Query 022068
Match_columns 303
No_of_seqs 240 out of 1695
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:47:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022068.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022068hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06999 Suc_Fer-like: Sucrase 100.0 7.5E-41 1.6E-45 302.9 19.5 206 79-290 1-230 (230)
2 cd03062 TRX_Fd_Sucrase TRX-lik 99.9 2.5E-24 5.5E-29 170.6 9.0 95 188-290 1-97 (97)
3 COG4759 Uncharacterized protei 99.9 3.6E-22 7.8E-27 182.7 11.1 209 76-298 13-232 (316)
4 cd03063 TRX_Fd_FDH_beta TRX-li 99.7 9.1E-17 2E-21 125.8 8.1 77 190-279 2-81 (92)
5 cd02980 TRX_Fd_family Thioredo 99.7 9.7E-17 2.1E-21 120.9 7.4 76 189-275 1-77 (77)
6 cd03064 TRX_Fd_NuoE TRX-like [ 99.6 4.3E-15 9.3E-20 113.3 7.0 74 188-274 1-79 (80)
7 COG3411 Ferredoxin [Energy pro 99.5 3.4E-15 7.3E-20 107.6 4.0 58 226-290 2-59 (64)
8 cd03081 TRX_Fd_NuoE_FDH_gamma 99.5 1.2E-13 2.6E-18 105.6 6.7 74 188-274 1-79 (80)
9 cd03083 TRX_Fd_NuoE_hoxF TRX-l 99.5 1.1E-13 2.5E-18 105.7 6.5 74 188-274 1-79 (80)
10 PRK07539 NADH dehydrogenase su 99.4 2.6E-13 5.7E-18 116.2 7.5 78 184-274 70-152 (154)
11 PF01257 2Fe-2S_thioredx: Thio 99.4 3.1E-13 6.7E-18 114.6 7.0 80 183-275 60-144 (145)
12 cd03062 TRX_Fd_Sucrase TRX-lik 99.4 9.6E-13 2.1E-17 104.3 7.8 87 89-179 2-90 (97)
13 TIGR01958 nuoE_fam NADH-quinon 99.4 1E-12 2.2E-17 111.8 7.8 78 184-274 64-146 (148)
14 COG3411 Ferredoxin [Energy pro 99.2 1.1E-11 2.4E-16 89.5 3.8 51 130-180 3-53 (64)
15 cd03082 TRX_Fd_NuoE_W_FDH_beta 99.2 3.7E-11 8E-16 90.1 5.3 68 189-273 2-70 (72)
16 PRK05988 formate dehydrogenase 99.2 1.2E-10 2.6E-15 99.9 8.4 79 184-275 71-154 (156)
17 PRK07571 bidirectional hydroge 99.1 1.3E-10 2.8E-15 100.9 7.9 79 184-275 84-167 (169)
18 COG1905 NuoE NADH:ubiquinone o 99.1 2.8E-10 6E-15 97.4 6.5 79 184-275 73-156 (160)
19 cd02980 TRX_Fd_family Thioredo 99.0 6.3E-10 1.4E-14 83.5 6.2 77 89-171 1-77 (77)
20 PRK12373 NADH dehydrogenase su 98.9 2.6E-09 5.7E-14 103.4 7.6 86 184-283 85-176 (400)
21 cd03063 TRX_Fd_FDH_beta TRX-li 98.8 8.8E-09 1.9E-13 80.8 6.2 78 90-175 2-81 (92)
22 cd03064 TRX_Fd_NuoE TRX-like [ 98.8 1E-08 2.2E-13 78.0 5.2 75 88-170 1-79 (80)
23 KOG3196 NADH:ubiquinone oxidor 98.6 3.2E-08 6.9E-13 86.4 5.0 86 185-284 110-200 (233)
24 cd03081 TRX_Fd_NuoE_FDH_gamma 98.4 5.5E-07 1.2E-11 68.7 5.4 74 89-170 2-79 (80)
25 PF01257 2Fe-2S_thioredx: Thio 98.3 9.1E-07 2E-11 75.0 6.0 83 81-171 58-144 (145)
26 cd03083 TRX_Fd_NuoE_hoxF TRX-l 98.2 2.1E-06 4.5E-11 65.5 5.1 74 89-170 2-79 (80)
27 PRK07539 NADH dehydrogenase su 98.2 2.2E-06 4.7E-11 73.4 5.6 81 82-170 68-152 (154)
28 TIGR01958 nuoE_fam NADH-quinon 98.1 4.3E-06 9.3E-11 71.1 5.6 81 82-170 62-146 (148)
29 PF07845 DUF1636: Protein of u 98.0 3E-05 6.6E-10 63.4 8.1 79 191-274 1-85 (116)
30 cd03082 TRX_Fd_NuoE_W_FDH_beta 97.6 5.3E-05 1.2E-09 56.7 3.5 69 89-169 2-70 (72)
31 PF06999 Suc_Fer-like: Sucrase 97.4 0.00065 1.4E-08 61.4 8.6 90 86-179 130-223 (230)
32 COG5469 Predicted metal-bindin 97.4 0.00088 1.9E-08 55.7 8.0 85 185-274 14-105 (143)
33 PRK05988 formate dehydrogenase 97.3 0.00061 1.3E-08 58.6 6.8 82 82-171 69-154 (156)
34 PRK07571 bidirectional hydroge 97.3 0.00074 1.6E-08 58.8 6.5 82 82-171 82-167 (169)
35 COG1905 NuoE NADH:ubiquinone o 96.6 0.0039 8.5E-08 53.7 5.3 80 85-172 74-157 (160)
36 PRK12373 NADH dehydrogenase su 96.3 0.011 2.4E-07 57.8 7.3 81 89-178 91-175 (400)
37 PF07845 DUF1636: Protein of u 95.0 0.069 1.5E-06 43.7 5.9 84 91-174 1-92 (116)
38 PF07293 DUF1450: Protein of u 93.4 0.35 7.5E-06 36.8 6.4 71 188-279 2-75 (78)
39 PRK13669 hypothetical protein; 91.3 0.68 1.5E-05 35.2 5.7 70 188-278 2-74 (78)
40 KOG3196 NADH:ubiquinone oxidor 83.1 2.4 5.1E-05 37.8 5.0 84 84-176 109-196 (233)
41 COG5469 Predicted metal-bindin 80.5 6.5 0.00014 33.0 6.4 86 89-174 18-112 (143)
42 COG4759 Uncharacterized protei 42.4 42 0.00091 31.9 4.6 80 87-170 130-209 (316)
43 PRK09566 nirA ferredoxin-nitri 39.2 82 0.0018 32.1 6.6 78 156-241 363-444 (513)
44 TIGR00853 pts-lac PTS system, 36.3 97 0.0021 24.0 5.2 36 189-232 4-39 (95)
45 cd05565 PTS_IIB_lactose PTS_II 34.3 1E+02 0.0022 24.3 5.1 26 204-231 10-35 (99)
46 PRK10310 PTS system galactitol 33.3 94 0.002 24.0 4.7 23 207-231 16-38 (94)
47 PLN02431 ferredoxin--nitrite r 30.5 1.8E+02 0.004 30.2 7.6 81 154-242 435-519 (587)
48 PRK09567 nirA ferredoxin-nitri 28.6 1.9E+02 0.0042 30.0 7.4 49 189-241 445-497 (593)
49 PF05569 Peptidase_M56: BlaR1 28.2 1E+02 0.0023 28.5 4.9 66 208-281 141-212 (299)
50 TIGR02066 dsrB sulfite reducta 28.0 1.4E+02 0.003 28.8 5.8 82 153-240 68-156 (341)
51 cd05564 PTS_IIB_chitobiose_lic 26.8 1.2E+02 0.0027 23.3 4.4 22 208-231 13-34 (96)
52 cd00248 Mth938-like Mth938-lik 25.9 1.3E+02 0.0028 24.0 4.4 32 190-232 55-87 (109)
53 PRK13504 sulfite reductase sub 25.7 2.7E+02 0.0058 28.8 7.8 52 188-243 428-487 (569)
54 PF09176 Mpt_N: Methylene-tetr 24.7 58 0.0013 24.9 2.0 19 258-276 16-34 (81)
55 COG1062 AdhC Zn-dependent alco 24.7 1.1E+02 0.0023 29.9 4.3 88 188-295 255-347 (366)
56 PRK09590 celB cellobiose phosp 24.5 1.7E+02 0.0036 23.3 4.8 21 208-230 15-35 (104)
57 COG0155 CysI Sulfite reductase 23.2 3.6E+02 0.0079 27.6 8.0 83 188-276 376-480 (510)
No 1
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=100.00 E-value=7.5e-41 Score=302.92 Aligned_cols=206 Identities=42% Similarity=0.720 Sum_probs=165.2
Q ss_pred CCCCCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCC----------CCCCCeEE
Q 022068 79 KLAGTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGG----------EGTDGDVL 148 (303)
Q Consensus 79 pL~GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~----------c~~gp~vl 148 (303)
||+||++.|.+||+|++ ++++|+++.+++. ..+++.|.++++........+..+++..+. ......++
T Consensus 1 pL~Gta~~~~~hvli~~-~~~~W~~~~~~~~-~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 78 (230)
T PF06999_consen 1 PLIGTAPPYDRHVLIET-GPGDWPSDALDSK-SSLPQALSAALKARKKKLGVRFLLIRRPGRISNSSLPEPSRPKPGDVL 78 (230)
T ss_pred CcCcccCcCcEEEEEEc-CCCCCCcchhcCC-cchHHHHHHHHHHhhcccCccccceecCCcccccccccccCCCCceEE
Confidence 79999999999999988 6899999776632 467888888887765554455544444433 23356899
Q ss_pred EecCcEEeccCCCCchhHHHHHHhhCCCC--------------CCCCCCCCCCCcEEEEcCCCCCCCccccccHHHHHHH
Q 022068 149 IFPEMIKYEGLKESDVDSFVDDVLVNGKP--------------WASGVQEGLTGSYVFVCSHGSRDKRCGVCGPALIEKF 214 (303)
Q Consensus 149 V~Pd~i~Y~~v~~~dvd~~v~~~L~~g~p--------------~~~~~~e~~~~~~IlVC~~~~rD~rC~~~G~~l~~~l 214 (303)
|||++++|..+.....+++++.++..... ......+...+++||||+|++||+|||+.|+.|+++|
T Consensus 79 v~p~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iLVCtHg~RD~rCg~~Gp~l~~~l 158 (230)
T PF06999_consen 79 VFPDFKIYRFVTRSNVQEFVEDLLDLDLPAVTALPRQSSAAPDKLPFPREPPDKPLILVCTHGKRDKRCGILGPPLAREL 158 (230)
T ss_pred EEcccEEeccccchhhHHHHHHhccccccccccccCccccccccCCCCcccCCCCEEEEcCCCCcCCchhcccHHHHHHH
Confidence 99999999988888888888765543322 0111223457899999999999999999999999999
Q ss_pred HHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCCCCHHHHHHHHHHCCccccceeeecc
Q 022068 215 NAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERLWRFVL 290 (303)
Q Consensus 215 ~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp~dv~~Iv~~~l~~g~~v~~l~rG~~ 290 (303)
++++.+.++...+ ||++||+|||+||||||+|.. ++.+|+|||+|+|++|+.||++++.+|++++++|||+|
T Consensus 159 ~~~~~~~~l~~~~-V~~iSHiGGHkfAgNvIiy~~---~~p~g~wyGrv~p~~v~~iv~~t~~~g~vi~~~~RG~~ 230 (230)
T PF06999_consen 159 EKELRERGLSRDR-VWEISHIGGHKFAGNVIIYSK---PKPDGIWYGRVTPEDVEGIVDATILDGKVIPELYRGRM 230 (230)
T ss_pred HHHhhhcCCccce-EEEecccccceecCeEEEEec---CCCcEEEEEeeCHHHHHHHHHHHHhCCcCcCccCcCCC
Confidence 9999999987644 999999999999999999920 01159999999999999999998999999999999997
No 2
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=99.91 E-value=2.5e-24 Score=170.58 Aligned_cols=95 Identities=47% Similarity=0.913 Sum_probs=83.6
Q ss_pred CcEEEEcCCCCCCCccccccHHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCC--CCCCCcccEEEeecCC
Q 022068 188 GSYVFVCSHGSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSP--DSEGKIMGHWYGYVTP 265 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p--~~~~~~~g~wYg~Vtp 265 (303)
.++||||+|.+||.||+..|++|+++|++++.++|. ++|.|+.+||+|||.++ |+|+++| + ++||++|+|
T Consensus 1 ~~~ilVCth~rrd~~C~~~g~~l~~~l~~~l~~~~~-~~v~v~~~~clG~c~~g-p~vvvyP~~~------g~wy~~v~p 72 (97)
T cd03062 1 DPLVLVCTHGKRDKRCGICGPPLAAELRAELPEHGP-GGVRVWEVSHVGGHKFA-GNVIIYPKGD------GIWYGRVTP 72 (97)
T ss_pred CCEEEEeCCCCCCcChhhcCHHHHHHHHHHHHHhCC-CceEEEeCCcCCccCcC-CEEEEEeCCC------eeEEeecCH
Confidence 368999999999999999999999999999999984 56999999999655555 5555566 5 899999999
Q ss_pred CCHHHHHHHHHHCCccccceeeecc
Q 022068 266 DDVPAILDQHIAKGEIIERLWRFVL 290 (303)
Q Consensus 266 ~dv~~Iv~~~l~~g~~v~~l~rG~~ 290 (303)
+|+++||++|+.+|++++++.|+.+
T Consensus 73 ~~v~~Iv~~hl~~g~~v~~~~~~~~ 97 (97)
T cd03062 73 EHVPPIVDRLILGGKIIPELRRGGI 97 (97)
T ss_pred HHHHHHHHHHhcCCcCCcccccCCC
Confidence 9999999999999999999998763
No 3
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=3.6e-22 Score=182.67 Aligned_cols=209 Identities=23% Similarity=0.378 Sum_probs=146.5
Q ss_pred cCCCCCCCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCC--C-CeEEEe--
Q 022068 76 YKEKLAGTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGT--D-GDVLIF-- 150 (303)
Q Consensus 76 ~~epL~GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~--g-p~vlV~-- 150 (303)
..|+++||+..++. ||+.|.|.+|+++..++ ..+++.|.+.++..-....+ ..+.+-..+... + ..+++|
T Consensus 13 ~~EDpIGTa~~~~~--ylliE~pqPW~~~~~~s--~~ip~~l~dl~~~~~~~~~~-~~l~i~~d~ey~~~g~tr~~~y~~ 87 (316)
T COG4759 13 NGEDPIGTANTRDG--YLLIEAPQPWTENVLDS--KPIPQNLQDLLEELYKAGGV-IPLAIAPDREYSQPGYTRVLIYRR 87 (316)
T ss_pred cCCCCCCcccccce--EEEEeCCCCcccccccC--CCCChhHHHHHHHHHhcCCc-eeEEEeeccccCCCCceEEEEEec
Confidence 48999999999888 88889999999987764 45555555554432211112 222222222211 2 245555
Q ss_pred cCcEE--ec----cCCCCchhHHHHHHhhCCCCCCCCCCCCCCCcEEEEcCCCCCCCccccccHHHHHHHHHHHHhcCCC
Q 022068 151 PEMIK--YE----GLKESDVDSFVDDVLVNGKPWASGVQEGLTGSYVFVCSHGSRDKRCGVCGPALIEKFNAEIDSRGLK 224 (303)
Q Consensus 151 Pd~i~--Y~----~v~~~dvd~~v~~~L~~g~p~~~~~~e~~~~~~IlVC~~~~rD~rC~~~G~~l~~~l~~~l~~~gl~ 224 (303)
|..+. |. -|+......++...+.+|+....-...+...+.|+||||+++|+||+..|.++++.+++..+...+.
