Query 008728
Match_columns 556
No_of_seqs 320 out of 1355
Neff 7.6
Searched_HMMs 46136
Date Thu Mar 28 15:50:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008728.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008728hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 1.4E-71 3.1E-76 599.9 34.7 409 113-529 65-479 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 8.1E-53 1.7E-57 440.6 11.6 337 147-491 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.6E-47 3.6E-52 413.1 32.9 324 110-442 91-420 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 9.1E-39 2E-43 334.5 15.8 309 116-437 2-319 (345)
5 KOG1267 Mitochondrial transcri 100.0 3.2E-30 7E-35 275.8 16.4 338 120-475 68-411 (413)
6 KOG1267 Mitochondrial transcri 99.9 2E-21 4.2E-26 208.1 16.3 313 107-440 87-409 (413)
7 smart00733 Mterf Mitochondrial 96.5 0.0017 3.6E-08 42.2 2.1 28 414-442 3-30 (31)
8 smart00733 Mterf Mitochondrial 96.4 0.0026 5.7E-08 41.2 2.4 28 378-406 3-30 (31)
9 PF11955 PORR: Plant organelle 91.7 0.68 1.5E-05 48.3 8.3 41 275-315 108-150 (335)
10 cd04790 HTH_Cfa-like_unk Helix 89.6 2.1 4.6E-05 40.3 8.9 20 145-164 50-69 (172)
11 cd04790 HTH_Cfa-like_unk Helix 87.7 5.3 0.00012 37.6 10.2 47 285-339 118-165 (172)
12 PRK14135 recX recombination re 87.5 33 0.00073 34.3 17.5 137 115-272 64-201 (263)
13 PF11955 PORR: Plant organelle 87.4 1 2.2E-05 47.1 5.6 101 142-243 37-150 (335)
14 PRK14136 recX recombination re 82.6 37 0.0008 34.9 13.9 138 114-277 168-306 (309)
15 PRK00117 recX recombination re 77.7 57 0.0012 29.9 14.9 135 114-272 17-152 (157)
16 PF04695 Pex14_N: Peroxisomal 77.3 4.1 9E-05 36.8 4.8 38 381-422 14-51 (136)
17 PHA01351 putative minor struct 75.7 43 0.00093 37.9 12.7 87 34-154 647-736 (1070)
18 TIGR01448 recD_rel helicase, p 74.6 23 0.00049 41.2 11.1 89 108-202 74-167 (720)
19 PRK14135 recX recombination re 72.1 97 0.0021 31.0 13.8 79 216-309 181-259 (263)
20 PF02631 RecX: RecX family; I 69.1 41 0.0009 29.3 9.2 60 138-200 7-67 (121)
21 TIGR01448 recD_rel helicase, p 68.9 34 0.00073 39.8 10.8 89 139-237 74-167 (720)
22 PF14490 HHH_4: Helix-hairpin- 60.0 23 0.00049 29.7 5.4 22 214-235 9-30 (94)
23 PRK00117 recX recombination re 58.6 1.5E+02 0.0032 27.1 12.5 18 254-271 83-100 (157)
24 PF11212 DUF2999: Protein of u 55.7 45 0.00098 26.5 5.8 15 253-267 33-47 (82)
25 KOG0011 Nucleotide excision re 54.3 18 0.00039 37.3 4.4 164 142-341 135-318 (340)
26 PF04695 Pex14_N: Peroxisomal 53.6 21 0.00045 32.3 4.4 34 167-203 15-48 (136)
27 PRK14134 recX recombination re 53.0 2.7E+02 0.0058 28.4 18.8 22 250-271 183-204 (283)
28 PRK14134 recX recombination re 52.6 1.3E+02 0.0029 30.6 10.7 24 285-308 255-278 (283)
29 PRK14137 recX recombination re 49.0 2.5E+02 0.0055 27.0 13.6 131 115-273 47-179 (195)
30 PF14490 HHH_4: Helix-hairpin- 48.6 78 0.0017 26.4 6.9 47 108-175 5-51 (94)
31 PF00627 UBA: UBA/TS-N domain; 48.5 39 0.00084 22.9 4.1 22 144-165 4-25 (37)
32 PHA01351 putative minor struct 47.2 5E+02 0.011 29.9 19.6 126 148-274 553-716 (1070)
33 PF02631 RecX: RecX family; I 46.9 62 0.0013 28.2 6.3 57 108-164 8-67 (121)
34 PRK00116 ruvA Holliday junctio 43.9 81 0.0018 30.2 7.1 26 213-238 149-174 (192)
35 PHA02591 hypothetical protein; 42.9 56 0.0012 26.5 4.7 30 103-132 39-69 (83)
36 TIGR00601 rad23 UV excision re 41.0 1.3E+02 0.0028 32.1 8.6 23 359-382 339-361 (378)
37 PRK14605 ruvA Holliday junctio 40.6 3.4E+02 0.0073 26.0 10.8 25 213-237 148-172 (194)
38 PF11212 DUF2999: Protein of u 40.4 1.9E+02 0.0041 23.1 7.6 47 113-162 3-49 (82)
39 COG2137 OraA Uncharacterized p 39.1 2.7E+02 0.0058 26.3 9.5 53 111-164 54-109 (174)
40 COG3620 Predicted transcriptio 38.3 76 0.0016 29.6 5.5 51 140-192 48-98 (187)
41 smart00165 UBA Ubiquitin assoc 38.0 78 0.0017 21.1 4.4 21 145-165 4-24 (37)
42 PF07499 RuvA_C: RuvA, C-termi 37.7 53 0.0011 23.7 3.6 23 143-165 4-26 (47)
43 PRK14137 recX recombination re 37.6 3.8E+02 0.0082 25.8 12.6 21 216-236 158-178 (195)
44 smart00657 RPOL4c DNA-directed 37.2 2.2E+02 0.0048 24.9 8.2 56 174-234 53-108 (118)
45 PRK00116 ruvA Holliday junctio 36.6 1.5E+02 0.0032 28.4 7.6 27 248-274 148-174 (192)
46 COG2137 OraA Uncharacterized p 35.1 3.9E+02 0.0085 25.2 12.1 135 115-273 27-164 (174)
47 KOG0400 40S ribosomal protein 34.3 61 0.0013 28.9 4.0 62 200-262 20-81 (151)
48 cd01392 HTH_LacI Helix-turn-he 33.5 97 0.0021 22.2 4.6 43 150-196 5-47 (52)
49 COG4974 XerD Site-specific rec 33.3 4E+02 0.0088 27.4 10.3 42 108-156 54-95 (300)
50 PF08069 Ribosomal_S13_N: Ribo 32.6 46 0.00099 25.7 2.7 34 202-235 22-55 (60)
51 PF11198 DUF2857: Protein of u 32.1 4.4E+02 0.0096 24.9 11.1 79 115-199 19-97 (180)
52 PF03960 ArsC: ArsC family; I 32.0 96 0.0021 26.5 5.0 20 154-174 71-90 (110)
53 COG1125 OpuBA ABC-type proline 31.8 86 0.0019 31.7 5.1 150 321-497 73-239 (309)
54 cd00194 UBA Ubiquitin Associat 31.2 1.2E+02 0.0026 20.3 4.4 20 145-164 4-23 (38)
55 COG1393 ArsC Arsenate reductas 30.1 87 0.0019 27.5 4.5 17 177-193 13-29 (117)
56 TIGR00084 ruvA Holliday juncti 28.3 5.3E+02 0.011 24.6 10.9 23 214-236 148-170 (191)
57 TIGR00601 rad23 UV excision re 28.3 7.6E+02 0.016 26.4 12.2 24 286-309 338-361 (378)
58 PRK08561 rps15p 30S ribosomal 28.2 2.3E+02 0.0049 26.1 6.8 37 201-237 21-57 (151)
59 KOG0400 40S ribosomal protein 26.8 37 0.0008 30.2 1.5 27 136-162 27-53 (151)
60 PF02433 FixO: Cytochrome C ox 26.4 1.7E+02 0.0037 28.7 6.1 15 212-226 210-224 (226)
61 PF06089 Asparaginase_II: L-as 26.4 5.9E+02 0.013 26.6 10.4 54 107-160 42-100 (324)
62 COG1393 ArsC Arsenate reductas 26.1 96 0.0021 27.2 4.0 19 108-126 11-29 (117)
63 PRK14601 ruvA Holliday junctio 26.1 5.8E+02 0.012 24.3 11.1 24 214-237 143-166 (183)
64 PF08069 Ribosomal_S13_N: Ribo 26.0 66 0.0014 24.8 2.5 47 153-201 10-56 (60)
65 PF03960 ArsC: ArsC family; I 25.7 1.3E+02 0.0029 25.6 4.9 22 332-353 70-91 (110)
66 PTZ00072 40S ribosomal protein 24.9 2.7E+02 0.0059 25.4 6.6 73 188-262 6-78 (148)
67 TIGR01616 nitro_assoc nitrogen 24.4 72 0.0016 28.4 2.9 45 333-383 73-117 (126)
68 cd01392 HTH_LacI Helix-turn-he 24.3 1.6E+02 0.0036 20.9 4.5 39 223-265 7-45 (52)
69 cd04777 HTH_MerR-like_sg1 Heli 24.1 1.7E+02 0.0036 24.9 5.1 23 178-200 44-66 (107)
70 PF11829 DUF3349: Protein of u 23.8 4.5E+02 0.0098 22.3 7.5 75 112-191 6-91 (96)
71 PF08671 SinI: Anti-repressor 23.5 62 0.0013 21.3 1.7 23 285-307 5-27 (30)
72 COG1125 OpuBA ABC-type proline 22.7 1.4E+02 0.003 30.3 4.7 66 356-425 72-139 (309)
73 PF02022 Integrase_Zn: Integra 22.0 1.5E+02 0.0031 20.9 3.4 29 393-421 7-36 (40)
74 KOG2561 Adaptor protein NUB1, 21.9 4.5E+02 0.0098 28.6 8.5 193 208-441 259-469 (568)
75 PF00356 LacI: Bacterial regul 21.6 1.3E+02 0.0028 21.7 3.2 18 222-239 8-25 (46)
76 PRK14601 ruvA Holliday junctio 21.5 7.1E+02 0.015 23.7 10.4 25 249-273 142-166 (183)
77 cd08316 Death_FAS_TNFRSF6 Deat 21.0 3E+02 0.0064 23.3 5.8 24 216-239 23-46 (97)
78 PF03874 RNA_pol_Rpb4: RNA pol 20.6 1.5E+02 0.0032 25.6 4.2 26 178-203 59-84 (117)
79 smart00354 HTH_LACI helix_turn 20.3 2.3E+02 0.0049 22.0 4.8 40 151-194 9-48 (70)
80 KOG2629 Peroxisomal membrane a 20.2 1.7E+02 0.0037 29.8 4.9 26 392-417 20-45 (300)
81 smart00657 RPOL4c DNA-directed 20.2 5.8E+02 0.013 22.2 7.9 31 209-239 53-83 (118)
82 PF08986 DUF1889: Domain of un 20.2 3.1E+02 0.0067 23.2 5.5 88 71-172 19-108 (119)
83 PRK13344 spxA transcriptional 20.1 37 0.00081 30.4 0.2 14 112-125 14-27 (132)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.4e-71 Score=599.94 Aligned_cols=409 Identities=26% Similarity=0.533 Sum_probs=391.4
Q ss_pred hHHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCChh-hHHHHHHHHHhCCCC
Q 008728 113 PLIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIE-ELNEIVEYLETNGVR 191 (556)
Q Consensus 113 ~~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~-~l~~~l~~L~s~G~~ 191 (556)
..++||.++|++++++.++.. ..+.+.++++++||+++|++.++|+ .+|.+|.++++ ++.|+++||+++|++
T Consensus 65 ~~~~~L~~lgi~~~~l~~~~~--p~~~~~~~~~l~~L~s~G~~~~~i~-----~~P~iL~~~v~~~l~Pvl~fL~~lG~s 137 (487)
T PLN03196 65 KVLDFLRGIGIDPDELDGLEL--PSTVDVMRERVEFLHKLGLTIEDIN-----EYPLVLGCSVKKNMIPVLDYLEKLGVT 137 (487)
T ss_pred HHHHHHHHcCCCchhhhccCC--CccHHHHHHHHHHHHHcCCChHHhc-----cCcHHhhcCHhhhhHHHHHHHHHcCCC
Confidence 478999999999999988765 4688999999999999999999997 39999999985 799999999999999
Q ss_pred hhhHHHHHhhCCCcccccHH-HHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHH
Q 008728 192 RDWMGYVMSRCPQLLSQSIE-EVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLL 270 (556)
Q Consensus 192 ~~~i~~lv~~~P~iL~~s~~-~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll 270 (556)
..+|++++.++|.+|.++++ ++.|+++||+++|++++++++++.++|++|+++.++++.++++||+++|++.++|++++
T Consensus 138 ~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il 217 (487)
T PLN03196 138 RSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPML 217 (487)
T ss_pred HHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 99999999999999999997 79999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCcccccCcccchHHHHHHHHHcCCChhhHHHHHhhCCcccccCccccchhHHHHHHHhCCChhhHhhhhhhcCcccc
Q 008728 271 AFRPHLMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRDEGIANMLVKFPSLLT 350 (556)
Q Consensus 271 ~~~P~lL~~s~e~~l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~~l~~kv~~L~~lG~s~~~i~~~i~~~P~iL~ 350 (556)
.++|++|+++++++++|+++||.++|++.++|.+++.++|++|+++++++++|++++|+++|++.+++..++.++|.+++
T Consensus 218 ~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~ 297 (487)
T PLN03196 218 TRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILG 297 (487)
T ss_pred HhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeE
Confidence 99999999999999999999999999999999999999999999999988999999999999999999999999999999
Q ss_pred chhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHHHhCCCHHHHHHHHhhcccccccchhhHH
Q 008728 351 YSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFLSLGIKLHQLGAMIADFPMLLRYNIDIFR 430 (556)
Q Consensus 351 ~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~~lG~~~~ei~~ml~~~P~lL~~s~e~l~ 430 (556)
+++++++.+++.|+.+.+|++++++..+++++|+++++|. +++.+|++||+++||+.++++.|++++|++|++|.++|+
T Consensus 298 ~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe-~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~ 376 (487)
T PLN03196 298 LDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNR-NVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMK 376 (487)
T ss_pred ecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccH-HHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHH
Confidence 9999999999999999999999999999999999999995 789999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCChhHHhhcCcccccCcccccHHHHHHHHHCCCCcccccccccChHHHHHHHHhhhhch----hhhhhc
Q 008728 431 PKYRYLRRTMVRPLQDLIEFPRFFSYSLEERIIPRHKIMVENRVNFKLRYMLACSNEEFNQKVADKVEGR----RLYELG 506 (556)
Q Consensus 431 ~k~~fL~~~mg~~~~~i~~~P~~L~ySLe~RI~pR~~~L~~~Gl~~~l~~~L~~sd~~F~~~~~~~~e~~----~~f~~~ 506 (556)
+|++||+++||+++++|++||+||+||||+||+|||++|+++|+.+++.++|+|||+.|+++|+..|.+- +.|.+|
T Consensus 377 ~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r~v~~y~e~~~~~~~~~~~ 456 (487)
T PLN03196 377 PSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQRMSGDFIEGEEMEPLFSMG 456 (487)
T ss_pred HHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHHHhhhcccccccCCCcccC
Confidence 9999999999999999999999999999999999999999999999999999999999999999988543 689999
Q ss_pred cccCCCCCCccchhhccCCcccc
Q 008728 507 LINEAPHSQTVDDSLRQQDAVDY 529 (556)
Q Consensus 507 ~~~e~~~~~~~~~~~~~~~~~~~ 529 (556)
+..|.|+++.++|+++++||+|.
