RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4925
(160 letters)
>gnl|CDD|235637 PRK05888, PRK05888, NADH dehydrogenase subunit I; Provisional.
Length = 164
Score = 254 bits (652), Expect = 2e-88
Identities = 100/159 (62%), Positives = 120/159 (75%)
Query: 2 VDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERC 61
+ + + + L E+ +G V + FK+ TI YP EK PLSPRFRG HALRR P+GEERC
Sbjct: 1 IKQYLKSMLLKELLKGLGVTLKYFFKKKVTIQYPEEKLPLSPRFRGRHALRRDPNGEERC 60
Query: 62 IACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNF 121
IACKLC AICPA AITIEA ER DG RRTTRYDI+ +CI+CGFC+EACP DAIVE P+F
Sbjct: 61 IACKLCAAICPADAITIEAAEREDGRRRTTRYDINFGRCIFCGFCEEACPTDAIVETPDF 120
Query: 122 EFSTESHEELLYNKEKLLSNGDKWESEIASNIHADHLYR 160
E +TE+ EEL+Y+KEKLL+NGD+ E EIA AD YR
Sbjct: 121 ELATETREELIYDKEKLLANGDRVEREIAPGKAADANYR 159
>gnl|CDD|224066 COG1143, NuoI, Formate hydrogenlyase subunit 6/NADH:ubiquinone
oxidoreductase 23 kD subunit (chain I) [Energy
production and conversion].
Length = 172
Score = 189 bits (483), Expect = 1e-62
Identities = 71/165 (43%), Positives = 94/165 (56%), Gaps = 10/165 (6%)
Query: 1 MVDRGIHAAFLTEIFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEER 60
+ FL + +G + ++FK+P TI YP EK PLSPRFRG H L R
Sbjct: 2 KLKEAAKVKFLLDFLKGLWTTLKNLFKKPVTIEYPEEKIPLSPRFRGRHVLDRDK----- 56
Query: 61 CIACKLCEAICPAQAITIEAEER-ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
CI C LC ICPA AIT+E ER DG ++ R DI++ +CI+CG C E CP A+V P
Sbjct: 57 CIGCGLCANICPANAITMETAERKVDGRKKPKRPDINLGRCIFCGLCVEVCPTGALVLTP 116
Query: 120 NFEFSTESHEELLYNKEKLLSNGDKWE----SEIASNIHADHLYR 160
FE ++ E+L+Y+KE+LL+ DK E EIA + D Y
Sbjct: 117 EFELASYKREDLVYDKERLLAPPDKKEEDKPFEIARLLALDAKYL 161
>gnl|CDD|233661 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 [Energy metabolism, Electron
transport].
Length = 122
Score = 177 bits (451), Expect = 2e-58
Identities = 60/122 (49%), Positives = 76/122 (62%)
Query: 17 GFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAI 76
G + + F +P T+ YP EK L PRFRG L R P+GEE+CI C LC A+CPA AI
Sbjct: 1 GLGLTLKYFFSKPVTVQYPEEKLYLPPRFRGRIVLTRDPNGEEKCIGCTLCAAVCPADAI 60
Query: 77 TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKE 136
+ E DG RR Y I+ +CI+CG C+EACP DAIV P FE +T + +L+Y KE
Sbjct: 61 RVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACPTDAIVLTPEFELATYTRSDLVYGKE 120
Query: 137 KL 138
L
Sbjct: 121 DL 122
>gnl|CDD|129498 TIGR00403, ndhI, NADH-plastoquinone oxidoreductase subunit I
protein. [Energy metabolism, Electron transport].
Length = 183
Score = 79.2 bits (195), Expect = 4e-19
Identities = 45/126 (35%), Positives = 65/126 (51%), Gaps = 6/126 (4%)
Query: 14 IFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPA 73
I +GF V H+ + P TI YP+EK S RFRG R ++CIAC++C +CP
Sbjct: 22 IGQGFAVTLDHMNRLPITIQYPYEKLIPSERFRG-----RIHFEFDKCIACEVCVRVCPI 76
Query: 74 QAITIEAE-ERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL 132
++ E +A ++ Y ID CI+CG C E CP + + +E ST EL
Sbjct: 77 NLPVVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELN 136
Query: 133 YNKEKL 138
Y++ L
Sbjct: 137 YDQIAL 142
>gnl|CDD|214334 CHL00014, ndhI, NADH dehydrogenase subunit I.
Length = 167
Score = 75.6 bits (186), Expect = 6e-18
Identities = 44/123 (35%), Positives = 62/123 (50%), Gaps = 6/123 (4%)
Query: 14 IFRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPA 73
I +GF + H + P TI YP+EK S RFRG R ++CIAC++C +CP
Sbjct: 19 IGQGFMITLSHANRLPVTIQYPYEKLITSERFRG-----RIHFEFDKCIACEVCVRVCPI 73
Query: 74 QAITIEAEERAD-GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL 132
++ + D +R Y ID CI+CG C E CP + + +E ST EL
Sbjct: 74 DLPVVDWKLETDIRKKRLLNYSIDFGVCIFCGNCVEYCPTNCLSMTEEYELSTYDRHELN 133
Query: 133 YNK 135
YN+
Sbjct: 134 YNQ 136
>gnl|CDD|183492 PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur
subunit; Provisional.
Length = 180
Score = 73.1 bits (180), Expect = 6e-17
Identities = 34/110 (30%), Positives = 52/110 (47%), Gaps = 13/110 (11%)
Query: 29 PATINYPFEKGPLSPRFRG--EHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADG 86
AT +YP E + FRG E+ ++CI C C CP+ A+T+E +
Sbjct: 13 TATSSYPLEPIAVDKNFRGKPEYNP-------QQCIGCAACVNACPSNALTVETDLATG- 64
Query: 87 SRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKE 136
++ ++ +CI+CG C+E CP AI FE + E+LL E
Sbjct: 65 ---ELAWEFNLGRCIFCGRCEEVCPTAAIKLSQEFELAVWKKEDLLQQSE 111
>gnl|CDD|181301 PRK08222, PRK08222, hydrogenase 4 subunit H; Validated.
Length = 181
Score = 72.5 bits (178), Expect = 1e-16
Identities = 37/102 (36%), Positives = 56/102 (54%), Gaps = 9/102 (8%)
Query: 30 ATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRR 89
AT+ YPF +SP FRG+ L +CIAC C CPA A+TI+ +++ +
Sbjct: 14 ATVKYPFAPLEVSPGFRGKPDL-----MPSQCIACGACTCACPANALTIQTDDQQN---- 64
Query: 90 TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEEL 131
+ + + + +CIYCG C+E CP AI NFE + + +L
Sbjct: 65 SRTWQLYLGRCIYCGRCEEVCPTRAIQLTNNFELTVTNKADL 106
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 62.9 bits (153), Expect = 3e-12
Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 15 FRGFFVATGHIFKEPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQ 74
F A +F++P TI P K + R+RG H + E+CI C C ICP
Sbjct: 6 FFAPLKAWKFLFRKPVTIKVPNVKREAAERYRGFHI-----NDWEKCIGCGTCSKICPTD 60
Query: 75 AIT-IEAEERADG-SRRTTRYDIDMTKCIYCGFCQEAC 110
AIT +E + ++ R ID +C +C C + C
Sbjct: 61 AITMVEVPDLPQEYGKKPQRPVIDYGRCSFCALCVDIC 98
Score = 28.2 bits (63), Expect = 2.0
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 60 RCIACKLCEAICPA 73
RC+ C +C CPA
Sbjct: 186 RCVECGICTDTCPA 199
>gnl|CDD|181399 PRK08348, PRK08348, NADH-plastoquinone oxidoreductase subunit;
Provisional.
Length = 120
Score = 57.2 bits (138), Expect = 2e-11
Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 14/103 (13%)
Query: 25 IFKEPATINYP-FEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEER 83
+FK+PAT +P E P+ FRG+ ++C+ C++C +CPA E R
Sbjct: 12 LFKKPATNLFPATEPVPVPEDFRGKILYDV-----DKCVGCRMCVTVCPAGVFVYLPEIR 66
Query: 84 ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTE 126
+ + +C++CG C + CP A+ +F ++
Sbjct: 67 --------KVALWTGRCVFCGQCVDVCPTGALQMSDDFLLASY 101
>gnl|CDD|221801 pfam12838, Fer4_7, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 48
Score = 52.9 bits (127), Expect = 2e-10
Identities = 20/53 (37%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
CI C C CP AIT++ E G +ID KC CG C CP
Sbjct: 1 CIGCGACVRACPYGAITLDEEGGKKG-----TVEIDPDKCTGCGACVAVCPTG 48
Score = 30.6 bits (69), Expect = 0.049
Identities = 10/23 (43%), Positives = 10/23 (43%)
Query: 100 CIYCGFCQEACPVDAIVEGPNFE 122
CI CG C ACP AI
Sbjct: 1 CIGCGACVRACPYGAITLDEEGG 23
Score = 25.2 bits (55), Expect = 4.0
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 58 EERCIACKLCEAICP 72
++C C C A+CP
Sbjct: 32 PDKCTGCGACVAVCP 46
>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A. 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
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 = 56.6 bits (137), Expect = 4e-10
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 60 RCIACKLCEAICPAQAIT--IEAEERADGSRRTTRYD--IDMTKCIYCGFCQEACPVDAI 115
+CI C C C I + R + ++ +D + CI CG C CPV AI
Sbjct: 8 KCIGCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGAI 67
Query: 116 VEGPNFEFSTESHEELLYNKEKL 138
E + + + L + +K+
Sbjct: 68 TEKDH----VDRVLKALADPKKV 86
Score = 34.6 bits (80), Expect = 0.013
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 95 IDMTKCIYCGFCQEACPVDAIV 116
DM+KCI CG C AC IV
Sbjct: 4 RDMSKCIGCGRCVRACTNVQIV 25
>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated.
Length = 280
Score = 55.7 bits (135), Expect = 6e-10
Identities = 23/57 (40%), Positives = 24/57 (42%), Gaps = 10/57 (17%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
CI C C CPA AIT+E ID KC CG C E CP AI
Sbjct: 215 CIGCGKCVKACPAGAITME----------NNLAVIDQEKCTSCGKCVEKCPTKAIRI 261
Score = 41.8 bits (99), Expect = 4e-05
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 58 EERCIACKLCEAICPAQAIT-IEAEERADGSRRTTRYDIDMTK-----CIYCGFCQEACP 111
E++C C C CP I I R + + + K CI CG C +ACP
Sbjct: 167 EDKCTGCGACVKACPRNVIELIPKSARVFVACNSKDKGKAVKKVCEVGCIGCGKCVKACP 226
Query: 112 VDAIV 116
AI
Sbjct: 227 AGAIT 231
Score = 33.4 bits (77), Expect = 0.033
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
C+ C A CP AI IE +G +D KC CG C +ACP + I
Sbjct: 141 CLGLGSCVAACPFDAIHIE-----NGLPV-----VDEDKCTGCGACVKACPRNVIE 186
Score = 26.0 bits (58), Expect = 8.8
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 59 ERCIACKLCEAICPAQAI 76
E+C +C C CP +AI
Sbjct: 242 EKCTSCGKCVEKCPTKAI 259
>gnl|CDD|224068 COG1145, NapF, Ferredoxin [Energy production and conversion].
Length = 99
Score = 51.1 bits (121), Expect = 3e-09
Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E+CI C LC +CP AI + E ID C+ CG C + CPVDA+
Sbjct: 28 AEKCIGCGLCVKVCPTGAIELIEEGLLLP-----EVVIDPDLCVLCGACLKVCPVDAL 80
Score = 31.8 bits (71), Expect = 0.041
Identities = 15/37 (40%), Positives = 18/37 (48%)
Query: 79 EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
EA S + + ID KCI CG C + CP AI
Sbjct: 10 EASASLRPSLKGKKLVIDAEKCIGCGLCVKVCPTGAI 46
Score = 31.8 bits (71), Expect = 0.053
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRT 90
+ C+ C C +CP A++I E G +
Sbjct: 62 PDLCVLCGACLKVCPVDALSIAEELVNAGEAKL 94
>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 [Unknown
function, General].
