Query 018378
Match_columns 357
No_of_seqs 262 out of 901
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:31:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018378.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018378hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1521 RNA polymerase I and I 100.0 2E-107 5E-112 772.6 23.6 295 29-354 1-310 (338)
2 cd07032 RNAP_I_II_AC40 AC40 su 100.0 5.4E-85 1.2E-89 629.9 27.7 250 76-354 1-265 (291)
3 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 2.1E-65 4.5E-70 489.0 23.3 229 76-354 1-235 (265)
4 PRK00783 DNA-directed RNA poly 100.0 7.1E-61 1.5E-65 455.6 21.5 227 76-354 1-232 (263)
5 cd07030 RNAP_D D subunit of Ar 100.0 5.1E-59 1.1E-63 442.0 22.0 227 76-354 1-232 (259)
6 KOG1522 RNA polymerase II, sub 100.0 1.1E-54 2.3E-59 404.2 16.9 207 73-304 3-213 (285)
7 cd07028 RNAP_RPB3_like RPB3 su 100.0 6.2E-52 1.4E-56 384.9 18.7 168 76-276 1-174 (212)
8 smart00662 RPOLD RNA polymeras 100.0 2.6E-48 5.7E-53 362.8 15.7 198 87-354 1-201 (224)
9 PRK14979 DNA-directed RNA poly 100.0 2.3E-39 4.9E-44 297.3 17.1 144 76-276 4-148 (195)
10 COG0202 RpoA DNA-directed RNA 100.0 5E-39 1.1E-43 314.1 9.7 250 74-354 3-285 (317)
11 cd06928 RNAP_alpha_NTD N-termi 100.0 1.4E-27 3E-32 222.3 15.5 142 80-277 3-174 (215)
12 PRK05182 DNA-directed RNA poly 99.9 2.5E-27 5.4E-32 231.4 15.7 149 71-276 2-181 (310)
13 PF01000 RNA_pol_A_bac: RNA po 99.9 1.5E-27 3.3E-32 200.2 7.0 105 119-265 1-112 (112)
14 TIGR02027 rpoA DNA-directed RN 99.9 3.9E-23 8.5E-28 200.9 13.3 133 88-276 2-164 (297)
15 CHL00013 rpoA RNA polymerase a 99.8 2.3E-19 4.9E-24 176.7 16.9 150 75-276 9-180 (327)
16 PF01193 RNA_pol_L: RNA polyme 98.7 2.1E-08 4.6E-13 77.0 4.0 31 88-118 1-31 (66)
17 COG0202 RpoA DNA-directed RNA 96.9 0.0016 3.5E-08 64.7 6.4 103 134-280 58-182 (317)
18 cd00460 RNAP_RPB11_RPB3 RPB11 96.7 0.0015 3.4E-08 52.8 3.7 32 78-109 1-32 (86)
19 PRK01146 DNA-directed RNA poly 95.0 0.047 1E-06 44.4 4.9 38 76-114 1-38 (85)
20 PRK15449 ferredoxin-like prote 94.6 0.035 7.6E-07 46.3 3.5 57 269-330 13-73 (95)
21 cd06927 RNAP_L L subunit of Ar 93.4 0.12 2.6E-06 41.9 4.2 35 78-113 1-35 (83)
22 cd07027 RNAP_RPB11_like RPB11 92.6 0.18 3.8E-06 40.9 4.1 33 78-110 1-33 (83)
23 COG1761 RPB11 DNA-directed RNA 91.0 0.4 8.6E-06 40.3 4.7 35 75-109 4-38 (99)
24 COG1146 Ferredoxin [Energy pro 85.5 1 2.2E-05 34.4 3.4 49 289-342 13-62 (68)
25 cd06926 RNAP_II_RPB11 RPB11 su 84.9 1.4 3.1E-05 36.3 4.2 37 76-113 7-43 (93)
26 TIGR02060 aprB adenosine phosp 82.6 1.5 3.3E-05 38.4 3.7 37 291-330 20-57 (132)
27 PLN00071 photosystem I subunit 82.4 2.3 4.9E-05 33.3 4.2 54 288-344 13-69 (81)
28 COG1143 NuoI Formate hydrogenl 80.4 1.3 2.9E-05 40.6 2.6 42 289-330 60-107 (172)
29 CHL00065 psaC photosystem I su 79.6 2.4 5.1E-05 33.3 3.5 55 288-345 13-70 (81)
30 PRK09626 oorD 2-oxoglutarate-a 78.4 1.4 3E-05 36.4 1.9 59 287-349 19-80 (103)
31 PF13247 Fer4_11: 4Fe-4S diclu 77.8 3.5 7.5E-05 34.4 4.1 36 291-330 16-52 (98)
32 COG2440 FixX Ferredoxin-like p 77.7 1.6 3.5E-05 36.7 2.1 48 276-328 25-74 (99)
33 cd07029 RNAP_I_III_AC19 AC19 s 76.2 3.4 7.3E-05 33.6 3.5 27 83-109 6-32 (85)
34 PRK08348 NADH-plastoquinone ox 75.6 2.8 6.1E-05 35.4 3.0 40 288-331 46-86 (120)
35 TIGR00402 napF ferredoxin-type 75.3 3.7 8.1E-05 33.8 3.6 42 287-331 37-79 (101)
36 PRK08222 hydrogenase 4 subunit 73.7 3.4 7.3E-05 37.8 3.3 51 288-341 42-93 (181)
37 PRK09625 porD pyruvate flavodo 73.3 4 8.7E-05 35.5 3.5 39 288-331 63-102 (133)
38 TIGR02700 flavo_MJ0208 archaeo 70.9 2.5 5.4E-05 40.0 1.8 39 287-331 151-190 (234)
39 PRK12387 formate hydrogenlyase 70.5 3.3 7.2E-05 37.5 2.5 44 288-331 42-86 (180)
40 PF13656 RNA_pol_L_2: RNA poly 70.4 2.5 5.4E-05 33.6 1.4 28 86-114 1-28 (77)
41 TIGR02179 PorD_KorD 2-oxoacid: 69.3 5.1 0.00011 30.9 3.0 39 288-331 29-68 (78)
42 PRK09624 porD pyuvate ferredox 68.5 5 0.00011 33.5 2.9 46 288-341 55-101 (105)
43 TIGR03048 PS_I_psaC photosyste 66.4 5.2 0.00011 31.3 2.5 44 288-331 12-58 (80)
44 TIGR01660 narH nitrate reducta 66.4 2.9 6.3E-05 44.0 1.3 16 289-304 219-234 (492)
45 PRK02651 photosystem I subunit 66.3 7.8 0.00017 30.1 3.5 43 289-331 14-59 (81)
46 COG2221 DsrA Dissimilatory sul 65.1 5.1 0.00011 40.2 2.7 37 289-331 177-214 (317)
47 PRK10194 ferredoxin-type prote 64.6 3.6 7.8E-05 36.6 1.4 51 288-342 108-159 (163)
48 PRK13795 hypothetical protein; 64.5 6.1 0.00013 43.0 3.4 41 287-331 584-625 (636)
49 PRK06273 ferredoxin; Provision 64.5 5.1 0.00011 36.4 2.4 45 287-331 52-104 (165)
50 TIGR03224 benzo_boxA benzoyl-C 64.3 4.2 9.1E-05 41.7 2.0 39 287-331 13-52 (411)
51 PRK05888 NADH dehydrogenase su 63.6 3.8 8.3E-05 36.5 1.4 44 288-331 62-110 (164)
52 PF13187 Fer4_9: 4Fe-4S diclus 62.6 7.1 0.00015 27.9 2.4 39 289-330 5-50 (55)
53 TIGR01944 rnfB electron transp 61.8 9.2 0.0002 34.3 3.5 39 288-331 117-156 (165)
54 PRK09623 vorD 2-ketoisovalerat 61.5 4.7 0.0001 33.6 1.5 39 288-331 55-94 (105)
55 COG0437 HybA Fe-S-cluster-cont 59.8 7.5 0.00016 36.7 2.6 34 292-329 77-110 (203)
56 TIGR02494 PFLE_PFLC glycyl-rad 59.3 4.3 9.3E-05 39.0 1.0 53 275-330 40-94 (295)
57 TIGR02163 napH_ ferredoxin-typ 57.8 6 0.00013 37.9 1.7 43 287-332 204-248 (255)
58 TIGR02936 fdxN_nitrog ferredox 55.5 11 0.00024 29.8 2.6 44 288-331 25-83 (91)
59 TIGR03478 DMSO_red_II_bet DMSO 54.2 7.6 0.00017 39.1 1.8 58 263-331 141-211 (321)
60 PF12838 Fer4_7: 4Fe-4S diclus 53.5 3.5 7.6E-05 29.5 -0.5 40 289-329 5-46 (52)
61 KOG3438 DNA-directed RNA polym 53.0 14 0.00031 31.4 2.9 36 84-125 14-49 (105)
62 PRK05113 electron transport co 51.4 11 0.00024 34.8 2.4 46 288-341 118-164 (191)
63 PRK06991 ferredoxin; Provision 50.0 7.6 0.00016 38.0 1.0 47 289-343 90-137 (270)
64 TIGR00397 mauM_napG MauM/NapG 49.2 16 0.00036 34.2 3.1 55 287-342 139-198 (213)
65 PRK07118 ferredoxin; Validated 47.8 16 0.00036 35.7 3.0 38 288-331 217-255 (280)
66 TIGR03294 FrhG coenzyme F420 h 47.8 18 0.00038 34.4 3.1 38 288-331 178-216 (228)
67 PRK14993 tetrathionate reducta 46.7 22 0.00047 34.2 3.5 35 288-330 134-178 (244)
68 TIGR02176 pyruv_ox_red pyruvat 46.5 11 0.00023 44.1 1.7 54 287-341 686-761 (1165)
69 PRK12771 putative glutamate sy 45.7 13 0.00028 39.3 2.1 44 290-340 516-560 (564)
70 TIGR03149 cyt_nit_nrfC cytochr 45.4 18 0.00039 34.1 2.8 70 262-344 103-185 (225)
71 TIGR01971 NuoI NADH-quinone ox 45.3 10 0.00022 31.8 0.9 44 288-331 47-95 (122)
72 TIGR03478 DMSO_red_II_bet DMSO 44.5 35 0.00075 34.5 4.7 41 287-331 132-175 (321)
73 PF13237 Fer4_10: 4Fe-4S diclu 44.2 14 0.00031 26.1 1.5 38 288-329 11-49 (52)
74 PRK10194 ferredoxin-type prote 44.2 20 0.00043 31.8 2.7 16 289-304 71-86 (163)
75 PRK09898 hypothetical protein; 43.2 19 0.0004 33.4 2.5 43 288-341 158-201 (208)
76 COG1145 NapF Ferredoxin [Energ 42.7 12 0.00027 29.2 1.1 42 289-331 34-76 (99)
77 PRK10882 hydrogenase 2 protein 42.6 15 0.00032 37.0 1.8 15 289-303 148-162 (328)
78 PRK09853 putative selenate red 41.6 18 0.00038 41.8 2.4 56 289-346 895-957 (1019)
79 PRK10882 hydrogenase 2 protein 41.1 9.8 0.00021 38.3 0.3 37 291-331 119-156 (328)
80 PRK09476 napG quinol dehydroge 41.1 16 0.00035 35.3 1.8 45 287-331 145-197 (254)
81 TIGR02912 sulfite_red_C sulfit 40.6 20 0.00044 35.2 2.4 38 287-330 172-213 (314)
82 PRK10330 formate dehydrogenase 39.8 23 0.00049 31.9 2.4 35 291-331 65-100 (181)
83 PRK09477 napH quinol dehydroge 39.2 12 0.00026 36.1 0.6 51 287-341 211-262 (271)
84 PRK13984 putative oxidoreducta 38.9 30 0.00065 36.9 3.5 64 287-350 48-122 (604)
85 TIGR02066 dsrB sulfite reducta 37.8 11 0.00024 37.9 0.1 39 291-331 188-227 (341)
86 TIGR00403 ndhI NADH-plastoquin 37.6 15 0.00033 33.6 0.9 44 288-331 66-115 (183)
87 KOG2415 Electron transfer flav 36.4 24 0.00051 37.4 2.2 35 294-329 562-598 (621)
88 PRK09898 hypothetical protein; 36.2 25 0.00053 32.6 2.1 41 287-331 124-167 (208)
89 PF12837 Fer4_6: 4Fe-4S bindin 35.8 18 0.00038 22.7 0.7 17 315-331 3-20 (24)
90 TIGR02745 ccoG_rdxA_fixG cytoc 35.6 25 0.00054 36.8 2.2 34 287-331 234-268 (434)
91 COG1142 HycB Fe-S-cluster-cont 34.8 22 0.00047 32.6 1.4 35 291-331 60-95 (165)
92 PRK08318 dihydropyrimidine deh 34.3 25 0.00055 35.9 2.0 52 288-344 346-401 (420)
93 PRK08764 ferredoxin; Provision 34.3 24 0.00053 30.6 1.6 39 288-331 89-128 (135)
94 TIGR02163 napH_ ferredoxin-typ 34.0 20 0.00043 34.4 1.1 41 291-331 173-214 (255)
95 TIGR01582 FDH-beta formate deh 33.0 21 0.00046 35.1 1.2 54 262-325 102-157 (283)
96 PRK09476 napG quinol dehydroge 33.0 58 0.0013 31.5 4.1 52 291-343 106-166 (254)
97 TIGR02064 dsrA sulfite reducta 31.9 26 0.00057 36.2 1.7 35 290-329 248-282 (402)
98 TIGR03149 cyt_nit_nrfC cytochr 31.9 63 0.0014 30.5 4.1 37 291-331 101-138 (225)
99 PRK14993 tetrathionate reducta 30.8 26 0.00056 33.6 1.4 36 291-331 107-143 (244)
100 PF00037 Fer4: 4Fe-4S binding 30.8 35 0.00076 21.0 1.5 17 315-331 2-19 (24)
101 KOG3256 NADH:ubiquinone oxidor 29.2 55 0.0012 30.5 3.0 43 289-331 116-163 (212)
102 PRK07118 ferredoxin; Validated 28.9 45 0.00097 32.7 2.7 37 289-331 144-181 (280)
103 PRK12809 putative oxidoreducta 28.8 36 0.00078 36.8 2.2 58 262-331 65-130 (639)
104 KOG3307 Molybdopterin converti 26.7 24 0.00053 31.2 0.3 43 88-145 50-95 (150)
105 PF14697 Fer4_21: 4Fe-4S diclu 26.3 15 0.00033 27.5 -0.9 48 289-340 11-59 (59)
106 TIGR01582 FDH-beta formate deh 26.3 30 0.00064 34.1 0.9 35 292-331 101-137 (283)
107 TIGR02512 Fe_only_hydrog hydro 25.6 30 0.00066 34.9 0.9 44 288-331 11-63 (374)
108 PRK12769 putative oxidoreducta 25.3 44 0.00095 36.2 2.0 73 262-341 65-145 (654)
109 PRK09326 F420H2 dehydrogenase 24.3 38 0.00082 33.8 1.3 44 288-331 16-66 (341)
110 TIGR02951 DMSO_dmsB DMSO reduc 23.3 63 0.0014 28.5 2.3 55 262-325 73-128 (161)
111 TIGR01444 fkbM_fam methyltrans 23.0 90 0.002 26.0 3.2 32 86-117 110-141 (143)
112 cd04932 ACT_AKiii-LysC-EC_1 AC 21.5 2.7E+02 0.0058 21.6 5.3 40 76-115 30-69 (75)
113 CHL00014 ndhI NADH dehydrogena 20.9 53 0.0011 29.5 1.4 44 288-331 63-112 (167)
114 TIGR00397 mauM_napG MauM/NapG 20.9 65 0.0014 30.2 2.0 53 276-330 47-105 (213)
No 1
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=100.00 E-value=2.3e-107 Score=772.62 Aligned_cols=295 Identities=57% Similarity=0.888 Sum_probs=282.5
Q ss_pred CcchhhccCeEEEccCCCccccccccCCCCcCCCCCcccchhhccCCceEEEEEecCceEEEEEEcCChhHHHHHHHHHH
Q 018378 29 PPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILI 108 (357)
Q Consensus 29 ~~~~~~~r~~v~~~~~~~~~~~~~~~~g~~~~~~~d~~~~~~~f~~~~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILi 108 (357)
|+|++.||++|.+++++|+|++|+||||.|. ++|+.|++++|+++++|.|.+++++.++|+|+|+|++||||||||||
T Consensus 1 ~~~~~~~~~~v~~~~~~v~~~~s~dfpg~Y~--~~d~~~~~~~f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILi 78 (338)
T KOG1521|consen 1 SAHLERMSTRVVLKEERVTNTTSTDFPGDYV--SEDDQWDLENFKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILI 78 (338)
T ss_pred ChhhhhhcceeeeccccccccccccCCcchh--cccccccHHHhhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHH
Confidence 5789999999999999999999999999999 78899999999999999999999999999999999999999999999
Q ss_pred hhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeecccCCCCCC-ceEEEEEEEEeecCCC----------
Q 018378 109 AELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEK-NTIVFKLHVLCERGGP---------- 177 (357)
Q Consensus 109 sEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~~~~~~~~-~tv~f~L~V~c~~~~~---------- 177 (357)
||||||||++|||++|||||||||||||||||||.+||++|+|..+.++..+. +|++|+|+|+|++++.