T Consensus 457 ~~~~~~~~~~~~~~~~~~~~~~~ 479 (487)
T PLN03196 457 GKLEMPGSESVSDEEDDDDDDEV 479 (487)
T ss_pred CcccCCCCccccCcccccchHHH
Confidence 99999999999988777666664
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=8.1e-53 Score=440.65 Aligned_cols=337 Identities=31% Similarity=0.566 Sum_probs=267.7
Q ss_pred HHHHhCCCChhHHHHHHHhhCCccccCChh-hHHHHHHHHHhCCCChhhHHHHHhhCCCcccccH-HHHHHHHHHHHHcC
Q 008728 147 EWLKSVHVKGEFLGVALLKTGGNILERSIE-ELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQSI-EEVKTRVHFYLDMG 224 (556)
Q Consensus 147 ~~L~~lGls~~~i~~il~r~~P~lL~~s~~-~l~~~l~~L~s~G~~~~~i~~lv~~~P~iL~~s~-~~l~~~v~fL~~lG 224 (556)
.+|+++||+.++|.+++.+ +|.++.++++ ++.|+++||.+.|++..+++++++++|.+|..+. +++.++++||+++|
T Consensus 2 ~~~~~~gf~~~~i~~~i~~-~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~ 80 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRR-YPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIG 80 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH--H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTS
T ss_pred hHHHHcCCCHHHHHHHHHh-CCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHc
Confidence 5789999999999999997 9999998874 7999999999999999999999999999999995 57999999999999
Q ss_pred CChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhhCCcccccCcccchHHHHHHHHHcCCChhhHHH
Q 008728 225 MNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPHLMGCGIGERWKPLVKYLYYLGVSRDGMRR 304 (556)
Q Consensus 225 ~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~~P~lL~~s~e~~l~~~v~~L~~lGls~~~i~~ 304 (556)
++++++.+++.++|++|..+...++.+++.+|+++|++.+.+.+++..+|.++... +++++.++++.++|++++++.+
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~ 158 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGR 158 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCC
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcc
Confidence 99999999999999999987778999999999999999998889999888877766 5899999999999999999999
Q ss_pred HHhhCCcccccCccccchhHHHHHHHhCCChhhHhhhhhhcCccccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccc
Q 008728 305 MLVIKPMVFCFDLETTIVPKVRFFQDIGVRDEGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPE 384 (556)
Q Consensus 305 il~~~P~iL~~~~e~~l~~kv~~L~~lG~s~~~i~~~i~~~P~iL~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~ 384 (556)
++..+|.++..+.+++++++++||+++|++.+++.+++.++|+++..++++.++++..++ ...|.... .++.++|+
T Consensus 159 vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~-~~~~~~~~---~~i~~~p~ 234 (345)
T PF02536_consen 159 VIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLL-SSGGVEEE---RVIKKFPQ 234 (345)
T ss_dssp CHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC-----------------------------
T ss_pred cccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccc-cccccccc---cccccccc
Confidence 999999888888888899999999999999999999999999999999998777765554 45554444 88899999
Q ss_pred eeeccchhhHHHHHHHHHHhCCCHHHHHHHHhhcccccccchhhHHHHHHHHHHHhCCChhHHhhcCcccccCcccccHH
Q 008728 385 LLGCSIGNKLEVNVKYFLSLGIKLHQLGAMIADFPMLLRYNIDIFRPKYRYLRRTMVRPLQDLIEFPRFFSYSLEERIIP 464 (556)
Q Consensus 385 iL~~s~~~~l~~kv~~L~~lG~~~~ei~~ml~~~P~lL~~s~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~ySLe~RI~p 464 (556)
++.++ .+++.++++||+++||+.++++.|+.++|++|.+|.+++++|++||.++||++.++|+++|++|+||||+||+|
T Consensus 235 il~~~-~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~P 313 (345)
T PF02536_consen 235 ILSLS-EEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKP 313 (345)
T ss_dssp --THH-HHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHH
T ss_pred ccccc-hHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhh
Confidence 99998 47899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred H---HHHHHHCC--CCcccccccccChHHHHH
Q 008728 465 R---HKIMVENR--VNFKLRYMLACSNEEFNQ 491 (556)
Q Consensus 465 R---~~~L~~~G--l~~~l~~~L~~sd~~F~~ 491 (556)
| +++|+++| ..+++.+||++||++|++
T Consensus 314 R~~~~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 314 RYEVLKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HHHHHHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 9 56788999 678899999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.6e-47 Score=413.09 Aligned_cols=324 Identities=23% Similarity=0.453 Sum_probs=306.2
Q ss_pred ChhhHHHHHHHCCCChHHHHHHHhhccCChh-hHHHHHHHHHhCCCChhHHHHHHHhhCCccccCChh-hHHHHHHHHHh
Q 008728 110 NVVPLIRWLKHNGLSYPKIAKLICMSGGNLE-SIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIE-ELNEIVEYLET 187 (556)
Q Consensus 110 ~~~~~~~~L~~~G~s~~~i~~~~~~~~~~~~-~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~-~l~~~l~~L~s 187 (556)
.+.+.++||+++||+.++|++.+.+...+++ .+.++++||+++|++..+|+++|.+ +|.+|.++++ ++.|+++||++
T Consensus 91 ~~~~~l~~L~s~G~~~~~i~~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~-~P~lL~~sve~~L~P~v~fL~~ 169 (487)
T PLN03196 91 VMRERVEFLHKLGLTIEDINEYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRR-YPQVLHASVVVDLAPVVKYLQG 169 (487)
T ss_pred HHHHHHHHHHHcCCChHHhccCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHh-CCceecccHHHHHHHHHHHHHH
Confidence 4667889999999999999987777677775 7999999999999999999999997 9999999986 79999999999
Q ss_pred CCCChhhHHHHHhhCCCcccccHH-HHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHH
Q 008728 188 NGVRRDWMGYVMSRCPQLLSQSIE-EVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDV 266 (556)
Q Consensus 188 ~G~~~~~i~~lv~~~P~iL~~s~~-~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I 266 (556)
+|++.++|++++.++|.+|+++++ ++.++++||.++|++.+++++++.++|.||+++.++++.++++||+++|++.++|
T Consensus 170 lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I 249 (487)
T PLN03196 170 LDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAV 249 (487)
T ss_pred cCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHH
Confidence 999999999999999999999998 5999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCcccccCcccchHHHHHHHHHcCCChhhHHHHHhhCCcccccCccccchhHHHHHH-HhCCChhhHhhhhhhc
Q 008728 267 GRLLAFRPHLMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQ-DIGVRDEGIANMLVKF 345 (556)
Q Consensus 267 ~~ll~~~P~lL~~s~e~~l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~~l~~kv~~L~-~lG~s~~~i~~~i~~~ 345 (556)
++++.++|++|+++++++++|++++|.++|++++++.+++.++|.+++++.++.+.+++.||. ++|++.+++..++.++
T Consensus 250 ~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~ 329 (487)
T PLN03196 250 ARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKL 329 (487)
T ss_pred HHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999888999999995 8999999999999999
Q ss_pred CccccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHH-HhCCCHHHHHHHHhhccccccc
Q 008728 346 PSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFL-SLGIKLHQLGAMIADFPMLLRY 424 (556)
Q Consensus 346 P~iL~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~-~lG~~~~ei~~ml~~~P~lL~~ 424 (556)
|++++++.+ +++++++||. ++||+.+++..|+.++|++|++|. ++|++|++||. ++|++.++ |+++|++|+|
T Consensus 330 P~il~lSe~-kl~~kvefL~-~~Gls~edI~~mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~----Iv~fP~~Lsy 402 (487)
T PLN03196 330 PQIVSLNRN-VALKHVEFLR-GRGFSAQDVAKMVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKE----LVEFPAYFTY 402 (487)
T ss_pred chhhcccHH-HHHHHHHHHH-HcCCCHHHHHHHHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHH----HHhChHHhcc
Confidence 999999976 5999999995 799999999999999999999997 89999999999 59999875 5799999999
Q ss_pred chh-hHHHHHHHHHHHhCC
Q 008728 425 NID-IFRPKYRYLRRTMVR 442 (556)
Q Consensus 425 s~e-~l~~k~~fL~~~mg~ 442 (556)
|.| +|+||+++|.++ |+
T Consensus 403 SLEkRI~PR~~~L~~k-Gl 420 (487)
T PLN03196 403 GLESRIKPRYERVAKK-GI 420 (487)
T ss_pred ChhhhhHHHHHHHHHc-CC
Confidence 999 999999998865 54
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=9.1e-39 Score=334.48 Aligned_cols=309 Identities=28% Similarity=0.516 Sum_probs=238.8
Q ss_pred HHHHHCCCChHHHHHHHhh----ccCChh-hHHHHHHHHHhCCCChhHHHHHHHhhCCccccCC-hhhHHHHHHHHHhCC
Q 008728 116 RWLKHNGLSYPKIAKLICM----SGGNLE-SIRHLAEWLKSVHVKGEFLGVALLKTGGNILERS-IEELNEIVEYLETNG 189 (556)
Q Consensus 116 ~~L~~~G~s~~~i~~~~~~----~~~~~~-~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s-~~~l~~~l~~L~s~G 189 (556)
++|+++||+..+|.++++. ...+++ ++.++++||.++|++..++++++.+ +|.++..+ .+++.+.+++|+++|
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~-~P~il~~s~~~~i~p~~~~L~~~~ 80 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSK-NPQILSRSLEKNIIPVFDFLKSIG 80 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH--GGGGGS--HHHHHHHHHHHTTTS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHh-ChHHHhccchhhHHHHHHHHHHHc
Confidence 5789999999999999873 245664 8999999999999999999999997 99999999 678999999999999
Q ss_pred CChhhHHHHHhhCCCcccccHH-HHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHH
Q 008728 190 VRRDWMGYVMSRCPQLLSQSIE-EVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGR 268 (556)
Q Consensus 190 ~~~~~i~~lv~~~P~iL~~s~~-~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ 268 (556)
++.+++++++.++|.+|..+.+ ++.+++.||+++|++.+.+.+++...|.++... +.+.+.+++|.++|++++++.+
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~ 158 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGR 158 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCC
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcc
Confidence 9999999999999999988775 799999999999999998999999999877653 8999999999999999999999
Q ss_pred HHhhCCcccccCcccchHHHHHHHHHcCCChhhHHHHHhhCCcccccCccccchhHHHHHHHhCCChhhHhhhhhhcCcc
Q 008728 269 LLAFRPHLMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRDEGIANMLVKFPSL 348 (556)
Q Consensus 269 ll~~~P~lL~~s~e~~l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~~l~~kv~~L~~lG~s~~~i~~~i~~~P~i 348 (556)
++..+|.++..+.+++++++++||+++|++.+++.+++.++|.++..+.++.+.++..++...|...+ .++.++|.+
T Consensus 159 vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~---~~i~~~p~i 235 (345)
T PF02536_consen 159 VIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE---RVIKKFPQI 235 (345)
T ss_dssp CHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC-----------------------------
T ss_pred cccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccc---ccccccccc
Confidence 99999988888888899999999999999999999999999999999988767766556666666655 889999999
Q ss_pred ccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHHH-hCCCHHHHHHHHhhcccccccchh
Q 008728 349 LTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFLS-LGIKLHQLGAMIADFPMLLRYNID 427 (556)
Q Consensus 349 L~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~~-lG~~~~ei~~ml~~~P~lL~~s~e 427 (556)
++++.+ ++.++++|| .++|++.+++.+|+.++|++|+++.+ ++++|++||.+ +|++.++| .++|++|+||.|
T Consensus 236 l~~~~~-~l~~~i~~L-~~lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe 308 (345)
T PF02536_consen 236 LSLSEE-KLKPKIEFL-QSLGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLE 308 (345)
T ss_dssp -THHHH-HHHHHHHHH-HTTT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HH
T ss_pred cccchH-hHHHHHHHH-HHhcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcCHHHH----hhCCceeEechh
Confidence 999966 599999999 57999999999999999999999974 59999999995 99998865 589999999998
Q ss_pred -hHHHHHHHHH
Q 008728 428 -IFRPKYRYLR 437 (556)
Q Consensus 428 -~l~~k~~fL~ 437 (556)
+++||++++.
T Consensus 309 ~ri~PR~~~~~ 319 (345)
T PF02536_consen 309 KRIKPRYEVLK 319 (345)
T ss_dssp HHHHHHHHHHH
T ss_pred hhhhhHHHHHH
Confidence 7999955554
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.97 E-value=3.2e-30 Score=275.81 Aligned_cols=338 Identities=26% Similarity=0.433 Sum_probs=292.8
Q ss_pred HCCCChHHHHHHHhhc-cCChhhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCChhh-HHHHHHHHHhCCCChhhHHH
Q 008728 120 HNGLSYPKIAKLICMS-GGNLESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEE-LNEIVEYLETNGVRRDWMGY 197 (556)
Q Consensus 120 ~~G~s~~~i~~~~~~~-~~~~~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~~-l~~~l~~L~s~G~~~~~i~~ 197 (556)
+.|.+...+..+.+.. ........+.+++|+++|++..++..++.. +|.++..+.++ +.+...+|.+.|++..++..
