RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12250
(235 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 = 66.7 bits (163), Expect = 8e-13
Identities = 42/186 (22%), Positives = 67/186 (36%), Gaps = 12/186 (6%)
Query: 5 FLHIWPRGTFMMIALPNQDHSWTVTLFMPFEKFGLLGTARALLDFFDKYFPDAIPLIGAE 64
G F ++ LP+ S +L + + L + + PL G
Sbjct: 198 GERFTHAGPFALLPLPDNRSSVVWSLPPGPAEDLQGLSDEEFLRELQRRLGERDPL-GRV 256
Query: 65 RLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLM 124
LV+ + PL Y + +V++IGDAAHAM P GQG N ED L + +
Sbjct: 257 TLVSSRSAF---PLSLRVAERYRR-GRVVLIGDAAHAMHPLAGQGANLALEDAAALAEAL 312
Query: 125 IQYDEDFG--KVLPKFTEVRQHDAEAICDLAMYNYIEMRDLVTKSSFLWRKRFDSFLFWM 182
L + R+ AEAI L+ + L + + + + +
Sbjct: 313 AAAPRPGADAAALAAYEARRRPRAEAIQKLSR----ALGRLFSADG-PFARFLRNLGLRL 367
Query: 183 FPRLWI 188
RL
Sbjct: 368 LDRLPP 373
>gnl|CDD|235727 PRK06183, mhpA, 3-(3-hydroxyphenyl)propionate hydroxylase;
Validated.
Length = 500
Score = 49.9 bits (120), Expect = 3e-07
Identities = 17/25 (68%), Positives = 19/25 (76%)
Query: 92 VLIIGDAAHAMVPFYGQGMNAGFED 116
VL+ GDAAH M PF GQGMN+G D
Sbjct: 288 VLLAGDAAHLMPPFAGQGMNSGIRD 312
>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 = 49.2 bits (118), Expect = 4e-07
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 51 DKYFPDAI-----PLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPF 105
+++ + +G + + + + S Y K +V + GDAAH P
Sbjct: 241 EEFTDEEAKQRLRSAVGIDLADVEILWKSIWGVRSRVATRYRK-GRVFLAGDAAHIHPPT 299
Query: 106 YGQGMNAGFED 116
GQG+N G +D
Sbjct: 300 GGQGLNTGIQD 310
>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 = 48.5 bits (116), Expect = 1e-06
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 73 RKAAPL-ISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDF 131
RK PL + I H +V++IG+AA + P GQG N G D L +++I D
Sbjct: 260 RKTYPLKLRIAETHVHP--RVVLIGNAAQTLHPIAGQGFNLGLRDVETLAEVLIDARIDL 317
Query: 132 GK--VLPKFTEVRQHD 145
G +L ++ RQ D
Sbjct: 318 GTYALLQEYLRRRQFD 333
>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 = 47.6 bits (114), Expect = 2e-06
Identities = 43/159 (27%), Positives = 62/159 (38%), Gaps = 34/159 (21%)
Query: 7 HIWPRGTFMMIALPNQDHS----WTVT-------LFMPFEKFGLLGTARALLDFFDKYFP 55
P G + LP D+ WT+ L + E+F L F
Sbjct: 202 RFTPTGPLAL--LPLPDNRSSLVWTLPPEEAERLLALSDEEF-----LAELQRAFGSRL- 253
Query: 56 DAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFE 115
GA LV R A PL Y ++ +IGDAAH + P GQG+N G
Sbjct: 254 ------GAITLVG---ERHAFPLSLTHAKRYVA-PRLALIGDAAHTIHPLAGQGLNLGLR 303
Query: 116 DCCILQDLMI---QYDEDFG--KVLPKFTEVRQHDAEAI 149
D L +++ + ED G +VL ++ R+ D A+
Sbjct: 304 DVAALAEVLEDARRRGEDIGSPRVLQRYERRRRFDNAAM 342
>gnl|CDD|136171 PRK07045, PRK07045, putative monooxygenase; Reviewed.
