Query 010056
Match_columns 519
No_of_seqs 282 out of 1362
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 20:31:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010056.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010056hhsearch_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 1.2E-90 2.5E-95 744.0 34.9 439 77-517 35-477 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1E-55 2.3E-60 458.3 5.7 335 135-475 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 6.2E-52 1.3E-56 445.0 24.9 347 85-450 83-439 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.7E-39 1.2E-43 333.0 9.7 305 106-421 2-319 (345)
5 KOG1267 Mitochondrial transcri 100.0 2.3E-30 5E-35 274.9 16.6 317 124-459 88-411 (413)
6 KOG1267 Mitochondrial transcri 99.9 7.3E-22 1.6E-26 209.9 14.1 281 161-458 90-376 (413)
7 smart00733 Mterf Mitochondrial 96.9 0.00068 1.5E-08 43.9 2.6 30 397-427 2-31 (31)
8 smart00733 Mterf Mitochondrial 96.5 0.0015 3.3E-08 42.2 1.7 25 220-245 5-29 (31)
9 PF11955 PORR: Plant organelle 95.2 0.24 5.2E-06 51.4 12.3 187 259-457 107-330 (335)
10 PF11955 PORR: Plant organelle 86.4 0.99 2.1E-05 46.9 4.9 238 171-422 46-328 (335)
11 cd04790 HTH_Cfa-like_unk Helix 84.0 6.1 0.00013 37.0 8.6 21 165-185 50-70 (172)
12 cd04790 HTH_Cfa-like_unk Helix 78.0 6.6 0.00014 36.8 6.6 18 380-397 149-166 (172)
13 PF14490 HHH_4: Helix-hairpin- 68.8 16 0.00035 30.5 6.2 47 161-232 7-53 (94)
14 COG1125 OpuBA ABC-type proline 67.9 9.7 0.00021 38.2 5.2 57 373-429 68-126 (309)
15 PF03960 ArsC: ArsC family; I 66.2 12 0.00025 32.2 4.9 81 104-195 12-92 (110)
16 PF04695 Pex14_N: Peroxisomal 63.8 10 0.00023 34.1 4.3 28 162-189 23-50 (136)
17 COG1393 ArsC Arsenate reductas 59.4 9.4 0.0002 33.5 3.1 39 105-146 18-56 (117)
18 PF04695 Pex14_N: Peroxisomal 49.8 24 0.00052 31.7 4.2 31 376-406 21-51 (136)
19 PF00627 UBA: UBA/TS-N domain; 46.4 28 0.00061 23.6 3.2 23 380-402 4-26 (37)
20 PF14490 HHH_4: Helix-hairpin- 45.0 65 0.0014 26.8 5.9 24 234-257 8-31 (94)
21 cd02977 ArsC_family Arsenate R 44.3 51 0.0011 27.7 5.2 78 105-195 16-95 (105)
22 cd03032 ArsC_Spx Arsenate Redu 44.3 49 0.0011 28.5 5.2 21 174-194 74-94 (115)
23 PRK14136 recX recombination re 43.9 42 0.00091 34.4 5.2 133 105-262 169-306 (309)
24 PRK01655 spxA transcriptional 42.1 55 0.0012 29.1 5.3 21 174-194 74-94 (131)
25 smart00165 UBA Ubiquitin assoc 41.4 35 0.00077 22.8 3.1 23 380-402 3-25 (37)
26 PRK13344 spxA transcriptional 40.0 63 0.0014 28.8 5.3 19 175-193 75-93 (132)
27 COG1393 ArsC Arsenate reductas 39.4 62 0.0013 28.3 5.0 42 126-175 10-53 (117)
28 cd00194 UBA Ubiquitin Associat 39.3 40 0.00086 22.7 3.1 23 380-402 3-25 (38)
29 PRK10026 arsenate reductase; P 39.0 66 0.0014 29.2 5.3 39 105-146 19-57 (141)
30 PF11212 DUF2999: Protein of u 38.5 64 0.0014 25.7 4.3 20 236-255 3-22 (82)
31 PRK14134 recX recombination re 36.7 2.6E+02 0.0057 28.3 9.8 58 125-186 90-151 (283)
32 PRK09875 putative hydrolase; P 35.7 1.4E+02 0.0031 30.4 7.8 112 105-224 169-288 (292)
33 PRK00117 recX recombination re 35.0 3.3E+02 0.0071 24.6 9.4 24 378-401 128-152 (157)
34 PRK00116 ruvA Holliday junctio 33.2 93 0.002 29.6 5.6 25 270-294 149-173 (192)
35 TIGR01617 arsC_related transcr 32.8 56 0.0012 28.2 3.7 77 105-195 16-96 (117)
36 TIGR00014 arsC arsenate reduct 32.8 1.1E+02 0.0023 26.5 5.4 36 105-143 16-51 (114)
37 PRK14134 recX recombination re 32.6 5.4E+02 0.012 26.1 12.5 175 197-400 94-277 (283)
38 PRK00117 recX recombination re 32.4 1.2E+02 0.0026 27.6 6.0 58 128-186 43-102 (157)
39 PF02022 Integrase_Zn: Integra 32.3 75 0.0016 22.4 3.5 29 377-405 7-36 (40)
40 PF03960 ArsC: ArsC family; I 32.0 70 0.0015 27.3 4.1 22 388-409 69-90 (110)
41 PRK12559 transcriptional regul 30.7 1.1E+02 0.0023 27.3 5.2 39 105-146 17-55 (131)
42 PTZ00217 flap endonuclease-1; 30.5 5.7E+02 0.012 27.3 11.6 73 104-184 143-230 (393)
43 TIGR01448 recD_rel helicase, p 30.1 1.8E+02 0.004 33.6 8.3 41 173-219 124-164 (720)
44 cd03034 ArsC_ArsC Arsenate Red 30.0 1.5E+02 0.0033 25.4 5.9 77 105-195 16-94 (112)
45 cd03036 ArsC_like Arsenate Red 29.6 1.5E+02 0.0031 25.4 5.7 79 104-195 15-96 (111)
46 cd03035 ArsC_Yffb Arsenate Red 28.8 97 0.0021 26.4 4.4 77 105-194 16-92 (105)
47 PF02631 RecX: RecX family; I 28.8 91 0.002 27.0 4.4 56 127-184 8-67 (121)
48 TIGR01616 nitro_assoc nitrogen 27.3 74 0.0016 28.2 3.6 18 390-407 73-90 (126)
49 PRK11613 folP dihydropteroate 26.4 5.5E+02 0.012 26.1 10.1 45 126-170 36-86 (282)
50 PHA02591 hypothetical protein; 26.0 1.4E+02 0.0031 24.2 4.5 23 232-254 46-68 (83)
51 PF11212 DUF2999: Protein of u 25.8 2.4E+02 0.0052 22.6 5.6 46 272-325 3-48 (82)
52 smart00657 RPOL4c DNA-directed 25.8 1.8E+02 0.0038 25.4 5.6 27 162-188 57-83 (118)
53 PRK14601 ruvA Holliday junctio 25.6 2.8E+02 0.006 26.3 7.3 24 271-294 143-166 (183)
54 PF02631 RecX: RecX family; I 24.8 3E+02 0.0065 23.7 7.0 26 376-401 92-118 (121)
55 PF07499 RuvA_C: RuvA, C-termi 24.7 92 0.002 22.4 3.0 24 163-186 4-27 (47)
56 KOG0400 40S ribosomal protein 24.5 74 0.0016 28.4 2.9 35 149-184 21-55 (151)
57 TIGR01448 recD_rel helicase, p 24.5 5.5E+02 0.012 29.8 10.8 87 161-257 76-166 (720)
58 PRK00116 ruvA Holliday junctio 24.3 1.2E+02 0.0027 28.7 4.8 50 240-292 74-126 (192)
59 PF08069 Ribosomal_S13_N: Ribo 23.9 55 0.0012 25.2 1.8 44 141-185 10-56 (60)
60 PRK14135 recX recombination re 23.9 7.1E+02 0.015 24.5 10.9 59 233-294 90-149 (263)
61 cd03033 ArsC_15kD Arsenate Red 23.4 1.8E+02 0.0039 25.2 5.2 21 174-194 72-92 (113)
62 TIGR00601 rad23 UV excision re 22.2 90 0.002 33.1 3.6 38 214-262 259-296 (378)
63 PHA02653 RNA helicase NPH-II; 21.4 1.6E+02 0.0034 33.9 5.6 45 102-147 528-572 (675)
64 COG2137 OraA Uncharacterized p 20.8 5.6E+02 0.012 24.1 8.2 26 376-401 137-163 (174)
65 cd03033 ArsC_15kD Arsenate Red 20.7 1.7E+02 0.0038 25.2 4.5 19 390-408 72-90 (113)
66 PF06757 Ins_allergen_rp: Inse 20.7 6.7E+02 0.015 23.3 8.9 21 377-397 157-177 (179)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.2e-90 Score=744.04 Aligned_cols=439 Identities=68% Similarity=1.126 Sum_probs=429.8
Q ss_pred cCCCCCCCCCCCh----hhHhhHHHHhhhhhHHHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccccCCc
Q 010056 77 KQGGSSSLYSRPS----ILEMKNERMANRAKVYDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDINNYPL 152 (519)
Q Consensus 77 ~~~~~~~~~~~p~----~~~~~~~~~~~~~~vv~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~~~P~ 152 (519)
++++++++|.+|+ +++++++++++|+.+++||+++||+++++.++.+|.+++.++++++||+++|++.++|++||+
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~lgi~~~~l~~~~~p~~~~~~~~~l~~L~s~G~~~~~i~~~P~ 114 (487)
T PLN03196 35 KQSSSPSLYERPSVTWGLLEMKKEKLVNREKVLDFLRGIGIDPDELDGLELPSTVDVMRERVEFLHKLGLTIEDINEYPL 114 (487)
T ss_pred ccCCCCccccCCchHHHHHHhhhhhhhhHHHHHHHHHHcCCCchhhhccCCCccHHHHHHHHHHHHHcCCChHHhccCcH
Confidence 4566668999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccchHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHhhhCcccccccccc
Q 010056 153 VLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPEVLGFKLEG 232 (519)
Q Consensus 153 lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~lL~~s~e~ 232 (519)
+|++++++++.|+++||.++|+++.+|++++.++|++|++++++++.|+++||+++|++.++|++++.++|++|++++++
T Consensus 115 iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~ 194 (487)
T PLN03196 115 VLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEG 194 (487)
T ss_pred HhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHHHHhCCChhHHHHHHhhCccccccccccchhhHHHHHHHhCCChHHHHHHHHhCCcccccccccchhhhHHH
Q 010056 233 TMSTSVAYLVGIGVSRREIGGVLTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARLIEKKPYILGFGLEERVKPNVES 312 (519)
Q Consensus 233 ~l~p~v~fL~~lGv~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~ 312 (519)
++.|+++||+++|++.++|++++.++|++|+++++++++|+++||+++|++.++|++++.++|++|+++++++++|++++
T Consensus 195 ~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~ 274 (487)
T PLN03196 195 TMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVEC 274 (487)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCccHHHHHhhCCcccccCcchhhhhHHHhhhhhcCCChhhHHHHHHhhhhhhhcChhHHHHhHHHHHHhCCcH
Q 010056 313 LLEFSVRKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSAIDSSSKDFGSIVEKMPQVVNASNSAVTRHVDFLKSCGFFL 392 (519)
Q Consensus 313 L~~lGv~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~lG~s~~~~~~~v~k~P~iL~~s~~~l~~kv~fL~~lG~s~ 392 (519)
|+++|++++++..+|+++|.+++.++++++.++++|+.+.+||+++++.++++++|+++++|.+++++|++||+++||+.
