RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9141
(379 letters)
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 89.4 bits (222), Expect = 8e-20
Identities = 44/173 (25%), Positives = 67/173 (38%), Gaps = 29/173 (16%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAR-EDIRNSGLSEGKSINLALSVRGREALRR 66
V IVG G G A A+ +V L E ++ G +ALS AL R
Sbjct: 4 DVAIVGAGPAGLALALALARAGLDVTLLERAPRELLERGR------GIALSPNALRALER 57
Query: 67 IGLEDKLLAHGIPMRARMIHGQNGKLREIPYDP-----------VHNQV-------ELEQ 108
+GL D+L A G+P M+ G+ + +D V
Sbjct: 58 LGLWDRLEALGVPPLHVMVVDDGGRRL-LIFDAAELGRGALGYVVPRSDLLNALLEAARA 116
Query: 109 YPDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGVRK 161
P+ + F ++ ++ + VT + D D L++GADGA S VR+
Sbjct: 117 LPNVTLRFGAEVEAVEQDGDGVTVTLSFDGET---LDADLLVGADGANSAVRR 166
>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 = 63.9 bits (156), Expect = 2e-11
Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 26/173 (15%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V+IVGGG G + A + A+ V L E S L +N R E LR+ G
Sbjct: 4 VLIVGGGPAGLMLALLLARAGVRVVLVERHAT--TSVLPRAGGLN----QRTMELLRQAG 57
Query: 69 LEDKLLAHGIPMRARMIHGQNGKLREIPYDP--------VHNQVELEQYPD--------- 111
LED++LA G P + N R D V+ Q ELE P
Sbjct: 58 LEDRILAEGAPHEGMGLAFYNTSRRRADLDFLTSPPRVTVYPQTELE--PILREHAEARG 115
Query: 112 CNIYFQHKLINLDVNSGNVT-FYRTEDNSETKITDNQLIIGADGAYSGVRKCL 163
+ F ++++L+ + VT R + E + ++G DG S VRK L
Sbjct: 116 AQVRFGTEVLSLEQDGDGVTAVVRDRRDGEEYTVRAKYLVGCDGGRSPVRKQL 168
>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 = 56.8 bits (138), Expect = 5e-09
Identities = 58/203 (28%), Positives = 79/203 (38%), Gaps = 58/203 (28%)
Query: 9 VVIVGGGLVGSLSACMFAKNQY-EVNLYEARE---------DIRNSGLSEGKSINLALSV 58
+VIVGGG VG A A++ +V L EA D R S LS SI L
Sbjct: 2 IVIVGGGPVGLALALALARSGGLKVALIEATPLPAPADPGFDNRVSALSAA-SIRL---- 56
Query: 59 RGREALRRIGLEDKLLAHGIPMRARMIH-------GQNGKLR----EIPYDPVHNQVELE 107
L ++G+ DK+ P RA+ I G G L EI + + VE
Sbjct: 57 -----LEKLGVWDKIE----PARAQPIRDIHVSDGGSFGALHFDADEIGLEALGYVVE-- 105
Query: 108 QYPDCNIYFQHKLINLDVNSGN----------VTFYRTEDNSETKITDNQ-----LIIGA 152
N Q L N V R D+ E + D Q L++GA
Sbjct: 106 -----NRVLQQALWERLQELPNRVTILCPARVVELPRHSDHVELTLDDGQQLRARLLVGA 160
Query: 153 DGAYSGVRKCL-MKQSMFNYSQT 174
DGA S VR+ + + ++Y Q+
Sbjct: 161 DGANSKVRQLAGIPTTGWDYGQS 183
>gnl|CDD|233669 TIGR01984, UbiH, 2-polyprenyl-6-methoxyphenol 4-hydroxylase. This
model represents the FAD-dependent monoxygenase
responsible for the second hydroxylation step in the
aerobic ubiquinone bioynthetic pathway. The scope of
this model is limited to the proteobacteria. This family
is closely related to the UbiF hydroxylase which
catalyzes the final hydroxylation step. The enzyme has
also been named VisB due to a mutant VISible light
sensitive phenotype [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 382
Score = 56.2 bits (136), Expect = 9e-09
Identities = 50/197 (25%), Positives = 72/197 (36%), Gaps = 45/197 (22%)
Query: 9 VVIVGGGLVGSLSACMFA-KNQYEVNLYEARE--------DIRNSGLSEGKSINLALSVR 59
V+IVGGGLVG A + + ++ L EA D R+ LS G S +
Sbjct: 2 VIIVGGGLVGLSLALALSRLGKIKIALIEANSPSAAQPGFDARSLALSYG-SKQI----- 55
Query: 60 GREALRRIGLEDKLLAHGIPMRARMIH----GQNGKLR---EIPYDPVHNQV-------- 104
L ++GL KL P+ IH G G P V
Sbjct: 56 ----LEKLGLWPKLAPFATPILD--IHVSDQGHFGATHLRASEFGLPALGYVVELADLGQ 109
Query: 105 ----ELEQYPDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGVR 160
L + +Y + + N V T DN + +L+I ADGA S VR
Sbjct: 110 ALLSRLALLTNIQLYCPARYKEIIRNQDYVRV--TLDNGQQLRA--KLLIAADGANSKVR 165
Query: 161 K-CLMKQSMFNYSQTYI 176
+ + +Y+QT +
Sbjct: 166 ELLSIPTEEHDYNQTAL 182
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 53.4 bits (129), Expect = 8e-08
Identities = 49/185 (26%), Positives = 77/185 (41%), Gaps = 51/185 (27%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYE----------AREDIRNSGLSEGKSINLALSV 58
+ IVGGG+VG+ A A++ + V + E ++ D+R S +S A SV
Sbjct: 8 IAIVGGGMVGAALALGLAQHGFSVAVLEHAAPAPFDADSQPDVRISAIS-------AASV 60
Query: 59 RGREALRRIGLEDKLLAHGIPMR--------------ARMI-HGQNGKLREIPYDPVHNQ 103
L+ +G+ D + A MR A ++ KL E+ Y V N+
Sbjct: 61 A---LLKGLGVWDAVQA----MRSHPYRRLETWEWETAHVVFDAAELKLPELGY-MVENR 112
Query: 104 V-------ELEQYPDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAY 156
V LE +P+ + L L + + T + E +L+IGADGA
Sbjct: 113 VLQLALWQALEAHPNVTLRCPASLQAL--QRDDDGWELTLADGEEIQA--KLVIGADGAN 168
Query: 157 SGVRK 161
S VR+
Sbjct: 169 SQVRQ 173
>gnl|CDD|235874 PRK06847, PRK06847, hypothetical protein; Provisional.