T Consensus 79 aEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDPrlFe~~~e~d~~~e~~ntlvF~L~VkC~~n~~a~~~~sdpk~ 158 (338)
T KOG1521|consen 79 AEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADPRLFEYRSENDEDDEKENTLVFKLNVKCTKNPNAKKDSSDPKE 158 (338)
T ss_pred hhcchhheeeeEEecCccccHHHHHHHhhcCcccccCcchhhccccCCCccCccceEEEEEEeeccCCCCcccCCCChhH
Confidence 99999999999999999999999999999999999999999999887776666 9999999999998842
Q ss_pred ---cceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCCEEEEEEEE
Q 018378 178 ---RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHA 253 (357)
Q Consensus 178 ---~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a 253 (357)
+..|||+|++|.|.|.|.+. |++++++++++ |+||||||||+|+|+|||
T Consensus 159 Ly~ns~vyS~~~~w~P~g~Q~~~---------------------------f~e~~i~~~~~DILiAkLrPGQEI~le~ha 211 (338)
T KOG1521|consen 159 LYNNSEVYSRDLTWKPKGYQAEI---------------------------FAENPIRPVHDDILIAKLRPGQEIELEAHA 211 (338)
T ss_pred hccCcEEecCcceeccccchhhh---------------------------cccCCccccCcceEEEecCCCCEeeeeeee
Confidence 68899999999999988642 77899999999 999999999999999999
Q ss_pred EecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHhcCCC
Q 018378 254 VKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEE 333 (357)
Q Consensus 254 ~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~rc~~~ 333 (357)
+|||||+|||||||+||||||+|.|.|++++.|++|++|++|||+|||+|++.+ |+++|+|+|||+||+||||+| |++
T Consensus 212 vkGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~-~kk~A~Vad~R~dT~sRe~~R-~ee 289 (338)
T KOG1521|consen 212 VKGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMG-GKKRAYVADPRKDTCSREVLR-HEE 289 (338)
T ss_pred ecccCcccccccCcccceeeccceeEecCcccchhHHHHHhhCCCCeEeeecCC-CceEEEecCcccchhhHHHhc-cHH
Confidence 999999999999999999999999999999999999999999999999999875 478999999999999999999 999
Q ss_pred cCCcEEEEEeCCEEEEEEEEE
Q 018378 334 WEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 334 ~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
|+|+|+|+|++|||||+||+.
T Consensus 290 ~~d~V~LgrvrdHfIFsvest 310 (338)
T KOG1521|consen 290 LKDKVQLGRVRDHFIFSVEST 310 (338)
T ss_pred hhhheeeccccceEEEEeecc
Confidence 999999999999999999986
No 2
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=100.00 E-value=5.4e-85 Score=629.93 Aligned_cols=250 Identities=61% Similarity=0.958 Sum_probs=231.9
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeecc-
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSE- 154 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~- 154 (357)
++|+|.++++++++|+|+|+|+||||||||||||||||||||.|+|++|||+|+|||||||||||||.+|++.|+|+.+
T Consensus 1 ~~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d~~~~~~~~~~ 80 (291)
T cd07032 1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADPRLFEYREDS 80 (291)
T ss_pred CeEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecCHHHccccccc
Confidence 4799999999999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred cCCCCCCceEEEEEEEEeecCCC-------------cceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 018378 155 NDTSNEKNTIVFKLHVLCERGGP-------------RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDL 221 (357)
Q Consensus 155 ~~~~~~~~tv~f~L~V~c~~~~~-------------~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~ 221 (357)
++.+|+.|+|+|+|+|+|++++. +..|||+||+|.|.|.|...
T Consensus 81 ~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~~~p~g~q~~~------------------------ 136 (291)
T cd07032 81 DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKR------------------------ 136 (291)
T ss_pred ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCEecCCCccccc------------------------
Confidence 46689999999999999986542 37899999999999977521
Q ss_pred CCCCCCCCccccCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCce
Q 018378 222 LPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNV 300 (357)
Q Consensus 222 ~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV 300 (357)
|.++++.++++ |+|+||++||+|+|+|+|+||+||+|||||||++|+||++|+|+|++++++++|++|+++||+||
T Consensus 137 ---~~~~~v~~v~~dI~I~kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~~~~~~~~~~~~cP~~V 213 (291)
T cd07032 137 ---FADNPIRPVHPDILIAKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGV 213 (291)
T ss_pred ---cCCCCcEEeCCCcEEEEECCCCEEEEEEEEEcCcccccceecCceeEEEEecceEEEcCcCCHHHHHHHHhhCCCcc
Confidence 34677999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeccCCCceEEEEccCCCCcchhhHHhcCCCcCCcEEEEEeCCEEEEEEEEE
Q 018378 301 FDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 301 ~~i~~~~~g~~~~~V~~~~~ct~crec~rc~~~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
|++++.+ |+++++|+|+++||+||||+| +.++.++|++++++|||||+||+.
T Consensus 214 f~i~~~~-~~~~~~V~~~~~ct~crec~~-~~~~~~~V~v~~~~d~fiF~VES~ 265 (291)
T cd07032 214 IDIEEVK-GKKKAVVANPRKDTLSREVLR-HEEFKDKVELGRVRDHFIFSIEST 265 (291)
T ss_pred EEecccC-CCceEEEcccccCcccHhHhh-hhccCCceeEEEeCCEEEEEEeCC
Confidence 9997643 346899999999999999999 777889999999999999999984
No 3
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=100.00 E-value=2.1e-65 Score=489.01 Aligned_cols=229 Identities=33% Similarity=0.433 Sum_probs=190.1
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecc-cceeee-c
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDP-RLFEYM-S 153 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~-~~~~~~-~ 153 (357)
++|+|.++++++++|.|+|+++|||||||||||||||||||+.|+|++|||+|+||+|||||||||+.+++ ..+.+. .
T Consensus 1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~~~~~~~~~~ 80 (265)
T cd07031 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLYYSR 80 (265)
T ss_pred CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCcccccceeeeecccCCCccCcHHHHhhhhh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999754 333332 2
Q ss_pred c--cCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCcc
Q 018378 154 E--NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIR 231 (357)
Q Consensus 154 ~--~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~ 231 (357)
. ++..|+.|+++|+|+++|++++ +..|||+||+|.|.+.|... ..|... +....
T Consensus 81 ~~~~~~~~~~~~v~~~L~v~~~~~~-~~~V~s~Dl~~~~~~~~~~~---------~~pi~~--------------~~~~~ 136 (265)
T cd07031 81 DCDCDEFCDKCSVELTLDVKCTGDQ-TREVTSRDLVSSGPKVNDVV---------PVPIRN--------------DSEDN 136 (265)
T ss_pred hccccCCCCCCeEEEEEEEEeccCC-CceEEHHHcccccccccccC---------Cccccc--------------ccccc
Confidence 2 3345677999999999998655 58999999999776544210 011110 01112
Q ss_pred ccCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCc
Q 018378 232 PMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGK 310 (357)
Q Consensus 232 ~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~ 310 (357)
++++ |+|+||+|||+|+|+|+|+||+||+|||||||++|+||++|+|+|++++.+.++.
T Consensus 137 ~~~~~i~I~kL~~gq~i~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~~~~~-------------------- 196 (265)
T cd07031 137 GEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYLED-------------------- 196 (265)
T ss_pred cCCCCeEEEEECCCCEEEEEEEEECCEeccCCEeccceEEEEEEccceEEccccccchhh--------------------
Confidence 5678 9999999999999999999999999999999999999999999998776432221
Q ss_pred eEEEEccCCCCcchhhHHhcCC-CcCCcEEEEEeCCEEEEEEEEE
Q 018378 311 KRATVAQPRACTLCRECLRCGE-EWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 311 ~~~~V~~~~~ct~crec~rc~~-~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
.|++.|++||+|++ +. ++++.|++++++|||||+||+.
T Consensus 197 -----~~~~~c~~c~~c~~-~~~~~~~~v~i~~~~~~fiF~VES~ 235 (265)
T cd07031 197 -----EDKEWPKSENACIE-EPPEKDALFDIDAKPDKFYFNVEST 235 (265)
T ss_pred -----cccccCchhHHHhh-cccccCCceEEEeeCCEEEEEEEec
Confidence 18899999999999 43 4789999999999999999984
No 4
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=7.1e-61 Score=455.59 Aligned_cols=227 Identities=36% Similarity=0.588 Sum_probs=204.3
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeeccc
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~~ 155 (357)
++|+|.+.++++++|.+.|+++|||||||||||||||||||+.|+|++|||+++||+|||||||||+.++++.++|+.++
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~~~~~~~~~~~ 80 (263)
T PRK00783 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTDLDKYKPPEEC 80 (263)
T ss_pred CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCcccccCHHHCCCcccc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999998888887654
Q ss_pred C---CCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccc
Q 018378 156 D---TSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRP 232 (357)
Q Consensus 156 ~---~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~ 232 (357)
+ ..|+.|++.|+|++++ +..|||+||++.| ..+++
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~-----~~~V~a~dl~~~~-------------------------------------~~v~~ 118 (263)
T PRK00783 81 TCEGEGCPDCTVTLSLEVEG-----PKTVYSGDLKSSD-------------------------------------PDVKP 118 (263)
T ss_pred cccCCCCCCcEEEEEEEecC-----CCcEEccccccCC-------------------------------------CCcee
Confidence 3 3577889999999985 3689999998621 23788
Q ss_pred cCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCce
Q 018378 233 MLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311 (357)
Q Consensus 233 v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~ 311 (357)
++| ++|+||++||+|+|+|+|.||+||+|||||||++++||+.|.|.+.+.+ ..|..|++.||.|||.+++ +
T Consensus 119 v~~~~~I~~L~~~~~l~~e~~~~~G~G~~HAKw~p~~~~~yr~~p~I~i~~~C--~~C~~C~~~CP~~vi~~~~-----~ 191 (263)
T PRK00783 119 VDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDC--DECEKCVEACPRGVLELKE-----G 191 (263)
T ss_pred cCCCcEEEEeCCCCEEEEEEEEEcCcccccCccCcceEeeecccccccccccC--CchHHHHHhCCccccEecC-----C
Confidence 999 9999999999999999999999999999999999999999999995555 5689999999999999964 3
Q ss_pred EEEEccCCCCcchhhHHh-cCCCcCCcEEEEEeCCEEEEEEEEE
Q 018378 312 RATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 312 ~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
.+.+.++..|++|++|++ |. .++|++.+++|+|+|+||+.
T Consensus 192 ~~~v~~~~~C~~C~~Ci~~CP---~~AI~i~~~~~~~if~vEs~ 232 (263)
T PRK00783 192 KLVVTDLLNCSLCKLCERACP---GKAIRVSDDENKFIFTVESD 232 (263)
T ss_pred eEEEeChhhCCCchHHHHhCC---CCceEEEEcCCeEEEEeccC
Confidence 477779999999999999 64 36899999999999999984
No 5
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=100.00 E-value=5.1e-59 Score=441.98 Aligned_cols=227 Identities=39% Similarity=0.640 Sum_probs=200.9
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeeccc
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~~ 155 (357)
++|+|.+.++++++|.++|+++++||||||+|||||||+||+.|+|++|||+|+||+|||||||||+..+...+.+..++
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~~~~~~ 80 (259)
T cd07030 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYRSEC 80 (259)
T ss_pred CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhcccccc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999765433333232
Q ss_pred ---CCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccc
Q 018378 156 ---DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRP 232 (357)
Q Consensus 156 ---~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~ 232 (357)
...++.|++.|+|+++|+ ..|||+||+|. +..+.+
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~~-----~~v~s~dl~~~-------------------------------------~~~v~~ 118 (259)
T cd07030 81 SCGGAGCPLCTVTLTLSVEGP-----GTVYSGDLKSS-------------------------------------DPDVKP 118 (259)
T ss_pred cccCCCCCCcEEEEEEEccCC-----ceEEccccccC-------------------------------------CCCccc
Confidence 245667899999999874 78999999972 123788
Q ss_pred cCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCce
Q 018378 233 MLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311 (357)
Q Consensus 233 v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~ 311 (357)
++| |+|+||++||+|+|+++|.||+||+||||+|+++++||++|.|.+.+.+.+ |.+|++.||.|+|.+++ +
T Consensus 119 ~~~~~~I~~l~~~~~l~~~~~~~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C~~--C~~C~~~CP~~vi~~d~-----~ 191 (259)
T cd07030 119 VYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDG--CGKCVEECPRGVLELEE-----G 191 (259)
T ss_pred cCCCcEEEEeCCCCEEEEEEEEecCccCCCCCCCCccEEEEEeecceechhhCCC--hHHHHHhCCccceEccC-----C
Confidence 999 999999999999999999999999999999999999999999999887754 89999999999999863 2
Q ss_pred EEEEccCCCCcchhhHHh-cCCCcCCcEEEEEeCCEEEEEEEEE
Q 018378 312 RATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 312 ~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
.+.+.++..|++|++|++ |. .+.|++.+++++|+|+||+.
T Consensus 192 ~~~v~~~~~C~~C~~C~~~Cp---~~AI~~~~~~~~~if~vEs~ 232 (259)
T cd07030 192 KVVVEDLEDCSLCKLCERACD---AGAIRVGWDEDRFIFEVESD 232 (259)
T ss_pred eeEEeChhhCcCchHHHHhCC---CCcEEEEecCCEEEEEEeCC
Confidence 477789999999999999 53 27999999999999999973
No 6
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=100.00 E-value=1.1e-54 Score=404.17 Aligned_cols=207 Identities=34% Similarity=0.518 Sum_probs=167.8
Q ss_pred cCCceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecc-cceee
Q 018378 73 CNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDP-RLFEY 151 (357)
Q Consensus 73 ~~~~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~-~~~~~ 151 (357)
.+.++|+|.+++++.++|.|.+.|.++||||||+|||||||+|||.|.|.-|||||+|||||||||||||.++- ..++|
T Consensus 3 ~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~l~y 82 (285)
T KOG1522|consen 3 ANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQY 82 (285)
T ss_pred CCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhhhhhh
Confidence 34578999999999999999999999999999999999999999999999999999999999999999999864 45778
Q ss_pred eccc--CCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCC
Q 018378 152 MSEN--DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNP 229 (357)
Q Consensus 152 ~~~~--~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~ 229 (357)
..+| +..|+.|+|.|.|+++|+..+ ...|||+||.. .+|.+.|+.+. .+... .
T Consensus 83 trdC~C~~~C~eCSVef~L~~kc~~d~-T~~VtsrDL~s--------------~~~~v~pv~~~---~~~~~------~- 137 (285)
T KOG1522|consen 83 TRDCECDEFCPECSVEFTLDVKCTDDQ-TRDVTSRDLVS--------------LDPTVTPVDSN---RGSEI------D- 137 (285)
T ss_pred cccCchhccCCcceEEEEEeeeecccc-eeeeehHhhhc--------------cCCcccccccC---CCCcc------c-
Confidence 7654 557999999999999998766 68999999983 12455666642 11110 1
Q ss_pred ccccCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEee
Q 018378 230 IRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIE 304 (357)
Q Consensus 230 v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~ 304 (357)
....++ |+|+|||+||+|+|+|+|+||+||+||||||+|+++|.|.|+-.+...+.......+.+.=+...++++
T Consensus 138 ~~~e~~gilI~KLRkgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~~Ewp~sk~~e~~ 213 (285)
T KOG1522|consen 138 DDSESKGILIVKLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSKNSELE 213 (285)
T ss_pred cccccCCcEEEEeecCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccchhhCCcccccCCC
Confidence 122345 999999999999999999999999999999999999999999877654443333334444444555554
No 7
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=100.00 E-value=6.2e-52 Score=384.93 Aligned_cols=168 Identities=40% Similarity=0.591 Sum_probs=145.7
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceeccc---ceeee
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPR---LFEYM 152 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~---~~~~~ 152 (357)
+.|+|.+.++++++|.|+|++++|||||||+|||||||+||+.|+|++|||+|+||+|||||||||+..++. .++.+
T Consensus 1 ~~i~i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~DE~iaHrlglIP~~~e~~~~~~~n~k 80 (212)
T cd07028 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPE 80 (212)
T ss_pred CcEEEEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccceeeeeeeeecccccCcHHHhhhccc
Confidence 468999999999999999999999999999999999999999999999999999999999999999997642 22323
Q ss_pred cc--cCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCc
Q 018378 153 SE--NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPI 230 (357)
Q Consensus 153 ~~--~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v 230 (357)
.. +...|+.|++.|+|+++|+.+. +..|||+||+|.+.|.. ++++
T Consensus 81 ~~~~~~~~~~~~~v~~~l~~~g~~~~-~~~V~s~DL~~~~~~~~--------------------------------~~~v 127 (212)
T cd07028 81 EDCECEDHCDKCSVVLTLQAFAESES-TTNVYSKDLVIVSNLMG--------------------------------RNIG 127 (212)
T ss_pred ccccccccccceeEEEEEEccCCCCC-cceEEHHHcccCCcccc--------------------------------CCCe
Confidence 22 2334666899999999986432 46899999999654421 2457
Q ss_pred cccCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeec
Q 018378 231 RPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLP 276 (357)
Q Consensus 231 ~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P 276 (357)
.|+++ |+|+||++||+|+|+|+|+||+||+|||||||++|+|+++|
T Consensus 128 ~pv~~di~I~kL~~gq~i~le~~~~~G~G~~hAk~sPV~~v~y~~~~ 174 (212)
T cd07028 128 HPIIQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIEFRYDP 174 (212)
T ss_pred EEeCCCcEEEEECCCCEEEEEEEEECCCcCCCCEeCCceEEEEEEEc
Confidence 89999 99999999999999999999999999999999999999999
No 8
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=2.6e-48 Score=362.78 Aligned_cols=198 Identities=40% Similarity=0.570 Sum_probs=175.4
Q ss_pred eEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeecc--cCCCCCCceE
Q 018378 87 DMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSE--NDTSNEKNTI 164 (357)
Q Consensus 87 ~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~--~~~~~~~~tv 164 (357)
+++|.|+|++.++||||||+|||+|||+||+.|+|++|+|.++||+++|||||+||..+.+.+.++.. |...|+.|++
T Consensus 1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~~~~~~~~~~~~~~~~~~~~~ 80 (224)
T smart00662 1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDPDGDEYQRDCECEEGCEKCSV 80 (224)
T ss_pred CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEechhccccccccccccCCCceE
Confidence 47899999999999999999999999999999999999999999999999999999987665566543 3456888999
Q ss_pred EEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCC
Q 018378 165 VFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGP 243 (357)
Q Consensus 165 ~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~-IlIaKL~p 243 (357)
.++|+++|+ ..|||+||+|.+ ++.+.+++| |+|+||++
T Consensus 81 ~~~L~~~gp-----~~V~a~Dl~~~~------------------------------------~~~v~~vnp~~~I~~L~~ 119 (224)
T smart00662 81 TLTLDVKGP-----GEVTAGDLKSDS------------------------------------DPDVEIVNPDIPIAKLRE 119 (224)
T ss_pred EEEEEEEcC-----CcEEHHHcccCC------------------------------------CCCcEEeCCCcEEEEECC
Confidence 999999985 679999999821 234789999 99999999
Q ss_pred CCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcc
Q 018378 244 GQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTL 323 (357)
Q Consensus 244 GQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~ 323 (357)
||+|+|+++|.||+||+||||+|+++++|++.|.|.++...++.++..+...||++++.++ |
T Consensus 120 gq~l~~e~~~~~G~G~~hak~~p~~~~~~~~~~~i~id~~~~pv~~v~~~~~~~~~~~~~~----------------~-- 181 (224)
T smart00662 120 GQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTD----------------C-- 181 (224)
T ss_pred CCEEEEEEEEECCcccccCccccccCCCcCcCCEEEECCCCChhhheeeeccCCccceecc----------------c--
Confidence 9999999999999999999999999999999999999988888888899999998876541 6
Q ss_pred hhhHHhcCCCcCCcEEEEEeCCEEEEEEEEE
Q 018378 324 CRECLRCGEEWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 324 crec~rc~~~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
||||++ +. +.|+|+|+|||-
T Consensus 182 ~~~c~~-~~----------~~d~l~f~IeT~ 201 (224)
T smart00662 182 CRECDE-GE----------EYDKLIFDVETN 201 (224)
T ss_pred chhhhc-cC----------CCCEEEEEEEec
Confidence 999998 32 579999999983
No 9
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=2.3e-39 Score=297.27 Aligned_cols=144 Identities=38% Similarity=0.598 Sum_probs=126.1
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCceecccceeeeccc
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D~~~~~~~~~~ 155 (357)
+++++....+++++|.|+ +++++||||||+|||+|||+||+.|+|++|||+++||++|||||||||+..+- +.