T Consensus 275 L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~~Gls~ 354 (487)
T PLN03196 275 LLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRGRGFSA 354 (487)
T ss_pred HHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHHcCCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCchhccCHHHHHHHHHHHHHHhCCChhhHhhcCcccccCccccchHHHHHHHHcCCCCCcchhhccChHH
Q 010056 393 QQVRQIVVECPQVLALNLDIMKLSFDYFQREMQRPLDDLVVFPAFFTYGLESTIKPRHKMIARKGLQCSLSWLLNCSDEK 472 (519)
Q Consensus 393 e~I~~mv~r~P~lL~~S~e~Lk~k~~fL~~~mg~~~~~i~~~P~~L~ySLekRI~PR~~~L~~kGl~~sl~~~l~~sd~~ 472 (519)
++|..||+++|++|++|.++|++|++||+++||+++++|++||+||+||||+||+|||++|++||+++++.|+++|||++
T Consensus 355 edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~ 434 (487)
T PLN03196 355 QDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDK 434 (487)
T ss_pred HHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccCCccccCcccccCCCCcccccccCCccc
Q 010056 473 FKERMNYDTIDLEEMDAMPSFDMNTLMEQRSDESASEYEEDSDDE 517 (519)
Q Consensus 473 F~~r~v~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~ 517 (519)
|++||+.+|.|+++++ |+|+|||++++|++++++|||||+|||
T Consensus 435 F~~r~v~~y~e~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (487)
T PLN03196 435 FEQRMSGDFIEGEEME--PLFSMGGKLEMPGSESVSDEEDDDDDD 477 (487)
T ss_pred HHHHHhhhcccccccC--CCcccCCcccCCCCccccCcccccchH
Confidence 9999999999999999 999999999999999999999775444
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=1e-55 Score=458.31 Aligned_cols=335 Identities=33% Similarity=0.611 Sum_probs=267.6
Q ss_pred HHHHhCCCCccccc----cCCcccccccccchHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCC
Q 010056 135 DFLHNLGLTIEDIN----NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDI 210 (519)
Q Consensus 135 ~~L~~lGls~~~i~----~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~ 210 (519)
++|+++||++++|. ++|.+|.+++++++.|+++||.+.|++..++++++.++|++|..++++++.|+++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 57899999999985 69999999999999999999999999999999999999999999999899999999999999
Q ss_pred CCCChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHHHhhCccccccccccchhhHHHHHHHhCCChHHHHHH
Q 010056 211 KPNDIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGVLTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARL 290 (519)
Q Consensus 211 s~~~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~i 290 (519)
+++++.+++.++|++|..+.++++.++++||+++|++.+.+.+++..+|.++... +++++.++++.++|++++++.++
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~v 159 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRV 159 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCC
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhccc
Confidence 9999999999999999999888999999999999999998889998888876665 58999999999999999999999
Q ss_pred HHhCCcccccccccchhhhHHHHHhhhcCCccHHHHHhhCCcccccCcchhhhhHHHhhhhhcCCChhhHHHHHHhhhhh
Q 010056 291 IEKKPYILGFGLEERVKPNVESLLEFSVRKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSAIDSSSKDFGSIVEKMPQV 370 (519)
Q Consensus 291 I~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~lG~s~~~~~~~v~k~P~i 370 (519)
+.++|+++..+.++++++++++|+++|++.+++..++.++|.++..+.+..++....++ ...|...+ +++.++|++
T Consensus 160 i~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~-~~~~~~~~---~~i~~~p~i 235 (345)
T PF02536_consen 160 IAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLL-SSGGVEEE---RVIKKFPQI 235 (345)
T ss_dssp HHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC------------------------------
T ss_pred ccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccc-cccccccc---ccccccccc
Confidence 99999999888888999999999999999999999999999999999988777766665 44444444 889999999
Q ss_pred hhcChhHHHHhHHHHHHhCCcHHHHHHHHHhcCchhccCHHHHHHHHHHHHHHhCCChhhHhhcCcccccCccccchHH-
Q 010056 371 VNASNSAVTRHVDFLKSCGFFLQQVRQIVVECPQVLALNLDIMKLSFDYFQREMQRPLDDLVVFPAFFTYGLESTIKPR- 449 (519)
Q Consensus 371 L~~s~~~l~~kv~fL~~lG~s~e~I~~mv~r~P~lL~~S~e~Lk~k~~fL~~~mg~~~~~i~~~P~~L~ySLekRI~PR- 449 (519)
+.++.+++..+++||.++||+.++|++|+.++|++|++|.+++++|++||+++||++.++|+++|++|+||||+||+||
T Consensus 236 l~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~ 315 (345)
T PF02536_consen 236 LSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRY 315 (345)
T ss_dssp -THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHH
T ss_pred cccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred --HHHHHHcC--CCCCcchhhccChHHHHH
Q 010056 450 --HKMIARKG--LQCSLSWLLNCSDEKFKE 475 (519)
Q Consensus 450 --~~~L~~kG--l~~sl~~~l~~sd~~F~~ 475 (519)
|++|+++| .++++.+++++||++|++
T Consensus 316 ~~~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 316 EVLKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HHHHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 56788999 679999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=6.2e-52 Score=444.95 Aligned_cols=347 Identities=26% Similarity=0.493 Sum_probs=318.5
Q ss_pred CCCChhhHhhHHHHhhhhhHHHHHHhCCCCccccCCcc--CCCChH-HHHHHHHHHHhCCCCccccc----cCCcccccc
Q 010056 85 YSRPSILEMKNERMANRAKVYDFLQGIGIVPDELDGLE--LPVTVE-VMRERVDFLHNLGLTIEDIN----NYPLVLGCS 157 (519)
Q Consensus 85 ~~~p~~~~~~~~~~~~~~~vv~yL~~~Gi~~~~l~~l~--~p~~~d-~v~~~l~~L~~lGls~~~i~----~~P~lL~~s 157 (519)
+.+|+.++..++++ +||+++|++.+++..++ +.++++ .++++++||+++|++.++|+ ++|.+|+++
T Consensus 83 ~~~p~~~~~~~~~l-------~~L~s~G~~~~~i~~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~s 155 (487)
T PLN03196 83 LELPSTVDVMRERV-------EFLHKLGLTIEDINEYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHAS 155 (487)
T ss_pred cCCCccHHHHHHHH-------HHHHHcCCChHHhccCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceeccc
Confidence 66788888777664 89999999999999876 345655 68899999999999999986 899999999
Q ss_pred cccchHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHhhhCccccccccccchhhH
Q 010056 158 VKKNMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPEVLGFKLEGTMSTS 237 (519)
Q Consensus 158 ~~~~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~lL~~s~e~~l~p~ 237 (519)
+++++.|+++||+++|+++++|.+++.++|++|+.+++.++.|+++||+++|++.++|++++.++|++|+++++++++|+
T Consensus 156 ve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~ 235 (487)
T PLN03196 156 VVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPK 235 (487)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCChhHHHHHHhhCccccccccccchhhHHHHHHHhCCChHHHHHHHHhCCcccccccccchhhhHHHHH-hh
Q 010056 238 VAYLVGIGVSRREIGGVLTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARLIEKKPYILGFGLEERVKPNVESLL-EF 316 (519)
Q Consensus 238 v~fL~~lGv~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~L~-~l 316 (519)
++||+++|++.++|++++.++|++|+++++++++|++++|.++|++++++..+|.++|.++++++++++.+++++|. ++
T Consensus 236 v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~l 315 (487)
T PLN03196 236 VDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKL 315 (487)
T ss_pred HHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999996 69
Q ss_pred hcCCccHHHHHhhCCcccccCcchhhhhHHHhhhhhcCCChhhHHHHHHhhhhhhhcChhHHHHhHHHHHH-hCCcHHHH
Q 010056 317 SVRKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSAIDSSSKDFGSIVEKMPQVVNASNSAVTRHVDFLKS-CGFFLQQV 395 (519)
Q Consensus 317 Gv~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~lG~s~~~~~~~v~k~P~iL~~s~~~l~~kv~fL~~-lG~s~e~I 395 (519)
|++++++..+++++|++++++. +++..+++||. .+||+.+++.+||+++|+++++|.++++.|++||++ ||++.++|
T Consensus 316 G~s~e~i~~~v~k~P~il~lSe-~kl~~kvefL~-~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~I 393 (487)
T PLN03196 316 KIDPEDFGRVIEKLPQIVSLNR-NVALKHVEFLR-GRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKEL 393 (487)
T ss_pred CCCHHHHHHHHHhcchhhcccH-HHHHHHHHHHH-HcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHH
Confidence 9999999999999999999986 57888899995 699999999999999999999999999999999998 99999997
Q ss_pred HHHHHhcCchhccCHH-HHHHHHHHHHHHhCCChhhHhhcCcccccCccccchHHH
Q 010056 396 RQIVVECPQVLALNLD-IMKLSFDYFQREMQRPLDDLVVFPAFFTYGLESTIKPRH 450 (519)
Q Consensus 396 ~~mv~r~P~lL~~S~e-~Lk~k~~fL~~~mg~~~~~i~~~P~~L~ySLekRI~PR~ 450 (519)
.++|++|+||+| +|+||+++|.. .|+.. .-..+|.+| |++..-|+
T Consensus 394 ----v~fP~~LsySLEkRI~PR~~~L~~-kGl~~----sL~~~L~~s-d~~F~~r~ 439 (487)
T PLN03196 394 ----VEFPAYFTYGLESRIKPRYERVAK-KGIKC----SLAWFLNCS-DDKFEQRM 439 (487)
T ss_pred ----HhChHHhccChhhhhHHHHHHHHH-cCCCC----CHHHHhccC-HHHHHHHH
Confidence 899999999999 89999999775 67631 122445665 54665554
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=5.7e-39 Score=333.03 Aligned_cols=305 Identities=28% Similarity=0.537 Sum_probs=232.4
Q ss_pred HHHHhCCCCccccCCcc--CC----CChH-HHHHHHHHHHhCCCCccccc----cCCcccccccccchHHHHHHHhhCCC
Q 010056 106 DFLQGIGIVPDELDGLE--LP----VTVE-VMRERVDFLHNLGLTIEDIN----NYPLVLGCSVKKNMIPVLDYLGKLGV 174 (519)
Q Consensus 106 ~yL~~~Gi~~~~l~~l~--~p----~~~d-~v~~~l~~L~~lGls~~~i~----~~P~lL~~s~~~~l~p~l~~L~~lGl 174 (519)
++|++.|++...+.++. .| ++++ .+.++++||.+.|++..+|+ ++|.+|..+.++++.|.++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 56888899988877753 22 3444 78999999999999999986 79999999999999999999999999
Q ss_pred ChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHH
Q 010056 175 RKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGV 254 (519)
Q Consensus 175 s~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~l 254 (519)
+++++.+++.++|.+|..+...++.+.+.||+++|++.+.+.+++..+|.++... +++.+.++++.++|+++++++++
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~v 159 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRV 159 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCC
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhccc
Confidence 9999999999999999998877899999999999999987888888888776655 68999999999999999999999
Q ss_pred HhhCccccccccccchhhHHHHHHHhCCChHHHHHHHHhCCcccccccccchhhhHHHHHhhhcCCccHHHHHhhCCccc
Q 010056 255 LTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARLIEKKPYILGFGLEERVKPNVESLLEFSVRKEALPVVVAQYPEII 334 (519)
Q Consensus 255 l~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~l~~vI~~~P~iL 334 (519)
+.++|+++..+.+++++|+++||+++|++.+++.+++.++|++++.++++.+++...++...|...+ .++.++|.++
T Consensus 160 i~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~---~~i~~~p~il 236 (345)
T PF02536_consen 160 IAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE---RVIKKFPQIL 236 (345)
T ss_dssp HHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC------------------------------
T ss_pred ccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccc---cccccccccc
Confidence 9999999999999999999999999999999999999999999999998666665555544454444 8899999999
Q ss_pred ccCcchhhhhHHHhhhhhcCCChhhHHHHHHhhhhhhhcChhHHHHhHHHHHH-hCCcHHHHHHHHHhcCchhccCHH-H
Q 010056 335 GIDLKPKLLGQQSLLNSAIDSSSKDFGSIVEKMPQVVNASNSAVTRHVDFLKS-CGFFLQQVRQIVVECPQVLALNLD-I 412 (519)
Q Consensus 335 ~~s~~~kl~~~~~~L~~~lG~s~~~~~~~v~k~P~iL~~s~~~l~~kv~fL~~-lG~s~e~I~~mv~r~P~lL~~S~e-~ 412 (519)
.++. +++..+.++|. .+|++.+++.+|+.++|+++++|.+++++|++||.+ +|++.++| .++|++|+||+| +
T Consensus 237 ~~~~-~~l~~~i~~L~-~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~r 310 (345)
T PF02536_consen 237 SLSE-EKLKPKIEFLQ-SLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKR 310 (345)
T ss_dssp THHH-HHHHHHHHHHH-TTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHH
T ss_pred ccch-HhHHHHHHHHH-HhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhh
Confidence 9884 57888999994 599999999999999999999999999999999998 99999998 799999999999 7
Q ss_pred HHHHHHHHH
Q 010056 413 MKLSFDYFQ 421 (519)
Q Consensus 413 Lk~k~~fL~ 421 (519)
|+||++++.