Length = 234
Score = 51.8 bits (124), Expect = 1e-08
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 54 YPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
Y +RC C +C CP AI + I + KC+ CG C+EACP +
Sbjct: 143 YMIDRKRCKGCGICVDACPRSAI----------DMVDGKAFIRLLKCVGCGKCKEACPYN 192
Query: 114 AIVEGPNFE 122
AI G +E
Sbjct: 193 AIHGGLEYE 201
Score = 34.1 bits (78), Expect = 0.016
Identities = 15/36 (41%), Positives = 17/36 (47%)
Query: 88 RRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEF 123
R T Y ID +C CG C +ACP AI F
Sbjct: 138 RTITPYMIDRKRCKGCGICVDACPRSAIDMVDGKAF 173
>gnl|CDD|225358 COG2768, COG2768, Uncharacterized Fe-S center protein [General
function prediction only].
Length = 354
Score = 51.7 bits (124), Expect = 2e-08
Identities = 37/118 (31%), Positives = 47/118 (39%), Gaps = 20/118 (16%)
Query: 23 GHIFKE--PATINYPFEKGPLSPRFRGEHALRRYPSG-EERCIACKLCEAICPAQAITIE 79
GH N L+ + +H L P EE+C C LC ICP AIT+
Sbjct: 156 GHGMTGFGGTIKNVGMGCASLAGKV-DQH-LDEKPVVVEEKCYDCGLCVKICPVGAITLT 213
Query: 80 AEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELL--YNK 135
+ ID KCI CG C EACP A+ N+E + E + Y K
Sbjct: 214 -----KVVK------IDYEKCIGCGQCMEACPYGAV--DQNWEEDSPEFLERMAEYAK 258
>gnl|CDD|222168 pfam13484, Fer4_16, 4Fe-4S double cluster binding domain.
Length = 67
Score = 46.8 bits (111), Expect = 7e-08
Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 13/65 (20%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSR-------RTTRYDIDMTKCI------YCGFC 106
C C C CP AI+ E E D R + ID KC+ CG C
Sbjct: 1 FCGTCGKCADACPTGAISGEDEPTWDARRCISYNTIGKKGWIIDELKCLLGGRIYGCGIC 60
Query: 107 QEACP 111
QE CP
Sbjct: 61 QEVCP 65
Score = 32.9 bits (75), Expect = 0.009
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 99 KCIYCGFCQEACPVDAIVEGPNFEF 123
C CG C +ACP AI +
Sbjct: 1 FCGTCGKCADACPTGAISGEDEPTW 25
>gnl|CDD|235764 PRK06273, PRK06273, ferredoxin; Provisional.
Length = 165
Score = 48.6 bits (116), Expect = 1e-07
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 58 EERCIACKLCEAICPAQAIT---IEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
EE CI C C +CP +AI +E + +G +T ID KC+YC +C + CPV
Sbjct: 48 EELCIGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPV 105
Score = 26.6 bits (59), Expect = 4.6
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 100 CIYCGFCQEACPVDAI 115
CI CG C CP AI
Sbjct: 51 CIGCGGCANVCPTKAI 66
>gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit
gamma/delta; Provisional.
Length = 312
Score = 49.2 bits (117), Expect = 1e-07
Identities = 26/60 (43%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSR----RTTRYDIDMTKCIYCGFCQEACPVDAI 115
+CI C+ C CP AI IEA A+G R R D D C CG C E CP AI
Sbjct: 248 KCIMCRKCWLYCPDDAI-IEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAI 306
Score = 33.0 bits (75), Expect = 0.047
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 84 ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
G R + ID +KCI C C CP DAI+E
Sbjct: 233 LTGGWRIDKPVIDHSKCIMCRKCWLYCPDDAIIE 266
>gnl|CDD|233895 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 = 48.9 bits (117), Expect = 2e-07
Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E RC+ C C +CPA + E ADG R I KC +CG C EACP A+
Sbjct: 47 ENRCLGCGKCVEVCPAGTARLS--ELADGR---NRIIIRREKCTHCGKCTEACPSGAL 99
Score = 30.8 bits (70), Expect = 0.29
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 59 ERCIACKLCEAICPAQAITIEAEE 82
E+C C C CP+ A++I EE
Sbjct: 82 EKCTHCGKCTEACPSGALSIVGEE 105
Score = 27.7 bits (62), Expect = 2.4
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 99 KCIYCGFCQEACPVDAIVEGPNFEFSTESH 128
+C+ CG C E CP +
Sbjct: 49 RCLGCGKCVEVCPAGTARLSELADGRNRII 78
>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3. See
PMID:20395274 for descriptions of different groups.
Length = 462
Score = 49.1 bits (118), Expect = 2e-07
Identities = 21/51 (41%), Positives = 24/51 (47%), Gaps = 9/51 (17%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
CE CP AI+ + RA ID KCI CG C ACP AI +
Sbjct: 166 CEKACPVGAISSDENGRAV---------IDYDKCISCGACMVACPFGAISD 207
Score = 48.4 bits (116), Expect = 3e-07
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 11/57 (19%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
C+A C +CP AI++ + R ID KCI CG C++ACP +AIVE
Sbjct: 116 CLA-HPCIEVCPKGAISM-------VNGRAY---IDQEKCIECGKCKKACPYNAIVE 161
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 49.2 bits (118), Expect = 2e-07
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
C+ C +C CP AI IE +R + +D KCI+CG C E CPV
Sbjct: 582 ECVGCGVCVGACPTGAIRIEEGKR--------KISVDEEKCIHCGKCTEVCPV 626
Score = 28.8 bits (65), Expect = 1.3
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 99 KCIYCGFCQEACPVDAI 115
+C+ CG C ACP AI
Sbjct: 582 ECVGCGVCVGACPTGAI 598
Score = 28.8 bits (65), Expect = 1.4
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 58 EERCIACKLCEAICPA 73
EE+CI C C +CP
Sbjct: 611 EEKCIHCGKCTEVCPV 626
>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 51
Score = 45.1 bits (106), Expect = 2e-07
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
++CI C C A CPA +ID +CI CG C E CP
Sbjct: 4 PDKCIGCGRCVAACPA------RVGAGAIRDEGGAVEIDPDRCIGCGACVEVCP 51
Score = 28.9 bits (64), Expect = 0.19
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 95 IDMTKCIYCGFCQEACPVDAIV 116
ID KCI CG C ACP
Sbjct: 2 IDPDKCIGCGRCVAACPARVGA 23
Score = 25.4 bits (55), Expect = 4.1
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 53 RYPSGEERCIACKLCEAICP 72
+RCI C C +CP
Sbjct: 32 AVEIDPDRCIGCGACVEVCP 51
>gnl|CDD|221966 pfam13187, Fer4_9, 4Fe-4S dicluster domain.
Length = 44
Score = 44.9 bits (106), Expect = 2e-07
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 12/56 (21%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
+CI C C +CPA I + + + KCI CG C E CPV AI
Sbjct: 1 KCIGCGACVKVCPAGVIMRDNGGKV------------VVKCIGCGACVEVCPVGAI 44
Score = 29.9 bits (67), Expect = 0.088
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 99 KCIYCGFCQEACPVDAIVEGPN 120
KCI CG C + CP I+
Sbjct: 1 KCIGCGACVKVCPAGVIMRDNG 22
Score = 25.3 bits (55), Expect = 3.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 59 ERCIACKLCEAICPAQAI 76
+CI C C +CP AI
Sbjct: 27 VKCIGCGACVEVCPVGAI 44
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 48.1 bits (115), Expect = 3e-07
Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 9/72 (12%)
Query: 48 EHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQ 107
E+CI C C +C AI + + ++ C CG C
Sbjct: 58 VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPGGK---------PVLNPDLCEGCGACS 108
Query: 108 EACPVDAIVEGP 119
CP AI E P
Sbjct: 109 IVCPEPAIEEEP 120
Score = 37.3 bits (87), Expect = 0.002
Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 79 EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
E E + R +ID KCI CG C E C AIV P
Sbjct: 51 EVLEEEE-VIRGEIPEIDPEKCIRCGKCAEVCRFGAIVVLPG 91
>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin),
alpha and beta subunits [Energy production and
conversion].
Length = 317
Score = 48.1 bits (115), Expect = 3e-07
Identities = 23/63 (36%), Positives = 28/63 (44%), Gaps = 11/63 (17%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
EE C C C +CP AIT + ++ ID +KCI CG C ACP A
Sbjct: 171 EELCRGCGKCVKVCPTGAITWDGKK----------LKIDGSKCIGCGKCIRACP-KAAFR 219
Query: 118 GPN 120
G
Sbjct: 220 GEK 222
Score = 30.4 bits (69), Expect = 0.31
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 90 TTRYDIDMTKCIYCGFCQEACPVDAI 115
+ +D C CG C + CP AI
Sbjct: 164 VWKPKVDEELCRGCGKCVKVCPTGAI 189
>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 = 45.0 bits (107), Expect = 4e-07
Identities = 23/58 (39%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
+E+CI CK C CP AI +E G ID C CG C CPV AI
Sbjct: 24 KEKCIKCKNCWLYCPEGAI----QEDEGGFVG-----IDYDYCKGCGICANVCPVKAI 72
Score = 31.5 bits (72), Expect = 0.037
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 86 GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPN 120
G R + +D KCI C C CP AI E
Sbjct: 13 GDWRVFKPVVDKEKCIKCKNCWLYCPEGAIQEDEG 47
Score = 25.4 bits (56), Expect = 6.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 61 CIACKLCEAICPAQAITIEAEE 82
C C +C +CP +AI + EE
Sbjct: 57 CKGCGICANVCPVKAIEMVREE 78
>gnl|CDD|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion].
Length = 68
Score = 44.4 bits (105), Expect = 6e-07
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
++CI C +C +CPA + +CI CG C+ ACPV AI
Sbjct: 7 YDKCIGCGICVEVCPAGVFDL------GEDEGGKPVVARPEECIDCGLCELACPVGAI 58
Score = 32.8 bits (75), Expect = 0.010
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 58 EERCIACKLCEAICPAQAITIEAE 81
E CI C LCE CP AI ++
Sbjct: 40 PEECIDCGLCELACPVGAIKVDIL 63
Score = 27.8 bits (62), Expect = 0.62
Identities = 12/25 (48%), Positives = 12/25 (48%)
Query: 95 IDMTKCIYCGFCQEACPVDAIVEGP 119
ID KCI CG C E CP G
Sbjct: 5 IDYDKCIGCGICVEVCPAGVFDLGE 29
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 46.8 bits (112), Expect = 1e-06
Identities = 21/59 (35%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
C C C CP AI R RY D KC C C + CP AI GP
Sbjct: 512 CFECDNCYGACPQDAIIKLGPGR--------RYHFDYDKCTGCHICADVCPCGAIEMGP 562
Score = 29.5 bits (67), Expect = 0.80
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 52 RRYPSGEERCIACKLCEAICPAQAITIEAEE 82
RRY ++C C +C +CP AI + E
Sbjct: 534 RRYHFDYDKCTGCHICADVCPCGAIEMGPGE 564
>gnl|CDD|224067 COG1144, COG1144, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, delta subunit
[Energy production and conversion].