Length = 375
Score = 47.9 bits (115), Expect = 5e-06
Identities = 45/176 (25%), Positives = 70/176 (39%), Gaps = 30/176 (17%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINL-ALSVRGREA 63
+ K V+IVGGG+ G +A + V+L E + R G I L ++R A
Sbjct: 3 AVKKVLIVGGGIGGLSAAIALRRAGIAVDLVEIDPEWR----VYGAGITLQGNALR---A 55
Query: 64 LRRIGLEDKLLAHGIPMRARMIHGQNG-KLREIPYDPVHNQVELEQYPDCN-IY---FQH 118
LR +G+ D+ L G + +G L E+P P ++ + P I
Sbjct: 56 LRELGVLDECLEAGFGFDGVDLFDPDGTLLAELP-TP---RLAGDDLPGGGGIMRPALAR 111
Query: 119 KLINLDVNSG-----NVTFYRTEDNSE---TKITDNQ-----LIIGADGAYSGVRK 161
L + +G T E + + +D L++GADG YS VR
Sbjct: 112 ILADAARAAGADVRLGTTVTAIEQDDDGVTVTFSDGTTGRYDLVVGADGLYSKVRS 167
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 46.5 bits (111), Expect = 1e-05
Identities = 49/181 (27%), Positives = 75/181 (41%), Gaps = 18/181 (9%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
VV+VGGGLVG+ A A++ V L R R + + + A+S + L R+G
Sbjct: 8 VVVVGGGLVGASLALALAQSGLRVALLAPRAPPRPADDAWDSRV-YAISPSSQAFLERLG 66
Query: 69 LEDKLLAHGI-PMRARMIHGQ-NGKLREIPYDPVHNQ----VE---LEQYPDCNIYFQHK 119
+ L A + P+ + G + +L Y Q VE +E+ + FQ
Sbjct: 67 VWQALDAARLAPVYDMRVFGDAHARLHFSAYQAGVPQLAWIVESSLIERALWAALRFQPN 126
Query: 120 LINLDVNSGNVTFYRTEDNSETKITDNQ-----LIIGADGAYSGVRK-CLMKQSMFNYSQ 173
L + D + + D Q L++GADGA+S VR +K Y Q
Sbjct: 127 LTWFPARA--QGLEVDPDAATLTLADGQVLRADLVVGADGAHSWVRSQAGIKAERRPYRQ 184
Query: 174 T 174
T
Sbjct: 185 T 185
>gnl|CDD|235584 PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 395
Score = 45.6 bits (109), Expect = 3e-05
Identities = 44/204 (21%), Positives = 68/204 (33%), Gaps = 58/204 (28%)
Query: 8 SVVIVGGGLVGS-----LSACMFAKNQYEVNLYEARE---------DIRNSGLSEGKSIN 53
V+IVGGG+ G+ LS + V L EA D R L+ G
Sbjct: 5 DVIIVGGGMAGATLALALSR--LSHGGLPVALIEAFAPESDAHPGFDARAIALAAGT--- 59
Query: 54 LALSVRGREALRRIGLEDKLLAHGIPMRARMIH----GQNGKLR----EIPYDPVHNQVE 105
+ L R+G+ L P+ IH G G +R + + VE
Sbjct: 60 -------CQQLARLGVWQALADCATPITH--IHVSDRGHAGFVRLDAEDYGVPALGYVVE 110
Query: 106 LEQYPDCNIYFQHKLINLDVNSGNVTFY---------RTEDNSETKITDNQ-----LIIG 151
L L VT + RT+ + + D + L++
Sbjct: 111 LHDVGQR---LFALLDKAP----GVTLHCPARVANVERTQGSVRVTLDDGETLTGRLLVA 163
Query: 152 ADGAYSGVRK-CLMKQSMFNYSQT 174
ADG++S +R+ + Y Q
Sbjct: 164 ADGSHSALREALGIDWQQHPYEQV 187
>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 = 43.4 bits (103), Expect = 6e-05
Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 22/97 (22%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI------RNSGL------SEGKSINLAL 56
VV++GGG+VG +A A+ V L E R D+ RN+GL E + L
Sbjct: 2 VVVIGGGIVGLSTAYELARRGLSVTLLE-RGDLASGASGRNAGLLHPGLRKERAPLLARL 60
Query: 57 SVRGREALRRIGLEDKLLAHGIPMRARMIHGQNGKLR 93
++ R+ R + + GI R + G L
Sbjct: 61 ALESRDLWREL-----IEELGIDCDFR----RTGVLV 88
>gnl|CDD|236046 PRK07538, PRK07538, hypothetical protein; Provisional.
Length = 413
Score = 44.5 bits (106), Expect = 6e-05
Identities = 45/181 (24%), Positives = 75/181 (41%), Gaps = 38/181 (20%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINL---ALSVRGREALR 65
V+I GGG+ G A + EV ++EA ++R G+ INL A+ RE L
Sbjct: 3 VLIAGGGIGGLTLALTLHQRGIEVVVFEAAPELRPLGV----GINLLPHAV----RE-LA 53
Query: 66 RIGLEDKLLAHGIPMRARMIHGQNGKLREIPYDP--VHNQVELEQY-------------- 109
+GL D L A GI R ++G+ I +P + + QY
Sbjct: 54 ELGLLDALDAIGIRTRELAYFNRHGQ--RIWSEPRGLAAGYDWPQYSIHRGELQMLLLDA 111
Query: 110 ------PDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKIT-DNQLIIGADGAYSGVRKC 162
PD + H+++ + ++ + + ++ ++IGADG +S VR
Sbjct: 112 VRERLGPDA-VRTGHRVVGFEQDADVTVVFLGDRAGGDLVSVRGDVLIGADGIHSAVRAQ 170
Query: 163 L 163
L
Sbjct: 171 L 171
>gnl|CDD|235727 PRK06183, mhpA, 3-(3-hydroxyphenyl)propionate hydroxylase;
Validated.
Length = 500
Score = 44.5 bits (106), Expect = 7e-05
Identities = 45/178 (25%), Positives = 68/178 (38%), Gaps = 37/178 (20%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINL--ALSVRGREALR- 65
VVIVG G VG A + + V + E + +L A+ + EALR
Sbjct: 13 VVIVGAGPVGLTLANLLGQYGVRVLVLERWPTL----------YDLPRAVGIDD-EALRV 61
Query: 66 --RIGLEDKLLAHGIPMRA-RMIHGQNGKLREIPYDPVH----------NQVELE----- 107
IGL D++L H P R + + L EI +Q LE
Sbjct: 62 LQAIGLADEVLPHTTPNHGMRFLDAKGRCLAEIARPSTGEFGWPRRNAFHQPLLEAVLRA 121
Query: 108 ---QYPDCNIYFQHKLINLDVNSGNVTF-YRTEDNSETKITDNQLIIGADGAYSGVRK 161
++P + F H++ L + VT D + + ++G DGA S VR+
Sbjct: 122 GLARFPHVRVRFGHEVTALTQDDDGVTVTLTDADGQRETVR-ARYVVGCDGANSFVRR 178
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 43.1 bits (102), Expect = 2e-04
Identities = 33/170 (19%), Positives = 67/170 (39%), Gaps = 13/170 (7%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINL--ALSVRG-REALR 65
+ I+G G+ G +A + + +EV ++E E ++ G G N+ L + ++
Sbjct: 3 IAIIGAGIGGLTAAALLQEQGHEVKVFEKNESVKEVGAGIGIGDNVIKKLGNHDLAKGIK 62
Query: 66 RIGLE----DKLLAHGIPMRARMIHGQNGKLREIPYDPVHNQVELEQYPDCNIYFQHKLI 121
G + L G + ++ N + + + + I+ ++
Sbjct: 63 NAGQILSTMNLLDDKGTLL-NKVKLKSNTLNVTLHRQTLI-DIIKSYVKEDAIFTGKEVT 120
Query: 122 NLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGVRKCLMKQSMFNY 171
++ + VT + + SE L IGADG +S VR+ + S Y
Sbjct: 121 KIENETDKVTIHFADGESE----AFDLCIGADGIHSKVRQSVNADSKVRY 166
>gnl|CDD|236001 PRK07364, PRK07364, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 415
Score = 41.9 bits (99), Expect = 3e-04
Identities = 36/169 (21%), Positives = 68/169 (40%), Gaps = 22/169 (13%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V IVGGG+VG A + + L EA+ + ++G++ ALS+ IG
Sbjct: 21 VAIVGGGIVGLTLAAALKDSGLRIALIEAQ--PAEAAAAKGQA--YALSLLSARIFEGIG 76
Query: 69 LEDKLLAHGIPMRA---------RMIHGQNGKLRE--IPYDPVHN------QVELEQYPD 111
+ +K+L R ++ Q L + Y H Q L+ P+
Sbjct: 77 VWEKILPQIGKFRQIRLSDADYPGVVKFQPTDLGTEALGYVGEHQVLLEALQEFLQSCPN 136
Query: 112 CNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGVR 160
++++++ T + + + ++L++ ADGA S +R
Sbjct: 137 ITWLCPAEVVSVEYQQDAATVTLEIEGKQQTL-QSKLVVAADGARSPIR 184
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 38.2 bits (90), Expect = 4e-04
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 11 IVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
IVG GL G ++A + AK +V + E R+ I
Sbjct: 1 IVGAGLSGLVAAYLLAKRGKDVLVLEKRDRI 31
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 41.2 bits (97), Expect = 7e-04
Identities = 33/104 (31%), Positives = 43/104 (41%), Gaps = 20/104 (19%)
Query: 7 KSVVIVGGGLVGSLSACMFAK---NQYEVNLYEAREDIRNSGLSE-----GKSINL---A 55
+ I+GGG+ G LSA + EV L+EA + + GL G
Sbjct: 1 MKIAIIGGGIAG-LSAAYRLQKAGPDVEVTLFEADDRV--GGLLRTVKIDGFLFERGPHH 57
Query: 56 LSVRGREALRRI---GLEDKLLAHGIPMRARMIHGQNGKLREIP 96
R E L I GLEDKLL R + + +GKL IP
Sbjct: 58 FLARKEEILDLIKELGLEDKLL-WNSTARKYIYY--DGKLHPIP 98
>gnl|CDD|235728 PRK06184, PRK06184, hypothetical protein; Provisional.
