RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5785
(340 letters)
>gnl|CDD|235652 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 232
Score = 223 bits (570), Expect = 4e-72
Identities = 74/122 (60%), Positives = 90/122 (73%), Gaps = 1/122 (0%)
Query: 219 DANDKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKK 278
D I PLP + V+KDLV DM FYAQY+SI+P+L D + LQS +DR+K
Sbjct: 78 DLKKGKIVIRPLPGLPVIKDLVVDMTQFYAQYRSIKPYLIND-TPPPARERLQSPEDREK 136
Query: 279 LDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPFS 338
LDGLYECILCACCSTSCPS+WWN +K+LGPA L+QAYR+I DSRDE T +RL+ L DPF
Sbjct: 137 LDGLYECILCACCSTSCPSFWWNPDKFLGPAALLQAYRFIADSRDEATGERLDILDDPFG 196
Query: 339 VY 340
V+
Sbjct: 197 VF 198
Score = 156 bits (396), Expect = 4e-46
Identities = 52/72 (72%), Positives = 62/72 (86%)
Query: 144 YLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTAD 203
LQS +DR+KLDGLYECILCACCSTSCPS+WWN +K+LGPA L+QAYR+I DSRDE T +
Sbjct: 127 RLQSPEDREKLDGLYECILCACCSTSCPSFWWNPDKFLGPAALLQAYRFIADSRDEATGE 186
Query: 204 RLNQLKDPFSVY 215
RL+ L DPF V+
Sbjct: 187 RLDILDDPFGVF 198
Score = 43.6 bits (104), Expect = 5e-05
Identities = 15/25 (60%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 99 TFAIYRWNPDKPDEKPTMQEYKVDL 123
TF IYR+NPD D P MQ Y+VD+
Sbjct: 1 TFKIYRYNPDV-DANPRMQTYEVDV 24
Score = 38.6 bits (91), Expect = 0.003
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 50 TFAIYRWNPDKPDEKPTMQEYK 71
TF IYR+NPD D P MQ Y+
Sbjct: 1 TFKIYRYNPDV-DANPRMQTYE 21
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 220 bits (562), Expect = 2e-70
Identities = 80/127 (62%), Positives = 95/127 (74%), Gaps = 2/127 (1%)
Query: 216 SKIDAN-DKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQR-DKENIGNAQYLQSL 273
+KID + + I PLPHM+V+KDLV DM NFY QYKSI+PWL+ G ++LQS
Sbjct: 118 TKIDRDESGPTTITPLPHMFVIKDLVVDMTNFYQQYKSIEPWLKTKKPPEDGQKEHLQSK 177
Query: 274 DDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQL 333
+DR KLDG+YECILCACCSTSCPSYWWN EK+LGPA L+ AYRWI DSRDE T +RL L
Sbjct: 178 EDRAKLDGMYECILCACCSTSCPSYWWNPEKFLGPAALLHAYRWISDSRDEYTKERLEAL 237
Query: 334 KDPFSVY 340
D F +Y
Sbjct: 238 DDEFKLY 244
Score = 146 bits (371), Expect = 6e-42
Identities = 52/74 (70%), Positives = 60/74 (81%)
Query: 142 AQYLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKT 201
++LQS +DR KLDG+YECILCACCSTSCPSYWWN EK+LGPA L+ AYRWI DSRDE T
Sbjct: 171 KEHLQSKEDRAKLDGMYECILCACCSTSCPSYWWNPEKFLGPAALLHAYRWISDSRDEYT 230
Query: 202 ADRLNQLKDPFSVY 215
+RL L D F +Y
Sbjct: 231 KERLEALDDEFKLY 244
Score = 58.3 bits (141), Expect = 1e-09
Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 82 SAAASSAVPAEKPAKYKTFAIYRWNPDKPDEKPTMQEYKVDLNN 125
SA ++ KP+ K F IYRWNPD P KP +Q YKVDLN+
Sbjct: 28 SAETKASSKGSKPSNLKEFQIYRWNPDNP-GKPHLQSYKVDLND 70
Score = 49.0 bits (117), Expect = 1e-06
Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 33 SAAASSAVPAEKPAKYKTFAIYRWNPDKPDEKPTMQEYK 71
SA ++ KP+ K F IYRWNPD P KP +Q YK
Sbjct: 28 SAETKASSKGSKPSNLKEFQIYRWNPDNP-GKPHLQSYK 65
>gnl|CDD|223555 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
protein subunit [Energy production and conversion].