T Consensus 4 ~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~~----~~-- 76 (195)
T PRK14979 4 IKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKPV----SG-- 76 (195)
T ss_pred cceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeeeeeeeec----cC--
Confidence 567777788899999999 99999999999999999999999999999999999999999999999987531 11
Q ss_pred CCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC
Q 018378 156 DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD 235 (357)
Q Consensus 156 ~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~ 235 (357)
.+++.|+|++++ ++.|||+||++. .+ .+++|
T Consensus 77 -----~~~~~l~L~~~g-----p~~Vta~Di~~~--------------------------------------~~-~ivnp 107 (195)
T PRK14979 77 -----DEVITFTLSKEG-----PCTVYSSDLKSE--------------------------------------NG-EVAFK 107 (195)
T ss_pred -----CCcEEEEEEEeC-----CceEEHHHcCCC--------------------------------------CC-cccCC
Confidence 257899999875 378999999971 11 47788
Q ss_pred -eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeec
Q 018378 236 -ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLP 276 (357)
Q Consensus 236 -IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P 276 (357)
++||+|++||+|+|+|+|.+|+||+||||+|+ .|.|+..+
T Consensus 108 di~I~tL~~g~~l~~e~~~~~G~Gy~hAk~~pv-da~y~~~~ 148 (195)
T PRK14979 108 NIPIVKLAEGQKLEIECEALVGTGKIHAKWQPC-NAVYKQIS 148 (195)
T ss_pred CcEEEEECCCCEEEEEEEEECCCccccccccce-eeEEecCC
Confidence 99999999999999999999999999999995 56777665
No 10
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=5e-39 Score=314.14 Aligned_cols=250 Identities=23% Similarity=0.289 Sum_probs=204.8
Q ss_pred CCceEEEEEec----CceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEee--C---c-ccccchhheecccCcCce
Q 018378 74 NNFRVEVIRLT----KDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIAN--N---T-SVIQDEVLAHRLGLIPII 143 (357)
Q Consensus 74 ~~~~I~i~~~~----~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~--N---T-Svl~DEvLAHRLGLIPi~ 143 (357)
++..|++.+++ ...++|...|+++++||||||||||+|||+||+.|+|++ | | +.++|||+||||||+||.
T Consensus 3 ~p~~i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~ 82 (317)
T COG0202 3 KPKKVKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLA 82 (317)
T ss_pred cccceEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCceee
Confidence 43448999988 668888888999999999999999999999999999999 3 4 489999999999999998
Q ss_pred eccc-----ceeeecc--cCCCCCCceEEEEEEEEeecCCC-----------cceEEcccceecCCCCCCCCCCCCCCCC
Q 018378 144 VDPR-----LFEYMSE--NDTSNEKNTIVFKLHVLCERGGP-----------RLTVKTNELKWLPNGSELPLETKPDSNP 205 (357)
Q Consensus 144 ~D~~-----~~~~~~~--~~~~~~~~tv~f~L~V~c~~~~~-----------~~~VyS~DL~~~p~g~q~~~~~~~~~~~ 205 (357)
.+.. .+.+... +...|..|++.+.|+|.|+...- ...||++|+.+.+.+++.
T Consensus 83 ~~~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~---------- 152 (317)
T COG0202 83 VKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNRE---------- 152 (317)
T ss_pred eecccccceEEEEeccCCccccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEeccccccc----------
Confidence 7653 2455443 33457789999999999863220 357899999996554431
Q ss_pred CCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCCEEEEEEEEEecccceeeeecceeeEEeeeeceEEEcCCC
Q 018378 206 SSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDV 284 (357)
Q Consensus 206 ~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwSPVata~Yr~~P~I~i~~~i 284 (357)
.+.++.+... +++++|+++|.+..+++|.+|+|++||||+|+++++|+.+|.+.+..++
T Consensus 153 --------------------~~~~v~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~i 212 (317)
T COG0202 153 --------------------DDPPVGPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKI 212 (317)
T ss_pred --------------------cCCCceeeeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHH
Confidence 2456777888 9999999999999999999999999999999999999999999888888
Q ss_pred ChHhHHHHHhhCCCc-eEEeeccC---CCceEEEEccCCCCcchhhHHhcCCCcCCcEEEEEeCCEEEEEEEEE
Q 018378 285 EDEDAEKLVKTCPVN-VFDIEDIG---SGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFICKYVML 354 (357)
Q Consensus 285 ~~~~a~~l~~~cp~g-V~~i~~~~---~g~~~~~V~~~~~ct~crec~rc~~~~~~~V~l~~~~dhFIF~Ve~~ 354 (357)
..+++..|+++||.. .+..++.. .+...+.+.+.+.|+.|++|++ ..+......|.+..++|+|+|+.+
T Consensus 213 l~e~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~I~~l~lsvrs~ncLk-~~~i~~i~~L~~~~e~~l~~v~n~ 285 (317)
T COG0202 213 LIEHLEVFVELCPKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLK-REGIETIGELVQRTEEELLKVENL 285 (317)
T ss_pred HHHHHHHHHhhccccceeecccccccccccccccccccccceeeehhhc-ccCchhhHHHHhcCHHHHhccccc
Confidence 899999999999976 34333210 1112347899999999999999 666666778899999999999875
No 11
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=99.95 E-value=1.4e-27 Score=222.31 Aligned_cols=142 Identities=26% Similarity=0.352 Sum_probs=120.4
Q ss_pred EEEecCceEEEEE----EcCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCce-ecc-------c
Q 018378 80 VIRLTKDDMEFDL----IGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDP-------R 147 (357)
Q Consensus 80 i~~~~~~~~~F~l----~Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~-~D~-------~ 147 (357)
+.+.++.+++|.+ .|++.++||||||+||+++|++||+.|.|++| +||||+||+. +|. +
T Consensus 3 ~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~---------~He~~~Ipgv~Edv~~IllNlk 73 (215)
T cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGV---------LHEFSTIPGVREDVLEILLNLK 73 (215)
T ss_pred eccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEccc---------ccccccCCCccccHHHHhhccc
Confidence 3455678999999 48999999999999999999999999999986 7999999976 563 3
Q ss_pred ceeeecccCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCC
Q 018378 148 LFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSN 227 (357)
Q Consensus 148 ~~~~~~~~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~ 227 (357)
.+.++..|. .|++.++|+++++ +.|||+||++ |
T Consensus 74 ~~~~~~~~~----~~~~~~~l~~~gp-----~~V~a~Di~~-~------------------------------------- 106 (215)
T cd06928 74 EIVFKSDSE----DEPQVLRLKVKGP-----GVVTAADIEL-P------------------------------------- 106 (215)
T ss_pred cEEEEecCC----CceEEEEEEEecC-----eEEEhHhcCc-C-------------------------------------
Confidence 344443332 5789999999863 7899999987 2
Q ss_pred CCccccCC-eEEEEeCCCCEEEEEEEEEecccceeeee-----------------cceeeEEeeeece
Q 018378 228 NPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKW-----------------SPVATAWYRMLPE 277 (357)
Q Consensus 228 ~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKw-----------------SPVata~Yr~~P~ 277 (357)
..+++++| ++||+|.+||+|+|+|++.+|+||.+|+| |||..+.|.+++.
T Consensus 107 ~~i~ivnp~~~IatL~~~~~l~ie~~i~~G~Gy~~~~~~~~~~~~~~~~~iDa~f~PV~~vny~v~~~ 174 (215)
T cd06928 107 SGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRKVNYSVEST 174 (215)
T ss_pred CCcEEeCCCcEEEEECCCCEEEEEEEEECcCcceeccccccccCCCceEEeCCCcCCeEEEEEEEEEe
Confidence 23789999 99999999999999999999999988765 9999999987763
No 12
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=99.95 E-value=2.5e-27 Score=231.40 Aligned_cols=149 Identities=23% Similarity=0.355 Sum_probs=125.6
Q ss_pred hccCCceEEEEEec--CceEEEEEE----cCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCce-
Q 018378 71 HFCNNFRVEVIRLT--KDDMEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII- 143 (357)
Q Consensus 71 ~f~~~~~I~i~~~~--~~~~~F~l~----Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~- 143 (357)
+|.++..+++.+.+ +.+++|.+. |++.++||||||+|||+|||+||+.|.|. .++|||++||+.
T Consensus 2 ~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~---------gv~hEf~~Ipgv~ 72 (310)
T PRK05182 2 EFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID---------GVLHEFSTIPGVR 72 (310)
T ss_pred CcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc---------ceeeeccccCCcc
Confidence 46677778888876 789999998 99999999999999999999999999994 489999999976
Q ss_pred ecc-------cceeeecccCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccC
Q 018378 144 VDP-------RLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFS 216 (357)
Q Consensus 144 ~D~-------~~~~~~~~~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~ 216 (357)
+|. +.+.++..| .|++.++|+++++ +.|||+||++ |
T Consensus 73 Edv~eIllNlk~i~~~~~~-----~~~~~~~l~~~gp-----~~VtA~Di~~-~-------------------------- 115 (310)
T PRK05182 73 EDVTEIILNLKGLRLKLHG-----DEPVTLTLSKKGP-----GEVTAGDIET-D-------------------------- 115 (310)
T ss_pred cchhHhhhhhccceeecCC-----CceEEEEEEecCC-----eEEEHHHcCC-C--------------------------
Confidence 553 233333222 2788999999863 7999999987 2
Q ss_pred CCCCCCCCCCCCCccccCC-eEEEEeCCCCEEEEEEEEEecccceeee----------------ecceeeEEeeeec
Q 018378 217 SSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAK----------------WSPVATAWYRMLP 276 (357)
Q Consensus 217 ~~q~~~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAK----------------wSPVata~Yr~~P 276 (357)
..+++++| ++||+|++||.|+|+|+|.+|+||.+|+ |+||..+.|.+.+
T Consensus 116 -----------~~v~ivn~d~~IatL~~~~~l~ie~~~~kG~Gy~~~~~~~~~~~~g~i~iDa~f~PV~~vny~ve~ 181 (310)
T PRK05182 116 -----------GDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKEDAPIGRIPVDAIFSPVKKVNYTVEN 181 (310)
T ss_pred -----------CCcEEeCCCeEEEEECCCCEEEEEEEEECcCCCcccccccccCCcccEEecCCcCCccceEEEecc
Confidence 22789999 9999999999999999999999997654 9999999997665
No 13
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=99.94 E-value=1.5e-27 Score=200.18 Aligned_cols=105 Identities=36% Similarity=0.526 Sum_probs=87.5
Q ss_pred EEEeeCcccccchhheecccCcCcee-cc-cc-eeeec---ccCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCC
Q 018378 119 VLIANNTSVIQDEVLAHRLGLIPIIV-DP-RL-FEYMS---ENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNG 192 (357)
Q Consensus 119 V~I~~NTSvl~DEvLAHRLGLIPi~~-D~-~~-~~~~~---~~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g 192 (357)
|+|++|||+|+||++|||||+||+.. |. +. ++.+. .+...++.|++.++|+++|+ ..|||+||+|.|
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~g~-----~~V~a~di~~~~-- 73 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVKGP-----GEVTAGDIKLEP-- 73 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEESS-----SCEEGGGSEESB--
T ss_pred CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEecCC-----CccccceeEecC--
Confidence 79999999999999999999999984 43 32 23332 12456788999999999985 679999999842
Q ss_pred CCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCCEEEEEEEEEecccceeeeec
Q 018378 193 SELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWS 265 (357)
Q Consensus 193 ~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~HAKwS 265 (357)
..+++++| ++||+|++||+|+|+|+|.+|+||+|||||
T Consensus 74 -----------------------------------~~i~ivn~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 74 -----------------------------------SGIEIVNPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS 112 (112)
T ss_dssp -----------------------------------TTEEESSTTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred -----------------------------------CceEEecCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence 33789999 999999999999999999999999999997
No 14
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=99.89 E-value=3.9e-23 Score=200.91 Aligned_cols=133 Identities=26% Similarity=0.349 Sum_probs=110.6
Q ss_pred EEEEEE----cCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCce-ecc-------cceeeeccc
Q 018378 88 MEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDP-------RLFEYMSEN 155 (357)
Q Consensus 88 ~~F~l~----Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~-~D~-------~~~~~~~~~ 155 (357)
.+|.+. |++.++||||||+|||++|++||+.|.|++ ++|+|++||.. +|. +.+.++..+
T Consensus 2 ~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~~~~~~ 72 (297)
T TIGR02027 2 GKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLVVKSEG 72 (297)
T ss_pred cEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceEEeccC
Confidence 578887 899999999999999999999999999977 89999999975 664 223333322
Q ss_pred CCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC
Q 018378 156 DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD 235 (357)
Q Consensus 156 ~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~v~~v~~ 235 (357)
+ ....++|+++| ++.|||+||+|.| +.+.+++|
T Consensus 73 ----~-~~~~~~l~~~g-----p~~VtA~Di~~~p-------------------------------------~~ieivnp 105 (297)
T TIGR02027 73 ----D-GERTMTLSKKG-----PGVVTAGDIKAPP-------------------------------------GDVEIVNP 105 (297)
T ss_pred ----C-CcEEEEEEEeC-----CEEEEhhhcccCC-------------------------------------CCcEEeCC
Confidence 2 23388888886 4899999999743 23789999
Q ss_pred -eEEEEeCCCCEEEEEEEEEeccccee-----------------eeecceeeEEeeeec
Q 018378 236 -ITIARLGPGQEIELEAHAVKGIGKTH-----------------AKWSPVATAWYRMLP 276 (357)
Q Consensus 236 -IlIaKL~pGQeI~le~~a~KGiGk~H-----------------AKwSPVata~Yr~~P 276 (357)
++||+|.+||.|+|++++.+|+||.+ |.||||..+.|.+++
T Consensus 106 d~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~~~~~~~~~i~iDa~FsPV~~Vny~ve~ 164 (297)
T TIGR02027 106 DLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNYEVEN 164 (297)
T ss_pred CeEEEEECCCCEEEEEEEEEcccccCcccccccccCccccccccccccCeEEEEEEEee
Confidence 99999999999999999999999864 469999999999875
No 15
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=99.82 E-value=2.3e-19 Score=176.69 Aligned_cols=150 Identities=22% Similarity=0.202 Sum_probs=121.0
Q ss_pred CceEEEEEecCceEEEEEE----cCChhHHHHHHHHHHhhCCcceEEEEEEeeCcccccchhheecccCcCce-eccc--
Q 018378 75 NFRVEVIRLTKDDMEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDPR-- 147 (357)
Q Consensus 75 ~~~I~i~~~~~~~~~F~l~----Gvd~siaNALRRILisEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~-~D~~-- 147 (357)
....++.+.++.+.+|.+. |++.+|||||||+|||++|++||..|.|++ +.|.+..||.. +|..