T Consensus 311 i~PR~~~~~ 319 (345)
T PF02536_consen 311 IKPRYEVLK 319 (345)
T ss_dssp HHHHHHHHH
T ss_pred hhhHHHHHH
Confidence 999965554
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.97 E-value=2.3e-30 Score=274.93 Aligned_cols=317 Identities=28% Similarity=0.489 Sum_probs=281.6
Q ss_pred CCChHHHHHHHHHHHhCCCCccccc----cCCcccccccccchHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchH
Q 010056 124 PVTVEVMRERVDFLHNLGLTIEDIN----NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLA 199 (519)
Q Consensus 124 p~~~d~v~~~l~~L~~lGls~~~i~----~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~ 199 (519)
..+++.+ +.+|+++|++..+|. .+|.++.++.++.+.+++.+|...|++.+++.+++...|.+|..+...++.
T Consensus 88 ~~~p~s~---~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~ 164 (413)
T KOG1267|consen 88 SVNPSSV---LSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLS 164 (413)
T ss_pred ccCcHHH---HHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchh
Confidence 4456655 889999999999986 689999999999999999999999999999999999999999988878999
Q ss_pred HHHHHHHhcC--CCCCChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHHHhhCccccccccccchhhHHHHH
Q 010056 200 PVVKYLQGLD--IKPNDIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGVLTRYPDILGMRVGRVIKPFVEYL 277 (519)
Q Consensus 200 p~v~fL~~lG--~s~~~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L 277 (519)
+.++|+++++ .....+.+.+...|.... .+..+. ++++++++|+..+++..++..+|....... .+...+.++
T Consensus 165 ~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~--~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i 239 (413)
T KOG1267|consen 165 TFIEFLKSIPPELLSSVVERLLTPVPSFLL--NENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFL 239 (413)
T ss_pred hHHHHhhccchhhhhhHHHHhccccccccc--cccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhH
Confidence 9999999985 777778877777764332 223344 889999999999999999999999987654 578888999
Q ss_pred HHhCCChHHHHHHHHhCCcccccccccchhhhHHHHHhhhcCCccHHHHHhhCCcccccCcchhhhhHHHhhhhhcCCCh
Q 010056 278 ESLGIPRLAVARLIEKKPYILGFGLEERVKPNVESLLEFSVRKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSAIDSSS 357 (519)
Q Consensus 278 ~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~lG~s~ 357 (519)
.++|+.+.. +++.+.|.+++++.++++++++++|+++|++.++++.|++++|++|+++.+.++.....++.. .
T Consensus 240 ~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~-----~ 312 (413)
T KOG1267|consen 240 LTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN-----P 312 (413)
T ss_pred HHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc-----c
Confidence 999987766 788899999999999999999999999999999999999999999999988776666555533 2
Q ss_pred hhHHHHHHhhhhhhhcChhHHHHhHHHHHHhCCcHHHHHHHHHhcCchhccCHH-HHHHHHHHHHHHhCCChhhHhhcCc
Q 010056 358 KDFGSIVEKMPQVVNASNSAVTRHVDFLKSCGFFLQQVRQIVVECPQVLALNLD-IMKLSFDYFQREMQRPLDDLVVFPA 436 (519)
Q Consensus 358 ~~~~~~v~k~P~iL~~s~~~l~~kv~fL~~lG~s~e~I~~mv~r~P~lL~~S~e-~Lk~k~~fL~~~mg~~~~~i~~~P~ 436 (519)
++ +.++|+++.++..++..+++|+...|++..++..|+.++|+++.+|.+ .++.+.+|+.+.|+++.+.++.+|+
T Consensus 313 ~~----~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~ 388 (413)
T KOG1267|consen 313 KH----ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPA 388 (413)
T ss_pred hh----hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccch
Confidence 33 889999999999999999999999999999999999999999999999 8999999999999999999999999
Q ss_pred ccccCccccchHHHHHHHHcCCC
Q 010056 437 FFTYGLESTIKPRHKMIARKGLQ 459 (519)
Q Consensus 437 ~L~ySLekRI~PR~~~L~~kGl~ 459 (519)
++.|++|+|++||+....++|.+
T Consensus 389 ~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 389 FFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred hhccchhhcchhHHHHHHHHhcc
Confidence 99999999999999998877643
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.87 E-value=7.3e-22 Score=209.94 Aligned_cols=281 Identities=20% Similarity=0.314 Sum_probs=245.6
Q ss_pred chHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHhhhCccccccccccchhhHHHH
Q 010056 161 NMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPEVLGFKLEGTMSTSVAY 240 (519)
Q Consensus 161 ~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~lL~~s~e~~l~p~v~f 240 (519)
+..+++++|+++|++..++.+++..+|.++..+.++.+.+.+.+|++.|++...+.+++...|.+|+.+...++.+.++|
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~ 169 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEF 169 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHH
Confidence 57889999999999999999999999999999999889999999999999999999999999999998888899999999
Q ss_pred HHHhC--CChhHHHHHHhhCccccccccccchhhHHHHHHHhCCChHHHHHHHHhCCcccccccccchhhhHHHHHhhhc
Q 010056 241 LVGIG--VSRREIGGVLTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARLIEKKPYILGFGLEERVKPNVESLLEFSV 318 (519)
Q Consensus 241 L~~lG--v~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~L~~lGv 318 (519)
+++++ .....+.+++...|..... +..+. ++++++++|..+..+...+..+|..+.... .+...+.++..+|+
T Consensus 170 l~~~~~~~~~s~~~~~~~~~~~~~~~--~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~ 244 (413)
T KOG1267|consen 170 LKSIPPELLSSVVERLLTPVPSFLLN--ENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGF 244 (413)
T ss_pred hhccchhhhhhHHHHhcccccccccc--ccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhcc
Confidence 99984 7777888888777743322 22344 899999999999999999999999887753 68888999999999
Q ss_pred CCccHHHHHhhCCcccccCcchhhhhHHHhhhhhcCCChhhHHHHHHhhhhhhhcChhHHHHhHHHHHHhCCcHHHHHHH
Q 010056 319 RKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSAIDSSSKDFGSIVEKMPQVVNASNSAVTRHVDFLKSCGFFLQQVRQI 398 (519)
Q Consensus 319 ~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~lG~s~~~~~~~v~k~P~iL~~s~~~l~~kv~fL~~lG~s~e~I~~m 398 (519)
++.. .++...|.+++.+.++.+++++.+| +.+||+.+++..|+.++|++++++.+++..+++|+.+. .++
T Consensus 245 ~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l-~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~---~~~---- 314 (413)
T KOG1267|consen 245 DPKT--REFVKAPILLSYSSEKTLEPKVEVL-KSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN---PKH---- 314 (413)
T ss_pred CCch--hHHHhhhhhhcccccccHHHHHHHH-HHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc---chh----
Confidence 8877 7888999999999999999999999 56799999999999999999999999999999999987 333
Q ss_pred HHhcCchhccCHHHHHHHHHHHHHHhCCChhhHh----hcCcccccCccccchHHHHHHHHcCC
Q 010056 399 VVECPQVLALNLDIMKLSFDYFQREMQRPLDDLV----VFPAFFTYGLESTIKPRHKMIARKGL 458 (519)
Q Consensus 399 v~r~P~lL~~S~e~Lk~k~~fL~~~mg~~~~~i~----~~P~~L~ySLekRI~PR~~~L~~kGl 458 (519)
+.++|+++.++..++.++++|+.. .|++..+++ .+|+++.||+++ +.+++.....+++
T Consensus 315 ~~k~p~~l~~s~~~l~~~ie~l~~-~g~~~~q~~~~~~~~Pq~l~~s~~~-~~~~~~~~~~~~~ 376 (413)
T KOG1267|consen 315 ILKFPQLLRSSEDKLKPRIEFLLS-LGFSDVQILEMVKRFPQYLSFSLEK-ILKRKYEYLLKGL 376 (413)
T ss_pred hhhhhhhhhccchhhhhhHHHHHH-cCCcHHHHHHHHhhccHHhhhhHHh-hhhhhHHHHHHHc
Confidence 699999999999999999999998 788876654 479999999998 6666654333443
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=96.95 E-value=0.00068 Score=43.92 Aligned_cols=30 Identities=20% Similarity=0.425 Sum_probs=24.0
Q ss_pred HHHHhcCchhccCHHHHHHHHHHHHHHhCCC
Q 010056 397 QIVVECPQVLALNLDIMKLSFDYFQREMQRP 427 (519)
Q Consensus 397 ~mv~r~P~lL~~S~e~Lk~k~~fL~~~mg~~ 427 (519)
.++.++|.+|+++.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4678888888888778888888888 68764
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=96.49 E-value=0.0015 Score=42.23 Aligned_cols=25 Identities=28% Similarity=0.830 Sum_probs=9.9
Q ss_pred hhCccccccccccchhhHHHHHHHhC
Q 010056 220 ERYPEVLGFKLEGTMSTSVAYLVGIG 245 (519)
Q Consensus 220 ~~~P~lL~~s~e~~l~p~v~fL~~lG 245 (519)
.++|.+|+++ +++++++++||+++|
T Consensus 5 ~~~P~il~~~-~~~l~~~~~~l~~~g 29 (31)
T smart00733 5 KKFPQILGYS-EKKLKPKVEFLKELG 29 (31)
T ss_pred hhCcCccccc-HHHhhHHHHHHHHcC
Confidence 3344444443 333444444444333
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=95.23 E-value=0.24 Score=51.43 Aligned_cols=187 Identities=16% Similarity=0.212 Sum_probs=92.9
Q ss_pred ccccccccccch-hhHHHHHH-HhCCChHHHHHHHHhCCccccccc---ccchhhhHHHHHhhhcCCccHHHHH------
Q 010056 259 PDILGMRVGRVI-KPFVEYLE-SLGIPRLAVARLIEKKPYILGFGL---EERVKPNVESLLEFSVRKEALPVVV------ 327 (519)
Q Consensus 259 P~lL~~s~e~~l-~p~v~~L~-~lG~~~~~i~~iI~~~P~iL~~s~---e~~l~~~v~~L~~lGv~~~~l~~vI------ 327 (519)
-.+|+++.++.| -.++..++ ++|++.+-...++.+||..|...- ....-+-+.|=.++.++.-+.....