Length = 234
Score = 169 bits (431), Expect = 3e-51
Identities = 63/122 (51%), Positives = 83/122 (68%), Gaps = 2/122 (1%)
Query: 219 DANDKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKK 278
D + V I PLP+ V++DLV DM FY + + I+P+L RD E + LQS ++R+K
Sbjct: 79 DLEEGVITIEPLPNFPVIRDLVVDMEEFYEKLRKIKPYLIRDDEP-DPGERLQSPEEREK 137
Query: 279 LDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPFS 338
LD L ECILC CC+ +CPS WWN +LGPA L QAYR++ DSRDE TA+RL L+DP
Sbjct: 138 LDELSECILCGCCTAACPSIWWN-PDFLGPAALRQAYRFLADSRDEGTAERLKILEDPDG 196
Query: 339 VY 340
V+
Sbjct: 197 VW 198
Score = 115 bits (289), Expect = 2e-30
Identities = 43/73 (58%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 144 YLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTAD 203
LQS ++R+KLD L ECILC CC+ +CPS WWN +LGPA L QAYR++ DSRDE TA+
Sbjct: 128 RLQSPEEREKLDELSECILCGCCTAACPSIWWN-PDFLGPAALRQAYRFLADSRDEGTAE 186
Query: 204 RLNQLKDPFSVYS 216
RL L+DP V+
Sbjct: 187 RLKILEDPDGVWR 199
Score = 36.5 bits (85), Expect = 0.010
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 99 TFAIYRWNPDKPDEKPTMQEYKVDLNNQLNF 129
F IYR+NPD D+KP Q Y+V + +
Sbjct: 4 KFKIYRYNPD--DDKPYWQTYEVPYDEGMTV 32
Score = 29.9 bits (68), Expect = 1.3
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 50 TFAIYRWNPDKPDEKPTMQEYK 71
F IYR+NPD D+KP Q Y+
Sbjct: 4 KFKIYRYNPD--DDKPYWQTYE 23
>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 = 156 bits (396), Expect = 3e-46
Identities = 61/122 (50%), Positives = 82/122 (67%), Gaps = 1/122 (0%)
Query: 219 DANDKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKK 278
D V KI PLP++ V+KDLV DM FYA+ ++I+P+L R + ++LQ+ + R+K
Sbjct: 74 DLGQPVMKIEPLPNLPVIKDLVVDMGPFYAKLEAIKPYLIRKSQPEPEGEFLQTPEQREK 133
Query: 279 LDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPFS 338
LD L CILC CC +SCP++WWN E +LGPA L AYR++IDSRD T DRL L D
Sbjct: 134 LDQLSGCILCGCCYSSCPAFWWNPE-FLGPAALTAAYRFLIDSRDHATKDRLEGLNDKNG 192
Query: 339 VY 340
V+
Sbjct: 193 VW 194
Score = 104 bits (262), Expect = 9e-27
Identities = 40/75 (53%), Positives = 52/75 (69%), Gaps = 1/75 (1%)
Query: 142 AQYLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKT 201
++LQ+ + R+KLD L CILC CC +SCP++WWN E +LGPA L AYR++IDSRD T
Sbjct: 122 GEFLQTPEQREKLDQLSGCILCGCCYSSCPAFWWNPE-FLGPAALTAAYRFLIDSRDHAT 180
Query: 202 ADRLNQLKDPFSVYS 216
DRL L D V+
Sbjct: 181 KDRLEGLNDKNGVWR 195
Score = 32.0 bits (73), Expect = 0.34
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 102 IYRWNPDKPDEKPTMQEYKVDLNNQ 126
+ R+NPD DEKP +Q Y+V +
Sbjct: 1 VLRFNPDV-DEKPHLQSYEVPADEG 24
>gnl|CDD|171592 PRK12575, PRK12575, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 235
Score = 147 bits (373), Expect = 8e-43
Identities = 63/112 (56%), Positives = 87/112 (77%), Gaps = 1/112 (0%)