Length = 388
Score = 44.9 bits (106), Expect = 1e-05
Identities = 33/109 (30%), Positives = 48/109 (44%), Gaps = 10/109 (9%)
Query: 44 RALLDFFDKYFPDAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMV 103
L +F DA+ IGA F PL + + YHK V+++GDAAH++
Sbjct: 246 ARLNEFVGDESADAMAAIGA---GTAF---PLIPLGRMNLDRYHK-RNVVLLGDAAHSIH 298
Query: 104 PFYGQGMNAGFEDCCILQDLMIQYDED---FGKVLPKFTEVRQHDAEAI 149
P GQGMN ED L + + L +F +R+ EA+
Sbjct: 299 PITGQGMNLAIEDAGELGACLDLHLSGQIALADALERFERIRRPVNEAV 347
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 44.6 bits (106), Expect = 2e-05
Identities = 16/35 (45%), Positives = 21/35 (60%)
Query: 92 VLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQ 126
V ++GDAAH + P GQGMN G D L D++
Sbjct: 282 VALVGDAAHLIHPLAGQGMNLGLRDVAALADVLAG 316
>gnl|CDD|132263 TIGR03219, salicylate_mono, salicylate 1-monooxygenase. Members of
this protein family are salicylate 1-monooxygenase, also
called salicylate hydroxylase. This enzyme converts
salicylate to catechol, which is a common intermediate
in the degradation of a number of aromatic compounds
(phenol, toluene, benzoate, etc.). The gene for this
protein may occur in catechol degradation genes, such as
those of the meta-cleavage pathway.
Length = 414
Score = 43.3 bits (102), Expect = 5e-05
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 85 PYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLM---IQYDEDFGKVLPKFTEV 141
P + + +V +IGDAAHAM+P G G G ED L L+ D +L + +V
Sbjct: 295 PGYVHGRVALIGDAAHAMLPHQGAGAGQGLEDAYFLARLLGDTELEAGDLPALLEAYDDV 354
Query: 142 RQHDA 146
R+ A
Sbjct: 355 RRPRA 359
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 43.4 bits (103), Expect = 5e-05
Identities = 19/52 (36%), Positives = 22/52 (42%), Gaps = 16/52 (30%)
Query: 65 RLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFED 116
RLVAD + R +V + GDAAH P G GMN G D
Sbjct: 294 RLVADSYRR----------------GRVFLAGDAAHLFTPTGGYGMNTGIGD 329
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 42.0 bits (99), Expect = 1e-04
Identities = 36/151 (23%), Positives = 63/151 (41%), Gaps = 23/151 (15%)
Query: 2 DPN-FLHIW-PRGTFMMIALPNQDHSWTVTL--------FMPFEKFGLLGTARALLDFFD 51
P+ W +G F ++ L N W +T+ + F K L +F
Sbjct: 183 LPDCAKEYWGTKGRFGIVPLLNNQAYWFITINAKERDPKYSSFGK-------PHLQAYF- 234
Query: 52 KYFPDAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMN 111
++P+ + I ++ L +K Y +++++GDAAHA P GQG
Sbjct: 235 NHYPNEVREILDKQSETGILHHDIYDLKPLKSFVY---GRIVLLGDAAHATTPNMGQGAG 291
Query: 112 AGFEDCCILQDLMIQYDEDFGKVLPKFTEVR 142
ED +L + + Y DF K L ++ ++R
Sbjct: 292 QAMEDAIVLANCLNAY--DFEKALQRYDKIR 320
>gnl|CDD|181552 PRK08773, PRK08773, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Validated.
Length = 392
Score = 41.8 bits (98), Expect = 2e-04
Identities = 38/128 (29%), Positives = 54/128 (42%), Gaps = 16/128 (12%)
Query: 14 FMMIALPNQDHSWTVTL------FMPF--EKFGLLGT-----ARALLDFFDKYFPDAIPL 60
F+ P+Q +W L +PF + ++ T A +L + F +
Sbjct: 192 FVDTEHPHQATAWQRFLPTGPLALLPFADGRSSIVWTLPDAEAERVLALDEAAFSRELTQ 251
Query: 61 IGAERL--VADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCC 118
A RL V R A PL Y + +VL +GDAAH + P GQG+N G D
Sbjct: 252 AFAARLGEVRVASPRTAFPLRRQLVQQY-VSGRVLTLGDAAHVVHPLAGQGVNLGLRDVA 310
Query: 119 ILQDLMIQ 126
LQ L+ Q
Sbjct: 311 ALQQLVRQ 318
>gnl|CDD|181564 PRK08849, PRK08849, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Provisional.
