Query 039791
Match_columns 552
No_of_seqs 287 out of 1197
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 13:14:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039791hhsearch_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 3.7E-63 8E-68 532.6 28.1 372 99-546 68-449 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 2.4E-50 5.2E-55 420.9 12.4 338 133-534 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 3.1E-45 6.7E-50 393.9 24.8 371 32-504 59-440 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 3E-36 6.6E-41 314.6 7.2 323 99-494 2-339 (345)
5 KOG1267 Mitochondrial transcri 100.0 1.1E-27 2.4E-32 255.4 18.9 327 80-512 78-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 8.6E-19 1.9E-23 187.2 14.6 247 231-514 89-341 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00033 7.1E-09 45.4 2.5 30 450-480 2-31 (31)
8 smart00733 Mterf Mitochondrial 96.7 0.0011 2.4E-08 42.8 1.9 28 289-317 3-30 (31)
9 PF11955 PORR: Plant organelle 92.6 0.45 9.7E-06 49.5 8.2 245 241-514 45-331 (335)
10 cd04790 HTH_Cfa-like_unk Helix 90.3 3.5 7.6E-05 38.6 11.0 51 99-152 19-71 (172)
11 cd04790 HTH_Cfa-like_unk Helix 70.1 26 0.00055 32.8 8.4 112 235-357 49-167 (172)
12 TIGR00601 rad23 UV excision re 66.6 57 0.0012 34.6 11.0 110 232-360 155-291 (378)
13 PF04695 Pex14_N: Peroxisomal 66.1 6.4 0.00014 35.4 3.3 42 288-333 10-51 (136)
14 COG1125 OpuBA ABC-type proline 60.7 15 0.00032 36.8 4.9 64 429-492 71-137 (309)
15 KOG2561 Adaptor protein NUB1, 55.3 60 0.0013 34.8 8.5 43 399-445 429-471 (568)
16 cd08306 Death_FADD Fas-associa 47.9 78 0.0017 25.9 6.6 38 239-280 19-57 (86)
17 PF14490 HHH_4: Helix-hairpin- 47.0 40 0.00087 28.0 4.9 25 233-257 8-32 (94)
18 PF06757 Ins_allergen_rp: Inse 47.0 1.3E+02 0.0028 28.2 8.9 62 245-322 15-76 (179)
19 PF04695 Pex14_N: Peroxisomal 46.6 29 0.00063 31.1 4.2 40 253-296 11-50 (136)
20 PF00627 UBA: UBA/TS-N domain; 44.6 30 0.00066 23.3 3.1 23 433-455 4-26 (37)
21 PF02631 RecX: RecX family; I 44.4 1.5E+02 0.0032 25.6 8.3 58 125-186 8-67 (121)
22 PRK09875 putative hydrolase; P 43.1 2.4E+02 0.0051 28.9 10.7 35 152-190 153-188 (292)
23 PRK13752 putative transcriptio 42.7 64 0.0014 29.2 5.9 51 99-150 25-75 (144)
24 cd00194 UBA Ubiquitin Associat 40.5 39 0.00084 22.6 3.1 23 433-455 3-25 (38)
25 smart00165 UBA Ubiquitin assoc 40.3 39 0.00085 22.5 3.1 23 433-455 3-25 (37)
26 PF02787 CPSase_L_D3: Carbamoy 38.6 88 0.0019 27.6 5.9 72 162-256 12-84 (123)
27 PHA02591 hypothetical protein; 37.8 80 0.0017 25.4 4.8 29 121-149 41-69 (83)
28 COG2137 OraA Uncharacterized p 36.6 2.6E+02 0.0056 26.3 9.0 19 310-328 145-163 (174)
29 cd04785 HTH_CadR-PbrR-like Hel 35.9 96 0.0021 27.2 5.8 50 100-150 19-68 (126)
30 cd04777 HTH_MerR-like_sg1 Heli 34.8 47 0.001 28.2 3.5 48 99-150 18-66 (107)
31 cd04784 HTH_CadR-PbrR Helix-Tu 34.5 1.1E+02 0.0024 26.8 5.9 49 99-150 18-68 (127)
32 PRK10227 DNA-binding transcrip 34.0 1.1E+02 0.0024 27.4 5.9 52 99-151 18-69 (135)
33 PRK14136 recX recombination re 33.9 5.4E+02 0.012 26.5 11.7 56 126-186 194-250 (309)
34 PF08004 DUF1699: Protein of u 33.6 1.4E+02 0.003 26.4 6.1 20 175-194 27-46 (131)
35 cd01108 HTH_CueR Helix-Turn-He 32.2 1.2E+02 0.0026 26.6 5.8 49 99-150 18-68 (127)
36 PF02022 Integrase_Zn: Integra 31.7 69 0.0015 22.4 3.2 29 430-458 7-36 (40)
37 cd04783 HTH_MerR1 Helix-Turn-H 31.4 1.3E+02 0.0027 26.4 5.8 50 99-151 18-69 (126)
38 PF02631 RecX: RecX family; I 31.4 1.3E+02 0.0029 25.9 6.0 24 305-328 95-118 (121)
39 KOG0011 Nucleotide excision re 31.4 2E+02 0.0043 29.8 7.7 108 235-360 137-259 (340)
40 PF10098 DUF2336: Uncharacteri 30.8 2.7E+02 0.0058 27.6 8.8 151 22-185 93-258 (262)
41 TIGR02047 CadR-PbrR Cd(II)/Pb( 29.9 1.4E+02 0.003 26.3 5.8 49 99-150 18-68 (127)
42 PRK11613 folP dihydropteroate 29.7 1.1E+02 0.0024 31.0 5.8 69 465-541 164-232 (282)
43 cd04770 HTH_HMRTR Helix-Turn-H 29.3 1.5E+02 0.0032 25.7 5.9 51 99-152 18-70 (123)
44 TIGR02044 CueR Cu(I)-responsiv 29.1 1.5E+02 0.0033 26.0 5.9 50 99-150 18-68 (127)
45 PF07499 RuvA_C: RuvA, C-termi 29.0 88 0.0019 22.4 3.6 27 431-457 3-29 (47)
46 PHA02591 hypothetical protein; 28.9 1E+02 0.0022 24.8 4.1 45 245-290 24-69 (83)
47 PF02022 Integrase_Zn: Integra 28.3 34 0.00074 23.9 1.2 25 40-64 12-36 (40)
48 TIGR02043 ZntR Zn(II)-responsi 28.0 1.5E+02 0.0033 26.2 5.8 50 99-150 19-69 (131)
49 PF07499 RuvA_C: RuvA, C-termi 27.8 73 0.0016 22.8 3.0 27 163-190 3-29 (47)
50 PF14698 ASL_C2: Argininosucci 27.6 56 0.0012 25.7 2.5 23 37-60 5-27 (70)
51 KOG3207 Beta-tubulin folding c 26.5 1.3E+02 0.0028 32.6 5.6 137 133-304 83-232 (505)
52 cd08785 CARD_CARD9-like Caspas 26.4 2E+02 0.0043 23.7 5.6 50 39-105 21-75 (86)
53 TIGR01448 recD_rel helicase, p 26.3 1.5E+02 0.0032 34.5 6.7 28 162-189 76-105 (720)
54 cd04788 HTH_NolA-AlbR Helix-Tu 25.4 1.4E+02 0.003 24.8 4.7 52 99-152 18-70 (96)
55 PHA01351 putative minor struct 25.3 4.7E+02 0.01 30.0 9.7 105 131-257 694-803 (1070)
56 cd04769 HTH_MerR2 Helix-Turn-H 25.2 2.1E+02 0.0046 24.6 6.1 50 99-151 18-68 (116)
57 PF13413 HTH_25: Helix-turn-he 24.7 1.3E+02 0.0029 22.9 4.1 28 44-71 6-33 (62)
58 TIGR02051 MerR Hg(II)-responsi 24.6 2.1E+02 0.0046 24.9 6.0 51 99-151 17-68 (124)
59 PRK00117 recX recombination re 24.3 5.3E+02 0.011 23.2 12.5 59 127-189 44-103 (157)