Query: 229 PLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKKLDGLYECILC 288
PLP + VV+DL+ DM +F+ QY SI+P+L D + LQ+ +R++LDGLYECILC
Sbjct: 91 PLPGLPVVRDLIVDMTDFFNQYHSIRPYLINDTVP-PERERLQTPQEREQLDGLYECILC 149
Query: 289 ACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPFSVY 340
ACCST+CPSYWWN +K++GPA L+QAYR+I DSRD+ TA RL+ L+DP+ ++
Sbjct: 150 ACCSTACPSYWWNPDKFVGPAGLLQAYRFIADSRDDATAARLDDLEDPYRLF 201
Score = 118 bits (298), Expect = 9e-32
Identities = 46/71 (64%), Positives = 62/71 (87%)
Query: 145 LQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADR 204
LQ+ +R++LDGLYECILCACCST+CPSYWWN +K++GPA L+QAYR+I DSRD+ TA R
Sbjct: 131 LQTPQEREQLDGLYECILCACCSTACPSYWWNPDKFVGPAGLLQAYRFIADSRDDATAAR 190
Query: 205 LNQLKDPFSVY 215
L+ L+DP+ ++
Sbjct: 191 LDDLEDPYRLF 201
Score = 29.5 bits (66), Expect = 1.8
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 95 AKYKTFAIYRWNPDKPDEKPTMQEYKVDL 123
A + IYR++PD D P MQ Y++
Sbjct: 2 ADTRILHIYRYDPD-DDAAPRMQRYEIAP 29
>gnl|CDD|237143 PRK12576, PRK12576, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 279
Score = 91.0 bits (226), Expect = 4e-21
Identities = 39/110 (35%), Positives = 63/110 (57%), Gaps = 2/110 (1%)
Query: 227 IYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENI-GNAQYLQSLDDRKKLDGLYEC 285
I P+ + VVKDL+ D + FY + ++P L R KE + G A++ +D+K+L +C
Sbjct: 95 IEPMDYFKVVKDLIVDFDEFYERMFKVKPRLYRAKEVLEGKAEHRLKPEDQKELWKFAQC 154
Query: 286 ILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKD 335
I C C ++CP + ++LGPA + YR++ D RD T +R+ L D
Sbjct: 155 IWCGLCVSACPVVAID-PEFLGPAAHAKGYRFLADPRDTITEERMKILID 203
Score = 57.1 bits (138), Expect = 2e-09
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 140 SNAQYLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDE 199
A++ +D+K+L +CI C C ++CP + ++LGPA + YR++ D RD
Sbjct: 134 GKAEHRLKPEDQKELWKFAQCIWCGLCVSACPVVAID-PEFLGPAAHAKGYRFLADPRDT 192
Query: 200 KTADRLNQLKD 210
T +R+ L D
Sbjct: 193 ITEERMKILID 203
Score = 27.8 bits (62), Expect = 8.9
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 7/48 (14%)
Query: 155 DGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTA 202
D + C C CS CP + + P ++ R K+
Sbjct: 203 DSSWRCTYCYSCSNVCP-------RDIEPVTAIKKTRSFTRVYKPKSE 243
>gnl|CDD|183605 PRK12577, PRK12577, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 329
Score = 89.4 bits (222), Expect = 3e-20
Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 1/110 (0%)
Query: 227 IYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKKLDGLYECI 286
I PL +M V+KDLV DM++F+ +++ P++ + ++LQ+ ++R KLD CI
Sbjct: 96 IAPLGNMPVIKDLVVDMSSFWQNLEAVDPYVSTAARQVPEREFLQTPEERSKLDQTGNCI 155
Query: 287 LCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDP 336
LC C + C + N E ++GP L +A R + DSRD T RL