Length = 91
Score = 43.9 bits (104), Expect = 2e-06
Identities = 24/59 (40%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
E++CI CKLC CP AI E G + YD C CG C CPV AI
Sbjct: 34 EDKCINCKLCWLYCPEPAI----LEEEGGYKVRIDYD----YCKGCGICANVCPVKAIE 84
Score = 28.5 bits (64), Expect = 0.56
Identities = 15/39 (38%), Positives = 17/39 (43%)
Query: 86 GSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS 124
GS R R +D KCI C C CP AI+E
Sbjct: 23 GSWRVFRPVVDEDKCINCKLCWLYCPEPAILEEEGGYKV 61
Score = 27.0 bits (60), Expect = 2.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 59 ERCIACKLCEAICPAQAITIEAEE 82
+ C C +C +CP +AI + EE
Sbjct: 66 DYCKGCGICANVCPVKAIEMVREE 89
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 44.7 bits (106), Expect = 6e-06
Identities = 24/95 (25%), Positives = 37/95 (38%), Gaps = 25/95 (26%)
Query: 33 NYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICP----AQAITIEAEERADGSR 88
N P+ K +P + + +CI C C C +A+TI D
Sbjct: 132 NPPYPKDESNPFYIYDPN---------QCILCGRCVEACQEVQVNEALTI------DWRG 176
Query: 89 RTTR------YDIDMTKCIYCGFCQEACPVDAIVE 117
R I+ + C+ CG C CPV+A++E
Sbjct: 177 EDPRVIWDNDVPINESSCVSCGACVTVCPVNALME 211
>gnl|CDD|215671 pfam00037, Fer4, 4Fe-4S binding domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich.
Length = 24
Score = 39.5 bits (93), Expect = 1e-05
Identities = 14/23 (60%), Positives = 14/23 (60%)
Query: 93 YDIDMTKCIYCGFCQEACPVDAI 115
ID KCI CG C E CPV AI
Sbjct: 1 VVIDEEKCIGCGACVEVCPVGAI 23
Score = 33.8 bits (78), Expect = 0.002
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 58 EERCIACKLCEAICPAQAIT 77
EE+CI C C +CP AIT
Sbjct: 5 EEKCIGCGACVEVCPVGAIT 24
>gnl|CDD|223514 COG0437, HybA, Fe-S-cluster-containing hydrogenase components 1
[Energy production and conversion].
Length = 203
Score = 42.4 bits (100), Expect = 2e-05
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 21/71 (29%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQE 108
++ CI C C A CP A ++ + KC +C C E
Sbjct: 99 KDLCIGCGYCIAACPYGAPQFNPDKGV------------VDKCTFCVDRVAVGKLPACVE 146
Query: 109 ACPVDAIVEGP 119
ACP A++ G
Sbjct: 147 ACPTGALIFGD 157
Score = 37.8 bits (88), Expect = 8e-04
Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 13/59 (22%)
Query: 62 IACKLCE-----AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
I+C CE +CP A+ E DG +D CI CG+C ACP A
Sbjct: 67 ISCMHCEDPPCVKVCPTGALFKREE---DGI-----VLVDKDLCIGCGYCIAACPYGAP 117
Score = 28.6 bits (64), Expect = 1.3
Identities = 15/71 (21%), Positives = 22/71 (30%), Gaps = 14/71 (19%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTK-----------CIYC--G 104
RCI CK C C + + R + D C++C
Sbjct: 17 SSRCIGCKACVVAC-KEENDRLPVGNSVFRRYVNYVEGDWGSGTVEYYYLSISCMHCEDP 75
Query: 105 FCQEACPVDAI 115
C + CP A+
Sbjct: 76 PCVKVCPTGAL 86
>gnl|CDD|224065 COG1142, HycB, Fe-S-cluster-containing hydrogenase components 2
[Energy production and conversion].
Length = 165
Score = 41.3 bits (97), Expect = 3e-05
Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 14/65 (21%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGF------CQEACP 111
EE+CI CKLC CP AIT+ ++ KC C C EACP
Sbjct: 81 EEKCIGCKLCVVACPFGAITM--VSYPVAAKAV------AVKCDLCAGREVGPACVEACP 132
Query: 112 VDAIV 116
+A+
Sbjct: 133 TEALE 137
Score = 39.8 bits (93), Expect = 1e-04
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 10/49 (20%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
C +CP AIT R DG+ + +D KCI C C ACP AI
Sbjct: 61 CAEVCPVGAIT-----RDDGAVQ-----VDEEKCIGCKLCVVACPFGAI 99
Score = 37.1 bits (86), Expect = 0.001
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 4/74 (5%)
Query: 52 RRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMT--KCIYC--GFCQ 107
R + E+CI C+ CE C I+++ + D + C +C C
Sbjct: 3 RFIIADPEKCIGCRTCEVACVVAHEEIQSQSIFLPRIMVIKNDGESAPVVCHHCEDAPCA 62
Query: 108 EACPVDAIVEGPNF 121
E CPV AI
Sbjct: 63 EVCPVGAITRDDGA 76
>gnl|CDD|182135 PRK09898, PRK09898, hypothetical protein; Provisional.
Length = 208
Score = 41.7 bits (98), Expect = 4e-05
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 12/58 (20%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
+RCI C C CP T+ E + +KC+ CG C ACP A+
Sbjct: 153 HKRCIGCSACTTACPWMMATVNTESKKS------------SKCVLCGECANACPTGAL 198
Score = 38.3 bits (89), Expect = 6e-04
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 59 ERCIACK--LCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
+ C CK C +CP AIT + +E +D +CI C C ACP
Sbjct: 121 DTCRQCKEPQCMNVCPIGAITWQQKEGC--------ITVDHKRCIGCSACTTACP 167
>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 [Energy metabolism,
Other].
Length = 411
Score = 41.8 bits (98), Expect = 6e-05
Identities = 19/57 (33%), Positives = 21/57 (36%), Gaps = 10/57 (17%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E CI C CE CP AIT + Y + C C C CP AI
Sbjct: 10 EICIRCNTCEETCPIDAITHD----------DRNYVVKADVCNGCMACVSPCPTGAI 56
Score = 33.3 bits (76), Expect = 0.042
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 95 IDMTKCIYCGFCQEACPVDAI 115
ID CI C C+E CP+DAI
Sbjct: 7 IDPEICIRCNTCEETCPIDAI 27
>gnl|CDD|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit
delta; Reviewed.
Length = 105
Score = 39.5 bits (92), Expect = 7e-05
Identities = 21/58 (36%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E +C+ C +C CP AI I + DG ID C CG C CP AI
Sbjct: 50 ESKCVKCYICWKFCPEPAIYI----KEDGY-----VAIDYDYCKGCGICANECPTKAI 98
Score = 28.8 bits (64), Expect = 0.62
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 61 CIACKLCEAICPAQAITIEAEER 83
C C +C CP +AIT+ EE+
Sbjct: 83 CKGCGICANECPTKAITMVKEEK 105
Score = 25.7 bits (56), Expect = 7.5
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 86 GSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
G RT +D +KC+ C C + CP AI
Sbjct: 39 GDWRTFMPVVDESKCVKCYICWKFCPEPAI 68
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 41.3 bits (97), Expect = 9e-05
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG------FCQEACP 111
+++CI CK C CP + I A G + T + KC C C E CP
Sbjct: 84 QQKCIGCKSCVVACPFGTMQIVLTPVAAGKVKATAH-----KCDLCAGRENGPACVENCP 138
Query: 112 VDAI 115
DA+
Sbjct: 139 ADAL 142
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 41.1 bits (97), Expect = 1e-04
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 58 EERCIACKLCEAIC---PAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
+++CI C C C QAI + DG+R ++ +C+ C C CPV+
Sbjct: 341 QDKCIGCGRCYIACEDTSHQAIEWDE----DGTRT---PEVIEEECVGCNLCAHVCPVEG 393
Query: 115 IVE 117
+
Sbjct: 394 CIT 396
Score = 31.5 bits (72), Expect = 0.16
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 52 RRYPSGEERCIACKLCEAICP-AQAITIEAEERADGSRRTTRY 93
R EE C+ C LC +CP IT+ + T +
Sbjct: 370 RTPEVIEEECVGCNLCAHVCPVEGCITMGEVKFGKPYANWTTH 412
Score = 26.1 bits (58), Expect = 9.2
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 95 IDMTKCIYCGFCQEAC 110
ID KCI CG C AC
Sbjct: 339 IDQDKCIGCGRCYIAC 354
>gnl|CDD|234170 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 = 40.9 bits (96), Expect = 1e-04
Identities = 25/76 (32%), Positives = 30/76 (39%), Gaps = 17/76 (22%)
Query: 44 RFRGEHALRRYP--SGEERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTK 99
R P +++CI CK C E CPA I E +E ID
Sbjct: 533 LSNKRAGKRAGPYKVDQDKCIGCKKCIKELGCPA--IEPEDKEAV----------IDPL- 579
Query: 100 CIYCGFCQEACPVDAI 115
C CG C + CP DAI
Sbjct: 580 CTGCGVCAQICPFDAI 595
>gnl|CDD|188518 TIGR04003, rSAM_BssD, [benzylsuccinate synthase]-activating enzyme.
Members of this radical SAM protein family are
[benzylsuccinate synthase]-activating enzyme, a glycyl
radical active site-creating enzyme related to [pyruvate
formate-lyase]-activating enzyme and additional
uncharacterized homologs activating additional glycyl
radical-containing enzymes [Protein fate, Protein
modification and repair].
Length = 314
Score = 40.6 bits (95), Expect = 1e-04
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
RC+ C C A+CPA + D S T +D TKC C C AC +A
Sbjct: 49 PNRCVGCGRCVAVCPAGTSRL-----VDNSDGRTIVVVDRTKCQRCMRCVAACLTEA 100
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 40.4 bits (95), Expect = 2e-04
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 58 EERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
EE+C C C + CP+ I + + + ID + C CG C E CP AI
Sbjct: 576 EEKCTGCGDCIVLSGCPS--IEPDPTFK--------KARIDPSSCNGCGSCVEVCPSFAI 625
Query: 116 VEG 118
EG
Sbjct: 626 KEG 628
Score = 28.1 bits (63), Expect = 2.3
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 61 CIACKLCEAICPAQAITIEAEERA 84
C C C +CP+ AI E
Sbjct: 610 CNGCGSCVEVCPSFAIKEGGENPK 633
>gnl|CDD|233648 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 [Energy
metabolism, Electron transport].
Length = 165
Score = 39.0 bits (91), Expect = 2e-04
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
E+ CI C C CP AI G+ + I +C C C E CP D I
Sbjct: 112 EDNCIGCTKCIQACPVDAIV--------GAAKAMHTVI-ADECTGCDLCVEPCPTDCIE 161
Score = 37.9 bits (88), Expect = 6e-04
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 95 IDMTKCIYCGFCQEACPVDAIVEGPNF 121
ID CI C C +ACPVDAIV
Sbjct: 110 IDEDNCIGCTKCIQACPVDAIVGAAKA 136
Score = 25.9 bits (57), Expect = 9.7
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 61 CIACKLCEAICPAQAITI 78
C C LC CP I +
Sbjct: 145 CTGCDLCVEPCPTDCIEM 162
>gnl|CDD|221963 pfam13183, Fer4_8, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 54
Score = 37.2 bits (86), Expect = 2e-04
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
+CI C C A+CP A R G R ++ C CG C E CPV
Sbjct: 3 SKCIRCGACRAVCPV----YRALGRFSGDPRGGALAAELWSCTSCGACTEVCPVG 53
Score = 30.7 bits (69), Expect = 0.044
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 96 DMTKCIYCGFCQEACPV 112
+++KCI CG C+ CPV
Sbjct: 1 ELSKCIRCGACRAVCPV 17
Score = 25.3 bits (55), Expect = 4.1
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 44 RFRGEHALRRYPSGEERCIACKLCEAICPA 73
RF G+ + C +C C +CP
Sbjct: 23 RFSGDPRGGALAAELWSCTSCGACTEVCPV 52
>gnl|CDD|224070 COG1148, HdrA, Heterodisulfide reductase, subunit A and related
polyferredoxins [Energy production and conversion].
