RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780861|ref|YP_003065274.1| NADH dehydrogenase subunit I
[Candidatus Liberibacter asiaticus str. psy62]
(163 letters)
>gnl|CDD|180305 PRK05888, PRK05888, NADH dehydrogenase subunit I; Provisional.
Length = 164
Score = 242 bits (621), Expect = 2e-65
Identities = 99/156 (63%), Positives = 113/156 (72%), Gaps = 1/156 (0%)
Query: 8 VSFLFLKEFVGAFFLCLRYFFKAKTTINYPFEKGSTSPRFRGEHALRRYPNGEERCIACK 67
+ + LKE + + L+YFFK K TI YP EK SPRFRG HALRR PNGEERCIACK
Sbjct: 5 LKSMLLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERCIACK 64
Query: 68 LCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFA 127
LC AICPA AITIE+ R DG RRT RYDI+ +CI+CG C+EACP DAIVE P+FE A
Sbjct: 65 LCAAICPADAITIEAAER-EDGRRRTTRYDINFGRCIFCGFCEEACPTDAIVETPDFELA 123
Query: 128 TETRQELYYDKERLLNNGDRWESEIVRNIVTDSPYR 163
TETR+EL YDKE+LL NGDR E EI D+ YR
Sbjct: 124 TETREELIYDKEKLLANGDRVEREIAPGKAADANYR 159
>gnl|CDD|162631 TIGR01971, NuoI, NADH-quinone oxidoreductase, chain I. This model
represents the I subunit (one of 14: A->N) of the
NADH-quinone oxidoreductase complex I which generally
couples NADH and ubiquinone oxidation/reduction in
bacteria and mammalian mitochondria, but may act on
NADPH and/or plastoquinone in cyanobacteria and plant
chloroplasts. This model excludes "I" subunits from the
closely related F420H2 dehydrogenase and formate
hydrogenlyase complexes.
Length = 122
Score = 161 bits (409), Expect = 9e-41
Identities = 65/122 (53%), Positives = 75/122 (61%), Gaps = 1/122 (0%)
Query: 20 FFLCLRYFFKAKTTINYPFEKGSTSPRFRGEHALRRYPNGEERCIACKLCEAICPAQAIT 79
L L+YFF T+ YP EK PRFRG L R PNGEE+CI C LC A+CPA AI
Sbjct: 2 LGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAIR 61
Query: 80 IESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFATETRQELYYDKE 139
+ DG RR Y I+ +CI+CGLC+EACP DAIV P FE AT TR +L Y KE
Sbjct: 62 VVPAEG-EDGKRRLKFYQINFGRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKE 120
Query: 140 RL 141
L
Sbjct: 121 DL 122
>gnl|CDD|181301 PRK08222, PRK08222, hydrogenase 4 subunit H; Validated.
Length = 181
Score = 72.5 bits (178), Expect = 5e-14
Identities = 38/104 (36%), Positives = 53/104 (50%), Gaps = 10/104 (9%)
Query: 32 TTINYPFEKGSTSPRFRGEHALRRYPNGEERCIACKLCEAICPAQAITIESGPRCHDGTR 91
T+ YPF SP FRG+ L +CIAC C CPA A+TI++ D +
Sbjct: 14 ATVKYPFAPLEVSPGFRGKPDL-----MPSQCIACGACTCACPANALTIQT-----DDQQ 63
Query: 92 RTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFATETRQELY 135
+ + + + +CIYCG C+E CP AI NFE + +LY
Sbjct: 64 NSRTWQLYLGRCIYCGRCEEVCPTRAIQLTNNFELTVTNKADLY 107
>gnl|CDD|129498 TIGR00403, ndhI, NADH-plastoquinone oxidoreductase subunit I
protein.
Length = 183
Score = 69.6 bits (170), Expect = 4e-13
Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 5/120 (4%)
Query: 19 AFFLCLRYFFKAKTTINYPFEKGSTSPRFRGEHALRRYPNGEERCIACKLCEAICPAQAI 78
F + L + + TI YP+EK S RFRG R ++CIAC++C +CP
Sbjct: 25 GFAVTLDHMNRLPITIQYPYEKLIPSERFRG-----RIHFEFDKCIACEVCVRVCPINLP 79
Query: 79 TIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFATETRQELYYDK 138
++ ++ Y ID CI+CG C E CP + + +E +T R EL YD+
Sbjct: 80 VVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELNYDQ 139
>gnl|CDD|183492 PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur
subunit; Provisional.
Length = 180
Score = 68.1 bits (167), Expect = 9e-13
Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 14/111 (12%)
Query: 31 KTTINYPFEKGSTSPRFRG--EHALRRYPNGEERCIACKLCEAICPAQAITIESGPRCHD 88
T +YP E + FRG E+ ++CI C C CP+ A+T+E+ D
Sbjct: 13 TATSSYPLEPIAVDKNFRGKPEYNP-------QQCIGCAACVNACPSNALTVET-----D 60
Query: 89 GTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFATETRQELYYDKE 139
+ ++ ++ +CI+CG C+E CP AI FE A +++L E
Sbjct: 61 LATGELAWEFNLGRCIFCGRCEEVCPTAAIKLSQEFELAVWKKEDLLQQSE 111
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 60.6 bits (147), Expect = 2e-10
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 7/104 (6%)
Query: 11 LFLKEFVGAFFLCLRYFFKAKTTINYPFEKGSTSPRFRGEHALRRYPNGEERCIACKLCE 70
+ K+F ++ F+ TI P K + R+RG H N E+CI C C
Sbjct: 1 MPEKDFFAPL-KAWKFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCS 54
Query: 71 AICPAQAIT-IESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEAC 113
ICP AIT +E + ++ R ID +C +C LC + C
Sbjct: 55 KICPTDAITMVEVPDLPQEYGKKPQRPVIDYGRCSFCALCVDIC 98
Score = 28.2 bits (63), Expect = 0.92
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 62 RCIACKLCEAICPA 75
RC+ C +C CPA
Sbjct: 186 RCVECGICTDTCPA 199
>gnl|CDD|180852 PRK07118, PRK07118, ferredoxin; Validated.
Length = 280
Score = 54.6 bits (132), Expect = 1e-08
Identities = 23/58 (39%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVE 120
CI C C CPA AIT+E+ ID KC CG C E CP AI
Sbjct: 215 CIGCGKCVKACPAGAITMENN-----------LAVIDQEKCTSCGKCVEKCPTKAIRI 261
Score = 39.1 bits (92), Expect = 5e-04
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 13/69 (18%)
Query: 60 EERCIACKLCEAICPAQAITIESGPR-------C--HDGTRRTVRYDIDMIKCIYCGLCQ 110
E++C C C CP I + P+ C D + V+ + + CI CG C
Sbjct: 167 EDKCTGCGACVKACPRNVIEL--IPKSARVFVACNSKD-KGKAVK-KVCEVGCIGCGKCV 222
Query: 111 EACPVDAIV 119
+ACP AI
Sbjct: 223 KACPAGAIT 231
Score = 36.1 bits (84), Expect = 0.004
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 63 CIACKLCEAICPAQAITIESG-PRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIV 119
C+ C A CP AI IE+G P +D KC CG C +ACP + I
Sbjct: 141 CLGLGSCVAACPFDAIHIENGLPV------------VDEDKCTGCGACVKACPRNVIE 186
Score = 25.7 bits (57), Expect = 6.2
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 61 ERCIACKLCEAICPAQAI 78
E+C +C C CP +AI
Sbjct: 242 EKCTSCGKCVEKCPTKAI 259
>gnl|CDD|184331 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 53.5 bits (129), Expect = 3e-08
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 27 FFKAKTTINYPFEKGSTSPRFR-GEHALRRYPNGEERCIACKLCEAICPAQAITIESGPR 85
F + +K + + F+ LRR C+ C +C CP AI IE G
Sbjct: 550 VFASGNIWARSEDKEAAASLFKDAARLLRR----AAECVGCGVCVGACPTGAIRIEEG-- 603
Query: 86 CHDGTRRTVRYDIDMIKCIYCGLCQEACPV 115
+R + D + KCI+CG C E CPV
Sbjct: 604 -----KRKISVDEE--KCIHCGKCTEVCPV 626
Score = 29.2 bits (66), Expect = 0.47
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 102 KCIYCGLCQEACPVDAI 118
+C+ CG+C ACP AI
Sbjct: 582 ECVGCGVCVGACPTGAI 598
>gnl|CDD|131747 TIGR02700, flavo_MJ0208, archaeoflavoprotein, MJ0208 family. This
model describes one of two paralogous families of
archaealflavoprotein. The other, described by TIGR02699
and typified by the partially characterized AF1518 of
Archaeoglobus fulgidus, is a homodimeric FMN-containing
flavoprotein that accepts electrons from ferredoxin and
can transfer them to various oxidoreductases. The
function of this protein family is unknown.