T Consensus 9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g---------v~hEfs~i~GV~Edv~eI 79 (327)
T CHL00013 9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG---------VPHEYSTIPGIRESVLEI 79 (327)
T ss_pred ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC---------ccccccCCCCcccCHHHH
Confidence 3567777888899999999 666799999999999999999999999976 66999999964 7742
Q ss_pred ceeeecccCCCCCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCC
Q 018378 148 LFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSN 227 (357)
Q Consensus 148 ~~~~~~~~~~~~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~ 227 (357)
.+|++.-.-.........+.|++++ ++.|||+||++ |
T Consensus 80 ilNLK~I~~k~~~~~~~~~~l~~~G-----p~~vtA~Di~~-p------------------------------------- 116 (327)
T CHL00013 80 LLNLKEIVLKSNLYGPQKASICVQG-----PKYVTAQDIIL-P------------------------------------- 116 (327)
T ss_pred HHhhhcCeEEccCCCcEEEEEEEeC-----CeEEEeeeecc-C-------------------------------------
Confidence 2333321111111245688888876 48999999986 2
Q ss_pred CCccccCC-eEEEEeCCCCEEEEEEEEEecccce--------------eeeecceeeEEeeeec
Q 018378 228 NPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKT--------------HAKWSPVATAWYRMLP 276 (357)
Q Consensus 228 ~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~--------------HAKwSPVata~Yr~~P 276 (357)
..+++++| .+||+|..|+.|+|++++.+|+||. .|.||||..+.|.+++
T Consensus 117 ~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~FsPV~kVny~Ve~ 180 (327)
T CHL00013 117 PSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVFMPVRNVNYSIHS 180 (327)
T ss_pred CCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCCCCeeEEEEEEEE
Confidence 23789999 9999999999999999999999995 3689999999999987
No 16
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=98.66 E-value=2.1e-08 Score=77.04 Aligned_cols=31 Identities=48% Similarity=0.792 Sum_probs=30.1
Q ss_pred EEEEEEcCChhHHHHHHHHHHhhCCcceEEE
Q 018378 88 MEFDLIGIDAAIANAFRRILIAELPTMAIEK 118 (357)
Q Consensus 88 ~~F~l~Gvd~siaNALRRILisEVPT~AIe~ 118 (357)
++|.+.|.|+++||||||+|+++||++||+.
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~ 31 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG 31 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe
Confidence 6899999999999999999999999999998
No 17
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=96.95 E-value=0.0016 Score=64.67 Aligned_cols=103 Identities=17% Similarity=0.153 Sum_probs=75.6
Q ss_pred eecccCcCce-ecc--cceeeecccCCC-CCCceEEEEEEEEeecCCCcceEEcccceecCCCCCCCCCCCCCCCCCCCC
Q 018378 134 AHRLGLIPII-VDP--RLFEYMSENDTS-NEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKP 209 (357)
Q Consensus 134 AHRLGLIPi~-~D~--~~~~~~~~~~~~-~~~~tv~f~L~V~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~ 209 (357)
.|++..||.. .|. -.++++.-.-.. .+.. +++++...| .+.||++|+...
T Consensus 58 ~hef~s~~gv~Edvl~~~LnLk~L~~~~~~~~~-~~~~~~~~g-----~g~v~a~d~~~~-------------------- 111 (317)
T COG0202 58 LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEE-VTLELDKEG-----PGEVTASDITVP-------------------- 111 (317)
T ss_pred ccccccCcCcHHHHHHHHhcCceeeeecccccc-eEEEEeccC-----CccccHhhcccc--------------------
Confidence 5888888644 453 123333211000 0111 788888876 388999999851
Q ss_pred CcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCCEEEEEEEEEeccccee-----------------eeecceeeEE
Q 018378 210 RTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTH-----------------AKWSPVATAW 271 (357)
Q Consensus 210 ~~~~~f~~~q~~~~~f~~~~v~~v~~-IlIaKL~pGQeI~le~~a~KGiGk~H-----------------AKwSPVata~ 271 (357)
..+..++| ..||.|..|.+|.|++++..|.|+.. |-||||..+.
T Consensus 112 ------------------~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~~~~~v~~i~~D~~~spv~kvq 173 (317)
T COG0202 112 ------------------LDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPIAVDAPFSPVRKVQ 173 (317)
T ss_pred ------------------eeEEEECCCceeeeccCCcceEEEEEEEcCccEeccccccccCCCceeeeCCCceeeeeece
Confidence 23788999 99999999999999999999999992 7899999999
Q ss_pred eeeeceEEE
Q 018378 272 YRMLPEIVL 280 (357)
Q Consensus 272 Yr~~P~I~i 280 (357)
|..+.-..-
T Consensus 174 y~ve~~r~~ 182 (317)
T COG0202 174 YIVEEARVG 182 (317)
T ss_pred EEEEeEEEe
Confidence 998876654
No 18
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=96.74 E-value=0.0015 Score=52.79 Aligned_cols=32 Identities=31% Similarity=0.555 Sum_probs=30.2
Q ss_pred EEEEEecCceEEEEEEcCChhHHHHHHHHHHh
Q 018378 78 VEVIRLTKDDMEFDLIGIDAAIANAFRRILIA 109 (357)
Q Consensus 78 I~i~~~~~~~~~F~l~Gvd~siaNALRRILis 109 (357)
|+|.+.+++.++|.+.|-|.++||+||+.|+.
T Consensus 1 ~ki~~~~~~~~~~~~~~edhTl~n~L~~~l~~ 32 (86)
T cd00460 1 VKILEKEKNYVDFVLENEDHTLGNSLRRILLK 32 (86)
T ss_pred CceecCCCCEEEEEEeCCCchHHHHHHHHHhC
Confidence 46788899999999999999999999999999
No 19
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=94.95 E-value=0.047 Score=44.45 Aligned_cols=38 Identities=18% Similarity=0.472 Sum_probs=33.6
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcc
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTM 114 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~ 114 (357)
++|+|.+.+++.++|.+.|=|.+++|+||-.|+. -|.+
T Consensus 1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~V 38 (85)
T PRK01146 1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLE-DPGV 38 (85)
T ss_pred CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhc-CCCe
Confidence 4789999999999999999999999999999885 4543
No 20
>PRK15449 ferredoxin-like protein FixX; Provisional
Probab=94.65 E-value=0.035 Score=46.26 Aligned_cols=57 Identities=25% Similarity=0.474 Sum_probs=43.1
Q ss_pred eEEeee---eceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-c
Q 018378 269 TAWYRM---LPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 269 ta~Yr~---~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c 330 (357)
...|.+ .|+|.|..+......+.++..||.|+|..++. + .++.+...|.-|+.|.- |
T Consensus 13 ~~~y~vd~~~~HI~i~~~~~~~~~k~C~~aCPagA~~~~e~----G-~V~vd~e~CigCg~C~~~C 73 (95)
T PRK15449 13 VNKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDD----G-SVRFDYAGCLECGTCRILG 73 (95)
T ss_pred cceeECCCCCCcEEEcCCCCchhhhHHHHHCCHhhcEeCCC----C-CEEEcCCCCCcchhhhhhc
Confidence 456765 48999987655456678999999999977532 2 44558899999999987 6
No 21
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=93.39 E-value=0.12 Score=41.85 Aligned_cols=35 Identities=23% Similarity=0.530 Sum_probs=31.4
Q ss_pred EEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCc
Q 018378 78 VEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPT 113 (357)
Q Consensus 78 I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT 113 (357)
|+|++.+++.++|.+.|=|.+++|+||-.|+.. |.
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~ 35 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD-PG 35 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC-CC
Confidence 578899999999999999999999999998875 44
No 22
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=92.56 E-value=0.18 Score=40.91 Aligned_cols=33 Identities=18% Similarity=0.393 Sum_probs=29.8
Q ss_pred EEEEEecCceEEEEEEcCChhHHHHHHHHHHhh
Q 018378 78 VEVIRLTKDDMEFDLIGIDAAIANAFRRILIAE 110 (357)
Q Consensus 78 I~i~~~~~~~~~F~l~Gvd~siaNALRRILisE 110 (357)
|+|.+.+++.++|.+.|=|.+++|+||-.|+..
T Consensus 1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~ 33 (83)
T cd07027 1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKD 33 (83)
T ss_pred CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcC
Confidence 468889999999999999999999999888765
No 23
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=91.02 E-value=0.4 Score=40.33 Aligned_cols=35 Identities=20% Similarity=0.499 Sum_probs=32.6
Q ss_pred CceEEEEEecCceEEEEEEcCChhHHHHHHHHHHh
Q 018378 75 NFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIA 109 (357)
Q Consensus 75 ~~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILis 109 (357)
.+++++.+.++++++|.++|=|.+++|.||-.|+.
T Consensus 4 ~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~ 38 (99)
T COG1761 4 EMELRIIKKDDNSLELEIEGEDHTLGNLLREELLK 38 (99)
T ss_pred ceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhC
Confidence 46889999999999999999999999999999887
No 24
>COG1146 Ferredoxin [Energy production and conversion]
Probab=85.52 E-value=1 Score=34.37 Aligned_cols=49 Identities=27% Similarity=0.563 Sum_probs=37.1
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEE
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIRR 342 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~ 342 (357)
+..+...||.++|.+.... .++.++.++..|..|..|+. |.. ++|.+..
T Consensus 13 c~~C~~~CP~~~~~~~~~~--~~~~~~~~~e~C~~C~~C~~~CP~---~aI~~~~ 62 (68)
T COG1146 13 CGICVEVCPAGVFDLGEDE--GGKPVVARPEECIDCGLCELACPV---GAIKVDI 62 (68)
T ss_pred CChheeccChhhEEecccc--CcceeEeccccCccchhhhhhCCc---ceEEEec
Confidence 6678899999999986431 15688999999999999998 632 2455543
No 25
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=84.91 E-value=1.4 Score=36.31 Aligned_cols=37 Identities=16% Similarity=0.182 Sum_probs=29.3
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCc
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPT 113 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT 113 (357)
..+......++.++|.+.|=|.++||+||-.|+. -|.
T Consensus 7 v~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~-~~~ 43 (93)
T cd06926 7 ITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLK-DPN 43 (93)
T ss_pred eEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhc-CCC
Confidence 3344444567899999999999999999999887 454
No 26
>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit. During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins.
Probab=82.62 E-value=1.5 Score=38.37 Aligned_cols=37 Identities=24% Similarity=0.650 Sum_probs=29.3
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-c
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c 330 (357)
.+++.||.++|.+++. ...+.+.++..|..|..|+. |
T Consensus 20 ~Cv~~CP~~ai~~~~~---~~~~~~id~~~C~~Cg~Cv~~C 57 (132)
T TIGR02060 20 ACVYICPNDLMHLDTE---IMKAYNIEPDMCWECYSCVKAC 57 (132)
T ss_pred cCHhhcCccceEecCC---CceeeecCchhCccHHHHHHhC
Confidence 8899999999987642 12455678899999999998 6
No 27
>PLN00071 photosystem I subunit VII; Provisional
Probab=82.36 E-value=2.3 Score=33.31 Aligned_cols=54 Identities=22% Similarity=0.538 Sum_probs=34.4
Q ss_pred hHHHHHhhCCCceEEeeccCCCc-eEE-EEccCCCCcchhhHHh-cCCCcCCcEEEEEeC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGK-KRA-TVAQPRACTLCRECLR-CGEEWEKRVSIRRVK 344 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~-~~~-~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~ 344 (357)
.+..+++.||.++|.+.+..+.. ... ...++..|+.|+.|.+ |.. +.+.+..-.
T Consensus 13 ~C~~C~~~CP~~~i~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP~---~Ai~~~~~~ 69 (81)
T PLN00071 13 GCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT---DFLSVRVYL 69 (81)
T ss_pred ChhHHHHHCCccceeeecccccccccccCcCCCCcCcChhhHHhhcCC---ccceEeeee
Confidence 47889999999999876421101 111 2346788999999998 643 245554433
No 28
>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]
Probab=80.44 E-value=1.3 Score=40.58 Aligned_cols=42 Identities=24% Similarity=0.628 Sum_probs=32.2
Q ss_pred HHHHHhhCCCceEEeeccC---CCce--EEEEccCCCCcchhhHHh-c
Q 018378 289 AEKLVKTCPVNVFDIEDIG---SGKK--RATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~---~g~~--~~~V~~~~~ct~crec~r-c 330 (357)
|..|+..||.++|.++... +|.+ +...-|..+|++|..|+. |
T Consensus 60 C~lCa~iCP~~aI~m~~~~~~~~g~~~~~~~~In~grCIfCg~C~e~C 107 (172)
T COG1143 60 CGLCANICPANAITMETAERKVDGRKKPKRPDINLGRCIFCGLCVEVC 107 (172)
T ss_pred hhHHHhhCCcCceEEEEcccCCCCccccccceeccccccccCchhhhC
Confidence 7889999999999996431 2332 344568899999999998 7
No 29
>CHL00065 psaC photosystem I subunit VII
Probab=79.58 E-value=2.4 Score=33.32 Aligned_cols=55 Identities=22% Similarity=0.529 Sum_probs=35.5
Q ss_pred hHHHHHhhCCCceEEeeccCC--CceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEEeCC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGS--GKKRATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKD 345 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~--g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~d 345 (357)
.+..+++.||.++|.+.+... +.......++..|+.|+.|.. |.. +.|++..-..
T Consensus 13 ~Cg~C~~~CP~~~i~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~---~Ai~~~~~~~ 70 (81)
T CHL00065 13 GCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT---DFLSVRVYLG 70 (81)
T ss_pred ChhHHHHHCCccchhheeccccccccccccCCCCcCCChhhhhhhcCc---cccEEEEEec
Confidence 477899999999988864210 111112345678999999998 643 3566654443
No 30
>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed
Probab=78.40 E-value=1.4 Score=36.41 Aligned_cols=59 Identities=24% Similarity=0.476 Sum_probs=37.9
Q ss_pred HhHHHHHhhCCCceEEeeccCCC--ceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEEeCCEEEE
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSG--KKRATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFIC 349 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g--~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~dhFIF 349 (357)
..+..++..||.++|.+.+.+.. .....+.++..|+.|+.|+. |.. +.|++... +.|.|
T Consensus 19 i~C~~Cv~aCP~~ai~~~~~~~~~~~~~~~~i~~~~C~~C~~C~~~CP~---~AI~~~~~-~~~~~ 80 (103)
T PRK09626 19 KACDICVSVCPAGVLAMRIDPHAVLGKMIKVVHPESCIGCRECELHCPD---FAIYVADR-KEFKF 80 (103)
T ss_pred cCCcchhhhcChhhhccccccccccCceeeEeCCccCCCcCcchhhCCh---hhEEEecc-cceee
Confidence 34778999999999987643210 11234557788999999998 642 35666543 34443
No 31
>PF13247 Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX_B 2VPZ_B 2VPW_F 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B ....
Probab=77.81 E-value=3.5 Score=34.36 Aligned_cols=36 Identities=25% Similarity=0.610 Sum_probs=25.6
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-c
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c 330 (357)
.+++.||.|+|..++.+ | +++.|..+|+.|+.|.. |
T Consensus 16 pC~~~CP~~Ai~~~~~~-G---~V~id~~~CigC~~C~~aC 52 (98)
T PF13247_consen 16 PCVEACPTGAIYKDPED-G---IVVIDEDKCIGCGYCVEAC 52 (98)
T ss_dssp HHHHHCTTTSEEEETTT-S----EEE-TTTCCTHHHHHHH-
T ss_pred chhhhCCccceEEEcCC-C---eEEechhhccCchhhhhhh
Confidence 67888999988876521 2 56778888999999988 5
No 32
>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]
Probab=77.68 E-value=1.6 Score=36.69 Aligned_cols=48 Identities=23% Similarity=0.579 Sum_probs=32.2
Q ss_pred ceEEEcCCCChHhHH--HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHH
Q 018378 276 PEIVLLEDVEDEDAE--KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECL 328 (357)
Q Consensus 276 P~I~i~~~i~~~~a~--~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~ 328 (357)
|+|.+.++-....++ .|...||.|++...+. +++++. -..|.-|..|-
T Consensus 25 pHI~v~~~~~~~~~~~~~l~~aCPA~~Y~~~~~----g~l~~~-yegClECGTCR 74 (99)
T COG2440 25 PHIIVKDPDDCQECEDKPLIKACPAGCYKLIDD----GKLRFD-YEGCLECGTCR 74 (99)
T ss_pred CcEecCCchhhhhccchhhhhcCCHHHeeECCC----CcEEEe-ecCeeecccee
Confidence 789887654333444 8999999999998753 346653 35566666653
No 33
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=76.25 E-value=3.4 Score=33.61 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=24.3
Q ss_pred ecCceEEEEEEcCChhHHHHHHHHHHh
Q 018378 83 LTKDDMEFDLIGIDAAIANAFRRILIA 109 (357)
Q Consensus 83 ~~~~~~~F~l~Gvd~siaNALRRILis 109 (357)
..++.++|.+.|=|.++||+||-.|+.
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~ 32 (85)
T cd07029 6 TDESCATFVFYGEDHTLGNSLRYVIMK 32 (85)
T ss_pred CCCCeEEEEEeCCCcchHHHHHHHHhh
Confidence 356789999999999999999999876
No 34
>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional
Probab=75.62 E-value=2.8 Score=35.43 Aligned_cols=40 Identities=23% Similarity=0.551 Sum_probs=29.7
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.+++.+.... ..+ ..+...|+.|..|+. |.
T Consensus 46 ~C~~C~~~CP~~ai~~~~~~---~~~-~i~~~~C~~Cg~Cv~~CP 86 (120)
T PRK08348 46 GCRMCVTVCPAGVFVYLPEI---RKV-ALWTGRCVFCGQCVDVCP 86 (120)
T ss_pred CcccHHHHCCccceEccccc---cce-EecCCcCcChhhhHHhCC
Confidence 47789999999998875321 223 346678999999998 64
No 35
>TIGR00402 napF ferredoxin-type protein NapF. The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation.
Probab=75.32 E-value=3.7 Score=33.83 Aligned_cols=42 Identities=17% Similarity=0.542 Sum_probs=30.6
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..+..++..||.+++.++.. | ......+...|+.|..|.. |.