T Consensus 107 ~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~ 186 (335)
T PF11955_consen 107 RKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKR 186 (335)
T ss_pred HHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhcccccc
Confidence 346666666654 25666666 788888777777888888776632 0111112222112333222211111
Q ss_pred -----------hhCCcccccCcchhhhhHHHhhhh---------hcCCCh--hhH-HHHHHhhhhhhhcChhH--HHHhH
Q 010056 328 -----------AQYPEIIGIDLKPKLLGQQSLLNS---------AIDSSS--KDF-GSIVEKMPQVVNASNSA--VTRHV 382 (519)
Q Consensus 328 -----------~~~P~iL~~s~~~kl~~~~~~L~~---------~lG~s~--~~~-~~~v~k~P~iL~~s~~~--l~~kv 382 (519)
..+|. +..++++...++.-+++ .-++++ ++. -++|.-.--+|+++.++ ..+++
T Consensus 187 ~~~~~~~~~Fp~~fp~--G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L 264 (335)
T PF11955_consen 187 EDGFDRPLAFPVSFPK--GFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHL 264 (335)
T ss_pred ccccCCceeeeecCCC--CccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHH
Confidence 11222 11122233222222221 112211 111 23444445667777654 44667
Q ss_pred HHHHH-hCCcHHHHHHHHHhcCchhccCHHHHHHHHHHHHHHhCCChhhHhhcCcccccCccccchHHHHHHHHcC
Q 010056 383 DFLKS-CGFFLQQVRQIVVECPQVLALNLDIMKLSFDYFQREMQRPLDDLVVFPAFFTYGLESTIKPRHKMIARKG 457 (519)
Q Consensus 383 ~fL~~-lG~s~e~I~~mv~r~P~lL~~S~e~Lk~k~~fL~~~mg~~~~~i~~~P~~L~ySLekRI~PR~~~L~~kG 457 (519)
..|.+ +|++ +.+..++.+||.|+-.|...-. -.-||.+..... +-|-.+|.+ .++-|+.-|...|
T Consensus 265 ~~fr~ef~lp-~k~~~~l~rHPgIFYvS~kg~~-~TVfLrEAY~~~-~Liek~Pl~-------~~r~k~~~Lm~~~ 330 (335)
T PF11955_consen 265 THFRKEFGLP-QKFRRLLLRHPGIFYVSLKGKR-HTVFLREAYDGG-ELIEKHPLV-------VIREKFLELMQEG 330 (335)
T ss_pred HHHHHHhCCc-HHHHHHHHhCCCeEEEeccCCc-eEEEEeeccCCC-CCCCCCchH-------HHHHHHHHHHhhc
Confidence 77876 8887 5678888888888888875211 123444444333 334455542 3555665555554
No 10
>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=86.44 E-value=0.99 Score=46.94 Aligned_cols=238 Identities=18% Similarity=0.319 Sum_probs=118.0
Q ss_pred hCCCChhHHHHHHhhcCccccccc---c----cchHHHHHHHH--hcCCCCCChhHHhhhCccccccccccch-hhHHHH
Q 010056 171 KLGVRKSTFTEFLRRYPQVLHSSV---V----VDLAPVVKYLQ--GLDIKPNDIPRVLERYPEVLGFKLEGTM-STSVAY 240 (519)
Q Consensus 171 ~lGls~~~i~~ll~~~P~iL~~s~---~----~~l~p~v~fL~--~lG~s~~~I~~il~~~P~lL~~s~e~~l-~p~v~f 240 (519)
.+|+..-.+...+.+||.++.... . ..+-+...-|. +..+-.+.-..++.+--.+|.++.++.| -.++..
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~ 125 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAH 125 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHH
Confidence 577755777777777777765432 0 11223222221 1221111113333444456666666555 345666
Q ss_pred HH-HhCCChhHHHHHHhhCcccccccc---ccchhhHHHHHHHhCCChHHHHHHH-----------------HhCCcccc
Q 010056 241 LV-GIGVSRREIGGVLTRYPDILGMRV---GRVIKPFVEYLESLGIPRLAVARLI-----------------EKKPYILG 299 (519)
Q Consensus 241 L~-~lGv~~~~I~~ll~~~P~lL~~s~---e~~l~p~v~~L~~lG~~~~~i~~iI-----------------~~~P~iL~ 299 (519)
++ ++|++.+=...++.++|..|...- ....-.-+.|=.++.++.-+..... .++|. |
T Consensus 126 l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~--G 203 (335)
T PF11955_consen 126 LRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPK--G 203 (335)
T ss_pred HHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCC--C
Confidence 66 567777767777777777765422 0011111111112222221111110 11221 2
Q ss_pred cccccchhhhHHHHHhhhc----------CCccH---HHHHhhCCcccccCcchhh-hhHHHhhhhhcCCChhhHHHHHH
Q 010056 300 FGLEERVKPNVESLLEFSV----------RKEAL---PVVVAQYPEIIGIDLKPKL-LGQQSLLNSAIDSSSKDFGSIVE 365 (519)
Q Consensus 300 ~s~e~~l~~~v~~L~~lGv----------~~~~l---~~vI~~~P~iL~~s~~~kl-~~~~~~L~~~lG~s~~~~~~~v~ 365 (519)
+.+.++.+..++-++++-+ +++.- ...++-.-.+|++.+++++ ......|.+.+|++ ..+..++.
T Consensus 204 ~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~ 282 (335)
T PF11955_consen 204 FRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLL 282 (335)
T ss_pred ccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHH
Confidence 2223344555554444321 11110 1234444566776666544 34556666788886 67889999
Q ss_pred hhhhhhhcChhHHHHhHHHHHHhCCcHHHHHHHHHhcCchhccCHHHHHHHHHHHHH
Q 010056 366 KMPQVVNASNSAVTRHVDFLKSCGFFLQQVRQIVVECPQVLALNLDIMKLSFDYFQR 422 (519)
Q Consensus 366 k~P~iL~~s~~~l~~kv~fL~~lG~s~e~I~~mv~r~P~lL~~S~e~Lk~k~~fL~~ 422 (519)
+||.|+.+|.. .....-||++ ++... .++.++|.+. ++.|+--|+.
T Consensus 283 rHPgIFYvS~k-g~~~TVfLrE-AY~~~---~Liek~Pl~~------~r~k~~~Lm~ 328 (335)
T PF11955_consen 283 RHPGIFYVSLK-GKRHTVFLRE-AYDGG---ELIEKHPLVV------IREKFLELMQ 328 (335)
T ss_pred hCCCeEEEecc-CCceEEEEee-ccCCC---CCCCCCchHH------HHHHHHHHHh
Confidence 99999988853 2222345555 33333 2457777764 6777666554
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=83.96 E-value=6.1 Score=37.03 Aligned_cols=21 Identities=14% Similarity=0.188 Sum_probs=11.6
Q ss_pred HHHHHhhCCCChhHHHHHHhh
Q 010056 165 VLDYLGKLGVRKSTFTEFLRR 185 (519)
Q Consensus 165 ~l~~L~~lGls~~~i~~ll~~ 185 (519)
.+..|+++|++-++|..++..
T Consensus 50 ~I~~lr~~G~sL~eI~~ll~~ 70 (172)
T cd04790 50 QICAYRSAGVSLEDIRSLLQQ 70 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHhc
Confidence 344555566666666655543
No 12
>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=78.01 E-value=6.6 Score=36.82 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=13.2
Q ss_pred HhHHHHHHhCCcHHHHHH
Q 010056 380 RHVDFLKSCGFFLQQVRQ 397 (519)
Q Consensus 380 ~kv~fL~~lG~s~e~I~~ 397 (519)
...+||.++|++.++|..
T Consensus 149 ~h~~~l~~~g~~~~~~~~ 166 (172)
T cd04790 149 AHQEFLQSLGIPEDEIER 166 (172)
T ss_pred HHHHHHHHcCCCHHHHHH
Confidence 456788888888887754
No 13
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=68.85 E-value=16 Score=30.48 Aligned_cols=47 Identities=17% Similarity=0.378 Sum_probs=29.2
Q ss_pred chHHHHHHHhhCCCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHhhhCcccccccccc
Q 010056 161 NMIPVLDYLGKLGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPEVLGFKLEG 232 (519)
Q Consensus 161 ~l~p~l~~L~~lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~lL~~s~e~ 232 (519)
.+..++.||..+|++.....++...+-. +...+|..+|+.|..++.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~-------------------------~ai~~l~~nPY~L~~~i~g 53 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGD-------------------------DAIEILKENPYRLIEDIDG 53 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-T-------------------------THHHHHHH-STCCCB-SSS
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhH-------------------------HHHHHHHHChHHHHHHccC
Confidence 3567788888999988887777765421 3446778899988876643
No 14
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=67.85 E-value=9.7 Score=38.21 Aligned_cols=57 Identities=14% Similarity=0.200 Sum_probs=40.2
Q ss_pred cChhHHHHhHHHHHH-hC-CcHHHHHHHHHhcCchhccCHHHHHHHHHHHHHHhCCChh
Q 010056 373 ASNSAVTRHVDFLKS-CG-FFLQQVRQIVVECPQVLALNLDIMKLSFDYFQREMQRPLD 429 (519)
Q Consensus 373 ~s~~~l~~kv~fL~~-lG-~s~e~I~~mv~r~P~lL~~S~e~Lk~k~~fL~~~mg~~~~ 429 (519)
+..-+++.++.|... .| |+.-.|.+=+.-.|.++.++.++++.|.+=|++-+|+++.
T Consensus 68 ~d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~ 126 (309)
T COG1125 68 LDPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPS 126 (309)
T ss_pred CCHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHH
Confidence 334456777777765 55 5666666666778888888888888888888777888763
No 15
>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=66.21 E-value=12 Score=32.18 Aligned_cols=81 Identities=22% Similarity=0.321 Sum_probs=46.9
Q ss_pred HHHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccccCCcccccccccchHHHHHHHhhCCCChhHHHHHH
Q 010056 104 VYDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDINNYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFL 183 (519)
Q Consensus 104 vv~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll 183 (519)
...||+.-|++.....-...|.+.+.+ .+++..+|.+..++-+. +. .... .+.-+....++.+++..++
T Consensus 12 a~~~L~~~gi~~~~~d~~k~p~s~~el---~~~l~~~~~~~~~lin~------~~-~~~k-~l~~~~~~~~s~~e~i~~l 80 (110)
T PF03960_consen 12 ALKWLEENGIEYEFIDYKKEPLSREEL---RELLSKLGNGPDDLINT------RS-KTYK-ELGKLKKDDLSDEELIELL 80 (110)
T ss_dssp HHHHHHHTT--EEEEETTTS---HHHH---HHHHHHHTSSGGGGB-T------TS-HHHH-HTTHHHCTTSBHHHHHHHH
T ss_pred HHHHHHHcCCCeEeehhhhCCCCHHHH---HHHHHHhcccHHHHhcC------cc-chHh-hhhhhhhhhhhhHHHHHHH
Confidence 468888888887765555456666665 67777777776665311 10 0011 1112334568888999999
Q ss_pred hhcCcccccccc
Q 010056 184 RRYPQVLHSSVV 195 (519)
Q Consensus 184 ~~~P~iL~~s~~ 195 (519)
..+|.++...+.
T Consensus 81 ~~~p~LikRPIi 92 (110)
T PF03960_consen 81 LENPKLIKRPII 92 (110)
T ss_dssp HHSGGGB-SSEE
T ss_pred HhChhheeCCEE
Confidence 999998887764
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=63.85 E-value=10 Score=34.06 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=19.3
Q ss_pred hHHHHHHHhhCCCChhHHHHHHhhcCcc
Q 010056 162 MIPVLDYLGKLGVRKSTFTEFLRRYPQV 189 (519)
Q Consensus 162 l~p~l~~L~~lGls~~~i~~ll~~~P~i 189 (519)
+..+++||++-|++.++|...+.+.+.-
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 5678888888888888888888776543
No 17
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=59.37 E-value=9.4 Score=33.49 Aligned_cols=39 Identities=28% Similarity=0.379 Sum_probs=17.2
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccc
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIED 146 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~ 146 (519)
..||+.-|++.....-...|-+.+.+ .++++..|...++
T Consensus 18 ~~~L~~~gi~~~~~~y~~~~~s~~eL---~~~l~~~g~~~~~ 56 (117)
T COG1393 18 LAWLEEHGIEYTFIDYLKTPPSREEL---KKILSKLGDGVEE 56 (117)
T ss_pred HHHHHHcCCCcEEEEeecCCCCHHHH---HHHHHHcCccHHH
Confidence 34555555554433333333444433 4444545544333
No 18
>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=49.76 E-value=24 Score=31.73 Aligned_cols=31 Identities=16% Similarity=0.286 Sum_probs=23.3
Q ss_pred hHHHHhHHHHHHhCCcHHHHHHHHHhcCchh
Q 010056 376 SAVTRHVDFLKSCGFFLQQVRQIVVECPQVL 406 (519)
Q Consensus 376 ~~l~~kv~fL~~lG~s~e~I~~mv~r~P~lL 406 (519)
..+.+|++||++-|++.+||..++.+.+.--
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3477999999999999999999999988765
No 19
>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=46.43 E-value=28 Score=23.59 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=17.5
Q ss_pred HhHHHHHHhCCcHHHHHHHHHhc
Q 010056 380 RHVDFLKSCGFFLQQVRQIVVEC 402 (519)
Q Consensus 380 ~kv~fL~~lG~s~e~I~~mv~r~ 402 (519)
.+++-|+++||+.+++.+.+..+
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 45778888999999988877665
No 20
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=45.03 E-value=65 Score=26.80 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=12.7
Q ss_pred hhhHHHHHHHhCCChhHHHHHHhh
Q 010056 234 MSTSVAYLVGIGVSRREIGGVLTR 257 (519)
Q Consensus 234 l~p~v~fL~~lGv~~~~I~~ll~~ 257 (519)
+...+.||.+.|++...+.++...