Length = 234
Score = 51.0 bits (122), Expect = 1e-07
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 61 ERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVE 120
+RC C +C CP AI + G + I ++KC+ CG C+EACP +AI
Sbjct: 148 KRCKGCGICVDACPRSAIDMVDG-----------KAFIRLLKCVGCGKCKEACPYNAIHG 196
Query: 121 GPNFE 125
G +E
Sbjct: 197 GLEYE 201
Score = 32.9 bits (75), Expect = 0.035
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 96 YDIDMIKCIYCGLCQEACPVDAIVEGPNFEF 126
Y ID +C CG+C +ACP AI F
Sbjct: 143 YMIDRKRCKGCGICVDACPRSAIDMVDGKAF 173
>gnl|CDD|162896 TIGR02512, Fe_only_hydrog, hydrogenases, Fe-only. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
Pfam model pfam02906. This family represents a division
among families that belong to pfam02906, which also
includes proteins such as nuclear prelamin A recognition
factor in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 50.8 bits (122), Expect = 1e-07
Identities = 20/62 (32%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 62 RCIACKLCEAICPAQAITIESGP-RCHDGTRRTVRYD--IDMIKCIYCGLCQEACPVDAI 118
+CI C C C I G T ++ +D CI CG C CPV AI
Sbjct: 8 KCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAI 67
Query: 119 VE 120
E
Sbjct: 68 TE 69
Score = 33.1 bits (76), Expect = 0.033
Identities = 15/41 (36%), Positives = 16/41 (39%), Gaps = 7/41 (17%)
Query: 98 IDMIKCIYCGLCQEACPVDAIV-------EGPNFEFATETR 131
DM KCI CG C AC IV G E A +
Sbjct: 4 RDMSKCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFG 44
Score = 25.4 bits (56), Expect = 7.5
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 60 EERCIACKLCEAICPAQAIT 79
E CI C C +CP AIT
Sbjct: 49 ESNCIGCGQCSLVCPVGAIT 68
>gnl|CDD|181399 PRK08348, PRK08348, NADH-plastoquinone oxidoreductase subunit;
Provisional.
Length = 120
Score = 47.1 bits (112), Expect = 2e-06
Identities = 26/109 (23%), Positives = 44/109 (40%), Gaps = 15/109 (13%)
Query: 24 LRYFFKAKTTINYPFEKGSTSP-RFRGEHALRRYPNGEERCIACKLCEAICPAQAITIES 82
LR FK T +P + P FRG+ ++C+ C++C +CPA
Sbjct: 9 LRNLFKKPATNLFPATEPVPVPEDFRGKILYDV-----DKCVGCRMCVTVCPAGVFVY-- 61
Query: 83 GPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPNFEFATETR 131
+ + +C++CG C + CP A+ +F A+ R
Sbjct: 62 -------LPEIRKVALWTGRCVFCGQCVDVCPTGALQMSDDFLLASYDR 103
>gnl|CDD|183735 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 46.8 bits (112), Expect = 2e-06
Identities = 21/60 (35%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGP 122
C C C CP AI G R +D D KC C +C + CP AI GP
Sbjct: 512 CFECDNCYGACPQDAII-------KLGPGRRYHFDYD--KCTGCHICADVCPCGAIEMGP 562
Score = 27.9 bits (63), Expect = 1.2
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 54 RRYPNGEERCIACKLCEAICPAQAITIESGP 84
RRY ++C C +C +CP AI + G
Sbjct: 534 RRYHFDYDKCTGCHICADVCPCGAIEMGPGE 564
>gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA
protein. Members of this protein family are BoxA, the A
component of the BoxAB benzoyl-CoA oxygenase/reductase.
This oxygen-requiring enzyme acts in an aerobic pathway
of benzoate catabolism via coenzyme A ligation. BoxA is
a homodimeric iron-sulphur-flavoprotein and acts as an
NADPH-dependent reductase for BoxB.
Length = 411
Score = 45.6 bits (108), Expect = 6e-06
Identities = 22/58 (37%), Positives = 24/58 (41%), Gaps = 11/58 (18%)
Query: 61 ERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
E CI C CE CP AIT HD V+ D+ C C C CP AI
Sbjct: 10 EICIRCNTCEETCPIDAIT-------HDDRNYVVKADV----CNGCMACVSPCPTGAI 56
Score = 32.9 bits (75), Expect = 0.041
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 98 IDMIKCIYCGLCQEACPVDAI 118
ID CI C C+E CP+DAI
Sbjct: 7 IDPEICIRCNTCEETCPIDAI 27
>gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2, ) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 43.9 bits (104), Expect = 2e-05
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
E RC+ C C +CPA + R R I KC +CG C EACP A+
Sbjct: 47 ENRCLGCGKCVEVCPAGTARLSE----LADGR--NRIIIRREKCTHCGKCTEACPSGAL 99
Score = 28.5 bits (64), Expect = 0.76
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 61 ERCIACKLCEAICPAQAITI 80
E+C C C CP+ A++I
Sbjct: 82 EKCTHCGKCTEACPSGALSI 101
>gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit
gamma/delta; Provisional.
Length = 312
Score = 43.4 bits (102), Expect = 3e-05
Identities = 25/62 (40%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 62 RCIACKLCEAICPAQAITIES-----GPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVD 116
+CI C+ C CP AI IE+ GPR R D D C CG+C E CP
Sbjct: 248 KCIMCRKCWLYCPDDAI-IEAWREAEGPRGR--KFRMKMIDFDYQYCKGCGVCAEVCPTG 304
Query: 117 AI 118
AI
Sbjct: 305 AI 306
Score = 30.7 bits (69), Expect = 0.17
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 98 IDMIKCIYCGLCQEACPVDAIVE 120
ID KCI C C CP DAI+E
Sbjct: 244 IDHSKCIMCRKCWLYCPDDAIIE 266
>gnl|CDD|180502 PRK06273, PRK06273, ferredoxin; Provisional.
Length = 165
Score = 43.2 bits (102), Expect = 4e-05
Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 60 EERCIACKLCEAICPAQAIT-IESGP-RCHDGTRRTVRYDIDMIKCIYCGLCQEACPV 115
EE CI C C +CP +AI I P + +G +T ID KC+YC C + CPV
Sbjct: 48 EELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPV 105
Score = 26.2 bits (58), Expect = 4.1
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 103 CIYCGLCQEACPVDAI 118
CI CG C CP AI
Sbjct: 51 CIGCGGCANVCPTKAI 66
>gnl|CDD|131234 TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoreductase, delta
subunit, pyruvate/2-ketoisovalerate family. A number of
anaerobic and microaerophilic species lack pyruvate
dehydrogenase and have instead a four subunit,
oxygen-sensitive pyruvate oxidoreductase, with either
ferredoxins or flavodoxins used as the acceptor. Several
related four-subunit enzymes may exist in the same
species. This model describes a subfamily of delta
subunits, representing mostly pyruvate,
2-ketoisovalerate, and 2-oxoglutarate specific enzymes.
The delta subunit is the smallest and resembles
ferredoxins.
Length = 78
Score = 43.1 bits (102), Expect = 4e-05
Identities = 23/59 (38%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
+E+CI CK C CP AI + G V D D C CG+C CPV AI
Sbjct: 24 KEKCIKCKNCWLYCPEGAIQEDEG--------GFVGIDYDY--CKGCGICANVCPVKAI 72
Score = 29.6 bits (67), Expect = 0.36
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 89 GTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEGPN 123
G R + +D KCI C C CP AI E
Sbjct: 13 GDWRVFKPVVDKEKCIKCKNCWLYCPEGAIQEDEG 47
>gnl|CDD|162616 TIGR01944, rnfB, electron transport complex, RnfABCDGE type, B
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the B subunit.
Length = 165
Score = 41.7 bits (98), Expect = 9e-05
Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIV 119
E+ CI C C CP AI G + + I +C C LC E CP D I
Sbjct: 112 EDNCIGCTKCIQACPVDAIV---------GAAKAMHTVI-ADECTGCDLCVEPCPTDCIE 161
Score = 38.2 bits (89), Expect = 0.001
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 98 IDMIKCIYCGLCQEACPVDAIVEGPNF 124
ID CI C C +ACPVDAIV
Sbjct: 110 IDEDNCIGCTKCIQACPVDAIVGAAKA 136
Score = 25.5 bits (56), Expect = 6.0
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 63 CIACKLCEAICPAQAITI 80
C C LC CP I +
Sbjct: 145 CTGCDLCVEPCPTDCIEM 162
>gnl|CDD|163218 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase,
alpha subunit. Indolepyruvate ferredoxin oxidoreductase
(IOR) is an alpha 2/beta 2 tetramer related to ketoacid
oxidoreductases for pyruvate (1.2.7.1, POR),
2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate
(1.2.7.7, VOR). These multi-subunit enzymes typically
are found in anaerobes and are inactiviated by oxygen.