T Consensus 37 ~~C~~C~~~CP~~~i~~~~~--g-~~~~~i~~~~C~~Cg~C~~~CP 79 (101)
T TIGR00402 37 TRCGECASACENNILQLGQQ--G-QPTVEFDNAECDFCGKCAEACP 79 (101)
T ss_pred cChhHHHHHcCcccceeccC--C-ceeeEecCccCcCccChhhHCC
Confidence 34788999999999887632 2 2233456678999999998 64
No 36
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=73.68 E-value=3.4 Score=37.83 Aligned_cols=51 Identities=18% Similarity=0.424 Sum_probs=33.7
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
.+..+++.||.++|.++....+.......++..|+.|..|.. |.. +.|++.
T Consensus 42 ~Cg~Cv~aCP~~Ai~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CPt---~AI~~~ 93 (181)
T PRK08222 42 ACGACTCACPANALTIQTDDQQNSRTWQLYLGRCIYCGRCEEVCPT---RAIQLT 93 (181)
T ss_pred chhHHHHhCCccceEcccccccCccceeeccCcCcCCCCcccccCc---CeEEec
Confidence 478899999999998764211111222346778999999998 642 355554
No 37
>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed
Probab=73.33 E-value=4 Score=35.55 Aligned_cols=39 Identities=21% Similarity=0.394 Sum_probs=29.6
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..++..||.++|...+ +...+.+...|+.|..|+. |.
T Consensus 63 ~C~~C~~~CP~~ai~~~~-----~~~~~i~~~~C~~Cg~Cv~vCP 102 (133)
T PRK09625 63 NCFNCWVYCPDAAILSRD-----KKLKGVDYSHCKGCGVCVEVCP 102 (133)
T ss_pred ChhhHHHhCCHhheEecC-----CceEEeCcCcCcChhHHHHHCC
Confidence 477899999999987643 1234456778999999999 74
No 38
>TIGR02700 flavo_MJ0208 archaeoflavoprotein, MJ0208 family. This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown.
Probab=70.93 E-value=2.5 Score=39.98 Aligned_cols=39 Identities=28% Similarity=0.659 Sum_probs=30.7
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..|.+|++.||.+++..++ + .. +.++..|+.|+.|.. |.
T Consensus 151 ~~C~~C~~~CP~~ai~~~~---~--~~-~i~~~~C~~Cg~C~~~CP 190 (234)
T TIGR02700 151 KGCGICVDACPRSAIDMVD---G--KA-FIRLLKCVGCGKCKEACP 190 (234)
T ss_pred cCcchHHHhCCcccEEecC---C--ce-EEchhhCCccchHHhhCC
Confidence 3578999999999998763 1 23 457788999999998 74
No 39
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=70.55 E-value=3.3 Score=37.54 Aligned_cols=44 Identities=23% Similarity=0.442 Sum_probs=31.2
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|.++....+.......++..|+.|..|.. |.
T Consensus 42 ~C~~Cv~~CP~~ai~~~~~~~~~~~~~~i~~~~C~~Cg~C~~vCP 86 (180)
T PRK12387 42 GCAACVNACPSNALTVETDLATGELAWEFNLGRCIFCGRCEEVCP 86 (180)
T ss_pred ChhHHHHhcCccCeEeeccccCCcccceeccccCcCccchhhhcC
Confidence 478899999999998864321112223457788999999988 64
No 40
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=70.39 E-value=2.5 Score=33.65 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=21.6
Q ss_pred ceEEEEEEcCChhHHHHHHHHHHhhCCcc
Q 018378 86 DDMEFDLIGIDAAIANAFRRILIAELPTM 114 (357)
Q Consensus 86 ~~~~F~l~Gvd~siaNALRRILisEVPT~ 114 (357)
+.++|.+.|=|.++||+||-.|+.. |.+
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~-p~V 28 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKD-PDV 28 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTS-TTE
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhC-CCe
Confidence 4689999999999999999987764 553
No 41
>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family. A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins.
Probab=69.25 E-value=5.1 Score=30.86 Aligned_cols=39 Identities=15% Similarity=0.309 Sum_probs=29.1
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..++..||.+++...+. + ....++..|+.|..|+. |.
T Consensus 29 ~C~~C~~~Cp~~ai~~~~~----~-~~~i~~~~C~~C~~C~~~CP 68 (78)
T TIGR02179 29 KCKNCWLYCPEGAIQEDEG----G-FVGIDYDYCKGCGICANVCP 68 (78)
T ss_pred ChhHHHhhcCccceEecCC----C-cEEecCccCcCccchhhhCC
Confidence 4788999999999887532 1 23346678999999988 53
No 42
>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed
Probab=68.51 E-value=5 Score=33.55 Aligned_cols=46 Identities=17% Similarity=0.319 Sum_probs=32.9
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
.+..+++.||.++|.+++. + ..+.++..|+.|..|+. |.. +.|.+.
T Consensus 55 ~C~~C~~~CP~~ai~~~~~----~-~~~id~~~C~~Cg~Cv~~CP~---~AI~~~ 101 (105)
T PRK09624 55 RCYLCYIYCPEPAIYLDEE----G-YPVFDYDYCKGCGICANECPT---KAIEMV 101 (105)
T ss_pred ChhhHHhhCCHhhEEecCC----C-cEEECchhCCCcCchhhhcCc---CcEEEe
Confidence 4788999999999988642 2 23447778999999998 643 345443
No 43
>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC. Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction center in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site (pfam00037) and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII.
Probab=66.43 E-value=5.2 Score=31.29 Aligned_cols=44 Identities=18% Similarity=0.584 Sum_probs=30.0
Q ss_pred hHHHHHhhCCCceEEeeccCC-CceEE-EEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGS-GKKRA-TVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~-g~~~~-~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|.+.+.++ ....+ ...++..|+.|+.|+. |.
T Consensus 12 ~C~~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP 58 (80)
T TIGR03048 12 GCTQCVRACPTDVLEMVPWDGCKAGQIASAPRTEDCVGCKRCESACP 58 (80)
T ss_pred CcchHHHHCCccceeeecccccccccccCcCCCCcCcChhHHHHhcC
Confidence 367899999999998864211 00111 2346678999999998 64
No 44
>TIGR01660 narH nitrate reductase, beta subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following: NarH and NarY, both E.Coli, sequences from B. Subtilis, Pseudomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans. This model also matches PFAM pfam00037 for 4Fe-4S binding domain.
Probab=66.41 E-value=2.9 Score=44.01 Aligned_cols=16 Identities=13% Similarity=0.276 Sum_probs=7.6
Q ss_pred HHHHHhhCCCceEEee
Q 018378 289 AEKLVKTCPVNVFDIE 304 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~ 304 (357)
|..|+..||-|++.++
T Consensus 219 Cg~CV~ACPygAI~~n 234 (492)
T TIGR01660 219 WRMCISGCPYKKIYFN 234 (492)
T ss_pred hHHHHHhCCCCCcEec
Confidence 4444555555554443
No 45
>PRK02651 photosystem I subunit VII; Provisional
Probab=66.33 E-value=7.8 Score=30.09 Aligned_cols=43 Identities=21% Similarity=0.623 Sum_probs=29.2
Q ss_pred HHHHHhhCCCceEEeeccCCCc-eEE-EEccCCCCcchhhHHh-cC
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGK-KRA-TVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~-~~~-~V~~~~~ct~crec~r-c~ 331 (357)
+..+++.||.++|...+...+. ... ...++..|..|+.|+. |.
T Consensus 14 C~~C~~~CP~~~i~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP 59 (81)
T PRK02651 14 CTQCVRACPLDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACP 59 (81)
T ss_pred cchHHHHCCccceecccccccccCcccccCCCCcCCChhhhhhhcC
Confidence 6789999999998875421111 111 2346688999999998 64
No 46
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=65.07 E-value=5.1 Score=40.16 Aligned_cols=37 Identities=30% Similarity=0.750 Sum_probs=30.3
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
+.+|++.||.|++++.. +++++ +-.+|..|-.|++ |.
T Consensus 177 c~~cv~~C~~gAI~~~~-----~~l~i-d~~~Ci~Cg~Ci~~Cp 214 (317)
T COG2221 177 CGKCVKVCPTGAITWDG-----KKLKI-DGSKCIGCGKCIRACP 214 (317)
T ss_pred hHhHHHhCCCCceeecc-----ceEEE-ehhhccCccHHhhhCC
Confidence 56999999999999973 45655 5678999999999 74
No 47
>PRK10194 ferredoxin-type protein; Provisional
Probab=64.64 E-value=3.6 Score=36.63 Aligned_cols=51 Identities=14% Similarity=0.305 Sum_probs=35.5
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEE
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIRR 342 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~ 342 (357)
.+..+++.||.++|.++....| ....+.+..+|+.|+.|.. |.. +.|+|..
T Consensus 108 ~C~~C~~~CP~~Ai~~~~~~~~-~~~~~i~~~~C~gCg~C~~~CP~---~AI~~~~ 159 (163)
T PRK10194 108 ECRRCQDSCEPMAIIFRPTLSG-IYQPQLNSQLCNGCGACAASCPV---SAITAEY 159 (163)
T ss_pred CcCcchhhCCHhHeEeeecCCC-cccceeCcccCcCcchhhhhCCc---cceEecc
Confidence 4678889999999998743212 1123457889999999998 642 4676654
No 48
>PRK13795 hypothetical protein; Provisional
Probab=64.47 E-value=6.1 Score=42.97 Aligned_cols=41 Identities=24% Similarity=0.608 Sum_probs=31.2
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..|..|+..||.+++.+++. ...+. .+...|+.|+.|.. |.
T Consensus 584 ~~Cg~C~~~CP~~ai~~~~~---~~~~~-id~~~C~~Cg~C~~aCP 625 (636)
T PRK13795 584 VGCGVCVGACPTGAIRIEEG---KRKIS-VDEEKCIHCGKCTEVCP 625 (636)
T ss_pred CCHhHHHHhCCcccEEeecC---CceEE-echhhcCChhHHHhhcC
Confidence 34888999999999988642 12344 46778999999998 74
No 49
>PRK06273 ferredoxin; Provisional
Probab=64.45 E-value=5.1 Score=36.35 Aligned_cols=45 Identities=18% Similarity=0.485 Sum_probs=31.8
Q ss_pred HhHHHHHhhCCCceEEeeccCC-----C--ceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGS-----G--KKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~-----g--~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..|..|+..||.++|.++.... + .....+.++..|+.|..|.. |.
T Consensus 52 igCg~C~~aCP~~AI~~~~~ep~~~~~~~~~~~~~~Id~~kCi~Cg~C~~aCP 104 (165)
T PRK06273 52 IGCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCP 104 (165)
T ss_pred cChhHHHHhcCccceeeecccccchhcccccccceecccccCcCCCCcchhCC
Confidence 3478899999999998763210 0 01234568889999999998 74
No 50
>TIGR03224 benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA protein. Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB.
Probab=64.25 E-value=4.2 Score=41.70 Aligned_cols=39 Identities=23% Similarity=0.651 Sum_probs=30.4
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..|..|+..||.++|..++ .. .+.++..|+.|..|+. |.
T Consensus 13 i~C~~C~~~CP~~ai~~~~-----~~-~~i~~~~C~~C~~C~~~CP 52 (411)
T TIGR03224 13 IRCNTCEETCPIDAITHDD-----RN-YVVKADVCNGCMACVSPCP 52 (411)
T ss_pred cCccchhhhCCcccEeccC-----Cc-eEeCcccCcCHHHHHhhcC
Confidence 4588899999999987753 12 3457889999999999 74
No 51
>PRK05888 NADH dehydrogenase subunit I; Provisional
Probab=63.60 E-value=3.8 Score=36.55 Aligned_cols=44 Identities=20% Similarity=0.493 Sum_probs=30.9
Q ss_pred hHHHHHhhCCCceEEeeccC--CCce--EEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIG--SGKK--RATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~--~g~~--~~~V~~~~~ct~crec~r-c~ 331 (357)
.|..|+..||.+++.+.... +|.. ...+.+...|+.|..|.. |.
T Consensus 62 ~C~~C~~~CP~~ai~~~~~~~~~g~~~~~~~~i~~~~C~~Cg~Cv~~CP 110 (164)
T PRK05888 62 ACKLCAAICPADAITIEAAEREDGRRRTTRYDINFGRCIFCGFCEEACP 110 (164)
T ss_pred cccChHHHcCccccccccccCCCCcccceeeecCCCcCcccCcchhhcC
Confidence 47789999999998765321 1211 234468899999999998 74
No 52
>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J.
Probab=62.61 E-value=7.1 Score=27.89 Aligned_cols=39 Identities=28% Similarity=0.813 Sum_probs=24.3
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEc------cCCCCcchhhHHh-c
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVA------QPRACTLCRECLR-C 330 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~------~~~~ct~crec~r-c 330 (357)
+..+++.||.+++.....+ ...... +...|+.|..|+. |
T Consensus 5 Cg~C~~~CP~~~~~~~~~~---~~~~~~~~~~~~~~~~C~~Cg~C~~~C 50 (55)
T PF13187_consen 5 CGRCVEACPVGVIEFDEDG---GKKVVDKDNERRNAEKCIGCGACVKAC 50 (55)
T ss_dssp TTHHHHHSTTT-EEEETTT---TCEECSECCESTTGGG--TTCHHHHHS
T ss_pred cchHHHHCCccCeEccCcc---ccccccccccCCCCCccccHhHHHHHc
Confidence 3468889999999987643 222222 2347999999997 5
No 53
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit.
Probab=61.76 E-value=9.2 Score=34.31 Aligned_cols=39 Identities=26% Similarity=0.572 Sum_probs=30.1
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+.++++.||.+++.... +...+.+...|+.|..|.. |.
T Consensus 117 ~Cg~C~~aCp~~ai~~~~-----~~~~~i~~~~C~~Cg~Cv~~CP 156 (165)
T TIGR01944 117 GCTKCIQACPVDAIVGAA-----KAMHTVIADECTGCDLCVEPCP 156 (165)
T ss_pred ChhHHHHhCCccceEecC-----CCceEeecccccChhHHHHhcC
Confidence 478899999999987653 2234557788999999998 64
No 54
>PRK09623 vorD 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed
Probab=61.48 E-value=4.7 Score=33.56 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=29.8
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|...+. + ..+.+...|+.|+.|++ |.
T Consensus 55 ~C~~C~~~CP~~ai~~~~~----~-~~~id~~~C~~Cg~Cv~~CP 94 (105)
T PRK09623 55 KCYICWKFCPEPAIYIKED----G-YVAIDYDYCKGCGICANECP 94 (105)
T ss_pred cccchhhhCCHhheEecCC----C-cEEeCchhCcCcchhhhhcC
Confidence 4778999999999877532 1 23457788999999998 64
No 55
>COG0437 HybA Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]
Probab=59.76 E-value=7.5 Score=36.70 Aligned_cols=34 Identities=21% Similarity=0.470 Sum_probs=19.2
Q ss_pred HHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh
Q 018378 292 LVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329 (357)
Q Consensus 292 l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r 329 (357)
+++.||.|+.-.... +-+++.|...|..|+.|+.
T Consensus 77 Cv~vCPtgA~~k~~~----dGiV~vd~d~CIGC~yCi~ 110 (203)
T COG0437 77 CVKVCPTGALFKREE----DGIVLVDKDLCIGCGYCIA 110 (203)
T ss_pred ccccCCCcceEEecC----CCEEEecCCcccCchHHHh
Confidence 556666665544321 1155566666666666665
No 56
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=59.28 E-value=4.3 Score=39.03 Aligned_cols=53 Identities=25% Similarity=0.654 Sum_probs=35.1
Q ss_pred eceEEEcC-CCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-c
Q 018378 275 LPEIVLLE-DVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 275 ~P~I~i~~-~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c 330 (357)
...+.+.. .+ -.|..|++.||.+++.+.....+ +...+.++..|+.|..|.. |
T Consensus 40 ~~~~~~~~~~C--~~C~~C~~~Cp~~a~~~~~~~~~-~~~~~~~~~~C~~Cg~C~~~C 94 (295)
T TIGR02494 40 SPELLFKENRC--LGCGKCVEVCPAGTARLSELADG-RNRIIIRREKCTHCGKCTEAC 94 (295)
T ss_pred CceEEEccccC--CCCchhhhhCcccccccccccCC-CcceeechhhcCchhHhhccC
Confidence 34445443 23 34678999999999874321112 2345678889999999998 6
No 57
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=57.81 E-value=6 Score=37.94 Aligned_cols=43 Identities=21% Similarity=0.488 Sum_probs=28.3
Q ss_pred HhHHHHHhhCCCce-EEeeccCCCceEEEEccCCCCcchhhHHh-cCC
Q 018378 287 EDAEKLVKTCPVNV-FDIEDIGSGKKRATVAQPRACTLCRECLR-CGE 332 (357)
Q Consensus 287 ~~a~~l~~~cp~gV-~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~ 332 (357)
.+|.++++.||.++ +.....+ .+... .+...|+.|.+|++ |..
T Consensus 204 ~~C~~C~~vCP~~~vl~~~~~~--~~~~~-i~~~~C~~Cg~Cv~~CP~ 248 (255)
T TIGR02163 204 TNCMDCFNVCPEPQVLRMPLKK--GGSTL-VLSGDCTLCGRCIDVCHE 248 (255)
T ss_pred eEcCCccCcCCCCceeeccccC--CCceE-eccccccchhHHHHhCCc
Confidence 45788999999885 4443211 12223 36678999999998 753
No 58
>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific. Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin.
Probab=55.46 E-value=11 Score=29.81 Aligned_cols=44 Identities=30% Similarity=0.637 Sum_probs=30.9
Q ss_pred hHHHHHhhCCCceEEeeccC-----------CCc---eEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIG-----------SGK---KRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~-----------~g~---~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|.+...+ .+. ....+.++..|+.|..|.. |.