60 PF11212 DUF2999: Protein of u 23.9 2.8E+02 0.0061 22.0 5.6 55 235-297 3-60 (82)
61 PRK14134 recX recombination re 23.2 7.9E+02 0.017 24.9 14.1 172 126-328 93-278 (283)
62 PF14490 HHH_4: Helix-hairpin- 23.0 1.9E+02 0.004 23.9 5.1 59 267-350 6-68 (94)
63 cd04787 HTH_HMRTR_unk Helix-Tu 23.0 1.4E+02 0.003 26.5 4.5 51 99-151 18-69 (133)
64 cd04768 HTH_BmrR-like Helix-Tu 22.9 1.5E+02 0.0033 24.6 4.5 50 99-151 18-69 (96)
65 COG1125 OpuBA ABC-type proline 22.6 2.5E+02 0.0054 28.4 6.4 64 128-194 73-138 (309)
66 PF03960 ArsC: ArsC family; I 22.3 1.3E+02 0.0029 25.5 4.2 21 280-300 70-90 (110)
67 KOG0995 Centromere-associated 21.8 2.5E+02 0.0055 31.2 6.9 112 104-242 51-169 (581)
68 cd04786 HTH_MerR-like_sg7 Heli 21.7 2.3E+02 0.0051 25.1 5.7 50 99-151 18-69 (131)
69 KOG1411 Aspartate aminotransfe 21.6 1.4E+02 0.0029 31.3 4.5 120 134-262 271-397 (427)
70 cd04782 HTH_BltR Helix-Turn-He 21.4 1.7E+02 0.0038 24.3 4.6 51 99-151 18-69 (97)
71 cd04781 HTH_MerR-like_sg6 Heli 21.0 1.8E+02 0.0038 25.3 4.7 52 99-152 18-69 (120)
72 cd04780 HTH_MerR-like_sg5 Heli 20.2 3.1E+02 0.0068 22.7 5.9 67 99-172 18-85 (95)
73 PRK13344 spxA transcriptional 20.1 94 0.002 27.6 2.8 21 175-195 73-93 (132)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=3.7e-63 Score=532.62 Aligned_cols=372 Identities=21% Similarity=0.337 Sum_probs=342.5
Q ss_pred HHHHhcCCCccccccc-CCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhhccccccChh-hHHHHHHHHHhhcCC
Q 039791 99 FFFESIGIDHAEVSCF-LPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEEVSIFSQSSQ-DLTAKLSRLKNYYGF 176 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~-~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~-~l~~~l~~L~~l~G~ 176 (552)
.|++++|+++.++..+ +|.++ +.++++++||+++|++.++|+ ++|.+++++++ .+.|+++||+++ |+
T Consensus 68 ~~L~~lgi~~~~l~~~~~p~~~------~~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~l-G~ 136 (487)
T PLN03196 68 DFLRGIGIDPDELDGLELPSTV------DVMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKL-GV 136 (487)
T ss_pred HHHHHcCCCchhhhccCCCccH------HHHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHc-CC
Confidence 6899999999999887 67544 799999999999999999997 57999999998 499999999999 99
Q ss_pred ChhHHhhHhhcCccccccccccccccHHHHHHHHhhhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHHhh
Q 039791 177 SNVILVGICLGFPHVLAGNGDEWGTEIATLFDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELMGR 256 (552)
Q Consensus 177 s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li~~ 256 (552)
+++++.++|.++|++|.. +++.++.|+++|| +++|+++++|++++.+
T Consensus 137 s~~~i~~lI~~~P~lL~~---sve~~L~P~v~fL------------------------------~~lGvs~~~i~~~l~r 183 (487)
T PLN03196 137 TRSSLPELLRRYPQVLHA---SVVVDLAPVVKYL------------------------------QGLDVKRQDIPRVLER 183 (487)
T ss_pred CHHHHHHHHHhCCceecc---cHHHHHHHHHHHH------------------------------HHcCCCHHHHHHHHHh
Confidence 999999999999999999 7777777766655 4789999999999999
Q ss_pred CCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCcccccc
Q 039791 257 NKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVLGRN 336 (552)
Q Consensus 257 ~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~ 336 (552)
+|++|++++++++.++++||.++|++.++|++++.++|+||+++++++++|+++||.++|++.++|++++.++|++|+++
T Consensus 184 ~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~s 263 (487)
T PLN03196 184 YPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFD 263 (487)
T ss_pred CchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred ---cccchHHHHHhCCc-hHHHHHHHHcccccccccccccCChhhhhHhhccchhhhhccCCCchhHHHHHHHHH-hcCc
Q 039791 337 ---KMANLPYVIRAVDL-QDWFFNKITNGYYKLLGNYALSNPDEDLDREFGDSLEKLLSSSRTPRHTMNKLTFLH-GIGY 411 (552)
Q Consensus 337 ---~lk~~~~~L~~lGv-~~~l~~iI~~~~~~l~~~~l~~~P~~l~~~~~g~~v~~~~~~s~~~~~~~~k~~fl~-~lG~ 411 (552)
.+++.+.+|.++|+ ++.+..+|.. +|.++. .+ ..+++..++.|+. ++|+
T Consensus 264 le~~lkp~v~~L~elGv~~~~i~~lI~~------------~P~iL~-----~s---------~e~kl~~~~~fL~~~lG~ 317 (487)
T PLN03196 264 LEETVKPNVECLLEFGVRKEALPSVIAQ------------YPDILG-----LD---------LKAKLAEQQYWLTSKLKI 317 (487)
T ss_pred HHHhHHHHHHHHHHcCCCHHHHHHHHHh------------CCceeE-----ec---------HHHhhhHHHHHHHHhhCC
Confidence 47788999999999 8999999999 998772 11 2457888899985 7999
Q ss_pred cCCchh--H-HHHHHHhcChhhHHHHHHHHHHcCCchHHHHHHHhhcCcccccChhhHHHHHHHHHHhhCCChHHHhhcC
Q 039791 412 GENTLT--L-KVLAKAHGTGSELQERFDCLLRNGVAFSKLCMMIRLTPKILNQNPETIEQKLDFLCQDLGSSLDYLYAFP 488 (552)
Q Consensus 412 ~~~~~~--~-~al~~l~~~~~~L~~r~~~L~~~G~s~~~v~~mi~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~l~~~P 488 (552)
++++.. + +.+.++..+++++++|++||+++||+.++|+.||+++|++|++|.++|++|++||+++||++.++|++||
T Consensus 318 s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP 397 (487)
T PLN03196 318 DPEDFGRVIEKLPQIVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFP 397 (487)
T ss_pred CHHHHHHHHHhcchhhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhCh
Confidence 998854 3 6667778889999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCcchhHHHHHHHHHHCCCCCCccccccccccchhHHHHHhcccCCCchHh
Q 039791 489 TFLCFDLEYRIKPRYKFHMWLVENGLCTKNYSIASMVATSEKSFISRIYGIHPAAPKQ 546 (552)
Q Consensus 489 ~~L~ysle~rikpR~~~~~~L~~~G~~~~~~sl~~il~~sd~~F~~~~~~~~p~~~~~ 546 (552)
+||+||+|+||+|||++ |+++|+ +++++++|+|||++|+++|+..|.|+.+.