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 445566777777766666665443
No 21
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=44.33 E-value=51 Score=27.73 Aligned_cols=78 Identities=24% Similarity=0.325 Sum_probs=42.7
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCcccccc--CCcccccccccchHHHHHHHhhCCCChhHHHHH
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDINN--YPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEF 182 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~~--~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~l 182 (519)
..||++.|++-..+.-...|.+.+.+ .+++...|....++-+ .+..-..+. -..-+++.+++.++
T Consensus 16 ~~~L~~~~i~~~~idi~~~~~~~~~l---~~~~~~~~~~~~~li~~~~~~~~~l~~----------~~~~~ls~~e~~~~ 82 (105)
T cd02977 16 LAWLEEHGIEYEFIDYLKEPPTKEEL---KELLAKLGLGVEDLFNTRGTPYRKLGL----------ADKDELSDEEALEL 82 (105)
T ss_pred HHHHHHcCCCcEEEeeccCCCCHHHH---HHHHHhcCCCHHHHHhcCCchHHHcCC----------ccccCCCHHHHHHH
Confidence 57788888776654433345555554 5566666655555421 110000000 00135677888888
Q ss_pred HhhcCcccccccc
Q 010056 183 LRRYPQVLHSSVV 195 (519)
Q Consensus 183 l~~~P~iL~~s~~ 195 (519)
+..+|.++...+.
T Consensus 83 l~~~p~LikRPii 95 (105)
T cd02977 83 MAEHPKLIKRPIV 95 (105)
T ss_pred HHhCcCeeeCCEE
Confidence 8888888776653
No 22
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=44.28 E-value=49 Score=28.55 Aligned_cols=21 Identities=14% Similarity=0.377 Sum_probs=12.4
Q ss_pred CChhHHHHHHhhcCccccccc
Q 010056 174 VRKSTFTEFLRRYPQVLHSSV 194 (519)
Q Consensus 174 ls~~~i~~ll~~~P~iL~~s~ 194 (519)
++.+++..++..+|.++...+
T Consensus 74 ls~~e~i~~l~~~p~LikRPi 94 (115)
T cd03032 74 LSLSELIRLISEHPSLLRRPI 94 (115)
T ss_pred CCHHHHHHHHHhChhheeCCE
Confidence 455566666666666665554
No 23
>PRK14136 recX recombination regulator RecX; Provisional
Probab=43.85 E-value=42 Score=34.43 Aligned_cols=133 Identities=11% Similarity=0.075 Sum_probs=72.0
Q ss_pred HHHHHhCCCCccccCCcc--CCCChHHHHHHHHHHHhCCCCcccc-c-cCCcccccccccchHHHHHHHhhCCCChhHHH
Q 010056 105 YDFLQGIGIVPDELDGLE--LPVTVEVMRERVDFLHNLGLTIEDI-N-NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFT 180 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~--~p~~~d~v~~~l~~L~~lGls~~~i-~-~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~ 180 (519)
+.||..---+..++..-. .-...+.+..+|+.|+++|+-.+.- + .|=..-... .-...+-..|+..|++.+.|.
T Consensus 169 L~lLSrReRSe~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~k--kGp~rIrqELrQKGId~eLIE 246 (309)
T PRK14136 169 LGYLSRREYSRAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASR--VGSARIVSELKRHAVGDALVE 246 (309)
T ss_pred HHHhhcccccHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhc--hhHHHHHHHHHHcCCCHHHHH
Confidence 556644333333333211 1234567778899999999876653 2 110000000 112345678889999999999
Q ss_pred HHHhhcCcccccccccchHHHHHHHHh-cCCCCCChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHHHhhCc
Q 010056 181 EFLRRYPQVLHSSVVVDLAPVVKYLQG-LDIKPNDIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGVLTRYP 259 (519)
Q Consensus 181 ~ll~~~P~iL~~s~~~~l~p~v~fL~~-lG~s~~~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~ll~~~P 259 (519)
..+.... +..+....+.++. ++- .+. .. ......+.||..-|++.+.|..+|..+-
T Consensus 247 qALeeie-------EDE~E~A~~L~eKK~~~-----------~~~----d~-kek~K~iRfL~rRGFS~D~I~~vLk~~~ 303 (309)
T PRK14136 247 SVGAQLR-------ETEFERAQAVWRKKFGA-----------LPQ----TP-AERAKQARFLAARGFSSATIVKLLKVGD 303 (309)
T ss_pred HHHHhcc-------HhHHHHHHHHHHHHhcc-----------cCc----CH-HHHHHHHHHHHHCCCCHHHHHHHHHhch
Confidence 8887431 1112222222221 111 110 11 1233457999999999999999987654
Q ss_pred ccc
Q 010056 260 DIL 262 (519)
Q Consensus 260 ~lL 262 (519)
..+
T Consensus 304 de~ 306 (309)
T PRK14136 304 DEF 306 (309)
T ss_pred hcc
Confidence 433
No 24
>PRK01655 spxA transcriptional regulator Spx; Reviewed
Probab=42.08 E-value=55 Score=29.10 Aligned_cols=21 Identities=10% Similarity=0.343 Sum_probs=12.1
Q ss_pred CChhHHHHHHhhcCccccccc
Q 010056 174 VRKSTFTEFLRRYPQVLHSSV 194 (519)
Q Consensus 174 ls~~~i~~ll~~~P~iL~~s~ 194 (519)
++.+++..++..+|.++...+
T Consensus 74 ls~~e~i~ll~~~p~LikRPI 94 (131)
T PRK01655 74 LSLQDLIKLISDNPGLLRRPI 94 (131)
T ss_pred CCHHHHHHHHHhCcceEeCCE
Confidence 344556666666666655554
No 25
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=41.37 E-value=35 Score=22.85 Aligned_cols=23 Identities=17% Similarity=0.267 Sum_probs=18.2
Q ss_pred HhHHHHHHhCCcHHHHHHHHHhc
Q 010056 380 RHVDFLKSCGFFLQQVRQIVVEC 402 (519)
Q Consensus 380 ~kv~fL~~lG~s~e~I~~mv~r~ 402 (519)
++++-|.+|||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45777888999999888777665
No 26
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=40.02 E-value=63 Score=28.81 Aligned_cols=19 Identities=16% Similarity=0.454 Sum_probs=9.3
Q ss_pred ChhHHHHHHhhcCcccccc
Q 010056 175 RKSTFTEFLRRYPQVLHSS 193 (519)
Q Consensus 175 s~~~i~~ll~~~P~iL~~s 193 (519)
+.+++..++..+|.++...
T Consensus 75 s~~e~i~ll~~~P~LikRP 93 (132)
T PRK13344 75 SVNEVIDLIQENPRILKSP 93 (132)
T ss_pred CHHHHHHHHHhCccceeCc
Confidence 3444455555555554444
No 27
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=39.37 E-value=62 Score=28.35 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=28.3
Q ss_pred ChHHHHHHHHHHHhCCCCccccc--cCCcccccccccchHHHHHHHhhCCCC
Q 010056 126 TVEVMRERVDFLHNLGLTIEDIN--NYPLVLGCSVKKNMIPVLDYLGKLGVR 175 (519)
Q Consensus 126 ~~d~v~~~l~~L~~lGls~~~i~--~~P~lL~~s~~~~l~p~l~~L~~lGls 175 (519)
+++..+...+||+++|+....+. +.| + +-....+++...|.+
T Consensus 10 ~C~t~rka~~~L~~~gi~~~~~~y~~~~------~--s~~eL~~~l~~~g~~ 53 (117)
T COG1393 10 NCSTCRKALAWLEEHGIEYTFIDYLKTP------P--SREELKKILSKLGDG 53 (117)
T ss_pred CChHHHHHHHHHHHcCCCcEEEEeecCC------C--CHHHHHHHHHHcCcc
Confidence 56778888999999999887553 332 1 234456666666655
No 28
>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=39.25 E-value=40 Score=22.71 Aligned_cols=23 Identities=17% Similarity=0.304 Sum_probs=17.7
Q ss_pred HhHHHHHHhCCcHHHHHHHHHhc
Q 010056 380 RHVDFLKSCGFFLQQVRQIVVEC 402 (519)
Q Consensus 380 ~kv~fL~~lG~s~e~I~~mv~r~ 402 (519)
.+++-|.+|||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45778888999988887776654
No 29
>PRK10026 arsenate reductase; Provisional
Probab=38.99 E-value=66 Score=29.21 Aligned_cols=39 Identities=21% Similarity=0.502 Sum_probs=18.8
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccc
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIED 146 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~ 146 (519)
..+|++-|++.....-...|-+.+.+ ..+|..+|....+
T Consensus 19 ~~wL~~~gi~~~~~d~~~~ppt~~eL---~~~l~~~g~~~~~ 57 (141)
T PRK10026 19 LEMIRNSGTEPTIIHYLETPPTRDEL---VKLIADMGISVRA 57 (141)
T ss_pred HHHHHHCCCCcEEEeeeCCCcCHHHH---HHHHHhCCCCHHH
Confidence 35555555555444333344444444 4444555554443
No 30
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=38.46 E-value=64 Score=25.69 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=11.3
Q ss_pred hHHHHHHHhCCChhHHHHHH
Q 010056 236 TSVAYLVGIGVSRREIGGVL 255 (519)
Q Consensus 236 p~v~fL~~lGv~~~~I~~ll 255 (519)
|.++.|++..++.+.|..++
T Consensus 3 PIia~LKehnvsd~qi~elF 22 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELF 22 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHH
Confidence 45555666655555555554
No 31
>PRK14134 recX recombination regulator RecX; Provisional
Probab=36.72 E-value=2.6e+02 Score=28.34 Aligned_cols=58 Identities=12% Similarity=0.158 Sum_probs=38.5
Q ss_pred CChHHHHHHHHHHHhCCCCcccc-c-cC--CcccccccccchHHHHHHHhhCCCChhHHHHHHhhc
Q 010056 125 VTVEVMRERVDFLHNLGLTIEDI-N-NY--PLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRRY 186 (519)
Q Consensus 125 ~~~d~v~~~l~~L~~lGls~~~i-~-~~--P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~~ 186 (519)
.+.+.+..+|+.|.+.|+-.+.- + .+ -.+-..+ ...+-.-|...|++.+.|...+...