IOR in Pyrococcus acts in fermentation of all three
aromatic amino acids, following removal of the amino
group by transamination. In Methanococcus maripaludis,
by contrast, IOR acts in the opposite direction, in
pathways of amino acid biosynthesis from phenylacetate,
indoleacetate, and p-hydroxyphenylacetate. In M.
maripaludis and many other species, iorA and iorB are
found next to an apparent phenylacetate-CoA ligase.
Length = 595
Score = 41.6 bits (98), Expect = 1e-04
Identities = 23/77 (29%), Positives = 28/77 (36%), Gaps = 18/77 (23%)
Query: 46 RFRGEHALRRYPN--GEERCIACKLC--EAICPAQAITIESGPRCHDGTRRTVRYDIDMI 101
R P +++CI CK C E CPA I E D
Sbjct: 533 LSNKRAGKRAGPYKVDQDKCIGCKKCIKELGCPA--IEPEDKEAVIDPL----------- 579
Query: 102 KCIYCGLCQEACPVDAI 118
C CG+C + CP DAI
Sbjct: 580 -CTGCGVCAQICPFDAI 595
>gnl|CDD|181383 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 41.5 bits (98), Expect = 1e-04
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 60 EERCIACKLCEAIC---PAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVD 116
+++CI C C C QAI + DGTR ++ +C+ C LC CPV+
Sbjct: 341 QDKCIGCGRCYIACEDTSHQAIEWDE-----DGTRT---PEVIEEECVGCNLCAHVCPVE 392
Query: 117 AIVE 120
+
Sbjct: 393 GCIT 396
Score = 30.3 bits (69), Expect = 0.24
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 60 EERCIACKLCEAICP-AQAITIE 81
EE C+ C LC +CP IT+
Sbjct: 376 EEECVGCNLCAHVCPVEGCITMG 398
Score = 28.0 bits (63), Expect = 1.3
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 94 VRYDIDMIKCIYCGLCQEAC 113
V ID KCI CG C AC
Sbjct: 335 VYARIDQDKCIGCGRCYIAC 354
>gnl|CDD|180786 PRK06991, PRK06991, ferredoxin; Provisional.
Length = 270
Score = 39.8 bits (93), Expect = 3e-04
Identities = 16/25 (64%), Positives = 17/25 (68%)
Query: 98 IDMIKCIYCGLCQEACPVDAIVEGP 122
ID CI C LC +ACPVDAIV P
Sbjct: 82 IDEQLCIGCTLCMQACPVDAIVGAP 106
Score = 39.4 bits (92), Expect = 4e-04
Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
E+ CI C LC CP AI + + + H TV D+ C C LC CPVD I
Sbjct: 84 EQLCIGCTLCMQACPVDAI-VGAPKQMH-----TVLADL----CTGCDLCVPPCPVDCI 132
>gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma. This
model represents that clade of F420-dependent
hydrogenases (FRH) beta subunits found exclusively and
universally in methanogenic archaea. This protein
contains two 4Fe-4S cluster binding domains (pfam00037)
and scores above the trusted cutoff to model pfam01058
for the "NADH ubiquinone oxidoreductase, 20 Kd subunit"
family.
Length = 228
Score = 39.1 bits (91), Expect = 6e-04
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
C+ C C A CP +AI +E G R +++ +CI CG C CP
Sbjct: 176 CMGCGTCAAACPTRAIEMEDG-----------RPNVNRDRCIKCGACYVQCP 216
Score = 25.6 bits (56), Expect = 7.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 103 CIYCGLCQEACPVDAI 118
C+ CG C ACP AI
Sbjct: 176 CMGCGTCAAACPTRAI 191
>gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin)
oxidoreductase, homodimeric. This model represents a
single chain form of pyruvate:ferredoxin (or flavodoxin)
oxidoreductase. This enzyme may transfer electrons to
nitrogenase in nitrogen-fixing species. Portions of this
protein are homologous to gamma subunit of the four
subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Length = 1165
Score = 38.2 bits (89), Expect = 0.001
Identities = 27/113 (23%), Positives = 42/113 (37%), Gaps = 37/113 (32%)
Query: 61 ERCIACKLCEAICPAQAITI--------ESGP----------RCHDGTRRTVRYDIDMIK 102
+ CI C C +CP AI E+ P + +G + ++ I +
Sbjct: 683 DNCIQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQ--ISPLD 740
Query: 103 CIYCGLCQEACPVD--AIV----------EGPNFEFATETRQELYYDKERLLN 143
C CG C + CP A+V + N+EFA + K+ LN
Sbjct: 741 CTGCGNCVDICPAKEKALVMQPLAEQREAQVANWEFAINIPE-----KDNKLN 788
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 38.2 bits (89), Expect = 0.001
Identities = 19/65 (29%), Positives = 25/65 (38%), Gaps = 12/65 (18%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCG------LCQEAC 113
+++CI CK C CP + I P + T KC C C E C
Sbjct: 84 QQKCIGCKSCVVACPFGTMQIVLTPVAAGKVKATAH------KCDLCAGRENGPACVENC 137
Query: 114 PVDAI 118
P DA+
Sbjct: 138 PADAL 142
>gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase,
anaerobic, C subunit. Members of this protein family
are the membrane-anchoring, non-catalytic C subunit,
product of the glpC gene, of a three-subunit,
FAD-dependent, anaerobic glycerol-3-phosphate
dehydrogenase. GlpC lasks classical hydrophobic
transmembrane helices; Cole, et al suggest interaction
with the membrane may involve amphipathic helices. GlcC
has conserved Cys-containing motifs suggestive of
iron-sulfur binding. This complex is found mostly in
Escherichia coli and closely related species.
Length = 397
Score = 37.8 bits (88), Expect = 0.001
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 61 ERCIACKLCEAICP-AQAITIESGPR--CHDGTRRTVR----YDIDMIKCIYCGLCQEAC 113
E CI C +C CP A+A + GP+ DG R ++ YD + C C C+ AC
Sbjct: 5 ESCIKCTVCTVYCPVAKANPLYPGPKQAGPDGERLRLKSAELYDEALKYCTNCKRCEVAC 64
Query: 114 PVD 116
P D
Sbjct: 65 PSD 67
>gnl|CDD|179940 PRK05113, PRK05113, electron transport complex protein RnfB;
Provisional.
Length = 191
Score = 37.6 bits (88), Expect = 0.001
Identities = 21/59 (35%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
E+ CI C C CP AI + + H TV D+ C C LC CP D I
Sbjct: 113 EDNCIGCTKCIQACPVDAI-VGATKAMH-----TVISDL----CTGCDLCVAPCPTDCI 161
Score = 36.8 bits (86), Expect = 0.002
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 98 IDMIKCIYCGLCQEACPVDAIV 119
ID CI C C +ACPVDAIV
Sbjct: 111 IDEDNCIGCTKCIQACPVDAIV 132
>gnl|CDD|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit
delta; Reviewed.
Length = 105
Score = 36.8 bits (85), Expect = 0.002
Identities = 26/82 (31%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 37 PFEKGSTSPRFRGEHALRRYPNGEERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRY 96
P G+T F G+ E +C+ C +C CP AI I+ DG
Sbjct: 27 PISLGTTLSNFTGDWRTFMPVVDESKCVKCYICWKFCPEPAIYIKE-----DGY-----V 76
Query: 97 DIDMIKCIYCGLCQEACPVDAI 118
ID C CG+C CP AI
Sbjct: 77 AIDYDYCKGCGICANECPTKAI 98
>gnl|CDD|179124 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 36.4 bits (85), Expect = 0.004
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 13/74 (17%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIV 119
E C C+ C CP + ++ G + V D++ C C LC+ ACP AI
Sbjct: 168 SEDCDECEKCVEACPRGVLELKEG-------KLVVT---DLLNCSLCKLCERACPGKAIR 217
Query: 120 EG--PN-FEFATET 130
N F F E+
Sbjct: 218 VSDDENKFIFTVES 231
Score = 28.7 bits (65), Expect = 0.76
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 58 NGEERCIACKLCEAICPAQAITIE 81
C CKLCE CP +AI +
Sbjct: 196 TDLLNCSLCKLCERACPGKAIRVS 219
>gnl|CDD|182135 PRK09898, PRK09898, hypothetical protein; Provisional.