Sbjct: 156 LCGACYSECNAREVNPE-FVGPHALAKAQRMVADSRDTATEQRLELYNQG 204
Score = 62.4 bits (152), Expect = 5e-11
Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 133 SSHATAISNAQYLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRW 192
S+ A + ++LQ+ ++R KLD CILC C + C + N E ++GP L +A R
Sbjct: 127 STAARQVPEREFLQTPEERSKLDQTGNCILCGACYSECNAREVNPE-FVGPHALAKAQRM 185
Query: 193 IIDSRDEKTADRLNQLKDP 211
+ DSRD T RL
Sbjct: 186 VADSRDTATEQRLELYNQG 204
>gnl|CDD|183490 PRK12385, PRK12385, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 244
Score = 66.6 bits (163), Expect = 8e-13
Identities = 32/108 (29%), Positives = 55/108 (50%), Gaps = 1/108 (0%)
Query: 226 KIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKKLDGLYEC 285
K+ L + + +DLV DM +F ++I+P++ + + Q+ K C
Sbjct: 90 KVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNDRTPDDGPNKQTPAQMAKYHQFSGC 149
Query: 286 ILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQL 333
I C C +CP + N E ++GPA + A+R+ +DSRD +R+ QL
Sbjct: 150 INCGLCYAACPQFGLNPE-FIGPAAITLAHRYNLDSRDHGKKERMKQL 196
Score = 46.6 bits (111), Expect = 5e-06
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 160 CILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPFSVYS 216
CI C C +CP + N E ++GPA + A+R+ +DSRD +R+ QL V+S
Sbjct: 149 CINCGLCYAACPQFGLNPE-FIGPAAITLAHRYNLDSRDHGKKERMKQLNGQNGVWS 204
>gnl|CDD|235756 PRK06259, PRK06259, succinate dehydrogenase/fumarate reductase
iron-sulfur subunit; Provisional.
Length = 486
Score = 62.7 bits (153), Expect = 6e-11
Identities = 36/96 (37%), Positives = 51/96 (53%), Gaps = 10/96 (10%)
Query: 235 VVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKKLDGLYECILCACCSTS 294
V+KDL+ D +Y + KS++ +LQR E I Y + ++D KKL G CI C C ++
Sbjct: 91 VIKDLIVDREPYYKKLKSLRNYLQRKNEKI---TYPEDIEDIKKLRG---CIECLSCVST 144
Query: 295 CPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRL 330
CP+ Y GP + Q R+ D RDE DR
Sbjct: 145 CPAR--KVSDYPGPTFMRQLARFAFDPRDEG--DRE 176
Score = 39.2 bits (92), Expect = 0.003
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 142 AQYLQSLDDRKKLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKT 201
Y + ++D KKL G CI C C ++CP+ Y GP + Q R+ D RDE
Sbjct: 120 ITYPEDIEDIKKLRG---CIECLSCVSTCPAR--KVSDYPGPTFMRQLARFAFDPRDEG- 173
Query: 202 ADRL 205
DR
Sbjct: 174 -DRE 176
>gnl|CDD|184136 PRK13552, frdB, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 239
Score = 51.5 bits (124), Expect = 1e-07
Identities = 30/111 (27%), Positives = 56/111 (50%), Gaps = 7/111 (6%)
Query: 222 DKVSKIYPLPHMYVVKDLVPDMNNFYAQ-YKSIQPWLQRDKENIGNAQYLQSLDDRKKLD 280
D V + PLP ++ DL + ++ + + ++ W+ DKE + L+ + ++ D
Sbjct: 86 DGVITLMPLPVFKLIGDLSVNTGKWFREMSERVESWIHTDKEFDIHR--LEERMEPEEAD 143
Query: 281 GLYE---CILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTAD 328