T Consensus 90 ~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~~~G----~~~I~~eL~qKGI~~~iIe~al~~~ 151 (283)
T PRK14134 90 YDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKINSYG----RNKIKYTLLNKGIKENIIIEKINNI 151 (283)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhh----HHHHHHHHHHCCCCHHHHHHHHHhC
Confidence 45677888899999999877653 2 11 0110111 2344677889999999999888754
No 32
>PRK09875 putative hydrolase; Provisional
Probab=35.70 E-value=1.4e+02 Score=30.42 Aligned_cols=112 Identities=15% Similarity=0.186 Sum_probs=53.8
Q ss_pred HHHHHhCCCCccc--cCCccCCCChHHHHHHHHHHHhCCCCcc--ccccCCcccccccccchHHHHHHHhhCCCChhHHH
Q 010056 105 YDFLQGIGIVPDE--LDGLELPVTVEVMRERVDFLHNLGLTIE--DINNYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFT 180 (519)
Q Consensus 105 v~yL~~~Gi~~~~--l~~l~~p~~~d~v~~~l~~L~~lGls~~--~i~~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~ 180 (519)
++.|++.|+++++ +.+.....+++.+++. .+.|.--+ .+... ...++......+..|.+.|..+.=+-
T Consensus 169 l~il~e~Gvd~~rvvi~H~d~~~d~~~~~~l----~~~G~~l~fD~~g~~----~~~pd~~r~~~i~~L~~~Gy~drilL 240 (292)
T PRK09875 169 LALLQAHGVDLSRVTVGHCDLKDNLDNILKM----IDLGAYVQFDTIGKN----SYYPDEKRIAMLHALRDRGLLNRVML 240 (292)
T ss_pred HHHHHHcCcCcceEEEeCCCCCCCHHHHHHH----HHcCCEEEeccCCCc----ccCCHHHHHHHHHHHHhcCCCCeEEE
Confidence 5778889998877 3455555566554222 23343322 12110 00011124555666666673221100
Q ss_pred -HHHhhcCcccc---cccccchHHHHHHHHhcCCCCCChhHHhhhCcc
Q 010056 181 -EFLRRYPQVLH---SSVVVDLAPVVKYLQGLDIKPNDIPRVLERYPE 224 (519)
Q Consensus 181 -~ll~~~P~iL~---~s~~~~l~p~v~fL~~lG~s~~~I~~il~~~P~ 224 (519)
.=+.+....-. .....-+...+-.|+..|+++++|.+|+..||.
T Consensus 241 S~D~~~~~~~~~~gg~G~~~i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 241 SMDITRRSHLKANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred eCCCCCcccccccCCCChhHHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 00000000000 000111445566778888888888888888885
No 33
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=35.00 E-value=3.3e+02 Score=24.62 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=17.9
Q ss_pred HHHh-HHHHHHhCCcHHHHHHHHHh
Q 010056 378 VTRH-VDFLKSCGFFLQQVRQIVVE 401 (519)
Q Consensus 378 l~~k-v~fL~~lG~s~e~I~~mv~r 401 (519)
.+.| +.+|..-||+.+.|...+..
T Consensus 128 ~k~Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 128 EKAKLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3344 68888899999998877654
No 34
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.23 E-value=93 Score=29.61 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=17.2
Q ss_pred hhhHHHHHHHhCCChHHHHHHHHhC
Q 010056 270 IKPFVEYLESLGIPRLAVARLIEKK 294 (519)
Q Consensus 270 l~p~v~~L~~lG~~~~~i~~iI~~~ 294 (519)
+...+.+|.++|+++..+.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4566777777777777777766654
No 35
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=32.80 E-value=56 Score=28.23 Aligned_cols=77 Identities=21% Similarity=0.149 Sum_probs=40.4
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccc--cCCcccccccccchHHHHHHHh--hCCCChhHHH
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDIN--NYPLVLGCSVKKNMIPVLDYLG--KLGVRKSTFT 180 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~--~~P~lL~~s~~~~l~p~l~~L~--~lGls~~~i~ 180 (519)
..||+..|++.....-...|.+.+.+ .+++...|...+++- +.+..-... +. --.++.+++.
T Consensus 16 ~~~L~~~~i~~~~idi~~~~~~~~el---~~l~~~~~~~~~~lin~~~~~~k~l~-----------~~~~~~~ls~~e~~ 81 (117)
T TIGR01617 16 RRWLEANGIEYQFIDIGEDGPTREEL---LDILSLLEDGIDPLLNTRGQSYRALN-----------TSNTFLDLSDKEAL 81 (117)
T ss_pred HHHHHHcCCceEEEecCCChhhHHHH---HHHHHHcCCCHHHheeCCCcchhhCC-----------chhhcccCCHHHHH
Confidence 56777777765544433334444443 666777776555542 111100000 00 0235667777
Q ss_pred HHHhhcCcccccccc
Q 010056 181 EFLRRYPQVLHSSVV 195 (519)
Q Consensus 181 ~ll~~~P~iL~~s~~ 195 (519)
.++..+|.++...+.
T Consensus 82 ~~i~~~p~LikRPIi 96 (117)
T TIGR01617 82 ELLAEDPALLRRPLI 96 (117)
T ss_pred HHHHhCcceEecCEE
Confidence 777777777766653
No 36
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=32.78 E-value=1.1e+02 Score=26.50 Aligned_cols=36 Identities=31% Similarity=0.451 Sum_probs=17.9
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCC
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLT 143 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls 143 (519)
..||++-|++.....-...|-+.+.+ ..+++.+|++
T Consensus 16 ~~~L~~~~i~~~~~di~~~p~t~~el---~~~l~~~g~~ 51 (114)
T TIGR00014 16 LALLEDKGIEPEVVKYLKNPPTKSEL---EAIFAKLGLT 51 (114)
T ss_pred HHHHHHCCCCeEEEeccCCCcCHHHH---HHHHHHcCCc
Confidence 45666666665543333344455544 4444445544
No 37
>PRK14134 recX recombination regulator RecX; Provisional
Probab=32.60 E-value=5.4e+02 Score=26.05 Aligned_cols=175 Identities=10% Similarity=0.098 Sum_probs=79.1
Q ss_pred chHHHHHHHHhcCC-CCCChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHHHhhCccccccccccchhhHHH
Q 010056 197 DLAPVVKYLQGLDI-KPNDIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGVLTRYPDILGMRVGRVIKPFVE 275 (519)
Q Consensus 197 ~l~p~v~fL~~lG~-s~~~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~ll~~~P~lL~~s~e~~l~p~v~ 275 (519)
.+..++++|++.|+ ++...+....+.-. -... -.....-|+.-|++.+.|...+...+ .+....
T Consensus 94 ~Ie~vI~~L~e~~yldD~ryA~~yv~~~~-~~~G----~~~I~~eL~qKGI~~~iIe~al~~~~------~e~e~e---- 158 (283)
T PRK14134 94 AVNRVIRFLKEYNFIDDDKYCDMYIREKI-NSYG----RNKIKYTLLNKGIKENIIIEKINNID------EEKEKK---- 158 (283)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHH-Hhhh----HHHHHHHHHHCCCCHHHHHHHHHhCC------hhhHHH----
Confidence 34556677777774 55555555443210 0110 01122455666998888887775321 111111
Q ss_pred HHHHhCCChHHHHHHHHh-CCccccc--ccccchhhhHHHHHhhhcCCccHHHHHhhCCcccccCcchhhhhHHHhhhhh
Q 010056 276 YLESLGIPRLAVARLIEK-KPYILGF--GLEERVKPNVESLLEFSVRKEALPVVVAQYPEIIGIDLKPKLLGQQSLLNSA 352 (519)
Q Consensus 276 ~L~~lG~~~~~i~~iI~~-~P~iL~~--s~e~~l~~~v~~L~~lGv~~~~l~~vI~~~P~iL~~s~~~kl~~~~~~L~~~ 352 (519)
.+.+++.+ ++..-.. +..+.-+..+.+|..-||+.+.+..++...=.--....+.+ -+-+...
T Consensus 159 ----------~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~~~~~~~~~~~~----~~~~~~~ 224 (283)
T PRK14134 159 ----------VAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNELIKNEALYKDNN----SQNIENN 224 (283)
T ss_pred ----------HHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhHhhhhhhcc----ccchhhc
Confidence 11122211 2211111 11112344567888889998888776644200000000000 0000000
Q ss_pred cCCChhhHH-H-HHHhhhhhhhcCh--hHHHHh-HHHHHHhCCcHHHHHHHHH
Q 010056 353 IDSSSKDFG-S-IVEKMPQVVNASN--SAVTRH-VDFLKSCGFFLQQVRQIVV 400 (519)
Q Consensus 353 lG~s~~~~~-~-~v~k~P~iL~~s~--~~l~~k-v~fL~~lG~s~e~I~~mv~ 400 (519)
.....-+.. . +-++++.+..... .++..| ..||..-||+.+.|..++.
T Consensus 225 ~~~~~~~~~~~~a~kr~~~~~~~e~d~~k~~~Kl~~~L~rkGf~~e~I~~vl~ 277 (283)
T PRK14134 225 IKDENIEELHNLARKRYDIIIKSEDDKNKIYRRLSNYLLRRGYSWEEVKKSLN 277 (283)
T ss_pred cccChHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 111111111 1 2233433322222 255666 6888889999999987764
No 38
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=32.38 E-value=1.2e+02 Score=27.57 Aligned_cols=58 Identities=19% Similarity=0.196 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCCCCccc-cc-cCCcccccccccchHHHHHHHhhCCCChhHHHHHHhhc
Q 010056 128 EVMRERVDFLHNLGLTIED-IN-NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRRY 186 (519)
Q Consensus 128 d~v~~~l~~L~~lGls~~~-i~-~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~~ 186 (519)
+.+..+|+.|...|+-.+. .+ .+=.-.... ..-...+...|..-|++.+.|..++...
T Consensus 43 ~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~-~~g~~~I~~~L~~kGi~~~~I~~~l~~~ 102 (157)
T PRK00117 43 EVIEAVLDRLKEEGLLDDERFAESFVRSRARK-GYGPRRIRQELRQKGVDREIIEEALAEL 102 (157)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhC-CchHHHHHHHHHHcCCCHHHHHHHHHHc
Confidence 3445557777777755443 22 000000000 1113445667777788777777777654
No 39
>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=32.35 E-value=75 Score=22.37 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=21.7
Q ss_pred HHHHhHHHHHH-hCCcHHHHHHHHHhcCch
Q 010056 377 AVTRHVDFLKS-CGFFLQQVRQIVVECPQV 405 (519)
Q Consensus 377 ~l~~kv~fL~~-lG~s~e~I~~mv~r~P~l 405 (519)
++-.....|.. +|++..+++++|..||.+
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 45566788885 999999999999999975
No 40
>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=70 Score=27.26 Aligned_cols=22 Identities=9% Similarity=0.229 Sum_probs=16.8
Q ss_pred hCCcHHHHHHHHHhcCchhccC
Q 010056 388 CGFFLQQVRQIVVECPQVLALN 409 (519)
Q Consensus 388 lG~s~e~I~~mv~r~P~lL~~S 409 (519)
..++.+++.+++..+|.++...
T Consensus 69 ~~~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 69 DDLSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp TTSBHHHHHHHHHHSGGGB-SS
T ss_pred hhhhhHHHHHHHHhChhheeCC
Confidence 4578888888899999887544
No 41
>PRK12559 transcriptional regulator Spx; Provisional
Probab=30.73 E-value=1.1e+02 Score=27.33 Aligned_cols=39 Identities=15% Similarity=0.064 Sum_probs=18.5
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccc
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIED 146 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~ 146 (519)
..||++.|++.....-...|.+.+.+ ..+|+..|+...+
T Consensus 17 ~~~L~~~gi~~~~~di~~~~~s~~el---~~~l~~~~~g~~~ 55 (131)
T PRK12559 17 KAWLEENQIDYTEKNIVSNSMTVDEL---KSILRLTEEGATE 55 (131)
T ss_pred HHHHHHcCCCeEEEEeeCCcCCHHHH---HHHHHHcCCCHHH
Confidence 35666666665444333334444444 4444444444333
No 42
>PTZ00217 flap endonuclease-1; Provisional
Probab=30.54 E-value=5.7e+02 Score=27.27 Aligned_cols=73 Identities=22% Similarity=0.275 Sum_probs=39.9
Q ss_pred HHHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccc--------cCCccc-cccc----cc--chHHHHHH
Q 010056 104 VYDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDIN--------NYPLVL-GCSV----KK--NMIPVLDY 168 (519)
Q Consensus 104 vv~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~--------~~P~lL-~~s~----~~--~l~p~l~~ 168 (519)
+...|+.+||+.=. .|.-.|.. +++|...|....-+. ..|.++ ..+. .. .....-..