Length = 208
Score = 36.0 bits (83), Expect = 0.004
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 61 ERCIACK--LCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
+ C CK C +CP AIT + C +D +CI C C ACP
Sbjct: 121 DTCRQCKEPQCMNVCPIGAITWQQKEGC---------ITVDHKRCIGCSACTTACP 167
Score = 35.2 bits (81), Expect = 0.008
Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 13/59 (22%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
+RCI C C CP T+ + KC+ CG C ACP A+
Sbjct: 153 HKRCIGCSACTTACPWMMATVNT-------------ESKKSSKCVLCGECANACPTGAL 198
>gnl|CDD|183604 PRK12576, PRK12576, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 279
Score = 35.9 bits (83), Expect = 0.005
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 103 CIYCGLCQEACPVDAIVE---GPN-----FEFATETRQELYYDKERLL 142
CI+CGLC ACPV AI GP + F + R + +ER+
Sbjct: 154 CIWCGLCVSACPVVAIDPEFLGPAAHAKGYRFLADPRDTIT--EERMK 199
Score = 35.5 bits (82), Expect = 0.007
Identities = 23/68 (33%), Positives = 27/68 (39%), Gaps = 14/68 (20%)
Query: 63 CIACKLCEAICPAQAITIE-SGPRCH------------DGTRRTVRYDIDMI-KCIYCGL 108
CI C LC + CP AI E GP H T ++ ID +C YC
Sbjct: 154 CIWCGLCVSACPVVAIDPEFLGPAAHAKGYRFLADPRDTITEERMKILIDSSWRCTYCYS 213
Query: 109 CQEACPVD 116
C CP D
Sbjct: 214 CSNVCPRD 221
>gnl|CDD|162996 TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein
FixG. Member of this ferredoxin-like protein family are
found exclusively in species with an operon encoding the
cbb3 type of cytochrome c oxidase (cco-cbb3), and near
the cco-cbb3 operon in about half the cases. The
cco-cbb3 is found in a variety of proteobacteria and
almost nowhere else, and is associated with oxygen use
under microaerobic conditions. Some (but not all) of
these proteobacteria are also nitrogen-fixing, hence the
gene symbol fixG. FixG was shown essential for
functional cco-cbb3 expression in Bradyrhizobium
japonicum.
Length = 434
Score = 35.7 bits (83), Expect = 0.006
Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 18/69 (26%)
Query: 45 PRFRGEHALRRYPNGEERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCI 104
PR + P G+ CI C LC +CP I I G + ++CI
Sbjct: 217 PRKGKKDPKAPGPLGD--CIDCNLCVQVCPT-GIDIRDGLQ---------------LECI 258
Query: 105 YCGLCQEAC 113
CGLC +AC
Sbjct: 259 NCGLCIDAC 267
>gnl|CDD|182382 PRK10330, PRK10330, formate dehydrogenase-H ferredoxin subunit;
Provisional.
Length = 181
Score = 35.3 bits (81), Expect = 0.008
Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRC-HDGTRRTVR-YDIDMIKCIYCG------LCQE 111
+ERCI CK C CP A+ + P + G VR + KC C C
Sbjct: 86 QERCIGCKTCVVACPYGAMEVVVRPVIRNSGAGLNVRAEKAEANKCDLCNHREDGPACMA 145
Query: 112 ACPVDAIV 119
ACP A++
Sbjct: 146 ACPTHALI 153
>gnl|CDD|185151 PRK15238, PRK15238, inner membrane transporter YjeM; Provisional.
Length = 496
Score = 34.5 bits (80), Expect = 0.014
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 14/44 (31%)
Query: 7 NVS----FLFLKEFVGAFFLCLRYFFKAKTTINYPFE--KGSTS 44
NVS +LFL GAF FFK K I+ PF K S
Sbjct: 402 NVSMTLPYLFL---AGAF-----PFFKKKKDIDRPFVVFKTKKS 437
>gnl|CDD|182001 PRK09626, oorD, 2-oxoglutarate-acceptor oxidoreductase subunit
OorD; Reviewed.
Length = 103
Score = 34.3 bits (79), Expect = 0.014
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI- 118
E RC AC +C ++CPA + + P G V + CI C C+ CP AI
Sbjct: 15 ESRCKACDICVSVCPAGVLAMRIDPHAVLGKMIKVVHP---ESCIGCRECELHCPDFAIY 71
Query: 119 -VEGPNFEFA--TETRQE 133
+ F+FA ++ +E
Sbjct: 72 VADRKEFKFAKLSKEAKE 89
>gnl|CDD|163201 TIGR03287, methan_mark_16, putative methanogenesis marker 16
metalloprotein. Members of this protein family, to
date, are found in a completed prokaryotic genome if and
only if the species is one of the archaeal methanogens.
The exact function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
This protein is a predicted to bind FeS clusters, based
on the presence of two copies of the Fer4 domain
(pfam00037), with each copy having four Cys residues
invariant across all members.
Length = 391
Score = 34.4 bits (79), Expect = 0.015
Identities = 22/59 (37%), Positives = 22/59 (37%), Gaps = 16/59 (27%)
Query: 61 ERCIACKLC--EAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDA 117
ERC C C E CP AI DGT T C CG C E CP A
Sbjct: 302 ERCENCDPCLVEEACPVPAIK-------KDGTLNTED-------CFGCGYCAEICPGGA 346
Score = 28.2 bits (63), Expect = 0.92
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 93 TVRYDIDMIKCIYCGLC--QEACPVDAIVEG 121
VR + +C C C +EACPV AI +
Sbjct: 294 DVRPKYNPERCENCDPCLVEEACPVPAIKKD 324
Score = 25.1 bits (55), Expect = 9.4
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 61 ERCIACKLCEAICPAQAITIESG 83
E C C C ICP A + G
Sbjct: 330 EDCFGCGYCAEICPGGAFEVNLG 352
>gnl|CDD|181550 PRK08764, PRK08764, ferredoxin; Provisional.
Length = 135
Score = 33.4 bits (76), Expect = 0.027
Identities = 22/60 (36%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIV 119
E CI C C CP AI + H TV + C C LC ACPVD I
Sbjct: 84 EADCIGCTKCIQACPVDAI-VGGAKHMH-----TVIAPL----CTGCELCVPACPVDCIE 133
Score = 31.4 bits (71), Expect = 0.10
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 103 CIYCGLCQEACPVDAIVEG 121
CI C C +ACPVDAIV G
Sbjct: 87 CIGCTKCIQACPVDAIVGG 105
>gnl|CDD|170017 PRK09624, porD, pyuvate ferredoxin oxidoreductase subunit delta;
Reviewed.
Length = 105
Score = 33.5 bits (76), Expect = 0.029
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIV 119
++C+ C LC CP AI ++ + YD C CG+C CP AI
Sbjct: 50 RDKCVRCYLCYIYCPEPAIYLD------EEGYPVFDYDY----CKGCGICANECPTKAIE 99
>gnl|CDD|181779 PRK09326, PRK09326, F420H2 dehydrogenase subunit F; Provisional.
Length = 341
Score = 33.3 bits (76), Expect = 0.030
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGT-----RRTVRYDIDMIKCIYCGLCQEACPV-D 116
C AC CEA+CP AIT++ D + ++ C C C CPV D
Sbjct: 14 CTACGACEAVCPIGAITVDKKAEIRDPNDLELYEKGAAPNV----CEGCLTCSRICPVVD 69
Query: 117 AIVE 120
+E
Sbjct: 70 GYIE 73
Score = 27.9 bits (62), Expect = 1.4
Identities = 13/38 (34%), Positives = 16/38 (42%)
Query: 98 IDMIKCIYCGLCQEACPVDAIVEGPNFEFATETRQELY 135
I+ C CG C+ CP+ AI E ELY
Sbjct: 9 IEYDVCTACGACEAVCPIGAITVDKKAEIRDPNDLELY 46
>gnl|CDD|183008 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 33.3 bits (77), Expect = 0.031
Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 13/64 (20%)
Query: 61 ERCIACKLCEAICPAQAITIE------SGPRCHDGTR----RTVRYDIDMIKCIYCGLCQ 110
+ CI C +C CP + +GP DG R YD + C C C+
Sbjct: 7 DSCIKCTVCTTACPVARVNPLYPGPKQAGP---DGERLRLKDGALYDESLKYCSNCKRCE 63
Query: 111 EACP 114
ACP
Sbjct: 64 VACP 67
>gnl|CDD|161798 TIGR00276, TIGR00276, iron-sulfur cluster binding protein,
putative. This series of proteins contain the prosite
signature for 4Fe-4S ferredoxins iron-sulfur binding
proteins (C-x(2)-C-x(2)-C-x(3)-C-[PEG]) between residues
175-188 of the model.