T Consensus 88 ~~~~fa~y~K~E~lv~d~~~~~l~l~l~~~~~~l~~~~~~~~h~RdiLVCTHgn~D~cCarfG~P~Y~~~r~~~a~l~~~ 167 (316)
T COG4759 88 PAKLFAGYSKQEFLVPDAELGVLILALLLQGKELAQFDIYPQHTRDILVCTHGNVDVCCARFGYPFYQQLRAQYADLNLE 167 (316)
T ss_pred HHHhhhhheeeEEecccchhhhhHHHHhcCCccchhhccchhhhceEEEecCCChhhhhhhcCcHHHHHHHHhhhhcccc
Confidence 32211 11 1333444455555566665443223333466789999999999999999999999999999988776
Q ss_pred CcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCCCCHHHHHHHHHHCCccccceeeeccCcccccce
Q 022068 225 DQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERLWRFVLYIFCLHGI 298 (303)
Q Consensus 225 ~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp~dv~~Iv~~~l~~g~~v~~l~rG~~~~~~~~~~ 298 (303)
+++||++||+|||.||..+|.++ +|.+||.++++....||... ..-+-++..+||+.+|+.+-||
T Consensus 168 -~lRvWq~SHfgGHrFAPTlidlP-------~GqyyG~Ld~~~~~~l~~r~-gdvk~L~~~YRGWg~L~~~~QI 232 (316)
T COG4759 168 -NLRVWQSSHFGGHRFAPTLIDLP-------QGQYYGHLDPESLDSLLTRT-GDVKQLKPFYRGWGGLPKFEQI 232 (316)
T ss_pred -ceEEEEecccCccccCchhhcCC-------CCceeeecCHHHHHHHHhcc-CchhhhhhhccCCcCCCHHHHH
Confidence 49999999999999999988886 48999999999999999754 2223488899999999998876
No 4
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=99.68 E-value=9.1e-17 Score=125.83 Aligned_cols=77 Identities=29% Similarity=0.421 Sum_probs=71.4
Q ss_pred EEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeC-CCCCCCccc-EEEeecCCC
Q 022068 190 YVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYS-PDSEGKIMG-HWYGYVTPD 266 (303)
Q Consensus 190 ~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~-p~~~~~~~g-~wYg~Vtp~ 266 (303)
+|+||+++. |..+| .+++++|+++++++|+ +++|.+|||+ |+|+.||+|.+. |+ + +.|++|+|+
T Consensus 2 ~I~Vc~gT~----ciAaGA~~V~~al~~ei~~~gl--~v~v~~tGC~-G~C~~ePlV~V~~p~------g~v~Y~~V~~e 68 (92)
T cd03063 2 RIYVPRDAA----ALALGADEVAEAIEAEAAARGL--AATIVRNGSR-GMYWLEPLVEVETPG------GRVAYGPVTPA 68 (92)
T ss_pred EEEEeCChh----hhhhCHHHHHHHHHHHHHHcCC--eEEEEEecCc-eecCCCCEEEEEeCC------CcEEEEeCCHH
Confidence 699999998 88888 9999999999999999 5999999999 899999999986 76 5 999999999
Q ss_pred CHHHHHHHHHHCC
Q 022068 267 DVPAILDQHIAKG 279 (303)
Q Consensus 267 dv~~Iv~~~l~~g 279 (303)
||++||++|+.+.
T Consensus 69 dv~~Iv~~~~~~~ 81 (92)
T cd03063 69 DVASLLDAGALEG 81 (92)
T ss_pred HHHHHHHHHhhcC
Confidence 9999999998854
No 5
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=99.68 E-value=9.7e-17 Score=120.85 Aligned_cols=76 Identities=33% Similarity=0.670 Sum_probs=71.2
Q ss_pred cEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCCCC
Q 022068 189 SYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTPDD 267 (303)
Q Consensus 189 ~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp~d 267 (303)
.+|+||++++ |..+| ++|+++|+++++..++++.|+|..++|+ |.|..||+|.++|+ +.||++|++++
T Consensus 1 ~~I~VC~~~~----C~~~G~~~l~~~l~~~~~~~~~~~~v~v~~~~Cl-g~C~~~P~v~i~~~------~~~y~~v~~~~ 69 (77)
T cd02980 1 HHILVCTGTA----CGLRGAEELLEALEKELGIRGGDGRVTVERVGCL-GACGLAPVVVVYPD------GVWYGRVTPED 69 (77)
T ss_pred CEEEEccCCC----cccCCHHHHHHHHHHHHhhhcCCCeEEEEEcCCc-CcccCCCEEEEeCC------CeEEccCCHHH
Confidence 4799999998 99997 9999999999999999888999999999 89999999999986 79999999999
Q ss_pred HHHHHHHH
Q 022068 268 VPAILDQH 275 (303)
Q Consensus 268 v~~Iv~~~ 275 (303)
+++||++|
T Consensus 70 ~~~il~~~ 77 (77)
T cd02980 70 VEEIVEEL 77 (77)
T ss_pred HHHHHHhC
Confidence 99999864
No 6
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=99.58 E-value=4.3e-15 Score=113.29 Aligned_cols=74 Identities=22% Similarity=0.421 Sum_probs=67.0
Q ss_pred CcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCC----CCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEee
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGL----KDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGY 262 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl----~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~ 262 (303)
+++|+||+++. |..+| .+++++|++++..+++ ++.|.|..++|+ |.|..||+|.++ +.||++
T Consensus 1 ~~~v~vC~~~~----C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~Cl-G~C~~gP~v~v~--------g~~y~~ 67 (80)
T cd03064 1 KHVIRVCTGTA----CHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECL-GACDLAPVMMIN--------DDVYGR 67 (80)
T ss_pred CEEEEECCCcH----HHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCc-CcCCCCCEEEEC--------CEEECC
Confidence 46899999998 99999 9999999999986633 667999999999 899999999996 799999
Q ss_pred cCCCCHHHHHHH
Q 022068 263 VTPDDVPAILDQ 274 (303)
Q Consensus 263 Vtp~dv~~Iv~~ 274 (303)
|||+++++|+++
T Consensus 68 vt~~~i~~i~~~ 79 (80)
T cd03064 68 LTPEKVDAILEA 79 (80)
T ss_pred CCHHHHHHHHHh
Confidence 999999999975
No 7
>COG3411 Ferredoxin [Energy production and conversion]
Probab=99.55 E-value=3.4e-15 Score=107.62 Aligned_cols=58 Identities=29% Similarity=0.503 Sum_probs=54.2
Q ss_pred cEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCCCCHHHHHHHHHHCCccccceeeecc
Q 022068 226 QIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQHIAKGEIIERLWRFVL 290 (303)
Q Consensus 226 ~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp~dv~~Iv~~~l~~g~~v~~l~rG~~ 290 (303)
.+.+..+||+ |.|..||+++++|+ |+||++|+|+|+++||++|+.+|++++++..++.
T Consensus 2 ~i~~t~tgCl-~~C~~gPvl~vYpe------gvWY~~V~p~~a~rIv~~hl~~Gr~Ve~~~~~~~ 59 (64)
T COG3411 2 SIRVTRTGCL-GVCQDGPVLVVYPE------GVWYTRVDPEDARRIVQSHLLGGRPVEELIYHTG 59 (64)
T ss_pred ceEEeecchh-hhhccCCEEEEecC------CeeEeccCHHHHHHHHHHHHhCCCcchhhcccCC
Confidence 4889999999 89999999999998 8999999999999999999999999999877653
No 8
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=99.46 E-value=1.2e-13 Score=105.60 Aligned_cols=74 Identities=19% Similarity=0.345 Sum_probs=66.9
Q ss_pred CcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHh----cCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEee
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDS----RGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGY 262 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~----~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~ 262 (303)
+++|.||.+.. |..+| .+|+++|+++|.. ...++.+.|..++|+ |.|..||+|++. +.||++
T Consensus 1 ~~~i~vC~~~~----C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~Cl-G~C~~gP~~~v~--------~~~~~~ 67 (80)
T cd03081 1 RHVLKLCRAEA----CQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCL-GLCACSPAAMID--------GEVHGR 67 (80)
T ss_pred CeEEEEcCChH----HHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeec-CccCCCCEEEEC--------CEEECC
Confidence 46899999999 99999 9999999999973 355678999999999 899999999995 799999
Q ss_pred cCCCCHHHHHHH
Q 022068 263 VTPDDVPAILDQ 274 (303)
Q Consensus 263 Vtp~dv~~Iv~~ 274 (303)
|+|++|++|+++
T Consensus 68 ~~~e~i~~il~~ 79 (80)
T cd03081 68 VDPEKFDALLAE 79 (80)
T ss_pred CCHHHHHHHHHc
Confidence 999999999974
No 9
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=99.46 E-value=1.1e-13 Score=105.73 Aligned_cols=74 Identities=14% Similarity=0.172 Sum_probs=66.6
Q ss_pred CcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcC--C--CCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEee
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRG--L--KDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGY 262 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~g--l--~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~ 262 (303)
+++|.||.+.. |..+| .+++++|+++|+.++ + ++.+.+..++|+ |.|+.||+|.++ +.||++
T Consensus 1 ~~~i~vC~~~~----C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gCl-G~C~~~P~v~V~--------~~~y~~ 67 (80)
T cd03083 1 KYRIYLSDSIT----DRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCT-GLCDQGPALLIN--------NRVFTR 67 (80)
T ss_pred CEEEEEcCChH----HHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEecee-cCcCCCCeEEEC--------CEEECC
Confidence 46899999999 99999 999999999997654 4 567999999999 899999999995 799999
Q ss_pred cCCCCHHHHHHH
Q 022068 263 VTPDDVPAILDQ 274 (303)
Q Consensus 263 Vtp~dv~~Iv~~ 274 (303)
|+|+++++||+.