Length = 502
Score = 40.7 bits (96), Expect = 0.001
Identities = 46/182 (25%), Positives = 67/182 (36%), Gaps = 40/182 (21%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V+IVG G G A A+ L E + S GK I R +E +G
Sbjct: 6 VLIVGAGPTGLTLAIELARRGVSFRLIEKAPEPFPG--SRGKGIQ----PRTQEVFDDLG 59
Query: 69 LEDKLLAHG---IPMRARMIHGQNGKLRE------------IPYD-----PVHNQVELEQ 108
+ D+++A G PMR I+ +G + E PY P Q E+
Sbjct: 60 VLDRVVAAGGLYPPMR---IYRDDGSVAESDMFAHLEPTPDEPYPLPLMVP---QWRTER 113
Query: 109 YP-------DCNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGVRK 161
+ F +L+ + ++ VT E + L +GADG S VRK
Sbjct: 114 ILRERLAELGHRVEFGCELVGFEQDADGVTARVAGPAGEETVRARYL-VGADGGRSFVRK 172
Query: 162 CL 163
L
Sbjct: 173 AL 174
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 40.7 bits (96), Expect = 0.001
Identities = 41/196 (20%), Positives = 69/196 (35%), Gaps = 44/196 (22%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE-DIRNSGLSEGKSINLALSVRGREA 63
S+ V+IVGGG VG A + + L E ++ N + S R E
Sbjct: 6 SETPVLIVGGGPVGLALALDLGRRGVDSILVERKDGTAFNPKAN-------TTSARSMEH 58
Query: 64 LRRIGLEDKLLAHGIP-------------------------MRARMIHGQNGKLREIPYD 98
RR+G+ D++ + G+P R + +
Sbjct: 59 FRRLGIADEVRSAGLPVDYPTDIAYFTRLTGYELARFRLPSAREAITPVGGPDGSWPSPE 118
Query: 99 PVH--NQVELE--------QYPDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKIT-DNQ 147
H Q LE P + + H+L + + ++ VT + + +T
Sbjct: 119 LPHRIPQKYLEPILLEHAAAQPGVTLRYGHRLTDFEQDADGVTATVEDLDGGESLTIRAD 178
Query: 148 LIIGADGAYSGVRKCL 163
++G DGA S VR+ L
Sbjct: 179 YLVGCDGARSAVRRSL 194
>gnl|CDD|181564 PRK08849, PRK08849, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Provisional.
Length = 384
Score = 39.8 bits (93), Expect = 0.002
Identities = 53/178 (29%), Positives = 84/178 (47%), Gaps = 31/178 (17%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE----------DIRNSGLSEGKSINLA 55
K + +VGGG+VG+ +A FAK V + E E DIR S +S+ S++L
Sbjct: 3 KYDIAVVGGGMVGAATALGFAKQGRSVAVIEGGEPKAFEPSQPMDIRVSAISQ-TSVDLL 61
Query: 56 LSVRGREALR--RIGLEDKLLAHGIP-MRARMIHGQNGKLREIPYDPVHNQV-------E 105
S+ ++ R+ +L P R R H L ++ Y V N++ +
Sbjct: 62 ESLGAWSSIVAMRVCPYKRLETWEHPECRTRF-HSDELNLDQLGY-IVENRLIQLGLWQQ 119
Query: 106 LEQYPDCNIYFQHKLINLDVNS-GN-VTFYRTEDNSETKITDNQLIIGADGAYSGVRK 161
QYP+ + KL +L+ ++ GN VT E +E + + +IGADGA S VR+
Sbjct: 120 FAQYPNLTLMCPEKLADLEFSAEGNRVTL---ESGAEIEA---KWVIGADGANSQVRQ 171
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 39.1 bits (91), Expect = 0.003
Identities = 28/101 (27%), Positives = 38/101 (37%), Gaps = 9/101 (8%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLA--LSVRGREA 63
K VV+VG G +G +A AK +V L EA + + L + LA L G E
Sbjct: 136 PKDVVVVGAGPIGLEAAEAAAKRGKKVTLIEAADRLGGQLLDPEVAEELAELLEKYGVEL 195
Query: 64 LRRIGLE--DKLLAHGIPMRARMIHGQNGKLREIPYDPVHN 102
L + + + R I G EI D V
Sbjct: 196 LLGTKVVGVEGKGNTLVVERVVGIDG-----EEIKADLVII 231
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 38.6 bits (90), Expect = 0.004
Identities = 38/186 (20%), Positives = 65/186 (34%), Gaps = 32/186 (17%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
VVIVG G GS +A AK +V + E + G LS R AL +
Sbjct: 6 VVIVGAGPAGSSAARRLAKAGLDVLVLEKGSEPGAKPCCGG-----GLSPR---ALEELI 57
Query: 69 LE-DKLLAHGIPMRARMIHGQNGKLREIPYDPVHNQVELEQYPD-----------CNIYF 116
+ D+ + + AR+ E+P + V+ ++ D +Y
Sbjct: 58 PDFDEEIERKVT-GARIYFPGEKVAIEVPVGEGYI-VDRAKF-DKWLAERAEEAGAELYP 114
Query: 117 QHKLINLDVNSGNV--TFYRTEDNSETKITDNQLIIGADGAYSGVRKCL--MKQSMFNYS 172
++ + V +D K+ +I ADG S + + L + +Y+
Sbjct: 115 GTRVTGVIREDDGVVVGVRAGDDEVRAKV-----VIDADGVNSALARKLGLKDRKPEDYA 169
Query: 173 QTYIEH 178
E
Sbjct: 170 IGVKEV 175
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 38.0 bits (88), Expect = 0.006
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 4 NSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
+ K VVI+GGG+VG +A A+ +V + EA E
Sbjct: 2 SMKMDVVIIGGGIVGLSAAYYLAERGADVTVLEAGE 37
>gnl|CDD|180582 PRK06475, PRK06475, salicylate hydroxylase; Provisional.
Length = 400
Score = 37.5 bits (87), Expect = 0.009
Identities = 41/182 (22%), Positives = 64/182 (35%), Gaps = 36/182 (19%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREAL 64
++ S +I G G+ G +A A + V + E +++ G L L+ L
Sbjct: 1 TRGSPLIAGAGVAGLSAALELAARGWAVTIIEKAQELSEVG------AGLQLAPNAMRHL 54
Query: 65 RRIGLEDKL-----------LAHGIPMRARMIHGQNGKLRE----IPYDPVHNQVELEQ- 108
R+G+ D+L L G R + Q G L PY H + +L+
Sbjct: 55 ERLGVADRLSGTGVTPKALYLMDGRKARPLL-AMQLGDLARKRWHHPYIVCH-RADLQSA 112
Query: 109 -YPDC--NIYFQHKL------INLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGV 159
C N + KL NS T RT + +I DG +S +
Sbjct: 113 LLDACRNNPGIEIKLGAEMTSQRQTGNSITATIIRTN---SVETVSAAYLIACDGVWSML 169
Query: 160 RK 161
R
Sbjct: 170 RA 171
>gnl|CDD|233693 TIGR02032, GG-red-SF, geranylgeranyl reductase family. This model
represents a subfamily which includes geranylgeranyl
reductases involved in chlorophyll and
bacteriochlorophyll biosynthesis as well as other
related enzymes which may also act on geranylgeranyl
groups or related substrates [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 295
Score = 36.5 bits (85), Expect = 0.015
Identities = 47/201 (23%), Positives = 73/201 (36%), Gaps = 30/201 (14%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
VV+VG G G+ +A A V L E + R K ALS R E L +
Sbjct: 3 VVVVGAGPAGASAAYRLADKGLRVLLLEKKSFPRY------KPCGGALSPRALEEL-DLP 55
Query: 69 LEDKLLAHGIPMRARMIHGQNGKLREIPYDPV-----------HNQVELEQYPDCNIYFQ 117
E + +R NG EIP + E Q +
Sbjct: 56 GELIVN----LVRGARFFSPNGDSVEIPIETELAYVIDRDAFDEQLAERAQEAGAELRLG 111
Query: 118 HKLINLDVNSGNVTF-YRTEDNSET-KITDNQLIIGADGAYSGVRKCL-MKQSMFNYSQT 174
++++++++ V R + + T KI +IGADG+ S V K L +K+ Y
Sbjct: 112 TRVLDVEIHDDRVVVIVRGSEGTVTAKI-----VIGADGSRSIVAKKLGLKKEPREYGVA 166
Query: 175 YIEHGYMELCIPPSEDNEVWL 195
M + EV++
Sbjct: 167 ARAEVEMPDEEVDEDFVEVYI 187
>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 = 37.0 bits (86), Expect = 0.016
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALR 65
+K V++VGGG G +A A+ + V L+E R L G + LA + GR
Sbjct: 379 RKRVLVVGGGPAGLEAAATAARRGHRVTLFE-----REDRL--GGQVRLAARLPGRGEFA 431
Query: 66 RI 67
+
Sbjct: 432 DL 433
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 36.8 bits (86), Expect = 0.017
Identities = 33/105 (31%), Positives = 46/105 (43%), Gaps = 22/105 (20%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQ---YEVNLYEAREDIRNSGL-----SEGKSINL---A 55
K V I+GGG+ G LSA + ++ L EA + R G +G I L +
Sbjct: 1 KKVAIIGGGITG-LSAAYRLHKKGPDADITLLEASD--RLGGKIQTVRKDGFPIELGPES 57
Query: 56 LSVRGREALR---RIGLEDKLLAHGIPMRAR-MIHGQNGKLREIP 96
R A +GLED+L+A + I+ NGKL IP
Sbjct: 58 FLARKPSAPALVKELGLEDELVA---NTTGQSYIY-VNGKLHPIP 98
>gnl|CDD|233672 TIGR01989, COQ6, ubiquinone biosynthesis monooxygenase COQ6. This
model represents the monooxygenase responsible for the
4-hydroxylateion of the phenol ring in the aerobic
biosynthesis of ubiquinone.