Length = 282
Score = 33.3 bits (76), Expect = 0.035
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 12/66 (18%)
Query: 60 EERCIACKLCEAICPAQAITIESG----PRC---HDGTRRTVRYD---IDMIKCIY-CGL 108
EE C C C CP QA+ +E PRC + + Y C +
Sbjct: 158 EEYCGRCTKCIDACPTQAL-VEPEFVDAPRCISYLTIEKDAALPKEFASNCGGRSYGCDI 216
Query: 109 CQEACP 114
CQE CP
Sbjct: 217 CQEVCP 222
Score = 28.7 bits (64), Expect = 0.68
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 103 CIYCGLCQEACPVDAIVE 120
C C C +ACP A+VE
Sbjct: 161 CGRCTKCIDACPTQALVE 178
>gnl|CDD|162737 TIGR02163, napH_, ferredoxin-type protein, NapH/MauN family. Most
members of this family are the NapH protein, found next
to NapG,in operons that encode the periplasmic nitrate
reductase. Some species with this reductase lack NapC
but accomplish electron transfer to NapAB in some other
manner, likely to involve NapH, NapG, and/or some other
protein. A few members of this protein are designated
MauN and are found in methylamine utilization operons in
species that appear to lack a periplasmic nitrate
reductase.
Length = 255
Score = 33.1 bits (76), Expect = 0.035
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 58 NGEERCIACKLCEAICP-AQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVD 116
+ E+C C C +CP Q + + P G+ + D C CG C + C D
Sbjct: 198 SDREKCTNCMDCFNVCPEPQVLRM---PLKKGGSTLVLSGD-----CTLCGRCIDVCHED 249
Query: 117 A 117
Sbjct: 250 V 250
>gnl|CDD|180493 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase
iron-sulfur subunit; Provisional.
Length = 486
Score = 33.1 bits (76), Expect = 0.039
Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 12/64 (18%)
Query: 63 CIACKLCEAICPAQAITIESGPRC------------HDGTRRTVRYDIDMIKCIYCGLCQ 110
CI C C + CPA+ ++ GP +G R +D + C CG C
Sbjct: 135 CIECLSCVSTCPARKVSDYPGPTFMRQLARFAFDPRDEGDREKEAFDEGLYNCTTCGKCV 194
Query: 111 EACP 114
E CP
Sbjct: 195 EVCP 198
>gnl|CDD|179919 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 33.0 bits (76), Expect = 0.039
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 103 CIYCGLCQEACPVD 116
CI CG C +ACP
Sbjct: 372 CIRCGACADACPAS 385
Score = 26.8 bits (60), Expect = 2.8
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 57 PNGEERCIACKLCEAICPA----QAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEA 112
P E+ CI C C CPA Q + + HD + Y++ CI CG C
Sbjct: 366 PPPEQPCIRCGACADACPASLLPQQLYWFAKAEEHD---KAQEYNLF--DCIECGACAYV 420
Query: 113 CP 114
CP
Sbjct: 421 CP 422
>gnl|CDD|162882 TIGR02486, RDH, reductive dehalogenase. This model represents a
family of corrin and 8-iron Fe-S cluster-containing
reductive dehalogenases found primarily in halorespiring
microorganisms such as dehalococcoides ethenogenes which
contains as many as 17 enzymes of this type with varying
substrate ranges. One example of a characterized species
is the tetrachloroethene reductive dehalogenase
(1.97.1.8) which also acts on trichloroethene converting
it to dichloroethene.
Length = 314
Score = 32.8 bits (75), Expect = 0.041
Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 19/71 (26%)
Query: 63 CIACKLCEAICPAQAIT--------IESGPRCHDGTRR-TVRYDIDMIKCI--------- 104
C C C CP+ AI+ E G +++ D +C+
Sbjct: 207 CETCGKCADECPSGAISKGGEPTWDPEDSNGDPPGENNPGLKWQYDGWRCLLFRCYNEGG 266
Query: 105 -YCGLCQEACP 114
CG+CQ CP
Sbjct: 267 GGCGVCQAVCP 277
Score = 28.9 bits (65), Expect = 0.70
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 97 DIDMIK-CIYCGLCQEACPVDAIVEGPN 123
D M K C CG C + CP AI +G
Sbjct: 200 DAGMAKFCETCGKCADECPSGAISKGGE 227
>gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta
subunit. This model describes the beta subunit of
sulfite reductase.
Length = 341
Score = 32.9 bits (75), Expect = 0.043
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 71 AICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
A CP A+ PR DG +++ ++D+ KCIYCG C CP
Sbjct: 191 AACPTGALK----PR-RDGKNKSL--EVDVEKCIYCGNCYTMCP 227
>gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex
subunit alpha; Validated.
Length = 781
Score = 32.6 bits (75), Expect = 0.045
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 48 RGEHALRRYPNGEE------RCIACKLCEAICPAQAITIESGPRCHDGTRRTVR--YDID 99
R ++ P EE +C C C +CP + E+ G + YD
Sbjct: 385 RKAKGIKALPTDEELKELAKKCTECGWCVRVCPNELPIPEAMEAAAKGDLSKLEDLYD-- 442
Query: 100 MIKCIYCGLCQEACP 114
KCI CG C++ CP
Sbjct: 443 --KCIGCGRCEQVCP 455
>gnl|CDD|181890 PRK09476, napG, quinol dehydrogenase periplasmic component;
Provisional.
Length = 254
Score = 32.3 bits (74), Expect = 0.061
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 102 KCIYCGLCQEACPVD 116
CI CGLC +ACP D
Sbjct: 60 ACIRCGLCVQACPYD 74
Score = 28.8 bits (65), Expect = 0.73
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 23/69 (33%)
Query: 60 EERCIA-----CKLCEAICPA--QAITIESGPRCHDGTRRTVRYD--------IDMIKCI 104
+E C+ C +C +CP +AIT+E R R + C
Sbjct: 136 QENCLNFQGLRCDVCYRVCPLIDKAITLE--------LERNERTGKHAFFLPTVHSDACT 187
Query: 105 YCGLCQEAC 113
CG C++AC
Sbjct: 188 GCGKCEKAC 196
>gnl|CDD|131958 TIGR02912, sulfite_red_C, sulfite reductase, subunit C. Members of
this protein family include the C subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum.
Note that any one of these enzymes may have secondary
substates such as NH2OH, SeO3(2-), and SO3(2-).
Heterologous expression of the anaerobic sulfite
reductase of Salmonella confers on Escherichia coli the
ability to produce hydrogen sulfide gas from sulfite.
Length = 314
Score = 32.1 bits (73), Expect = 0.066
Identities = 19/58 (32%), Positives = 23/58 (39%), Gaps = 12/58 (20%)
Query: 62 RCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDI--DMIKCIYCGLCQEACPVDA 117
RCI C C +C +A+ G Y + D KCI CG C CP A
Sbjct: 170 RCIGCGACVKVCKKKAV----------GALSFENYKVVRDHSKCIGCGECVLKCPTGA 217
>gnl|CDD|182000 PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta;
Reviewed.
Length = 133
Score = 32.0 bits (73), Expect = 0.080
Identities = 18/54 (33%), Positives = 21/54 (38%), Gaps = 10/54 (18%)
Query: 61 ERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
E CI C C CP AI +R +D C CG+C E CP
Sbjct: 59 EICINCFNCWVYCPDAAIL----------SRDKKLKGVDYSHCKGCGVCVEVCP 102
>gnl|CDD|182807 PRK10882, PRK10882, hydrogenase 2 protein HybA; Provisional.
Length = 328
Score = 31.9 bits (73), Expect = 0.083
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 9/46 (19%)
Query: 69 CEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
C ++CP A+T D V YD D C C C ACP
Sbjct: 120 CVSVCPVSALT-------KDPKTGIVHYDKD--VCTGCRYCMVACP 156
>gnl|CDD|132333 TIGR03290, CoB_CoM_SS_C, CoB--CoM heterodisulfide reductase,
subunit C. The last step in methanogenesis leaves two
coenzymes of methanogenesis, CoM and CoB, linked by a
disulfide bond. Members of this protein family are the C
subunit of the enzyme that reduces the heterodisulfide
to CoB-SH and CoM-SH. Similar enzyme complex subunits
are found in various other species, but likely act on a
different substrate.
Length = 144
Score = 31.7 bits (72), Expect = 0.092
Identities = 22/70 (31%), Positives = 25/70 (35%), Gaps = 19/70 (27%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGTRRTVRY-----------DIDMIKCIYCGLCQE 111
C C C CP SG R TR +R D D+ C C CQE
Sbjct: 4 CYQCGTCTGSCP-------SGRRTSYRTRLIIRKALLGLKDEVISDDDLWMCTTCYTCQE 56
Query: 112 ACPVD-AIVE 120
CP D I +
Sbjct: 57 RCPRDVKITD 66
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 31.3 bits (72), Expect = 0.13
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 69 CEAICP-----AQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
C CP + I I+ + + V I CI CG+C + CP DAI
Sbjct: 21 CIKYCPVVRTGEETIEID------EDDGKPV---ISEELCIGCGICVKKCPFDAI 66
Score = 30.9 bits (71), Expect = 0.16
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 60 EERCIACKLCEAICPAQAITI 80
EE CI C +C CP AI+I
Sbjct: 48 EELCIGCGICVKKCPFDAISI 68
>gnl|CDD|129414 TIGR00314, cdhA, CO dehydrogenase/acetyl-CoA synthase complex,
epsilon subunit. Acetyl-CoA decarbonylase/synthase
(ACDS) is a multienzyme complex. Carbon monoxide
dehydrogenase is a synonym. The ACDS complex carries out
an unusual reaction involving the reversible cleavage
and synthesis of acetyl-CoA in methanogens. The model
contains the prosite signature for 4Fe-4S ferredoxins
[C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462
of the model.