T Consensus 398 ~~LsySLEkRI~PR~~~---L~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~~~~ 449 (487)
T PLN03196 398 AYFTYGLESRIKPRYER---VAKKGI---KCSLAWFLNCSDDKFEQRMSGDFIEGEEM 449 (487)
T ss_pred HHhccChhhhhHHHHHH---HHHcCC---CCCHHHHhccCHHHHHHHHhhhccccccc
Confidence 99999999999999994 889998 68999999999999999999999886543
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=2.4e-50 Score=420.90 Aligned_cols=338 Identities=23% Similarity=0.354 Sum_probs=243.9
Q ss_pred HHHHhCCCChhhHHHHHhhhccccccChhh-HHHHHHHHHhhcCCChhHHhhHhhcCccccccccccccccHHHHHHHHh
Q 039791 133 CALSSFGFPWDKLGKLYKEEVSIFSQSSQD-LTAKLSRLKNYYGFSNVILVGICLGFPHVLAGNGDEWGTEIATLFDDLK 211 (552)
Q Consensus 133 ~~L~~~G~~~~~i~~~~~~~P~ll~~~~~~-l~~~l~~L~~l~G~s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~ 211 (552)
++|+++|++..+|.++++++|.++.+++++ +.|+++||.+. |++..++.+++.++|++|.. ++..++.|++++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~-G~s~~~i~~il~~~P~il~~---s~~~~i~p~~~~L~ 77 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSL-GFSSSDIAKILSKNPQILSR---SLEKNIIPVFDFLK 77 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHT-T--HHHHHHHHHH-GGGGGS-----HHHHHHHHHHHT
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHC-CCCHHHHHHHHHhChHHHhc---cchhhHHHHHHHHH
Confidence 467888888888888888888888888874 88888888888 88888888888888888888 65666666655544
Q ss_pred hhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHh
Q 039791 212 TVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLL 291 (552)
Q Consensus 212 ~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~ 291 (552)
++|.+++++.+++.++|++|..+.++++.+.++||+++|++.+.+.+++.
T Consensus 78 ------------------------------~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~ 127 (345)
T PF02536_consen 78 ------------------------------SIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLI 127 (345)
T ss_dssp ------------------------------TTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred ------------------------------HHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHH
Confidence 67888888888888888888887777888888888888888887778888
Q ss_pred hCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCcccccc---cccchHHHHHhCCc-hHHHHHHHHcccccccc
Q 039791 292 KSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVLGRN---KMANLPYVIRAVDL-QDWFFNKITNGYYKLLG 367 (552)
Q Consensus 292 ~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~---~lk~~~~~L~~lGv-~~~l~~iI~~~~~~l~~ 367 (552)
.+|.++... +++.+.++++.++|++++++.+++.++|+++..+ .+++.+.+|+++|+ ++++.+++..
T Consensus 128 ~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~------- 198 (345)
T PF02536_consen 128 SRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRK------- 198 (345)
T ss_dssp H-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHH-------
T ss_pred hcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhc-------
Confidence 787765544 6688888888888888888888888888766654 36677888888888 8888888888
Q ss_pred cccccCChhhhhHhhccchhhhhccCCCchhHHHHHHHHHhcCccCCchhH-HHHHHHhcChhhHHHHHHHHHHcCCchH
Q 039791 368 NYALSNPDEDLDREFGDSLEKLLSSSRTPRHTMNKLTFLHGIGYGENTLTL-KVLAKAHGTGSELQERFDCLLRNGVAFS 446 (552)
Q Consensus 368 ~~l~~~P~~l~~~~~g~~v~~~~~~s~~~~~~~~k~~fl~~lG~~~~~~~~-~al~~l~~~~~~L~~r~~~L~~~G~s~~ 446 (552)
+|..+. .+.++..+.+..+.+.|...+...+ +.+.++..+.++++++++||.++||+.+
T Consensus 199 -----~P~~l~---------------~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ 258 (345)
T PF02536_consen 199 -----CPRLLS---------------LSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEE 258 (345)
T ss_dssp -----TTTGGG---------------CGCHC---------------------------THHHHHHHHHHHHHHTTT--HH
T ss_pred -----ccceec---------------ccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHH
Confidence 887762 2344444444555544444444323 6666666678999999999999999999
Q ss_pred HHHHHHhhcCcccccChhhHHHHHHHHHHhhCCChHHHhhcCcccccccCCcchhHHHHHHHHHHCCCCCCccccccccc
Q 039791 447 KLCMMIRLTPKILNQNPETIEQKLDFLCQDLGSSLDYLYAFPTFLCFDLEYRIKPRYKFHMWLVENGLCTKNYSIASMVA 526 (552)
Q Consensus 447 ~v~~mi~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~l~~~P~~L~ysle~rikpR~~~~~~L~~~G~~~~~~sl~~il~ 526 (552)
+|++|++++|+||++|.|++++|++||+++||++.++|+++|+||+||+|+||+|||+++++|+++|. ...+++++|++
T Consensus 259 ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~sl~~~l~ 337 (345)
T PF02536_consen 259 EIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPSLSSMLS 337 (345)
T ss_dssp HHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGGS-HHHH
T ss_pred HHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCCHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999997 67899999999
Q ss_pred cchhHHHH
Q 039791 527 TSEKSFIS 534 (552)
Q Consensus 527 ~sd~~F~~ 534 (552)
+||++|++
T Consensus 338 ~s~~~F~~ 345 (345)
T PF02536_consen 338 CSDEEFLK 345 (345)
T ss_dssp HHHHHHT-
T ss_pred ccHHHhcC
Confidence 99999975
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=3.1e-45 Score=393.94 Aligned_cols=371 Identities=17% Similarity=0.243 Sum_probs=320.3
Q ss_pred HHHHHHHHHHHHHhcCCCChhhHHHHhhcChHHHHHHHHhcCCCCChhhHHHHHHHHHhhcCcchhHHHHHhcCCCcccc
Q 039791 32 IKEAQQAVTEYLHYTKSIPFTYAEHISKHSLNTLSKLIADLGVSYSAPSFSSTFQRFLRYHPINEFEFFFESIGIDHAEV 111 (552)
Q Consensus 32 ~~~a~~~~~~yL~~~~gl~~~~A~~is~~sp~~~~~ll~~~~~~~~~~~~~~~~~r~l~~~pi~~~e~f~eslGl~~~~~ 111 (552)
+.+.++.+.+||. .-|+....++..- -|..++.+-+ -..||+|+|++++++
T Consensus 59 ~~~~~~~~~~~L~-~lgi~~~~l~~~~--~p~~~~~~~~--------------------------~l~~L~s~G~~~~~i 109 (487)
T PLN03196 59 KLVNREKVLDFLR-GIGIDPDELDGLE--LPSTVDVMRE--------------------------RVEFLHKLGLTIEDI 109 (487)
T ss_pred hhhhHHHHHHHHH-HcCCCchhhhccC--CCccHHHHHH--------------------------HHHHHHHcCCChHHh
Confidence 5667788999999 6999987765422 2322221111 115899999999998
Q ss_pred cccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhhccccccChh-hHHHHHHHHHhhcCCChhHHhhHhhcCcc
Q 039791 112 SCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEEVSIFSQSSQ-DLTAKLSRLKNYYGFSNVILVGICLGFPH 190 (552)
Q Consensus 112 ~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~-~l~~~l~~L~~l~G~s~~~i~~lv~~~P~ 190 (552)
.. .|. ++..+.++++.|+++||.++|++..+|++++.++|.++.++++ .+.|+++||+++ |++++++.+++.++|+
T Consensus 110 ~~-~P~-iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~l-Gvs~~~i~~~l~r~P~ 186 (487)
T PLN03196 110 NE-YPL-VLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGL-DVKRQDIPRVLERYPE 186 (487)
T ss_pred cc-CcH-HhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHc-CCCHHHHHHHHHhCch
Confidence 85 576 6678889999999999999999999999999999999999998 599999999999 9999999999999999
Q ss_pred ccccccccccccHHHHHHHHhhhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHH
Q 039791 191 VLAGNGDEWGTEIATLFDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLV 270 (552)
Q Consensus 191 lL~~s~~~~~~~l~~~~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~ 270 (552)
+|+. +++..+.+. ++||.++|++.++|++++.++|++|.+++++++.