Length = 437
Score = 36.7 bits (85), Expect = 0.017
Identities = 57/237 (24%), Positives = 92/237 (38%), Gaps = 52/237 (21%)
Query: 9 VVIVGGGLVGSLSACMFAKNQY----EVNLYEAREDIRNSGLSEGKSINL---------A 55
VVIVGGG VG A N +V L +A + N L +
Sbjct: 3 VVIVGGGPVGLALAAALGNNPLTKDLKVLLLDA---VDNPKLKSRNYEKPDGPYSNRVSS 59
Query: 56 LSVRGREALRRIGLEDKLLAHGIPMRARM----------IHGQNGKLRE-----IPYDPV 100
++ ++IG D + + I RM I +E I D +
Sbjct: 60 ITPASISFFKKIGAWDHIQSDRIQPFGRMQVWDGCSLALIRFDRDNGKEDMACIIENDNI 119
Query: 101 HNQV--ELEQYPDCNIYFQHKLINLD-VNSGNVTFYRTEDNS---ETKITDNQ-----LI 149
N + L++Y N+ K++N + S + DNS ++D Q L+
Sbjct: 120 QNSLYNRLQEYNGDNV----KILNPARLISVTIPSKYPNDNSNWVHITLSDGQVLYTKLL 175
Query: 150 IGADGAYSGVRKCL-MKQSMFNYSQTYIEHGYMELCIPPSEDNEVWLYKNRLLSSVP 205
IGADG+ S VRK + + +NY+Q + ++L +E++ W R L + P
Sbjct: 176 IGADGSNSNVRKAANIDTTGWNYNQHAVV-ATLKLE-EATENDVAW---QRFLPTGP 227
>gnl|CDD|181552 PRK08773, PRK08773,
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Validated.
Length = 392
Score = 36.4 bits (84), Expect = 0.021
Identities = 18/42 (42%), Positives = 22/42 (52%)
Query: 1 MKCNSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIR 42
M S++ VIVGGG+VG+ A A V L E RE R
Sbjct: 1 MSRRSRRDAVIVGGGVVGAACALALADAGLSVALVEGREPPR 42
>gnl|CDD|202367 pfam02737, 3HCDH_N, 3-hydroxyacyl-CoA dehydrogenase, NAD binding
domain. This family also includes lambda crystallin.
Length = 180
Score = 35.6 bits (83), Expect = 0.021
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGL 46
V ++G G +G+ A +FA+ EV L + E+
Sbjct: 1 KVAVIGAGTMGAGIAQVFARAGLEVVLVDISEEALEKAR 39
>gnl|CDD|235416 PRK05335, PRK05335, tRNA (uracil-5-)-methyltransferase Gid;
Reviewed.
Length = 436
Score = 35.9 bits (84), Expect = 0.034
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAR 38
K V ++G GL GS +A AK V LYE R
Sbjct: 1 MMKPVNVIGAGLAGSEAAWQLAKRGVPVELYEMR 34
>gnl|CDD|215691 pfam00070, Pyr_redox, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 82
Score = 32.6 bits (75), Expect = 0.056
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIR 42
VV+VGGG +G A AK +V + E R+ +
Sbjct: 1 RVVVVGGGYIGLEFASALAKLGSKVTVVERRDRLL 35
>gnl|CDD|233987 TIGR02733, desat_CrtD, C-3',4' desaturase CrtD. Members of this
family are slr1293, a carotenoid biosynthesis protein
which was shown to be the C-3',4' desaturase (CrtD) of
myxoxanthophyll biosynthesis in Synechocystis sp.
strain PCC 6803, and close homologs (presumed to be
functionally equivalent) from other cyanobacteria,
where myxoxanthophyll biosynthesis is either known or
expected. This enzyme can act on neurosporene and so
presumably catalyzes the first step that is committed
to myxoxanthophyll [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 492
Score = 35.1 bits (81), Expect = 0.056
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEA 37
+ SVV++G G+ G +A + AK Y V L E
Sbjct: 1 ETSVVVIGAGIAGLTAAALLAKRGYRVTLLEQ 32
>gnl|CDD|169028 PRK07588, PRK07588, hypothetical protein; Provisional.
Length = 391
Score = 34.7 bits (80), Expect = 0.064
Identities = 42/182 (23%), Positives = 61/182 (33%), Gaps = 47/182 (25%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRR 66
V I G G+ G A + +E L E ++R G + G E +R
Sbjct: 1 MKVAISGAGIAGPTLAYWLRRYGHEPTLIERAPELRTGGYM------VDFWGVGYEVAKR 54
Query: 67 IGLEDKLLAHGIPMRA--------------------RMIHGQ-----NGKLREIPYDPVH 101
+G+ D+L G + RM+ G L Y +
Sbjct: 55 MGITDQLREAGYQIEHVRSVDPTGRRKADLNVDSFRRMVGDDFTSLPRGDLAAAIYTAID 114
Query: 102 NQVELEQYPDCNIYFQHKLINLDVNSGNV--TFYRTEDNSETKITDNQLIIGADGAYSGV 159
QVE F + +D + V TF R D L+IGADG +S V
Sbjct: 115 GQVE--------TIFDDSIATIDEHRDGVRVTFERGTPR------DFDLVIGADGLHSHV 160
Query: 160 RK 161
R+
Sbjct: 161 RR 162
>gnl|CDD|224154 COG1233, COG1233, Phytoene dehydrogenase and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 487
Score = 34.7 bits (80), Expect = 0.067
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 4 NSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
VV++G GL G +A + A+ +V + E +
Sbjct: 1 MPMYDVVVIGAGLNGLAAAALLARAGLKVTVLEKND 36
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 34.8 bits (81), Expect = 0.073
Identities = 41/174 (23%), Positives = 72/174 (41%), Gaps = 27/174 (15%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
VV+VG G VG A A+ V L + + LS G S + + R E R+G
Sbjct: 26 VVVVGAGPVGLALAIDLAQQGVPVVLLDD-----DDTLSTG-SRAICFAKRSLEIFDRLG 79
Query: 69 LEDKLLAHGIPMR-ARMIHGQNGKLR-EIPYDPVHN--------QVELEQY--------P 110
++++ G+ ++ R ++ +P H Q +E Y P
Sbjct: 80 CGERMVDKGVSWNVGKVFLRDEEVYRFDLLPEPGHRRPAFINLQQYYVEGYLVERAQALP 139
Query: 111 DCNIYFQHKLINLDVNSGNVTFY-RTEDNSETKITDNQLIIGADGAYSGVRKCL 163
+ ++ +++K+ L+ + VT T D T + +I DGA S +R+ L
Sbjct: 140 NIDLRWKNKVTGLEQHDDGVTLTVETPDGPYT--LEADWVIACDGARSPLREML 191
>gnl|CDD|235373 PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase;
Provisional.