Length = 622
Score = 39.8 bits (93), Expect = 3e-04
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E++C C +C CP AI+++ + +++ +C CG C ACP AI
Sbjct: 560 EDKCTGCGICAE-CPFGAISVD------------KAEVNPLRCKGCGICSAACPSGAI 604
Score = 39.0 bits (91), Expect = 4e-04
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 18/71 (25%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTR-------------YDIDMTKCIYCGF 105
++C C C +CP +E + + Y+ID CI CG
Sbjct: 224 DKCTGCGACSEVCP-----VEVPNEFNEGLGKRKAIYIPFPQAVPLNYNIDPKHCIECGL 278
Query: 106 CQEACPVDAIV 116
C++ACP +A+
Sbjct: 279 CEKACPNEAVD 289
Score = 27.8 bits (62), Expect = 3.1
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 88 RRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
+ RY D KC CG C E CPV+ E
Sbjct: 216 EKKPRYVDD--KCTGCGACSEVCPVEVPNE 243
Score = 27.0 bits (60), Expect = 5.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 61 CIACKLCEAICPAQAITIEAEER 83
CI C LCE CP +A+ + E
Sbjct: 273 CIECGLCEKACPNEAVDLNQEPE 295
>gnl|CDD|224516 COG1600, COG1600, Uncharacterized Fe-S protein [Energy production
and conversion].
Length = 337
Score = 39.3 bits (92), Expect = 4e-04
Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 14/69 (20%)
Query: 55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID-----------MTKCIY- 102
P E+ C +C C CP A+ A D R + I+ + IY
Sbjct: 181 PEEEDHCGSCTRCLDACPTGALV--APYTVDARRCISYLTIEKGGAPEEFRPLIGNRIYG 238
Query: 103 CGFCQEACP 111
C CQ+ CP
Sbjct: 239 CDICQKVCP 247
>gnl|CDD|211993 TIGR04270, Rama_corrin_act, methylamine methyltransferase corrinoid
protein reductive activase. Members of this family
occur as paralogs in species capable of generating
methane from mono-, di-, and tri-methylamine. Members
include RamA (Reductive Activation of Methyltransfer,
Amines) from Methanosarcina barkeri MS (DSM 800). Member
proteins have two C-terminal motifs with four Cys each,
likely to bind one 4Fe-4S cluster per motif.
Length = 535
Score = 39.0 bits (91), Expect = 5e-04
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
E CIAC+ C CP +A++I E R D D C C+ CP
Sbjct: 479 EGCIACQKCVKECPGKALSILESEPP-------RIDTDRCLGTACRRCERVCPEKVF 528
>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 = 38.3 bits (89), Expect = 7e-04
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 10/51 (19%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
C+ C C A CP +AI +E DG R +++ +CI CG C CP
Sbjct: 176 CMGCGTCAAACPTRAIEME-----DG-----RPNVNRDRCIKCGACYVQCP 216
>gnl|CDD|223425 COG0348, NapH, Polyferredoxin [Energy production and conversion].
Length = 386
Score = 38.2 bits (89), Expect = 8e-04
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 17/65 (26%)
Query: 58 EERCIA-CKLCEAICPAQA-----ITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
++R CK C+ +CP + + DG +CI CG C +AC
Sbjct: 210 DKRGCPRCKRCKKVCPEPIPLWVQVCPAGIDIRDGL-----------ECIGCGRCIDACD 258
Query: 112 VDAIV 116
D +
Sbjct: 259 DDMLK 263
>gnl|CDD|233754 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 = 37.7 bits (88), Expect = 0.001
Identities = 18/70 (25%), Positives = 25/70 (35%), Gaps = 12/70 (17%)
Query: 56 SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
S E+C C C +CP + + + GS D C CG C + C D
Sbjct: 198 SDREKCTNCMDCFNVCPEPQV-LRMPLKKGGSTLVLSGD-----CTLCGRCIDVCHEDV- 250
Query: 116 VEGPNFEFST 125
F+T
Sbjct: 251 -----LGFTT 255
>gnl|CDD|235903 PRK06991, PRK06991, ferredoxin; Provisional.
Length = 270
Score = 37.9 bits (88), Expect = 0.001
Identities = 15/25 (60%), Positives = 16/25 (64%)
Query: 95 IDMTKCIYCGFCQEACPVDAIVEGP 119
ID CI C C +ACPVDAIV P
Sbjct: 82 IDEQLCIGCTLCMQACPVDAIVGAP 106
Score = 35.2 bits (81), Expect = 0.008
Identities = 20/66 (30%), Positives = 23/66 (34%), Gaps = 25/66 (37%)
Query: 58 EERCIACKLCEAICPAQAI--------TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEA 109
E+ CI C LC CP AI T+ A+ C C C
Sbjct: 84 EQLCIGCTLCMQACPVDAIVGAPKQMHTVLADL-----------------CTGCDLCVPP 126
Query: 110 CPVDAI 115
CPVD I
Sbjct: 127 CPVDCI 132
>gnl|CDD|170017 PRK09624, porD, pyuvate ferredoxin oxidoreductase subunit delta;
Reviewed.
Length = 105
Score = 36.5 bits (84), Expect = 0.001
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 11/60 (18%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI-DMTKCIYCGFCQEACPVDAIV 116
++C+ C LC CP AI ++ E Y + D C CG C CP AI
Sbjct: 50 RDKCVRCYLCYIYCPEPAIYLDEEG----------YPVFDYDYCKGCGICANECPTKAIE 99
>gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional.
Length = 244
Score = 37.5 bits (87), Expect = 0.001
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
C +CP QA +R DG +D +C+ C +C +ACP DA
Sbjct: 108 CVPVCPVQATF----QREDGI-----VVVDNKRCVGCAYCVQACPYDA 146
Score = 27.5 bits (61), Expect = 2.7
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 14/60 (23%)
Query: 59 ERCIACKLCEAICPAQAITIEAEER-ADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
+RC+ C C CP A I E + AD KC +C EA + A VE
Sbjct: 130 KRCVGCAYCVQACPYDARFINHETQTAD-------------KCTFCVHRLEAGLLPACVE 176
>gnl|CDD|227003 COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfC [Energy production and conversion].
Length = 529
Score = 37.7 bits (88), Expect = 0.001
Identities = 18/58 (31%), Positives = 25/58 (43%)
Query: 55 PSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
P E+ CI C LC CP + + A G + + ++ CI CG C CP
Sbjct: 361 PIKEQSCIRCSLCADACPVNLLPQQLYWFAKGEQHDEEEEHNLLDCIECGACAYVCPS 418
Score = 26.6 bits (59), Expect = 6.4
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 100 CIYCGFCQEACPVD 113
CI C C +ACPV+
Sbjct: 367 CIRCSLCADACPVN 380
>gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex
subunit alpha; Validated.
Length = 781
Score = 37.6 bits (88), Expect = 0.002
Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 46 RGEHALRRYPSGEE------RCIACKLCEAICPAQAITIEAEERA---DGSRRTTRYDID 96
R ++ P+ EE +C C C +CP + EA E A D S+ YD
Sbjct: 385 RKAKGIKALPTDEELKELAKKCTECGWCVRVCPNELPIPEAMEAAAKGDLSKLEDLYD-- 442
Query: 97 MTKCIYCGFCQEACP 111
KCI CG C++ CP
Sbjct: 443 --KCIGCGRCEQVCP 455
>gnl|CDD|188556 TIGR04041, activase_YjjW, glycine radical enzyme activase, YjjW
family. Members of this family are radical SAM enzymes,
designated YjjW in E. coli, that are paired with and
appear to activate a glycyl radical enzyme of unknown
function, designated YjjI. This activase and its target
are found in Clostridial species as well as E. coli and
cousins. Members of this family may be misannotated as
pyruvate formate lyase activating enzyme [Protein fate,
Protein modification and repair].
Length = 276
Score = 37.2 bits (87), Expect = 0.002
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
C C C A CPA A+++ DG +D + +CI C C + CP
Sbjct: 42 HCDHCGDCVAGCPAGALSLV-----DGK---VVWDKE--RCIGCDTCIKVCP 83
>gnl|CDD|235347 PRK05113, PRK05113, electron transport complex protein RnfB;
Provisional.
Length = 191
Score = 36.8 bits (86), Expect = 0.002
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 95 IDMTKCIYCGFCQEACPVDAIV 116
ID CI C C +ACPVDAIV
Sbjct: 111 IDEDNCIGCTKCIQACPVDAIV 132
Score = 32.6 bits (75), Expect = 0.044
Identities = 17/66 (25%), Positives = 21/66 (31%), Gaps = 25/66 (37%)
Query: 58 EERCIACKLCEAICPAQAI--------TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEA 109
E+ CI C C CP AI T+ ++ C C C
Sbjct: 113 EDNCIGCTKCIQACPVDAIVGATKAMHTVISDL-----------------CTGCDLCVAP 155
Query: 110 CPVDAI 115
CP D I
Sbjct: 156 CPTDCI 161
>gnl|CDD|205098 pfam12837, Fer4_6, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 24
Score = 33.7 bits (78), Expect = 0.002
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 95 IDMTKCIYCGFCQEACPVDAI 115
ID KCI CG C CP AI
Sbjct: 4 IDPDKCIGCGRCVAVCPEGAI 24
Score = 31.8 bits (73), Expect = 0.012
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 58 EERCIACKLCEAICPAQAI 76
++CI C C A+CP AI
Sbjct: 6 PDKCIGCGRCVAVCPEGAI 24
>gnl|CDD|222145 pfam13459, Fer4_15, 4Fe-4S single cluster domain.
Length = 60
Score = 34.6 bits (80), Expect = 0.002
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEA---CPVDA 114
+ CI C LC A+ P ++ + +A D+ + QEA CPVDA
Sbjct: 4 RDTCIGCGLCVALAPD-VFELDEDGKARVILDEGEVPDDLEEDA-----QEAADACPVDA 57
Query: 115 IV 116
I
Sbjct: 58 IH 59
Score = 25.0 bits (55), Expect = 5.3
Identities = 7/17 (41%), Positives = 8/17 (47%)
Query: 95 IDMTKCIYCGFCQEACP 111
+D CI CG C P
Sbjct: 2 VDRDTCIGCGLCVALAP 18
>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 [Central
intermediary metabolism, Sulfur metabolism].
Length = 132
Score = 36.1 bits (83), Expect = 0.002
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 12/75 (16%)
Query: 59 ERCIACKL-----CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
+C CK C ICP + ++ E Y+I+ C C C +ACP
Sbjct: 8 TKCDGCKAGEKTACVYICPNDLMHLDTEIM-------KAYNIEPDMCWECYSCVKACPQG 60
Query: 114 AIVEGPNFEFSTESH 128
AI +F+
Sbjct: 61 AIDVRGYADFAPLGG 75
>gnl|CDD|222205 pfam13534, Fer4_17, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 61
Score = 34.4 bits (79), Expect = 0.002
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 5/57 (8%)
Query: 60 RCIACKLCEAICPAQAITIE-----AEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
RCI C C +CP+ + + +G + C CG C+ CP
Sbjct: 1 RCIQCGYCVPVCPSYLLNGDEPKKLMRAAYNGDLEELLANEAADSCSECGLCEYVCP 57
Score = 26.3 bits (58), Expect = 2.1
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 99 KCIYCGFCQEACPV 112
+CI CG+C CP
Sbjct: 1 RCIQCGYCVPVCPS 14
Score = 25.9 bits (57), Expect = 2.5
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 59 ERCIACKLCEAICPA 73
+ C C LCE +CP
Sbjct: 44 DSCSECGLCEYVCPM 58
>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase. The D
subunit of archaeal RNA polymerase (RNAP) is involved in
the assembly of RNAP subunits. RNAP is a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. A single distinct RNAP complex is found in
archaea, which may be responsible for the synthesis of
all RNAs. The archaeal RNAP harbors homologues of all
eukaryotic RNAP II subunits with two exceptions (RPB8
and RPB9). The 12 archaeal subunits are designated by
letters and can be divided into three functional groups
that are engaged in: (I) catalysis (A'/A", B'/B" or B);
(II) assembly (L, N, D and P); and (III) auxiliary
functions (F, E, H and K). The D subunit is equivalent
to the RPB3 subunit of eukaryotic RNAP II. It contains
two subdomains: one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The assembly of the two largest archaeal RNAP
subunits that provide most of the enzyme's catalytic
functions depends on the presence of the archaeal D/L
heterodimer.