T Consensus 68 s~~~~~~~~~~~~~~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~-~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~ 146 (413)
T KOG1267|consen 68 SLGLSIKLARKLSREVSSEDSVNPSSVLSSLRSLGFTDSQISSIILS-SPKLLYLSSENILKPKLRLLDSLGLPSSELSS 146 (413)
T ss_pred ccccchhhHHHHHHHHHhhhccCcHHHHHHHHhcCCchhhccccccc-CchhhhccchhhhhhhhhhhhccCccccccch
Confidence 4566666666666532 344556778899999999999999999996 99999998765 66777899999999999999
Q ss_pred HHhhCCCcccccHH-HHHHHHHHHHHcC--CChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhhCC
Q 008728 198 VMSRCPQLLSQSIE-EVKTRVHFYLDMG--MNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRP 274 (556)
Q Consensus 198 lv~~~P~iL~~s~~-~l~~~v~fL~~lG--~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~~P 274 (556)
+++..|.+|..+.. ++.+.++|+++++ .....+.+++...|.... .+..+. ++++++++|+....+..++..+|
T Consensus 147 i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~--~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~ 223 (413)
T KOG1267|consen 147 IVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLL--NENSVE-RLDIRRELGVKPRLLKSLLESQP 223 (413)
T ss_pred hhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccc--cccccc-cchhhHHhCCCHHHHHHHHhcCc
Confidence 99998999887665 7999999999984 777888888877774432 223444 99999999999999999999999
Q ss_pred cccccCcccchHHHHHHHHHcCCChhhHHHHHhhCCcccccCccccchhHHHHHHHhCCChhhHhhhhhhcCccccchhh
Q 008728 275 HLMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRDEGIANMLVKFPSLLTYSLY 354 (556)
Q Consensus 275 ~lL~~s~e~~l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~~l~~kv~~L~~lG~s~~~i~~~i~~~P~iL~~s~~ 354 (556)
.+..... .+...+.++..+|+.+.. +++...|.++.++.++++++++++|+++|++.++++.|+.++|++|+++.+
T Consensus 224 ~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~ 299 (413)
T KOG1267|consen 224 RPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVK 299 (413)
T ss_pred cceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehh
Confidence 9998764 588889999999988877 888999999999999999999999999999999999999999999999998
Q ss_pred hhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHHHhCCCHHHHHHHHhhcccccccchh-hHHHHH
Q 008728 355 KKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFLSLGIKLHQLGAMIADFPMLLRYNID-IFRPKY 433 (556)
Q Consensus 355 ~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~~lG~~~~ei~~ml~~~P~lL~~s~e-~l~~k~ 433 (556)
+++ ..+.|+++. .++ +.++|+++.++ +.++.++++||...|++..++..|++++|+++.++.+ .++.+.
T Consensus 300 ~~~-~~~~~~~~~----~~~----~~k~p~~l~~s-~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~ 369 (413)
T KOG1267|consen 300 KNL-KTTEYLLKN----PKH----ILKFPQLLRSS-EDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKY 369 (413)
T ss_pred hhh-HHHHHHHhc----chh----hhhhhhhhhcc-chhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhH
Confidence 755 556666555 233 77999999666 5899999999999999999999999999999999999 999999
Q ss_pred HHHHHHhCCChhHHhhcCcccccCcccccHHHHHHHHHCCCC
Q 008728 434 RYLRRTMVRPLQDLIEFPRFFSYSLEERIIPRHKIMVENRVN 475 (556)
Q Consensus 434 ~fL~~~mg~~~~~i~~~P~~L~ySLe~RI~pR~~~L~~~Gl~ 475 (556)
+|+.+.|+++.+.++.+|.+++|++|.|+.||+.....+|..
T Consensus 370 ~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 370 EYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred HHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 999999999999999999999999999999999988776643
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.87 E-value=2e-21 Score=208.15 Aligned_cols=313 Identities=20% Similarity=0.347 Sum_probs=263.8
Q ss_pred cCCChhhHHHHHHHCCCChHHHHHHHhhc----cCCh-hhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCCh-hhHHH
Q 008728 107 EDSNVVPLIRWLKHNGLSYPKIAKLICMS----GGNL-ESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSI-EELNE 180 (556)
Q Consensus 107 ~~~~~~~~~~~L~~~G~s~~~i~~~~~~~----~~~~-~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~-~~l~~ 180 (556)
...+..+....|+++|++..+|.++...+ ..+. ..+.+++.+|.+.|++.+.+..++.. .|.+|..+. .++..
T Consensus 87 ~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~-~~~il~~~~~~~~~~ 165 (413)
T KOG1267|consen 87 DSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSV-VPKILLKSKGESLST 165 (413)
T ss_pred hccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhc-cHHHHHhhcCCchhh
Confidence 35566778899999999999999998632 3344 46788888999999999999999996 888888654 58999
Q ss_pred HHHHHHhCC--CChhhHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHH
Q 008728 181 IVEYLETNG--VRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKE 258 (556)
Q Consensus 181 ~l~~L~s~G--~~~~~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~ 258 (556)
.++||++++ +....+..++...|... ..+..+. ++++++++|+...++..++..+|.+..... .+...+.++..
T Consensus 166 ~~~~l~~~~~~~~~s~~~~~~~~~~~~~-~~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~ 241 (413)
T KOG1267|consen 166 FIEFLKSIPPELLSSVVERLLTPVPSFL-LNENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLT 241 (413)
T ss_pred HHHHhhccchhhhhhHHHHhcccccccc-ccccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHH
Confidence 999999985 77777777766665311 1122344 899999999999999999999999987643 78888999999
Q ss_pred cCCChHHHHHHHhhCCcccccCcccchHHHHHHHHHcCCChhhHHHHHhhCCcccccCccccchhHHHHHHHhCCChhhH
Q 008728 259 FGLSTEDVGRLLAFRPHLMGCGIGERWKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLETTIVPKVRFFQDIGVRDEGI 338 (556)
Q Consensus 259 lG~~~~~I~~ll~~~P~lL~~s~e~~l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~~l~~kv~~L~~lG~s~~~i 338 (556)
+|+.+.. +++...|.++.++.++++++++++|+++|++.++++.++.++|.+|+++.+. +..+++++... . ++
T Consensus 242 ~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~-~~~~~~~~~~~--~-~~- 314 (413)
T KOG1267|consen 242 LGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKK-NLKTTEYLLKN--P-KH- 314 (413)
T ss_pred hccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhh-hhHHHHHHHhc--c-hh-
Confidence 9987766 8888999999999999999999999999999999999999999999999764 77778887765 3 33
Q ss_pred hhhhhhcCccccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHH-HhCCCHHHHHHHHhh
Q 008728 339 ANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFL-SLGIKLHQLGAMIAD 417 (556)
Q Consensus 339 ~~~i~~~P~iL~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~-~lG~~~~ei~~ml~~ 417 (556)
+.++|+++.++.. ++.++++|+ ..+|++..++..+++++|++++++.+..++.+.+++. .++++.+ ++..
T Consensus 315 ---~~k~p~~l~~s~~-~l~~~ie~l-~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~----~~~~ 385 (413)
T KOG1267|consen 315 ---ILKFPQLLRSSED-KLKPRIEFL-LSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLS----ALVS 385 (413)
T ss_pred ---hhhhhhhhhccch-hhhhhHHHH-HHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHH----HHhc
Confidence 8999999966655 699999999 5999999999999999999999998667888899998 5998855 6679
Q ss_pred cccccccchh-hHHHHHHHHHHHh
Q 008728 418 FPMLLRYNID-IFRPKYRYLRRTM 440 (556)
Q Consensus 418 ~P~lL~~s~e-~l~~k~~fL~~~m 440 (556)
+|.++.|+.+ ++.+|+......+
T Consensus 386 ~p~~~~y~le~ri~pr~~~~~~~~ 409 (413)
T KOG1267|consen 386 FPAFFGYSLEKRIRPRFNVIKKLG 409 (413)
T ss_pred cchhhccchhhcchhHHHHHHHHh
Confidence 9999999999 9999999887654
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.54 E-value=0.0017 Score=42.17 Aligned_cols=28 Identities=25% Similarity=0.619 Sum_probs=17.0
Q ss_pred HHhhcccccccchhhHHHHHHHHHHHhCC
Q 008728 414 MIADFPMLLRYNIDIFRPKYRYLRRTMVR 442 (556)
Q Consensus 414 ml~~~P~lL~~s~e~l~~k~~fL~~~mg~ 442 (556)
++.++|.+++++.++++++++||. .+|+
T Consensus 3 ~~~~~P~il~~~~~~l~~~~~~l~-~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYSEKKLKPKVEFLK-ELGF 30 (31)
T ss_pred hhhhCcCcccccHHHhhHHHHHHH-HcCC
Confidence 455666666666556666666666 5554
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.39 E-value=0.0026 Score=41.18 Aligned_cols=28 Identities=36% Similarity=0.577 Sum_probs=15.0
Q ss_pred HHhhccceeeccchhhHHHHHHHHHHhCC
Q 008728 378 CLALGPELLGCSIGNKLEVNVKYFLSLGI 406 (556)
Q Consensus 378 vi~~~P~iL~~s~~~~l~~kv~~L~~lG~ 406 (556)
++.++|.+++++ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 344555555555 4555555555555554
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=91.67 E-value=0.68 Score=48.33 Aligned_cols=41 Identities=20% Similarity=0.154 Sum_probs=24.7
Q ss_pred cccccCcccch-HHHHHHHH-HcCCChhhHHHHHhhCCccccc
Q 008728 275 HLMGCGIGERW-KPLVKYLY-YLGVSRDGMRRMLVIKPMVFCF 315 (556)
Q Consensus 275 ~lL~~s~e~~l-~~~v~~L~-~lGls~~~i~~il~~~P~iL~~ 315 (556)
.+|.++.++.| -.++..++ ++|++.+=...++.+||..+..
T Consensus 108 KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 108 KLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 44555554333 23455565 6777777667777777776654
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=89.62 E-value=2.1 Score=40.33 Aligned_cols=20 Identities=20% Similarity=-0.084 Sum_probs=12.1
Q ss_pred HHHHHHhCCCChhHHHHHHH
Q 008728 145 LAEWLKSVHVKGEFLGVALL 164 (556)
Q Consensus 145 ~l~~L~~lGls~~~i~~il~ 164 (556)
.+..|+++|++-.+|..++.
T Consensus 50 ~I~~lr~~G~sL~eI~~ll~ 69 (172)
T cd04790 50 QICAYRSAGVSLEDIRSLLQ 69 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHh
Confidence 44455666666666666554
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=87.69 E-value=5.3 Score=37.61 Aligned_cols=47 Identities=23% Similarity=0.323 Sum_probs=25.3
Q ss_pred hHHHHHHHHHcCCChhhHHHHHhhCCcccccCccc-cchhHHHHHHHhCCChhhHh
Q 008728 285 WKPLVKYLYYLGVSRDGMRRMLVIKPMVFCFDLET-TIVPKVRFFQDIGVRDEGIA 339 (556)
Q Consensus 285 l~~~v~~L~~lGls~~~i~~il~~~P~iL~~~~e~-~l~~kv~~L~~lG~s~~~i~ 339 (556)
....++.++.+|++++++.+.=..+ ++ +=..-.+||..+|++.+++.
T Consensus 118 ~~~w~~l~~~~g~~~~~m~~wh~~f--------e~~~p~~h~~~l~~~g~~~~~~~ 165 (172)
T cd04790 118 KEKWVAILKAAGMDEADMRRWHIEF--------EKMEPEAHQEFLQSLGIPEDEIE 165 (172)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHH--------HHhCcHHHHHHHHHcCCCHHHHH
Confidence 3445566667777776654432211 11 11233567777777777653
No 12
>PRK14135 recX recombination regulator RecX; Provisional
Probab=87.45 E-value=33 Score=34.35 Aligned_cols=137 Identities=12% Similarity=0.108 Sum_probs=67.0
Q ss_pred HHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChh
Q 008728 115 IRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRD 193 (556)
Q Consensus 115 ~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~ 193 (556)
+.+|....-|..++..-...-+++.+.+..+++.|...|+ +....+....+.+ +.........+...|...|++.+
T Consensus 64 l~~L~~r~~s~~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~---~~~~~~g~~~I~~kL~~kGi~~~ 140 (263)
T PRK14135 64 LYYLSYQMRTEKEVRDYLKKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTN---INTGDKGPRVIKQKLLQKGIEDE 140 (263)
T ss_pred HHHhhhccccHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH---HhccccchHHHHHHHHHcCCCHH
Confidence 4444444555555544444334556666777777777775 3333333322201 11111223345667778888888
Q ss_pred hHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhh
Q 008728 194 WMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAF 272 (556)
Q Consensus 194 ~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~ 272 (556)
.|..++.... ..++ +.....+ +.+.+.++.. .+....-.....+|..-|++.+.|..++..
T Consensus 141 ~Ie~~l~~l~---~~~~--~d~a~~~----------~~k~~~~~~~---~~~~~~k~Ki~~~L~rkGf~~~~I~~~l~~ 201 (263)
T PRK14135 141 IIEEALSEYT---EEDQ--IEVAQKL----------AEKLLKKYQK---LPFKALKQKIIQSLLTKGFSYEVIKAALEE 201 (263)
T ss_pred HHHHHHHhCC---hhhH--HHHHHHH----------HHHHHHHhcC---CCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 8887776532 1111 1110001 1111122210 111112234567788888888888777764
No 13
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=87.37 E-value=1 Score=47.05 Aligned_cols=101 Identities=22% Similarity=0.245 Sum_probs=58.1
Q ss_pred HHHHHHHHHhCCCChhHHHHHHHhhCCccccCCh--------hhHHHHHHHH--HhCCCChhhHHHHHhhCCCcccccHH
Q 008728 142 IRHLAEWLKSVHVKGEFLGVALLKTGGNILERSI--------EELNEIVEYL--ETNGVRRDWMGYVMSRCPQLLSQSIE 211 (556)
Q Consensus 142 l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~--------~~l~~~l~~L--~s~G~~~~~i~~lv~~~P~iL~~s~~ 211 (556)
+...-.+-..+|+....+...+.| ||.++.... -.+-+...-| +...+-.+.-..++.+--.+|-+|.+
T Consensus 37 l~~l~k~~~~L~l~~~~~~~flrk-yP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~ 115 (335)
T PF11955_consen 37 LRDLSKLRRQLGLKPRKVSRFLRK-YPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKD 115 (335)
T ss_pred HHHHHHHHHhcCCCcccHHHHHHh-CCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCC
Confidence 333334446789977888889997 999996421 0111111111 01111101112222333346666665
Q ss_pred H--HHHHHHHHH-HcCCChhHHHHHHHhCCccccc
Q 008728 212 E--VKTRVHFYL-DMGMNKNDFGTMVFDYPKILGF 243 (556)
Q Consensus 212 ~--l~~~v~fL~-~lG~s~~~l~~ll~~~P~iL~~ 243 (556)
. -..+|..++ ++|++++-...++.+||..+.-
T Consensus 116 ~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 116 RRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred CcccHHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 3 245677776 8999999999999999998754
No 14
>PRK14136 recX recombination regulator RecX; Provisional
Probab=82.55 E-value=37 Score=34.91 Aligned_cols=138 Identities=14% Similarity=0.164 Sum_probs=86.3
Q ss_pred HHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCCh
Q 008728 114 LIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRR 192 (556)
Q Consensus 114 ~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~ 192 (556)
.+.||..---+..++..-.....+..+.+..+|+.|++.|+ +.........+ . .. .. .-...+..-|+..||+.