Length = 461
Score = 34.4 bits (80), Expect = 0.082
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
+S++I G G++G A +FA +V L R+
Sbjct: 176 RSLIIYGAGVIGCEYASIFAALGVKVTLINTRD 208
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 34.3 bits (79), Expect = 0.10
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAR 38
V I G GL G +A A Y+V LYEAR
Sbjct: 1 MRVAIAGAGLAGLAAAYELADAGYDVTLYEAR 32
>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
Length = 472
Score = 34.1 bits (79), Expect = 0.11
Identities = 17/35 (48%), Positives = 22/35 (62%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
KS+VIVGGG++G A M A EV + EA + I
Sbjct: 181 KSLVIVGGGVIGLEWASMLADFGVEVTVVEAADRI 215
>gnl|CDD|180297 PRK05868, PRK05868, hypothetical protein; Validated.
Length = 372
Score = 34.2 bits (78), Expect = 0.11
Identities = 43/175 (24%), Positives = 71/175 (40%), Gaps = 32/175 (18%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGR--EAL 64
K+VV+ G + G+ +A ++ Y V + E R+ GL G A+ VRG + L
Sbjct: 2 KTVVVSGASVAGTAAAYWLGRHGYSVTMVE-----RHPGLRPGGQ---AIDVRGPALDVL 53
Query: 65 RRIGLEDKLLAHGIPMRARMIHGQNGK--LREIPYDPVHNQVELEQYPDCNIYFQHKLIN 122
R+GL H +R ++G R+ P V PD + + L+
Sbjct: 54 ERMGLLAAAQEHKTRIRGASFVDRDGNELFRDTESTPTGGPVN---SPDIEL-LRDDLVE 109
Query: 123 LDVNSGNVTFYRTEDNSETKITDN----------------QLIIGADGAYSGVRK 161
L + + D+S + + D+ L+IGADG +S VR+
Sbjct: 110 LLYGATQPSVEYLFDDSISTLQDDGDSVRVTFERAAAREFDLVIGADGLHSNVRR 164
>gnl|CDD|178515 PLN02927, PLN02927, antheraxanthin epoxidase/zeaxanthin epoxidase.
Length = 668
Score = 34.3 bits (78), Expect = 0.13
Identities = 48/194 (24%), Positives = 82/194 (42%), Gaps = 37/194 (19%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQ-YEVNLYEAR-EDIRNSGLSEGKSINLALSVRGREA 63
KKS V+V GG +G L + AK + ++V ++E IR G G + + A
Sbjct: 80 KKSRVLVAGGGIGGLVFALAAKKKGFDVLVFEKDLSAIRGEGKYRGP---IQIQSNALAA 136
Query: 64 LRRIGLE--DKLLAHGIPMRAR---MIHGQNGKL------------REIPYDPVHNQVEL 106
L I ++ ++++ G R ++ G +G R +P V +++ L
Sbjct: 137 LEAIDIDVAEQVMEAGCITGDRINGLVDGISGSWYVKFDTFTPAASRGLPVTRVISRMTL 196
Query: 107 EQYPDCNIYFQHKLINLDV--NSGNVTFYRTEDNSETKITDN------QLIIGADGAYSG 158
+Q + + DV N NV + + T + +N L++GADG +S
Sbjct: 197 QQ-------ILARAVGEDVIRNESNVVDFEDSGDKVTVVLENGQRYEGDLLVGADGIWSK 249
Query: 159 VRKCLMKQSMFNYS 172
VR L +S YS
Sbjct: 250 VRNNLFGRSEATYS 263
>gnl|CDD|181262 PRK08163, PRK08163, salicylate hydroxylase; Provisional.
Length = 396
Score = 33.9 bits (78), Expect = 0.14
Identities = 45/184 (24%), Positives = 70/184 (38%), Gaps = 37/184 (20%)
Query: 4 NSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRN--SGLSEGKSINLALSVRG- 60
V+IVGGG+ G +A A+ +V L E +I +G+ G + AL G
Sbjct: 2 TKVTPVLIVGGGIGGLAAALALARQGIKVKLLEQAAEIGEIGAGIQLGPNAFSALDALGV 61
Query: 61 REALRR-------IGLEDKLLAH-------GIPMRARMIHGQNGKLREIPYDPVH----N 102
EA R+ + + D + A G RAR PY +H +
Sbjct: 62 GEAARQRAVFTDHLTMMDAVDAEEVVRIPTGQAFRARF-GN--------PYAVIHRADIH 112
Query: 103 QVELE---QYPDCNIYFQHKLINLDVNSGNVTFYRTEDNSETKITDNQLIIGADGAYSGV 159
LE +P ++ ++ + VT + + N T +IG DG S V
Sbjct: 113 LSLLEAVLDHPLVEFRTSTHVVGIEQDGDGVTVFDQQGNRWT----GDALIGCDGVKSVV 168
Query: 160 RKCL 163
R+ L
Sbjct: 169 RQSL 172
>gnl|CDD|224152 COG1231, COG1231, Monoamine oxidase [Amino acid transport and
metabolism].
Length = 450
Score = 33.6 bits (77), Expect = 0.17
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
V+IVG GL G +A K Y+V + EAR+
Sbjct: 8 ADVIIVGAGLAGLSAAYELKKAGYQVQILEARD 40
>gnl|CDD|203096 pfam04820, Trp_halogenase, Tryptophan halogenase. Tryptophan
halogenase catalyzes the chlorination of tryptophan to
form 7-chlorotryptophan. This is the first step in the
biosynthesis of pyrrolnitrin, an antibiotic with
broad-spectrum anti-fungal activity. Tryptophan
halogenase is NADH-dependent.
Length = 457
Score = 33.1 bits (76), Expect = 0.21
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 9 VVIVGGGLVGSLSACMFAK---NQYEVNLYEAREDI 41
+VIVGGG G ++A A+ +V L E+ E+I
Sbjct: 2 IVIVGGGTAGWMAAAALARALKGGLDVTLVES-EEI 36
>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
Length = 569
Score = 33.2 bits (76), Expect = 0.22
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
K V I+G GL G +A +EV++YE+R I
Sbjct: 75 KLKVAIIGAGLAGMSTAVELLDQGHEVDIYESRPFI 110
>gnl|CDD|224127 COG1206, Gid, NAD(FAD)-utilizing enzyme possibly involved in
translation [Translation, ribosomal structure and
biogenesis].
Length = 439
Score = 33.1 bits (76), Expect = 0.26
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAR 38
++ + ++G GL GS +A AK V LYE R
Sbjct: 2 MQQPINVIGAGLAGSEAAWQIAKRGVPVILYEMR 35
>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 = 32.7 bits (75), Expect = 0.29
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSE 48
K VV+VGGG +G A AK EV + E R+ + E
Sbjct: 143 KRVVVVGGGYIGLELAAALAKLGKEVTVVERRDRLLARADDE 184
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 32.5 bits (75), Expect = 0.35
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 13/53 (24%)
Query: 55 ALSVRGREALRRIGLEDKLL--AHGIPMRARMIHGQNGKLREIPYDPVHNQVE 105
AL+ REAL ++G D+LL AHG+P R + G DP Q E
Sbjct: 164 ALADSIREALAKLGDPDRLLFSAHGLPERYI----KKG-------DPYPAQCE 205
>gnl|CDD|235706 PRK06129, PRK06129, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 308
Score = 32.3 bits (74), Expect = 0.38
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEARED 40
SV I+G GL+G A +FA+ +EV L++A
Sbjct: 4 SVAIIGAGLIGRAWAIVFARAGHEVRLWDADPA 36
>gnl|CDD|236385 PRK09126, PRK09126, hypothetical protein; Provisional.