T Consensus 187 LL~~---~~e~~l~p~------------------------------v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~ 233 (487)
T PLN03196 187 LLGF---KLEGTMSTS------------------------------VAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIK 233 (487)
T ss_pred hhcC---CHHHHHHHH------------------------------HHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHH
Confidence 9999 666555554 5556689999999999999999999999999999
Q ss_pred HHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCcccccc---cccchHHHH-H
Q 039791 271 QKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVLGRN---KMANLPYVI-R 346 (552)
Q Consensus 271 ~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~---~lk~~~~~L-~ 346 (552)
|+++||.++|++.++|++++.++|++|+++++++++|+++||.++|++.+++..++.++|.+++.+ .+++...++ .
T Consensus 234 P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~ 313 (487)
T PLN03196 234 PKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTS 313 (487)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999986 355666777 5
Q ss_pred hCCc-hHHHHHHHHcccccccccccccCChhhhhHhhccchhhhhccCCCchhHHHHHHHHHhcCccCCchh--H-HHHH
Q 039791 347 AVDL-QDWFFNKITNGYYKLLGNYALSNPDEDLDREFGDSLEKLLSSSRTPRHTMNKLTFLHGIGYGENTLT--L-KVLA 422 (552)
Q Consensus 347 ~lGv-~~~l~~iI~~~~~~l~~~~l~~~P~~l~~~~~g~~v~~~~~~s~~~~~~~~k~~fl~~lG~~~~~~~--~-~al~ 422 (552)
.+|+ .+++..++.+ .|+++ +.+.+++.+|++|++++||++++.. + +.|.
T Consensus 314 ~lG~s~e~i~~~v~k------------~P~il---------------~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~ 366 (487)
T PLN03196 314 KLKIDPEDFGRVIEK------------LPQIV---------------SLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQ 366 (487)
T ss_pred hhCCCHHHHHHHHHh------------cchhh---------------cccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCc
Confidence 8999 8899999988 89876 3467899999999999999998864 3 8888
Q ss_pred HHhcChhhHHHHHHHHH-HcCCchHHHHHHHhhcCcccccChh-hHHHHHHHHHHhhCCChHHHhhcCcccccccCCcch
Q 039791 423 KAHGTGSELQERFDCLL-RNGVAFSKLCMMIRLTPKILNQNPE-TIEQKLDFLCQDLGSSLDYLYAFPTFLCFDLEYRIK 500 (552)
Q Consensus 423 ~l~~~~~~L~~r~~~L~-~~G~s~~~v~~mi~~~P~iL~~s~e-~l~~k~~fL~~~mg~~~~~l~~~P~~L~ysle~rik 500 (552)
++..+.++|+++++||+ ++|++.++ |.++|++|+||.| +|+||+++|.++ |+.. .-..+|.+| |+++.
T Consensus 367 lL~~S~~~l~~k~dFlvneMg~~~~~----Iv~fP~~LsySLEkRI~PR~~~L~~k-Gl~~----sL~~~L~~s-d~~F~ 436 (487)
T PLN03196 367 ILALNLEIMKPSLEFFKKEMKRPLKE----LVEFPAYFTYGLESRIKPRYERVAKK-GIKC----SLAWFLNCS-DDKFE 436 (487)
T ss_pred eeeccHHHHHHHHHHHHHHhCCCHHH----HHhChHHhccChhhhhHHHHHHHHHc-CCCC----CHHHHhccC-HHHHH
Confidence 88999999999999999 89999876 5799999999999 999999999875 8732 234567777 55888
Q ss_pred hHHH
Q 039791 501 PRYK 504 (552)
Q Consensus 501 pR~~ 504 (552)
.||.
T Consensus 437 ~r~v 440 (487)
T PLN03196 437 QRMS 440 (487)
T ss_pred HHHh
Confidence 8876
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=3e-36 Score=314.62 Aligned_cols=323 Identities=19% Similarity=0.332 Sum_probs=229.7
Q ss_pred HHHHhcCCCccccccc---CCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhhccccccChh-hHHHHHHHHHhhc
Q 039791 99 FFFESIGIDHAEVSCF---LPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEEVSIFSQSSQ-DLTAKLSRLKNYY 174 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~---~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~-~l~~~l~~L~~l~ 174 (552)
.+|++.|.+++.+..+ .|. ++..+.++.+.|.++||++.|++..++++++.++|.++..+.+ .+.|.+++|+++
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~-~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~- 79 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPR-LLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSI- 79 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-H-HHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTT-
T ss_pred hHHHHcCCCHHHHHHHHHhCCc-eEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHH-
Confidence 4566666666666555 465 5567889999999999999999999999999999999999965 699999999999
Q ss_pred CCChhHHhhHhhcCccccccccccccccHHHHHHHHhhhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHH
Q 039791 175 GFSNVILVGICLGFPHVLAGNGDEWGTEIATLFDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELM 254 (552)
Q Consensus 175 G~s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li 254 (552)
|.+++++.+++.++|++|.. +.+.++. +++++|.++|++.+.+..++
T Consensus 80 ~~s~~d~~~~l~r~p~~l~~---~~~~~l~------------------------------~~v~~L~~lGv~~~~~~~~l 126 (345)
T PF02536_consen 80 GLSDEDIVKVLKRYPRILSF---SVEENLS------------------------------PNVAFLRSLGVPPSQIISLL 126 (345)
T ss_dssp SS-HHHHHHHHHH-SHHHHS------HHHH------------------------------HHHHHHHHTT--HHHHHHHH
T ss_pred cCCHHHHHHHHHhcchhhcc---chHhhhh------------------------------hhhhHHhhcCCcHHHHHHHH
Confidence 99999999999999999998 4443444 45667778999999899999
Q ss_pred hhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCcccc
Q 039791 255 GRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVLG 334 (552)
Q Consensus 255 ~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~ 334 (552)
...|.++... +++.+.++++.++|++.+++++++.++|+++..+.+++++|+++||+++|++.+++.+++.++|.+++
T Consensus 127 ~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~ 204 (345)
T PF02536_consen 127 ISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLS 204 (345)
T ss_dssp HH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGG
T ss_pred HhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceec
Confidence 9998877655 89999999999999999999999999999888888999999999999999999999999999999999
Q ss_pred ccc---ccchHHHHHhCCchHHHHHHHHcccccccccccccCChhhhhHhhccchhhhhccCCCchhHHHHHHHHHhcCc
Q 039791 335 RNK---MANLPYVIRAVDLQDWFFNKITNGYYKLLGNYALSNPDEDLDREFGDSLEKLLSSSRTPRHTMNKLTFLHGIGY 411 (552)
Q Consensus 335 ~~~---lk~~~~~L~~lGv~~~l~~iI~~~~~~l~~~~l~~~P~~l~~~~~g~~v~~~~~~s~~~~~~~~k~~fl~~lG~ 411 (552)
.+. ++....++...|..+. .++.. +|.++. .+.+++..++++|+++||
T Consensus 205 ~s~~~~l~~~~~l~~~~~~~~~--~~i~~------------~p~il~---------------~~~~~l~~~i~~L~~lG~ 255 (345)
T PF02536_consen 205 LSVEKILEPVLYLLSSGGVEEE--RVIKK------------FPQILS---------------LSEEKLKPKIEFLQSLGF 255 (345)
T ss_dssp CGCHC-----------------------------------------T---------------HHHHHHHHHHHHHHTTT-
T ss_pred cccccccccccccccccccccc--ccccc------------cccccc---------------cchHhHHHHHHHHHHhcC
Confidence 974 3445555555555333 66666 887762 256789999999999999
Q ss_pred cCCchh-H--HHHHHHhcChhhHHHHHHHHH-HcCCchHHHHHHHhhcCcccccChh-hHHHH---HHHHHHhhCCChHH
Q 039791 412 GENTLT-L--KVLAKAHGTGSELQERFDCLL-RNGVAFSKLCMMIRLTPKILNQNPE-TIEQK---LDFLCQDLGSSLDY 483 (552)
Q Consensus 412 ~~~~~~-~--~al~~l~~~~~~L~~r~~~L~-~~G~s~~~v~~mi~~~P~iL~~s~e-~l~~k---~~fL~~~mg~~~~~ 483 (552)
++++.. | +.|.++..+.++++++++||. ++|++.++| .++|++|+||.| +|+|| +++|.+ .|. ..