Length = 784
Score = 30.6 bits (69), Expect = 0.19
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 60 EERCIACKLCEAICP 74
EE+C AC CE CP
Sbjct: 436 EEQCYACGRCEQACP 450
Score = 29.8 bits (67), Expect = 0.34
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 62 RCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIK-CIYCGLCQEACP 114
+C C C CP E+ G + + + C CG C++ACP
Sbjct: 400 KCTQCGNCVRTCPNSLRVDEAMAHAQKGDLSKL---EQLEEQCYACGRCEQACP 450
>gnl|CDD|181515 PRK08640, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 249
Score = 30.0 bits (68), Expect = 0.27
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 83 GPRCHDGTRRTVRYDIDMIKCIYCGLCQEACP 114
GPR + +R Y++ KC+ CG C EACP
Sbjct: 137 GPRMPE-EKRQWAYELS--KCMTCGCCLEACP 165
>gnl|CDD|131115 TIGR02060, aprB, adenosine phosphosulphate reductase, beta subunit.
During dissimilatory sulfate reduction and sulfur
oxidation, adenylylsulfate (APS) reductase catalyzes
reversibly the two-electron reduction of APS to sulfite
and AMP. Found in several bacterial lineages and in
Archaeoglobales, APS reductase is a heterodimer composed
of an alpha subunit containing a noncovalently bound
FAD, and a beta subunit containing two [4Fe-4S]
clusters. Described by this model is the beta subunit of
APS reductase, sharing common evolutionary origin with
other iron-sulfur cluster-binding proteins.
Length = 132
Score = 29.9 bits (67), Expect = 0.28
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 61 ERCIACKL-----CEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPV 115
+C CK C ICP + +++ Y+I+ C C C +ACP
Sbjct: 8 TKCDGCKAGEKTACVYICPNDLMHLDTEIM--------KAYNIEPDMCWECYSCVKACPQ 59
Query: 116 DAIVEGPNFEFA 127
AI +FA
Sbjct: 60 GAIDVRGYADFA 71
>gnl|CDD|129492 TIGR00397, mauM_napG, MauM/NapG family ferredoxin-type protein.
MauM is involved in methylamine utilization. NapG is
associated with nitrate reductase activity. The two
proteins are highly similar.
Length = 213
Score = 29.9 bits (67), Expect = 0.30
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 103 CIYCGLCQEACPVDAI 118
C+ CGLC EACP D +
Sbjct: 55 CVRCGLCVEACPYDIL 70
Score = 29.1 bits (65), Expect = 0.59
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 59 GEERCI-----ACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEAC 113
G E C+ C +C +CP + I P ++ R + +D KC CG C++ C
Sbjct: 129 GHETCLNYKGLNCSICVRVCPIRGEAISLKPIENERGRLQIPT-VDSAKCTGCGTCEKHC 187
>gnl|CDD|162435 TIGR01582, FDH-beta, formate dehydrogenase, beta subunit, Fe-S
containing. In addition to the gamma proteobacteria, a
sequence from Aquifex aolicus falls within the scope of
this model. This appears to be the case for the alpha,
gamma and epsilon (accessory protein TIGR01562) chains
as well.
Length = 283
Score = 29.9 bits (67), Expect = 0.30
Identities = 25/103 (24%), Positives = 33/103 (32%), Gaps = 27/103 (26%)
Query: 52 ALRRYPNG-----EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYC 106
A+ +Y NG +CI C C CP PR R KC C
Sbjct: 110 AIIQYQNGIVDFDHSKCIGCGYCIVGCPFNI------PRYDKVDNRPY-------KCTLC 156
Query: 107 ------GL---CQEACPVDAIVEGPNFEFATETRQELYYDKER 140
G C + CP +AI G + + + K R
Sbjct: 157 IDRVSVGQEPACVKTCPTNAISFGFKEDMKERAEKRVADLKSR 199
Score = 25.3 bits (55), Expect = 7.5
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 98 IDMIKCIYCGLCQEAC 113
ID+ CI C CQ AC
Sbjct: 26 IDVSSCIGCKACQAAC 41
>gnl|CDD|161860 TIGR00402, napF, ferredoxin-type protein NapF. The gene codes for
a ferredoxin-type cytosolic protein, NapF, of the
periplasmic nitrate reductase system, as in Escherichia
coli. NapF interacts with the catalytic subunit, NapA,
and may be an accessory protein for NapA maturation.
Length = 101
Score = 29.9 bits (67), Expect = 0.35
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 10/70 (14%)
Query: 62 RCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVEG 121
C C C + C + + + TV +D +C +CG C EACP +A
Sbjct: 35 VCTRCGECASACENNILQLG------QQGQPTVEFDNA--ECDFCGKCAEACPTNAF--H 84
Query: 122 PNFEFATETR 131
P F R
Sbjct: 85 PRFPGDWLLR 94
>gnl|CDD|163157 TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S
protein. Members of this protein family are the Fe-S
protein, NrfC, of a cytochrome c nitrite reductase
system for which the pentaheme cytochrome c protein,
NrfB (family TIGR03146) is an unambiguous marker.
Members of this protein family show similarity to other
ferredoxin-like proteins, including a subunit of a
polysulfide reductase.
Length = 225
Score = 29.4 bits (66), Expect = 0.40
Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 27/90 (30%)
Query: 61 ERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYC----------GLCQ 110
+ C+ C+ C A CP + I + D KC +C C
Sbjct: 125 DLCVGCQYCIAACPYRVRFIHPVTKSAD-------------KCNFCRDTNLAEGKLPACV 171
Query: 111 EACPVDAIVEG----PNFEFATETRQELYY 136
E+CP A+ G PN E + + +Q+ Y
Sbjct: 172 ESCPTKALTFGDLNDPNSEVSQKLKQKPVY 201
Score = 25.5 bits (56), Expect = 6.0
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 16/66 (24%)
Query: 56 YPNGEERC--IACKLCE-----AICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGL 108
+P+ E R +C+ C+ A+CP A + T D+ C+ C
Sbjct: 82 FPDVEYRFFRKSCQHCDNAPCVAVCPTGASFKD---------EETGIVDVHKDLCVGCQY 132
Query: 109 CQEACP 114
C ACP
Sbjct: 133 CIAACP 138
>gnl|CDD|181891 PRK09477, napH, quinol dehydrogenase membrane component;
Provisional.
Length = 271
Score = 29.5 bits (67), Expect = 0.47
Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 61 ERCIACKLCEAICP-AQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
++C C C +CP Q + P + D CI CG C + C D
Sbjct: 208 QKCTRCMDCFHVCPEPQVLR----PPLKGKQSPSQVTSGD---CITCGRCIDVCSEDVF 259
>gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional.