Length = 392
Score = 32.2 bits (74), Expect = 0.40
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 15/87 (17%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNS--GLSE----GKSINLALSVRGRE 62
+V+VG G G A A + +V L E R L++ G+ I AL+ RE
Sbjct: 6 IVVVGAGPAGLSFARSLAGSGLKVTLIE-----RQPLAALADPAFDGREI--ALTHASRE 58
Query: 63 ALRRIGLEDKLLAHGI-PMR-ARMIHG 87
L+R+G D++ I P+R A++++G
Sbjct: 59 ILQRLGAWDRIPEDEISPLRDAKVLNG 85
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 32.5 bits (75), Expect = 0.40
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLA 55
+ I+GGG+ G+ A A+ ++V LYE + ++G S N
Sbjct: 261 RDAAIIGGGIAGAALALALARRGWQVTLYE-----ADEAPAQGASGNRQ 304
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 31.5 bits (72), Expect = 0.56
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 13/70 (18%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRG-------R 61
++I+G G VG A ++ + V L + E+ L++ L
Sbjct: 3 IIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLAD------ELDTHVVIGDATDE 56
Query: 62 EALRRIGLED 71
+ L G++D
Sbjct: 57 DVLEEAGIDD 66
>gnl|CDD|224170 COG1250, FadB, 3-hydroxyacyl-CoA dehydrogenase [Lipid
metabolism].
Length = 307
Score = 31.8 bits (73), Expect = 0.58
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSE 48
K V ++G G++G+ A +FA Y+V L + + L+
Sbjct: 4 KKVAVIGAGVMGAGIAAVFALAGYDVVLKDISPEALERALAY 45
>gnl|CDD|227035 COG4691, StbC, Plasmid stability protein [General function
prediction only].
Length = 80
Score = 29.0 bits (65), Expect = 0.89
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 36 EAREDIRNSGLSEGKSINLALSVRGREAL----RRIGLEDKLLAHGIPMR 81
EARE + + L E + +AL+ + R+GL + R
Sbjct: 31 EAREILTAALLGEEVPMPVALAADSGREIDLEPERLGLIARTRPQSRDER 80
>gnl|CDD|129243 TIGR00137, gid_trmFO, tRNA:m(5)U-54 methyltransferase. This
model represents an orthologous set of proteins present
in relatively few bacteria but very tightly conserved
where it occurs. It is closely related to gidA
(glucose-inhibited division protein A), which appears
to be present in all complete eubacterial genomes so
far and in Saccharomyces cerevisiae. It was designated
gid but is now recognized as a tRNA:m(5)U-54
methyltransferase and is now designated trmFO [Protein
synthesis, tRNA and rRNA base modification].
Length = 433
Score = 31.4 bits (71), Expect = 0.90
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAR 38
V ++GGGL GS +A A+ V LYE R
Sbjct: 1 TPVHVIGGGLAGSEAAWQLAQAGVPVILYEMR 32
>gnl|CDD|183139 PRK11445, PRK11445, putative oxidoreductase; Provisional.
Length = 351
Score = 31.2 bits (71), Expect = 0.94
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 130 VTFYRTEDNSETKITDNQLIIGADGAYSGVRKCLMKQ 166
V F D E IT + ++GADGA S VR+ L
Sbjct: 133 VIFR--ADGWEQHIT-ARYLVGADGANSMVRRHLYPD 166
>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 = 31.0 bits (70), Expect = 1.0
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAR 38
V IVG GL G +A +EV++YE+R
Sbjct: 2 VAIVGAGLAGLSTAVELVDAGHEVDIYESR 31
>gnl|CDD|235870 PRK06834, PRK06834, hypothetical protein; Provisional.
Length = 488
Score = 30.8 bits (70), Expect = 1.2
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRI 67
+VVI GGG G + A A +V + E R + G G L R E L +
Sbjct: 5 AVVIAGGGPTGLMLAGELALAGVDVAIVERRPNQELVGSRAG-----GLHARTLEVLDQR 59
Query: 68 GLEDKLLAHG 77
G+ D+ LA G
Sbjct: 60 GIADRFLAQG 69
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 30.9 bits (70), Expect = 1.2
Identities = 17/33 (51%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 7 KSVVIVGGGLVGSLSACMF-AKNQYEVNLYEAR 38
K V IVG G G LSA F A YEV +YE+
Sbjct: 284 KKVAIVGSGPAG-LSAAYFLATMGYEVTVYESL 315
>gnl|CDD|181001 PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 388
Score = 30.6 bits (70), Expect = 1.3
Identities = 41/185 (22%), Positives = 68/185 (36%), Gaps = 39/185 (21%)
Query: 1 MKCNSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYE---AREDIRNSGLSEGKSINLALS 57
+ + ++GGG G +A A+ V L D+R + L G SI
Sbjct: 2 LMEKEHTDIAVIGGGPAGLAAAIALARAGASVALVAPEPPYADLRTTALL-GPSIRF--- 57
Query: 58 VRGREALRRIGLEDKLLAHGIPMRA-RMIHGQNGKLREIPYDPVH---NQVELEQY---- 109
L R+GL +L H P+++ R++ G+L P V ++ + +
Sbjct: 58 ------LERLGLWARLAPHAAPLQSMRIVDA-TGRLIRAP--EVRFRAAEIGEDAFGYNI 108
Query: 110 PDCNIYFQHKLI-------NLDVNSGNVTFYRTEDNSET-KITDNQ-----LIIGADGAY 156
P N L N+ R ++ T + D L++GADG
Sbjct: 109 P--NWLLNRALEARVAELPNITRFGDEAESVRPREDEVTVTLADGTTLSARLVVGADGRN 166
Query: 157 SGVRK 161
S VR+
Sbjct: 167 SPVRE 171
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the E3
component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to have
distinct functions (ferric leghemoglobin reductase and
NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 30.7 bits (70), Expect = 1.5
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
+S+VI+GGG++G A +FA +V + E + I
Sbjct: 171 ESLVIIGGGVIGVEFASIFASLGSKVTVIEMLDRI 205
>gnl|CDD|215205 PLN02357, PLN02357, serine acetyltransferase.
Length = 360
Score = 30.2 bits (68), Expect = 1.6
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 257 DRDQPC----KPLLDFKNPIKIQSHAVVNEFYKQESLIVASLCQEKIEKMF 303
+RD C L+FK + Q+H + ++ + Q I+A L Q ++ + F
Sbjct: 175 ERDPACISYVHCFLNFKGFLACQAHRIAHKLWTQGRKILALLIQNRVSEAF 225
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 30.2 bits (69), Expect = 1.7
Identities = 28/82 (34%), Positives = 39/82 (47%), Gaps = 23/82 (28%)
Query: 9 VVIVGGGLVGSLSACM-FAKNQYEVNLYEAREDIRNSGLS-----EGKSI---------- 52
+ IVGGG+ G L+A AK +EV ++EA + + GL+ G I
Sbjct: 2 IAIVGGGIAG-LAAAYRLAKRGHEVTVFEADDQL--GGLAASFEFGGLPIERFYHHIFKS 58
Query: 53 NLALSVRGREALRRIGLEDKLL 74
+ AL E L +GLEDKL
Sbjct: 59 DEAL----LELLDELGLEDKLR 76
>gnl|CDD|144583 pfam01043, SecA_PP_bind, SecA preprotein cross-linking domain. The
SecA ATPase is involved in the insertion and retraction
of preproteins through the plasma membrane. This domain
has been found to cross-link to preproteins, thought to
indicate a role in preprotein binding. The pre-protein
cross-linking domain is comprised of two sub domains
that are inserted within the ATPase domain.
Length = 113
Score = 28.6 bits (65), Expect = 1.9
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 297 EKIEKMFDNTSTYKSRHINFIH------RSYHLYTVDI 328
EK EK+ + Y +I +H R++HL+ D+
Sbjct: 42 EKAEKLLGIENLYDPENIELLHHINQALRAHHLFKRDV 79
>gnl|CDD|236541 PRK09496, trkA, potassium transporter peripheral membrane
component; Reviewed.
Length = 453
Score = 30.1 bits (69), Expect = 1.9
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEARED 40
K V+IVGGG +G A + K Y V L E +
Sbjct: 232 KRVMIVGGGNIGYYLAKLLEKEGYSVKLIERDPE 265
>gnl|CDD|180361 PRK06035, PRK06035, 3-hydroxyacyl-CoA dehydrogenase; Validated.
Length = 291
Score = 29.8 bits (67), Expect = 2.0
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRR 66
K + +VG G++G A +FA+ Y+V + + E+I + + + I G LR
Sbjct: 4 KVIGVVGSGVMGQGIAQVFARTGYDVTIVDVSEEILKNAM---ELIE-----SGPYGLRN 55
Query: 67 I 67
+
Sbjct: 56 L 56
>gnl|CDD|223652 COG0579, COG0579, Predicted dehydrogenase [General function
prediction only].