T Consensus 143 ~~~lL~~~Gip~i~-----AP~EAdaq---~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v 214 (393)
T PTZ00217 143 AKKLLRLMGIPVIE-----APCEAEAQ---CAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTV 214 (393)
T ss_pred HHHHHHHcCCceEE-----CCcCHHHH---HHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHH
Confidence 35667778877433 25555554 888888886554333 233332 1110 00 01122345
Q ss_pred HhhCCCChhHHHHHHh
Q 010056 169 LGKLGVRKSTFTEFLR 184 (519)
Q Consensus 169 L~~lGls~~~i~~ll~ 184 (519)
+..+|++++++..+..
T Consensus 215 ~~~~gl~~~q~id~~i 230 (393)
T PTZ00217 215 LEELGLSMDQFIDLCI 230 (393)
T ss_pred HHHhCCCHHHHHHHHH
Confidence 5678888888887764
No 43
>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=30.06 E-value=1.8e+02 Score=33.59 Aligned_cols=41 Identities=27% Similarity=0.414 Sum_probs=20.5
Q ss_pred CCChhHHHHHHhhcCcccccccccchHHHHHHHHhcCCCCCChhHHh
Q 010056 173 GVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGLDIKPNDIPRVL 219 (519)
Q Consensus 173 Gls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~lG~s~~~I~~il 219 (519)
|++...+..+...+-. .......+.||..+|++.....++.
T Consensus 124 gi~~~~~~~i~~~~~~------~~~~~~~~~~L~~~gi~~~~a~ki~ 164 (720)
T TIGR01448 124 GISKANLEKFVSQWSQ------QGDERRLLAGLQGLGIGIKLAQRIY 164 (720)
T ss_pred CCCHHHHHHHHHHHHH------hHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 5555555555554411 1124455566666666555444443
No 44
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=29.98 E-value=1.5e+02 Score=25.41 Aligned_cols=77 Identities=18% Similarity=0.319 Sum_probs=46.5
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccc--cCCcccccccccchHHHHHHHhhCCCChhHHHHH
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDIN--NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEF 182 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~--~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~l 182 (519)
..||+.-|++.....-...|-+.+.+ ..+|...|...+++- +.+..-... +..-+++.+++..+
T Consensus 16 ~~~L~~~~i~~~~~di~~~~~t~~el---~~~l~~~~~~~~~lin~~~~~y~~l~-----------~~~~~ls~~e~i~l 81 (112)
T cd03034 16 LALLEEAGIEPEIVEYLKTPPTAAEL---RELLAKLGISPRDLLRTKEAPYKELG-----------LADPELSDEELIDA 81 (112)
T ss_pred HHHHHHCCCCeEEEecccCCcCHHHH---HHHHHHcCCCHHHHHhcCCchHHHcC-----------CCccCCCHHHHHHH
Confidence 57888888887665544456666666 666677776555542 111110000 11235677888888
Q ss_pred HhhcCcccccccc
Q 010056 183 LRRYPQVLHSSVV 195 (519)
Q Consensus 183 l~~~P~iL~~s~~ 195 (519)
+..+|.++...+.
T Consensus 82 l~~~P~LikRPIi 94 (112)
T cd03034 82 MAAHPILIERPIV 94 (112)
T ss_pred HHhCcCcccCCEE
Confidence 8888888877754
No 45
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=29.58 E-value=1.5e+02 Score=25.42 Aligned_cols=79 Identities=16% Similarity=0.195 Sum_probs=45.8
Q ss_pred HHHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccc-cC-CcccccccccchHHHHHHHhh-CCCChhHHH
Q 010056 104 VYDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDIN-NY-PLVLGCSVKKNMIPVLDYLGK-LGVRKSTFT 180 (519)
Q Consensus 104 vv~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~-~~-P~lL~~s~~~~l~p~l~~L~~-lGls~~~i~ 180 (519)
..+||++-|++.+...-...|.+.+.+ ..++...|....++- .. +..-.... . .. .+++.+++.
T Consensus 15 a~~~L~~~~i~~~~idi~~~~~~~~el---~~~~~~~~~~~~~l~~~~~~~~~~l~~----~------~~~~~~s~~e~~ 81 (111)
T cd03036 15 AKKWLDEHGVDYTAIDIVEEPPSKEEL---KKWLEKSGLPLKKFFNTSGKSYRELGL----K------DKLPSLSEEEAL 81 (111)
T ss_pred HHHHHHHcCCceEEecccCCcccHHHH---HHHHHHcCCCHHHHHhcCCchHHhCCc----c------cccccCCHHHHH
Confidence 357888888887665443344454444 566677776655542 11 10000000 0 01 256778888
Q ss_pred HHHhhcCcccccccc
Q 010056 181 EFLRRYPQVLHSSVV 195 (519)
Q Consensus 181 ~ll~~~P~iL~~s~~ 195 (519)
.++..+|.++...+.
T Consensus 82 ~~l~~~p~LikRPIi 96 (111)
T cd03036 82 ELLSSDGMLIKRPFV 96 (111)
T ss_pred HHHHhCcCeeeCCEE
Confidence 899999998887764
No 46
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=28.80 E-value=97 Score=26.38 Aligned_cols=77 Identities=14% Similarity=0.157 Sum_probs=38.3
Q ss_pred HHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCccccccCCcccccccccchHHHHHHHhhCCCChhHHHHHHh
Q 010056 105 YDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDINNYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLR 184 (519)
Q Consensus 105 v~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i~~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~ 184 (519)
..||+.-|++.....-...|-+.+.+ .+++...|+ .+-++..- ..... +..=..-.++.+++..++.
T Consensus 16 ~~~L~~~~i~~~~~di~~~p~s~~eL---~~~l~~~g~-~~li~~~~--------~~yk~-l~l~~~~~~s~~e~~~~l~ 82 (105)
T cd03035 16 RKWLEARGVAYTFHDYRKDGLDAATL---ERWLAKVGW-ETLLNKRG--------TTWRK-LDDAQKAALDAAKAIALML 82 (105)
T ss_pred HHHHHHcCCCeEEEecccCCCCHHHH---HHHHHHhCh-HHHHccCc--------hHHHh-CChhhhccCCHHHHHHHHH
Confidence 46777777776665544456666665 445555662 22222110 00000 0000012355667777777
Q ss_pred hcCccccccc
Q 010056 185 RYPQVLHSSV 194 (519)
Q Consensus 185 ~~P~iL~~s~ 194 (519)
.+|.++...+
T Consensus 83 ~~p~LikRPI 92 (105)
T cd03035 83 EHPSLIKRPV 92 (105)
T ss_pred hCcCeeecce
Confidence 7777776654
No 47
>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=28.77 E-value=91 Score=26.99 Aligned_cols=56 Identities=21% Similarity=0.280 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHhCCCCcccc-c-cC--CcccccccccchHHHHHHHhhCCCChhHHHHHHh
Q 010056 127 VEVMRERVDFLHNLGLTIEDI-N-NY--PLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLR 184 (519)
Q Consensus 127 ~d~v~~~l~~L~~lGls~~~i-~-~~--P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~ 184 (519)
.+.+..+|+.|...|+-++.- + .+ -.+- .. ..-..-+..-|..-|++...|...+.
T Consensus 8 ~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~-~~-~~G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYIDDERYAESYVRSRLR-RK-GKGPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH-HT-T--HHHHHHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcc-cc-cccHHHHHHHHHHHCCChHHHHHHHH
Confidence 345666688888877765543 1 10 0010 00 01134566778888998888888877
No 48
>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=27.30 E-value=74 Score=28.20 Aligned_cols=18 Identities=11% Similarity=0.117 Sum_probs=10.7
Q ss_pred CcHHHHHHHHHhcCchhc
Q 010056 390 FFLQQVRQIVVECPQVLA 407 (519)
Q Consensus 390 ~s~e~I~~mv~r~P~lL~ 407 (519)
++.+++.+++..+|.++.
T Consensus 73 ls~~e~i~lm~~~P~LIK 90 (126)
T TIGR01616 73 IDEASALALMVSDPLLIR 90 (126)
T ss_pred CCHHHHHHHHHhCcCeEe
Confidence 455666666666666653
No 49
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=26.38 E-value=5.5e+02 Score=26.09 Aligned_cols=45 Identities=24% Similarity=0.392 Sum_probs=27.1
Q ss_pred ChHHHHHHHHHHHhCCCCccccc---cCCcccccccccc---hHHHHHHHh
Q 010056 126 TVEVMRERVDFLHNLGLTIEDIN---NYPLVLGCSVKKN---MIPVLDYLG 170 (519)
Q Consensus 126 ~~d~v~~~l~~L~~lGls~~~i~---~~P~lL~~s~~~~---l~p~l~~L~ 170 (519)
+++....+...+.+-|-+--||+ ..|..-..+.++. +.|+++.++
T Consensus 36 ~~~~a~~~a~~~~~~GAdIIDIGgeSTrPg~~~v~~eeE~~Rv~pvI~~l~ 86 (282)
T PRK11613 36 SLIDAVKHANLMINAGATIIDVGGESTRPGAAEVSVEEELDRVIPVVEAIA 86 (282)
T ss_pred CHHHHHHHHHHHHHCCCcEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 56666666777777787777776 3454333344433 555666665
No 50
>PHA02591 hypothetical protein; Provisional
Probab=26.04 E-value=1.4e+02 Score=24.25 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=15.0
Q ss_pred cchhhHHHHHHHhCCChhHHHHH
Q 010056 232 GTMSTSVAYLVGIGVSRREIGGV 254 (519)
Q Consensus 232 ~~l~p~v~fL~~lGv~~~~I~~l 254 (519)
+.+.....-|.+.|++.++|+..
T Consensus 46 dd~~~vA~eL~eqGlSqeqIA~~ 68 (83)
T PHA02591 46 DDLISVTHELARKGFTVEKIASL 68 (83)
T ss_pred chHHHHHHHHHHcCCCHHHHHHH
Confidence 34555666677777777777665
No 51
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.85 E-value=2.4e+02 Score=22.56 Aligned_cols=46 Identities=11% Similarity=0.248 Sum_probs=21.7
Q ss_pred hHHHHHHHhCCChHHHHHHHHhCCcccccccccchhhhHHHHHhhhcCCccHHH
Q 010056 272 PFVEYLESLGIPRLAVARLIEKKPYILGFGLEERVKPNVESLLEFSVRKEALPV 325 (519)
Q Consensus 272 p~v~~L~~lG~~~~~i~~iI~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~l~~ 325 (519)
|.+..|++..++.+.|..++.... - +--..+..+.++|++++++..
T Consensus 3 PIia~LKehnvsd~qi~elFq~lT----~----NPl~AMa~i~qLGip~eKLQ~ 48 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQALT----Q----NPLAAMATIQQLGIPQEKLQQ 48 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHHh----h----CHHHHHHHHHHcCCCHHHHHH
Confidence 445555555566555554443211 1 111234445556666555443
No 52
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=25.76 E-value=1.8e+02 Score=25.40 Aligned_cols=27 Identities=15% Similarity=0.122 Sum_probs=12.7
Q ss_pred hHHHHHHHhhCCCChhHHHHHHhhcCc
Q 010056 162 MIPVLDYLGKLGVRKSTFTEFLRRYPQ 188 (519)
Q Consensus 162 l~p~l~~L~~lGls~~~i~~ll~~~P~ 188 (519)
+....+.|...|+.+.++..++.-+|.
