect = 3.3
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 52 GKKVAIVGSGPSGLGAAHQLN-KEAGTELI 80
GK VAI+G G G A LN +++G +I
Sbjct: 3 GKTVAIIGYGSQGH--AQALNLRDSGLNVI 30
>gnl|CDD|215749 pfam00148, Oxidored_nitro, Nitrogenase component 1 type
Oxidoreductase.
Length = 397
Score = 25.7 bits (57), Expect = 3.3
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 52 GKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
GK+VAI G G A L +E G E++
Sbjct: 272 GKRVAIYGDPDLAWGLARFL-EELGMEVV 299
>gnl|CDD|233383 TIGR01373, soxB, sarcosine oxidase, beta subunit family,
heterotetrameric form. This model describes the beta
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 = 407
Score = 25.5 bits (56), Expect = 3.6
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 37 FEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKEAG 76
++ W PE P + V IVG G GL A+ L KE G
Sbjct: 18 WKPAWRSPE-P--KPTYDVIIVGGGGHGLATAYYLAKEHG 54
>gnl|CDD|234093 TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl
glycosylphosphotransferase. Members of this family are
generally found near other genes involved in the
biosynthesis of a variety of exopolysaccharides. These
proteins consist of two fused domains, an N-terminal
hydrophobic domain of generally low conservation and a
highly conserved C-terminal sugar transferase domain
(pfam02397). Characterized and partially characterized
members of this subfamily include Salmonella WbaP
(originally RfbP) , E. coli WcaJ , Methylobacillus EpsB,
Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B
Streptococcus CpsE (originally CpsD), and Streptococcus
suis Cps2E. Each of these is believed to act in
transferring the sugar from, for instance, UDP-glucose
or UDP-galactose, to a lipid carrier such as
undecaprenyl phosphate as the first (priming) step in
the synthesis of an oligosaccharide "block". This
function is encoded in the C-terminal domain. The
liposaccharide is believed to be subsequently
transferred through a "flippase" function from the
cytoplasmic to the periplasmic face of the inner
membrane by the N-terminal domain. Certain closely
related transferase enzymes such as Sinorhizobium ExoY
and Lactococcus EpsD lack the N-terminal domain and are
not found by this model.
Length = 445
Score = 25.2 bits (56), Expect = 3.6
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 52 GKKVAIVGSGPSGLGAAHQL--NKEAGTELI 80
++V IVG+G + A L N G ++
Sbjct: 125 LRRVLIVGTGEAAEELAKALSRNPALGYRVV 155
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 25.5 bits (56), Expect = 3.6
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 9/32 (28%)
Query: 42 IKPEIP-------TLRTGKKVAIVGSGPSGLG 66
+P++P TL G+ VA+V GPSG G
Sbjct: 490 NRPDVPVLKGLTFTLHPGEVVALV--GPSGSG 519
>gnl|CDD|176230 cd08269, Zn_ADH9, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 312
Score = 25.4 bits (56), Expect = 4.0
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 36 AFEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
F +GWI+ GK VA++G+G GL QL AG +
Sbjct: 121 VFRRGWIRA-------GKTVAVIGAGFIGLLFL-QLAAAAGARRV 157
>gnl|CDD|180054 PRK05396, tdh, L-threonine 3-dehydrogenase; Validated.
Length = 341
Score = 25.2 bits (56), Expect = 4.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 51 TGKKVAIVGSGPSGLGAA 68
G+ V I G+GP G+ AA
Sbjct: 163 VGEDVLITGAGPIGIMAA 180
>gnl|CDD|235412 PRK05329, PRK05329, anaerobic glycerol-3-phosphate dehydrogenase
subunit B; Validated.
Length = 422
Score = 25.2 bits (56), Expect = 4.1
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 50 RTGKKVAIVGSGPSGL 65
GK+VA+V G L
Sbjct: 23 EAGKRVALVAKGQGAL 38
>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 = 25.2 bits (56), Expect = 4.1
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 55 VAIVGSGPSGLGAA 68
+ IVG GP GL A
Sbjct: 2 IVIVGGGPVGLALA 15
>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 25.2 bits (56), Expect = 4.3
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 48 TLRTGKKVAIVGSG---PSGLGAAHQLNKE 74
L+ G+KVAI+ G P L A +LN
Sbjct: 497 LLKEGEKVAILAFGTMLPEALKVAEKLNAY 526
>gnl|CDD|237575 PRK13977, PRK13977, myosin-cross-reactive antigen; Provisional.
Length = 576
Score = 25.2 bits (56), Expect = 4.3
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 43 KPEIPTLRTGKKVAIVGSGPSGLGAA 68
+P P KK I+GSG + L AA
Sbjct: 13 RPRKPEGVDNKKAYIIGSGLASLAAA 38
>gnl|CDD|183782 PRK12834, PRK12834, putative FAD-binding dehydrogenase; Reviewed.