T Consensus 25 ~C~~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~C~~Cg~C~~~CP 83 (91)
T TIGR02936 25 GCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVANPGNCIGCGACARVCP 83 (91)
T ss_pred CcchHHHHcChhhceeeccccccccccccccccccccceeeecCCccCcChhhhhhhCC
Confidence 37889999999999876310 000 1233568899999999998 64
No 59
>TIGR03478 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit. This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase.
Probab=54.22 E-value=7.6 Score=39.06 Aligned_cols=58 Identities=17% Similarity=0.406 Sum_probs=35.2
Q ss_pred eecceeeEEeeee--ceEEEcC-CCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcch---------hhHHh-
Q 018378 263 KWSPVATAWYRML--PEIVLLE-DVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLC---------RECLR- 329 (357)
Q Consensus 263 KwSPVata~Yr~~--P~I~i~~-~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~c---------rec~r- 329 (357)
+-.|+. |.|+-. -.+.++. .+ ..+..|+..||-+++.++... .+..+|++| ..|+.
T Consensus 141 ~aCPtg-AI~k~eedGiV~ID~ekC--iGCg~Cv~ACPygAi~~n~~~--------~~~eKC~~C~~Rie~G~~PaCv~a 209 (321)
T TIGR03478 141 AACPTG-AIYKREEDGIVLVDQERC--KGYRYCVEACPYKKVYFNPQS--------QKSEKCIGCYPRIEKGIAPACVKQ 209 (321)
T ss_pred hhCCcC-cEEEecCCCeEEECHHHC--cchHHHHHhCCCCCcEecCCC--------CchhhCCCchhhhccCCCCHHHhh
Confidence 345654 344322 2334443 23 347888999999988876421 245789999 57887
Q ss_pred cC
Q 018378 330 CG 331 (357)
Q Consensus 330 c~ 331 (357)
|.
T Consensus 210 CP 211 (321)
T TIGR03478 210 CP 211 (321)
T ss_pred cC
Confidence 64
No 60
>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3CF4_A 1K0T_A 2VKR_C 1JB0_C 3PCQ_C.
Probab=53.49 E-value=3.5 Score=29.48 Aligned_cols=40 Identities=25% Similarity=0.674 Sum_probs=23.7
Q ss_pred HHHHHhhCCCceEEeeccCC--CceEEEEccCCCCcchhhHHh
Q 018378 289 AEKLVKTCPVNVFDIEDIGS--GKKRATVAQPRACTLCRECLR 329 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~--g~~~~~V~~~~~ct~crec~r 329 (357)
+..+++.||.++|.+....+ +...+. .++..|+.|..|+.
T Consensus 5 C~~C~~~CP~~~i~~~~~~~~~~~~~~~-~~~~~C~~C~~C~~ 46 (52)
T PF12838_consen 5 CGACVEACPTGAIRLDEEENEEGKPKMV-IDPDKCTGCGACVE 46 (52)
T ss_dssp --HHHHH-TTHHCEEEETTT-SSSTTSE-ETGGG----SHHHH
T ss_pred cCchHHhcCccccCcccccccCCceEEE-EechhCcCcChhhh
Confidence 45788999999999876421 223344 47899999999987
No 61
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=52.99 E-value=14 Score=31.41 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=28.3
Q ss_pred cCceEEEEEEcCChhHHHHHHHHHHhhCCcceEEEEEEeeCc
Q 018378 84 TKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNT 125 (357)
Q Consensus 84 ~~~~~~F~l~Gvd~siaNALRRILisEVPT~AIe~V~I~~NT 125 (357)
+.....|.|..=|.+||||||=+++- =..|.+-+.|
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k------~peVefcGYt 49 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMK------NPEVEFCGYT 49 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhc------CCceEEEecc
Confidence 34578999999999999999998776 3456666655
No 62
>PRK05113 electron transport complex protein RnfB; Provisional
Probab=51.44 E-value=11 Score=34.76 Aligned_cols=46 Identities=20% Similarity=0.446 Sum_probs=32.5
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
.+.++++.||.+++..... .....++..|+.|..|+. |.. +.|.+.
T Consensus 118 ~Cg~Cv~aCp~~ai~~~~~-----~~~~v~~~~C~~Cg~Cv~vCP~---~AI~~~ 164 (191)
T PRK05113 118 GCTKCIQACPVDAIVGATK-----AMHTVISDLCTGCDLCVAPCPT---DCIEMI 164 (191)
T ss_pred CCChhhhhCCHhhhecccC-----CceeecCCcCCchHHHHHHcCc---CceEEe
Confidence 3778999999999876431 233456789999999998 743 345444
No 63
>PRK06991 ferredoxin; Provisional
Probab=50.04 E-value=7.6 Score=38.01 Aligned_cols=47 Identities=21% Similarity=0.444 Sum_probs=33.9
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEEe
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIRRV 343 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~ 343 (357)
+..|+..||.++|.+.. +...+.+...|+.|..|+. |.. +.|.+...
T Consensus 90 Cg~Cv~aCP~~AI~~~~-----~~~~~v~~~~CigCg~Cv~vCP~---~AI~~~~~ 137 (270)
T PRK06991 90 CTLCMQACPVDAIVGAP-----KQMHTVLADLCTGCDLCVPPCPV---DCIDMVPV 137 (270)
T ss_pred CcHHHHhCCHhheeccc-----ccceeeCHhhCCCchHHHhhCCc---CCeEeecC
Confidence 77899999999987753 1234456789999999998 743 35555433
No 64
>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.
Probab=49.25 E-value=16 Score=34.22 Aligned_cols=55 Identities=18% Similarity=0.468 Sum_probs=36.1
Q ss_pred HhHHHHHhhCCC--ceEEeeccCCCce--EEEEccCCCCcchhhHHh-cCCCcCCcEEEEE
Q 018378 287 EDAEKLVKTCPV--NVFDIEDIGSGKK--RATVAQPRACTLCRECLR-CGEEWEKRVSIRR 342 (357)
Q Consensus 287 ~~a~~l~~~cp~--gV~~i~~~~~g~~--~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~ 342 (357)
-.+..+++.||. ++|.++....... ..-+.++.+|+.|..|.. | +-.+..|++..
T Consensus 139 ~~C~~C~~~CP~~~~AI~~~~~~~~~~~~~~p~Vd~~~C~gCG~C~~~C-P~~~~AI~v~~ 198 (213)
T TIGR00397 139 LNCSICVRVCPIRGEAISLKPIENERGRLQIPTVDSAKCTGCGTCEKHC-VLSEAAIRVLP 198 (213)
T ss_pred CCcccchhhCCCCcceEEEecccccCCcccceEEecccCCCcchhhHhC-CCCCCeEEEee
Confidence 357889999998 6887764311111 233557889999999998 6 32234666554
No 65
>PRK07118 ferredoxin; Validated
Probab=47.84 E-value=16 Score=35.72 Aligned_cols=38 Identities=32% Similarity=0.775 Sum_probs=30.6
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|.+++ . ..+.|+.+|+.|..|.. |.
T Consensus 217 ~Cg~Cv~~CP~~AI~~~~-----~-~~vId~~~C~~Cg~C~~~CP 255 (280)
T PRK07118 217 GCGKCVKACPAGAITMEN-----N-LAVIDQEKCTSCGKCVEKCP 255 (280)
T ss_pred cchHHHhhCCcCcEEEeC-----C-cEEEcCCcCCCHHHHHHhCC
Confidence 367899999999999863 1 34558899999999998 63
No 66
>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family.
Probab=47.80 E-value=18 Score=34.39 Aligned_cols=38 Identities=24% Similarity=0.656 Sum_probs=29.7
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..+++.||.++|..+. ++.. .+...|+.|+.|.. |.
T Consensus 178 ~C~~C~~aCP~~ai~~~~-----~~~~-i~~~~C~~C~~C~~~CP 216 (228)
T TIGR03294 178 GCGTCAAACPTRAIEMED-----GRPN-VNRDRCIKCGACYVQCP 216 (228)
T ss_pred ChhHHHHhCCHhhEEEeC-----CcEE-EChhhccCHHHHHHHcC
Confidence 488999999999998863 1233 46678999999998 74
No 67
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=46.66 E-value=22 Score=34.17 Aligned_cols=35 Identities=26% Similarity=0.636 Sum_probs=27.3
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh---------hHHh-c
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR---------ECLR-C 330 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr---------ec~r-c 330 (357)
.+..++..||.+++.++... .+..+|++|. .|+. |
T Consensus 134 gC~~Cv~aCP~~Ai~~~~~~--------~~~~KC~~C~~r~~~G~~PaCv~~C 178 (244)
T PRK14993 134 GCAYCVQACPYDARFINHET--------QTADKCTFCVHRLEAGLLPACVESC 178 (244)
T ss_pred CHHHHHHhcCCCCCEEeCCC--------CCcccCcCCcchhhCCCCcccchhc
Confidence 47889999999999986421 2457899997 6887 6
No 68
>TIGR02176 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric. This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase.
Probab=46.51 E-value=11 Score=44.07 Aligned_cols=54 Identities=24% Similarity=0.480 Sum_probs=34.0
Q ss_pred HhHHHHHhhCCCceEEeecc------------------C---CCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 287 EDAEKLVKTCPVNVFDIEDI------------------G---SGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~------------------~---~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
-.|..|+..||.++|..... + .+.......++..|+.|..|.. |..+ .+.+.+.
T Consensus 686 i~Cg~C~~vCP~~ai~~~~~~~~~~~~ap~~~~~~~~~~~~~~~~~~~i~i~~~~C~gCg~Cv~~CP~~-~~Al~m~ 761 (1165)
T TIGR02176 686 IQCNQCAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISPLDCTGCGNCVDICPAK-EKALVMQ 761 (1165)
T ss_pred CCccchHHhcChhhccccccchhhhhcCcccchhhhhhcccccccceeEEeccccCcCccchhhhcCCC-Ccccccc
Confidence 45888999999999875310 0 0101113458899999999999 8532 2344443
No 69
>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional
Probab=45.68 E-value=13 Score=39.29 Aligned_cols=44 Identities=20% Similarity=0.393 Sum_probs=30.6
Q ss_pred HHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEE
Q 018378 290 EKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSI 340 (357)
Q Consensus 290 ~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l 340 (357)
..|...||.+++..... + .....+...|+.|..|.+ |.. +.|++
T Consensus 516 ~~C~~~Cp~~ai~~~~~--~--~~~~i~~~~C~~Cg~C~~~CP~---~Ai~~ 560 (564)
T PRK12771 516 DNCYGACPQDAIIKLGP--G--RRYHFDYDKCTGCHICADVCPC---GAIEM 560 (564)
T ss_pred chhhhhCChhheeeecC--C--ceEEEecccCcChhHHHhhcCc---CceEe
Confidence 56777799999877532 1 224457789999999999 743 35554
No 70
>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein. Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase.
Probab=45.36 E-value=18 Score=34.12 Aligned_cols=70 Identities=16% Similarity=0.383 Sum_probs=41.5
Q ss_pred eeecceeeEEeee-eceEEEcC-CCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh----------hHHh
Q 018378 262 AKWSPVATAWYRM-LPEIVLLE-DVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR----------ECLR 329 (357)
Q Consensus 262 AKwSPVata~Yr~-~P~I~i~~-~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr----------ec~r 329 (357)
++-.|+......- ...+.++. .. -.+..++..||.+++.+... ..+..+|++|. .|+.
T Consensus 103 v~~CP~gAi~~~~~~g~v~id~~~C--~~C~~C~~aCP~~A~~~~~~--------~~~~~kC~~C~~~~~~~g~~P~Cv~ 172 (225)
T TIGR03149 103 VAVCPTGASFKDEETGIVDVHKDLC--VGCQYCIAACPYRVRFIHPV--------TKSADKCNFCRDTNLAEGKLPACVE 172 (225)
T ss_pred HhhCCCCcEEEeCCCCeEEechhhC--CcchHHHHhCCCCCcEecCC--------CCccccCCCCCcchhhCCCCCcccc
Confidence 5667776544332 22344543 23 34788999999998766431 12467899996 6887
Q ss_pred -cCCCcCCcEEEEEeC
Q 018378 330 -CGEEWEKRVSIRRVK 344 (357)
Q Consensus 330 -c~~~~~~~V~l~~~~ 344 (357)
|.. +.+.++...
T Consensus 173 ~Cp~---~Ai~f~~~~ 185 (225)
T TIGR03149 173 SCPT---KALTFGDLN 185 (225)
T ss_pred cCcc---CCEEEeccc
Confidence 642 355555433
No 71
>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I. This model represents the I subunit (one of 14: A-N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes.
Probab=45.25 E-value=10 Score=31.78 Aligned_cols=44 Identities=18% Similarity=0.469 Sum_probs=30.0
Q ss_pred hHHHHHhhCCCceEEeeccC--CCce--EEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIG--SGKK--RATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~--~g~~--~~~V~~~~~ct~crec~r-c~ 331 (357)
.+..++..||.+++.+.... ++.. ...+.+...|..|+.|.. |.
T Consensus 47 ~C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~Cv~~CP 95 (122)
T TIGR01971 47 GCTLCAAVCPADAIRVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACP 95 (122)
T ss_pred CcchhhhhcCHhHeeeeeeccCCCceecccceECcccCCCCCchhhhCC
Confidence 47788999999988765321 1111 124457788999999998 63
No 72
>TIGR03478 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit. This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase.
Probab=44.49 E-value=35 Score=34.48 Aligned_cols=41 Identities=17% Similarity=0.480 Sum_probs=30.2
Q ss_pred HhHH--HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAE--KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~--~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+|. .+++.||.|+|...+. +| +++.|..+|..|+.|+. |.
T Consensus 132 ~hC~nP~Cv~aCPtgAI~k~ee-dG---iV~ID~ekCiGCg~Cv~ACP 175 (321)
T TIGR03478 132 NHCTNPACLAACPTGAIYKREE-DG---IVLVDQERCKGYRYCVEACP 175 (321)
T ss_pred CCCCCccchhhCCcCcEEEecC-CC---eEEECHHHCcchHHHHHhCC
Confidence 4455 7889999999865432 12 45568889999999999 73
No 73
>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.
Probab=44.23 E-value=14 Score=26.11 Aligned_cols=38 Identities=32% Similarity=0.767 Sum_probs=18.4
Q ss_pred hHHHHHhhCCC-ceEEeeccCCCceEEEEccCCCCcchhhHHh
Q 018378 288 DAEKLVKTCPV-NVFDIEDIGSGKKRATVAQPRACTLCRECLR 329 (357)
Q Consensus 288 ~a~~l~~~cp~-gV~~i~~~~~g~~~~~V~~~~~ct~crec~r 329 (357)
.+..+++.||. ++..+... .+...+ ++.+|+.|..|+.
T Consensus 11 ~C~~C~~~CP~~~~~~~~~~---~~~~~~-~~~~C~~Cg~C~~ 49 (52)
T PF13237_consen 11 GCGRCVKVCPADNAIAIDDG---EKKVEI-DPERCIGCGACVE 49 (52)
T ss_dssp ---TTGGG-TT-----EEE----SSSEEE--TTT--TTSHHHH
T ss_pred CCcChHHHccchhHHHhhcc---CCCeEe-CcccccccChhhh
Confidence 35678889998 33333321 133444 8999999999986
No 74
>PRK10194 ferredoxin-type protein; Provisional
Probab=44.20 E-value=20 Score=31.84 Aligned_cols=16 Identities=19% Similarity=0.486 Sum_probs=10.1
Q ss_pred HHHHHhhCCCceEEee
Q 018378 289 AEKLVKTCPVNVFDIE 304 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~ 304 (357)
+..++..||.+++...
T Consensus 71 C~~C~~~CP~~ai~~~ 86 (163)
T PRK10194 71 CYACAQACPESLFSPR 86 (163)
T ss_pred chhhHhhCcchheecc
Confidence 5566667777766553
No 75
>PRK09898 hypothetical protein; Provisional
Probab=43.16 E-value=19 Score=33.43 Aligned_cols=43 Identities=21% Similarity=0.525 Sum_probs=30.6
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
.+..+++.||.+++.++... .++.+|++|..|++ |.. +.+.+.
T Consensus 158 gC~~C~~aCP~~ai~~~~~~--------~~~~kC~~Cg~Cv~~CP~---~Ai~~~ 201 (208)
T PRK09898 158 GCSACTTACPWMMATVNTES--------KKSSKCVLCGECANACPT---GALKII 201 (208)
T ss_pred CcCcccccCCCCCCEecCCC--------CcCCcCcChHHHHHhCCc---ccEEEe
Confidence 36778899999998876321 24678999999998 643 245444
No 76
>COG1145 NapF Ferredoxin [Energy production and conversion]
Probab=42.69 E-value=12 Score=29.21 Aligned_cols=42 Identities=31% Similarity=0.690 Sum_probs=30.2
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
+..+.+.||.++|.+...... ....+.++..|+.|..|.+ |.
T Consensus 34 Cg~C~~~CP~~ai~~~~~~~~-~~~~~~~~~~C~~C~~C~~~Cp 76 (99)
T COG1145 34 CGLCVKVCPTGAIELIEEGLL-LPEVVIDPDLCVLCGACLKVCP 76 (99)
T ss_pred CCCchhhCCHHHhhcccccCc-cceEEEccccCccccchHhhCC
Confidence 778899999999887421100 1234557899999999998 64
No 77
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=42.58 E-value=15 Score=37.01 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=7.8
Q ss_pred HHHHHhhCCCceEEe
Q 018378 289 AEKLVKTCPVNVFDI 303 (357)
Q Consensus 289 a~~l~~~cp~gV~~i 303 (357)
|..|+..||.+++.+
T Consensus 148 Cg~Cv~aCP~gai~~ 162 (328)
T PRK10882 148 CRYCMVACPFNVPKY 162 (328)
T ss_pred ccHHHHhCCccceec
Confidence 445555555555544
No 78
>PRK09853 putative selenate reductase subunit YgfK; Provisional
Probab=41.58 E-value=18 Score=41.77 Aligned_cols=56 Identities=16% Similarity=0.520 Sum_probs=34.2
Q ss_pred HHHHHhhCCCce---EEeeccCCCceEEEEccCCCCcchhhHHh-cC---CCcCCcEEEEEeCCE
Q 018378 289 AEKLVKTCPVNV---FDIEDIGSGKKRATVAQPRACTLCRECLR-CG---EEWEKRVSIRRVKDH 346 (357)
Q Consensus 289 a~~l~~~cp~gV---~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~---~~~~~~V~l~~~~dh 346 (357)
|..|+..||.++ +.+.... +....++. +..|+-|..|.. |. ..++|+.+|=..++.