Length = 429
Score = 29.9 bits (68), Expect = 2.1
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 9 VVIVGGGLVGSLSACMFAK--NQYEVNLYEAREDIRNSGLSEGKSIN 53
VVI+GGG++G+ +A ++ V L E + G+++ S N
Sbjct: 6 VVIIGGGIMGAATAYELSEYEPDLSVALLE-----KEDGVAQESSSN 47
>gnl|CDD|226268 COG3745, CpaB, Flp pilus assembly protein CpaB [Intracellular
trafficking and secretion].
Length = 276
Score = 29.7 bits (67), Expect = 2.1
Identities = 6/31 (19%), Positives = 13/31 (41%), Gaps = 6/31 (19%)
Query: 221 LMNFPRADQGGDKRDCLLHEGTSRILVPNMR 251
++ + D G D + ++PN+R
Sbjct: 155 ILTVRKDDAGADS------SKLAETVLPNIR 179
>gnl|CDD|240384 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
Length = 567
Score = 30.2 bits (68), Expect = 2.3
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V+IVGG + G + A +K +V + E R+ + + L G AL+ +G
Sbjct: 36 VIIVGGSIAGPVLAKALSKQGRKVLMLE-----RDLFSKPDRIVGELLQPGGVNALKELG 90
Query: 69 LEDKLLAHGIPMRARMIHGQNGKLREIPY 97
+E+ G+P ++ GK ++PY
Sbjct: 91 MEECAEGIGMPCFGYVVFDHKGKQVKLPY 119
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and 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.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 29.8 bits (68), Expect = 2.4
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 1 MKCNSKKSVVIVGGGLVGSLSACMFAK 27
+K S+ + G G VG L+A M AK
Sbjct: 182 LKPRPGSSIAVFGAGAVG-LAAVMAAK 207
>gnl|CDD|233018 TIGR00551, nadB, L-aspartate oxidase. L-aspartate oxidase is the
B protein, NadB, of the quinolinate synthetase complex.
Quinolinate synthetase makes a precursor of the
pyridine nucleotide portion of NAD. This model
identifies proteins that cluster as L-aspartate oxidase
(a flavoprotein difficult to separate from the set of
closely related flavoprotein subunits of succinate
dehydrogenase and fumarate reductase) by both UPGMA and
neighbor-joining trees. The most distant protein
accepted as an L-aspartate oxidase (NadB), that from
Pyrococcus horikoshii, not only clusters with other
NadB but is just one gene away from NadA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Pyridine
nucleotides].
Length = 488
Score = 29.8 bits (67), Expect = 2.4
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
VV++G G G LSA + +Q V +
Sbjct: 1 HSCDVVVIGSGAAG-LSAALALADQGRVIVLSKAP 34
>gnl|CDD|181018 PRK07530, PRK07530, 3-hydroxybutyryl-CoA dehydrogenase;
Validated.
Length = 292
Score = 29.6 bits (67), Expect = 2.4
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSI--NLALSV-RGR-- 61
K V ++G G +G+ A + A Y+V L + D +GL+ +I NLA V +G+
Sbjct: 5 KKVGVIGAGQMGNGIAHVCALAGYDVLLNDVSADRLEAGLA---TINGNLARQVAKGKIS 61
Query: 62 -----EALRRIGLEDKLLAHG 77
AL RI L
Sbjct: 62 EEARAAALARISTATDLEDLA 82
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 29.9 bits (68), Expect = 2.4
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 4 NSKKSVVIVGGGLVGSLSACMF-AKNQYEVNLYEARED 40
S+K V ++G G G L+A F A+ + V ++E E+
Sbjct: 537 GSRKKVAVIGAGPAG-LAAAYFLARAGHPVTVFEREEN 573
>gnl|CDD|225915 COG3380, COG3380, Predicted NAD/FAD-dependent oxidoreductase
[General function prediction only].
Length = 331
Score = 29.8 bits (67), Expect = 2.6
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYE 36
S+ IVG G+ G +A + EV ++E
Sbjct: 3 SIAIVGAGIAGLAAAYALREAGREVTVFE 31
>gnl|CDD|177909 PLN02268, PLN02268, probable polyamine oxidase.
Length = 435
Score = 29.7 bits (67), Expect = 2.7
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
SV+++GGG+ G +A ++V L E+R+ I
Sbjct: 2 SVIVIGGGIAGIAAARALHDASFKVTLLESRDRI 35
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e)
SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR
that catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR
subfamily, with a characteristic active site tetrad and
NAD-binding motif. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 29.6 bits (67), Expect = 2.7
Identities = 20/79 (25%), Positives = 28/79 (35%), Gaps = 9/79 (11%)
Query: 7 KSVVIVGG-GLVGSLSACMFAKNQYEV----NL---YEAREDIRNSGLSEGKSINLA-LS 57
V+I GG G +GS A F K +EV NL E +
Sbjct: 1 MRVLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRGSFGNLAWLKANREDGGVRFVHGD 60
Query: 58 VRGREALRRIGLEDKLLAH 76
+R R L + + L+ H
Sbjct: 61 IRNRNDLEDLFEDIDLIIH 79
>gnl|CDD|178578 PLN03000, PLN03000, amine oxidase.
Length = 881
Score = 30.0 bits (67), Expect = 2.7
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEARE 39
SK SVVIVG GL G +A + ++V + E R+
Sbjct: 183 SKSSVVIVGAGLSGLAAARQLMRFGFKVTVLEGRK 217
>gnl|CDD|168629 PRK06617, PRK06617, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 374
Score = 29.5 bits (66), Expect = 2.7
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAR--------EDIRNSGLS 47
+ VI+G GL G L+A FA+ + ++E++ +DIR + L+
Sbjct: 3 NTVILGCGLSGMLTALSFAQKGIKTTIFESKSVKSPEFFKDIRTTALT 50
>gnl|CDD|236341 PRK08850, PRK08850, 2-octaprenyl-6-methoxyphenol hydroxylase;
Validated.
Length = 405
Score = 29.7 bits (67), Expect = 2.8
Identities = 42/173 (24%), Positives = 69/173 (39%), Gaps = 27/173 (15%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINL-ALSVRGREALRRI 67
V I+GGG+VG A ++ + + E + + L+E + + ALS LR +
Sbjct: 7 VAIIGGGMVGLALAAALKESDLRIAVIEGQ--LPEEALNELPDVRVSALSRSSEHILRNL 64
Query: 68 GLEDKLLAHGIPMRARMIHGQNGKLREIPYDPVHNQVELEQYPDCNIYFQHKLINLDV-- 125
G + A M + I +D + Q PD ++++I L +
Sbjct: 65 GAWQGIEARRAAPYIAMEVWEQDSFARIEFD----AESMAQ-PDLGHIVENRVIQLALLE 119
Query: 126 ---NSGNVTFYRTE-------DNSETKIT-DN------QLIIGADGAYSGVRK 161
NVT SE +T DN +L++GADGA S +R+
Sbjct: 120 QVQKQDNVTLLMPARCQSIAVGESEAWLTLDNGQALTAKLVVGADGANSWLRR 172
>gnl|CDD|118773 pfam10249, NDUFB10, NADH-ubiquinone oxidoreductase subunit 10.
NDUFB10 is a family of conserved proteins of up to 180
residues. It is one of the 41 protein subunits within
the hydrophobic fraction of the NADH:ubiquinone
oxidoreductase (complex I), a multiprotein complex
located in the inner mitochondrial membrane whose main
function is the transport of electrons from NADH to
ubiquinone, which is accompanied by translocation of
protons from the mitochondrial matrix to the
intermembrane space. NDUFB10 is encoded in the nucleus.
Length = 128
Score = 28.2 bits (63), Expect = 3.5
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 154 GAYSGVRKCLMKQ 166
GAY+ RKCLMKQ
Sbjct: 107 GAYANARKCLMKQ 119
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 29.4 bits (67), Expect = 3.7
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 15/79 (18%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYE------ARED------IRNSGLSEGKSINL 54
+ +VI+GGG +G A MF + EV + E RED +R EG + L
Sbjct: 172 EHLVIIGGGYIGLEFAQMFRRFGSEVTVIERGPRLLPREDEDVAAAVREILEREGIDVRL 231
Query: 55 ---ALSVRGREALRRIGLE 70
+ V +GL+
Sbjct: 232 NAECIRVERDGDGIAVGLD 250
>gnl|CDD|214937 smart00957, SecA_DEAD, SecA DEAD-like domain. SecA protein binds
to the plasma membrane where it interacts with proOmpA
to support translocation of proOmpA through the
membrane. SecA protein achieves this translocation, in
association with SecY protein, in an ATP dependent
manner. This domain represents the N-terminal
ATP-dependent helicase domain, which is related to the.