T Consensus 68 v~~~~v~~iv~~ 79 (80)
T cd03083 68 LTPGRIDQIAEL 79 (80)
T ss_pred CCHHHHHHHHhc
Confidence 999999999974
No 10
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=99.43 E-value=2.6e-13 Score=116.17 Aligned_cols=78 Identities=15% Similarity=0.370 Sum_probs=70.1
Q ss_pred CCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHH-hcC---CCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 184 EGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEID-SRG---LKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 184 e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~-~~g---l~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
++..+.+|+||.++. |..+| .+|+++|+++|. +.| .++.+.+..++|+ |.|..||+|.++ +.
T Consensus 70 ~p~gk~~I~VC~g~~----C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~Cl-G~C~~gPvv~V~--------~~ 136 (154)
T PRK07539 70 QPVGRHVIQVCTSTP----CWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECL-GACDNAPVVMIN--------DD 136 (154)
T ss_pred CCCCCEEEEEcCCch----HHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEcccc-CccCCCCEEEEC--------CE
Confidence 356688999999998 99999 999999999998 555 3677999999999 899999999998 68
Q ss_pred EEeecCCCCHHHHHHH
Q 022068 259 WYGYVTPDDVPAILDQ 274 (303)
Q Consensus 259 wYg~Vtp~dv~~Iv~~ 274 (303)
||++||++++++||++
T Consensus 137 ~y~~vt~e~v~~il~~ 152 (154)
T PRK07539 137 TYEDLTPEKIDELLDE 152 (154)
T ss_pred EeCCCCHHHHHHHHHh
Confidence 9999999999999976
No 11
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=99.42 E-value=3.1e-13 Score=114.59 Aligned_cols=80 Identities=25% Similarity=0.482 Sum_probs=69.2
Q ss_pred CCCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHH----hcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCccc
Q 022068 183 QEGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEID----SRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMG 257 (303)
Q Consensus 183 ~e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~----~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g 257 (303)
.++..+.+|+||++.. |..+| .+|+++|+++|. +...++.+.|..++|+ |+|..||+|.|. +
T Consensus 60 ~~p~gk~~I~VC~g~~----C~~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~Cl-G~C~~aP~v~V~--------~ 126 (145)
T PF01257_consen 60 LEPKGKHHIRVCTGTS----CHLRGAEELLEALEEELGIKPGETTEDGKFTLEETGCL-GACDQAPVVMVD--------G 126 (145)
T ss_dssp SSS--SEEEEEE-SHH----HHTTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSS-SSGGGSSEEEEC--------C
T ss_pred cCCCCCcEEEeCCCch----HHhCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCc-cccCCCCEEEEC--------C
Confidence 3456788999999998 99999 999999999995 3456788999999999 899999999996 7
Q ss_pred EEEeecCCCCHHHHHHHH
Q 022068 258 HWYGYVTPDDVPAILDQH 275 (303)
Q Consensus 258 ~wYg~Vtp~dv~~Iv~~~ 275 (303)
.||++|||+++.+||++.
T Consensus 127 ~~y~~vt~e~v~~il~~l 144 (145)
T PF01257_consen 127 EWYGNVTPEKVDEILEEL 144 (145)
T ss_dssp CEEESSSCCHHHHHHHHH
T ss_pred EEECCCCHHHHHHHHHhc
Confidence 899999999999999863
No 12
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=99.39 E-value=9.6e-13 Score=104.27 Aligned_cols=87 Identities=24% Similarity=0.360 Sum_probs=73.4
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEec--CcEEeccCCCCchhH
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIFP--EMIKYEGLKESDVDS 166 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~P--d~i~Y~~v~~~dvd~ 166 (303)
.|||||+....+ .+|...+ ..+.++|++++.+++. ..+++..+.|+|.|..+|+++||| |++||..++++|+++
T Consensus 2 ~~ilVCth~rrd--~~C~~~g-~~l~~~l~~~l~~~~~-~~v~v~~~~clG~c~~gp~vvvyP~~~g~wy~~v~p~~v~~ 77 (97)
T cd03062 2 PLVLVCTHGKRD--KRCGICG-PPLAAELRAELPEHGP-GGVRVWEVSHVGGHKFAGNVIIYPKGDGIWYGRVTPEHVPP 77 (97)
T ss_pred CEEEEeCCCCCC--cChhhcC-HHHHHHHHHHHHHhCC-CceEEEeCCcCCccCcCCEEEEEeCCCeeEEeecCHHHHHH
Confidence 599999865433 4666554 5788999999988763 357888899999999999999999 999999999999999
Q ss_pred HHHHHhhCCCCCC
Q 022068 167 FVDDVLVNGKPWA 179 (303)
Q Consensus 167 ~v~~~L~~g~p~~ 179 (303)
||++|+.++.++.
T Consensus 78 Iv~~hl~~g~~v~ 90 (97)
T cd03062 78 IVDRLILGGKIIP 90 (97)
T ss_pred HHHHHhcCCcCCc
Confidence 9999999887763
No 13
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=99.38 E-value=1e-12 Score=111.83 Aligned_cols=78 Identities=15% Similarity=0.395 Sum_probs=69.5
Q ss_pred CCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhc----CCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 184 EGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSR----GLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 184 e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~----gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
++..+.+|+||+++. |..+| .+|+++|+++|... ..|+.+.+..++|+ |.|..||+|.++ +.
T Consensus 64 ~p~gk~~I~VC~g~~----C~~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~Cl-G~C~~aP~v~V~--------~~ 130 (148)
T TIGR01958 64 EPVGRYHLQVCTNVP----CALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECL-GACGNAPVMMIN--------DD 130 (148)
T ss_pred CCCCCEEEEEcCCch----hhhcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCcc-CccCCCCEEEEC--------CE
Confidence 356678999999998 99999 99999999999854 23667999999999 899999999998 57
Q ss_pred EEeecCCCCHHHHHHH
Q 022068 259 WYGYVTPDDVPAILDQ 274 (303)
Q Consensus 259 wYg~Vtp~dv~~Iv~~ 274 (303)
||++|||+++++||++
T Consensus 131 ~y~~vt~e~v~~il~~ 146 (148)
T TIGR01958 131 YYEFLTPEKLDELLER 146 (148)
T ss_pred EeCCCCHHHHHHHHHh
Confidence 9999999999999975
No 14
>COG3411 Ferredoxin [Energy production and conversion]
Probab=99.21 E-value=1.1e-11 Score=89.46 Aligned_cols=51 Identities=22% Similarity=0.391 Sum_probs=47.6
Q ss_pred ceeeeeccCCCCCCCCeEEEecCcEEeccCCCCchhHHHHHHhhCCCCCCC
Q 022068 130 VKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDVDSFVDDVLVNGKPWAS 180 (303)
Q Consensus 130 v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dvd~~v~~~L~~g~p~~~ 180 (303)
++++.++|++.|..||+++||||++||.+++++|+++||++||++|.+++.
T Consensus 3 i~~t~tgCl~~C~~gPvl~vYpegvWY~~V~p~~a~rIv~~hl~~Gr~Ve~ 53 (64)
T COG3411 3 IRVTRTGCLGVCQDGPVLVVYPEGVWYTRVDPEDARRIVQSHLLGGRPVEE 53 (64)
T ss_pred eEEeecchhhhhccCCEEEEecCCeeEeccCHHHHHHHHHHHHhCCCcchh
Confidence 567889999999999999999999999999999999999999999988743
No 15
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=99.17 E-value=3.7e-11 Score=90.13 Aligned_cols=68 Identities=21% Similarity=0.272 Sum_probs=62.1
Q ss_pred cEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCCCC
Q 022068 189 SYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTPDD 267 (303)
Q Consensus 189 ~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp~d 267 (303)
.+|.||.+.. |..+| .+|+++|+++|... .+.+..++|+ |.|..||+|+++ +..|+++|+++
T Consensus 2 ~~I~vC~~~~----C~~~Ga~~l~~~l~~~L~~~----~v~l~~~~Cl-G~C~~gP~v~V~--------~~~~~~~t~~~ 64 (72)
T cd03082 2 LTVRVCDSLS----CAMAGAEELLAALEAGLGPE----GVRVVRAPCV-GRCERAPAALVG--------QRPVDGATPAA 64 (72)
T ss_pred eEEEEcCChH----HHHCCHHHHHHHHHHHhCCC----eEEEEecCcC-CccCCCCeEEEC--------CEEeCCcCHHH
Confidence 5799999999 99999 99999999998542 5999999999 899999999998 67999999999
Q ss_pred HHHHHH
Q 022068 268 VPAILD 273 (303)
Q Consensus 268 v~~Iv~ 273 (303)
++++++
T Consensus 65 i~~~~~ 70 (72)
T cd03082 65 VAAAVE 70 (72)
T ss_pred HHHHHh
Confidence 999886
No 16
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=99.15 E-value=1.2e-10 Score=99.90 Aligned_cols=79 Identities=16% Similarity=0.285 Sum_probs=70.7
Q ss_pred CCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHH----hcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 184 EGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEID----SRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 184 e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~----~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
++..+++|.||++.. |..+| .+|+++|+++|. +...|+.+.+..+.|+ |.|..||+|.++ +.
T Consensus 71 ~p~Gk~~I~VC~~~~----C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~Cl-G~C~~aP~~~in--------~~ 137 (156)
T PRK05988 71 HPPGRHVLKLCRAEA----CQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCL-GLCACSPAAMLD--------GE 137 (156)
T ss_pred CCCCCEEEEEeCCch----hhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeec-CccCCCCeEEEC--------CE
Confidence 456788999999999 99999 999999999987 3345778999999999 899999999997 78
Q ss_pred EEeecCCCCHHHHHHHH
Q 022068 259 WYGYVTPDDVPAILDQH 275 (303)
Q Consensus 259 wYg~Vtp~dv~~Iv~~~ 275 (303)
.|++||++++++|+++.
T Consensus 138 ~~~~lt~~~~~~il~~~ 154 (156)
T PRK05988 138 VHGRLDPQRLDALLAEA 154 (156)
T ss_pred EeCCCCHHHHHHHHHHh
Confidence 99999999999999864
No 17
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=99.14 E-value=1.3e-10 Score=100.86 Aligned_cols=79 Identities=19% Similarity=0.312 Sum_probs=71.0
Q ss_pred CCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHH----hcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 184 EGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEID----SRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 184 e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~----~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
++..+++|.||.+.. |..+| ..|+++|+++|. +...|+.+.+..+.|+ |.|..||+|.++ +.
T Consensus 84 ~P~Gk~~I~VC~g~a----C~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~Cl-G~C~~AP~~~Vn--------~~ 150 (169)
T PRK07571 84 KPSGEHTCVVCTGTA----CYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCL-GACGIAPAVVFD--------GK 150 (169)
T ss_pred CCCCCEEEEEcCChH----HHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEeccc-CccCCCCeEEEC--------CE
Confidence 356788999999999 99999 999999999997 3345778999999999 899999999998 78
Q ss_pred EEeecCCCCHHHHHHHH
Q 022068 259 WYGYVTPDDVPAILDQH 275 (303)
Q Consensus 259 wYg~Vtp~dv~~Iv~~~ 275 (303)
.|++||++++++||+++
T Consensus 151 ~~~~lt~e~v~~il~~~ 167 (169)
T PRK07571 151 VAGKQTPESVLEKVQGW 167 (169)
T ss_pred EeCCCCHHHHHHHHHHH
Confidence 99999999999999875
No 18
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=99.06 E-value=2.8e-10 Score=97.41 Aligned_cols=79 Identities=18% Similarity=0.410 Sum_probs=71.6
Q ss_pred CCCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHH----hcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 184 EGLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEID----SRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 184 e~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~----~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
.+..+++|-||++.. |..+| .+|++.|++.|. +-.-|+.+.+.++.|+ |.|..+|+|+|+ +.