T Consensus 256 s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~ri~PR~~~~~~l~~-~g~--~~ 328 (345)
T PF02536_consen 256 SEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKRIKPRYEVLKVLKS-KGL--II 328 (345)
T ss_dssp -HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHHHHHHHHHHHTT---TTT--GG
T ss_pred cHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhhhhhHHHHHHHHHH-CcC--CC
Confidence 998754 4 778888889888999999999 899999875 699999999998 89999 666655 363 22
Q ss_pred HhhcCcccccc
Q 039791 484 LYAFPTFLCFD 494 (552)
Q Consensus 484 l~~~P~~L~ys 494 (552)
......+|++|
T Consensus 329 ~~sl~~~l~~s 339 (345)
T PF02536_consen 329 NPSLSSMLSCS 339 (345)
T ss_dssp GGGS-HHHHHH
T ss_pred CCCHHHHhhcc
Confidence 33334444444
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.95 E-value=1.1e-27 Score=255.44 Aligned_cols=327 Identities=21% Similarity=0.323 Sum_probs=268.3
Q ss_pred hHHHHHHHHHhhcCcchhHHHHHhcCCCccccccc---CCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhhcccc
Q 039791 80 SFSSTFQRFLRYHPINEFEFFFESIGIDHAEVSCF---LPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEEVSIF 156 (552)
Q Consensus 80 ~~~~~~~r~l~~~pi~~~e~f~eslGl~~~~~~~~---~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll 156 (552)
.+.+.+......+|.+.++ +|+|+|+++++++++ .|+ ++..+.++.+.+...+|++.|++...++++++.-|.++
T Consensus 78 ~~~~~~~~~~~~~p~s~~~-~l~s~g~~~~~i~s~i~~~p~-ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il 155 (413)
T KOG1267|consen 78 KLSREVSSEDSVNPSSVLS-SLRSLGFTDSQISSIILSSPK-LLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKIL 155 (413)
T ss_pred HHHHHHHhhhccCcHHHHH-HHHhcCCchhhcccccccCch-hhhccchhhhhhhhhhhhccCccccccchhhhccHHHH
Confidence 3444555566678888887 899999999999988 444 66788888999999999999999999999998888888
Q ss_pred ccChh-hHHHHHHHHHhhcC--CChhHHhhHhhcCccccccccccccccHHHHHHHHhhhhhcccccccccCCccchhhH
Q 039791 157 SQSSQ-DLTAKLSRLKNYYG--FSNVILVGICLGFPHVLAGNGDEWGTEIATLFDDLKTVFVDFGLMSSVEGNVEVWYDI 233 (552)
Q Consensus 157 ~~~~~-~l~~~l~~L~~l~G--~s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~~l~~~~~~~~l~~~~~~s~~~~ 233 (552)
+..-+ .+...++++.+. + +....+.+++...|..... |..+
T Consensus 156 ~~~~~~~~~~~~~~l~~~-~~~~~~s~~~~~~~~~~~~~~~-----------------------------------~~~v 199 (413)
T KOG1267|consen 156 LKSKGESLSTFIEFLKSI-PPELLSSVVERLLTPVPSFLLN-----------------------------------ENSV 199 (413)
T ss_pred HhhcCCchhhHHHHhhcc-chhhhhhHHHHhcccccccccc-----------------------------------cccc
Confidence 87776 588999999988 5 6666666666666533322 1122
Q ss_pred hHHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHh
Q 039791 234 CRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLN 313 (552)
Q Consensus 234 ~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~ 313 (552)
. .++++.++|....++...+..+|+.+.... .+...+.++..+|+.+.. +++...|.+++++.+++++|++++|+
T Consensus 200 ~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~ 274 (413)
T KOG1267|consen 200 E-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLK 274 (413)
T ss_pred c-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHH
Confidence 2 566778999999999999999999998664 788999999999988776 89999999999999999999999999
Q ss_pred hcCCCHHHHHHHHHhCCcccccccccchHHHHHhCCchHHHHHHHHcccccccccccccCChhhhhHhhccchhhhhccC
Q 039791 314 HLGLSAKELKSVSEMYPYVLGRNKMANLPYVIRAVDLQDWFFNKITNGYYKLLGNYALSNPDEDLDREFGDSLEKLLSSS 393 (552)
Q Consensus 314 ~lG~s~~~i~~~l~~~P~iL~~~~lk~~~~~L~~lGv~~~l~~iI~~~~~~l~~~~l~~~P~~l~~~~~g~~v~~~~~~s 393 (552)
++|++.+||.+++.++|++|+.+.-+.