T Consensus 168 AL~lLSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr-~-R~--~k-kGp~rIrqELrQKGId~ 242 (309)
T PRK14136 168 ALGYLSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVH-R-RA--SR-VGSARIVSELKRHAVGD 242 (309)
T ss_pred HHHHhhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHH-H-Hh--hc-hhHHHHHHHHHHcCCCH
Confidence 56777777788888877766556788899999999999987 45555555444 2 11 11 12334567799999999
Q ss_pred hhHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhh
Q 008728 193 DWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAF 272 (556)
Q Consensus 193 ~~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~ 272 (556)
+.|...+.... .+.+......+++ ++..+ .. ........+.||..-||+.+.|..+|..
T Consensus 243 eLIEqALeeie------EDE~E~A~~L~eK-------------K~~~~-~~-d~kek~K~iRfL~rRGFS~D~I~~vLk~ 301 (309)
T PRK14136 243 ALVESVGAQLR------ETEFERAQAVWRK-------------KFGAL-PQ-TPAERAKQARFLAARGFSSATIVKLLKV 301 (309)
T ss_pred HHHHHHHHhcc------HhHHHHHHHHHHH-------------Hhccc-Cc-CHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 99988876431 1222222222221 11111 01 1233456689999999999999998876
Q ss_pred CCccc
Q 008728 273 RPHLM 277 (556)
Q Consensus 273 ~P~lL 277 (556)
+-.-+
T Consensus 302 ~~de~ 306 (309)
T PRK14136 302 GDDEF 306 (309)
T ss_pred chhcc
Confidence 54433
No 15
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=77.69 E-value=57 Score=29.86 Aligned_cols=135 Identities=18% Similarity=0.181 Sum_probs=71.2
Q ss_pred HHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCCh
Q 008728 114 LIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRR 192 (556)
Q Consensus 114 ~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~ 192 (556)
.+.+|....-|..++..-....+++.+.+..+++.|...|+ +....+....+.+ .- ...-...+...|...|++.
T Consensus 17 al~~L~~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~-~~---~~~g~~~I~~~L~~kGi~~ 92 (157)
T PRK00117 17 ALRLLARREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSR-AR---KGYGPRRIRQELRQKGVDR 92 (157)
T ss_pred HHHHHccchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-Hh---CCchHHHHHHHHHHcCCCH
Confidence 44555555566666555554445566677777777777775 4434444433311 11 1122344566788888888
Q ss_pred hhHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhh
Q 008728 193 DWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAF 272 (556)
Q Consensus 193 ~~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~ 272 (556)
+.|..++...+ .+..+ .....+. .++...-..+. ..-...+.+|..-|++.+.|..++..
T Consensus 93 ~~I~~~l~~~~----~d~~e--~a~~~~~-------------k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 93 EIIEEALAELD----IDWEE--LARELAR-------------KKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHHcC----ccHHH--HHHHHHH-------------HHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 88887777654 12211 1111111 11222111111 33456667777888888777766653
No 16
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=77.28 E-value=4.1 Score=36.80 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=26.8
Q ss_pred hccceeeccchhhHHHHHHHHHHhCCCHHHHHHHHhhccccc
Q 008728 381 LGPELLGCSIGNKLEVNVKYFLSLGIKLHQLGAMIADFPMLL 422 (556)
Q Consensus 381 ~~P~iL~~s~~~~l~~kv~~L~~lG~~~~ei~~ml~~~P~lL 422 (556)
.+|.+-.- -+..|++||++.|++.+||..++.+.+.--
T Consensus 14 ~~p~V~~s----p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 14 QDPKVRNS----PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp CTTTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCcccccC----CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 45666443 477999999999999999999998876654
No 17
>PHA01351 putative minor structural protein
Probab=75.75 E-value=43 Score=37.92 Aligned_cols=87 Identities=17% Similarity=0.076 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHH-hhccccccchhcccccchhHHHHHHHHHHHhccCcccccccccccccccccCCChh
Q 008728 34 ELIMKALDIRRQVTAEIFKEAMW-RKGKFGITYSTNVADRLPDFIDHVMIKAAALKKLPEFADSSFNVRAKWFIEDSNVV 112 (556)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~r~~~~l~~~~~~ 112 (556)
+.=.++|.+--..|+++..+|.. ++-..+.|..+++.+..|--.|+
T Consensus 647 itELKKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~--------------------------------- 693 (1070)
T PHA01351 647 ETELKKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQ--------------------------------- 693 (1070)
T ss_pred HHHHHHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHH---------------------------------
Confidence 33345688889999999888842 35566777777777765553333
Q ss_pred hHHHHHHHCCCChHHHHHHHhhccCCh--hhHHHHHHHHHhCCC
Q 008728 113 PLIRWLKHNGLSYPKIAKLICMSGGNL--ESIRHLAEWLKSVHV 154 (556)
Q Consensus 113 ~~~~~L~~~G~s~~~i~~~~~~~~~~~--~~l~~~l~~L~~lGl 154 (556)
...-|+.+|++.+.|.-+...+++.+ ..+..-..-|.++|.
T Consensus 694 -~~~ELKKL~IpdSqInil~t~yy~~~~~~kls~~~~sl~~~g~ 736 (1070)
T PHA01351 694 -LSGELKKIHKDKTALELYITKFYYEYIYPKISNYHLQLARHGI 736 (1070)
T ss_pred -HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 44557777888888777666543332 455555555566776
No 18
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=74.61 E-value=23 Score=41.21 Aligned_cols=89 Identities=10% Similarity=0.090 Sum_probs=67.2
Q ss_pred CCChhhHHHHHHH---CCCChHHHHHHHhhccCCh-hhHHHHHHHHHhC-CCChhHHHHHHHhhCCccccCChhhHHHHH
Q 008728 108 DSNVVPLIRWLKH---NGLSYPKIAKLICMSGGNL-ESIRHLAEWLKSV-HVKGEFLGVALLKTGGNILERSIEELNEIV 182 (556)
Q Consensus 108 ~~~~~~~~~~L~~---~G~s~~~i~~~~~~~~~~~-~~l~~~l~~L~~l-Gls~~~i~~il~r~~P~lL~~s~~~l~~~l 182 (556)
......++.||.+ .|+-+....+++..|+.+. +.+..-.+.|.++ |++...+..+... +. .......++
T Consensus 74 p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~-~~-----~~~~~~~~~ 147 (720)
T TIGR01448 74 PTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQ-WS-----QQGDERRLL 147 (720)
T ss_pred CCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHH-HH-----HhHHHHHHH
Confidence 3445578899985 3888988899998875553 5677777778776 9999998887775 31 233477889
Q ss_pred HHHHhCCCChhhHHHHHhhC
Q 008728 183 EYLETNGVRRDWMGYVMSRC 202 (556)
Q Consensus 183 ~~L~s~G~~~~~i~~lv~~~ 202 (556)
.||.++|++...+.++...+
T Consensus 148 ~~L~~~gi~~~~a~ki~~~y 167 (720)
T TIGR01448 148 AGLQGLGIGIKLAQRIYKFY 167 (720)
T ss_pred HHHHHcCCCHHHHHHHHHHH
Confidence 99999999998887777654
No 19
>PRK14135 recX recombination regulator RecX; Provisional
Probab=72.08 E-value=97 Score=30.99 Aligned_cols=79 Identities=16% Similarity=0.066 Sum_probs=41.5
Q ss_pred HHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhhCCcccccCcccchHHHHHHHHHc
Q 008728 216 RVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPHLMGCGIGERWKPLVKYLYYL 295 (556)
Q Consensus 216 ~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~~P~lL~~s~e~~l~~~v~~L~~l 295 (556)
...+|..-|++...|..++.....=. ..+. -.+.|... +.+...++. .....+.-.....||..=
T Consensus 181 i~~~L~rkGf~~~~I~~~l~~~~~e~---d~~~---e~e~l~~~------~~k~~~k~~---~~~~~k~k~K~~~~L~rr 245 (263)
T PRK14135 181 IIQSLLTKGFSYEVIKAALEELDLEQ---DEEE---EQELLQKE------LEKAYRKYS---KYDGYELKQKLKQALYRK 245 (263)
T ss_pred HHHHHHhCCCCHHHHHHHHHHcccCC---ChHH---HHHHHHHH------HHHHHHHHh---cCCHHHHHHHHHHHHHHC
Confidence 45788899999999988887642100 0000 00111100 000111111 001112345677888899
Q ss_pred CCChhhHHHHHhhC
Q 008728 296 GVSRDGMRRMLVIK 309 (556)
Q Consensus 296 Gls~~~i~~il~~~ 309 (556)
||+.+.|..++...
T Consensus 246 GF~~~~I~~~l~~~ 259 (263)
T PRK14135 246 GFSYDDIDSFLREY 259 (263)
T ss_pred CCCHHHHHHHHHHh
Confidence 99999988887653
No 20
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=69.15 E-value=41 Score=29.33 Aligned_cols=60 Identities=18% Similarity=0.275 Sum_probs=25.9
Q ss_pred ChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhhHHHHHh
Q 008728 138 NLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMGYVMS 200 (556)
Q Consensus 138 ~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~i~~lv~ 200 (556)
+.+.+..+++.|.+.|+ +....+....+ .- +.....-...+..-|+..|++...|...+.
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~-~~--~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVR-SR--LRRKGKGPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHH-HH--HHHTT--HHHHHHHHHHTT--HHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHH-Hh--cccccccHHHHHHHHHHHCCChHHHHHHHH
Confidence 44455566666666665 22222222221 00 000111233345566777777777766665
No 21
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=68.86 E-value=34 Score=39.78 Aligned_cols=89 Identities=12% Similarity=0.089 Sum_probs=60.9
Q ss_pred hhhHHHHHHHHHh---CCCChhHHHHHHHhhCCccccCCh-hhHHHHHHHHHhC-CCChhhHHHHHhhCCCcccccHHHH
Q 008728 139 LESIRHLAEWLKS---VHVKGEFLGVALLKTGGNILERSI-EELNEIVEYLETN-GVRRDWMGYVMSRCPQLLSQSIEEV 213 (556)
Q Consensus 139 ~~~l~~~l~~L~~---lGls~~~i~~il~r~~P~lL~~s~-~~l~~~l~~L~s~-G~~~~~i~~lv~~~P~iL~~s~~~l 213 (556)
+.+.+..+.||.+ -|+.+....+|+.+ |+.+. +.+..-.+.|..+ |++...+..+...+. .....
T Consensus 74 p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~-----fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~-----~~~~~ 143 (720)
T TIGR01448 74 PTSKEGIVAYLSSRSIKGVGKKLAQRIVKT-----FGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS-----QQGDE 143 (720)
T ss_pred CCCHHHHHHHHhcCCCCCcCHHHHHHHHHH-----hCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH-----HhHHH
Confidence 3456678889976 38888888888886 44332 3344445566664 899888887776542 11236
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhC
Q 008728 214 KTRVHFYLDMGMNKNDFGTMVFDY 237 (556)
Q Consensus 214 ~~~v~fL~~lG~s~~~l~~ll~~~ 237 (556)
...+.||..+|++.....++...|
T Consensus 144 ~~~~~~L~~~gi~~~~a~ki~~~y 167 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQRIYKFY 167 (720)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 677899999999988777766654
No 22
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=60.01 E-value=23 Score=29.70 Aligned_cols=22 Identities=9% Similarity=0.128 Sum_probs=9.3
Q ss_pred HHHHHHHHHcCCChhHHHHHHH
Q 008728 214 KTRVHFYLDMGMNKNDFGTMVF 235 (556)
Q Consensus 214 ~~~v~fL~~lG~s~~~l~~ll~ 235 (556)
...+.||..+|++.....++..
T Consensus 9 ~~~~~~L~~~gl~~~~a~kl~~ 30 (94)
T PF14490_consen 9 RELMAFLQEYGLSPKLAMKLYK 30 (94)
T ss_dssp HHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 3444555555555544444333
No 23
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=58.55 E-value=1.5e+02 Score=27.10 Aligned_cols=18 Identities=28% Similarity=0.350 Sum_probs=9.1
Q ss_pred HHHHHcCCChHHHHHHHh
Q 008728 254 TYLKEFGLSTEDVGRLLA 271 (556)
Q Consensus 254 ~~L~~lG~~~~~I~~ll~ 271 (556)
..|..-|++.+.|...+.
T Consensus 83 ~~L~~kGi~~~~I~~~l~ 100 (157)
T PRK00117 83 QELRQKGVDREIIEEALA 100 (157)
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 344555555555544444
No 24
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=55.66 E-value=45 Score=26.46 Aligned_cols=15 Identities=13% Similarity=0.512 Sum_probs=6.7
Q ss_pred HHHHHHcCCChHHHH
Q 008728 253 VTYLKEFGLSTEDVG 267 (556)
Q Consensus 253 v~~L~~lG~~~~~I~ 267 (556)
+..+..+|++++.+.