Length = 384
Score = 41.3 bits (97), Expect = 2e-04
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 77 PLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDFGKVLP 136
PL Y KN+ VL+ GDAAH + P GQG+N GF+D +L +
Sbjct: 267 PLTRRHAQQYVKNNCVLL-GDAAHTINPLAGQGVNLGFKDVDVLLAETEKQGVLNDASFA 325
Query: 137 KFTEVRQHD 145
++ R+ D
Sbjct: 326 RYERRRRPD 334
>gnl|CDD|168201 PRK05714, PRK05714, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Provisional.
Length = 405
Score = 40.6 bits (95), Expect = 4e-04
Identities = 15/33 (45%), Positives = 23/33 (69%)
Query: 94 IIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQ 126
+IGDAAH + P GQG+N GF D +L ++++
Sbjct: 289 LIGDAAHTIHPLAGQGVNLGFLDAAVLAEVLLH 321
>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 = 40.1 bits (94), Expect = 5e-04
Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 72 SRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCIL 120
SR A PL + Y +V ++GDAAH + P GQG+N GF D L
Sbjct: 316 SRAAFPLGLGHADEYVT-KRVALVGDAAHRVHPLAGQGVNLGFGDVASL 363
>gnl|CDD|236001 PRK07364, PRK07364, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 415
Score = 39.6 bits (93), Expect = 8e-04
Identities = 40/147 (27%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 9 WPRGTFMMIALPNQDHS--WTVTLFMPFEKFGLLGTARALLDFFDKYFPDAI-----PLI 61
WP G F ++ LP WT P + A+ALL + F + +
Sbjct: 220 WPSGPFAILPLPGNRCQIVWT----APHAQ------AKALLALPEAEFLAELQQRYGDQL 269
Query: 62 GAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQ 121
G L+ D R P+ ++ + Y + ++ ++GDAAH P GQG+N G D L
Sbjct: 270 GKLELLGD---RFLFPVQLMQSDRYVQ-HRLALVGDAAHCCHPVGGQGLNLGIRDAAALA 325
Query: 122 DLMI---QYDEDFG--KVLPKFTEVRQ 143
++ Q ED G VL ++ R+
Sbjct: 326 QVLQTAHQRGEDIGSLAVLKRYERWRK 352
>gnl|CDD|235729 PRK06185, PRK06185, hypothetical protein; Provisional.
Length = 407
Score = 39.5 bits (93), Expect = 9e-04
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 90 DKVLIIGDAAHAMVPFYGQGMN 111
+L IGDAAHAM P G G+N
Sbjct: 284 PGLLCIGDAAHAMSPVGGVGIN 305
>gnl|CDD|180582 PRK06475, PRK06475, salicylate hydroxylase; Provisional.
Length = 400
Score = 38.7 bits (90), Expect = 0.001
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 77 PLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDFGKVLP 136
PL + + D+ + +GDA+HA+ PF QG ED L + + +D L
Sbjct: 279 PLFEMADAQFVGPDRTIFLGDASHAVTPFAAQGAAMAIEDAAALAEALDS--DDQSAGLK 336
Query: 137 KFTEVR 142
+F VR
Sbjct: 337 RFDSVR 342
>gnl|CDD|235870 PRK06834, PRK06834, hypothetical protein; Provisional.