+YE CI C CC +C + E ++G L + R+ +D RDE+T +
Sbjct: 144 EIYELDRCIECGCCVAACGTKQMR-EDFVGAVGLNRIARFELDPRDERTDE 193
Score = 41.9 bits (99), Expect = 2e-04
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 155 DGLYE---CILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTAD 203
D +YE CI C CC +C + E ++G L + R+ +D RDE+T +
Sbjct: 143 DEIYELDRCIECGCCVAACGTKQMR-EDFVGAVGLNRIARFELDPRDERTDE 193
Score = 35.7 bits (83), Expect = 0.023
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 99 TFAIYRWNPDKPDEKPTMQEYKVD 122
TF I+R+NP P KP M Y+++
Sbjct: 6 TFNIFRYNPQDPGSKPHMVTYQLE 29
Score = 33.8 bits (78), Expect = 0.091
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 50 TFAIYRWNPDKPDEKPTMQEYK 71
TF I+R+NP P KP M Y+
Sbjct: 6 TFNIFRYNPQDPGSKPHMVTYQ 27
>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 = 39.4 bits (92), Expect = 1e-04
Identities = 14/34 (41%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 159 ECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRW 192
CI C C CPSY NG P LM+A
Sbjct: 1 RCIQCGYCVPVCPSYLLNG---DEPKKLMRAAYN 31
Score = 39.4 bits (92), Expect = 1e-04
Identities = 14/34 (41%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 284 ECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRW 317
CI C C CPSY NG P LM+A
Sbjct: 1 RCIQCGYCVPVCPSYLLNG---DEPKKLMRAAYN 31
Score = 31.0 bits (70), Expect = 0.098
Identities = 8/34 (23%), Positives = 12/34 (35%)
Query: 139 ISNAQYLQSLDDRKKLDGLYECILCACCSTSCPS 172
+ A Y L++ + C C C CP
Sbjct: 25 LMRAAYNGDLEELLANEAADSCSECGLCEYVCPM 58
Score = 31.0 bits (70), Expect = 0.12
Identities = 7/29 (24%), Positives = 10/29 (34%)
Query: 269 YLQSLDDRKKLDGLYECILCACCSTSCPS 297
Y L++ + C C C CP
Sbjct: 30 YNGDLEELLANEAADSCSECGLCEYVCPM 58
>gnl|CDD|221911 pfam13085, Fer2_3, 2Fe-2S iron-sulfur cluster binding domain. The
2Fe-2S ferredoxin family have a general core structure
consisting of beta(2)-alpha-beta(2) which abeta-grasp
type fold. The domain is around one hundred amino acids
with four conserved cysteine residues to which the
2Fe-2S cluster is ligated.
Length = 107
Score = 38.3 bits (90), Expect = 8e-04
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 226 KIYPLPHMYVVKDLVPDMNNFY 247
I PLP V++DLV D + F+
Sbjct: 85 TIEPLPGFPVIRDLVVDRSPFF 106
Score = 31.4 bits (72), Expect = 0.21
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 99 TFAIYRWNPDKPDEKPTMQEYKVDLNNQLNF 129
T I+R++P + D +P QEY+V+ +
Sbjct: 1 TLRIFRYDPPR-DAEPYYQEYEVEYEEGMTV 30
Score = 27.5 bits (62), Expect = 4.6
Identities = 9/22 (40%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 50 TFAIYRWNPDKPDEKPTMQEYK 71
T I+R++P + D +P QEY+
Sbjct: 1 TLRIFRYDPPR-DAEPYYQEYE 21
>gnl|CDD|181515 PRK08640, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 249