T Consensus 73 ~P~Gr~~i~VC~~t~----C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~Cl-GaC~~AP~vmin--------d~ 139 (160)
T COG1905 73 KPVGRHHIRVCTGTA----CHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECL-GACGQAPVVMIN--------DD 139 (160)
T ss_pred CcCCCeEEEEeCCcH----HhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeee-cccccCCEEEEC--------Cc
Confidence 466789999999999 99999 999999999998 4445788999999999 899999999998 67
Q ss_pred EEeecCCCCHHHHHHHH
Q 022068 259 WYGYVTPDDVPAILDQH 275 (303)
Q Consensus 259 wYg~Vtp~dv~~Iv~~~ 275 (303)
.|+++|||.+.+||++.
T Consensus 140 ~~~~lt~e~l~eil~~~ 156 (160)
T COG1905 140 VYGRLTPEKLEEILEKL 156 (160)
T ss_pred hhccCCHHHHHHHHHHH
Confidence 89999999999999875
No 19
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=99.02 E-value=6.3e-10 Score=83.54 Aligned_cols=77 Identities=22% Similarity=0.392 Sum_probs=66.6
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCchhHHH
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDVDSFV 168 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dvd~~v 168 (303)
.||+||+.. .|...++..+.++|+++++..+.+..+++..+.|.|.|..+|.|+|+|++.||.+++++++++|+
T Consensus 1 ~~I~VC~~~------~C~~~G~~~l~~~l~~~~~~~~~~~~v~v~~~~Clg~C~~~P~v~i~~~~~~y~~v~~~~~~~il 74 (77)
T cd02980 1 HHILVCTGT------ACGLRGAEELLEALEKELGIRGGDGRVTVERVGCLGACGLAPVVVVYPDGVWYGRVTPEDVEEIV 74 (77)
T ss_pred CEEEEccCC------CcccCCHHHHHHHHHHHHhhhcCCCeEEEEEcCCcCcccCCCEEEEeCCCeEEccCCHHHHHHHH
Confidence 379999842 45566678899999999988877667888999999999999999999999999999999999999
Q ss_pred HHH
Q 022068 169 DDV 171 (303)
Q Consensus 169 ~~~ 171 (303)
++|
T Consensus 75 ~~~ 77 (77)
T cd02980 75 EEL 77 (77)
T ss_pred HhC
Confidence 864
No 20
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=98.91 E-value=2.6e-09 Score=103.37 Aligned_cols=86 Identities=17% Similarity=0.327 Sum_probs=74.6
Q ss_pred CCCCC-cEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhc----CCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCccc
Q 022068 184 EGLTG-SYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSR----GLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMG 257 (303)
Q Consensus 184 e~~~~-~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~----gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g 257 (303)
++..+ .+|.||++.. |..+| ..|++.|+++|.-. .-|+.+.+..+.|| |.|..+|+|.|+ +
T Consensus 85 ~P~Gk~~~I~VC~~t~----C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCL-GaC~~APv~~In--------d 151 (400)
T PRK12373 85 QPVGTRAHIQVCGTTP----CMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECL-GACVNAPMVQIG--------K 151 (400)
T ss_pred cCCCCceEEEEcCChH----HHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeec-CccCCCCeEEEC--------C
Confidence 35665 7999999999 99999 99999999998743 24677999999999 899999999998 6
Q ss_pred EEEeecCCCCHHHHHHHHHHCCcccc
Q 022068 258 HWYGYVTPDDVPAILDQHIAKGEIIE 283 (303)
Q Consensus 258 ~wYg~Vtp~dv~~Iv~~~l~~g~~v~ 283 (303)
.+|++||++++.+||++ +..|+++.
T Consensus 152 ~~y~~LTpe~v~~IL~~-l~ag~~~~ 176 (400)
T PRK12373 152 DYYEDLTPERLEEIIDA-FAAGKGPV 176 (400)
T ss_pred EEeCCCCHHHHHHHHHH-HhCCCCCC
Confidence 89999999999999987 57777653
No 21
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=98.81 E-value=8.8e-09 Score=80.79 Aligned_cols=78 Identities=15% Similarity=0.156 Sum_probs=67.1
Q ss_pred EEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEe-cCc-EEeccCCCCchhHH
Q 022068 90 HVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIF-PEM-IKYEGLKESDVDSF 167 (303)
Q Consensus 90 HVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~-Pd~-i~Y~~v~~~dvd~~ 167 (303)
+|+||.. + .|.+.++..+.++|.+++++++. .+.+..++|.|.|..+|.|.|+ |++ +.|.+++++|+++|
T Consensus 2 ~I~Vc~g--T----~ciAaGA~~V~~al~~ei~~~gl--~v~v~~tGC~G~C~~ePlV~V~~p~g~v~Y~~V~~edv~~I 73 (92)
T cd03063 2 RIYVPRD--A----AALALGADEVAEAIEAEAAARGL--AATIVRNGSRGMYWLEPLVEVETPGGRVAYGPVTPADVASL 73 (92)
T ss_pred EEEEeCC--h----hhhhhCHHHHHHHHHHHHHHcCC--eEEEEEecCceecCCCCEEEEEeCCCcEEEEeCCHHHHHHH
Confidence 5788863 2 34567788899999999999886 4778889999999999999997 999 99999999999999
Q ss_pred HHHHhhCC
Q 022068 168 VDDVLVNG 175 (303)
Q Consensus 168 v~~~L~~g 175 (303)
+++|+.+.
T Consensus 74 v~~~~~~~ 81 (92)
T cd03063 74 LDAGALEG 81 (92)
T ss_pred HHHHhhcC
Confidence 99998754
No 22
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=98.77 E-value=1e-08 Score=77.97 Aligned_cols=75 Identities=16% Similarity=0.170 Sum_probs=61.1
Q ss_pred CeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccC----CCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCc
Q 022068 88 GRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKD----DMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESD 163 (303)
Q Consensus 88 ~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~----~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~d 163 (303)
++||+||... .|...++..+.++|.++++.+.. +..+.+..++|+|.|..+|.|+|+ ++||.++++++
T Consensus 1 ~~~v~vC~~~------~C~~~Ga~~~~~~l~~~l~~~~~~~~~~~~v~v~~t~ClG~C~~gP~v~v~--g~~y~~vt~~~ 72 (80)
T cd03064 1 KHVIRVCTGT------ACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMIN--DDVYGRLTPEK 72 (80)
T ss_pred CEEEEECCCc------HHHhCCHHHHHHHHHHHhCCCCCCcCCCCEEEEEEecCcCcCCCCCEEEEC--CEEECCCCHHH
Confidence 4689999842 56677788899999988865432 334677889999999999999994 89999999999
Q ss_pred hhHHHHH
Q 022068 164 VDSFVDD 170 (303)
Q Consensus 164 vd~~v~~ 170 (303)
+++|+++
T Consensus 73 i~~i~~~ 79 (80)
T cd03064 73 VDAILEA 79 (80)
T ss_pred HHHHHHh
Confidence 9999875
No 23
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=98.64 E-value=3.2e-08 Score=86.39 Aligned_cols=86 Identities=17% Similarity=0.347 Sum_probs=73.0
Q ss_pred CCCCcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhc-C---CCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEE
Q 022068 185 GLTGSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSR-G---LKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHW 259 (303)
Q Consensus 185 ~~~~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~-g---l~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~w 259 (303)
+..++||.||+.+- |-.+| +.+.++.++.+.-. | -+....|.++.|+ |.|..||+|.++ +.+
T Consensus 110 p~gKy~v~VC~ttp----C~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~eCl-GaCvnaPmi~IN--------D~y 176 (233)
T KOG3196|consen 110 PVGKYHVQVCTTTP----CMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVECL-GACVNAPMIAIN--------DDY 176 (233)
T ss_pred CCCCceEEEecCcH----HhhhccHHHHHHHHHHhCccccccccccceeeecchhh-hhhccCceeeec--------chh
Confidence 46789999999999 99999 89999999887642 2 2456889999999 899999999998 579
Q ss_pred EeecCCCCHHHHHHHHHHCCccccc
Q 022068 260 YGYVTPDDVPAILDQHIAKGEIIER 284 (303)
Q Consensus 260 Yg~Vtp~dv~~Iv~~~l~~g~~v~~ 284 (303)
|+.+|++++.+|+++ |.+|+....
T Consensus 177 yedlt~k~l~eIle~-L~~~k~pp~ 200 (233)
T KOG3196|consen 177 YEDLTPKKLVEILED-LKAGKKPPA 200 (233)
T ss_pred hccCCHHHHHHHHHH-HhcCCCCCC
Confidence 999999999999987 677775443
No 24
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=98.39 E-value=5.5e-07 Score=68.72 Aligned_cols=74 Identities=15% Similarity=0.164 Sum_probs=59.0
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhc----cCCCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCch
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTR----KDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDV 164 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r----~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dv 164 (303)
++|.||.+. .|...++..+.++|.+++... ..+..+.+..+.|+|.|+.+|.++| ++.||.+++++++
T Consensus 2 ~~i~vC~~~------~C~~~G~~~ll~~l~~~l~~~~g~~~~dg~~~l~~~~ClG~C~~gP~~~v--~~~~~~~~~~e~i 73 (80)
T cd03081 2 HVLKLCRAE------ACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMI--DGEVHGRVDPEKF 73 (80)
T ss_pred eEEEEcCCh------HHHhCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEeeecCccCCCCEEEE--CCEEECCCCHHHH
Confidence 578899742 455667788889998888633 2334467788999999999999987 9999999999999
Q ss_pred hHHHHH
Q 022068 165 DSFVDD 170 (303)
Q Consensus 165 d~~v~~ 170 (303)
++|+++
T Consensus 74 ~~il~~ 79 (80)
T cd03081 74 DALLAE 79 (80)
T ss_pred HHHHHc
Confidence 999874
No 25
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=98.33 E-value=9.1e-07 Score=75.02 Aligned_cols=83 Identities=16% Similarity=0.185 Sum_probs=63.2
Q ss_pred CCCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHh----ccCCCCceeeeeccCCCCCCCCeEEEecCcEEe
Q 022068 81 AGTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKT----RKDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKY 156 (303)
Q Consensus 81 ~GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~----r~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y 156 (303)
.-+.|..++||+||.+. .|...|+..+.+.|++++.- ...+..+.+..+.|+|.|+.+|.|+| ++.||
T Consensus 58 f~~~p~gk~~I~VC~g~------~C~~~Ga~~l~~~l~~~l~i~~g~~~~dg~~~l~~~~ClG~C~~aP~v~V--~~~~y 129 (145)
T PF01257_consen 58 FRLEPKGKHHIRVCTGT------SCHLRGAEELLEALEEELGIKPGETTEDGKFTLEETGCLGACDQAPVVMV--DGEWY 129 (145)
T ss_dssp S-SSS--SEEEEEE-SH------HHHTTTHHHHHHHHHHHHCTSCCCCSTTTTEEEEEESSSSSGGGSSEEEE--CCCEE
T ss_pred cccCCCCCcEEEeCCCc------hHHhCCCHHHHHHHHHHhCCcccccCCCceEEEEECCCccccCCCCEEEE--CCEEE
Confidence 33556667899999842 55667778888999888842 22344567788999999999999999 88899
Q ss_pred ccCCCCchhHHHHHH
Q 022068 157 EGLKESDVDSFVDDV 171 (303)
Q Consensus 157 ~~v~~~dvd~~v~~~ 171 (303)
.+++++++++|++++
T Consensus 130 ~~vt~e~v~~il~~l 144 (145)
T PF01257_consen 130 GNVTPEKVDEILEEL 144 (145)
T ss_dssp ESSSCCHHHHHHHHH
T ss_pred CCCCHHHHHHHHHhc
Confidence 999999999999863
No 26
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=98.22 E-value=2.1e-06 Score=65.53 Aligned_cols=74 Identities=18% Similarity=0.180 Sum_probs=58.2
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccC----CCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCch
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKD----DMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDV 164 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~----~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dv 164 (303)
++|.||... .|...++..+.++|++++..+.. +..+++..++|.|.|..+|.+.| ++.+|.+++++++
T Consensus 2 ~~i~vC~~~------~C~~~Ga~~v~~~l~~~l~~~~~~~t~d~~v~l~~~gClG~C~~~P~v~V--~~~~y~~v~~~~v 73 (80)
T cd03083 2 YRIYLSDSI------TDRMNGYKAVLDALCRELGIRFGEVDEDGMVGLFFTSCTGLCDQGPALLI--NNRVFTRLTPGRI 73 (80)
T ss_pred EEEEEcCCh------HHHhCCHHHHHHHHHHHHCCCCCCcCCCCeEEEEEeceecCcCCCCeEEE--CCEEECCCCHHHH
Confidence 578899742 33456778899999999865542 22356677899999999999999 6789999999999
Q ss_pred hHHHHH
Q 022068 165 DSFVDD 170 (303)
Q Consensus 165 d~~v~~ 170 (303)
++|++.