Length = 488
Score = 38.1 bits (89), Expect = 0.003
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 91 KVLIIGDAAHAMVPFYGQGMNAGFED 116
+VL+ GDAAH P GQG+N G +D
Sbjct: 266 RVLLAGDAAHVHSPVGGQGLNTGVQD 291
>gnl|CDD|168629 PRK06617, PRK06617, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 374
Score = 37.6 bits (87), Expect = 0.003
Identities = 40/149 (26%), Positives = 65/149 (43%), Gaps = 31/149 (20%)
Query: 7 HIWPRGTFMMIALPNQDHS---WTVT-------LFMPFEKFGLLGTARALLDFFDKYFPD 56
H P G F ++ L +Q S W+ + + +P E+ L T R + K
Sbjct: 196 HFLPLGPFALLPLKDQYASSVIWSTSSDQAALIVNLPVEEVRFL-TQRNAGNSLGK---- 250
Query: 57 AIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFED 116
I + ++ F PL + N Y N ++++I D AH + P GQG+N G +D
Sbjct: 251 ----ITIDSEISSF------PLKARIANRYFHN-RIVLIADTAHTVHPLAGQGLNQGIKD 299
Query: 117 CCILQDLMIQYDEDFGKVLPKFTEVRQHD 145
IL MI + L ++ ++RQ D
Sbjct: 300 IEILS--MIVSNNG---TLQEYQKLRQED 323
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 37.7 bits (88), Expect = 0.003
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 92 VLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQ 126
+ ++GDAAH + P GQG+N G+ D L D+++
Sbjct: 283 LALVGDAAHTINPLAGQGVNLGYRDVDALLDVLVN 317
>gnl|CDD|181001 PRK07494, PRK07494, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 388
Score = 37.6 bits (88), Expect = 0.004
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 72 SRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDF 131
R+A PL + + + ++G+AAH P QG+N G D L +++ ED
Sbjct: 263 GRQAWPLSGQVAHRFAAG-RTALVGEAAHVFPPIGAQGLNLGLRDVATLVEIVEDRPEDP 321
Query: 132 G 132
G
Sbjct: 322 G 322
>gnl|CDD|180935 PRK07333, PRK07333, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 403
Score = 37.7 bits (88), Expect = 0.004
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 94 IIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYD---EDFG 132
++GDAAH + P GQG+N G +D L +++++ D G
Sbjct: 284 LVGDAAHGIHPIAGQGLNLGLKDVAALAEVVVEAARLGLDIG 325
>gnl|CDD|235874 PRK06847, PRK06847, hypothetical protein; Provisional.
Length = 375
Score = 37.2 bits (87), Expect = 0.004
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 85 PYHKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCIL 120
P+H+ +V++IGDAAHA P QG ED +L
Sbjct: 278 PWHRG-RVVLIGDAAHATTPHLAQGAGMAIEDAIVL 312
>gnl|CDD|236199 PRK08244, PRK08244, hypothetical protein; Provisional.
Length = 493
Score = 36.6 bits (85), Expect = 0.008
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 87 HKNDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLM 124
+++ ++ + GDAAH P GQG+N G LQD M
Sbjct: 269 YRSGRIFLAGDAAHIHFPAGGQGLNVG------LQDAM 300
>gnl|CDD|236341 PRK08850, PRK08850, 2-octaprenyl-6-methoxyphenol hydroxylase;
Validated.
Length = 405
Score = 35.5 bits (82), Expect = 0.017
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 90 DKVLIIGDAAHAMVPFYGQGMNAGFED-CCILQDLMI--QYDEDFG 132
++V ++GDAAH + P GQG+N G D + Q+++ Q D G
Sbjct: 282 ERVALVGDAAHTIHPLAGQGVNLGLLDAASLAQEILALWQQGRDIG 327
>gnl|CDD|235728 PRK06184, PRK06184, hypothetical protein; Provisional.
Length = 502
Score = 35.7 bits (83), Expect = 0.018
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 91 KVLIIGDAAHAMVPFYGQGMNAGFED 116
+V + GDAAH P GQG+N +D
Sbjct: 282 RVFLAGDAAHVHPPAGGQGLNTSVQD 307
>gnl|CDD|182273 PRK10157, PRK10157, putative oxidoreductase FixC; Provisional.
Length = 428
Score = 35.3 bits (81), Expect = 0.019
Identities = 42/124 (33%), Positives = 49/124 (39%), Gaps = 29/124 (23%)
Query: 46 LLDFFDKYFPDAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPF 105
L DF K P PLI +LV +S P I P D VLI GDAA
Sbjct: 255 LEDF--KQHPAVAPLIAGGKLVE--YSAHVVPEAGINMLPELVGDGVLIAGDAA------ 304
Query: 106 YGQGMNAGFEDCCILQDLMIQYDE-------------DFGKVLPKFTEVRQH-DAEAICD 151
G MN GF + DL I E DF K K E RQH ++ + D
Sbjct: 305 -GMCMNLGFTIRGM--DLAIAAGEAAAKTVLSAMKSDDFSK--QKLAEYRQHLESGPLRD 359
Query: 152 LAMY 155
+ MY
Sbjct: 360 MRMY 363
>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 = 35.1 bits (81), Expect = 0.025
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 58 IPLIGAERLV-ADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAGFED 116
+P AERLV + APL S C P + ++ + GDAAH + P +G+N D
Sbjct: 247 LPSEAAERLVTGPSIEKSIAPLRSFVCEPM-QYGRLFLAGDAAHIVPPTGAKGLNLAASD 305
Query: 117 CCILQDLMIQ-YDE 129
L + +++ Y E
Sbjct: 306 VHYLYEALLEHYQE 319
>gnl|CDD|236139 PRK08013, PRK08013, oxidoreductase; Provisional.