Length = 259
Score = 36.5 bits (85), Expect = 0.003
Identities = 26/94 (27%), Positives = 32/94 (34%), Gaps = 23/94 (24%)
Query: 48 EHA---------LRRYPSGE--ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDID 96
EHA + YP E E C C C CP + +E + D
Sbjct: 147 EHAKWQPTTACGYKYYPVIEIDEDCDGCGKCVEECPRGVLELEEGKVVVE---------D 197
Query: 97 MTKCIYCGFCQEACPVDAIVEGP---NFEFSTES 127
+ C C C+ AC AI G F F ES
Sbjct: 198 LEDCSLCKLCERACDAGAIRVGWDEDRFIFEVES 231
Score = 27.2 bits (61), Expect = 4.2
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 57 GEERCIACKLCEAICPAQAITIEAEERA-------DGS 87
E C CKLCE C A AI + +E DGS
Sbjct: 197 DLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGS 234
>gnl|CDD|234157 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 [Energy metabolism,
Methanogenesis].
Length = 391
Score = 36.3 bits (84), Expect = 0.003
Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 15/58 (25%)
Query: 59 ERCIACKLC--EAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
ERC C C E CP AI + DG ++ C CG+C E CP A
Sbjct: 302 ERCENCDPCLVEEACPVPAI------KKDG-------TLNTEDCFGCGYCAEICPGGA 346
Score = 28.6 bits (64), Expect = 1.6
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 90 TTRYDIDMTKCIYCGFC--QEACPVDAIVEG 118
R + +C C C +EACPV AI +
Sbjct: 294 DVRPKYNPERCENCDPCLVEEACPVPAIKKD 324
>gnl|CDD|225433 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfB [Energy production and conversion].
Length = 198
Score = 35.9 bits (83), Expect = 0.003
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 95 IDMTKCIYCGFCQEACPVDAIVEGPNF 121
ID CI C C +ACPVDAIV
Sbjct: 112 IDEANCIGCTKCIQACPVDAIVGATKA 138
Score = 33.6 bits (77), Expect = 0.020
Identities = 18/66 (27%), Positives = 20/66 (30%), Gaps = 25/66 (37%)
Query: 58 EERCIACKLCEAICPAQAI--------TIEAEERADGSRRTTRYDIDMTKCIYCGFCQEA 109
E CI C C CP AI T+ A+ C C C
Sbjct: 114 EANCIGCTKCIQACPVDAIVGATKAMHTVIADL-----------------CTGCDLCVAP 156
Query: 110 CPVDAI 115
CP D I
Sbjct: 157 CPTDCI 162
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 36.0 bits (84), Expect = 0.004
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 12/73 (16%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
E C C+ C CP + ++ + D+ C C C+ ACP AI
Sbjct: 168 SEDCDECEKCVEACPRGVLELKEGKLVVT---------DLLNCSLCKLCERACPGKAIRV 218
Query: 118 G--PN-FEFSTES 127
N F F+ ES
Sbjct: 219 SDDENKFIFTVES 231
Score = 32.2 bits (74), Expect = 0.090
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERA-------DGS 87
C CKLCE CP +AI + +E DGS
Sbjct: 198 LLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGS 234
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 36.1 bits (84), Expect = 0.005
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 15/61 (24%)
Query: 60 RCIACKLCEAICP-----AQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
+C C CP + I I+ + T + I CI CG C + CP DA
Sbjct: 17 KC--GYECIKYCPVVRTGKETIEIDED--------TGKPVISEELCIGCGICVKKCPFDA 66
Query: 115 I 115
I
Sbjct: 67 I 67
Score = 29.2 bits (66), Expect = 0.87
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 58 EERCIACKLCEAICPAQAITI 78
EE CI C +C CP AI+I
Sbjct: 49 EELCIGCGICVKKCPFDAISI 69
>gnl|CDD|235756 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase
iron-sulfur subunit; Provisional.
Length = 486
Score = 35.8 bits (83), Expect = 0.007
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 13/64 (20%)
Query: 61 CIACKLCEAICPAQAIT-------------IEAEERADGSRRTTRYDIDMTKCIYCGFCQ 107
CI C C + CPA+ ++ + R +G R +D + C CG C
Sbjct: 135 CIECLSCVSTCPARKVSDYPGPTFMRQLARFAFDPRDEGDREKEAFDEGLYNCTTCGKCV 194
Query: 108 EACP 111
E CP
Sbjct: 195 EVCP 198
>gnl|CDD|233890 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 = 35.5 bits (82), Expect = 0.007
Identities = 17/71 (23%), Positives = 20/71 (28%), Gaps = 20/71 (28%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYD----------IDMTKC---------- 100
C C C CP+ AI+ E D D +C
Sbjct: 207 CETCGKCADECPSGAISKGGEPTWDPEDSNGDPPGENNPGLKWQYDGWRCLLFRCYNEGG 266
Query: 101 IYCGFCQEACP 111
CG CQ CP
Sbjct: 267 GGCGVCQAVCP 277
Score = 29.7 bits (67), Expect = 0.51
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 94 DIDMTK-CIYCGFCQEACPVDAIVEGPN 120
D M K C CG C + CP AI +G
Sbjct: 200 DAGMAKFCETCGKCADECPSGAISKGGE 227
>gnl|CDD|181779 PRK09326, PRK09326, F420H2 dehydrogenase subunit F; Provisional.
Length = 341
Score = 35.2 bits (81), Expect = 0.008
Identities = 22/60 (36%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 61 CIACKLCEAICPAQAITIE--AEERADGSRRTTRYDIDMTKCIYCGFCQEACPV-DAIVE 117
C AC CEA+CP AIT++ AE R C C C CPV D +E
Sbjct: 14 CTACGACEAVCPIGAITVDKKAEIRDPNDLELYEKGAAPNVCEGCLTCSRICPVVDGYIE 73
Score = 27.9 bits (62), Expect = 2.4
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 95 IDMTKCIYCGFCQEACPVDAIV 116
I+ C CG C+ CP+ AI
Sbjct: 9 IEYDVCTACGACEAVCPIGAIT 30
>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
kD subunit (chain G) [Energy production and conversion].
Length = 693
Score = 35.4 bits (82), Expect = 0.008
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 59 ERCIACKLCEAICP--AQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIV 116
RCI C C C A + +R + Y + CG C + CPV A+
Sbjct: 144 NRCILCTRCVRFCKEIAGTHELGVIKR-GENSEIGTYLDQPLESELCGNCVDVCPVGALT 202
Query: 117 EGPNFEF 123
P F F
Sbjct: 203 SKP-FAF 208
Score = 26.6 bits (59), Expect = 8.1
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 95 IDMTKCIYCGFCQEAC 110
DM +CI C C C
Sbjct: 141 YDMNRCILCTRCVRFC 156
>gnl|CDD|236597 PRK09626, oorD, 2-oxoglutarate-acceptor oxidoreductase subunit
OorD; Reviewed.
Length = 103
Score = 33.5 bits (77), Expect = 0.011
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERAD-GSRRTTRYDIDMTKCIYCGFCQEACPVDAI- 115
E RC AC +C ++CPA + + + A G + CI C C+ CP AI
Sbjct: 15 ESRCKACDICVSVCPAGVLAMRIDPHAVLGKMIKVVHP---ESCIGCRECELHCPDFAIY 71
Query: 116 -VEGPNFEFSTESHE 129
+ F+F+ S E
Sbjct: 72 VADRKEFKFAKLSKE 86
>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 = 35.1 bits (81), Expect = 0.012
Identities = 18/70 (25%), Positives = 23/70 (32%), Gaps = 17/70 (24%)
Query: 59 ERCIACKLCEAICPAQAITI---EAEERADGSRRTT--------------RYDIDMTKCI 101
+ CI C C +CP AI + EE + R I C
Sbjct: 683 DNCIQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISPLDCT 742
Query: 102 YCGFCQEACP 111
CG C + CP
Sbjct: 743 GCGNCVDICP 752
>gnl|CDD|236596 PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta;
Reviewed.
Length = 133
Score = 34.0 bits (78), Expect = 0.013
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
E CI C C CP AI + +++ G +D + C CG C E CP
Sbjct: 59 EICINCFNCWVYCPDAAI-LSRDKKLKG--------VDYSHCKGCGVCVEVCP 102
>gnl|CDD|182382 PRK10330, PRK10330, formate dehydrogenase-H ferredoxin subunit;
Provisional.
Length = 181
Score = 34.1 bits (78), Expect = 0.013
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 58 EERCIACKLCEAICP--AQAITIEAEERADGSRRTTR-YDIDMTKCIYCGF------CQE 108
+ERCI CK C CP A + + R G+ R + KC C C
Sbjct: 86 QERCIGCKTCVVACPYGAMEVVVRPVIRNSGAGLNVRAEKAEANKCDLCNHREDGPACMA 145
Query: 109 ACPVDAIV 116
ACP A++
Sbjct: 146 ACPTHALI 153
>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
[Central intermediary metabolism, Sulfur metabolism].
Length = 314
Score = 34.5 bits (79), Expect = 0.015
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI--DMTKCIYCGFCQEACPVDA 114
RCI C C +C +++A G+ Y + D +KCI CG C CP A
Sbjct: 170 RCIGCGACVKVC---------KKKAVGALSFENYKVVRDHSKCIGCGECVLKCPTGA 217
>gnl|CDD|238897 cd01916, ACS_1, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
decarbonylase, is found in acetogenic and methanogenic
organisms and is responsible for the synthesis and
breakdown of acetyl-CoA. ACS forms a heterotetramer
with carbon monoxide dehydrogenase (CODH) consisting of
two ACS and two CODH subunits. CODH reduces carbon
dioxide to carbon monoxide and ACS then synthesizes
acetyl-CoA from carbon monoxide, CoA, and a methyl group
donated by another protein (CoFeSP). ACS has three
structural domains, an N-terminal rossman fold domain
with a helical region at its N-terminus which interacts
with CODH, and two alpha + beta fold domains. A Ni-Fe-S
center referred to as the A-cluster is located in the
C-terminal domain. A large cavity exists between the
three domains which may bind CoA.
Length = 731
Score = 34.7 bits (80), Expect = 0.017
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 13/71 (18%)
Query: 50 ALRRYPSGEE------RCIACKLCEAICPAQAITIEAEERA---DGSRRTTRYDIDMTKC 100
++ P+ EE +C C C CP EA E A D S +D C
Sbjct: 350 GEKKLPTDEEFQELAAKCTDCGWCTRACPNSLRIKEAMEAAKEGDFSGLADLFDQ----C 405
Query: 101 IYCGFCQEACP 111
+ CG C++ CP
Sbjct: 406 VGCGRCEQECP 416
>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 [Energy
metabolism, Anaerobic].
Length = 397
Score = 34.4 bits (79), Expect = 0.019
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 59 ERCIACKLCEAICPAQAITIE----AEERADGSRRTTR----YDIDMTKCIYCGFCQEAC 110
E CI C +C CP + DG R + YD + C C C+ AC
Sbjct: 5 ESCIKCTVCTVYCPVAKANPLYPGPKQAGPDGERLRLKSAELYDEALKYCTNCKRCEVAC 64
Query: 111 PVD 113
P D
Sbjct: 65 PSD 67
>gnl|CDD|233993 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 = 34.2 bits (79), Expect = 0.021
Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 17/72 (23%)
Query: 39 GPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMT 98
P PR + P G+ CI C LC +CP I I DG +
Sbjct: 213 EPRGPRKGKKDPKAPGPLGD--CIDCNLCVQVCPT-GIDIR-----DGLQ---------L 255
Query: 99 KCIYCGFCQEAC 110
+CI CG C +AC
Sbjct: 256 ECINCGLCIDAC 267
>gnl|CDD|223325 COG0247, GlpC, Fe-S oxidoreductase [Energy production and
conversion].