T Consensus 74 ~~iv~~ 79 (80)
T cd03083 74 DQIAEL 79 (80)
T ss_pred HHHHhc
Confidence 999874
No 27
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=98.21 E-value=2.2e-06 Score=73.43 Aligned_cols=81 Identities=17% Similarity=0.158 Sum_probs=63.2
Q ss_pred CCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHH-hccC---CCCceeeeeccCCCCCCCCeEEEecCcEEec
Q 022068 82 GTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALK-TRKD---DMTVKSLMTVCGGGEGTDGDVLIFPEMIKYE 157 (303)
Q Consensus 82 GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik-~r~~---~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~ 157 (303)
.+.|..++||+||.+. .|...|+..+.++|.+++. +.+. +..+.+..+.|+|.|+.+|.++|. +.||.
T Consensus 68 ~~~p~gk~~I~VC~g~------~C~~~Ga~~l~~~l~~~L~i~~g~tt~dg~~~l~~~~ClG~C~~gPvv~V~--~~~y~ 139 (154)
T PRK07539 68 FRQPVGRHVIQVCTST------PCWLRGGEAILAALKKKLGIKPGETTADGRFTLLEVECLGACDNAPVVMIN--DDTYE 139 (154)
T ss_pred CcCCCCCEEEEEcCCc------hHHHCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEEccccCccCCCCEEEEC--CEEeC
Confidence 3456667889999742 4566677889999998886 3332 333566778999999999999997 46999
Q ss_pred cCCCCchhHHHHH
Q 022068 158 GLKESDVDSFVDD 170 (303)
Q Consensus 158 ~v~~~dvd~~v~~ 170 (303)
+++++++++|+++
T Consensus 140 ~vt~e~v~~il~~ 152 (154)
T PRK07539 140 DLTPEKIDELLDE 152 (154)
T ss_pred CCCHHHHHHHHHh
Confidence 9999999999876
No 28
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=98.12 E-value=4.3e-06 Score=71.14 Aligned_cols=81 Identities=20% Similarity=0.224 Sum_probs=63.0
Q ss_pred CCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccC----CCCceeeeeccCCCCCCCCeEEEecCcEEec
Q 022068 82 GTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKD----DMTVKSLMTVCGGGEGTDGDVLIFPEMIKYE 157 (303)
Q Consensus 82 GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~----~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~ 157 (303)
.+.|..++||+||.+. .|...|+..+.++|++++..... +..+.+..+.|.|.|+.+|.++|.+ .||.
T Consensus 62 ~~~p~gk~~I~VC~g~------~C~~~Ga~~v~~~l~~~L~i~~g~~t~dg~~~l~~~~ClG~C~~aP~v~V~~--~~y~ 133 (148)
T TIGR01958 62 DTEPVGRYHLQVCTNV------PCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGACGNAPVMMIND--DYYE 133 (148)
T ss_pred CcCCCCCEEEEEcCCc------hhhhcCHHHHHHHHHHHhCCCCCCCCCCCeEEEEEcCccCccCCCCEEEECC--EEeC
Confidence 3455557889999742 35566778889999988864422 3345677789999999999999984 6999
Q ss_pred cCCCCchhHHHHH
Q 022068 158 GLKESDVDSFVDD 170 (303)
Q Consensus 158 ~v~~~dvd~~v~~ 170 (303)
+++++++++++++
T Consensus 134 ~vt~e~v~~il~~ 146 (148)
T TIGR01958 134 FLTPEKLDELLER 146 (148)
T ss_pred CCCHHHHHHHHHh
Confidence 9999999999875
No 29
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=98.00 E-value=3e-05 Score=63.37 Aligned_cols=79 Identities=23% Similarity=0.395 Sum_probs=63.3
Q ss_pred EEEcCCCCCCC----ccccc-cHHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccEEEeecCC
Q 022068 191 VFVCSHGSRDK----RCGVC-GPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGHWYGYVTP 265 (303)
Q Consensus 191 IlVC~~~~rD~----rC~~~-G~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~wYg~Vtp 265 (303)
|+||+. +|.. .-+.. |..|+++|++.++..++...|+|..+.|| .-|..+-.|.+.-.++ ..+.||.++|
T Consensus 1 l~VC~t-Cr~~~~~~~~~~~~G~~L~~aL~~~~~~~~~~~~v~v~~v~CL-~~C~r~CtVA~~~~gK---~tYlfGdl~p 75 (116)
T PF07845_consen 1 LFVCTT-CRRSGEDPEDGPRPGAALLDALRAALADAPLPDGVEVRPVECL-SACDRPCTVALQAPGK---WTYLFGDLDP 75 (116)
T ss_pred CEEeCC-CCCCCCCCCCCCChHHHHHHHHHHHHhcCCCCCceEEEeccHH-hcCCCceEEEEEcCCC---cEEEEecCCc
Confidence 588884 3332 33334 48999999999998888888999999999 8999999998874432 4689999999
Q ss_pred -CCHHHHHHH
Q 022068 266 -DDVPAILDQ 274 (303)
Q Consensus 266 -~dv~~Iv~~ 274 (303)
++++.|++.
T Consensus 76 ~~~a~~il~~ 85 (116)
T PF07845_consen 76 DEDAEDILAF 85 (116)
T ss_pred ccCHHHHHHH
Confidence 999999974
No 30
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=97.63 E-value=5.3e-05 Score=56.72 Aligned_cols=69 Identities=17% Similarity=0.206 Sum_probs=53.9
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCchhHHH
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDVDSFV 168 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dvd~~v 168 (303)
++|.||.+. .|...++..+.++|++++... .+.+..+.|+|.|+.+|.++|+.+ .|.+++++++++++
T Consensus 2 ~~I~vC~~~------~C~~~Ga~~l~~~l~~~L~~~----~v~l~~~~ClG~C~~gP~v~V~~~--~~~~~t~~~i~~~~ 69 (72)
T cd03082 2 LTVRVCDSL------SCAMAGAEELLAALEAGLGPE----GVRVVRAPCVGRCERAPAALVGQR--PVDGATPAAVAAAV 69 (72)
T ss_pred eEEEEcCCh------HHHHCCHHHHHHHHHHHhCCC----eEEEEecCcCCccCCCCeEEECCE--EeCCcCHHHHHHHH
Confidence 578899743 445567777888888777432 467788999999999999999754 68899999999887
Q ss_pred H
Q 022068 169 D 169 (303)
Q Consensus 169 ~ 169 (303)
+
T Consensus 70 ~ 70 (72)
T cd03082 70 E 70 (72)
T ss_pred h
Confidence 6
No 31
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=97.43 E-value=0.00065 Score=61.43 Aligned_cols=90 Identities=24% Similarity=0.370 Sum_probs=64.5
Q ss_pred CCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEe----cCcEEeccCCC
Q 022068 86 PYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIF----PEMIKYEGLKE 161 (303)
Q Consensus 86 ~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~----Pd~i~Y~~v~~ 161 (303)
..+.+||||+-+.-|- +|... +..|.++|.+.+..++..... +-.+.-.|.+.=.++|++| |+++||.+|++
T Consensus 130 ~~~~~iLVCtHg~RD~--rCg~~-Gp~l~~~l~~~~~~~~l~~~~-V~~iSHiGGHkfAgNvIiy~~~~p~g~wyGrv~p 205 (230)
T PF06999_consen 130 PDKPLILVCTHGKRDK--RCGIL-GPPLARELEKELRERGLSRDR-VWEISHIGGHKFAGNVIIYSKPKPDGIWYGRVTP 205 (230)
T ss_pred CCCCEEEEcCCCCcCC--chhcc-cHHHHHHHHHHhhhcCCccce-EEEecccccceecCeEEEEecCCCcEEEEEeeCH
Confidence 3577899998543332 55543 356778888888777654322 4334444555557899999 99999999999
Q ss_pred CchhHHHHHHhhCCCCCC
Q 022068 162 SDVDSFVDDVLVNGKPWA 179 (303)
Q Consensus 162 ~dvd~~v~~~L~~g~p~~ 179 (303)
++++.||+..+.+|+.+.
T Consensus 206 ~~v~~iv~~t~~~g~vi~ 223 (230)
T PF06999_consen 206 EDVEGIVDATILDGKVIP 223 (230)
T ss_pred HHHHHHHHHHHhCCcCcC
Confidence 999999999777877653
No 32
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=97.38 E-value=0.00088 Score=55.67 Aligned_cols=85 Identities=21% Similarity=0.431 Sum_probs=65.3
Q ss_pred CCCCcEEEEcCCCCCCC-----ccccc-cHHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCCCCCCcccE
Q 022068 185 GLTGSYVFVCSHGSRDK-----RCGVC-GPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPDSEGKIMGH 258 (303)
Q Consensus 185 ~~~~~~IlVC~~~~rD~-----rC~~~-G~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~~~~~~~g~ 258 (303)
...++.+|||.. +||. +=+-. |..|++.|.+...+..+...+.|..++|+ ..|..|-+|.+.-+++ ..+
T Consensus 14 ~~~~htlfVCks-C~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~~~~~e~~I~~VeCl-~~C~r~c~vA~~~~~k---~sY 88 (143)
T COG5469 14 GMPKHTLFVCKS-CRDVSQEGKENGPSDGSILLDKLQELAQEWEIAHEFEIQTVECL-AACNRGCVVAFSGPGK---PSY 88 (143)
T ss_pred ccCceEEEEecc-ccccccCCccCCCCcHHHHHHHHHHHHhhhhhhccceeeeeHhh-hhcCCCeEEEEecCCC---ceE
Confidence 456789999994 4442 22233 37889999877777777777899999999 8999999998864422 268
Q ss_pred EEeecCCCC-HHHHHHH
Q 022068 259 WYGYVTPDD-VPAILDQ 274 (303)
Q Consensus 259 wYg~Vtp~d-v~~Iv~~ 274 (303)
.||.++|+| +..||+-
T Consensus 89 LFgdL~p~d~a~dLl~~ 105 (143)
T COG5469 89 LFGDLTPDDSASDLLEF 105 (143)
T ss_pred EEccCCccccHHHHHHH
Confidence 999999999 8888874
No 33
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=97.33 E-value=0.00061 Score=58.56 Aligned_cols=82 Identities=17% Similarity=0.129 Sum_probs=61.7
Q ss_pred CCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhcc----CCCCceeeeeccCCCCCCCCeEEEecCcEEec
Q 022068 82 GTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRK----DDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYE 157 (303)
Q Consensus 82 GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~----~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~ 157 (303)
.+-|..+++|.||.+. .|...|+..+.+.|.+++.-.. .+....+..+.|.|.|+.+|.++| ++..|.
T Consensus 69 ~~~p~Gk~~I~VC~~~------~C~~~G~~~ll~~l~~~Lgi~~gett~Dg~ftL~~~~ClG~C~~aP~~~i--n~~~~~ 140 (156)
T PRK05988 69 RTHPPGRHVLKLCRAE------ACQAMGGDALAAHAKARLGIDFHQTTADGAVTLEPVYCLGLCACSPAAML--DGEVHG 140 (156)
T ss_pred CCCCCCCEEEEEeCCc------hhhcCCHHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEE--CCEEeC
Confidence 3445667789999742 4455677888888888875322 223345667899999999999988 778899
Q ss_pred cCCCCchhHHHHHH
Q 022068 158 GLKESDVDSFVDDV 171 (303)
Q Consensus 158 ~v~~~dvd~~v~~~ 171 (303)
++++++++++++.+
T Consensus 141 ~lt~~~~~~il~~~ 154 (156)
T PRK05988 141 RLDPQRLDALLAEA 154 (156)
T ss_pred CCCHHHHHHHHHHh
Confidence 99999999998864
No 34
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=97.26 E-value=0.00074 Score=58.79 Aligned_cols=82 Identities=13% Similarity=0.084 Sum_probs=62.0
Q ss_pred CCccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhc----cCCCCceeeeeccCCCCCCCCeEEEecCcEEec
Q 022068 82 GTVNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTR----KDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYE 157 (303)
Q Consensus 82 GTa~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r----~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~ 157 (303)
-+.|..+++|.||.+. .|...|+..+.+.|.+++.-. ..+....+....|.|.|+.+|.++| ++..|.