T Consensus 895 C~~C~~vCP~~A~~~i~~~g~~-~~~~~~~~-~~~C~~CG~C~~~CP~~~~py~dk~t~f~~~~d 957 (1019)
T PRK09853 895 CEKCVDVCPNRANVSIAVPGFQ-NRFQIVHL-DAMCNECGNCAQFCPWNGKPYKDKITLFSLEED 957 (1019)
T ss_pred cchhhhhCCcccccccccCCcc-cCCceEEc-CccCccccchhhhCCCCCCcccccceEEcchhh
Confidence 466777799999 4433211 11233333 478999999998 72 345777777655443
No 79
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=41.12 E-value=9.8 Score=38.25 Aligned_cols=37 Identities=27% Similarity=0.591 Sum_probs=28.5
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.|++.||.|+|..++. ...++.+...|+.|+.|.. |.
T Consensus 119 ~Cv~aCP~gAi~k~~~----~g~V~id~dkCigCg~Cv~aCP 156 (328)
T PRK10882 119 NCVSVCPVSALTKDPK----TGIVHYDKDVCTGCRYCMVACP 156 (328)
T ss_pred hhHhhCCCCCEEeccc----CCcccCCHHHcCcccHHHHhCC
Confidence 6889999999987542 1244568889999999998 64
No 80
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=41.09 E-value=16 Score=35.27 Aligned_cols=45 Identities=24% Similarity=0.532 Sum_probs=31.7
Q ss_pred HhHHHHHhhCCC--ceEEeeccCC---Cce--EEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPV--NVFDIEDIGS---GKK--RATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~--gV~~i~~~~~---g~~--~~~V~~~~~ct~crec~r-c~ 331 (357)
..+..+++.||. ++|.++...+ |.. ..-+.+...|+.|..|.. |.
T Consensus 145 ~~C~~C~~~CP~~~~AI~~~~~~~~r~g~~~~~~p~Id~d~C~gCG~C~~aCP 197 (254)
T PRK09476 145 LRCDVCYRVCPLIDKAITLELERNERTGKHAFFLPTVHSDACTGCGKCEKACV 197 (254)
T ss_pred CchHHHhhhCCCccCeEEEEcccccccccccccceEEeHHHCcCcChhhHhcC
Confidence 468899999995 8998874321 111 123457788999999998 74
No 81
>TIGR02912 sulfite_red_C sulfite reductase, subunit C. Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite.
Probab=40.57 E-value=20 Score=35.20 Aligned_cols=38 Identities=26% Similarity=0.586 Sum_probs=28.0
Q ss_pred HhHHHHHhhCCC---ceEEeeccCCCceEEEEccCCCCcchhhHHh-c
Q 018378 287 EDAEKLVKTCPV---NVFDIEDIGSGKKRATVAQPRACTLCRECLR-C 330 (357)
Q Consensus 287 ~~a~~l~~~cp~---gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c 330 (357)
..|..|++.||. +++...+ .++ +.++..|+.|..|+. |
T Consensus 172 ~~Cg~C~~~Cp~~a~~ai~~~~-----~~~-~id~~~C~~Cg~Cv~~C 213 (314)
T TIGR02912 172 IGCGACVKVCKKKAVGALSFEN-----YKV-VRDHSKCIGCGECVLKC 213 (314)
T ss_pred CcchHHHHhcChhhcCceeccC-----CeE-EeCCCcCcCcchhhhhC
Confidence 357789999996 5565542 233 458889999999998 7
No 82
>PRK10330 formate dehydrogenase-H ferredoxin subunit; Provisional
Probab=39.75 E-value=23 Score=31.93 Aligned_cols=35 Identities=20% Similarity=0.551 Sum_probs=26.8
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+++.||.|++..++ +.+.+ +..+|+.|+.|.. |.
T Consensus 65 ~C~~~Cp~~ai~~~~-----~~v~i-~~~~C~~C~~C~~~CP 100 (181)
T PRK10330 65 PCANVCPNGAISRDK-----GFVHV-MQERCIGCKTCVVACP 100 (181)
T ss_pred HHHHHcCcccEEccC-----CeEEe-ChhhCCCcchhhhhCC
Confidence 788999999987642 23444 7788999999998 63
No 83
>PRK09477 napH quinol dehydrogenase membrane component; Provisional
Probab=39.23 E-value=12 Score=36.14 Aligned_cols=51 Identities=18% Similarity=0.451 Sum_probs=29.7
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEE
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIR 341 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~ 341 (357)
..|.+|++.||.+.+.-... .++....+.+...|+.|.+|+. |.. +.++..
T Consensus 211 ~~C~~C~~~CP~~~i~~~~~-~~~~~~~~i~~~~C~~Cg~Cv~~CP~---~Ai~~~ 262 (271)
T PRK09477 211 TRCMDCFHVCPEPQVLRPPL-KGKQSPSQVTSGDCITCGRCIDVCSE---DVFNFT 262 (271)
T ss_pred cccCCcCCcCCCcceecccc-cCCCccceeCcccCcChhHHHhhcCc---cceeec
Confidence 35778888999886321000 0111111245667999999998 753 345543
No 84
>PRK13984 putative oxidoreductase; Provisional
Probab=38.85 E-value=30 Score=36.86 Aligned_cols=64 Identities=22% Similarity=0.490 Sum_probs=39.1
Q ss_pred HhHHHHHhhCCCceEEeeccC-----CCce-EEEEccCCCCcchhhHHh-cCCC---c-CCcEEEEEeCCEEEEE
Q 018378 287 EDAEKLVKTCPVNVFDIEDIG-----SGKK-RATVAQPRACTLCRECLR-CGEE---W-EKRVSIRRVKDHFICK 350 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~-----~g~~-~~~V~~~~~ct~crec~r-c~~~---~-~~~V~l~~~~dhFIF~ 350 (357)
-.|.+|++.||.+++...+.. .|.. ...+.+...|+.|..|+. |..+ + .+.+.+......|+|+
T Consensus 48 i~C~~C~~~Cp~~ai~~~~~~~~~~~~g~~~~~~~i~~~~c~~c~~c~~~Cp~~Ai~~~~~~~~~~~~~~~~~~~ 122 (604)
T PRK13984 48 IGCGTCSKICPTDAITMVEVPDLPQEYGKKPQRPVIDYGRCSFCALCVDICTTGSLKMTREYIHISPDPEDFIFM 122 (604)
T ss_pred cCccchhhhCCccceEeeccccccccccccccccccCcccCcCcchHHhhCCcCcEEecceEEEeecChhhEEEe
Confidence 348899999999988765320 0111 123567788999999998 7421 1 1234445555555554
No 85
>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit. This model describes the beta subunit of sulfite reductase.
Probab=37.78 E-value=11 Score=37.93 Aligned_cols=39 Identities=23% Similarity=0.600 Sum_probs=28.6
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+++.||.+++.+++.+ +.++ .+.|+..|..|..|++ |.
T Consensus 188 ~Cv~~CP~~Ai~~~~~~-~~~~-~~id~~~Ci~Cg~Ci~~CP 227 (341)
T TIGR02066 188 SVVAACPTGALKPRRDG-KNKS-LEVDVEKCIYCGNCYTMCP 227 (341)
T ss_pred ceEeeCchhhceecccC-CCCc-eeeccccCCcCCchHHhCc
Confidence 56778999999885321 1234 4568889999999999 73
No 86
>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein.
Probab=37.55 E-value=15 Score=33.65 Aligned_cols=44 Identities=20% Similarity=0.499 Sum_probs=27.1
Q ss_pred hHHHHHhhCCCceEEeecc-----CCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDI-----GSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~-----~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.|..|++.||.+++.+... ..........+...|+.|..|.. |.
T Consensus 66 ~Cg~C~~aCP~~ai~~~~~~~~~~~~~~~~~~~id~~~Ci~Cg~Cv~aCP 115 (183)
T TIGR00403 66 ACEVCVRVCPINLPVVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCP 115 (183)
T ss_pred CcCChhhhCCCCcccccccccccccccccceeecCcccccCcCchhhhcC
Confidence 4677888999987533210 00011223456778999999998 63
No 87
>KOG2415 consensus Electron transfer flavoprotein ubiquinone oxidoreductase [Energy production and conversion]
Probab=36.43 E-value=24 Score=37.44 Aligned_cols=35 Identities=23% Similarity=0.575 Sum_probs=25.2
Q ss_pred hhCCCceEEeeccCC--CceEEEEccCCCCcchhhHHh
Q 018378 294 KTCPVNVFDIEDIGS--GKKRATVAQPRACTLCRECLR 329 (357)
Q Consensus 294 ~~cp~gV~~i~~~~~--g~~~~~V~~~~~ct~crec~r 329 (357)
+-||.||+++-++.. ..+++.+ |..+|.-|..|--
T Consensus 562 rfCPAgVYEyV~dE~~~~~krlqI-NaQNCiHCKtCDI 598 (621)
T KOG2415|consen 562 RFCPAGVYEYVPDEAGPVGKRLQI-NAQNCIHCKTCDI 598 (621)
T ss_pred ccCCccceeecccccCCCcceEEE-ccccceecccccc
Confidence 469999999854322 2246665 8899999999943
No 88
>PRK09898 hypothetical protein; Provisional
Probab=36.23 E-value=25 Score=32.63 Aligned_cols=41 Identities=15% Similarity=0.533 Sum_probs=30.2
Q ss_pred HhHH--HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAE--KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~--~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.++. .+++.||.|+|...+.. + ..+.+...|..|+.|.+ |.
T Consensus 124 ~~C~~~~C~~~CP~gAi~~~~~~---g-~v~vd~~~CigC~~C~~aCP 167 (208)
T PRK09898 124 RQCKEPQCMNVCPIGAITWQQKE---G-CITVDHKRCIGCSACTTACP 167 (208)
T ss_pred CCccCcchhhhCCcceEEeeccC---C-eEEeccccCCCcCcccccCC
Confidence 4454 68899999999876421 2 34457788999999998 63
No 89
>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=35.84 E-value=18 Score=22.69 Aligned_cols=17 Identities=41% Similarity=1.136 Sum_probs=14.2
Q ss_pred EccCCCCcchhhHHh-cC
Q 018378 315 VAQPRACTLCRECLR-CG 331 (357)
Q Consensus 315 V~~~~~ct~crec~r-c~ 331 (357)
+.|+.+|+.|..|++ |.
T Consensus 3 ~id~~~C~~Cg~C~~~Cp 20 (24)
T PF12837_consen 3 VIDPDKCIGCGDCVRVCP 20 (24)
T ss_pred EEChhhCcChhHHHHhcc
Confidence 458899999999998 53
No 90
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=35.56 E-value=25 Score=36.76 Aligned_cols=34 Identities=35% Similarity=0.812 Sum_probs=25.1
Q ss_pred HhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 287 EDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 287 ~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
..|..|++.||.| +++++ + ....|+.|..|+. |.
T Consensus 234 i~C~~Cv~vCP~g-i~~~~---~-------~~~~Ci~Cg~CidaCp 268 (434)
T TIGR02745 234 IDCNLCVQVCPTG-IDIRD---G-------LQLECINCGLCIDACD 268 (434)
T ss_pred CChhhhHHhCCCC-CEeCC---C-------CchhChhhhHHHHhCC
Confidence 3588999999999 45432 1 2257999999999 74
No 91
>COG1142 HycB Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]
Probab=34.85 E-value=22 Score=32.61 Aligned_cols=35 Identities=26% Similarity=0.645 Sum_probs=27.1
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
-+++.||.|+|..++ .+++.|..+|..|..|.- |.
T Consensus 60 PC~~vCP~~AI~~~~------~~v~V~~ekCiGC~~C~~aCP 95 (165)
T COG1142 60 PCAEVCPVGAITRDD------GAVQVDEEKCIGCKLCVVACP 95 (165)
T ss_pred chhhhCchhheeecC------CceEEchhhccCcchhhhcCC
Confidence 477889999988762 256678888999999987 63
No 92
>PRK08318 dihydropyrimidine dehydrogenase subunit B; Validated
Probab=34.27 E-value=25 Score=35.88 Aligned_cols=52 Identities=17% Similarity=0.427 Sum_probs=33.5
Q ss_pred hHHHHHhhCCCc---eEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEEEEeC
Q 018378 288 DAEKLVKTCPVN---VFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSIRRVK 344 (357)
Q Consensus 288 ~a~~l~~~cp~g---V~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l~~~~ 344 (357)
.|..|.+.||.+ +|.+++. |..... .+...|+.|..|+. |.. ++.|++....
T Consensus 346 ~C~~C~~~Cp~~~~~ai~~~~~--~~~~~~-i~~~~C~~Cg~C~~~CP~--~~Ai~~~~~~ 401 (420)
T PRK08318 346 GCGRCYIACEDTSHQAIEWDED--GTRTPE-VIEEECVGCNLCAHVCPV--EGCITMGEVK 401 (420)
T ss_pred CCCcccccCCCcchhheeeccC--CCceEE-echhhCcccchHHhhCCC--CCCEEEeccC
Confidence 477888899975 5665432 222333 46788999999998 753 1356665543
No 93
>PRK08764 ferredoxin; Provisional
Probab=34.25 E-value=24 Score=30.59 Aligned_cols=39 Identities=23% Similarity=0.510 Sum_probs=28.4
Q ss_pred hHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+.++++.||.++|..+.. ...+.+...|+.|..|+. |.
T Consensus 89 ~C~~Cv~aCp~~ai~~~~~-----~~~~v~~~~C~~Cg~Cv~~CP 128 (135)
T PRK08764 89 GCTKCIQACPVDAIVGGAK-----HMHTVIAPLCTGCELCVPACP 128 (135)
T ss_pred CcchHHHhCChhhcCccCC-----CceeecCCcCcCccchhhhcC
Confidence 3678999999998876421 123345678999999998 64
No 94
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=34.00 E-value=20 Score=34.42 Aligned_cols=41 Identities=20% Similarity=0.385 Sum_probs=26.5
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
-|...||-|++--.-.....-++.+.|+.+|+-|+.|.+ |.
T Consensus 173 ~C~~~CP~Ga~~~~~~~~~~~~i~~~~~~~C~~C~~C~~vCP 214 (255)
T TIGR02163 173 WCGHLCPLGAFYGLIGRKSLIKIAASDREKCTNCMDCFNVCP 214 (255)
T ss_pred hhhCcCCCcchhhhhhccCceEEEeeccccCeEcCCccCcCC
Confidence 355689999983211111113455556899999999998 64
No 95
>TIGR01582 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing. In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well.
Probab=32.98 E-value=21 Score=35.14 Aligned_cols=54 Identities=20% Similarity=0.332 Sum_probs=32.1
Q ss_pred eeecceeeEEeee-eceEEEcC-CCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh
Q 018378 262 AKWSPVATAWYRM-LPEIVLLE-DVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR 325 (357)
Q Consensus 262 AKwSPVata~Yr~-~P~I~i~~-~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr 325 (357)
++-.|+..+.++. .-.+.++. .+. .+..++..||.+++.+++.+ ....+|++|.
T Consensus 102 v~aCP~~gA~~~~~~G~V~id~dkCi--gC~~Cv~aCP~~a~~~~~~~--------~~~~KC~~C~ 157 (283)
T TIGR01582 102 LKACPAPGAIIQYQNGIVDFDHSKCI--GCGYCIVGCPFNIPRYDKVD--------NRPYKCTLCI 157 (283)
T ss_pred cCCCCcCCeEEEcCCCcEEEeHHHCC--cchHHHhhCCCCCcEEcCCC--------CChhhhcccc
Confidence 4557763333332 23344443 233 37789999999999886421 1246899995
No 96
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=32.96 E-value=58 Score=31.46 Aligned_cols=52 Identities=25% Similarity=0.540 Sum_probs=34.1
Q ss_pred HHHhhCCCceEEeeccC--CCc-eEEEEccCCCCc-----chhhHHh-cCCCcCCcEEEEEe
Q 018378 291 KLVKTCPVNVFDIEDIG--SGK-KRATVAQPRACT-----LCRECLR-CGEEWEKRVSIRRV 343 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~--~g~-~~~~V~~~~~ct-----~crec~r-c~~~~~~~V~l~~~ 343 (357)
.+++.||.+++.+.... ... ..+++.+...|. .|..|.+ |.. -.+.|.+...
T Consensus 106 ~Cv~aCPtgAL~~~~~~~~~~~~g~av~id~~~Ci~~~~~~C~~C~~~CP~-~~~AI~~~~~ 166 (254)
T PRK09476 106 PCVKACPSGALDRELVDIDDARMGLAVLVDQENCLNFQGLRCDVCYRVCPL-IDKAITLELE 166 (254)
T ss_pred chhhccCccceEeecccccccccCceeecchhhccccCCCchHHHhhhCCC-ccCeEEEEcc
Confidence 58889999999875321 101 223347888998 7999999 632 1257777654
No 97
>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit. This model describes the alpha subunit of sulfite reductase.