T Consensus 33 Ma~i~qLGip~eKLQ 47 (82)
T PF11212_consen 33 MATIQQLGIPQEKLQ 47 (82)
T ss_pred HHHHHHcCCCHHHHH
Confidence 334444455444443
No 25
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=54.29 E-value=18 Score=37.31 Aligned_cols=164 Identities=13% Similarity=0.110 Sum_probs=85.5
Q ss_pred HHHHHHHHHhCCCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhhHHHHHhhCCCcccc-----cHHHH---
Q 008728 142 IRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQ-----SIEEV--- 213 (556)
Q Consensus 142 l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~i~~lv~~~P~iL~~-----s~~~l--- 213 (556)
....+.-+-++|....++.+.+.- +..+....++||-+ |++.+.-.-.....|....- .+..+
T Consensus 135 ~e~~V~~Im~MGy~re~V~~AlRA--------afNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~ 205 (340)
T KOG0011|consen 135 YEQTVQQIMEMGYDREEVERALRA--------AFNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQ 205 (340)
T ss_pred hHHHHHHHHHhCccHHHHHHHHHH--------hhCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCCc
Confidence 345566666788888887766553 55667777888876 56542111111111111111 11111
Q ss_pred -------HHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhhCCcccc----cCcc
Q 008728 214 -------KTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPHLMG----CGIG 282 (556)
Q Consensus 214 -------~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~~P~lL~----~s~e 282 (556)
...++||++- -.-.+++.+|..+|.+|.. .|..+|-..-++.++|..|+.-|. ..++
T Consensus 206 ~~~~~~~~~~l~fLr~~-~qf~~lR~~iqqNP~ll~~-----------~Lqqlg~~nP~L~q~Iq~nqe~Fl~mlnep~~ 273 (340)
T KOG0011|consen 206 GAVEASGGDPLEFLRNQ-PQFQQLRQMIQQNPELLHP-----------LLQQLGKQNPQLLQLIQENQEAFLQLLNEPVE 273 (340)
T ss_pred cchhhhcCCchhhhhcc-HHHHHHHHHHhhCHHHHHH-----------HHHHHhhhCHHHHHHHHHHHHHHHHHhhcccc
Confidence 1225555431 0114577788888887642 466777777777777777764332 2222
Q ss_pred cchHHHHHHHHHcCCChhhHHHHHhhCC-cccccCccccchhHHHHHHHhCCChhhHhhh
Q 008728 283 ERWKPLVKYLYYLGVSRDGMRRMLVIKP-MVFCFDLETTIVPKVRFFQDIGVRDEGIANM 341 (556)
Q Consensus 283 ~~l~~~v~~L~~lGls~~~i~~il~~~P-~iL~~~~e~~l~~kv~~L~~lG~s~~~i~~~ 341 (556)
. .+.| .....=..-| .-+....++ +.-++-|+.+||++.-+..+
T Consensus 274 ~---------~~~~----~~~~~~~~~~~~~I~vtpee--~eAIeRL~alGF~ralViqa 318 (340)
T KOG0011|consen 274 G---------GDGG----GTGAPAAEGPGHQIQVTPEE--KEAIERLEALGFPRALVIQA 318 (340)
T ss_pred c---------cccc----ccccccccCCcceEecCHHH--HHHHHHHHHhCCcHHHHHHH
Confidence 1 1111 1122222333 333444443 67788889999977655443
No 26
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=53.55 E-value=21 Score=32.28 Aligned_cols=34 Identities=15% Similarity=0.366 Sum_probs=19.8
Q ss_pred CCccccCChhhHHHHHHHHHhCCCChhhHHHHHhhCC
Q 008728 167 GGNILERSIEELNEIVEYLETNGVRRDWMGYVMSRCP 203 (556)
Q Consensus 167 ~P~lL~~s~~~l~~~l~~L~s~G~~~~~i~~lv~~~P 203 (556)
+|.+-..+ +..+++||++.|++.++|..++.+.+
T Consensus 15 ~p~V~~sp---~~~k~~FL~sKGLt~~EI~~al~~a~ 48 (136)
T PF04695_consen 15 DPKVRNSP---LEKKIAFLESKGLTEEEIDEALGRAG 48 (136)
T ss_dssp TTTCCCS----HHHHHHHHHHCT--HHHHHHHHHHHT
T ss_pred CcccccCC---HHHHHHHHHcCCCCHHHHHHHHHhcC
Confidence 45554444 45567777777777777777776554
No 27
>PRK14134 recX recombination regulator RecX; Provisional
Probab=52.97 E-value=2.7e+02 Score=28.42 Aligned_cols=22 Identities=23% Similarity=0.231 Sum_probs=11.7
Q ss_pred HHHHHHHHHcCCChHHHHHHHh
Q 008728 250 HQKVTYLKEFGLSTEDVGRLLA 271 (556)
Q Consensus 250 ~~~v~~L~~lG~~~~~I~~ll~ 271 (556)
...+.||..-|++.+.|..++.
T Consensus 183 ~Kl~~~L~rrGFs~~~I~~vl~ 204 (283)
T PRK14134 183 KKLGPYLISRGYSSNIAEWILN 204 (283)
T ss_pred HHHHHHHHHCCCCHHHHHHHHH
Confidence 3444555556666555554443
No 28
>PRK14134 recX recombination regulator RecX; Provisional
Probab=52.61 E-value=1.3e+02 Score=30.60 Aligned_cols=24 Identities=25% Similarity=0.421 Sum_probs=17.6
Q ss_pred hHHHHHHHHHcCCChhhHHHHHhh
Q 008728 285 WKPLVKYLYYLGVSRDGMRRMLVI 308 (556)
Q Consensus 285 l~~~v~~L~~lGls~~~i~~il~~ 308 (556)
-+.+..||..-||+-+.|..++..
T Consensus 255 ~~Kl~~~L~rkGf~~e~I~~vl~~ 278 (283)
T PRK14134 255 YRRLSNYLLRRGYSWEEVKKSLNE 278 (283)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHH
Confidence 456677788888888888777654
No 29
>PRK14137 recX recombination regulator RecX; Provisional
Probab=49.00 E-value=2.5e+02 Score=26.97 Aligned_cols=131 Identities=9% Similarity=0.061 Sum_probs=69.3
Q ss_pred HHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChh
Q 008728 115 IRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRD 193 (556)
Q Consensus 115 ~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~ 193 (556)
+++|..-.-|..++..-.....++.+.+..+++.|.+.|+ +....+....+ ....-...+-.-|+..|++.+
T Consensus 47 l~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~-------~k~~Gp~rI~~eL~qKGI~~~ 119 (195)
T PRK14137 47 FRALAARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENS-------RRGVGALRVRQTLRRRGVEET 119 (195)
T ss_pred HHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH-------hcCchHHHHHHHHHHcCCCHH
Confidence 3444444455555544444334555666677777777776 33333332110 111122335667889999998
Q ss_pred hHHHHHhhCCCcccccHH-HHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhh
Q 008728 194 WMGYVMSRCPQLLSQSIE-EVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAF 272 (556)
Q Consensus 194 ~i~~lv~~~P~iL~~s~~-~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~ 272 (556)
.|...+... +.+ ........++. +++.+-. ....-...+.||..-|++.+.|..++..
T Consensus 120 lI~~al~~~------d~ede~e~a~~l~~K-------------K~~~~~~--~~~~k~K~~~~L~rRGFs~~~I~~al~~ 178 (195)
T PRK14137 120 LIEETLAAR------DPQEEQQEARNLLER-------------RWSSFAR--KRDPRASAYAFLARRGFSGAVIWPAIRE 178 (195)
T ss_pred HHHHHHHhc------CchhHHHHHHHHHHH-------------hccccCc--chhHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 888877643 221 22222222221 1111111 0122355777899999999888877765
Q ss_pred C
Q 008728 273 R 273 (556)
Q Consensus 273 ~ 273 (556)
.
T Consensus 179 ~ 179 (195)
T PRK14137 179 V 179 (195)
T ss_pred H
Confidence 3
No 30
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=48.63 E-value=78 Score=26.42 Aligned_cols=47 Identities=21% Similarity=0.064 Sum_probs=27.5
Q ss_pred CCChhhHHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCCh
Q 008728 108 DSNVVPLIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSI 175 (556)
Q Consensus 108 ~~~~~~~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~ 175 (556)
...+..++.||..+|+++..+.+++..+ |- +...+|.. +|..|..+.
T Consensus 5 ~~~~~~~~~~L~~~gl~~~~a~kl~~~y-----------------g~---~ai~~l~~-nPY~L~~~i 51 (94)
T PF14490_consen 5 NRGLRELMAFLQEYGLSPKLAMKLYKKY-----------------GD---DAIEILKE-NPYRLIEDI 51 (94)
T ss_dssp ----HHHHHHHHHTT--HHHHHHHHHHH------------------T---THHHHHHH--STCCCB-S
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHH-----------------hH---HHHHHHHH-ChHHHHHHc
Confidence 3456678889999999998888888755 21 22245664 999888754
No 31
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=48.50 E-value=39 Score=22.90 Aligned_cols=22 Identities=18% Similarity=0.007 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCChhHHHHHHHh
Q 008728 144 HLAEWLKSVHVKGEFLGVALLK 165 (556)
Q Consensus 144 ~~l~~L~~lGls~~~i~~il~r 165 (556)
..+.-|.++||+..+..+.|.+
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~ 25 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRA 25 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 3455556666666655555554
No 32
>PHA01351 putative minor structural protein
Probab=47.16 E-value=5e+02 Score=29.90 Aligned_cols=126 Identities=12% Similarity=0.019 Sum_probs=74.0
Q ss_pred HHHhCCCChhHHHHHHHhhCCccccCCh-----h--------hHHHHHHHHHhCCCChhhHHHHHhhCCCcccccHH--H
Q 008728 148 WLKSVHVKGEFLGVALLKTGGNILERSI-----E--------ELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQSIE--E 212 (556)
Q Consensus 148 ~L~~lGls~~~i~~il~r~~P~lL~~s~-----~--------~l~~~l~~L~s~G~~~~~i~~lv~~~P~iL~~s~~--~ 212 (556)
-|+++|++..-|..++.. +=.+-.... + +.+..-.-|+.+|..+.-+.++..-+.++.....+ -
T Consensus 553 ELKkLg~s~alIqaiI~E-yftepL~KlQLnvyEsLakKGY~d~qq~ksElk~LGidKe~i~klin~Y~ql~qt~~eIkY 631 (1070)
T PHA01351 553 DLKHLGFDSAIISALIYE-NQVEQLIKFQLNNIESLAKKGYLSLDEIKKQFKAIGIIKEYEDAFINFYNQELQISAFLTI 631 (1070)
T ss_pred HHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 455677777766666553 322111100 1 22333445667788887777776666555333222 1
Q ss_pred H-----------HHHHHHHHHcCCChhHHHHHHHhC---Cccccc---------chhhhHHHHHHHHHHcCCChHHHHHH
Q 008728 213 V-----------KTRVHFYLDMGMNKNDFGTMVFDY---PKILGF---------LTLEEMHQKVTYLKEFGLSTEDVGRL 269 (556)
Q Consensus 213 l-----------~~~v~fL~~lG~s~~~l~~ll~~~---P~iL~~---------~~~~~l~~~v~~L~~lG~~~~~I~~l 269 (556)
+ +....-|+.+|++++-+..++..+ |.+-.- .+.-+....-.-|+.+|.+++.+-.+
T Consensus 632 Iqe~LK~f~IspkeAitELKKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil 711 (1070)
T PHA01351 632 LKSQLRQFQIDPKEAETELKKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELY 711 (1070)
T ss_pred HHHHHHHcccCHHHHHHHHHHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHH
Confidence 1 234567788999998888888777 432110 11122344567899999999999888
Q ss_pred HhhCC
Q 008728 270 LAFRP 274 (556)
Q Consensus 270 l~~~P 274 (556)
++.+-
T Consensus 712 ~t~yy 716 (1070)
T PHA01351 712 ITKFY 716 (1070)
T ss_pred HHHHH
Confidence 87653
No 33
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=46.86 E-value=62 Score=28.22 Aligned_cols=57 Identities=19% Similarity=0.158 Sum_probs=27.3
Q ss_pred CCChhhHHHHHHHCCCC-hHHHHHHHhh--ccCChhhHHHHHHHHHhCCCChhHHHHHHH
Q 008728 108 DSNVVPLIRWLKHNGLS-YPKIAKLICM--SGGNLESIRHLAEWLKSVHVKGEFLGVALL 164 (556)
Q Consensus 108 ~~~~~~~~~~L~~~G~s-~~~i~~~~~~--~~~~~~~l~~~l~~L~~lGls~~~i~~il~ 164 (556)
+..+..++.+|..+|+= ....+..+-. .............-|..-|++...|..++.
T Consensus 8 ~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHH
Confidence 33455567777777743 3334433321 110122333445566777888777765544
No 34
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=43.92 E-value=81 Score=30.16 Aligned_cols=26 Identities=12% Similarity=0.178 Sum_probs=20.2
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhCC
Q 008728 213 VKTRVHFYLDMGMNKNDFGTMVFDYP 238 (556)
Q Consensus 213 l~~~v~fL~~lG~s~~~l~~ll~~~P 238 (556)
+...+.+|..+|++..++.+++..+-
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKIL 174 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 56677888888888888888887763
No 35
>PHA02591 hypothetical protein; Provisional
Probab=42.95 E-value=56 Score=26.50 Aligned_cols=30 Identities=23% Similarity=0.615 Sum_probs=23.2
Q ss_pred cccc-cCCChhhHHHHHHHCCCChHHHHHHH
Q 008728 103 KWFI-EDSNVVPLIRWLKHNGLSYPKIAKLI 132 (556)
Q Consensus 103 ~~~l-~~~~~~~~~~~L~~~G~s~~~i~~~~ 132 (556)
+.|+ ++.++.++.+-|...|++.++|+...
T Consensus 39 ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 39 RYFVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEEEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 4455 67788888888888888888887765
No 36
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.01 E-value=1.3e+02 Score=32.14 Aligned_cols=23 Identities=9% Similarity=-0.049 Sum_probs=14.9
Q ss_pred HHHHHHHHHcCCCcchHhHHHhhc
Q 008728 359 PVVIFLMTKAGVSERDIGKCLALG 382 (556)
Q Consensus 359 ~~~~fL~~~lGl~~~~i~~vi~~~ 382 (556)
..++-| ..|||++..+..+...|
T Consensus 339 ~AIeRL-~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 339 EAIERL-CALGFDRGLVIQAYFAC 361 (378)
T ss_pred HHHHHH-HHcCCCHHHHHHHHHhc
Confidence 455555 58888888777664433
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.64 E-value=3.4e+02 Score=26.03 Aligned_cols=25 Identities=4% Similarity=0.068 Sum_probs=18.1
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhC
Q 008728 213 VKTRVHFYLDMGMNKNDFGTMVFDY 237 (556)
Q Consensus 213 l~~~v~fL~~lG~s~~~l~~ll~~~ 237 (556)
....+.+|..+|++..++.+++...
T Consensus 148 ~~e~~~aL~~LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 148 NSDILATLTALGYSSSEAAKAISSL 172 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3456677778888888877777765
No 38
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=40.40 E-value=1.9e+02 Score=23.07 Aligned_cols=47 Identities=21% Similarity=0.183 Sum_probs=25.3
Q ss_pred hHHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCChhHHHHH
Q 008728 113 PLIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKGEFLGVA 162 (556)
Q Consensus 113 ~~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~~~i~~i 162 (556)
|.+..|+...+|.++|..++.-+..|+= .-......+|++++.+..+
T Consensus 3 PIia~LKehnvsd~qi~elFq~lT~NPl---~AMa~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQALTQNPL---AAMATIQQLGIPQEKLQQL 49 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHHhhCHH---HHHHHHHHcCCCHHHHHHH
Confidence 3455666666666666666654433331 1223445566666666544
No 39
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=39.08 E-value=2.7e+02 Score=26.33 Aligned_cols=53 Identities=23% Similarity=0.236 Sum_probs=29.7
Q ss_pred hhhHHHHHHHCC-CChHHHHHHHhhc--cCChhhHHHHHHHHHhCCCChhHHHHHHH
Q 008728 111 VVPLIRWLKHNG-LSYPKIAKLICMS--GGNLESIRHLAEWLKSVHVKGEFLGVALL 164 (556)
Q Consensus 111 ~~~~~~~L~~~G-~s~~~i~~~~~~~--~~~~~~l~~~l~~L~~lGls~~~i~~il~ 164 (556)
+..++++|...| ++..+++..+-.. ... ........-|...|++...|..++.