Length = 549
Score = 25.2 bits (56), Expect = 4.5
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 55 VAIVGSGPSGLGAAHQL 71
V +VG+G +GL AA +L
Sbjct: 7 VIVVGAGLAGLVAAAEL 23
>gnl|CDD|235368 PRK05225, PRK05225, ketol-acid reductoisomerase; Validated.
Length = 487
Score = 24.9 bits (55), Expect = 4.8
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 52 GKKVAIVGSGPSGL 65
GKK+ IVG G GL
Sbjct: 36 GKKIVIVGCGAQGL 49
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production
and conversion].
Length = 313
Score = 24.8 bits (55), Expect = 4.8
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 53 KKVAIVGSGPSGLGAAHQL-NKEAGTELI 80
KVA++G+G G A L + G+EL+
Sbjct: 1 MKVAVIGAGNVGSSLAFLLLLQGLGSELV 29
>gnl|CDD|215362 PLN02676, PLN02676, polyamine oxidase.
Length = 487
Score = 25.1 bits (55), Expect = 5.0
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 55 VAIVGSGPSGLGAAHQLNKEAGTE 78
V IVG+G SG+ AA L+ EAG E
Sbjct: 29 VIIVGAGMSGISAAKTLS-EAGIE 51
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 25.0 bits (55), Expect = 5.4
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 59 GSGPSGLGAAHQLNKEAGTELIK 81
GSGP+GL A +++ AGT LI+
Sbjct: 134 GSGPAGLSAMAEVSPFAGTRLIR 156
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 25.0 bits (55), Expect = 5.4
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 47 PTLRTGKKVAIVGSGPSGLG 66
L G++VAI+ GPSG G
Sbjct: 356 LDLPPGERVAIL--GPSGSG 373
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 25.1 bits (54), Expect = 5.4
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
L GK VA++G G G A L +++G E++
Sbjct: 13 LLQGKTVAVIGYGSQGHAQAQNL-RDSGVEVV 43
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 24.6 bits (54), Expect = 5.8
Identities = 11/27 (40%), Positives = 12/27 (44%)
Query: 51 TGKKVAIVGSGPSGLGAAHQLNKEAGT 77
GKKV +VG G L A L K
Sbjct: 11 EGKKVLVVGGGSVALRKARLLLKAGAD 37
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 24.9 bits (55), Expect = 5.8
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 45 EIPTLRTGKKVAIVGSGP 62
E KKV I+GSGP
Sbjct: 548 EAEPSSEKKKVLILGSGP 565
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 24.8 bits (54), Expect = 5.9
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 54 KVAIVGSGPSGLGAAHQLNK 73
KV IVG G +GL AA L K
Sbjct: 3 KVGIVGGGLAGLTAAISLAK 22
>gnl|CDD|181001 PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 388
Score = 24.9 bits (55), Expect = 5.9
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 55 VAIVGSGPSGLGAA 68
+A++G GP+GL AA
Sbjct: 10 IAVIGGGPAGLAAA 23
>gnl|CDD|180442 PRK06175, PRK06175, L-aspartate oxidase; Provisional.
Length = 433
Score = 24.6 bits (54), Expect = 6.0
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 55 VAIVGSGPSGLGAAHQLNK 73
V IVGSG +GL +A L K
Sbjct: 7 VLIVGSGVAGLYSALNLRK 25
>gnl|CDD|236374 PRK09077, PRK09077, L-aspartate oxidase; Provisional.
Length = 536
Score = 24.9 bits (55), Expect = 6.4
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 55 VAIVGSGPSGLGAAHQL 71
V I+GSG +GL A +L
Sbjct: 11 VLIIGSGAAGLSLALRL 27
>gnl|CDD|235470 PRK05444, PRK05444, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 580
Score = 24.7 bits (55), Expect = 6.4
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 49 LRTGKKVAIVGSG---PSGLGAAHQLNK 73
LR G+ VAI+ G L AA +L
Sbjct: 460 LREGEDVAILAFGTMLAEALKAAERLAS 487
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 24.5 bits (54), Expect = 6.4
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 35 HAFEQGWIKPEIPTLRTGKKVAIVGSGPSGLGAA 68
H E IKP G VA++G+GP GL A
Sbjct: 158 HGAELAGIKP-------GSTVAVIGAGPVGLCAV 184
>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 = 24.7 bits (54), Expect = 6.5
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 55 VAIVGSGPSGLGAAHQLNK 73
+A++G GP+GL A +L +
Sbjct: 2 LAVIGGGPAGLAIALELAR 20
>gnl|CDD|176223 cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 24.6 bits (54), Expect = 6.6
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQL 71
L G+ ++G GP GL L
Sbjct: 159 LTPGEVALVIGCGPIGLAVIAAL 181
>gnl|CDD|183139 PRK11445, PRK11445, putative oxidoreductase; Provisional.