Length = 244
Score = 29.5 bits (66), Expect = 0.48
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 10/49 (20%)
Query: 69 CEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDA 117
C +CP QA R +D +C+ C C +ACP DA
Sbjct: 108 CVPVCPVQATF----------QREDGIVVVDNKRCVGCAYCVQACPYDA 146
Score = 25.6 bits (56), Expect = 5.7
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 13/60 (21%)
Query: 61 ERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAIVE 120
+RC+ C C CP A I + D KC +C EA + A VE
Sbjct: 130 KRCVGCAYCVQACPYDARFINHETQTAD-------------KCTFCVHRLEAGLLPACVE 176
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 29.2 bits (65), Expect = 0.50
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 11/50 (22%)
Query: 69 CEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
C CP A+T +S +D KCI C C ACP +
Sbjct: 64 CVTACPVNALTFQSD-----------SVQLDEQKCIGCKRCAIACPFGVV 102
Score = 27.7 bits (61), Expect = 1.6
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 63 CIACKLCEAICPAQAITIESGPRCHDGTRRTV-----RYDIDMIKCIYC--GLCQEACPV 115
CI C CE C A A E+ P H R + + + C +C C ACPV
Sbjct: 12 CIGCHACEIAC-AVAHNQENWPLSHSDFRPRIHVVGKGQAANPVACHHCNNAPCVTACPV 70
Query: 116 DAIV 119
+A+
Sbjct: 71 NALT 74
Score = 25.8 bits (56), Expect = 5.7
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 60 EERCIACKLCEAICPAQAI 78
E++CI CK C CP +
Sbjct: 84 EQKCIGCKRCAIACPFGVV 102
>gnl|CDD|180322 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 232
Score = 28.6 bits (65), Expect = 0.69
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 95 RYDIDMIKCIYCGLCQEACPV 115
+ D + +CI C C +CP
Sbjct: 136 KLD-GLYECILCACCSTSCPS 155
>gnl|CDD|183490 PRK12385, PRK12385, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 244
Score = 28.5 bits (64), Expect = 0.76
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 103 CIYCGLCQEACP 114
CI CGLC ACP
Sbjct: 149 CINCGLCYAACP 160
Score = 25.8 bits (57), Expect = 5.4
Identities = 20/71 (28%), Positives = 25/71 (35%), Gaps = 22/71 (30%)
Query: 63 CIACKLCEAICPAQAITIE-SGPRCHDGTRRTVRYDID------------------MIKC 103
CI C LC A CP + E GP RY++D + C
Sbjct: 149 CINCGLCYAACPQFGLNPEFIGPA---AITLAHRYNLDSRDHGKKERMKQLNGQNGVWSC 205
Query: 104 IYCGLCQEACP 114
+ G C E CP
Sbjct: 206 TFVGYCSEVCP 216
>gnl|CDD|179457 PRK02651, PRK02651, photosystem I subunit VII; Provisional.
Length = 81
Score = 28.5 bits (63), Expect = 0.82
Identities = 22/77 (28%), Positives = 28/77 (36%), Gaps = 29/77 (37%)
Query: 51 HALRRYPNGEERCIACKLCEAICP-----------AQAITIESGPRCHDGTRRTVRYDID 99
HA++ Y + CI C C CP +A I S PR D
Sbjct: 3 HAVKIY----DTCIGCTQCVRACPLDVLEMVPWDGCKAGQIASSPRTED----------- 47
Query: 100 MIKCIYCGLCQEACPVD 116
C+ C C+ ACP D
Sbjct: 48 ---CVGCKRCETACPTD 61
Score = 26.5 bits (58), Expect = 3.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 61 ERCIACKLCEAICPAQAITI 80
E C+ CK CE CP ++I
Sbjct: 46 EDCVGCKRCETACPTDFLSI 65
>gnl|CDD|129374 TIGR00273, TIGR00273, iron-sulfur cluster-binding protein. Members
of this family have a perfect 4Fe-4S binding motif
C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or
imperfect (the first Cys replaced by Ser) second copy.
Members probably bind two 4fe-4S iron-sulfur clusters.
Length = 432
Score = 28.7 bits (64), Expect = 0.83
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 99 DMIKCIYCGLCQEACPV 115
+++ CI CG CQ CPV
Sbjct: 291 EVLACIRCGACQNECPV 307
Score = 27.9 bits (62), Expect = 1.4
Identities = 17/64 (26%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 62 RCIACKLCEAICPA-QAITIESGPRCHDGTRRTV---------RYDIDMIKCIYCGLCQE 111
CI C C+ CP + I + G V Y CG C+E
Sbjct: 294 ACIRCGACQNECPVYRHIGGHWYGSIYPGPIGAVWSPLLGGYTDYKHLPYLSSLCGACRE 353
Query: 112 ACPV 115
CPV
Sbjct: 354 VCPV 357
>gnl|CDD|132092 TIGR03048, PS_I_psaC, photosystem I iron-sulfur protein PsaC.
Members of this family are PsaC, an essential component
of photosystem I (PS-I) reaction center in Cyanobacteria
and chloroplasts. This small protein, about 80 amino
acids in length, contains two copies of the
ferredoxin-like 4Fe-4S binding site (pfam00037) and
therefore eight conserved Cys residues. This protein is
also called photosystem I subunit VII.
Length = 80
Score = 27.9 bits (62), Expect = 1.4
Identities = 19/65 (29%), Positives = 22/65 (33%), Gaps = 25/65 (38%)
Query: 63 CIACKLCEAICPA-----------QAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQE 111
CI C C CP +A I S PR D C+ C C+
Sbjct: 10 CIGCTQCVRACPTDVLEMVPWDGCKAGQIASAPRTED--------------CVGCKRCES 55
Query: 112 ACPVD 116
ACP D
Sbjct: 56 ACPTD 60
Score = 25.2 bits (55), Expect = 7.9
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 61 ERCIACKLCEAICPAQAITI 80
E C+ CK CE+ CP +++
Sbjct: 45 EDCVGCKRCESACPTDFLSV 64
>gnl|CDD|183296 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 27.8 bits (63), Expect = 1.4
Identities = 7/15 (46%), Positives = 9/15 (60%), Gaps = 2/15 (13%)
Query: 103 CIYCG--LCQEACPV 115
C+ C C +ACPV
Sbjct: 42 CLQCKDAPCVKACPV 56
>gnl|CDD|162617 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit.
Length = 435
Score = 27.7 bits (62), Expect = 1.5
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 103 CIYCGLCQEACPV 115
CI CG C + CP+
Sbjct: 365 CIRCGKCVQVCPM 377
Score = 27.3 bits (61), Expect = 2.0
Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 11/66 (16%)
Query: 53 LRRYPNGEERCIACKLCEAICPA----QAITIESGPRCHDGTRRTVRYDIDMIKCIYCGL 108
P CI C C +CP Q + + D + +++ CI CG
Sbjct: 357 TPESPEKP--CIRCGKCVQVCPMNLLPQQLNWLALADEFDEAE-----EHNLMDCIECGC 409
Query: 109 CQEACP 114
C CP
Sbjct: 410 CSYVCP 415
>gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 27.7 bits (62), Expect = 1.5
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 99 DMIKCIYCGLCQEACPVDAIV 119
+ + C +CG C CPV A+
Sbjct: 202 ETLDCSFCGECIAVCPVGALS 222
>gnl|CDD|161850 TIGR00384, dhsB, succinate dehydrogenase and fumarate reductase
iron-sulfur protein. Succinate dehydrogenase and
fumarate reductase are reverse directions of the same
enzymatic interconversion, succinate + FAD+ = fumarate +
FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse
reactions are catalyzed by distinct complexes: fumarate
reductase operates under anaerobic conditions and
succinate dehydrogenase operates under aerobic
conditions. This model also describes a region of the B
subunit of a cytosolic archaeal fumarate reductase.
Length = 220
Score = 27.4 bits (61), Expect = 1.8
Identities = 15/52 (28%), Positives = 18/52 (34%), Gaps = 15/52 (28%)
Query: 103 CIYCGLCQEACPVDAIVE---GPNF------------EFATETRQELYYDKE 139
CI CG C +CP GP + AT+ R E DK
Sbjct: 140 CILCGCCYSSCPAFWWNPEFLGPAALTAAYRFLIDSRDHATKDRLEGLNDKN 191
Score = 27.0 bits (60), Expect = 2.7
Identities = 19/71 (26%), Positives = 23/71 (32%), Gaps = 22/71 (30%)
Query: 63 CIACKLCEAICPAQAITIE-SGPRCHDGTRRTVRYDID------------------MIKC 103
CI C C + CPA E GP R+ ID + +C
Sbjct: 140 CILCGCCYSSCPAFWWNPEFLGPA---ALTAAYRFLIDSRDHATKDRLEGLNDKNGVWRC 196
Query: 104 IYCGLCQEACP 114
C C E CP
Sbjct: 197 TTCMNCSEVCP 207
>gnl|CDD|163077 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of
this family are homodimeric ferredoxins from nitrogen
fixation regions of many nitrogen-fixing bacteria. As
characterized in Rhodobacter capsulatus, these proteins
are homodimeric, with two 4Fe-4S clusters bound per
monomer. Although nif-specific, this protein family is
not usiveral, as other nitrogenase systems may
substitute flavodoxins, or different types of
ferredoxin.
Length = 91
Score = 27.4 bits (61), Expect = 1.9
Identities = 7/22 (31%), Positives = 9/22 (40%)
Query: 58 NGEERCIACKLCEAICPAQAIT 79
CI C C +CP + T
Sbjct: 67 ANPGNCIGCGACARVCPKKCQT 88
Score = 27.0 bits (60), Expect = 2.6
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 88 DGTRRTVRY--DIDMIKCIYCGLCQEACPVD 116
G+ T ++ ID KCI CG C + C D
Sbjct: 6 GGSEWTPQFVTSIDQEKCIGCGRCYKVCGRD 36
Score = 26.2 bits (58), Expect = 4.1
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 9/67 (13%)
Query: 60 EERCIACKLCEAICPAQAITI----ESGPRCH-----DGTRRTVRYDIDMIKCIYCGLCQ 110
+E+CI C C +C +T+ E G D R V + CI CG C
Sbjct: 20 QEKCIGCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVANPGNCIGCGACA 79
Query: 111 EACPVDA 117
CP
Sbjct: 80 RVCPKKC 86
>gnl|CDD|177700 PLN00071, PLN00071, photosystem I subunit VII; Provisional.