T Consensus 54 Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g-~G~~rl~qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 54 IEEVIDRLAEEGYLDDTRFAEAYIRSRSRKG-KGPARLKQELKQKGIDDEIIEEALE 109 (174)
T ss_pred HHHHHHHHHHcCcccHHHHHHHHHHHHHhcc-cChHHHHHHHHHcCCCHHHHHHHHh
Confidence 556677776665 4555555554321 111 1223344456677888877777666
No 40
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=38.33 E-value=76 Score=29.60 Aligned_cols=51 Identities=8% Similarity=0.196 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCCh
Q 008728 140 ESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRR 192 (556)
Q Consensus 140 ~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~ 192 (556)
..++..+++|+++-=..-....+.. .|.+...+.+.+..+++..+..|++-
T Consensus 48 St~k~Il~aL~e~e~~~ita~~iM~--spvv~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 48 STVKRILEALEEAEKTRITAKTIMH--SPVVSVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred HHHHHHHHHHHHhhcceEeHhhhcc--CCeeEECchhhHHHHHHHHHHcCCcc
Confidence 4677777777765223333333333 67766666677888888888888763
No 41
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=38.02 E-value=78 Score=21.14 Aligned_cols=21 Identities=19% Similarity=-0.080 Sum_probs=10.2
Q ss_pred HHHHHHhCCCChhHHHHHHHh
Q 008728 145 LAEWLKSVHVKGEFLGVALLK 165 (556)
Q Consensus 145 ~l~~L~~lGls~~~i~~il~r 165 (556)
.++-|.++||+..++...+.+
T Consensus 4 ~v~~L~~mGf~~~~a~~aL~~ 24 (37)
T smart00165 4 KIDQLLEMGFSREEALKALRA 24 (37)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 344455555555554444443
No 42
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=37.67 E-value=53 Score=23.71 Aligned_cols=23 Identities=22% Similarity=-0.022 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCChhHHHHHHHh
Q 008728 143 RHLAEWLKSVHVKGEFLGVALLK 165 (556)
Q Consensus 143 ~~~l~~L~~lGls~~~i~~il~r 165 (556)
++.++.|.++|++..++.+++.+
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 44555666666666666665554
No 43
>PRK14137 recX recombination regulator RecX; Provisional
Probab=37.60 E-value=3.8e+02 Score=25.75 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=13.2
Q ss_pred HHHHHHHcCCChhHHHHHHHh
Q 008728 216 RVHFYLDMGMNKNDFGTMVFD 236 (556)
Q Consensus 216 ~v~fL~~lG~s~~~l~~ll~~ 236 (556)
.+.||..-||+...|..++..
T Consensus 158 ~~~~L~rRGFs~~~I~~al~~ 178 (195)
T PRK14137 158 AYAFLARRGFSGAVIWPAIRE 178 (195)
T ss_pred HHHHHHHCCCCHHHHHHHHHH
Confidence 445666677776666665554
No 44
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=37.21 E-value=2.2e+02 Score=24.86 Aligned_cols=56 Identities=9% Similarity=0.176 Sum_probs=29.6
Q ss_pred ChhhHHHHHHHHHhCCCChhhHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHH
Q 008728 174 SIEELNEIVEYLETNGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMV 234 (556)
Q Consensus 174 s~~~l~~~l~~L~s~G~~~~~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll 234 (556)
+.+.+......|...|+.+..+..++.-+| .+++.+...|.-+.+- ++++++.+++
T Consensus 53 ~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P----~s~~E~~~lI~sl~~r-~~ee~l~~iL 108 (118)
T smart00657 53 NREIVRAVRTLLKSKKLHKFEIAQLGNLRP----ETAEEAQLLIPSLEER-IDEEELEELL 108 (118)
T ss_pred CHHHHHHHHHHHHhcCCCHHHHHHHhCCCC----CCHHHHHHHhhhhhcc-CCHHHHHHHH
Confidence 444555556666666666666666666666 2444454444444322 4444444433
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=36.57 E-value=1.5e+02 Score=28.35 Aligned_cols=27 Identities=15% Similarity=0.254 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHcCCChHHHHHHHhhCC
Q 008728 248 EMHQKVTYLKEFGLSTEDVGRLLAFRP 274 (556)
Q Consensus 248 ~l~~~v~~L~~lG~~~~~I~~ll~~~P 274 (556)
.+...+.+|..+|+++.++.+++...-
T Consensus 148 ~~~ev~~aL~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 148 ALEEAVSALVALGYKPKEASKAVAKIL 174 (192)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 367889999999999999999988763
No 46
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=35.12 E-value=3.9e+02 Score=25.20 Aligned_cols=135 Identities=12% Similarity=0.088 Sum_probs=70.0
Q ss_pred HHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCC-ChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChh
Q 008728 115 IRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHV-KGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRD 193 (556)
Q Consensus 115 ~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGl-s~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~ 193 (556)
+++|..---|..++..-......+.+.++.++.+|...|+ +....+....+ .-.--+ .-....-+-|...|++++
T Consensus 27 l~~Ls~R~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~-~r~~~g---~G~~rl~qeL~qkGi~~~ 102 (174)
T COG2137 27 LRLLSRRDRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAYIR-SRSRKG---KGPARLKQELKQKGIDDE 102 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHHHH-HHHhcc---cChHHHHHHHHHcCCCHH
Confidence 3444433444444444444334455567788888888877 44444433332 111111 223445667888999999
Q ss_pred hHHHHHhhCCCcccccHHH-HHHHHHHHH-HcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHh
Q 008728 194 WMGYVMSRCPQLLSQSIEE-VKTRVHFYL-DMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLA 271 (556)
Q Consensus 194 ~i~~lv~~~P~iL~~s~~~-l~~~v~fL~-~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~ 271 (556)
.|..++.. .+.++ .......+. .+ +.+.+.. ....=.....+|..-|++.+.|..++.
T Consensus 103 ~Ie~aL~~------~~~~~~~~~a~~~~~kk~------------~~~~~~~--~~~~k~Ki~r~L~~rGFs~~~i~~~l~ 162 (174)
T COG2137 103 IIEEALEL------IDEEDEQERARKVLRKKF------------KRENKPP--DKKEKAKIQRFLLRRGFSYEVIKEALN 162 (174)
T ss_pred HHHHHHhc------cchHHHHHHHHHHHHHHh------------CccccCc--chhHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 99888762 22221 211122221 11 1121111 112224455677888999998888876
Q ss_pred hC
Q 008728 272 FR 273 (556)
Q Consensus 272 ~~ 273 (556)
..
T Consensus 163 ~~ 164 (174)
T COG2137 163 EA 164 (174)
T ss_pred Hh
Confidence 54
No 47
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=34.31 E-value=61 Score=28.89 Aligned_cols=62 Identities=19% Similarity=0.268 Sum_probs=33.9
Q ss_pred hhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCC
Q 008728 200 SRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLS 262 (556)
Q Consensus 200 ~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~ 262 (556)
.+.|.-|..+.+++..-+--|..-|+++.+|+-+++....|=... .-.=...+.+|+..|+-
T Consensus 20 r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r-~v~G~kI~Rilk~~Gl~ 81 (151)
T KOG0400|consen 20 RSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVR-FVTGNKILRILKSNGLA 81 (151)
T ss_pred cCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhh-eechhHHHHHHHHcCCC
Confidence 345666666666666666666666777777765555443321111 11113455666666664
No 48
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=33.45 E-value=97 Score=22.15 Aligned_cols=43 Identities=16% Similarity=0.066 Sum_probs=24.8
Q ss_pred HhCCCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhhHH
Q 008728 150 KSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMG 196 (556)
Q Consensus 150 ~~lGls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~i~ 196 (556)
+.+|++...+.+++.. .| ..+.+....+.+..+.+|+.+.++.
T Consensus 5 ~~~gvs~~tvs~~l~g-~~---~vs~~~~~~i~~~~~~l~~~~~~~~ 47 (52)
T cd01392 5 RAAGVSVATVSRVLNG-KP---RVSEETRERVLAAAEELGYRPNAAA 47 (52)
T ss_pred HHHCcCHHHHHHHHcC-CC---CCCHHHHHHHHHHHHHhCCCCCHHH
Confidence 4457777777766553 33 2344555556666666666665543
No 49
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=33.28 E-value=4e+02 Score=27.40 Aligned_cols=42 Identities=19% Similarity=0.373 Sum_probs=22.0
Q ss_pred CCChhhHHHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCCh
Q 008728 108 DSNVVPLIRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKG 156 (556)
Q Consensus 108 ~~~~~~~~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~ 156 (556)
..++..-+.+|...|++...+++... .++....||..-|+..
T Consensus 54 ~~di~~yl~~l~~~g~s~~S~aR~ls-------alR~fy~fl~~E~~~~ 95 (300)
T COG4974 54 EADIREYLTELAEQGLSATSIARALS-------ALRSFYQFLIREGLRE 95 (300)
T ss_pred HHHHHHHHHHHHhCCcChhhHHHHHH-------HHHHHHHHHHHCCCcc
Confidence 44455555555566666666554443 3344455665555544
No 50
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=32.61 E-value=46 Score=25.66 Aligned_cols=34 Identities=24% Similarity=0.305 Sum_probs=14.5
Q ss_pred CCCcccccHHHHHHHHHHHHHcCCChhHHHHHHH
Q 008728 202 CPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVF 235 (556)
Q Consensus 202 ~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~ 235 (556)
.|.-+.++.+++...|.-|.+-|+++.+|+-+|+
T Consensus 22 ~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLR 55 (60)
T PF08069_consen 22 PPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_dssp --TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHH
T ss_pred CCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhh
Confidence 3444444455555555555555555555554444
No 51
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=32.10 E-value=4.4e+02 Score=24.88 Aligned_cols=79 Identities=16% Similarity=0.175 Sum_probs=46.5
Q ss_pred HHHHHHCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhh
Q 008728 115 IRWLKHNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDW 194 (556)
Q Consensus 115 ~~~L~~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~ 194 (556)
++....+||++++|..+-.....+...+....-.+-++-++.+.+.+++.. ......-...++.+-.+|-+..-
T Consensus 19 ~~~c~~lG~~~eel~~L~~ls~~~l~~L~~~~v~~~~i~in~~~l~~~L~~------~~~~~~~~~~idr~L~lGAS~~m 92 (180)
T PF11198_consen 19 IRRCEALGFSPEELDALQQLSLDDLHYLANSSVSFVSISINHDVLWRLLEQ------ARREQQEQQLIDRALRLGASIEM 92 (180)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHhcCCcceeeeeeCHHHHHHHHHH------HHHHHHHHHHHHHHHHcCCCHHH
Confidence 456678899999998887643233333333333344466667777766664 11123344566666677777765
Q ss_pred HHHHH
Q 008728 195 MGYVM 199 (556)
Q Consensus 195 i~~lv 199 (556)
+..++
T Consensus 93 m~~~F 97 (180)
T PF11198_consen 93 MQRLF 97 (180)
T ss_pred HHHHH
Confidence 55444
No 52
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=31.97 E-value=96 Score=26.49 Aligned_cols=20 Identities=25% Similarity=0.315 Sum_probs=10.1
Q ss_pred CChhHHHHHHHhhCCccccCC
Q 008728 154 VKGEFLGVALLKTGGNILERS 174 (556)
Q Consensus 154 ls~~~i~~il~r~~P~lL~~s 174 (556)
++..++..++.. +|.++.++
T Consensus 71 ~s~~e~i~~l~~-~p~LikRP 90 (110)
T PF03960_consen 71 LSDEELIELLLE-NPKLIKRP 90 (110)
T ss_dssp SBHHHHHHHHHH-SGGGB-SS
T ss_pred hhhHHHHHHHHh-ChhheeCC
Confidence 455555555553 55555544
No 53
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=31.79 E-value=86 Score=31.73 Aligned_cols=150 Identities=17% Similarity=0.261 Sum_probs=85.4
Q ss_pred chhHHHHH-HHhCC-ChhhHhhhhhhcCccccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHH
Q 008728 321 IVPKVRFF-QDIGV-RDEGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNV 398 (556)
Q Consensus 321 l~~kv~~L-~~lG~-s~~~i~~~i~~~P~iL~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv 398 (556)
++.++.|. +..|+ +.-.+..=|.-.|.+++++-+ +++.+++-|+..+|+++.+.. .++|.-|+-... .|+
T Consensus 73 LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~-~i~~r~~ELl~lvgL~p~~~~---~RyP~eLSGGQQ----QRV 144 (309)
T COG1125 73 LRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKE-RIKKRADELLDLVGLDPSEYA---DRYPHELSGGQQ----QRV 144 (309)
T ss_pred HHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHH-HHHHHHHHHHHHhCCCHHHHh---hcCchhcCcchh----hHH
Confidence 55566655 34443 445566666777777777755 477777777777888776543 477777655432 222
Q ss_pred HHHHHhCCCHHHHHHHHhhcccccccch----------hhHHHHHHHHHHHhCCChhHHhhcCcccccCcccccH--HHH
Q 008728 399 KYFLSLGIKLHQLGAMIADFPMLLRYNI----------DIFRPKYRYLRRTMVRPLQDLIEFPRFFSYSLEERII--PRH 466 (556)
Q Consensus 399 ~~L~~lG~~~~ei~~ml~~~P~lL~~s~----------e~l~~k~~fL~~~mg~~~~~i~~~P~~L~ySLe~RI~--pR~ 466 (556)
| +..++...|.++.+++ ..++.-+.-+.+++|.. -.+.+...+.-++ -|.