T Consensus 82 ~~~P~Gk~~I~VC~g~------aC~~~G~~~ll~~l~~~Lgi~~gett~DG~ftL~~~~ClG~C~~AP~~~V--n~~~~~ 153 (169)
T PRK07571 82 SLKPSGEHTCVVCTGT------ACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVF--DGKVAG 153 (169)
T ss_pred CcCCCCCEEEEEcCCh------HHHHCCcHHHHHHHHHHhCCCCCCcCCCCeEEEEEecccCccCCCCeEEE--CCEEeC
Confidence 3445567788899742 445567788888888887522 2233355677899999999999998 677899
Q ss_pred cCCCCchhHHHHHH
Q 022068 158 GLKESDVDSFVDDV 171 (303)
Q Consensus 158 ~v~~~dvd~~v~~~ 171 (303)
+++++++++|++++
T Consensus 154 ~lt~e~v~~il~~~ 167 (169)
T PRK07571 154 KQTPESVLEKVQGW 167 (169)
T ss_pred CCCHHHHHHHHHHH
Confidence 99999999999876
No 35
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=96.60 E-value=0.0039 Score=53.69 Aligned_cols=80 Identities=18% Similarity=0.202 Sum_probs=58.5
Q ss_pred cCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhc----cCCCCceeeeeccCCCCCCCCeEEEecCcEEeccCC
Q 022068 85 NPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTR----KDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLK 160 (303)
Q Consensus 85 ~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r----~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~ 160 (303)
|.-++||-||++. .|...|++.+.+.|.+.+.-. ..+....+.-+.|+|.|+.+|.|.|. +-.|.+++
T Consensus 74 P~Gr~~i~VC~~t------~C~l~Gs~~l~~~l~~~lgi~~gett~DG~ftl~~v~ClGaC~~AP~vmin--d~~~~~lt 145 (160)
T COG1905 74 PVGRHHIRVCTGT------ACHLKGSEALLKALEKKLGIKPGETTADGKFTLEPVECLGACGQAPVVMIN--DDVYGRLT 145 (160)
T ss_pred cCCCeEEEEeCCc------HHhhcChHHHHHHHHHHhCCCCCCcCCCCeEEEeeeeeecccccCCEEEEC--CchhccCC
Confidence 3346889999742 345567778888888877522 22334455668999999999999884 55678899
Q ss_pred CCchhHHHHHHh
Q 022068 161 ESDVDSFVDDVL 172 (303)
Q Consensus 161 ~~dvd~~v~~~L 172 (303)
++.+++|++.+.
T Consensus 146 ~e~l~eil~~~~ 157 (160)
T COG1905 146 PEKLEEILEKLK 157 (160)
T ss_pred HHHHHHHHHHHh
Confidence 999999999764
No 36
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=96.33 E-value=0.011 Score=57.82 Aligned_cols=81 Identities=20% Similarity=0.203 Sum_probs=60.3
Q ss_pred eEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccC----CCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCch
Q 022068 89 RHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKD----DMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDV 164 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~----~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dv 164 (303)
.||.||.+. .|...|+..+.+.|.+.|.-... +....+....|+|.|..+|.++| +...|.+++++++
T Consensus 91 ~~I~VC~~t------~C~l~Ga~~ll~~le~~Lgik~GeTT~DG~FTLe~veCLGaC~~APv~~I--nd~~y~~LTpe~v 162 (400)
T PRK12373 91 AHIQVCGTT------PCMLRGSEALMAVCKSKIHAHPHELNADGTLSWEEVECLGACVNAPMVQI--GKDYYEDLTPERL 162 (400)
T ss_pred eEEEEcCCh------HHHhCChHHHHHHHHHHhCCCCCCcCCCCeEEEEeeeecCccCCCCeEEE--CCEEeCCCCHHHH
Confidence 589999743 34556777888888888754322 22345566889999999999999 5668999999999
Q ss_pred hHHHHHHhhCCCCC
Q 022068 165 DSFVDDVLVNGKPW 178 (303)
Q Consensus 165 d~~v~~~L~~g~p~ 178 (303)
++|++.+ ..|.+.
T Consensus 163 ~~IL~~l-~ag~~~ 175 (400)
T PRK12373 163 EEIIDAF-AAGKGP 175 (400)
T ss_pred HHHHHHH-hCCCCC
Confidence 9999985 455543
No 37
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=94.97 E-value=0.069 Score=43.70 Aligned_cols=84 Identities=13% Similarity=0.052 Sum_probs=54.6
Q ss_pred EEEEeeCCCCc-ccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEecCcEE---eccCCC-Cchh
Q 022068 91 VFLCFKGPEMW-VARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIFPEMIK---YEGLKE-SDVD 165 (303)
Q Consensus 91 VfLc~~~p~~W-p~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~---Y~~v~~-~dvd 165 (303)
||||++....| ...-....+..|.+.|.++++.......+++.-..|+..|..+.+|-+-=.++| |..+++ ++++
T Consensus 1 l~VC~tCr~~~~~~~~~~~~G~~L~~aL~~~~~~~~~~~~v~v~~v~CL~~C~r~CtVA~~~~gK~tYlfGdl~p~~~a~ 80 (116)
T PF07845_consen 1 LFVCTTCRRSGEDPEDGPRPGAALLDALRAALADAPLPDGVEVRPVECLSACDRPCTVALQAPGKWTYLFGDLDPDEDAE 80 (116)
T ss_pred CEEeCCCCCCCCCCCCCCChHHHHHHHHHHHHhcCCCCCceEEEeccHHhcCCCceEEEEEcCCCcEEEEecCCcccCHH
Confidence 58998765543 221122233456777777776666555688888999999998877776644444 557777 7777
Q ss_pred HHHH---HHhhC
Q 022068 166 SFVD---DVLVN 174 (303)
Q Consensus 166 ~~v~---~~L~~ 174 (303)
+|++ .|...
T Consensus 81 ~il~~a~~Y~~s 92 (116)
T PF07845_consen 81 DILAFAALYAAS 92 (116)
T ss_pred HHHHHHHHHHhC
Confidence 7765 45544
No 38
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=93.37 E-value=0.35 Score=36.83 Aligned_cols=71 Identities=15% Similarity=0.216 Sum_probs=48.1
Q ss_pred CcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCCCCcEEEEEeccCC--CCCCCCceeEeCCCCCCCcccEEEeecC
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGLKDQIFVKPCSHIG--GHKYAGNLIVYSPDSEGKIMGHWYGYVT 264 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl~~~v~v~~~sclG--G~c~agpvv~v~p~~~~~~~g~wYg~Vt 264 (303)
++.|-+|.+.- ..| ..+++.|++ +.++.|.+.||+| |.|...|-.+|+ |.+-.--|
T Consensus 2 ~piVefC~~Nl------~~g~~~~~~~Le~-------~p~~~Vie~gCl~~Cg~C~~~pFAlVn--------G~~V~A~t 60 (78)
T PF07293_consen 2 NPIVEFCVSNL------ASGTDQVYEKLEK-------DPDIDVIEYGCLSYCGPCAKKPFALVN--------GEIVAAET 60 (78)
T ss_pred CceEEEcccCc------hhhhHHHHHHHhc-------CCCccEEEcChhhhCcCCCCCccEEEC--------CEEEecCC
Confidence 35688899764 567 777877764 1347899999993 445678888887 66666666
Q ss_pred CCCHHHHHHHHHHCC
Q 022068 265 PDDVPAILDQHIAKG 279 (303)
Q Consensus 265 p~dv~~Iv~~~l~~g 279 (303)
++++-+-|.++|.+.
T Consensus 61 ~eeL~~kI~~~i~e~ 75 (78)
T PF07293_consen 61 AEELLEKIKEKIEEN 75 (78)
T ss_pred HHHHHHHHHHHHhcc
Confidence 666655555665443
No 39
>PRK13669 hypothetical protein; Provisional
Probab=91.31 E-value=0.68 Score=35.21 Aligned_cols=70 Identities=20% Similarity=0.283 Sum_probs=45.5
Q ss_pred CcEEEEcCCCCCCCcccccc-HHHHHHHHHHHHhcCCCCcEEEEEeccCC--CCCCCCceeEeCCCCCCCcccEEEeecC
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-PALIEKFNAEIDSRGLKDQIFVKPCSHIG--GHKYAGNLIVYSPDSEGKIMGHWYGYVT 264 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-~~l~~~l~~~l~~~gl~~~v~v~~~sclG--G~c~agpvv~v~p~~~~~~~g~wYg~Vt 264 (303)
++.|=+|.+.. ..| +.+++.|++ ++++.|.+.||++ |.|..+|-.+|. |.+-..-|
T Consensus 2 ~piVEfC~sNl------~~G~~~~~~~Le~-------dP~~dVie~gCls~CG~C~~~~FAlVn--------g~~V~a~t 60 (78)
T PRK13669 2 NPIVEFCVSNL------ASGSQAAFEKLEK-------DPNLDVLEYGCLGYCGICSEGLFALVN--------GEVVEGET 60 (78)
T ss_pred Cceeeehhcch------hhhHHHHHHHHHh-------CCCceEEEcchhhhCcCcccCceEEEC--------CeEeecCC
Confidence 35678899874 667 666665632 3457899999983 456788989997 55555555
Q ss_pred CCCHHHHHHHHHHC
Q 022068 265 PDDVPAILDQHIAK 278 (303)
Q Consensus 265 p~dv~~Iv~~~l~~ 278 (303)
+|+.-+-|.++|..