T Consensus 275 ~~Gf~~~di~~~~~k~P~~l~~s~~~~----------------------------------------------------- 301 (413)
T KOG1267|consen 275 SLGFSREEIWKMVKKCPQILGYSVKKN----------------------------------------------------- 301 (413)
T ss_pred HcCCCHHHHHHHHHhCchheEeehhhh-----------------------------------------------------
Confidence 999999999999999999999873111
Q ss_pred CCchhHHHHHHHHHhcCccCCchhHHHHHHHhcChhhHHHHHHHHHHcCCchHHHHHHHhhcCcccccChh-hHHHHHHH
Q 039791 394 RTPRHTMNKLTFLHGIGYGENTLTLKVLAKAHGTGSELQERFDCLLRNGVAFSKLCMMIRLTPKILNQNPE-TIEQKLDF 472 (552)
Q Consensus 394 ~~~~~~~~k~~fl~~lG~~~~~~~~~al~~l~~~~~~L~~r~~~L~~~G~s~~~v~~mi~~~P~iL~~s~e-~l~~k~~f 472 (552)
..+++++.+. .++ .++-+.++.+++.+++++++|+...|++..++..|++++|+++++|.+ .++++.+|
T Consensus 302 ------~~~~~~~~~~--~~~--~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~ 371 (413)
T KOG1267|consen 302 ------LKTTEYLLKN--PKH--ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEY 371 (413)
T ss_pred ------hHHHHHHHhc--chh--hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHH
Confidence 1112222221 111 114444556678999999999999999999999999999999999999 99999999
Q ss_pred HHHhhCCChHHHhhcCcccccccCCcchhHHHHHHHHHHC
Q 039791 473 LCQDLGSSLDYLYAFPTFLCFDLEYRIKPRYKFHMWLVEN 512 (552)
Q Consensus 473 L~~~mg~~~~~l~~~P~~L~ysle~rikpR~~~~~~L~~~ 512 (552)
+.+.|++|.+.++.+|+++.|++|+|+.||+.++.++..+
T Consensus 372 ~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 372 LLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred HHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 9999999999999999999999999999999987776654
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.79 E-value=8.6e-19 Score=187.17 Aligned_cols=247 Identities=15% Similarity=0.261 Sum_probs=208.2
Q ss_pred hhHhHHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHH
Q 039791 231 YDICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKG 310 (552)
Q Consensus 231 ~~~~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~ 310 (552)
.+...++++|++.|+++.+|.+++..+|.++..+.++.+.++..+|...|++..+++.++...|.+|+.+...++.+.++
T Consensus 89 ~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~ 168 (413)
T KOG1267|consen 89 VNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIE 168 (413)
T ss_pred cCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHH
Confidence 45567889999999999999999999999999999999999999999999999999999999999999888889999999
Q ss_pred HHhhcC--CCHHHHHHHHHhCCccccc-ccccchHHHHHhCCc-hHHHHHHHHcccccccccccccCChhhhhHhhccch
Q 039791 311 LLNHLG--LSAKELKSVSEMYPYVLGR-NKMANLPYVIRAVDL-QDWFFNKITNGYYKLLGNYALSNPDEDLDREFGDSL 386 (552)
Q Consensus 311 fL~~lG--~s~~~i~~~l~~~P~iL~~-~~lk~~~~~L~~lGv-~~~l~~iI~~~~~~l~~~~l~~~P~~l~~~~~g~~v 386 (552)
||++++ .....+.+.+...|..... ..+. .+.+++.+|+ +..+...+.. +|....
T Consensus 169 ~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~-~~~~~~~lg~~~~~L~~~l~~------------~~~~~~-------- 227 (413)
T KOG1267|consen 169 FLKSIPPELLSSVVERLLTPVPSFLLNENSVE-RLDIRRELGVKPRLLKSLLES------------QPRPVL-------- 227 (413)
T ss_pred HhhccchhhhhhHHHHhccccccccccccccc-cchhhHHhCCCHHHHHHHHhc------------Ccccee--------
Confidence 999975 6777777777777654443 2345 8899999999 8888877777 676552
Q ss_pred hhhhccCCCchhHHHHHHHHHhcCccCCchhH-HHHHHHhc-ChhhHHHHHHHHHHcCCchHHHHHHHhhcCcccccChh
Q 039791 387 EKLLSSSRTPRHTMNKLTFLHGIGYGENTLTL-KVLAKAHG-TGSELQERFDCLLRNGVAFSKLCMMIRLTPKILNQNPE 464 (552)
Q Consensus 387 ~~~~~~s~~~~~~~~k~~fl~~lG~~~~~~~~-~al~~l~~-~~~~L~~r~~~L~~~G~s~~~v~~mi~~~P~iL~~s~e 464 (552)
....+..++.++..+||++.+.++ +|+..+.+ +++++++++++|.+.||+.+||+.|++++|++|++|.+
T Consensus 228 --------~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~ 299 (413)
T KOG1267|consen 228 --------LYLKLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVK 299 (413)
T ss_pred --------eehhhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehh
Confidence 112678889999999999999877 88888876 58999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhCCChHHHhhcCcccccccCCcchhHHHHHHHHHHCCC
Q 039791 465 TIEQKLDFLCQDLGSSLDYLYAFPTFLCFDLEYRIKPRYKFHMWLVENGL 514 (552)
Q Consensus 465 ~l~~k~~fL~~~mg~~~~~l~~~P~~L~ysle~rikpR~~~~~~L~~~G~ 514 (552)
.+..+++|+.+. .+++.++|++++++.. .+.+|++ .+...|+
T Consensus 300 ~~~~~~~~~~~~----~~~~~k~p~~l~~s~~-~l~~~ie---~l~~~g~ 341 (413)
T KOG1267|consen 300 KNLKTTEYLLKN----PKHILKFPQLLRSSED-KLKPRIE---FLLSLGF 341 (413)
T ss_pred hhhHHHHHHHhc----chhhhhhhhhhhccch-hhhhhHH---HHHHcCC
Confidence 888888888876 3338888888866644 8888887 4556554
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=97.15 E-value=0.00033 Score=45.36 Aligned_cols=30 Identities=30% Similarity=0.580 Sum_probs=26.9
Q ss_pred HHHhhcCcccccChhhHHHHHHHHHHhhCCC
Q 039791 450 MMIRLTPKILNQNPETIEQKLDFLCQDLGSS 480 (552)
Q Consensus 450 ~mi~~~P~iL~~s~e~l~~k~~fL~~~mg~~ 480 (552)
.++.++|.+|+++.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 5789999999999779999999999 68874
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=96.66 E-value=0.0011 Score=42.81 Aligned_cols=28 Identities=32% Similarity=0.587 Sum_probs=15.0
Q ss_pred HHhhCCceecccccccHhhHHHHHhhcCC
Q 039791 289 LLLKSPEILSFDLETQVISVKGLLNHLGL 317 (552)
Q Consensus 289 il~~~P~iL~~s~e~~L~~~v~fL~~lG~ 317 (552)
++.++|++++++ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 445555555555 4555555555555554
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=92.62 E-value=0.45 Score=49.46 Aligned_cols=245 Identities=14% Similarity=0.103 Sum_probs=134.5
Q ss_pred hhCCCChhHHHHHHhhCCcceecCch-------hhHHHHHHHHH--hcCCChhHHHHHHhhCCceecccccccH-hhHHH
Q 039791 241 YDFRFEKGKLGELMGRNKSIFLDYPE-------EVLVQKVEYFC--RFGVGNEDVGLLLLKSPEILSFDLETQV-ISVKG 310 (552)
Q Consensus 241 ~~lG~~~~~i~~li~~~P~lL~~~~~-------~~l~~~v~fL~--~lG~~~~~i~~il~~~P~iL~~s~e~~L-~~~v~ 310 (552)
..+|++...+...+.+||.++..... =.+.+...-|. +..+-.+.-..++.+--.+|.++.++.| -.++.