Length = 380
Score = 29.3 bits (67), Expect = 3.7
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 297 EKIEKMFDNTSTYKSRHINFIH------RSYHLYTVDI 328
EK EK+ + Y +I +H R+++L+ D+
Sbjct: 265 EKAEKLLGIDNLYDPENIELLHHVNQALRAHYLFKRDV 302
>gnl|CDD|236223 PRK08294, PRK08294, phenol 2-monooxygenase; Provisional.
Length = 634
Score = 29.2 bits (66), Expect = 3.8
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 VTFYRT--EDNSETKITDNQLIIGADGAYSGVRKCL 163
VT RT E E + + ++G DGA S VRK +
Sbjct: 181 VTLRRTDGEHEGEEETVRAKYVVGCDGARSRVRKAI 216
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 29.1 bits (66), Expect = 4.1
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 7 KSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDI 41
KS+VIVGGG +G A +FA +V + E + I
Sbjct: 174 KSLVIVGGGYIGLEFASVFAALGSKVTVVERGDRI 208
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 29.0 bits (66), Expect = 4.2
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 5 SKKSVVIVGGGLVGSLS-ACMFAKNQYEVNLYEAREDI 41
+ K V ++G G G L+ A A+ Y+V ++EAR+
Sbjct: 139 TGKKVAVIGAGPAG-LTAAHRLARKGYDVTIFEARDKA 175
>gnl|CDD|235967 PRK07208, PRK07208, hypothetical protein; Provisional.
Length = 479
Score = 29.1 bits (66), Expect = 4.3
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 4 NSKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLS 47
+KKSVVI+G G G +A K Y V + EA + G+S
Sbjct: 2 TNKKSVVIIGAGPAGLTAAYELLKRGYPVTVLEADPVV--GGIS 43
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 28.8 bits (65), Expect = 4.5
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKN-QYEVNL----YEAREDIRNSGLSEGKSINLALSVRG 60
++++G G VGS+ A A+N EV + E I + ++ L +
Sbjct: 1 MMKILVIGAGGVGSVVAHKLAQNGDGEVTIADRSKEKCARIAELIGGKVEA--LQVDAAD 58
Query: 61 REALRRI 67
+AL +
Sbjct: 59 VDALVAL 65
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 28.8 bits (65), Expect = 4.6
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 3/74 (4%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V IVG GL+G A + V + D + L + + +
Sbjct: 6 VGIVGLGLMGGSLARALKEAGLVVRIIGR--DRSAATLKAALELGVIDELTVAGLAEAAA 63
Query: 69 LEDKLLAHGIPMRA 82
D L+ +P+ A
Sbjct: 64 EAD-LVIVAVPIEA 76
>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 = 4.6
Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 17/109 (15%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQY-----EVNLYEAREDI-------RNSG--LSEGKS 51
KK VVI+GGG+ G L A + + + E+ L EA + + + G + G
Sbjct: 2 KKHVVIIGGGISG-LCAAYYLEKEIPELPVELTLVEASDRVGGKIQTVKEDGYLIERGPD 60
Query: 52 INLALSVRGREALRRIGLEDKLLAHGIPMRARMIHGQNGKLREIPYDPV 100
L + ++ +GLE L++ R + GKL +P
Sbjct: 61 SFLERKKSAPDLVKDLGLEHVLVSD--ATGQRYVLVNRGKLMPVPTKIA 107
>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 = 28.4 bits (64), Expect = 5.4
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 7 KSVVIVGGGLVGSLSACMFAK 27
+V+++G G VG L A AK
Sbjct: 136 DTVLVLGAGGVG-LLAAQLAK 155
>gnl|CDD|237771 PRK14619, PRK14619, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 308
Score = 28.4 bits (64), Expect = 6.1
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLS 47
K++ I+G G GS A + + N + V ++ R SGLS
Sbjct: 3 QPKTIAILGAGAWGSTLAGLASANGHRVRVWS-----RRSGLS 40
>gnl|CDD|236319 PRK08641, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 589
Score = 28.4 bits (64), Expect = 6.7
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 4 NSKKSVVIVGGGLVGSLSACM 24
+K V++VGGGL G L A +
Sbjct: 1 MAKGKVIVVGGGLAG-LMATI 20
>gnl|CDD|215439 PLN02819, PLN02819, lysine-ketoglutarate reductase/saccharopine
dehydrogenase.
Length = 1042
Score = 28.6 bits (64), Expect = 7.1
Identities = 29/163 (17%), Positives = 61/163 (37%), Gaps = 26/163 (15%)
Query: 148 LIIGADGAYSGVRKCLMKQSMFNYSQTYIEHGYMELCIPPSEDNEVWLYKNRLLSS---- 203
+I A G++ + KC + QS S + +E G ++D EV ++++ S
Sbjct: 482 VIEAAGGSFH-LAKCQVGQSADAESYSELEVG--------ADDKEVL---DQIIDSLTRL 529
Query: 204 -VPEVRKRISLRAQSLKSLMNFPRADQGGDKRDCLLHEGTSRILVPNMRLSNHLDRDQPC 262
P R + L + + + + +L+ L + C
Sbjct: 530 ANPNEDYISPAREANKIFLKIGKVQQENECNEKAEVTKKSQNVLI--------LGAGRVC 581
Query: 263 KPLLDFKNPIK-IQSHAVVNEFYKQESLIVASLCQEKIEKMFD 304
+P ++ +K I + +E +IVASL + ++ +
Sbjct: 582 RPAAEYLASVKTISYYGDDSEEPTDVHVIVASLYLKDAKETVE 624
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 28.2 bits (63), Expect = 7.8
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 8 SVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSE 48
V IVGGGL G +A AK ++V + NS L++
Sbjct: 3 KVGIVGGGLAGLTAAISLAKKGFDVTIIGPGIKKSNSYLAQ 43
>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 = 28.3 bits (63), Expect = 8.3
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 5 SKKSVVIVGGGLVGSLSACMFAKNQYEVNLYEA 37
+ K V ++G G G A AK + V ++EA
Sbjct: 132 THKKVAVIGAGPAGLACASELAKAGHSVTVFEA 164
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase
[Cell envelope biogenesis, outer membrane].
Length = 448
Score = 28.0 bits (63), Expect = 8.5
Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 2/81 (2%)
Query: 6 KKSVVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALR 65
K V+++G G G +A K EV + + R + + + G
Sbjct: 7 GKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDRPAPEGLAAQPLLLEGIEVEL-GSHDDE 65
Query: 66 RIGLEDKL-LAHGIPMRARMI 85
+ D + + GIP ++
Sbjct: 66 DLAEFDLVVKSPGIPPTHPLV 86
>gnl|CDD|234847 PRK00847, thyX, FAD-dependent thymidylate synthase; Reviewed.
Length = 217
Score = 27.5 bits (62), Expect = 9.0
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 171 YSQTYIEHGYMELCIPPSEDNEVWLYKNRLLSSVPEVRKRISLRAQSLKSLMNFPRADQG 230
SQ Y+ E IPPS + N S E+ + + + + +
Sbjct: 90 QSQRYVLLDEFEFYIPPSIRKDNQSNSN----SQEELLELF--EEAAEAAYEAYEELLEK 143
Query: 231 GDKRDCLLHEGTSRILVPN 249
G R+ +R ++P
Sbjct: 144 GIAREL------ARYVLPL 156
>gnl|CDD|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 27.9 bits (62), Expect = 9.8
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 9 VVIVGGGLVGSLSACMFAKNQYEVNLYEAREDIRNSGLSEGKSINLALSVRGREALRRIG 68
V+IVG G+ GS A AK+ V++ E D+R G+ + GR L ++G
Sbjct: 46 VIIVGAGVGGSALAYALAKDGRRVHVIE--RDLREPERMMGEFMQPG----GRFMLSKLG 99
Query: 69 LEDKL 73
LED L
Sbjct: 100 LEDCL 104
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.395
Gapped
Lambda K H
0.267 0.0863 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,911,839
Number of extensions: 1805589
Number of successful extensions: 1818
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1792
Number of HSP's successfully gapped: 116
Length of query: 379
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 280
Effective length of database: 6,546,556
Effective search space: 1833035680
Effective search space used: 1833035680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.6 bits)