Length = 351
Score = 24.6 bits (54), Expect = 6.7
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 55 VAIVGSGPSGLGAAHQLNKE 74
VAI+G GP+G A L +
Sbjct: 4 VAIIGLGPAGSALARLLAGK 23
>gnl|CDD|238936 cd01977, Nitrogenase_VFe_alpha, Nitrogenase_VFe_alpha -like:
Nitrogenase VFe protein, alpha subunit like. This group
contains proteins similar to the alpha subunits of, the
VFe protein of the vanadium-dependent (V-) nitrogenase
and the FeFe protein of the iron only (Fe-) nitrogenase
Nitrogenase catalyzes the ATP-dependent reduction of
dinitrogen (N2) to ammonia. In addition to V- and Fe-
nitrogenases there is a molybdenum (Mo)-dependent
nitrogenase which is the most widespread and best
characterized of these systems. These systems consist
of component 1 (VFe protein, FeFe protein or, MoFe
protein respectively) and, component 2 (Fe protein).
MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases
are alpha2beta2delta2 hexamers. The alpha and beta
subunits of VFe and FeFe are similar to the alpha and
beta subunits of MoFe. For MoFe each alphabeta pair
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein which
has a practically identical structure in all three
systems, it contains a single [4Fe-4S] cluster.
Electrons are transferred from the [4Fe-4S] cluster of
the Fe protein to the P-cluster of the MoFe and in turn
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 415
Score = 24.7 bits (54), Expect = 6.7
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 31 AIIDHAFEQGWIKPEIPTLRT---GKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
A+I + KPE+ + GKKV I GP + E G +++
Sbjct: 266 AVIAEEMAK--WKPELDWYKERLKGKKVCIWTGGPKLWHWTKVIEDELGMQVV 316
>gnl|CDD|235608 PRK05786, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 238
Score = 24.7 bits (54), Expect = 6.9
Identities = 11/17 (64%), Positives = 12/17 (70%), Gaps = 1/17 (5%)
Query: 52 GKKVAIVGSGPSGLGAA 68
GKKVAI+G GLG A
Sbjct: 5 GKKVAIIGVSE-GLGYA 20
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 24.8 bits (54), Expect = 7.0
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 49 LRTGKKVAIVGSGPSGLGAAHQLNKEAG 76
R G V + G+GP GL A L K AG
Sbjct: 201 FRPGAYVVVYGAGPIGLAAI-ALAKAAG 227
>gnl|CDD|236385 PRK09126, PRK09126, hypothetical protein; Provisional.
Length = 392
Score = 24.5 bits (54), Expect = 7.0
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 55 VAIVGSGPSGLGAAHQL 71
+ +VG+GP+GL A L
Sbjct: 6 IVVVGAGPAGLSFARSL 22
>gnl|CDD|235059 PRK02705, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 459
Score = 24.5 bits (54), Expect = 7.2
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 53 KKVAIVGSGPSGLGAAHQLNKE 74
++G G SG+ AA L +
Sbjct: 1 AIAHVIGLGRSGIAAARLLKAQ 22
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 24.6 bits (54), Expect = 8.4
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 46 IPTLRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
+PT R GK V I+ GP+G+G + L AG EL
Sbjct: 94 LPTPRPGKVVGIL--GPNGIGKSTALKILAG-ELK 125
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 24.3 bits (53), Expect = 8.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 54 KVAIVGSGPSGLGAAHQLNK 73
K+AI+G+G GL AA L +
Sbjct: 2 KIAIIGAGIGGLTAAALLQE 21
>gnl|CDD|233878 TIGR02467, CbiE, precorrin-6y C5,15-methyltransferase
(decarboxylating), CbiE subunit. This model recognizes
the CbiE methylase which is responsible, in part (along
with CbiT), for methylating precorrin-6y (or
cobalt-precorrin-6y) at both the 5 and 15 positions as
well as the concomitant decarbozylation at C-12. In
many organisms, this protein is fused to the CbiT
subunit. The fused protein, when found in organisms
catalyzing the oxidative version of the cobalamin
biosynthesis pathway, is called CobL.
Length = 204
Score = 24.2 bits (53), Expect = 9.1
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 24 TIKNIECAIIDHAFEQGWIKPEIPTLRTGKKVAIVGSG-P--SGLGA 67
+ + II + + I R K+V ++ SG P G+G
Sbjct: 38 ELIGEKREIILTYKDLDELLEFIAATRKEKRVVVLASGDPLFYGIGR 84
>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 = 24.1 bits (53), Expect = 9.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 54 KVAIVGSGPSGLGAA 68
V I+G+GP GL A
Sbjct: 1 DVIIIGAGPCGLACA 15
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent alcohol dehydrogenases. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 306
Score = 24.2 bits (53), Expect = 9.5
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 48 TLRTGKKVAIVGSGPSGLGAAHQLNKEAGTELI 80
+R G V + G GP GL AA Q+ K G ++
Sbjct: 161 GIRPGDTVVVFGPGPIGLLAA-QVAKLQGATVV 192
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
0.318 0.138 0.432
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,093,969
Number of extensions: 322980
Number of successful extensions: 881
Number of sequences better than 10.0: 1
Number of HSP's gapped: 864
Number of HSP's successfully gapped: 211
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)