Length = 81
Score = 27.2 bits (60), Expect = 2.2
Identities = 19/65 (29%), Positives = 22/65 (33%), Gaps = 25/65 (38%)
Query: 63 CIACKLCEAICP-----------AQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQE 111
CI C C CP +A I S PR D C+ C C+
Sbjct: 11 CIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTED--------------CVGCKRCES 56
Query: 112 ACPVD 116
ACP D
Sbjct: 57 ACPTD 61
Score = 24.9 bits (54), Expect = 9.2
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 61 ERCIACKLCEAICPAQAITI 80
E C+ CK CE+ CP +++
Sbjct: 46 EDCVGCKRCESACPTDFLSV 65
>gnl|CDD|184993 PRK15033, PRK15033, tricarballylate utilization protein B;
Provisional.
Length = 389
Score = 26.5 bits (59), Expect = 3.4
Identities = 26/89 (29%), Positives = 31/89 (34%), Gaps = 32/89 (35%)
Query: 63 CIACKLCEAIC---PAQAITIESGPRCHDGTRRT--VRYDIDMIK--CIYCGLCQEACPV 115
C AC+ CE C PA TRR + DI + C CG C AC
Sbjct: 35 CNACRYCEGFCAVFPAM-------------TRRLEFGKADIHYLANLCHNCGACLHACQY 81
Query: 116 DAIVEGPNFEFA-------TETRQELYYD 137
P EFA + R E Y +
Sbjct: 82 -----APPHEFAVNVPKAMAQVRLETYQE 105
>gnl|CDD|182296 PRK10194, PRK10194, ferredoxin-type protein; Provisional.
Length = 163
Score = 26.5 bits (58), Expect = 3.4
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 12/60 (20%)
Query: 62 RCIACKLCEAICPAQAITIE---SGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDAI 118
+ + C+ C+ C AI SG + ++ C CG C +CPV AI
Sbjct: 105 QSVECRRCQDSCEPMAIIFRPTLSG---------IYQPQLNSQLCNGCGACAASCPVSAI 155
Score = 25.8 bits (56), Expect = 6.0
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 63 CIACKLCEAICPAQAITIE 81
C C C A CP AIT E
Sbjct: 140 CNGCGACAASCPVSAITAE 158
>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 = 26.3 bits (58), Expect = 3.6
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 61 ERCIAC----KLCEAICPAQA-ITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPV 115
+RC+ C + C +CP +A I I + V D C CG C CP
Sbjct: 881 QRCLECSYVCEKCVDVCPNRANIVIYVPG--FRDQFQIVHLDG---MCNECGNCATFCPY 935
Query: 116 D 116
D
Sbjct: 936 D 936
>gnl|CDD|181964 PRK09575, vmrA, multidrug efflux pump VmrA; Reviewed.
Length = 453
Score = 26.1 bits (58), Expect = 4.0
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 22 LCLRYFFKAKTTINYPFEKGSTSPRF 47
L L YFF ++ I ++ +
Sbjct: 207 LGLGYFFSSRANIRLTLKELRFNWSL 232
>gnl|CDD|181037 PRK07569, PRK07569, bidirectional hydrogenase complex protein HoxU;
Validated.
Length = 234
Score = 26.2 bits (58), Expect = 4.1
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 103 CIYCGLCQEACPVDAIVE 120
C CG C +ACP AI
Sbjct: 192 CTSCGKCVQACPTGAIFR 209
>gnl|CDD|131996 TIGR02951, DMSO_dmsB, DMSO reductase, iron-sulfur subunit. This
family consists of the iron-sulfur subunit, or chain B,
of an enzyme called the anaerobic dimethyl sulfoxide
reductase. Chains A and B are catalytic, while chain C
is a membrane anchor.
Length = 161
Score = 26.2 bits (58), Expect = 4.6
Identities = 20/55 (36%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 64 IACKLC-EAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCGLCQEACPVDA 117
I+C C + C T R DG V D D KCI C C ACP A
Sbjct: 62 ISCNHCADPACVKNCPTGAMYKREEDGL---VLVDQD--KCIGCRYCVWACPYGA 111
Score = 25.1 bits (55), Expect = 9.2
Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 22/72 (30%)
Query: 60 EERCIACKLCEAICPAQAITIESGPRCHDGTRRTVRYDIDMIKCIYCG---------LCQ 110
+++CI C+ C CP A P+ M KC C C
Sbjct: 94 QDKCIGCRYCVWACPYGA------PQYDPQQGV-------MGKCDGCYDRVEKGLRPACV 140
Query: 111 EACPVDAIVEGP 122
+ACP+ A+ GP
Sbjct: 141 DACPMRALDFGP 152
>gnl|CDD|183491 PRK12386, PRK12386, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 251
Score = 25.8 bits (57), Expect = 5.0
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 102 KCIYCGLCQEACPV 115
KCI C LCQ C V
Sbjct: 143 KCIECFLCQNVCHV 156
>gnl|CDD|185058 PRK15103, PRK15103, paraquat-inducible membrane protein A;
Provisional.
Length = 419
Score = 25.8 bits (57), Expect = 5.9
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 65 ACKLCEAICPAQAITIESGPRCHDGTRRTVR 95
+C C AI PA PRCH T+ VR
Sbjct: 223 SCSCCTAILPADQPVC---PRCH--TKGYVR 248
>gnl|CDD|183763 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 25.5 bits (57), Expect = 6.9
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 103 CIYCGL--CQEACPVDAIVEGPNF 124
C+ CG+ C CPV + P +
Sbjct: 46 CMDCGIPFCHWGCPVHNYI--PEW 67
>gnl|CDD|181495 PRK08596, PRK08596, acetylornithine deacetylase; Validated.
Length = 421
Score = 25.4 bits (56), Expect = 7.0
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 78 ITIESGPRCHDGTRR 92
IT++S HDGTRR
Sbjct: 193 ITVKSPQTFHDGTRR 207
>gnl|CDD|132518 TIGR03478, DMSO_red_II_bet, DMSO reductase family type II enzyme,
iron-sulfur subunit. This model represents the
iron-sulfur subunit, typically called the beta subunit,
of various proteins that also contain a molybdopterin
subunit and a heme b subunit. The group includes two
distinct but very closely related periplasmic proteins
of anaerobic respiration, selenate reductase and
chlorate reductase. Other members of this family include
dimethyl sulphide dehydrogenase and ethylbenzene
dehydrogenase.
Length = 321
Score = 25.5 bits (56), Expect = 7.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 91 RRTVRYDIDMIKCIYCGLCQEAC 113
+R + Y ID+ KCI C C AC
Sbjct: 1 KRQLAYVIDLNKCIGCQTCTVAC 23
>gnl|CDD|131956 TIGR02910, sulfite_red_A, sulfite reductase, subunit A. Members of
this protein family include the A subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum.
Note that any one of these enzymes may have secondary
substates such as NH2OH, SeO3(2-), and SO3(2-).
Heterologous expression of the anaerobic sulfite
reductase of Salmonella confers on Escherichia coli the
ability to produce hydrogen sulfide gas from sulfite.
Length = 334
Score = 25.2 bits (55), Expect = 7.9
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 46 RFRGEHALRRYP--NGEERCIACKLCEAICP 74
RF+ H + Y NG C+ C C+ ICP
Sbjct: 284 RFKVMHKVNDYKKRNGYHMCVGCGRCDDICP 314
>gnl|CDD|183069 PRK11274, glcF, glycolate oxidase iron-sulfur subunit; Provisional.
Length = 407
Score = 25.2 bits (56), Expect = 9.1
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 22/81 (27%)
Query: 53 LRRYPNGEE------RCIACKLCEAICPA-QAITIE-SGPR-----------CHDGTRRT 93
+R P GEE +C+ C C A CP Q + E GPR + T +T
Sbjct: 9 IRDTPEGEEAEAILRKCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQVLEGAEVTEKT 68
Query: 94 VRYDIDMIKCIYCGLCQEACP 114
+ +D +C+ C C+ CP
Sbjct: 69 -QLHLD--RCLTCRNCETTCP 86
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.328 0.143 0.465
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,695,017
Number of extensions: 158245
Number of successful extensions: 624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 526
Number of HSP's successfully gapped: 174
Length of query: 163
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 77
Effective length of database: 4,136,185
Effective search space: 318486245
Effective search space used: 318486245
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: 53 (24.4 bits)