T Consensus 57 i~~~~~~L~~~~L~k~E~~~i~Nl~P~ 83 (118)
T smart00657 57 VRAVRTLLKSKKLHKFEIAQLGNLRPE 83 (118)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCCC
Confidence 344444444445555555554444443
No 53
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.56 E-value=2.8e+02 Score=26.32 Aligned_cols=24 Identities=13% Similarity=0.221 Sum_probs=14.6
Q ss_pred hhHHHHHHHhCCChHHHHHHHHhC
Q 010056 271 KPFVEYLESLGIPRLAVARLIEKK 294 (519)
Q Consensus 271 ~p~v~~L~~lG~~~~~i~~iI~~~ 294 (519)
...++.|..+|+++.++.+++.+-
T Consensus 143 ~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 143 SEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhc
Confidence 445566666666666666666543
No 54
>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=24.81 E-value=3e+02 Score=23.69 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=17.3
Q ss_pred hHHHHh-HHHHHHhCCcHHHHHHHHHh
Q 010056 376 SAVTRH-VDFLKSCGFFLQQVRQIVVE 401 (519)
Q Consensus 376 ~~l~~k-v~fL~~lG~s~e~I~~mv~r 401 (519)
.+.+.| +.+|..-||+.+.|..++..
T Consensus 92 ~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 92 RKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 344444 78888999999999876653
No 55
>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=24.69 E-value=92 Score=22.40 Aligned_cols=24 Identities=21% Similarity=0.213 Sum_probs=17.2
Q ss_pred HHHHHHHhhCCCChhHHHHHHhhc
Q 010056 163 IPVLDYLGKLGVRKSTFTEFLRRY 186 (519)
Q Consensus 163 ~p~l~~L~~lGls~~~i~~ll~~~ 186 (519)
..+++-|.++|+++.++.+++..-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 456777888888888888877764
No 56
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=24.54 E-value=74 Score=28.40 Aligned_cols=35 Identities=23% Similarity=0.249 Sum_probs=19.6
Q ss_pred cCCcccccccccchHHHHHHHhhCCCChhHHHHHHh
Q 010056 149 NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLR 184 (519)
Q Consensus 149 ~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~ 184 (519)
+.|..|..++++ +..-+--|..-|++++||+-+++
T Consensus 21 ~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400|consen 21 SVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred CCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeee
Confidence 455555555543 45555555566666666665444
No 57
>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=24.51 E-value=5.5e+02 Score=29.78 Aligned_cols=87 Identities=15% Similarity=0.261 Sum_probs=48.1
Q ss_pred chHHHHHHHhh---CCCChhHHHHHHhhcCcccccccccchHHHHHHHHhc-CCCCCChhHHhhhCccccccccccchhh
Q 010056 161 NMIPVLDYLGK---LGVRKSTFTEFLRRYPQVLHSSVVVDLAPVVKYLQGL-DIKPNDIPRVLERYPEVLGFKLEGTMST 236 (519)
Q Consensus 161 ~l~p~l~~L~~---lGls~~~i~~ll~~~P~iL~~s~~~~l~p~v~fL~~l-G~s~~~I~~il~~~P~lL~~s~e~~l~p 236 (519)
+....+.||.+ -|+.+....+++..++.=... .|..--+-|.++ |++.+....+...+.. ......
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~----~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~ 145 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFD----VLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERR 145 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHH----HHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHH
Confidence 35677888875 578888888888766432221 222223344443 6666655555554321 112445
Q ss_pred HHHHHHHhCCChhHHHHHHhh
Q 010056 237 SVAYLVGIGVSRREIGGVLTR 257 (519)
Q Consensus 237 ~v~fL~~lGv~~~~I~~ll~~ 257 (519)
.+.||.++|++...+.++...
T Consensus 146 ~~~~L~~~gi~~~~a~ki~~~ 166 (720)
T TIGR01448 146 LLAGLQGLGIGIKLAQRIYKF 166 (720)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 556666677766666555433
No 58
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.29 E-value=1.2e+02 Score=28.75 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=22.7
Q ss_pred HHHHh-CCChhHHHHHHhhCcc-ccccccccchhhHHHHHHHh-CCChHHHHHHHH
Q 010056 240 YLVGI-GVSRREIGGVLTRYPD-ILGMRVGRVIKPFVEYLESL-GIPRLAVARLIE 292 (519)
Q Consensus 240 fL~~l-Gv~~~~I~~ll~~~P~-lL~~s~e~~l~p~v~~L~~l-G~~~~~i~~iI~ 292 (519)
.|..+ |+.++-..+++..+.. -+... -.....+.|.++ |+.++...+++.
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~---i~~~d~~~L~~v~Gig~k~A~~I~~ 126 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQA---IANGDVKALTKVPGIGKKTAERIVL 126 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHH---HHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 34444 6666666666654431 11000 011223445554 666665555543
No 59
>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=23.92 E-value=55 Score=25.25 Aligned_cols=44 Identities=23% Similarity=0.229 Sum_probs=25.3
Q ss_pred CCCccccc---cCCcccccccccchHHHHHHHhhCCCChhHHHHHHhh
Q 010056 141 GLTIEDIN---NYPLVLGCSVKKNMIPVLDYLGKLGVRKSTFTEFLRR 185 (519)
Q Consensus 141 Gls~~~i~---~~P~lL~~s~~~~l~p~l~~L~~lGls~~~i~~ll~~ 185 (519)
|.|....- ..|..+..+.++ +...+.-|..-|+++++|+-+|+-
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~~e-Ve~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 10 GISGSTRPYRRSPPSWLKYSPEE-VEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp --------S-SS--TT--S-HHH-HHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CccCCCCCCCCCCCCCcCCCHHH-HHHHHHHHHHcCCCHHHhhhhhhh
Confidence 44444432 467777777764 888888888999999999988764
No 60
>PRK14135 recX recombination regulator RecX; Provisional
Probab=23.86 E-value=7.1e+02 Score=24.54 Aligned_cols=59 Identities=12% Similarity=0.110 Sum_probs=29.8
Q ss_pred chhhHHHHHHHhC-CChhHHHHHHhhCccccccccccchhhHHHHHHHhCCChHHHHHHHHhC
Q 010056 233 TMSTSVAYLVGIG-VSRREIGGVLTRYPDILGMRVGRVIKPFVEYLESLGIPRLAVARLIEKK 294 (519)
Q Consensus 233 ~l~p~v~fL~~lG-v~~~~I~~ll~~~P~lL~~s~e~~l~p~v~~L~~lG~~~~~i~~iI~~~ 294 (519)
.+...++.|.+.| ++....+....+.= +... ...-.....-|..-|++.+.|..++...
T Consensus 90 ~Ie~vl~~l~~~~~ldD~~~a~~~~~~~--~~~~-~~g~~~I~~kL~~kGi~~~~Ie~~l~~l 149 (263)
T PRK14135 90 IISEVIDKLKEEKYIDDKEYAESYVRTN--INTG-DKGPRVIKQKLLQKGIEDEIIEEALSEY 149 (263)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHH--Hhcc-ccchHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 3445566777666 44444444433321 0000 0112233455667788888777777653
No 61
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=23.35 E-value=1.8e+02 Score=25.16 Aligned_cols=21 Identities=5% Similarity=0.183 Sum_probs=11.2
Q ss_pred CChhHHHHHHhhcCccccccc
Q 010056 174 VRKSTFTEFLRRYPQVLHSSV 194 (519)
Q Consensus 174 ls~~~i~~ll~~~P~iL~~s~ 194 (519)
++.+++..++..+|.++...+
T Consensus 72 ls~~e~~~ll~~~P~LikRPI 92 (113)
T cd03033 72 LDEEEALALMIADPLLIRRPL 92 (113)
T ss_pred CCHHHHHHHHHhCcceeeCCe
Confidence 344555555555555555443
No 62
>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=22.18 E-value=90 Score=33.14 Aligned_cols=38 Identities=18% Similarity=0.413 Sum_probs=23.6
Q ss_pred ChhHHhhhCccccccccccchhhHHHHHHHhCCChhHHHHHHhhCcccc
Q 010056 214 DIPRVLERYPEVLGFKLEGTMSTSVAYLVGIGVSRREIGGVLTRYPDIL 262 (519)
Q Consensus 214 ~I~~il~~~P~lL~~s~e~~l~p~v~fL~~lGv~~~~I~~ll~~~P~lL 262 (519)
+++.+|..||.+|- .+|+.+|-+.-++..+|..+|.-|
T Consensus 259 ~lR~~vq~NP~~L~-----------~lLqql~~~nP~l~q~I~~n~e~F 296 (378)
T TIGR00601 259 QLRQVVQQNPQLLP-----------PLLQQIGQENPQLLQQISQHPEQF 296 (378)
T ss_pred HHHHHHHHCHHHHH-----------HHHHHHHhhCHHHHHHHHHCHHHH
Confidence 45666777776653 346666666666666666666543
No 63
>PHA02653 RNA helicase NPH-II; Provisional
Probab=21.41 E-value=1.6e+02 Score=33.88 Aligned_cols=45 Identities=11% Similarity=0.271 Sum_probs=29.7
Q ss_pred hhHHHHHHhCCCCccccCCccCCCChHHHHHHHHHHHhCCCCcccc
Q 010056 102 AKVYDFLQGIGIVPDELDGLELPVTVEVMRERVDFLHNLGLTIEDI 147 (519)
Q Consensus 102 ~~vv~yL~~~Gi~~~~l~~l~~p~~~d~v~~~l~~L~~lGls~~~i 147 (519)
+.++-+|+.+|++..+.. +..|-+.+.+...++.|..+|..++++
T Consensus 528 ~~~vL~lk~~g~~~~~~~-~ldpP~~~~l~~A~~~L~~lga~~~~l 572 (675)
T PHA02653 528 HNYILYAKYFNLTLPEDL-FVIPSNLDRLRKTEEYIDSFNISIEKW 572 (675)
T ss_pred HHHHHHHHHcCCCCcccc-cCCCCCHHHHHHHHHHHHHcCCCchhh
Confidence 345667788998643322 334566677878888888888776643
No 64
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=20.76 E-value=5.6e+02 Score=24.11 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=18.0
Q ss_pred hHHHHh-HHHHHHhCCcHHHHHHHHHh
Q 010056 376 SAVTRH-VDFLKSCGFFLQQVRQIVVE 401 (519)
Q Consensus 376 ~~l~~k-v~fL~~lG~s~e~I~~mv~r 401 (519)
.+.+.| ..+|..-||+.+.|..++..
T Consensus 137 ~~~k~Ki~r~L~~rGFs~~~i~~~l~~ 163 (174)
T COG2137 137 KKEKAKIQRFLLRRGFSYEVIKEALNE 163 (174)
T ss_pred hhHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 345555 56777789999888776643
No 65
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=20.72 E-value=1.7e+02 Score=25.25 Aligned_cols=19 Identities=5% Similarity=0.141 Sum_probs=12.1
Q ss_pred CcHHHHHHHHHhcCchhcc
Q 010056 390 FFLQQVRQIVVECPQVLAL 408 (519)
Q Consensus 390 ~s~e~I~~mv~r~P~lL~~ 408 (519)
++.+++.+++..+|.++.-
T Consensus 72 ls~~e~~~ll~~~P~LikR 90 (113)
T cd03033 72 LDEEEALALMIADPLLIRR 90 (113)
T ss_pred CCHHHHHHHHHhCcceeeC
Confidence 4556666777777776643
No 66
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=20.67 E-value=6.7e+02 Score=23.29 Aligned_cols=21 Identities=14% Similarity=0.202 Sum_probs=13.0
Q ss_pred HHHHhHHHHHHhCCcHHHHHH
Q 010056 377 AVTRHVDFLKSCGFFLQQVRQ 397 (519)
Q Consensus 377 ~l~~kv~fL~~lG~s~e~I~~ 397 (519)
..+.-++-|.+.|++.+.+.+
T Consensus 157 ~~~~~~~~L~~~Gvdv~~l~~ 177 (179)
T PF06757_consen 157 EFQRLLNELRENGVDVDYLLE 177 (179)
T ss_pred HHHHHHHHHHHcCCCHHHHHH
Confidence 445556666677777666643
Done!