Length = 400
Score = 35.0 bits (81), Expect = 0.025
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 94 IIGDAAHAMVPFYGQGMNAGFED 116
++GDAAH + P GQG+N GF D
Sbjct: 286 LVGDAAHTIHPLAGQGVNLGFMD 308
>gnl|CDD|181262 PRK08163, PRK08163, salicylate hydroxylase; Provisional.
Length = 396
Score = 33.5 bits (77), Expect = 0.088
Identities = 16/52 (30%), Positives = 22/52 (42%)
Query: 91 KVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDFGKVLPKFTEVR 142
+V ++GDAAH M + QG ED L + D D + VR
Sbjct: 287 RVTLLGDAAHPMTQYMAQGACMALEDAVTLGKALEGCDGDAEAAFALYESVR 338
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 33.3 bits (77), Expect = 0.11
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 92 VLIIGDAAHAMVPFYGQGMNAGFED 116
VL GDAAH + PF +G N+G +D
Sbjct: 301 VLFAGDAAHQVSPFGARGANSGIQD 325
>gnl|CDD|240384 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
Length = 567
Score = 32.5 bits (74), Expect = 0.19
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 92 VLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQ 126
+ IGD A+ P G GM F DC L +
Sbjct: 339 YVGIGDHANQRHPLTGGGMTCCFSDCIRLAKSLTG 373
>gnl|CDD|235584 PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 395
Score = 32.1 bits (74), Expect = 0.24
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 94 IIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQY---DEDFG--KVLPKFTEVRQHDAEA 148
++G+AA + P GQG N G D L + + Q ED G VL ++ + RQ D EA
Sbjct: 286 LVGNAAQTLHPIAGQGFNLGLRDVMSLAETLTQALARGEDIGDYAVLQRYQQRRQQDREA 345
>gnl|CDD|235905 PRK06996, PRK06996, hypothetical protein; Provisional.
Length = 398
Score = 31.2 bits (71), Expect = 0.38
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 89 NDKVLIIGDAAHAMVPFYGQGMNAGFEDCCILQD 122
N ++ +G+AA + P GQG+N G D L D
Sbjct: 290 NGRIAAVGNAAQTLHPVAGQGLNLGLRDAHTLAD 323
>gnl|CDD|223717 COG0644, FixC, Dehydrogenases (flavoproteins) [Energy production
and conversion].
Length = 396
Score = 31.3 bits (71), Expect = 0.41
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 45 ALLDFFDKYF--PDAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAM 102
L+ +++ P L+ +++ ++ P P D VL++GDAA +
Sbjct: 225 PFLELLERFKEHPAIRKLLLGGKILE--YAAGGIPEGGPASRPLVG-DGVLLVGDAAGFV 281
Query: 103 VPFYGQGMNAG 113
P G+G+
Sbjct: 282 NPLTGEGIRYA 292
>gnl|CDD|236223 PRK08294, PRK08294, phenol 2-monooxygenase; Provisional.
Length = 634
Score = 30.3 bits (69), Expect = 0.82
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 91 KVLIIGDAAHAMVPFYGQGMNAGFED 116
+V I GDA H GQGMN +D
Sbjct: 341 RVFIAGDACHTHSAKAGQGMNVSMQD 366
>gnl|CDD|236046 PRK07538, PRK07538, hypothetical protein; Provisional.
Length = 413
Score = 30.2 bits (69), Expect = 0.96
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 90 DKVLIIGDAAHAMVP 104
+V ++GDAAH M P
Sbjct: 297 GRVTLLGDAAHPMYP 311
>gnl|CDD|233689 TIGR02023, BchP-ChlP, geranylgeranyl reductase. This model
represents a group of geranylgeranyl reductases specific
for the biosyntheses of bacteriochlorophyll and
chlorophyll. It is unclear whether the processes of
isoprenoid ligation to the chlorin ring and reduction of
the geranylgeranyl chain to a phytyl chain are
necessarily ordered the same way in all species (see
introduction to ) [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 388
Score = 30.1 bits (68), Expect = 1.1
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 73 RKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGM 110
R+AAP I +K P + +++GDAA + P G+G+
Sbjct: 248 REAAP-IPMKPRPRWDFGRAMLVGDAAGLVTPASGEGI 284
>gnl|CDD|233618 TIGR01887, dipeptidaselike, dipeptidase, putative. This model
represents a clade of probable zinc dipeptidases,
closely related to the characterized non-specific
dipeptidase, PepV. Many enzymes in this clade have been
given names including the terms "Xaa-His" and
"carnosinase" due to the early mis-characterization of
the Lactobacillus delbrueckii PepV enzyme. These names
are likely too specific.