T Consensus 45 ~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~ 124 (335)
T PF11955_consen 45 RQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIA 124 (335)
T ss_pred HhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHH
Confidence 46899778999999999999866431 01222222222 1111100011222222345666665554 35667
Q ss_pred HHh-hcCCCHHHHHHHHHhCCccccccc------ccchHHHHHhCCc---hHHHHHH--HHcccccccccccccCChhhh
Q 039791 311 LLN-HLGLSAKELKSVSEMYPYVLGRNK------MANLPYVIRAVDL---QDWFFNK--ITNGYYKLLGNYALSNPDEDL 378 (552)
Q Consensus 311 fL~-~lG~s~~~i~~~l~~~P~iL~~~~------lk~~~~~L~~lGv---~~~l~~i--I~~~~~~l~~~~l~~~P~~l~ 378 (552)
-++ ++|++.+-..+++.+||..|.... .-.++.|=.++.+ +.+...- ...+. -...-+. +|-
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~--~~~~~~~-Fp~--- 198 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKRED--GFDRPLA-FPV--- 198 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhcccccccc--ccCCcee-eee---
Confidence 776 499999999999999999988632 1113444444544 1111110 00000 0000000 110
Q ss_pred hHhhccchhhhhccCCCchhHHHHHHHHHhc----------CccCCchhH--HHHHHHhc------ChhhHHHHHHHHH-
Q 039791 379 DREFGDSLEKLLSSSRTPRHTMNKLTFLHGI----------GYGENTLTL--KVLAKAHG------TGSELQERFDCLL- 439 (552)
Q Consensus 379 ~~~~g~~v~~~~~~s~~~~~~~~k~~fl~~l----------G~~~~~~~~--~al~~l~~------~~~~L~~r~~~L~- 439 (552)
..--|.+ -.....++++-++++ |+++++..+ +|..+++- .+....+++..|+
T Consensus 199 ~fp~G~~---------l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ 269 (335)
T PF11955_consen 199 SFPKGFR---------LKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRK 269 (335)
T ss_pred cCCCCcc---------ccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHH
Confidence 0000111 224566677777665 445556666 77776543 2567788899999
Q ss_pred HcCCchHHHHHHHhhcCcccccChhhHHHHHHHHHHhhCCChHHH-hhcCcccccccCCcchhHHHHHHHHHHCCC
Q 039791 440 RNGVAFSKLCMMIRLTPKILNQNPETIEQKLDFLCQDLGSSLDYL-YAFPTFLCFDLEYRIKPRYKFHMWLVENGL 514 (552)
Q Consensus 440 ~~G~s~~~v~~mi~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~l-~~~P~~L~ysle~rikpR~~~~~~L~~~G~ 514 (552)
++|++ +.+..|+.+||.|+..|...-. -.=||.+ +|.-.++ ..+|-+ .++-||. .|...|.
T Consensus 270 ef~lp-~k~~~~l~rHPgIFYvS~kg~~-~TVfLrE--AY~~~~Liek~Pl~-------~~r~k~~---~Lm~~~~ 331 (335)
T PF11955_consen 270 EFGLP-QKFRRLLLRHPGIFYVSLKGKR-HTVFLRE--AYDGGELIEKHPLV-------VIREKFL---ELMQEGR 331 (335)
T ss_pred HhCCc-HHHHHHHHhCCCeEEEeccCCc-eEEEEee--ccCCCCCCCCCchH-------HHHHHHH---HHHhhcc
Confidence 99999 5789999999999999976211 1125555 4544443 445542 3555554 4555553
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=90.32 E-value=3.5 Score=38.64 Aligned_cols=51 Identities=24% Similarity=0.395 Sum_probs=31.1
Q ss_pred HHHHhcCCC-cccccccCCCcceeec-cccchHHHHHHHHhCCCChhhHHHHHhhh
Q 039791 99 FFFESIGID-HAEVSCFLPANKFFLS-EDSCLLNAACALSSFGFPWDKLGKLYKEE 152 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l~~ls-~d~~l~~~~~~L~~~G~~~~~i~~~~~~~ 152 (552)
-|+|..|+= |+.-. +.+-=.++ +|-.-...+..|++.|++-+.|..++...
T Consensus 19 RyYe~~GLl~p~~r~---~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 19 LYYERIGLLSPSARS---ESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHCCCCCCCccC---CCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 368889974 32211 11111122 23344578888999999999999987543
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=70.12 E-value=26 Score=32.84 Aligned_cols=112 Identities=11% Similarity=0.146 Sum_probs=63.0
Q ss_pred HHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHH----hcCCChhHHHHHHhhCCceecccccccHhhHHH
Q 039791 235 RKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFC----RFGVGNEDVGLLLLKSPEILSFDLETQVISVKG 310 (552)
Q Consensus 235 ~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~----~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~ 310 (552)
..+.+++++|++-++|..++..... .....+...++.+. .+--....+..++...+..-.-. .-+....++
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~~~~~-~V~~~~w~~ 123 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLLKEQR-LVTKEKWVA 123 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc-cCCHHHHHH
Confidence 4677889999999999999876543 12233444444443 22222344555544333331111 112344556
Q ss_pred HHhhcCCCHHHHHHHHHhCCcccccccccc--hHHHHHhCCc-hHHHHHH
Q 039791 311 LLNHLGLSAKELKSVSEMYPYVLGRNKMAN--LPYVIRAVDL-QDWFFNK 357 (552)
Q Consensus 311 fL~~lG~s~~~i~~~l~~~P~iL~~~~lk~--~~~~L~~lGv-~~~l~~i 357 (552)
.++.+|++++++.+.=..+ ....| -..||..+|+ .+++..+
T Consensus 124 l~~~~g~~~~~m~~wh~~f------e~~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 124 ILKAAGMDEADMRRWHIEF------EKMEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHcCCChHHHHHHHHHH------HHhCcHHHHHHHHHcCCCHHHHHHH
Confidence 6777898888764322211 22333 4589999999 7776654
No 12
>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=66.65 E-value=57 Score=34.64 Aligned_cols=110 Identities=11% Similarity=0.161 Sum_probs=65.3
Q ss_pred hHhHHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHH-----------H-----HhhCCc
Q 039791 232 DICRKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGL-----------L-----LLKSPE 295 (552)
Q Consensus 232 ~~~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~-----------i-----l~~~P~ 295 (552)
.....++-+.++||+++++.+.++.. -++-.+.|+||.. |++.. +.. . --..|.
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAa--------fNNPdRAVEYL~t-GIP~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAA--------FNNPDRAVEYLLT-GIPED-PEQPEPVQQTAASTAAATTETPQHGS 224 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHH--------hCCHHHHHHHHHh-CCCcc-ccccccCCCcccccccccCCCCCCcc
Confidence 45678999999999999999998875 2567889999984 35421 100 0 000001
Q ss_pred eeccccccc----------HhhHHHHHhhcCCCHHHHHHHHHhCCcccccccccchHHHHHhCCc-hHHHHHHHHc
Q 039791 296 ILSFDLETQ----------VISVKGLLNHLGLSAKELKSVSEMYPYVLGRNKMANLPYVIRAVDL-QDWFFNKITN 360 (552)
Q Consensus 296 iL~~s~e~~----------L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~~lk~~~~~L~~lGv-~~~l~~iI~~ 360 (552)
++....... =...++||++.= --.+++.+|..+|++|- .+|+.+|- ...+.++|..