T Consensus 145 ------G-----v~RALAadP~ilLMDEPFgALDpI~R~~lQ~e~~~lq~~l~kT-------ivfVTHDidEA~kLadri 206 (309)
T COG1125 145 ------G-----VARALAADPPILLMDEPFGALDPITRKQLQEEIKELQKELGKT-------IVFVTHDIDEALKLADRI 206 (309)
T ss_pred ------H-----HHHHHhcCCCeEeecCCccccChhhHHHHHHHHHHHHHHhCCE-------EEEEecCHHHHHhhhceE
Confidence 2 3346778888887765 34444444455554432 1233444332111 111
Q ss_pred HHHHHCCCCc---ccccccccChHHHHHHHHhhh
Q 008728 467 KIMVENRVNF---KLRYMLACSNEEFNQKVADKV 497 (556)
Q Consensus 467 ~~L~~~Gl~~---~l~~~L~~sd~~F~~~~~~~~ 497 (556)
..+ ..|... ....++...-.+|.+.+.+.-
T Consensus 207 ~vm-~~G~i~Q~~~P~~il~~Pan~FV~~f~g~~ 239 (309)
T COG1125 207 AVM-DAGEIVQYDTPDEILANPANDFVEDFFGES 239 (309)
T ss_pred EEe-cCCeEEEeCCHHHHHhCccHHHHHHHhccc
Confidence 122 234321 234688888999999888764
No 54
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=31.19 E-value=1.2e+02 Score=20.31 Aligned_cols=20 Identities=25% Similarity=-0.012 Sum_probs=9.9
Q ss_pred HHHHHHhCCCChhHHHHHHH
Q 008728 145 LAEWLKSVHVKGEFLGVALL 164 (556)
Q Consensus 145 ~l~~L~~lGls~~~i~~il~ 164 (556)
.++-|.++|++...+...+.
T Consensus 4 ~v~~L~~mGf~~~~~~~AL~ 23 (38)
T cd00194 4 KLEQLLEMGFSREEARKALR 23 (38)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34445555555555544444
No 55
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=30.09 E-value=87 Score=27.47 Aligned_cols=17 Identities=18% Similarity=0.432 Sum_probs=11.6
Q ss_pred hHHHHHHHHHhCCCChh
Q 008728 177 ELNEIVEYLETNGVRRD 193 (556)
Q Consensus 177 ~l~~~l~~L~s~G~~~~ 193 (556)
....+.+||+..|+...
T Consensus 13 t~rka~~~L~~~gi~~~ 29 (117)
T COG1393 13 TCRKALAWLEEHGIEYT 29 (117)
T ss_pred HHHHHHHHHHHcCCCcE
Confidence 45666777777777754
No 56
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=28.32 E-value=5.3e+02 Score=24.60 Aligned_cols=23 Identities=4% Similarity=0.144 Sum_probs=14.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHHh
Q 008728 214 KTRVHFYLDMGMNKNDFGTMVFD 236 (556)
Q Consensus 214 ~~~v~fL~~lG~s~~~l~~ll~~ 236 (556)
...+..|..+|+++.++.+++..
T Consensus 148 ~e~~~aL~~LGy~~~e~~~ai~~ 170 (191)
T TIGR00084 148 DELFEALVSLGYKPQEIQQALKK 170 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 44556666666666666666554
No 57
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.27 E-value=7.6e+02 Score=26.38 Aligned_cols=24 Identities=21% Similarity=0.188 Sum_probs=19.8
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhC
Q 008728 286 KPLVKYLYYLGVSRDGMRRMLVIK 309 (556)
Q Consensus 286 ~~~v~~L~~lGls~~~i~~il~~~ 309 (556)
+..|+-|+.+||++..+......|
T Consensus 338 ~~AIeRL~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 338 KEAIERLCALGFDRGLVIQAYFAC 361 (378)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhc
Confidence 578899999999999887776666
No 58
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=28.23 E-value=2.3e+02 Score=26.11 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=26.0
Q ss_pred hCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhC
Q 008728 201 RCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDY 237 (556)
Q Consensus 201 ~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~ 237 (556)
..|.-+.++.+++...|.-|..-|+++.+|+-+++..
T Consensus 21 ~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 21 EPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 4455566777777777777777777777777766643
No 59
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=26.81 E-value=37 Score=30.20 Aligned_cols=27 Identities=11% Similarity=0.065 Sum_probs=14.4
Q ss_pred cCChhhHHHHHHHHHhCCCChhHHHHH
Q 008728 136 GGNLESIRHLAEWLKSVHVKGEFLGVA 162 (556)
Q Consensus 136 ~~~~~~l~~~l~~L~~lGls~~~i~~i 162 (556)
..+++.+.+-+--|-+-|+++++|+-+
T Consensus 27 K~~~ddvkeqI~K~akKGltpsqIGvi 53 (151)
T KOG0400|consen 27 KLTADDVKEQIYKLAKKGLTPSQIGVI 53 (151)
T ss_pred hcCHHHHHHHHHHHHHcCCChhHceee
Confidence 445555555555555556666666533
No 60
>PF02433 FixO: Cytochrome C oxidase, mono-heme subunit/FixO; InterPro: IPR003468 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) []. Cytochrome cbb3 oxidases are required both to support symbiotic nitrogen fixation, whilst ensuring that the oxygen-labile nitrogenase is not compromised. Cytochrome cbb3 oxidases consist of four subunits: FixN (or CcoN), FixO (or CcoO), FixP (or CcoP) and FixQ (or CcoQ). The catalytic core is comprised of subunits FixN, FixO and FixP, where FixN acts as the catalytic subunit, and Fix O and FixP are membrane-bound mono- and di-haem cytochromes c, respectively. The FixQ subunit protects the core complex in the presence of oxygen from proteolytic degradation []. This entry represents the mono-haem FixO subunit.
Probab=26.39 E-value=1.7e+02 Score=28.74 Aligned_cols=15 Identities=13% Similarity=0.443 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHcCCC
Q 008728 212 EVKTRVHFYLDMGMN 226 (556)
Q Consensus 212 ~l~~~v~fL~~lG~s 226 (556)
++...|+||+.||-.
T Consensus 210 Ei~ALIAYLQ~LGt~ 224 (226)
T PF02433_consen 210 EIVALIAYLQRLGTD 224 (226)
T ss_pred HHHHHHHHHHHcccc
Confidence 577777777777753
No 61
>PF06089 Asparaginase_II: L-asparaginase II; InterPro: IPR010349 This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (3.5.1.1 from EC) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source [].
Probab=26.39 E-value=5.9e+02 Score=26.61 Aligned_cols=54 Identities=17% Similarity=0.179 Sum_probs=41.9
Q ss_pred cCCChhhHHHHHH-----HCCCChHHHHHHHhhccCChhhHHHHHHHHHhCCCChhHHH
Q 008728 107 EDSNVVPLIRWLK-----HNGLSYPKIAKLICMSGGNLESIRHLAEWLKSVHVKGEFLG 160 (556)
Q Consensus 107 ~~~~~~~~~~~L~-----~~G~s~~~i~~~~~~~~~~~~~l~~~l~~L~~lGls~~~i~ 160 (556)
+..++...+..+. .+|++.++++=+--.....+..++.+..+|+++|++.+++.
T Consensus 42 Sa~KP~QAlp~l~sGa~e~~~l~~~elAl~cASH~Ge~~H~~~v~~~L~k~gL~e~~L~ 100 (324)
T PF06089_consen 42 SAAKPFQALPLLESGAAEAFGLTDEELALACASHSGEPEHVEAVRSMLAKAGLSEEDLQ 100 (324)
T ss_pred hhccHHHHHHHHHcCchhhcCCCHHHHHHHhhcccChHHHHHHHHHHHHHcCCCHHHcC
Confidence 3445555555654 67999999886666667778889999999999999999886
No 62
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=26.07 E-value=96 Score=27.21 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=12.8
Q ss_pred CCChhhHHHHHHHCCCChH
Q 008728 108 DSNVVPLIRWLKHNGLSYP 126 (556)
Q Consensus 108 ~~~~~~~~~~L~~~G~s~~ 126 (556)
.+..+....||.++|+.+.
T Consensus 11 C~t~rka~~~L~~~gi~~~ 29 (117)
T COG1393 11 CSTCRKALAWLEEHGIEYT 29 (117)
T ss_pred ChHHHHHHHHHHHcCCCcE
Confidence 3445567888888776664
No 63
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.06 E-value=5.8e+02 Score=24.27 Aligned_cols=24 Identities=8% Similarity=0.203 Sum_probs=14.4
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhC
Q 008728 214 KTRVHFYLDMGMNKNDFGTMVFDY 237 (556)
Q Consensus 214 ~~~v~fL~~lG~s~~~l~~ll~~~ 237 (556)
...++.|..||+++.++.+++..-
T Consensus 143 ~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 143 SEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhc
Confidence 345566666666666666666554
No 64
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=26.00 E-value=66 Score=24.80 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=25.0
Q ss_pred CCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhhHHHHHhh
Q 008728 153 HVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDWMGYVMSR 201 (556)
Q Consensus 153 Gls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~i~~lv~~ 201 (556)
|.+.+... .-. ..|.=+..+.+++...+--|...|+++++|+-++..
T Consensus 10 G~S~S~~P-~~~-~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 10 GISGSTRP-YRR-SPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp ---------S-S-S--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CccCCCCC-CCC-CCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 55554443 112 357777777788888888888888888888877753
No 65
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=25.67 E-value=1.3e+02 Score=25.57 Aligned_cols=22 Identities=23% Similarity=0.528 Sum_probs=15.3
Q ss_pred CCChhhHhhhhhhcCccccchh
Q 008728 332 GVRDEGIANMLVKFPSLLTYSL 353 (556)
Q Consensus 332 G~s~~~i~~~i~~~P~iL~~s~ 353 (556)
.++.+++..++..+|.++..++
T Consensus 70 ~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 70 DLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp TSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhHHHHHHHHhChhheeCCE
Confidence 4677777788888887776653
No 66
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=24.91 E-value=2.7e+02 Score=25.44 Aligned_cols=73 Identities=19% Similarity=0.251 Sum_probs=40.8
Q ss_pred CCCChhhHHHHHhhCCCcccccHHHHHHHHHHHHHcCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCC
Q 008728 188 NGVRRDWMGYVMSRCPQLLSQSIEEVKTRVHFYLDMGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLS 262 (556)
Q Consensus 188 ~G~~~~~i~~lv~~~P~iL~~s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~ 262 (556)
.|.+.+.+. .-...|..+.++.+++...+.-|..-|+++.+|+-+++..-.|=..... +=......|++-|+.
T Consensus 6 kG~S~S~~P-~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~v-tG~kI~rILk~~Gla 78 (148)
T PTZ00072 6 KGISSSALP-YRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNV-TGSKILRILKKNGLA 78 (148)
T ss_pred CCCCCCCCC-CCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeec-cchHHHHHHHhcCCC
Confidence 355544333 1123565577777788888888888888888888777654321110000 012345566666653
No 67
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=24.36 E-value=72 Score=28.38 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=24.4
Q ss_pred CChhhHhhhhhhcCccccchhhhhhHHHHHHHHHHcCCCcchHhHHHhhcc
Q 008728 333 VRDEGIANMLVKFPSLLTYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGP 383 (556)
Q Consensus 333 ~s~~~i~~~i~~~P~iL~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P 383 (556)
++.+++..++..+|.++-.++-.. ..+ -.+|++++.+...+...|
T Consensus 73 ls~~e~i~lm~~~P~LIKRPIi~~-~~~-----~~iGf~~e~~~~~l~~~~ 117 (126)
T TIGR01616 73 IDEASALALMVSDPLLIRRPLMDL-GGI-----RCAGFDREPVLSWIGLQT 117 (126)
T ss_pred CCHHHHHHHHHhCcCeEeCCEEEE-CCE-----EEEcCCHHHHHHHhCCCC
Confidence 455667777777777776553210 000 135666666655554443
No 68
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=24.34 E-value=1.6e+02 Score=20.89 Aligned_cols=39 Identities=13% Similarity=0.275 Sum_probs=16.5
Q ss_pred cCCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHH
Q 008728 223 MGMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTED 265 (556)
Q Consensus 223 lG~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~ 265 (556)
+|++...+.+++...|.+ +........+....+|+.++.
T Consensus 7 ~gvs~~tvs~~l~g~~~v----s~~~~~~i~~~~~~l~~~~~~ 45 (52)
T cd01392 7 AGVSVATVSRVLNGKPRV----SEETRERVLAAAEELGYRPNA 45 (52)
T ss_pred HCcCHHHHHHHHcCCCCC----CHHHHHHHHHHHHHhCCCCCH
Confidence 455555555544443321 122333334444445544433
No 69
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.09 E-value=1.7e+02 Score=24.89 Aligned_cols=23 Identities=17% Similarity=-0.015 Sum_probs=15.6
Q ss_pred HHHHHHHHHhCCCChhhHHHHHh
Q 008728 178 LNEIVEYLETNGVRRDWMGYVMS 200 (556)
Q Consensus 178 l~~~l~~L~s~G~~~~~i~~lv~ 200 (556)
....+..|+++||+-++|..++.
T Consensus 44 ~l~~I~~lr~~G~sL~eI~~~l~ 66 (107)
T cd04777 44 DLEFILELKGLGFSLIEIQKIFS 66 (107)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHH
Confidence 34556667777777777777665
No 70
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=23.79 E-value=4.5e+02 Score=22.28 Aligned_cols=75 Identities=17% Similarity=0.305 Sum_probs=37.7
Q ss_pred hhHHHHHH-HC--CCChHHHHHHHhhc--cCChhhHHHHHHHHHhC---CCChhHHHHHHHhhCCccccC---ChhhHHH
Q 008728 112 VPLIRWLK-HN--GLSYPKIAKLICMS--GGNLESIRHLAEWLKSV---HVKGEFLGVALLKTGGNILER---SIEELNE 180 (556)
Q Consensus 112 ~~~~~~L~-~~--G~s~~~i~~~~~~~--~~~~~~l~~~l~~L~~l---Gls~~~i~~il~r~~P~lL~~---s~~~l~~ 180 (556)
.+++.||+ .| |++..+..-+.-.. ..+-+.+..+..-|..- ..+..+|+..|.+ ... +.+++..
T Consensus 6 ~~iv~WLRaGYP~GvP~~Dy~PLlALL~r~Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~I~~-----vt~~~P~~~di~R 80 (96)
T PF11829_consen 6 ASIVDWLRAGYPEGVPPTDYVPLLALLRRRLTDDEVAEVAAELAARGDPPVDRIDIGVAITR-----VTDELPTPEDIER 80 (96)
T ss_dssp HHHHHHHHHH-TT-B-HHHHHHHHHHHTTTS-HHHHHHHHHHHHHHTSS-BSCCHHHHHHHH-----HCSS-S-HHHHHH
T ss_pred HHHHHHHHccCCCCCCCCccHHHHHHhcccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH-----HHcCCcCHHHHHH
Confidence 34566664 33 66666655444322 34445666666666322 2366666666665 221 2356666
Q ss_pred HHHHHHhCCCC
Q 008728 181 IVEYLETNGVR 191 (556)
Q Consensus 181 ~l~~L~s~G~~ 191 (556)
+...|...|.+
T Consensus 81 V~~~Laa~GWP 91 (96)
T PF11829_consen 81 VRARLAAAGWP 91 (96)
T ss_dssp HHHHHHTTT-G
T ss_pred HHHHHHhCCCC
Confidence 77777766644
No 71
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=23.51 E-value=62 Score=21.30 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=11.2
Q ss_pred hHHHHHHHHHcCCChhhHHHHHh
Q 008728 285 WKPLVKYLYYLGVSRDGMRRMLV 307 (556)
Q Consensus 285 l~~~v~~L~~lGls~~~i~~il~ 307 (556)
+...+.--++.|++.++|...+.