Length = 447
Score = 29.3 bits (66), Expect = 2.0
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 2/45 (4%)
Query: 69 DFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPFYGQGMNAG 113
F A + + + G +AH P +G+NA
Sbjct: 224 LKFVFFIAKELEGDFEVNDGTLTITLEGKSAHGSAP--EKGINAA 266
>gnl|CDD|238943 cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a
specific electron acceptor for various mitochondrial
dehydrogenases. ETF transfers electrons to the main
respiratory chain via ETF-ubiquinone oxidoreductase. ETF
is an heterodimer that consists of an alpha and a beta
subunit which binds one molecule of FAD per dimer . A
similar system also exists in some bacteria. The
homologous pair of proteins (FixA/FixB) are essential
for nitrogen fixation. The alpha subunit of ETF is
structurally related to the bacterial nitrogen fixation
protein fixB which could play a role in a redox process
and feed electrons to ferredoxin. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 181
Score = 28.7 bits (65), Expect = 2.1
Identities = 17/51 (33%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 34 FEKFGLLGTARALLDFFDKYFPDAIPLIGAERLVADFFSRKAA----PLIS 80
+ TA+AL K PD I L GA + R AA P IS
Sbjct: 71 LAGYDPEATAKALAALIKKEKPDLI-LAGATSIGKQLAPRVAALLGVPQIS 120
>gnl|CDD|178515 PLN02927, PLN02927, antheraxanthin epoxidase/zeaxanthin epoxidase.
Length = 668
Score = 28.9 bits (64), Expect = 2.5
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 91 KVLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLMIQYDEDFGKVLPKFTEV 141
+V ++GD+ HAM P GQG ED L ++ DE + + + T V
Sbjct: 368 RVTLLGDSIHAMQPNMGQGGCMAIEDSF---QLALELDEAWKQSVETNTPV 415
>gnl|CDD|235955 PRK07190, PRK07190, hypothetical protein; Provisional.
Length = 487
Score = 28.6 bits (64), Expect = 3.0
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 90 DKVLIIGDAAHAMVPFYGQGMNAGFED 116
D++ + GDA H GQG+N G D
Sbjct: 275 DRIFLAGDACHIHSVNGGQGLNTGLAD 301
>gnl|CDD|236639 PRK10002, PRK10002, outer membrane protein F; Provisional.
Length = 362
Score = 28.3 bits (63), Expect = 3.8
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 106 YGQGMNA-----------GFEDCCILQDLMIQYDEDFGKVLPK--FTEVRQHDAEAICDL 152
YG+ NA GF + L+ QY DFG + P +T+ + D E I D+
Sbjct: 253 YGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFG-LRPSIAYTKSKAKDVEGIGDV 311
Query: 153 AMYNYIEM 160
+ NY E+
Sbjct: 312 DLVNYFEV 319
>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
Length = 429
Score = 28.4 bits (63), Expect = 4.1
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 11/69 (15%)
Query: 46 LLDFFDKYFPDAIPLIGAERLVADFFSRKAAPLISIKCNPYHKNDKVLIIGDAAHAMVPF 105
L DF K P PLI +L+ +S P + P ND V+I+GDAA
Sbjct: 255 LEDF--KQHPAIRPLISGGKLLE--YSAHMVPEGGLAMVPQLVNDGVMIVGDAA------ 304
Query: 106 YGQGMNAGF 114
G +N GF
Sbjct: 305 -GFCLNLGF 312
>gnl|CDD|129908 TIGR00828, EIID-AGA, PTS system, mannose/fructose/sorbose family,
IID component. Bacterial PTS transporters transport and
concomitantly phosphorylate their sugar substrates, and
typically consist of multiple subunits or protein
domains. The Man family is unique in several respects
among PTS permease families.It is the only PTS family in
which members possess a IID protein. It is the only PTS
family in which the IIB constituent is phosphorylated on
a histidyl rather than a cysteyl residue. Its permease
members exhibit broad specificity for a range of sugars,
rather than being specific for just one or a few sugars.