Score = 36.1 bits (84), Expect = 0.018
Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 1/97 (1%)
Query: 218 IDANDKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRK 277
ID ++ ++ P+ VV+DL D + + K ++ W+ D + R+
Sbjct: 87 IDQLEQPIRLEPMSTFPVVRDLQVDRSRMFDNLKRVKAWIPIDGTYDLGPGPRMPEEKRQ 146
Query: 278 KLDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQA 314
L +C+ C CC +CP+ ++GPA + Q
Sbjct: 147 WAYELSKCMTCGCCLEACPNV-NEKSDFIGPAAISQV 182
Score = 31.9 bits (73), Expect = 0.36
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 157 LYECILCACCSTSCPSYWWNGEKYLGPAVLMQA 189
L +C+ C CC +CP+ ++GPA + Q
Sbjct: 151 LSKCMTCGCCLEACPNV-NEKSDFIGPAAISQV 182
>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 = 31.4 bits (71), Expect = 0.061
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 156 GLYECILCACCSTSCPSY 173
L +CI C C CP Y
Sbjct: 1 ELSKCIRCGACRAVCPVY 18
Score = 31.4 bits (71), Expect = 0.061
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 281 GLYECILCACCSTSCPSY 298
L +CI C C CP Y
Sbjct: 1 ELSKCIRCGACRAVCPVY 18
Score = 29.9 bits (67), Expect = 0.25
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 138 AISNAQYLQSLDDRKKLDGLYECILCACCSTSCPS 172
+ ++ L+ C C C+ CP
Sbjct: 18 YRALGRFSGDPRGGALAAELWSCTSCGACTEVCPV 52
Score = 29.5 bits (66), Expect = 0.28
Identities = 6/31 (19%), Positives = 10/31 (32%)
Query: 267 AQYLQSLDDRKKLDGLYECILCACCSTSCPS 297
++ L+ C C C+ CP
Sbjct: 22 GRFSGDPRGGALAAELWSCTSCGACTEVCPV 52
>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 = 32.9 bits (75), Expect = 0.14
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 160 CILCACCSTSCPSYWWNGE 178
CI C C CP +W
Sbjct: 205 CIKCGACYVQCPRAFWPEY 223
Score = 32.9 bits (75), Expect = 0.14
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 285 CILCACCSTSCPSYWWNGE 303
CI C C CP +W
Sbjct: 205 CIKCGACYVQCPRAFWPEY 223
>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 = 30.0 bits (67), Expect = 0.20
Identities = 6/32 (18%), Positives = 7/32 (21%)
Query: 140 SNAQYLQSLDDRKKLDGLYECILCACCSTSCP 171
+ CI C C CP
Sbjct: 20 RVGAGAIRDEGGAVEIDPDRCIGCGACVEVCP 51
Score = 30.0 bits (67), Expect = 0.20
Identities = 6/32 (18%), Positives = 7/32 (21%)
Query: 265 GNAQYLQSLDDRKKLDGLYECILCACCSTSCP 296
+ CI C C CP
Sbjct: 20 RVGAGAIRDEGGAVEIDPDRCIGCGACVEVCP 51
>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 = 32.7 bits (75), Expect = 0.25
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 156 GLYECILCACCSTSCPS 172
L +CI C CCS CPS
Sbjct: 400 NLMDCIECGCCSYVCPS 416
Score = 32.7 bits (75), Expect = 0.25
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 281 GLYECILCACCSTSCPS 297
L +CI C CCS CPS
Sbjct: 400 NLMDCIECGCCSYVCPS 416
>gnl|CDD|237086 PRK12386, PRK12386, fumarate reductase iron-sulfur subunit;
Provisional.