Length = 388
Score = 33.8 bits (77), Expect = 0.025
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 10/65 (15%)
Query: 59 ERCIACKLCEAICPA----------QAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQE 108
++C+ C C +CP+ I + E + + C+ CG C
Sbjct: 9 DKCVHCGFCTNVCPSYRATEALSPRGRIVLVREVLRGKAPGDEEVYEALDTCLACGACAT 68
Query: 109 ACPVD 113
ACP
Sbjct: 69 ACPSG 73
>gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta
subunit. Dissimilatory sulfite reductase catalyzes the
six-electron reduction of sulfite to sulfide, as the
terminal reaction in dissimilatory sulfate reduction. It
remains unclear however, whether trithionate and
thiosulfate serve as intermediate compounds to sulfide,
or as end products of sulfite reduction. Sulfite
reductase is a multisubunit enzyme composed of dimers of
either alpha/beta or alpha/beta/gamma subunits, each
containing a siroheme and iron sulfur cluster prosthetic
center. Found in sulfate-reducing bacteria, these genes
are commonly located in an unidirectional gene cluster.
This model describes the beta subunit of sulfite
reductase [Central intermediary metabolism, Sulfur
metabolism].
Length = 341
Score = 33.7 bits (77), Expect = 0.030
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 69 AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
A CP A+ R DG ++ ++D+ KCIYCG C CP
Sbjct: 191 AACPTGALKP----RRDGKNKSL--EVDVEKCIYCGNCYTMCP 227
>gnl|CDD|205077 pfam12797, Fer4_2, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 22
Score = 30.5 bits (69), Expect = 0.030
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 91 TRYDIDMTKCIYCGFCQEACPV 112
+ ID KCI CG C ACP
Sbjct: 1 PKPLIDEDKCIGCGACVSACPA 22
Score = 28.6 bits (64), Expect = 0.16
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 58 EERCIACKLCEAICPA 73
E++CI C C + CPA
Sbjct: 7 EDKCIGCGACVSACPA 22
>gnl|CDD|181550 PRK08764, PRK08764, ferredoxin; Provisional.
Length = 135
Score = 32.6 bits (74), Expect = 0.038
Identities = 24/74 (32%), Positives = 28/74 (37%), Gaps = 10/74 (13%)
Query: 44 RFRGEHALRRYP-SGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIY 102
R RG H L + E CI C C CP AI A+ + + C
Sbjct: 69 RSRGTHKLPQVAWIVEADCIGCTKCIQACPVDAIVGGAKHM---------HTVIAPLCTG 119
Query: 103 CGFCQEACPVDAIV 116
C C ACPVD I
Sbjct: 120 CELCVPACPVDCIE 133
Score = 31.4 bits (71), Expect = 0.082
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 100 CIYCGFCQEACPVDAIVEG 118
CI C C +ACPVDAIV G
Sbjct: 87 CIGCTKCIQACPVDAIVGG 105
>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 [Energy metabolism, Electron
transport].
Length = 213
Score = 33.0 bits (75), Expect = 0.039
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 57 GEERCI-----ACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEAC 110
G E C+ C +C +CP + I + + R +D KC CG C++ C
Sbjct: 129 GHETCLNYKGLNCSICVRVCPIRGEAISLKPIENERGRLQIPTVDSAKCTGCGTCEKHC 187
Score = 28.7 bits (64), Expect = 0.97
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 100 CIYCGFCQEACPVDAI 115
C+ CG C EACP D +
Sbjct: 55 CVRCGLCVEACPYDIL 70
>gnl|CDD|232959 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
[Energy metabolism, Electron transport].
Length = 101
Score = 31.8 bits (72), Expect = 0.049
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 9/66 (13%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
C C C + C + + + T D +C +CG C EACP +A P
Sbjct: 35 VCTRCGECASACENNIL-----QLGQQGQPTVE--FDNAECDFCGKCAEACPTNAF--HP 85
Query: 120 NFEFST 125
F
Sbjct: 86 RFPGDW 91
>gnl|CDD|224072 COG1150, HdrC, Heterodisulfide reductase, subunit C [Energy
production and conversion].
Length = 195
Score = 32.4 bits (74), Expect = 0.055
Identities = 20/110 (18%), Positives = 32/110 (29%), Gaps = 32/110 (29%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRY-----------DIDMTKCIYCGFCQ 107
E C C C CP+ T R+ R + C+ C C
Sbjct: 39 EGCYQCGTCTGSCPSGRFT------DYSPRKIIRKARLGLVDLILSSESLWACVTCYTCT 92
Query: 108 EACPVDAIVEGPNFEF------------STESHEELLYNKEKLLSNGDKW 145
E CP + ++H E+L E +++ G+
Sbjct: 93 ERCPRGVKIVEVVKALRNIAVKEGLIEPMLKAHREVL---ETVITTGNHA 139
>gnl|CDD|224074 COG1152, CdhA, CO dehydrogenase/acetyl-CoA synthase alpha subunit
[Energy production and conversion].
Length = 772
Score = 32.9 bits (75), Expect = 0.055
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 50 ALRRYPSGEE------RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYC 103
+ P EE +C C C CP + EA E A + D+ CI C
Sbjct: 385 GRKEKPDDEEFMEYARKCTYCGNCMRACPNELDIPEAMEYAAKGDFSKLEDLH-DVCIGC 443
Query: 104 GFCQEACP 111
G C++ CP
Sbjct: 444 GRCEQVCP 451
Score = 29.0 bits (65), Expect = 1.4
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSR 88
+ CI C CE +CP + E+A R
Sbjct: 437 HDVCIGCGRCEQVCPKNIPILNMIEKAAQKR 467
>gnl|CDD|237143 PRK12576, PRK12576, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 279
Score = 32.8 bits (75), Expect = 0.060
Identities = 21/68 (30%), Positives = 27/68 (39%), Gaps = 15/68 (22%)
Query: 61 CIACKLCEAICPAQAITIE--------------AEERADGSRRTTRYDIDMT-KCIYCGF 105
CI C LC + CP AI E A+ R + + ID + +C YC
Sbjct: 154 CIWCGLCVSACPVVAIDPEFLGPAAHAKGYRFLADPRDTITEERMKILIDSSWRCTYCYS 213
Query: 106 CQEACPVD 113
C CP D
Sbjct: 214 CSNVCPRD 221
Score = 31.3 bits (71), Expect = 0.20
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 98 TKCIYCGFCQEACPVDAI 115
+CI+CG C ACPV AI
Sbjct: 152 AQCIWCGLCVSACPVVAI 169
>gnl|CDD|236535 PRK09477, napH, quinol dehydrogenase membrane component;
Provisional.
Length = 271
Score = 32.2 bits (74), Expect = 0.074
Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 13/68 (19%)
Query: 59 ERCIACKLCEAICP-AQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVE 117
++C C C +CP Q + R + + + CI CG C + C D
Sbjct: 208 QKCTRCMDCFHVCPEPQVL------RPPLKGKQSPSQVTSGDCITCGRCIDVCSEDV--- 258
Query: 118 GPNFEFST 125
F F+
Sbjct: 259 ---FNFTI 263
>gnl|CDD|235652 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 232
Score = 32.1 bits (74), Expect = 0.082
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 81 EERADGSRRTTRYDIDMTKCIYCGFCQEACPV 112
E+R + D + +CI C C +CP
Sbjct: 132 EDRE-------KLD-GLYECILCACCSTSCPS 155
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 32.1 bits (74), Expect = 0.11
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 13/54 (24%)
Query: 67 CEAICP-----AQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
C CP + I I+ ++ + I CI CG C + CP DAI
Sbjct: 21 CIKYCPVVRTGEETIEIDEDDG--------KPVISEELCIGCGICVKKCPFDAI 66
Score = 30.9 bits (71), Expect = 0.23
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 58 EERCIACKLCEAICPAQAITI 78
EE CI C +C CP AI+I
Sbjct: 48 EELCIGCGICVKKCPFDAISI 68
>gnl|CDD|224064 COG1141, Fer, Ferredoxin [Energy production and conversion].
Length = 68
Score = 30.1 bits (68), Expect = 0.11
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERA---DGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
+ CI C C A+ P + E A DG+ ++ + EACP DA
Sbjct: 7 RDTCIGCGACLAVAP-DVFDYDDEGIAFVLDGNIGEGEVPEELEEDAE--DAAEACPTDA 63
Query: 115 I 115
I
Sbjct: 64 I 64
Score = 28.5 bits (64), Expect = 0.44
Identities = 7/17 (41%), Positives = 8/17 (47%)
Query: 95 IDMTKCIYCGFCQEACP 111
+D CI CG C P
Sbjct: 5 VDRDTCIGCGACLAVAP 21
>gnl|CDD|233649 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 [Energy
metabolism, Electron transport].
Length = 435
Score = 31.9 bits (73), Expect = 0.12
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 51 LRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEAC 110
P E+ CI C C +CP + + A + ++ CI CG C C
Sbjct: 357 TPESP--EKPCIRCGKCVQVCPMNLLPQQLNWLALADEFDEAEEHNLMDCIECGCCSYVC 414
Query: 111 P 111
P
Sbjct: 415 P 415
Score = 27.3 bits (61), Expect = 4.2
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 100 CIYCGFCQEACPVDAIVEGPNFEFSTESHEEL 131
CI CG C + CP++ + + N+ + +E
Sbjct: 365 CIRCGKCVQVCPMNLLPQQLNWLALADEFDEA 396
>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 [Energy metabolism, Chemoautotrophy].
Length = 784
Score = 31.7 bits (72), Expect = 0.17
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGP 119
+C C C CP EA A + ++ +C CG C++ACP + P
Sbjct: 400 KCTQCGNCVRTCPNSLRVDEAMAHAQKGDLSKLEQLE-EQCYACGRCEQACPKNI----P 454
Query: 120 NFEFSTESHEELLYNK 135
T++ E+ L N+
Sbjct: 455 IISMITKAGEDRLKNE 470
Score = 30.6 bits (69), Expect = 0.41
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 58 EERCIACKLCEAICP 72
EE+C AC CE CP
Sbjct: 436 EEQCYACGRCEQACP 450
Score = 27.1 bits (60), Expect = 5.6
Identities = 10/31 (32%), Positives = 11/31 (35%), Gaps = 5/31 (16%)
Query: 86 GSRRTTRYDID-----MTKCIYCGFCQEACP 111
G R D + KC CG C CP
Sbjct: 382 GDERKFLPDDEELMELANKCTQCGNCVRTCP 412
>gnl|CDD|175989 cd04022, C2A_MCTP_PRT_plant, C2 domain first repeat found in
Multiple C2 domain and Transmembrane region Proteins
(MCTP); plant subset. MCTPs are involved in Ca2+
signaling at the membrane. Plant-MCTPs are composed of
a variable N-terminal sequence, four C2 domains, two
transmembrane regions (TMRs), and a short C-terminal
sequence. It is one of four protein classes that are
anchored to membranes via a transmembrane region; the
others being synaptotagmins, extended synaptotagmins,
and ferlins. MCTPs are the only membrane-bound C2 domain
proteins that contain two functional TMRs. MCTPs are
unique in that they bind Ca2+ but not phospholipids. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-II topology.