The mannose permease of E. coli, for example, can
transport and phosphorylate glucose, mannose, fructose,
glucosamine,N-acetylglucosamine, and other sugars. Other
members of this can transport sorbose, fructose and
N-acetylglucosamine. This family is specific for the IID
subunits of this family of PTS transporters [Transport
and binding proteins, Carbohydrates, organic alcohols,
and acids, Signal transduction, PTS].
Length = 271
Score = 27.5 bits (61), Expect = 5.7
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 48 DFFDKYFPDAIPLIGAERLVADFFSRKAAPLISI 81
+ D+ P +PL G L+ +K P++ I
Sbjct: 223 NILDQLMPGLLPL-GLTLLMYWLLRKKVNPVLLI 255
>gnl|CDD|219864 pfam08491, SE, Squalene epoxidase. This domain is found in
squalene epoxidase (SE) and related proteins which are
found in taxonomically diverse groups of eukaryotes and
also in bacteria. SE was first cloned from Saccharomyces
cerevisiae where it was named ERG1. It contains a
putative FAD binding site and is a key enzyme in the
sterol biosynthetic pathway. Putative transmembrane
regions are found to the protein's C-terminus.
Length = 276
Score = 27.7 bits (62), Expect = 5.9
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 85 PYHKNDK--VLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLM-----IQYDEDFGKVLPK 137
P KN K ++++GDA + P G GM D +L+ L+ + E KVL
Sbjct: 123 PASKNRKKGLILLGDALNMRHPLTGGGMTVALNDIVLLRKLLGPLRDLSDREKVSKVLKS 182
Query: 138 FTEVRQHDAEAICDLAMYNY 157
F +R+ I L++ Y
Sbjct: 183 FHWLRKPYDAVINTLSIALY 202
>gnl|CDD|220167 pfam09296, NUDIX-like, NADH pyrophosphatase-like rudimentary
NUDIX domain. The N-terminal domain in NADH
pyrophosphatase, which has a rudiment Nudix fold
according to SCOP.
Length = 91
Score = 26.2 bits (58), Expect = 6.0
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 32 MPFEKFGLLGTARALLDF 49
+ E GL G AR LL +
Sbjct: 74 LDEELAGLAGRARQLLHW 91
>gnl|CDD|218101 pfam04467, DUF483, Protein of unknown function (DUF483). Family of
uncharacterized prokaryotic proteins.
Length = 127
Score = 26.8 bits (59), Expect = 6.2
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 108 QGMNAGFEDCCILQDLMIQYDEDFGKVLPKFTEVRQHDAEAICDLAMY---NYI----EM 160
G G+ DCCI + L + +E+ Q D A+Y N+I
Sbjct: 40 IGKLLGYPDCCIRSFNEKHRKAIDIEHLKEVSEMSQFDKNQKGIWAIYEPSNFIPCSLLC 99
Query: 161 RDLVTKS--SFLWRKRFDSFL 179
++ + + L F + L
Sbjct: 100 KEALKRGLIGTLIHDEFQTIL 120
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 26.8 bits (60), Expect = 9.6
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 28 VTLFMPFEKFGLLGTARALLDFFDKYFPDAIPLIGAERLVADFFSRKAA 76
V+L + + LG L++ + + P I + G R+ F +RKA
Sbjct: 67 VSLKVIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKAC 115
>gnl|CDD|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 27.2 bits (60), Expect = 9.8
Identities = 25/94 (26%), Positives = 36/94 (38%), Gaps = 24/94 (25%)
Query: 54 FPDAIPLIGAERLVADFFSRKAAPLI----------------SIKCNPYHK-----NDK- 91
PD IP I A ++ F AP + IK P + +DK
Sbjct: 268 LPDNIPSI-ANGEMSTFVKNTIAPQVPPKLRKIFLKGIDEGAHIKVVPTKRMSATLSDKK 326
Query: 92 -VLIIGDAAHAMVPFYGQGMNAGFEDCCILQDLM 124
V+++GDA + P GM D IL+ L+
Sbjct: 327 GVIVLGDAFNMRHPAIASGMMVLLSDILILRRLL 360
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
0.328 0.141 0.456
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,404,841
Number of extensions: 1193517
Number of successful extensions: 1256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1255
Number of HSP's successfully gapped: 62
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 57 (25.8 bits)