Probab=31.94 E-value=26 Score=36.20 Aligned_cols=35 Identities=23% Similarity=0.727 Sum_probs=27.7
Q ss_pred HHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh
Q 018378 290 EKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329 (357)
Q Consensus 290 ~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r 329 (357)
.++++.||.+++.+++ .+++.+ |..+|+.|-.|++
T Consensus 248 ~~~v~~Cp~~ai~~~~----~~~~~i-d~~~C~~Cm~Ci~ 282 (402)
T TIGR02064 248 NEVVNRCPTKAISWDG----SKELSI-DNRECVRCMHCIN 282 (402)
T ss_pred hhHhhcCCccccccCC----CceEEE-cchhcCcCccccc
Confidence 4578899999999963 135555 6678999999998
No 98
>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein. Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase.
Probab=31.93 E-value=63 Score=30.47 Aligned_cols=37 Identities=22% Similarity=0.527 Sum_probs=27.1
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+++.||.|+|..++. .| .+..|...|+.|+.|.. |.
T Consensus 101 ~Cv~~CP~gAi~~~~~-~g---~v~id~~~C~~C~~C~~aCP 138 (225)
T TIGR03149 101 PCVAVCPTGASFKDEE-TG---IVDVHKDLCVGCQYCIAACP 138 (225)
T ss_pred ChHhhCCCCcEEEeCC-CC---eEEechhhCCcchHHHHhCC
Confidence 4888999999876532 12 34457788999999998 64
No 99
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=30.83 E-value=26 Score=33.61 Aligned_cols=36 Identities=28% Similarity=0.612 Sum_probs=27.4
Q ss_pred HHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 291 KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 291 ~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
.+++.||.|++..++. | +.+.+...|+.|+.|+. |.
T Consensus 107 ~Cv~~CP~~Ai~~~~~--G---~v~id~~~CigC~~Cv~aCP 143 (244)
T PRK14993 107 PCVPVCPVQATFQRED--G---IVVVDNKRCVGCAYCVQACP 143 (244)
T ss_pred cCccccCCCCEEECCC--C---CEEEcHHHCCCHHHHHHhcC
Confidence 3888999999865432 2 45567888999999998 74
No 100
>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....
Probab=30.82 E-value=35 Score=21.03 Aligned_cols=17 Identities=35% Similarity=1.007 Sum_probs=13.0
Q ss_pred EccCCCCcchhhHHh-cC
Q 018378 315 VAQPRACTLCRECLR-CG 331 (357)
Q Consensus 315 V~~~~~ct~crec~r-c~ 331 (357)
+.|...|+.|..|++ |.
T Consensus 2 ~id~~~C~~Cg~C~~~CP 19 (24)
T PF00037_consen 2 VIDPDKCIGCGRCVEACP 19 (24)
T ss_dssp EEETTTSSS-THHHHHST
T ss_pred EEchHHCCCcchhhhhcc
Confidence 457889999999998 53
No 101
>KOG3256 consensus NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion]
Probab=29.18 E-value=55 Score=30.47 Aligned_cols=43 Identities=23% Similarity=0.511 Sum_probs=29.5
Q ss_pred HHHHHhhCCCceEEeec--cCCCceEE--EEccCCCCcchhhHHh-cC
Q 018378 289 AEKLVKTCPVNVFDIED--IGSGKKRA--TVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~--~~~g~~~~--~V~~~~~ct~crec~r-c~ 331 (357)
|+-|...||..++.|+- ..+|+++. +--|--+|.+|..|.+ |.
T Consensus 116 CklCeavCPaqaitieae~r~dgsrRttrYdIDmtkCIyCG~CqEaCP 163 (212)
T KOG3256|consen 116 CKLCEAVCPAQAITIEAEERTDGSRRTTRYDIDMTKCIYCGFCQEACP 163 (212)
T ss_pred HHHHHHhCCcccceeeceecCCccccceeecccceeeeeecchhhhCC
Confidence 45677789999988753 23444433 2346678999999998 63
No 102
>PRK07118 ferredoxin; Validated
Probab=28.94 E-value=45 Score=32.69 Aligned_cols=37 Identities=30% Similarity=0.713 Sum_probs=29.2
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
+..+++.||.++|.+.+ +.+ +.|+.+|+.|+.|++ |.
T Consensus 144 Cg~C~~aCp~~AI~~~~-----g~~-~id~~~C~~Cg~Cv~aCP 181 (280)
T PRK07118 144 LGSCVAACPFDAIHIEN-----GLP-VVDEDKCTGCGACVKACP 181 (280)
T ss_pred hhHHHHhCCccCeEccC-----CeE-EEChhhCcChhHHHHhcC
Confidence 67889999999988753 233 447889999999998 63
No 103
>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=28.80 E-value=36 Score=36.78 Aligned_cols=58 Identities=22% Similarity=0.535 Sum_probs=33.8
Q ss_pred eeecceeeEEeeeeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh-------hHHh-cC
Q 018378 262 AKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR-------ECLR-CG 331 (357)
Q Consensus 262 AKwSPVata~Yr~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr-------ec~r-c~ 331 (357)
++-.|+....+. .-.+.+... ....|..|+..||.+++.+.+ . .+.+|.+|. .|+. |.
T Consensus 65 ~~~CP~~ai~~~-~~~v~~d~~-~C~gC~~C~~~CP~~ai~~~~-----~-----~~~kC~~C~~~~~~~~~Cv~~CP 130 (639)
T PRK12809 65 VTACPVNALTFQ-SDSVQLDEQ-KCIGCKRCAIACPFGVVEMVD-----T-----IAQKCDLCNQRSSGTQACIEVCP 130 (639)
T ss_pred HhhCCcCceecc-ccceecChh-hCcchhhHhhhcCCCCEEccC-----C-----CcccccCCcccCCCCChhhhhCc
Confidence 456777655443 123333321 123477888889988887642 1 245788876 5777 63
No 104
>KOG3307 consensus Molybdopterin converting factor subunit 2 [Coenzyme transport and metabolism]
Probab=26.69 E-value=24 Score=31.17 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=28.0
Q ss_pred EEEEEEcCChhHHHHHHHHHH---hhCCcceEEEEEEeeCcccccchhheecccCcCceec
Q 018378 88 MEFDLIGIDAAIANAFRRILI---AELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVD 145 (357)
Q Consensus 88 ~~F~l~Gvd~siaNALRRILi---sEVPT~AIe~V~I~~NTSvl~DEvLAHRLGLIPi~~D 145 (357)
+.+.-+-+++---|.||-|.- ++-| |.++- ++||||++|+-+.
T Consensus 50 ~~L~Yeay~pMA~~~lr~IC~~iR~~wp---vkkIA------------vfHRLG~VpvgEs 95 (150)
T KOG3307|consen 50 SNLSYEAYDPMAYKKLRGICAEIRAEWP---VKKIA------------VFHRLGKVPVGES 95 (150)
T ss_pred eeeehhhhcHHHHHHHHHHHHHHHhhCc---hhhhh------------hhhhccCcccCcc
Confidence 344445677777788988863 3444 44433 5699999998643
No 105
>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B ....
Probab=26.28 E-value=15 Score=27.54 Aligned_cols=48 Identities=25% Similarity=0.694 Sum_probs=24.3
Q ss_pred HHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchhhHHh-cCCCcCCcEEE
Q 018378 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR-CGEEWEKRVSI 340 (357)
Q Consensus 289 a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~~~~~~~V~l 340 (357)
+.++...||.++|+.-...++ +.+. .++..|+.|..|.. |.- ++.|++
T Consensus 11 Cg~C~~~Cp~~~~~~i~~~~~-~~~~-v~~~~C~GCg~C~~~CPv--~~AI~m 59 (59)
T PF14697_consen 11 CGKCVRACPDGAIDAIEVDEG-KKVP-VNPDKCIGCGLCVKVCPV--KDAITM 59 (59)
T ss_dssp -SCCCHHCCCCS-S-ECCTTT-TSSE-CE-TT--S-SCCCCCSSS--TTSEEE
T ss_pred hhhHHhHcCccceeeEEecCC-eeEE-eccccCcCcCcccccCCC--ccCCCC
Confidence 445677899977766433222 2333 34689999999987 531 145553
No 106
>TIGR01582 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing. In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well.
Probab=26.27 E-value=30 Score=34.13 Aligned_cols=35 Identities=23% Similarity=0.485 Sum_probs=26.4
Q ss_pred HHhhCCC-ceEEeeccCCCceEEEEccCCCCcchhhHHh-cC
Q 018378 292 LVKTCPV-NVFDIEDIGSGKKRATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 292 l~~~cp~-gV~~i~~~~~g~~~~~V~~~~~ct~crec~r-c~ 331 (357)
|++.||. +++...+. | +++.+..+|+.|+.|.. |.
T Consensus 101 Cv~aCP~~gA~~~~~~--G---~V~id~dkCigC~~Cv~aCP 137 (283)
T TIGR01582 101 CLKACPAPGAIIQYQN--G---IVDFDHSKCIGCGYCIVGCP 137 (283)
T ss_pred ccCCCCcCCeEEEcCC--C---cEEEeHHHCCcchHHHhhCC
Confidence 8889996 77765432 2 45568888999999998 73
No 107
>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only. This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length.
Probab=25.64 E-value=30 Score=34.95 Aligned_cols=44 Identities=16% Similarity=0.412 Sum_probs=28.3
Q ss_pred hHHHHHhhCCCceEE--eeccCCCc-eEE-----EEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFD--IEDIGSGK-KRA-----TVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~--i~~~~~g~-~~~-----~V~~~~~ct~crec~r-c~ 331 (357)
.|.+|++.||.+++. +.....+. ..+ ...+...|+.|..|+. |.
T Consensus 11 ~Cg~Cv~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~id~~~C~~Cg~Cv~~CP 63 (374)
T TIGR02512 11 GCGRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCP 63 (374)
T ss_pred cChHhhhhCCHhhccccccccccCCccccccccccccCcccCcCccCHHHhCC
Confidence 488999999999875 22111111 111 1246678999999999 73
No 108
>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=25.30 E-value=44 Score=36.18 Aligned_cols=73 Identities=18% Similarity=0.351 Sum_probs=42.0
Q ss_pred eeecceeeEEeeeeceEEEcC-CCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh------hHHh-cCCC
Q 018378 262 AKWSPVATAWYRMLPEIVLLE-DVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR------ECLR-CGEE 333 (357)
Q Consensus 262 AKwSPVata~Yr~~P~I~i~~-~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr------ec~r-c~~~ 333 (357)
+.-.|+... ++....+.+.. .+ -.|..|+..||.+++.+...... ......++.+|.+|. .|+. |..
T Consensus 65 ~~~CP~~ai-~~~~~~~~id~~~C--~~C~~C~~~CP~~ai~~~~~~~~-~~~~~~~~~~C~~C~~~~~~p~Cv~~CP~- 139 (654)
T PRK12769 65 ARSCPNGAI-SHVDDSIQVNQQKC--IGCKSCVVACPFGTMQIVLTPVA-AGKVKATAHKCDLCAGRENGPACVENCPA- 139 (654)
T ss_pred hhhCCccce-eccCCeEEEecccc--cCcChhcccCCccCeeecccCCc-ccceeeecCcCcCCCCCCCCCceeccCCc-
Confidence 455676543 33344455543 23 34778889999999887642111 111234567899998 6777 553
Q ss_pred cCCcEEEE
Q 018378 334 WEKRVSIR 341 (357)
Q Consensus 334 ~~~~V~l~ 341 (357)
+.+.+.
T Consensus 140 --~Ai~~~ 145 (654)
T PRK12769 140 --DALQLV 145 (654)
T ss_pred --CcEEEe
Confidence 355554
No 109
>PRK09326 F420H2 dehydrogenase subunit F; Provisional
Probab=24.35 E-value=38 Score=33.81 Aligned_cols=44 Identities=20% Similarity=0.515 Sum_probs=29.7
Q ss_pred hHHHHHhhCCCceEEeeccCCCce------EEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDIGSGKK------RATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~~~g~~------~~~V~~~~~ct~crec~r-c~ 331 (357)
.|..|+..||.++|.+.+...... ...+.+...|+.|..|.+ |.
T Consensus 16 gCg~C~~~CP~~aI~~~~~~~~~~~~~~~~~~~~~d~~~C~~Cg~C~~vCP 66 (341)
T PRK09326 16 ACGACEAVCPIGAITVDKKAEIRDPNDLELYEKGAAPNVCEGCLTCSRICP 66 (341)
T ss_pred ChHHHHHhCCHhhhecccCcccccccchhhhccCCCcCcCcCcCchhhhCC
Confidence 488899999999998864210000 001236678999999998 74
No 110
>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit. This family consists of the iron-sulfur subunit, or chain B, of an enzyme called the anaerobic dimethyl sulfoxide reductase. Chains A and B are catalytic, while chain C is a membrane anchor.
Probab=23.25 E-value=63 Score=28.47 Aligned_cols=55 Identities=16% Similarity=0.198 Sum_probs=31.2
Q ss_pred eeecceeeEEee-eeceEEEcCCCChHhHHHHHhhCCCceEEeeccCCCceEEEEccCCCCcchh
Q 018378 262 AKWSPVATAWYR-MLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR 325 (357)
Q Consensus 262 AKwSPVata~Yr-~~P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g~~~~~V~~~~~ct~cr 325 (357)
.+..|+.....+ -...+.+... ....+..++..||.++|.++... ..+.+|++|.
T Consensus 73 ~~~CP~~ai~~~~~~~~~~i~~~-~C~~C~~C~~aCP~~ai~~~~~~--------~~~~kC~~C~ 128 (161)
T TIGR02951 73 VKNCPTGAMYKREEDGLVLVDQD-KCIGCRYCVWACPYGAPQYDPQQ--------GVMGKCDGCY 128 (161)
T ss_pred HHhCCCCCEEeecCCCcEEECHH-hCCCchHHHhhCCCCCcEEcCCC--------CccccCCCCH
Confidence 456676544333 1223344321 11236778889999998876421 1346899996
No 111
>TIGR01444 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.
Probab=23.04 E-value=90 Score=25.98 Aligned_cols=32 Identities=19% Similarity=0.422 Sum_probs=29.8
Q ss_pred ceEEEEEEcCChhHHHHHHHHHHhhCCcceEE
Q 018378 86 DDMEFDLIGIDAAIANAFRRILIAELPTMAIE 117 (357)
Q Consensus 86 ~~~~F~l~Gvd~siaNALRRILisEVPT~AIe 117 (357)
+.++.|++|....+-..+++.|..-+|.+.||
T Consensus 110 ~~lKiDiEG~E~~vL~g~~~~l~~~~~~i~~E 141 (143)
T TIGR01444 110 DLLKIDVEGAELEVLRGAKETLLRKRPGIVLE 141 (143)
T ss_pred CEEEEeCCCchHHHHhChHHHHHHhCCeEEEE
Confidence 57899999999999999999999999999887
No 112
>cd04932 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.49 E-value=2.7e+02 Score=21.62 Aligned_cols=40 Identities=15% Similarity=0.279 Sum_probs=29.9
Q ss_pred ceEEEEEecCceEEEEEEcCChhHHHHHHHHHHhhCCcce
Q 018378 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMA 115 (357)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNALRRILisEVPT~A 115 (357)
..|....-+...+.|.+..-+..--|+|++.|++|+-.+|
T Consensus 30 I~VDmI~~s~~~iSftv~~~d~~~~~~~~~~l~~~l~~~~ 69 (75)
T cd04932 30 ISVDLITTSEISVALTLDNTGSTSDQLLTQALLKELSQIC 69 (75)
T ss_pred CcEEEEeecCCEEEEEEeccccchhHHHHHHHHHHHHhcc
Confidence 4555554467889999998775545789989999988865
No 113
>CHL00014 ndhI NADH dehydrogenase subunit I
Probab=20.86 E-value=53 Score=29.48 Aligned_cols=44 Identities=23% Similarity=0.503 Sum_probs=27.1
Q ss_pred hHHHHHhhCCCceEEeecc---CCCce--EEEEccCCCCcchhhHHh-cC
Q 018378 288 DAEKLVKTCPVNVFDIEDI---GSGKK--RATVAQPRACTLCRECLR-CG 331 (357)
Q Consensus 288 ~a~~l~~~cp~gV~~i~~~---~~g~~--~~~V~~~~~ct~crec~r-c~ 331 (357)
.|..|+..||.+++.+... +.+.. .....+...|+.|..|.. |.
T Consensus 63 ~Cg~C~~aCP~~~~~~~~~~~~~~~~~~~~~~~id~~~C~~Cg~C~~~CP 112 (167)
T CHL00014 63 ACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGVCIFCGNCVEYCP 112 (167)
T ss_pred CcCcHHHhCCCCCccccccccccccccccccccCCCCcCcCccchHhhcC
Confidence 3778999999986543211 00001 122346677999999998 74
No 114
>TIGR00397 mauM_napG MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar.
Probab=20.86 E-value=65 Score=30.24 Aligned_cols=53 Identities=21% Similarity=0.544 Sum_probs=32.0
Q ss_pred ceEEEcCCCChHhHHHHHhhCCCceEEeeccCCC--ceEE-EEccCCCCcchh--hHHh-c
Q 018378 276 PEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSG--KKRA-TVAQPRACTLCR--ECLR-C 330 (357)
Q Consensus 276 P~I~i~~~i~~~~a~~l~~~cp~gV~~i~~~~~g--~~~~-~V~~~~~ct~cr--ec~r-c 330 (357)
|+..|+....+ +..+++.||.++|.+...+.+ .+.. ...+...|++|. .|+. |
T Consensus 47 ~e~~F~~~Ci~--Cg~Cv~aCP~~ai~~~~~~~~~~~g~p~~~~~~~~C~~C~d~~Cv~~C 105 (213)
T TIGR00397 47 PEQDFLAACVR--CGLCVEACPYDILSLASWSDPAPLGTPFFTPREVPCRMCKDIPCARAC 105 (213)
T ss_pred cchhhcccccc--hhHHHHhCCcccccccccccccccCCccccccCCcCCCCCCchHHhHc
Confidence 55566555543 788899999999877532110 0111 222345699996 5887 6
Done!