Length = 127
Score = 30.4 bits (69), Expect = 0.17
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 27 KEPATINYPFEKGPLSPRFRGEHALRRYPS 56
E YP EK L R RGE L+ Y +
Sbjct: 97 SEAVVQRYPLEKRGLFSRVRGEIGLKVYIT 126
>gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 639
Score = 31.5 bits (71), Expect = 0.18
Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 16/86 (18%)
Query: 33 NYPFEKGPLSPRFRGEHAL-RRYPSGEERCIACK--LCEAICPAQAITIEAEERADGSRR 89
N+P PR H + + + C C C CP A+T +++
Sbjct: 30 NWPLSHSDFRPRI---HVVGKGQAANPVACHHCNNAPCVTACPVNALTFQSDS------- 79
Query: 90 TTRYDIDMTKCIYCGFCQEACPVDAI 115
+D KCI C C ACP +
Sbjct: 80 ---VQLDEQKCIGCKRCAIACPFGVV 102
>gnl|CDD|205080 pfam12800, Fer4_4, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 17
Score = 28.2 bits (63), Expect = 0.20
Identities = 7/17 (41%), Positives = 8/17 (47%)
Query: 58 EERCIACKLCEAICPAQ 74
E+CI C C CP
Sbjct: 1 PEKCIGCGACVDACPYG 17
Score = 25.1 bits (55), Expect = 3.0
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 97 MTKCIYCGFCQEACPVD 113
KCI CG C +ACP
Sbjct: 1 PEKCIGCGACVDACPYG 17
>gnl|CDD|234122 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 [Energy metabolism, Electron
transport].
Length = 225
Score = 30.9 bits (70), Expect = 0.21
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
C A+CP A + E T D+ C+ C +C ACP
Sbjct: 102 CVAVCPTGASFKDEE--------TGIVDVHKDLCVGCQYCIAACP 138
Score = 30.5 bits (69), Expect = 0.25
Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 28/90 (31%)
Query: 59 ERCIACKLCEAICPAQAITIEAEER-ADGSRRTTRYDIDMTKCIYC----------GFCQ 107
+ C+ C+ C A CP + I + AD KC +C C
Sbjct: 125 DLCVGCQYCIAACPYRVRFIHPVTKSAD-------------KCNFCRDTNLAEGKLPACV 171
Query: 108 EACPVDAIVEG----PNFEFSTESHEELLY 133
E+CP A+ G PN E S + ++ +Y
Sbjct: 172 ESCPTKALTFGDLNDPNSEVSQKLKQKPVY 201
>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 = 30.5 bits (69), Expect = 0.25
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 21/71 (29%)
Query: 58 EERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQE 108
+++CI C+ C CP A + ++ M KC C C +
Sbjct: 94 QDKCIGCRYCVWACPYGAPQYDPQQGV------------MGKCDGCYDRVEKGLRPACVD 141
Query: 109 ACPVDAIVEGP 119
ACP+ A+ GP
Sbjct: 142 ACPMRALDFGP 152
Score = 28.2 bits (63), Expect = 1.3
Identities = 19/58 (32%), Positives = 23/58 (39%), Gaps = 13/58 (22%)
Query: 62 IACKLCE-----AICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDA 114
I+C C CP A+ E DG +D KCI C +C ACP A
Sbjct: 62 ISCNHCADPACVKNCPTGAMYKREE---DGLVL-----VDQDKCIGCRYCVWACPYGA 111
Score = 27.4 bits (61), Expect = 2.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 95 IDMTKCIYCGFCQEAC 110
+D T+C C CQ AC
Sbjct: 6 VDQTRCSGCKTCQIAC 21
>gnl|CDD|236786 PRK10882, PRK10882, hydrogenase 2 protein HybA; Provisional.
Length = 328
Score = 30.8 bits (70), Expect = 0.27
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFST 125
C ++CP A+T + + G YD D C C +C ACP + P ++++
Sbjct: 120 CVSVCPVSALTKDPK---TG---IVHYDKD--VCTGCRYCMVACPFNV----PKYDYNN 166
>gnl|CDD|181515 PRK08640, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 249
Score = 30.3 bits (69), Expect = 0.30
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 88 RRTTRYDIDMTKCIYCGFCQEACP 111
+R Y++ +KC+ CG C EACP
Sbjct: 144 KRQWAYEL--SKCMTCGCCLEACP 165
>gnl|CDD|234064 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
[Central intermediary metabolism, Nitrogen fixation].
Length = 91
Score = 29.3 bits (66), Expect = 0.31
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 10/67 (14%)
Query: 58 EERCIACKLCEAICPAQAITIEA----------EERADGSRRTTRYDIDMTKCIYCGFCQ 107
+E+CI C C +C +T++ ++ D R + CI CG C
Sbjct: 20 QEKCIGCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVANPGNCIGCGACA 79
Query: 108 EACPVDA 114
CP
Sbjct: 80 RVCPKKC 86
Score = 28.5 bits (64), Expect = 0.50
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 85 DGSRRTTRY--DIDMTKCIYCGFCQEACPVD 113
GS T ++ ID KCI CG C + C D
Sbjct: 6 GGSEWTPQFVTSIDQEKCIGCGRCYKVCGRD 36
Score = 27.7 bits (62), Expect = 1.1
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 56 SGEERCIACKLCEAICPAQAIT 77
+ CI C C +CP + T
Sbjct: 67 ANPGNCIGCGACARVCPKKCQT 88
>gnl|CDD|236869 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 30.2 bits (69), Expect = 0.37
Identities = 16/64 (25%), Positives = 21/64 (32%), Gaps = 14/64 (21%)
Query: 59 ERCIACKLCEAICPAQAITIE---------AEERADGSRRTTRYDID--MTKCIYCGFCQ 107
+ CI C +C CP + ER R D + C C C+
Sbjct: 7 DSCIKCTVCTTACPVARVNPLYPGPKQAGPDGERL---RLKDGALYDESLKYCSNCKRCE 63
Query: 108 EACP 111
ACP
Sbjct: 64 VACP 67
>gnl|CDD|236534 PRK09476, napG, quinol dehydrogenase periplasmic component;
Provisional.
Length = 254
Score = 30.0 bits (68), Expect = 0.41
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 99 KCIYCGFCQEACPVD 113
CI CG C +ACP D
Sbjct: 60 ACIRCGLCVQACPYD 74
Score = 28.8 bits (65), Expect = 0.98
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 22/68 (32%)
Query: 58 EERCIA-----CKLCEAICPA--QAITIEAEERADGSRRTTRYD--------IDMTKCIY 102
+E C+ C +C +CP +AIT+E R R + C
Sbjct: 136 QENCLNFQGLRCDVCYRVCPLIDKAITLE-------LERNERTGKHAFFLPTVHSDACTG 188
Query: 103 CGFCQEAC 110
CG C++AC
Sbjct: 189 CGKCEKAC 196
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 30.3 bits (69), Expect = 0.48
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 100 CIYCGFCQEACPVD 113
CI CG C +ACP
Sbjct: 372 CIRCGACADACPAS 385
Score = 26.8 bits (60), Expect = 5.6
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 19/67 (28%)
Query: 55 PSGEER-CIACKLCEAICPAQ---------AITIEAEERADGSRRTTRYDIDMTKCIYCG 104
P E+ CI C C CPA A +A+ + Y++ CI CG
Sbjct: 365 PPPPEQPCIRCGACADACPASLLPQQLYWFA-------KAEEHDKAQEYNLF--DCIECG 415
Query: 105 FCQEACP 111
C CP
Sbjct: 416 ACAYVCP 422
>gnl|CDD|205427 pfam13247, Fer4_11, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 99
Score = 28.7 bits (65), Expect = 0.49
Identities = 14/49 (28%), Positives = 17/49 (34%), Gaps = 8/49 (16%)
Query: 67 CEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
C A CP+ AI + E G +D C C ACP
Sbjct: 18 CVASCPSGAIYKDEE---TGIVL-----VDQKTCRGWRMCVSACPYKKP 58
>gnl|CDD|223555 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
protein subunit [Energy production and conversion].
Length = 234
Score = 29.6 bits (67), Expect = 0.52
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 96 DMTKCIYCGFCQEACPVDAIVEGPNF 121
++++CI CG C ACP I P+F
Sbjct: 140 ELSECILCGCCTAACPS--IWWNPDF 163
Score = 27.3 bits (61), Expect = 3.1
Identities = 21/93 (22%), Positives = 26/93 (27%), Gaps = 19/93 (20%)
Query: 37 EKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICP--------------AQAITIEAEE 82
+ P R CI C C A CP QA A+
Sbjct: 120 DDEPDPGERLQSPEEREKLDELSECILCGCCTAACPSIWWNPDFLGPAALRQAYRFLADS 179
Query: 83 RADGSRRTTRYDIDMTK----CIYCGFCQEACP 111
R +G ++ C CG C E CP
Sbjct: 180 RDEG-TAERLKILEDPDGVWRCTTCGNCTEVCP 211
>gnl|CDD|236967 PRK11749, PRK11749, dihydropyrimidine dehydrogenase subunit A;
Provisional.
Length = 457
Score = 29.8 bits (68), Expect = 0.61
Identities = 7/15 (46%), Positives = 9/15 (60%), Gaps = 2/15 (13%)
Query: 100 CIYCG--FCQEACPV 112
C+ C C +ACPV
Sbjct: 42 CLQCKDAPCVKACPV 56
>gnl|CDD|205078 pfam12798, Fer4_3, 4Fe-4S binding domain. This superfamily
includes proteins containing domains which bind to
iron-sulfur clusters. Members include bacterial
ferredoxins, various dehydrogenases, and various
reductases. Structure of the domain is an
alpha-antiparallel beta sandwich.
Length = 15
Score = 26.9 bits (60), Expect = 0.64
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 100 CIYCGFCQEACPVDA 114
C CG C E CPV A
Sbjct: 1 CTGCGACVEVCPVGA 15
>gnl|CDD|179457 PRK02651, PRK02651, photosystem I subunit VII; Provisional.
Length = 81
Score = 28.1 bits (62), Expect = 0.70
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSR 88
E C+ CK CE CP ++I A+ +R
Sbjct: 46 EDCVGCKRCETACPTDFLSIRVYLGAETTR 75
Score = 27.3 bits (60), Expect = 1.6
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 18/71 (25%)
Query: 49 HALRRYPSGEERCIACKLCEAICPAQAITI------EAEERADGSRRTTRYDIDMTKCIY 102
HA++ Y + CI C C CP + + +A + A R C+
Sbjct: 3 HAVKIY----DTCIGCTQCVRACPLDVLEMVPWDGCKAGQIASSPR--------TEDCVG 50
Query: 103 CGFCQEACPVD 113
C C+ ACP D
Sbjct: 51 CKRCETACPTD 61
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 29.7 bits (67), Expect = 0.71
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 96 DMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHE 129
+ C +CG C CPV A+ +F++++ + E
Sbjct: 202 ETLDCSFCGECIAVCPVGALS-SSDFQYTSNAWE 234
>gnl|CDD|237213 PRK12810, gltD, glutamate synthase subunit beta; Reviewed.
Length = 471
Score = 29.4 bits (67), Expect = 0.73
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 100 CIYCG--FCQEACPVDAIVEGPNF 121
C+ CG FC CPV + P +
Sbjct: 46 CMDCGIPFCHWGCPVHNYI--PEW 67
>gnl|CDD|233481 TIGR01582, FDH-beta, formate dehydrogenase, beta subunit, Fe-S
containing. This model represents the beta subunit of
the gamma-proteobacterial formate dehydrogenase. This
subunit contains four 4Fe-4S clusters and is involved in
transmitting electrons from the alpha subunit
(TIGR01553) at the periplasmic space to the gamma
subunit which spans the cytoplasmic membrane. 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
[Energy metabolism, Anaerobic, Energy metabolism,
Electron transport].
Length = 283
Score = 29.1 bits (65), Expect = 0.85
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 94 DIDMTKCIYCGFCQEACPVD 113
D D +KCI CG+C CP +
Sbjct: 120 DFDHSKCIGCGYCIVGCPFN 139
Score = 27.6 bits (61), Expect = 3.2
Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 21/69 (30%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCG---------FCQEA 109
+CI C C CP R + D KC C C +
Sbjct: 124 SKCIGCGYCIVGCPFNI------------PRYDKVDNRPYKCTLCIDRVSVGQEPACVKT 171
Query: 110 CPVDAIVEG 118
CP +AI G
Sbjct: 172 CPTNAISFG 180
Score = 26.8 bits (59), Expect = 6.1
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 95 IDMTKCIYCGFCQEAC 110
ID++ CI C CQ AC
Sbjct: 26 IDVSSCIGCKACQAAC 41
>gnl|CDD|181037 PRK07569, PRK07569, bidirectional hydrogenase complex protein HoxU;
Validated.