T Consensus 61 ~eeL~~kI~~~i~e 74 (78)
T PRK13669 61 PEELVENIYAHLEE 74 (78)
T ss_pred HHHHHHHHHHHHhh
Confidence 55554444455544
No 40
>KOG3196 consensus NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion]
Probab=83.11 E-value=2.4 Score=37.78 Aligned_cols=84 Identities=18% Similarity=0.154 Sum_probs=51.2
Q ss_pred ccCCCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCC----CceeeeeccCCCCCCCCeEEEecCcEEeccC
Q 022068 84 VNPYGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDM----TVKSLMTVCGGGEGTDGDVLIFPEMIKYEGL 159 (303)
Q Consensus 84 a~~y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~----~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v 159 (303)
.+.-+-||-||++ || |...+++...+...+.+.....+. .-.+.-..|+|.|-.+|.+-|- | -.|..+
T Consensus 109 ~p~gKy~v~VC~t----tp--C~lrg~d~i~ea~~k~lgi~~Gett~d~~Ftl~e~eClGaCvnaPmi~IN-D-~yyedl 180 (233)
T KOG3196|consen 109 KPVGKYHVQVCTT----TP--CMLRGSDDILEACKKQLGIKVGETTKDGLFTLEEVECLGACVNAPMIAIN-D-DYYEDL 180 (233)
T ss_pred cCCCCceEEEecC----cH--HhhhccHHHHHHHHHHhCccccccccccceeeecchhhhhhccCceeeec-c-hhhccC
Confidence 3444678999974 32 222334444444444442211111 1234557899999999988774 3 368889
Q ss_pred CCCchhHHHHHHhhCCC
Q 022068 160 KESDVDSFVDDVLVNGK 176 (303)
Q Consensus 160 ~~~dvd~~v~~~L~~g~ 176 (303)
++.++.+|+++ |.+++
T Consensus 181 t~k~l~eIle~-L~~~k 196 (233)
T KOG3196|consen 181 TPKKLVEILED-LKAGK 196 (233)
T ss_pred CHHHHHHHHHH-HhcCC
Confidence 99999999987 55443
No 41
>COG5469 Predicted metal-binding protein [Function unknown]
Probab=80.52 E-value=6.5 Score=33.01 Aligned_cols=86 Identities=14% Similarity=0.120 Sum_probs=48.3
Q ss_pred eEEEEEeeCCCCcccccc--cccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEe-cCcEE--eccCCCCc
Q 022068 89 RHVFLCFKGPEMWVARVE--ASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIF-PEMIK--YEGLKESD 163 (303)
Q Consensus 89 rHVfLc~~~p~~Wp~~~e--~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~-Pd~i~--Y~~v~~~d 163 (303)
+-+|||......|...-+ ..+...|.+.|.++-..........++-..|+..|..+.+|.+- |+..- |..++++|
T Consensus 18 htlfVCksC~~~~~~~~~~~p~~G~~Ll~kl~~l~qe~~~~~e~~I~~VeCl~~C~r~c~vA~~~~~k~sYLFgdL~p~d 97 (143)
T COG5469 18 HTLFVCKSCRDVSQEGKENGPSDGSILLDKLQELAQEWEIAHEFEIQTVECLAACNRGCVVAFSGPGKPSYLFGDLTPDD 97 (143)
T ss_pred eEEEEeccccccccCCccCCCCcHHHHHHHHHHHHhhhhhhccceeeeeHhhhhcCCCeEEEEecCCCceEEEccCCccc
Confidence 448999876777754222 22233455555544444443344567778899999976544333 55432 44666665
Q ss_pred -hhHHH---HHHhhC
Q 022068 164 -VDSFV---DDVLVN 174 (303)
Q Consensus 164 -vd~~v---~~~L~~ 174 (303)
..+++ +.|..+
T Consensus 98 ~a~dLl~~a~ly~~~ 112 (143)
T COG5469 98 SASDLLEFAQLYANS 112 (143)
T ss_pred cHHHHHHHHHHhhhc
Confidence 44544 445543
No 42
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=42.43 E-value=42 Score=31.90 Aligned_cols=80 Identities=14% Similarity=0.169 Sum_probs=51.4
Q ss_pred CCeEEEEEeeCCCCcccccccccCCcHHHHHHHHHHhccCCCCceeeeeccCCCCCCCCeEEEecCcEEeccCCCCchhH
Q 022068 87 YGRHVFLCFKGPEMWVARVEASDTDTLPKLLASALKTRKDDMTVKSLMTVCGGGEGTDGDVLIFPEMIKYEGLKESDVDS 166 (303)
Q Consensus 87 y~rHVfLc~~~p~~Wp~~~e~~~s~~L~~~L~~~Ik~r~~~~~v~~~~t~c~g~c~~gp~vlV~Pd~i~Y~~v~~~dvd~ 166 (303)
+.|-++||+-+ .--+.|..- +-++++.++..++...++ .+|+=...=.|...=.|+++-+|.+..|..++++.++.
T Consensus 130 h~RdiLVCTHg--n~D~cCarf-G~P~Y~~~r~~~a~l~~~-~lRvWq~SHfgGHrFAPTlidlP~GqyyG~Ld~~~~~~ 205 (316)
T COG4759 130 HTRDILVCTHG--NVDVCCARF-GYPFYQQLRAQYADLNLE-NLRVWQSSHFGGHRFAPTLIDLPQGQYYGHLDPESLDS 205 (316)
T ss_pred hhceEEEecCC--Chhhhhhhc-CcHHHHHHHHhhhhcccc-ceEEEEecccCccccCchhhcCCCCceeeecCHHHHHH
Confidence 45678999833 223345443 357888888888766543 23331111123334489999999999999888887777
Q ss_pred HHHH
Q 022068 167 FVDD 170 (303)
Q Consensus 167 ~v~~ 170 (303)
|+..
T Consensus 206 l~~r 209 (316)
T COG4759 206 LLTR 209 (316)
T ss_pred HHhc
Confidence 7653
No 43
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=39.21 E-value=82 Score=32.06 Aligned_cols=78 Identities=10% Similarity=0.169 Sum_probs=41.7
Q ss_pred eccCCCCchhHHHHHHhhCCCCCCCCCCCCCCCcEEEEcCCCCCCCcccccc---HHHHHHHHHHHHh-cCCCCcEEEEE
Q 022068 156 YEGLKESDVDSFVDDVLVNGKPWASGVQEGLTGSYVFVCSHGSRDKRCGVCG---PALIEKFNAEIDS-RGLKDQIFVKP 231 (303)
Q Consensus 156 Y~~v~~~dvd~~v~~~L~~g~p~~~~~~e~~~~~~IlVC~~~~rD~rC~~~G---~~l~~~l~~~l~~-~gl~~~v~v~~ 231 (303)
+..++.++++++.++.+..+.+..++ .....+.-|++.. .|...- ..+..+|.++|.+ .+++..+.|.-
T Consensus 363 l~~i~~~~v~~l~~~~~~~~~~~~~~----~~~~~~vaC~G~~---~C~~a~~dT~~~a~~l~~~l~~~~~lp~~~kI~i 435 (513)
T PRK09566 363 IPNIPDENLETFLAEPLLQKFSLEPG----PLARGLVSCTGNQ---YCNFALIETKNRALALAKELDAELDLPQPVRIHW 435 (513)
T ss_pred EeCCCHHHHHHHHHHHhhccCCCCCC----ccccCceeCcCcc---cccccHhhHHHHHHHHHHHHHHhcCCCCceEEEE
Confidence 34455555666555533333222111 1234678898763 365432 4445555555543 36666788888
Q ss_pred eccCCCCCCC
Q 022068 232 CSHIGGHKYA 241 (303)
Q Consensus 232 ~sclGG~c~a 241 (303)
+||- -.|..
T Consensus 436 SGCp-n~C~~ 444 (513)
T PRK09566 436 TGCP-NSCGQ 444 (513)
T ss_pred ECCh-hhhhc
Confidence 8887 56654
No 44
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=36.34 E-value=97 Score=24.03 Aligned_cols=36 Identities=14% Similarity=0.342 Sum_probs=23.3
Q ss_pred cEEEEcCCCCCCCccccccHHHHHHHHHHHHhcCCCCcEEEEEe
Q 022068 189 SYVFVCSHGSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPC 232 (303)
Q Consensus 189 ~~IlVC~~~~rD~rC~~~G~~l~~~l~~~l~~~gl~~~v~v~~~ 232 (303)
.+|++|+++ |..-..+.+.+++.++++|++ ++|..+
T Consensus 4 ~~ILl~C~~------G~sSS~l~~k~~~~~~~~gi~--~~v~a~ 39 (95)
T TIGR00853 4 TNILLLCAA------GMSTSLLVNKMNKAAEEYGVP--VKIAAG 39 (95)
T ss_pred cEEEEECCC------chhHHHHHHHHHHHHHHCCCc--EEEEEe
Confidence 455555544 222246789999999999997 455543
No 45
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=34.29 E-value=1e+02 Score=24.30 Aligned_cols=26 Identities=19% Similarity=0.258 Sum_probs=19.7
Q ss_pred ccccHHHHHHHHHHHHhcCCCCcEEEEE
Q 022068 204 GVCGPALIEKFNAEIDSRGLKDQIFVKP 231 (303)
Q Consensus 204 ~~~G~~l~~~l~~~l~~~gl~~~v~v~~ 231 (303)
|..-.-+.+.+++.++++|++ ++|..
T Consensus 10 GaSSs~la~km~~~a~~~gi~--~~i~a 35 (99)
T cd05565 10 GGTSGLLANALNKGAKERGVP--LEAAA 35 (99)
T ss_pred CCCHHHHHHHHHHHHHHCCCc--EEEEE
Confidence 434478899999999999997 55554
No 46
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=33.35 E-value=94 Score=24.00 Aligned_cols=23 Identities=9% Similarity=0.082 Sum_probs=17.7
Q ss_pred cHHHHHHHHHHHHhcCCCCcEEEEE
Q 022068 207 GPALIEKFNAEIDSRGLKDQIFVKP 231 (303)
Q Consensus 207 G~~l~~~l~~~l~~~gl~~~v~v~~ 231 (303)
...+...+++.++++|++ ++|..
T Consensus 16 S~m~~~ki~~~l~~~gi~--~~v~~ 38 (94)
T PRK10310 16 STMAAEEIKELCQSHNIP--VELIQ 38 (94)
T ss_pred HHHHHHHHHHHHHHCCCe--EEEEE
Confidence 366689999999999986 55554
No 47
>PLN02431 ferredoxin--nitrite reductase
Probab=30.49 E-value=1.8e+02 Score=30.23 Aligned_cols=81 Identities=15% Similarity=0.123 Sum_probs=43.4
Q ss_pred EEeccCCCCchhHHHHHHhhCCCCCCCCCCCCCCCcEEEEcCCCCCCCcccccc---HHHHHHHHHHHHh-cCCCCcEEE
Q 022068 154 IKYEGLKESDVDSFVDDVLVNGKPWASGVQEGLTGSYVFVCSHGSRDKRCGVCG---PALIEKFNAEIDS-RGLKDQIFV 229 (303)
Q Consensus 154 i~Y~~v~~~dvd~~v~~~L~~g~p~~~~~~e~~~~~~IlVC~~~~rD~rC~~~G---~~l~~~l~~~l~~-~gl~~~v~v 229 (303)
+.+..++.+++++++++.+..+....+ ......|..|++.. -|...- ..+..+|.+++.+ ..++..+.|
T Consensus 435 i~i~~V~~~~v~~l~~~l~~~g~~~~~----~~~~r~vvACtG~~---~C~~ai~eTk~~A~~L~~~l~~~~~lp~k~kI 507 (587)
T PLN02431 435 IIIPNVPNSKVEALLAEPLLQRFSPNP----GLLLKGLVACTGNQ---FCGQAIIETKARALKVTEELERLVEVPRPVRM 507 (587)
T ss_pred EEECCCCHHHHHHHHHHHHhcCCCCCC----CCCccceeECCCcc---ccCccHHHHHHHHHHHHHHHHHhhcCCCCeEE
Confidence 344455555666665543332221111 12234688998753 255432 4555566655543 356666788
Q ss_pred EEeccCCCCCCCC
Q 022068 230 KPCSHIGGHKYAG 242 (303)
Q Consensus 230 ~~~sclGG~c~ag 242 (303)
.-+||- -.|...
T Consensus 508 ~vSGCp-n~C~~~ 519 (587)
T PLN02431 508 HWTGCP-NSCGQV 519 (587)
T ss_pred EEECCc-cccccc
Confidence 888887 566543
No 48
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=28.61 E-value=1.9e+02 Score=30.02 Aligned_cols=49 Identities=8% Similarity=0.123 Sum_probs=30.3
Q ss_pred cEEEEcCCCCCCCcccccc---HHHHHHHHHHHHhc-CCCCcEEEEEeccCCCCCCC
Q 022068 189 SYVFVCSHGSRDKRCGVCG---PALIEKFNAEIDSR-GLKDQIFVKPCSHIGGHKYA 241 (303)
Q Consensus 189 ~~IlVC~~~~rD~rC~~~G---~~l~~~l~~~l~~~-gl~~~v~v~~~sclGG~c~a 241 (303)
..+..|++.. -|.... ..+..+|.+.|.++ +++..+.|.-+||- -.|..
T Consensus 445 ~~~vAC~G~~---~C~~a~~dT~~~a~~l~~~l~~~~~l~~~ikI~vSGCp-n~Ca~ 497 (593)
T PRK09567 445 AGLVACTGNA---GCKFAAADTKGHALAIADYCEPRVALDQPVNIHLTGCH-HSCAQ 497 (593)
T ss_pred eccEecCCCC---CCCccHhhHHHHHHHHHHHHHHhcCCCCCcEEEEECCC-ccccc
Confidence 3578899763 265442 45555555555443 56666888888887 55653
No 49
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=28.24 E-value=1e+02 Score=28.55 Aligned_cols=66 Identities=21% Similarity=0.286 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCC---ceeEeCCCCCCCcccEEEeecCCCCHHHHHHH---HHHCCcc
Q 022068 208 PALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAG---NLIVYSPDSEGKIMGHWYGYVTPDDVPAILDQ---HIAKGEI 281 (303)
Q Consensus 208 ~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~ag---pvv~v~p~~~~~~~g~wYg~Vtp~dv~~Iv~~---~l~~g~~ 281 (303)
..+.+.+++...+.|+..++.+..+..+-..+-.| |.|+++ .......++++.+.|+.. |+.++..