Length = 251
Score = 32.0 bits (73), Expect = 0.36
Identities = 25/119 (21%), Positives = 50/119 (42%), Gaps = 7/119 (5%)
Query: 222 DKVSKIYPLPHMYVVKDLVPDMNNFYAQYKSIQPWLQRDKENIGNAQYLQSLDDRKKLDG 281
D+ + P+ V++DLV D++ Y + + I + +++ +Y D ++
Sbjct: 83 DETVTVTPMRTFPVIRDLVTDVSFNYEKAREIPSFTPP--KDLQPGEYRMQQVDVERSQE 140
Query: 282 LYECILCACCSTSC---PSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPF 337
+CI C C C + N + GP LM+ ++ TADR + ++
Sbjct: 141 FRKCIECFLCQNVCHVVRDHEENKPAFAGPRFLMRIAE--LEMHPLDTADRRAEAQEEH 197
>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 = 30.2 bits (68), Expect = 1.9
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 15/57 (26%)
Query: 257 LQRDKENIGNAQYLQSLDDRKKLDGLYECILCACCSTSCPSY-----WWNGEKYLGP 308
L + NI ++ + L CI C C CP Y W G Y GP
Sbjct: 277 LDNGRSNILATEFREVL----------ACIRCGACQNECPVYRHIGGHWYGSIYPGP 323
Score = 29.5 bits (66), Expect = 3.2
Identities = 12/29 (41%), Positives = 12/29 (41%), Gaps = 5/29 (17%)
Query: 160 CILCACCSTSCPSY-----WWNGEKYLGP 183
CI C C CP Y W G Y GP
Sbjct: 295 CIRCGACQNECPVYRHIGGHWYGSIYPGP 323
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 29.9 bits (68), Expect = 2.0
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 157 LYECILCACCSTSCPSY 173
L++CI C C+ CPS
Sbjct: 408 LFDCIECGACAYVCPSN 424
Score = 29.9 bits (68), Expect = 2.0
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 282 LYECILCACCSTSCPSY 298
L++CI C C+ CPS
Sbjct: 408 LFDCIECGACAYVCPSN 424
>gnl|CDD|179457 PRK02651, PRK02651, photosystem I subunit VII; Provisional.
Length = 81
Score = 27.3 bits (60), Expect = 2.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 159 ECILCACCSTSCPSYWWNGEKYLGP 183
+C+ C C T+CP+ + + YLG
Sbjct: 47 DCVGCKRCETACPTDFLSIRVYLGA 71
Score = 27.3 bits (60), Expect = 2.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 284 ECILCACCSTSCPSYWWNGEKYLGP 308
+C+ C C T+CP+ + + YLG
Sbjct: 47 DCVGCKRCETACPTDFLSIRVYLGA 71
>gnl|CDD|224062 COG1139, COG1139, Uncharacterized conserved protein containing a
ferredoxin-like domain [Energy production and
conversion].
Length = 459
Score = 29.2 bits (66), Expect = 3.8
Identities = 11/29 (37%), Positives = 11/29 (37%), Gaps = 5/29 (17%)
Query: 160 CILCACCSTSCPSY-----WWNGEKYLGP 183
CI C C CP Y G Y GP
Sbjct: 310 CIRCGACLNHCPVYRHIGGHAYGSIYPGP 338
Score = 29.2 bits (66), Expect = 3.8
Identities = 11/29 (37%), Positives = 11/29 (37%), Gaps = 5/29 (17%)
Query: 285 CILCACCSTSCPSY-----WWNGEKYLGP 308
CI C C CP Y G Y GP
Sbjct: 310 CIRCGACLNHCPVYRHIGGHAYGSIYPGP 338
>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin),
alpha and beta subunits [Energy production and
conversion].
Length = 317
Score = 28.5 bits (64), Expect = 4.7
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 150 DRKKLDGLYE-CILCACCSTSCPSYWWNGEK 179
D KKL CI C C +CP + GEK
Sbjct: 192 DGKKLKIDGSKCIGCGKCIRACPKAAFRGEK 222
Score = 28.5 bits (64), Expect = 4.7
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 275 DRKKLDGLYE-CILCACCSTSCPSYWWNGEK 304
D KKL CI C C +CP + GEK
Sbjct: 192 DGKKLKIDGSKCIGCGKCIRACPKAAFRGEK 222
>gnl|CDD|223325 COG0247, GlpC, Fe-S oxidoreductase [Energy production and
conversion].