Length = 234
Score = 28.8 bits (65), Expect = 0.99
Identities = 23/84 (27%), Positives = 31/84 (36%), Gaps = 22/84 (26%)
Query: 43 PRFRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEERADGSRRTTRYDI--DM--- 97
PRF +H RC+ C C +C IE D + R + + D+
Sbjct: 139 PRFGIDH---------NRCVLCTRCVRVCDE----IEGAHTWDVAGRGAKSRVITDLNQP 185
Query: 98 ----TKCIYCGFCQEACPVDAIVE 117
C CG C +ACP AI
Sbjct: 186 WGTSETCTSCGKCVQACPTGAIFR 209
>gnl|CDD|185089 PRK15135, PRK15135, histidine/lysine/arginine/ornithine ABC
transporter permease HisQ; Provisional.
Length = 228
Score = 29.0 bits (65), Expect = 1.00
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 4/28 (14%)
Query: 6 IHAAFLTEIFRGFFVA--TGHIFKEPAT 31
I+ A+ TE FRG F+A GHI E AT
Sbjct: 103 IYGAYFTETFRGAFMAVPKGHI--EAAT 128
>gnl|CDD|177005 CHL00065, psaC, photosystem I subunit VII.
Length = 81
Score = 27.8 bits (62), Expect = 1.0
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSR 88
E C+ CK CE+ CP +++ + +R
Sbjct: 46 EDCVGCKRCESACPTDFLSVRVYLGHETTR 75
Score = 25.5 bits (56), Expect = 5.0
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 14/59 (23%)
Query: 61 CIACKLCEAICPAQAITI------EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
CI C C CP + + +A++ A R C+ C C+ ACP D
Sbjct: 11 CIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPR--------TEDCVGCKRCESACPTD 61
>gnl|CDD|182296 PRK10194, PRK10194, ferredoxin-type protein; Provisional.
Length = 163
Score = 28.1 bits (62), Expect = 1.4
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 60 RCIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVDAI 115
+ + C+ C+ C AI + ++ C CG C +CPV AI
Sbjct: 105 QSVECRRCQDSCEPMAIIFRPTLSG-----IYQPQLNSQLCNGCGACAASCPVSAI 155
Score = 26.1 bits (57), Expect = 7.3
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 61 CIACKLCEAICPAQAITIE 79
C C C A CP AIT E
Sbjct: 140 CNGCGACAASCPVSAITAE 158
>gnl|CDD|222081 pfam13370, Fer4_13, 4Fe-4S single cluster domain.
Length = 58
Score = 26.9 bits (60), Expect = 1.4
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 58 EERCIACKLCEAICP 72
+ CI C LC I P
Sbjct: 3 RDTCIGCGLCREIAP 17
>gnl|CDD|236890 PRK11274, glcF, glycolate oxidase iron-sulfur subunit; Provisional.
Length = 407
Score = 28.7 bits (65), Expect = 1.5
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 99 KCIYCGFCQEACP 111
KC++CGFC CP
Sbjct: 24 KCVHCGFCTATCP 36
>gnl|CDD|232950 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
[Energy metabolism, Aerobic, Energy metabolism,
Anaerobic, Energy metabolism, TCA cycle].
Length = 220
Score = 28.2 bits (63), Expect = 1.9
Identities = 17/70 (24%), Positives = 22/70 (31%), Gaps = 21/70 (30%)
Query: 61 CIACKLCEAICPA--------------QAITIEAEERADGSRRTTRYDIDMTK-----CI 101
CI C C + CPA A + R ++ R + K C
Sbjct: 140 CILCGCCYSSCPAFWWNPEFLGPAALTAAYRFLIDSRDHATK--DRLEGLNDKNGVWRCT 197
Query: 102 YCGFCQEACP 111
C C E CP
Sbjct: 198 TCMNCSEVCP 207
Score = 27.0 bits (60), Expect = 4.8
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 96 DMTKCIYCGFCQEACPVDAIVEGPNF 121
++ CI CG C +CP A P F
Sbjct: 136 QLSGCILCGCCYSSCP--AFWWNPEF 159
>gnl|CDD|226972 COG4624, COG4624, Iron only hydrogenase large subunit, C-terminal
domain [General function prediction only].
Length = 411
Score = 28.2 bits (63), Expect = 2.0
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 95 IDMTKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLS 140
I ++ C+ C C +C V AI S +S +++L E L
Sbjct: 31 ISLSDCLACSGCITSCEVKAI--------SLQSGKKVLEELEDLFC 68
>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 [Energy
metabolism, Photosynthesis].
Length = 80
Score = 26.8 bits (59), Expect = 2.3
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 59 ERCIACKLCEAICPAQAITIEAEERADGSR 88
E C+ CK CE+ CP +++ A+ +R
Sbjct: 45 EDCVGCKRCESACPTDFLSVRVYLGAETTR 74
Score = 25.2 bits (55), Expect = 6.4
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 14/59 (23%)
Query: 61 CIACKLCEAICPAQAITI------EAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
CI C C CP + + +A + A R C+ C C+ ACP D
Sbjct: 10 CIGCTQCVRACPTDVLEMVPWDGCKAGQIASAPR--------TEDCVGCKRCESACPTD 60
>gnl|CDD|212975 cd12042, SH3_CACNB3, Src Homology 3 domain of Voltage-dependent
L-type calcium channel subunit beta3. The beta3 subunit
of voltage-dependent calcium channels (Ca(V)s) is one of
four beta subunits present in vertebrates. It is the
main beta subunit present in smooth muscles and is
strongly expressed in the brain; it is predominant in
the olfactory bulb, cortex, and hippocampus. It may play
a role in regulating the NMDAR (N-methyl-d-aspartate
receptor) activity in the hippocampus and thus,
activity-dependent synaptic plasticity and cognitive
behaviors. Ca(V)s are multi-protein complexes that
regulate the entry of calcium into cells. They impact
muscle contraction, neuronal migration, hormone and
neurotransmitter release, and the activation of
calcium-dependent signaling pathways. They are composed
of four subunits: alpha1, alpha2delta, beta, and gamma.
The beta subunit is a soluble and intracellular protein
that interacts with the transmembrane alpha1 subunit. It
facilitates the trafficking and proper localization of
the alpha1 subunit to the cellular plasma membrane.
Vertebrates contain four different beta subunits from
distinct genes (beta1-4); each exists as multiple splice
variants. All are expressed in the brain while other
tissues show more specific expression patterns. The beta
subunits show similarity to MAGUK (membrane-associated
guanylate kinase) proteins in that they contain SH3 and
inactive guanylate kinase (GuK) domains; however, they
do not appear to contain a PDZ domain. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 68
Score = 26.1 bits (57), Expect = 2.5
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 98 TKCIYCGFCQEACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDKW 145
T YCG E CPV NFE ++ L+ KEK + D W
Sbjct: 9 TNVSYCGALDEECPVQG--AAINFE-----AKDFLHIKEKY--SNDWW 47
>gnl|CDD|183376 PRK11909, PRK11909, cobalt transport protein CbiM; Provisional.
Length = 230
Score = 27.8 bits (62), Expect = 2.7
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 109 ACPVDAIVEGPNFEFSTESHEELLYNKEKLLSNGDK 144
A V+AIV G + ++ EE L K+ GD
Sbjct: 194 AGIVEAIVTGLVVYYLQKADEENLLYKKSYKLRGDN 229
>gnl|CDD|183490 PRK12385, PRK12385, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 244
Score = 27.7 bits (62), Expect = 2.8
Identities = 21/69 (30%), Positives = 26/69 (37%), Gaps = 19/69 (27%)
Query: 61 CIACKLCEAICPA----------QAITIEAEERADGSR---RTTRYDIDMTK-----CIY 102
CI C LC A CP AIT+ D SR + R + C +
Sbjct: 149 CINCGLCYAACPQFGLNPEFIGPAAITLAHRYNLD-SRDHGKKERMKQLNGQNGVWSCTF 207
Query: 103 CGFCQEACP 111
G+C E CP
Sbjct: 208 VGYCSEVCP 216
>gnl|CDD|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit
[Energy production and conversion].
Length = 247
Score = 27.0 bits (60), Expect = 4.1
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 12/51 (23%)
Query: 61 CIACKLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACP 111
C+ C C A CP++AI G R ++ +CI CG C +CP
Sbjct: 192 CMGCGTCAASCPSRAIPC------RGCR------GNIPRCIKCGACFVSCP 230
>gnl|CDD|177700 PLN00071, PLN00071, photosystem I subunit VII; Provisional.
Length = 81
Score = 25.7 bits (56), Expect = 5.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 59 ERCIACKLCEAICPAQAITI 78
E C+ CK CE+ CP +++
Sbjct: 46 EDCVGCKRCESACPTDFLSV 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
[Energy metabolism, Electron transport].
Length = 432
Score = 26.8 bits (59), Expect = 5.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 96 DMTKCIYCGFCQEACPV 112
++ CI CG CQ CPV
Sbjct: 291 EVLACIRCGACQNECPV 307
>gnl|CDD|161920 TIGR00545, lipoyltrans, lipoyltransferase and lipoate-protein
ligase. One member of this group of proteins is bovine
lipoyltransferase, which transfers the lipoyl group from
lipoyl-AMP to the specific Lys of lipoate-dependent
enzymes. However, it does not first activate lipoic acid
with ATP to create lipoyl-AMP and pyrophosphate. Another
member of this group, lipoate-protein ligase A from E.
coli, catalyzes both the activation and the transfer of
lipoate. Homology between the two is full-length, except
for the bovine mitochondrial targeting signal, but is
strongest toward the N-terminus [Protein fate, Protein
modification and repair].
Length = 324
Score = 26.7 bits (59), Expect = 6.1
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 7 HAAFLTEIFRGFFVATGHI 25
FL E+ + FF T +
Sbjct: 195 TEQFLEEMTQAFFTYTERV 213
>gnl|CDD|224062 COG1139, COG1139, Uncharacterized conserved protein containing a
ferredoxin-like domain [Energy production and
conversion].
Length = 459
Score = 26.5 bits (59), Expect = 6.7
Identities = 17/74 (22%), Positives = 18/74 (24%), Gaps = 31/74 (41%)
Query: 60 RCIACKLCEAICPA---------------------QAITIEAEERADGSRRTTRYDIDMT 98
RCI C C CP I + D
Sbjct: 309 RCIRCGACLNHCPVYRHIGGHAYGSIYPGPIGVVWSPILGGYDAAGDLP----------Y 358
Query: 99 KCIYCGFCQEACPV 112
C CG C E CPV
Sbjct: 359 ACSLCGACTEVCPV 372
>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 = 26.7 bits (59), Expect = 7.2
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 59 ERCIAC----KLCEAICPAQAITIEAEERADGSRRTTRYDIDMTKCIYCGFCQEACPVD 113
+RC+ C + C +CP +A + + D C CG C CP D
Sbjct: 881 QRCLECSYVCEKCVDVCPNRANIVIYVPGFRDQFQIVHLD---GMCNECGNCATFCPYD 936
>gnl|CDD|205920 pfam13746, Fer4_18, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 69
Score = 24.7 bits (54), Expect = 9.8
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 2/56 (3%)
Query: 60 RCIACKLCE-AICPAQAITIEAEERADGSRRTTRYDID-MTKCIYCGFCQEACPVD 113
RC + + E + A R R D + + C+ CG C E CP
Sbjct: 10 RCQSAMIDEDTLVVAYDFRPGGRGRPRYRRLHKVKDNEGLGDCVGCGRCVEVCPTG 65
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
0.322 0.138 0.435
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,214,470
Number of extensions: 727385
Number of successful extensions: 1026
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 275
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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 (21.9 bits)
S2: 55 (25.0 bits)