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Confidence 44444445556666666655554
No 72
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=22.73 E-value=1.4e+02 Score=30.35 Aligned_cols=66 Identities=17% Similarity=0.359 Sum_probs=43.0
Q ss_pred hhHHHHHHHHHHcC-CCcchHhHHHhhccceeeccchhhHHHHHHHHH-HhCCCHHHHHHHHhhcccccccc
Q 008728 356 KIRPVVIFLMTKAG-VSERDIGKCLALGPELLGCSIGNKLEVNVKYFL-SLGIKLHQLGAMIADFPMLLRYN 425 (556)
Q Consensus 356 ~L~~~~~fL~~~lG-l~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~-~lG~~~~ei~~ml~~~P~lL~~s 425 (556)
+|+.++.|..++.| ++...+..-|+..|++++.+. ++++.|++-|. -+|++..+. ..|+|.=|+=.
T Consensus 72 ~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k-~~i~~r~~ELl~lvgL~p~~~---~~RyP~eLSGG 139 (309)
T COG1125 72 ELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDK-ERIKKRADELLDLVGLDPSEY---ADRYPHELSGG 139 (309)
T ss_pred HHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCH-HHHHHHHHHHHHHhCCCHHHH---hhcCchhcCcc
Confidence 47777777777777 566666666777777777774 56777766665 377776543 34666655543
No 73
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=21.96 E-value=1.5e+02 Score=20.90 Aligned_cols=29 Identities=21% Similarity=0.248 Sum_probs=21.0
Q ss_pred hHHHHHHHHH-HhCCCHHHHHHHHhhcccc
Q 008728 393 KLEVNVKYFL-SLGIKLHQLGAMIADFPML 421 (556)
Q Consensus 393 ~l~~kv~~L~-~lG~~~~ei~~ml~~~P~l 421 (556)
+.-...+.|. ++|++......+|..||.+
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 4555677888 6899999999999999876
No 74
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=21.88 E-value=4.5e+02 Score=28.64 Aligned_cols=193 Identities=12% Similarity=0.094 Sum_probs=96.8
Q ss_pred ccHHH-HHHHHHHHHHc-----CCChhHHHHHHHhCCcccccchhhhHHHHHHHHHHcCCChHHHHHHHhhCCcccccCc
Q 008728 208 QSIEE-VKTRVHFYLDM-----GMNKNDFGTMVFDYPKILGFLTLEEMHQKVTYLKEFGLSTEDVGRLLAFRPHLMGCGI 281 (556)
Q Consensus 208 ~s~~~-l~~~v~fL~~l-----G~s~~~l~~ll~~~P~iL~~~~~~~l~~~v~~L~~lG~~~~~I~~ll~~~P~lL~~s~ 281 (556)
.+++. +.-++..|+++ |..++....+=.....++.. .-....+..+.++|+.+.+-...++.+-.
T Consensus 259 ~spEraL~lRL~LLQGV~~yHqg~~deAye~le~a~~~l~el---ki~d~~lsllv~mGfeesdaRlaLRsc~g------ 329 (568)
T KOG2561|consen 259 QSPERALILRLELLQGVVAYHQGQRDEAYEALESAHAKLLEL---KINDETLSLLVGMGFEESDARLALRSCNG------ 329 (568)
T ss_pred CChhHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHe---eccchHHHHHHHcCCCchHHHHHHHhccc------
Confidence 45553 56667777653 66665555444443333332 22356777888999988887766665533
Q ss_pred ccchHHHHHHHHHcCCChhhHH--------HHHhhCCcccccCcccc--chhHHHHHHHhCCChhhHhhhhhh--cCccc
Q 008728 282 GERWKPLVKYLYYLGVSRDGMR--------RMLVIKPMVFCFDLETT--IVPKVRFFQDIGVRDEGIANMLVK--FPSLL 349 (556)
Q Consensus 282 e~~l~~~v~~L~~lGls~~~i~--------~il~~~P~iL~~~~e~~--l~~kv~~L~~lG~s~~~i~~~i~~--~P~iL 349 (556)
++...+.|+.+---.-.+.+ .+..+. .++-+.... ....+.+|.++|+...-...++++ +|..-
T Consensus 330 --~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~--k~~n~~~~~wvn~rs~~rL~~mGyer~la~eaL~r~~Ndi~~ 405 (568)
T KOG2561|consen 330 --DVDSAVQFIIERREKLAQKREKDLAREREILERK--KYGNTPMKKWVNPRSLERLVSMGYERELAAEALRRNENDIQK 405 (568)
T ss_pred --cHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH--HhcCCCcccccCHHHHHHHHhcchHhHHHHHHHHhccCcHHH
Confidence 56666777653110001111 111111 111111111 234577888999998888788777 33211
Q ss_pred cchhhhhhHHHHHHHHHHcCCCcchHhHHHhhccceeeccchhhHHHHHHHHHHhCCCHHHHHHHHhhcccccccchhhH
Q 008728 350 TYSLYKKIRPVVIFLMTKAGVSERDIGKCLALGPELLGCSIGNKLEVNVKYFLSLGIKLHQLGAMIADFPMLLRYNIDIF 429 (556)
Q Consensus 350 ~~s~~~~L~~~~~fL~~~lGl~~~~i~~vi~~~P~iL~~s~~~~l~~kv~~L~~lG~~~~ei~~ml~~~P~lL~~s~e~l 429 (556)
-++. +.=..+++. ...|.. .+..-..++.-|..+||+.-..+..+...- .++
T Consensus 406 ----------aldl----lq~esdel~---~n~~~~----p~~vd~~~la~Lv~mGF~e~~A~~ALe~~g-------nn~ 457 (568)
T KOG2561|consen 406 ----------ALDL----LQDESDELE---SNKPKR----PEQVDGISLAELVSMGFEEGKARSALEAGG-------NNE 457 (568)
T ss_pred ----------HHHh----cCCcchhhh---ccCCCC----CcccchhhHHHHHHhccccchHHHHHHhcC-------CcH
Confidence 1111 111111111 111111 111234457788999999887776665332 234
Q ss_pred HHHHHHHHHHhC
Q 008728 430 RPKYRYLRRTMV 441 (556)
Q Consensus 430 ~~k~~fL~~~mg 441 (556)
..-.++|....+
T Consensus 458 ~~a~~~L~~s~~ 469 (568)
T KOG2561|consen 458 DTAQRLLSASVA 469 (568)
T ss_pred HHHHHHHHHhCC
Confidence 444555554433
No 75
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.57 E-value=1.3e+02 Score=21.72 Aligned_cols=18 Identities=17% Similarity=0.429 Sum_probs=9.3
Q ss_pred HcCCChhHHHHHHHhCCc
Q 008728 222 DMGMNKNDFGTMVFDYPK 239 (556)
Q Consensus 222 ~lG~s~~~l~~ll~~~P~ 239 (556)
..|++...+.+++...|.
T Consensus 8 ~agvS~~TVSr~ln~~~~ 25 (46)
T PF00356_consen 8 EAGVSKSTVSRVLNGPPR 25 (46)
T ss_dssp HHTSSHHHHHHHHTTCSS
T ss_pred HHCcCHHHHHHHHhCCCC
Confidence 345555555555555443
No 76
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.50 E-value=7.1e+02 Score=23.66 Aligned_cols=25 Identities=20% Similarity=0.282 Sum_probs=16.7
Q ss_pred HHHHHHHHHHcCCChHHHHHHHhhC
Q 008728 249 MHQKVTYLKEFGLSTEDVGRLLAFR 273 (556)
Q Consensus 249 l~~~v~~L~~lG~~~~~I~~ll~~~ 273 (556)
....++-|..+|+++.++.+.+..-
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 3456666777777777777766665
No 77
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=20.98 E-value=3e+02 Score=23.34 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=15.7
Q ss_pred HHHHHHHcCCChhHHHHHHHhCCc
Q 008728 216 RVHFYLDMGMNKNDFGTMVFDYPK 239 (556)
Q Consensus 216 ~v~fL~~lG~s~~~l~~ll~~~P~ 239 (556)
.-+|-+.+|+++.+|-.+-..+|.
T Consensus 23 wK~faR~lglse~~Id~I~~~~~~ 46 (97)
T cd08316 23 VKKFVRKSGLSEPKIDEIKLDNPQ 46 (97)
T ss_pred HHHHHHHcCCCHHHHHHHHHcCCC
Confidence 334556777777777777776665
No 78
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=20.55 E-value=1.5e+02 Score=25.58 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=11.3
Q ss_pred HHHHHHHHHhCCCChhhHHHHHhhCC
Q 008728 178 LNEIVEYLETNGVRRDWMGYVMSRCP 203 (556)
Q Consensus 178 l~~~l~~L~s~G~~~~~i~~lv~~~P 203 (556)
+...++.|.++|++...+..++.-+|
T Consensus 59 ~~~l~~~L~~~~L~~~E~~qi~Nl~P 84 (117)
T PF03874_consen 59 IKELREELKKFGLTEFEILQIINLRP 84 (117)
T ss_dssp HHHHHHHHTTSTS-HHHHHHHHHH--
T ss_pred HHHHHHHHhcccCCHHHHHHHhcCCC
Confidence 44444444555555555555554444
No 79
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=20.27 E-value=2.3e+02 Score=22.03 Aligned_cols=40 Identities=18% Similarity=0.161 Sum_probs=20.1
Q ss_pred hCCCChhHHHHHHHhhCCccccCChhhHHHHHHHHHhCCCChhh
Q 008728 151 SVHVKGEFLGVALLKTGGNILERSIEELNEIVEYLETNGVRRDW 194 (556)
Q Consensus 151 ~lGls~~~i~~il~r~~P~lL~~s~~~l~~~l~~L~s~G~~~~~ 194 (556)
.+|++.+.+.+++.. .|.+ +.+....+.+.++.+|..+..
T Consensus 9 ~~gvS~~TVSr~ln~-~~~v---~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 9 LAGVSKATVSRVLNG-NGRV---SEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred HHCCCHHHHHHHHCC-CCCC---CHHHHHHHHHHHHHhCCCCCH
Confidence 346666665555442 3332 344455555555555555443
No 80
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.20 E-value=1.7e+02 Score=29.79 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=22.1
Q ss_pred hhHHHHHHHHHHhCCCHHHHHHHHhh
Q 008728 392 NKLEVNVKYFLSLGIKLHQLGAMIAD 417 (556)
Q Consensus 392 ~~l~~kv~~L~~lG~~~~ei~~ml~~ 417 (556)
.-+..|.+||++.|++.+||-.++.+
T Consensus 20 aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 20 APLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred chHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 45778999999999999999888774
No 81
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=20.20 E-value=5.8e+02 Score=22.17 Aligned_cols=31 Identities=13% Similarity=0.082 Sum_probs=16.9
Q ss_pred cHHHHHHHHHHHHHcCCChhHHHHHHHhCCc
Q 008728 209 SIEEVKTRVHFYLDMGMNKNDFGTMVFDYPK 239 (556)
Q Consensus 209 s~~~l~~~v~fL~~lG~s~~~l~~ll~~~P~ 239 (556)
+.+.+......|...|+....+..++.-.|.
T Consensus 53 ~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~ 83 (118)
T smart00657 53 NREIVRAVRTLLKSKKLHKFEIAQLGNLRPE 83 (118)
T ss_pred CHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC
Confidence 3444555555555556665555555555554
No 82
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=20.19 E-value=3.1e+02 Score=23.21 Aligned_cols=88 Identities=14% Similarity=0.226 Sum_probs=38.9
Q ss_pred ccchhHHHHHHHHHHHhccCcccccccccccccccccCCChhhHHHHHHHCCCChHHHHHHHh--hccCChhhHHHHHHH
Q 008728 71 DRLPDFIDHVMIKAAALKKLPEFADSSFNVRAKWFIEDSNVVPLIRWLKHNGLSYPKIAKLIC--MSGGNLESIRHLAEW 148 (556)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~r~~~~l~~~~~~~~~~~L~~~G~s~~~i~~~~~--~~~~~~~~l~~~l~~ 148 (556)
+++|.-||+.+-=...+.-.... ....+++.-.-.+.||..+|++.+...-..+ .-+++++--..+..|
T Consensus 19 k~MpavIdKALDFIggMntSas~---------P~sMdESTAKGi~KyL~elGvPasa~dv~aRg~qeGWn~gFT~k~agw 89 (119)
T PF08986_consen 19 KSMPAVIDKALDFIGGMNTSASV---------PHSMDESTAKGIFKYLKELGVPASAADVTARGEQEGWNPGFTEKVAGW 89 (119)
T ss_dssp S----HHHHHHHHHHTS-TT-SS-----------HCCCHHHHHHHHHHHHCT----HHHHHHHHHHCT--HHHHHHHHHH
T ss_pred CcchHHHHHHHHHhcccccCCCC---------CCccchHHHHHHHHHHHHcCCCCCHHHHHHhcccccCChhHHHHHHHH
Confidence 67888777755333321111111 1122456666789999999987655333333 236677766677777
Q ss_pred HHhCCCChhHHHHHHHhhCCcccc
Q 008728 149 LKSVHVKGEFLGVALLKTGGNILE 172 (556)
Q Consensus 149 L~~lGls~~~i~~il~r~~P~lL~ 172 (556)
-+++--. .+++.| +|..+.
T Consensus 90 aeki~sG----~rivIK-nPEyFs 108 (119)
T PF08986_consen 90 AEKIASG----ERIVIK-NPEYFS 108 (119)
T ss_dssp HHHHHCT---------S-SGGGS-
T ss_pred HHHHhcC----Ceeeec-ChHHHH
Confidence 7765322 245565 887765
No 83
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=20.09 E-value=37 Score=30.41 Aligned_cols=14 Identities=36% Similarity=0.634 Sum_probs=7.7
Q ss_pred hhHHHHHHHCCCCh
Q 008728 112 VPLIRWLKHNGLSY 125 (556)
Q Consensus 112 ~~~~~~L~~~G~s~ 125 (556)
.....||.+.|++.
T Consensus 14 rkA~~~L~~~~i~~ 27 (132)
T PRK13344 14 KKAKTWLNAHQLSY 27 (132)
T ss_pred HHHHHHHHHcCCCe
Confidence 34556666665443
Done!