Length = 388
Score = 28.4 bits (63), Expect = 5.7
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 154 LDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWI 193
+ L +C+ C C+ CPSY + L P + R +
Sbjct: 5 FESLDKCVHCGFCTNVCPSY--RATEALSPRGRIVLVREV 42
Score = 28.4 bits (63), Expect = 5.7
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 279 LDGLYECILCACCSTSCPSYWWNGEKYLGPAVLMQAYRWI 318
+ L +C+ C C+ CPSY + L P + R +
Sbjct: 5 FESLDKCVHCGFCTNVCPSY--RATEALSPRGRIVLVREV 42
>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 = 25.6 bits (56), Expect = 6.9
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 159 ECILCACCSTSCPS 172
+C C C CP+
Sbjct: 34 KCTGCGACVAVCPT 47
Score = 25.6 bits (56), Expect = 6.9
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 284 ECILCACCSTSCPS 297
+C C C CP+
Sbjct: 34 KCTGCGACVAVCPT 47
>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 = 26.2 bits (58), Expect = 6.9
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 166 CSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDP 211
C+ CP+ L+ AY + R RL+++KD
Sbjct: 2 CTYMCPTCRCQSAMI-DEDTLVVAYDFRPGGRGRPRYRRLHKVKDN 46
Score = 26.2 bits (58), Expect = 6.9
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 291 CSTSCPSYWWNGEKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDP 336
C+ CP+ L+ AY + R RL+++KD
Sbjct: 2 CTYMCPTCRCQSAMI-DEDTLVVAYDFRPGGRGRPRYRRLHKVKDN 46
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 27.9 bits (62), Expect = 6.9
Identities = 21/89 (23%), Positives = 29/89 (32%), Gaps = 1/89 (1%)
Query: 13 KMSKFSAIGLTAKNIRSFQLSAAASSAVPAEKPAKYKTFAIYRWNPDKPDEKPTMQEYKT 72
+ AK + + + A SA A K A K + K +K K
Sbjct: 212 AKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAA-KAAKKAKKTAKKALKKAAKAVKKA 270
Query: 73 AKNIRSFQLSAAASSAVPAEKPAKYKTFA 101
AK AA +A + AK K A
Sbjct: 271 AKKAAKAAAKAAKGAAKATKGKAKAKKKA 299
>gnl|CDD|183492 PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur
subunit; Provisional.
Length = 180
Score = 27.7 bits (62), Expect = 7.3
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 160 CILCACCSTSCPS 172
CI CA C +CPS
Sbjct: 40 CIGCAACVNACPS 52
Score = 27.7 bits (62), Expect = 7.3
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 285 CILCACCSTSCPS 297
CI CA C +CPS
Sbjct: 40 CIGCAACVNACPS 52
>gnl|CDD|221966 pfam13187, Fer4_9, 4Fe-4S dicluster domain.
Length = 44
Score = 25.3 bits (55), Expect = 7.4
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 158 YECILCACCSTSCP 171
+CI C C CP
Sbjct: 27 VKCIGCGACVEVCP 40
Score = 25.3 bits (55), Expect = 7.4
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 283 YECILCACCSTSCP 296
+CI C C CP
Sbjct: 27 VKCIGCGACVEVCP 40
>gnl|CDD|184390 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Provisional.
Length = 218
Score = 27.5 bits (61), Expect = 8.9
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 171 PSYWWNG----EKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPF 212
P++WW E LG AVL Q ++ E L LK+ F
Sbjct: 21 PAWWWPNALKFEALLG-AVLTQNTKF------EAVEKSLENLKNAF 59
Score = 27.5 bits (61), Expect = 8.9
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 296 PSYWWNG----EKYLGPAVLMQAYRWIIDSRDEKTADRLNQLKDPF 337
P++WW E LG AVL Q ++ E L LK+ F
Sbjct: 21 PAWWWPNALKFEALLG-AVLTQNTKF------EAVEKSLENLKNAF 59
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
0.317 0.131 0.407
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,659,113
Number of extensions: 1499512
Number of successful extensions: 1673
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1643
Number of HSP's successfully gapped: 93
Length of query: 340
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 242
Effective length of database: 6,590,910
Effective search space: 1595000220
Effective search space used: 1595000220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)