T Consensus 141 ~~~~~~l~~~~~~~~~~~~~~i~~s~~i~sP~~~G~~~p~I~lP--------~~~~~~~~~~el~~il~HEl~Hikr~D~ 212 (299)
T PF05569_consen 141 EELQALLEECKEELGIKRPIRIRVSSGISSPFVFGFLRPVIVLP--------ESLLEDLSEEELRAILLHELAHIKRRDL 212 (299)
T ss_pred HHHHHHHHHHHHHhCCCCceEEEEcCCCCCCeeecCcceEEEec--------CccccccCHHHHHHHHHHHHHHHHCCCh
Confidence 45666777777777887788888777665566566 788887 234568899999988874 6656554
No 50
>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit. This model describes the beta subunit of sulfite reductase.
Probab=27.97 E-value=1.4e+02 Score=28.84 Aligned_cols=82 Identities=10% Similarity=0.147 Sum_probs=47.1
Q ss_pred cEEeccCCCCchhHHHHHHhhCCCCCCCCCCCCCCCcEEEEcCCCCCCCcccccc---HHH----HHHHHHHHHhcCCCC
Q 022068 153 MIKYEGLKESDVDSFVDDVLVNGKPWASGVQEGLTGSYVFVCSHGSRDKRCGVCG---PAL----IEKFNAEIDSRGLKD 225 (303)
Q Consensus 153 ~i~Y~~v~~~dvd~~v~~~L~~g~p~~~~~~e~~~~~~IlVC~~~~rD~rC~~~G---~~l----~~~l~~~l~~~gl~~ 225 (303)
++.+..++.+|++++.++....|.... +.+ ..-+..|.-|.+.. .|...+ .++ .++|.+.+...+++.
T Consensus 68 nI~l~~I~~edl~~i~~~L~~~Gl~~~-~~G-~~vrrni~aC~G~~---~C~~a~~dt~~l~~~l~~~l~~~~~~~~lP~ 142 (341)
T TIGR02066 68 NVEFLVSDESKIQPLIDELEEVGFPVG-GTG-DAVKGNIVHTQGWL---HCHIPAIDASGIVKAVMDELYEYFTDHKLPA 142 (341)
T ss_pred CEEEecCCHHHHHHHHHHHHhccCCCC-CCC-CccccccccCcCCC---CCCcchhchHHHHHHHHHHHHHHHhcccccc
Confidence 345667899999999887554454321 111 11222477888763 264443 333 445555555556776
Q ss_pred cEEEEEeccCCCCCC
Q 022068 226 QIFVKPCSHIGGHKY 240 (303)
Q Consensus 226 ~v~v~~~sclGG~c~ 240 (303)
.+.|.-+||- -.|.
T Consensus 143 KfKI~vSGC~-~~C~ 156 (341)
T TIGR02066 143 MVRISLSCCA-NMCG 156 (341)
T ss_pred cceecccccc-cccc
Confidence 6777766765 4443
No 51
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=26.77 E-value=1.2e+02 Score=23.35 Aligned_cols=22 Identities=18% Similarity=0.450 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEE
Q 022068 208 PALIEKFNAEIDSRGLKDQIFVKP 231 (303)
Q Consensus 208 ~~l~~~l~~~l~~~gl~~~v~v~~ 231 (303)
..+.+.+++.++++|++ ++|..
T Consensus 13 S~~~~ki~~~~~~~~~~--~~v~~ 34 (96)
T cd05564 13 SILVKKMKKAAEKRGID--AEIEA 34 (96)
T ss_pred HHHHHHHHHHHHHCCCc--eEEEE
Confidence 46788999999999987 44444
No 52
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=25.92 E-value=1.3e+02 Score=23.95 Aligned_cols=32 Identities=13% Similarity=0.132 Sum_probs=18.0
Q ss_pred EEEEcCCCCCCCccccc-cHHHHHHHHHHHHhcCCCCcEEEEEe
Q 022068 190 YVFVCSHGSRDKRCGVC-GPALIEKFNAEIDSRGLKDQIFVKPC 232 (303)
Q Consensus 190 ~IlVC~~~~rD~rC~~~-G~~l~~~l~~~l~~~gl~~~v~v~~~ 232 (303)
.|++.|+.+ ... -+++.++| .++|+. +++..|
T Consensus 55 iliiGTG~~-----~~~~~~~~~~~l----~~~gI~--vE~m~T 87 (109)
T cd00248 55 ILLIGTGAE-----IAFLPRALRAAL----RAAGIG--VEVMST 87 (109)
T ss_pred EEEEcCCCC-----CCcCCHHHHHHH----HHcCCe--EEEeCc
Confidence 788998775 222 25555444 456654 455443
No 53
>PRK13504 sulfite reductase subunit beta; Provisional
Probab=25.74 E-value=2.7e+02 Score=28.78 Aligned_cols=52 Identities=17% Similarity=0.349 Sum_probs=34.4
Q ss_pred CcEEEEcCCCCCCCcccccc-------HHHHHHHHHHHHhcCC-CCcEEEEEeccCCCCCCCCc
Q 022068 188 GSYVFVCSHGSRDKRCGVCG-------PALIEKFNAEIDSRGL-KDQIFVKPCSHIGGHKYAGN 243 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G-------~~l~~~l~~~l~~~gl-~~~v~v~~~sclGG~c~agp 243 (303)
...+.-|++.. -|...- ..|.++|++.+...++ +..+.|.-+||- -.|...-
T Consensus 428 ~~~ivAC~G~~---~C~~a~~~t~~~a~~l~~~l~~~~~~~~l~~~~i~I~vSGCp-n~Ca~~~ 487 (569)
T PRK13504 428 RRNSMACVALP---TCGLAMAEAERYLPSFIDRIEALLAKHGLSDEHIVIRMTGCP-NGCARPY 487 (569)
T ss_pred eeceeecCCcc---cccchhhhHHHHHHHHHHHHHHHHhhcCCCCCceEEEEeCCc-ccccccc
Confidence 45678898753 264432 2466667776666677 567888888998 7776543
No 54
>PF09176 Mpt_N: Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; InterPro: IPR015259 Prokaryotic methylene-tetrahydromethanopterin dehydrogenase catalyses the dehydrogenation of methylene-tetrahydromethanopterin during growth on one-carbon compounds such as methanol. It can also catalyse the reversible dehydrogenation of methylene-tetrahydrofolate, though at much lower efficiency []. The pterin domain of this protein is composed of two alpha-beta segments found at the N- and C-terminal ends of the polypeptide respectivly. This entry represents the N-terminal segment of the pterin domain, with a core comprising three alpha/beta/alpha layers in which each sheet contains four strands. ; PDB: 1LUA_A 1LU9_C.
Probab=24.73 E-value=58 Score=24.92 Aligned_cols=19 Identities=42% Similarity=0.644 Sum_probs=14.8
Q ss_pred EEEeecCCCCHHHHHHHHH
Q 022068 258 HWYGYVTPDDVPAILDQHI 276 (303)
Q Consensus 258 ~wYg~Vtp~dv~~Iv~~~l 276 (303)
+=|++|++++|..|++..|
T Consensus 16 ~py~~V~~~~V~~LvqdaI 34 (81)
T PF09176_consen 16 IPYGGVTPDEVRGLVQDAI 34 (81)
T ss_dssp EEESS--TTTHHHHHHHHH
T ss_pred eccCCcCHHHhhhhhccee
Confidence 4699999999999998764
No 55
>COG1062 AdhC Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]
Probab=24.66 E-value=1.1e+02 Score=29.95 Aligned_cols=88 Identities=19% Similarity=0.317 Sum_probs=52.4
Q ss_pred CcEEEEcCCCCCCCccccccHHHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCCceeEeCCC---CCCCcccEEEeecC
Q 022068 188 GSYVFVCSHGSRDKRCGVCGPALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAGNLIVYSPD---SEGKIMGHWYGYVT 264 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~G~~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~agpvv~v~p~---~~~~~~g~wYg~Vt 264 (303)
-.+.|-|+++. +.+++.++.....+++-+..+.- +|..+.++|- ......|.|||.+.
T Consensus 255 ~d~~~e~~G~~-------------~~~~~al~~~~~~G~~v~iGv~~------~~~~i~~~~~~lv~gr~~~Gs~~G~~~ 315 (366)
T COG1062 255 ADYAFECVGNV-------------EVMRQALEATHRGGTSVIIGVAG------AGQEISTRPFQLVTGRVWKGSAFGGAR 315 (366)
T ss_pred CCEEEEccCCH-------------HHHHHHHHHHhcCCeEEEEecCC------CCceeecChHHeeccceEEEEeecCCc
Confidence 45778888763 24444444433344445554443 3343433321 01223578999987
Q ss_pred C-CCHHHHHHHHHHCCc-cccceeeeccCcccc
Q 022068 265 P-DDVPAILDQHIAKGE-IIERLWRFVLYIFCL 295 (303)
Q Consensus 265 p-~dv~~Iv~~~l~~g~-~v~~l~rG~~~~~~~ 295 (303)
| -|+++||+.+ ++|+ ++.+|+-.++.|.+.
T Consensus 316 p~~diP~lv~~y-~~Gkl~~d~lvt~~~~Le~I 347 (366)
T COG1062 316 PRSDIPRLVDLY-MAGKLPLDRLVTHTIPLEDI 347 (366)
T ss_pred cccchhHHHHHH-HcCCCchhHHhhccccHHHH
Confidence 7 5799999987 4555 578888888877654
No 56
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=24.49 E-value=1.7e+02 Score=23.26 Aligned_cols=21 Identities=19% Similarity=0.251 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEE
Q 022068 208 PALIEKFNAEIDSRGLKDQIFVK 230 (303)
Q Consensus 208 ~~l~~~l~~~l~~~gl~~~v~v~ 230 (303)
-.+.+.+++.++++|++ +.|.
T Consensus 15 Slla~k~k~~~~e~gi~--~~i~ 35 (104)
T PRK09590 15 SMMAKKTTEYLKEQGKD--IEVD 35 (104)
T ss_pred HHHHHHHHHHHHHCCCc--eEEE
Confidence 58889999999999987 4444
No 57
>COG0155 CysI Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]
Probab=23.18 E-value=3.6e+02 Score=27.64 Aligned_cols=83 Identities=17% Similarity=0.283 Sum_probs=44.2
Q ss_pred CcEEEEcCCCCCCCccccc-c--H----HHHHHHHHHHHhcCCCCcEEEEEeccCCCCCCCC---ceeEe---------C
Q 022068 188 GSYVFVCSHGSRDKRCGVC-G--P----ALIEKFNAEIDSRGLKDQIFVKPCSHIGGHKYAG---NLIVY---------S 248 (303)
Q Consensus 188 ~~~IlVC~~~~rD~rC~~~-G--~----~l~~~l~~~l~~~gl~~~v~v~~~sclGG~c~ag---pvv~v---------~ 248 (303)
...+.-|.+.. -|+.. . . .+.++|++.+.+.++ .+.+.-+||. .-|..- ++=++ +
T Consensus 376 ~~~~~AC~G~p---~C~lA~aet~~~a~~i~~~l~~~~~~~~~--~i~i~isGCp-n~Ca~~~~a~Igl~G~~~~~y~v~ 449 (510)
T COG0155 376 RRNSIACVGLP---TCALALAETERDAPRIIARLEDLLDKHGL--PITLHISGCP-NGCGRPHLAEIGLVGKAKGGYQVY 449 (510)
T ss_pred hhhcccCCCCC---chhhhHhhHHHHHHHHHHHHHhhhcccCC--ceeEEeccCc-chhcCcccCceeEeeccCcceEEE
Confidence 45788999843 26654 1 3 444444444444444 4778888888 666543 21111 1
Q ss_pred CCC--CCCcccEEEee-cCCCCHHHHHHHHH
Q 022068 249 PDS--EGKIMGHWYGY-VTPDDVPAILDQHI 276 (303)
Q Consensus 249 p~~--~~~~~g~wYg~-Vtp~dv~~Iv~~~l 276 (303)
-.+ .+..-+.+|+. ++.+++...++..+
T Consensus 450 lGG~~~~~~~~~~~~~~~~~~~i~~~~~~l~ 480 (510)
T COG0155 450 LGGGADGTRGGKLYGENVPAEEILDAIDRLI 480 (510)
T ss_pred ecCCCCCCccceeecCCCCHHHHHHHHHHHH
Confidence 111 01112456544 88888766666543
Done!