T Consensus 225 lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~p-qf~~lR~~vq~NP~~L~--------~lLqql~~~nP~l~q~I~~ 291 (378)
T TIGR00601 225 VFEQAAQGGTEQPATEAAQGGNPLEFLRNQP-QFQQLRQVVQQNPQLLP--------PLLQQIGQENPQLLQQISQ 291 (378)
T ss_pred hhhhhhcccccccccccccCCchHHHhhcCH-HHHHHHHHHHHCHHHHH--------HHHHHHHhhCHHHHHHHHH
Confidence 100000000 001345655310 12357777888887764 57888888 7888888888
No 13
>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=66.07 E-value=6.4 Score=35.39 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=27.4
Q ss_pred HHHhhCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCccc
Q 039791 288 LLLLKSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVL 333 (552)
Q Consensus 288 ~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL 333 (552)
.-+.++|.|-..+ +..+++||++-|++.+||..++.+.+.--
T Consensus 10 ~~FL~~p~V~~sp----~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 10 VKFLQDPKVRNSP----LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHCTTTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHhCCcccccCC----HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3445577776644 56688899888999998888888766544
No 14
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=60.70 E-value=15 Score=36.81 Aligned_cols=64 Identities=23% Similarity=0.385 Sum_probs=40.9
Q ss_pred hhHHHHHHHHH-HcCC-chHHHHHHHhhcCcccccChhhHHHHHHHHHHhhCCCh-HHHhhcCcccc
Q 039791 429 SELQERFDCLL-RNGV-AFSKLCMMIRLTPKILNQNPETIEQKLDFLCQDLGSSL-DYLYAFPTFLC 492 (552)
Q Consensus 429 ~~L~~r~~~L~-~~G~-s~~~v~~mi~~~P~iL~~s~e~l~~k~~fL~~~mg~~~-~~l~~~P~~L~ 492 (552)
.+|+.++-|-. ..|+ +.--|.+=|...|++++++.++++.|.+=|.+.+|+++ ++.-++|.=|+
T Consensus 71 ~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLS 137 (309)
T COG1125 71 VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELS 137 (309)
T ss_pred HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcC
Confidence 34555555554 5554 44455566777788888887778888777777778776 35555555444
No 15
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=55.30 E-value=60 Score=34.83 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCccCCchhHHHHHHHhcChhhHHHHHHHHHHcCCch
Q 039791 399 TMNKLTFLHGIGYGENTLTLKVLAKAHGTGSELQERFDCLLRNGVAF 445 (552)
Q Consensus 399 ~~~k~~fl~~lG~~~~~~~~~al~~l~~~~~~L~~r~~~L~~~G~s~ 445 (552)
-..+++-|..+||+++... .|+....++.+ .-..+|...+=+.
T Consensus 429 d~~~la~Lv~mGF~e~~A~-~ALe~~gnn~~---~a~~~L~~s~~n~ 471 (568)
T KOG2561|consen 429 DGISLAELVSMGFEEGKAR-SALEAGGNNED---TAQRLLSASVANE 471 (568)
T ss_pred chhhHHHHHHhccccchHH-HHHHhcCCcHH---HHHHHHHHhCCCC
Confidence 3568899999999998754 45555444433 3445555333333
No 16
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=47.89 E-value=78 Score=25.93 Aligned_cols=38 Identities=8% Similarity=0.061 Sum_probs=28.5
Q ss_pred HHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHh-cC
Q 039791 239 VFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCR-FG 280 (552)
Q Consensus 239 fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~-lG 280 (552)
+-+.+|+++.+|..+-..||. +..+.....+..++. -|
T Consensus 19 laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g 57 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHC
Confidence 446789999999999999984 445667777766663 45
No 17
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=47.02 E-value=40 Score=28.02 Aligned_cols=25 Identities=4% Similarity=0.094 Sum_probs=14.5
Q ss_pred HhHHHHHHhhCCCChhHHHHHHhhC
Q 039791 233 ICRKIRVFYDFRFEKGKLGELMGRN 257 (552)
Q Consensus 233 ~~~~l~fl~~lG~~~~~i~~li~~~ 257 (552)
+...+.+|.++|++.....++...+
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~~y 32 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYKKY 32 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3445677778888877666665553
No 18
>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=46.98 E-value=1.3e+02 Score=28.22 Aligned_cols=62 Identities=16% Similarity=0.190 Sum_probs=44.5
Q ss_pred CChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHhhcCCCHHHH
Q 039791 245 FEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLNHLGLSAKEL 322 (552)
Q Consensus 245 ~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i 322 (552)
++.++|..++.+| +.-+...+..++|+.+-.+ .++..-+...|. ++.-+.||.+-|+.....
T Consensus 15 Ip~~~i~~i~~~Y-----~~~D~efq~~~~yl~s~~f--~~l~~~l~~~pE---------~~~l~~yL~~~gldv~~~ 76 (179)
T PF06757_consen 15 IPMEEIQDIVQRY-----YLEDAEFQAAVRYLNSSEF--KQLWQQLEALPE---------VKALLDYLESAGLDVYYY 76 (179)
T ss_pred cCHHHHHHHHHHH-----HHcCHHHHHHHHHHcChHH--HHHHHHHHcCHH---------HHHHHHHHHHCCCCHHHH
Confidence 3456788898887 2334689999999987653 456555555553 567889999999976653
No 19
>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=46.63 E-value=29 Score=31.13 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=27.7
Q ss_pred HHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCce
Q 039791 253 LMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEI 296 (552)
Q Consensus 253 li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~i 296 (552)
-+.++|.+-. ..+..+++||++-|++.+||...+.+.+.-
T Consensus 11 ~FL~~p~V~~----sp~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 11 KFLQDPKVRN----SPLEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HHHCTTTCCC----S-HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred HHhCCccccc----CCHHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 3455777753 246789999999999999999999876543
No 20
>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=44.61 E-value=30 Score=23.28 Aligned_cols=23 Identities=17% Similarity=0.232 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCchHHHHHHHhhc
Q 039791 433 ERFDCLLRNGVAFSKLCMMIRLT 455 (552)
Q Consensus 433 ~r~~~L~~~G~s~~~v~~mi~~~ 455 (552)
+.+.-|+++||+.+++.+.+..+
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 45666777788888777666654
No 21
>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=44.40 E-value=1.5e+02 Score=25.63 Aligned_cols=58 Identities=12% Similarity=0.200 Sum_probs=34.8
Q ss_pred ccchHHHHHHHHhCCC-ChhhHHHHHhhhccc-cccChhhHHHHHHHHHhhcCCChhHHhhHhh
Q 039791 125 DSCLLNAACALSSFGF-PWDKLGKLYKEEVSI-FSQSSQDLTAKLSRLKNYYGFSNVILVGICL 186 (552)
Q Consensus 125 d~~l~~~~~~L~~~G~-~~~~i~~~~~~~P~l-l~~~~~~l~~~l~~L~~l~G~s~~~i~~lv~ 186 (552)
++.+...++.|.+.|+ +.......+.+.-.- -++++..|. .-|... |++.+.|...+.
T Consensus 8 ~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~---~~L~~k-Gi~~~~i~~~l~ 67 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIR---QKLKQK-GIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHH---HHHHHT-T--HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHH---HHHHHH-CCChHHHHHHHH
Confidence 4677888999999994 444555544333222 444544444 467778 999998888887
No 22
>PRK09875 putative hydrolase; Provisional
Probab=43.12 E-value=2.4e+02 Score=28.85 Aligned_cols=35 Identities=14% Similarity=0.015 Sum_probs=21.7
Q ss_pred hccccccChh-hHHHHHHHHHhhcCCChhHHhhHhhcCcc
Q 039791 152 EVSIFSQSSQ-DLTAKLSRLKNYYGFSNVILVGICLGFPH 190 (552)
Q Consensus 152 ~P~ll~~~~~-~l~~~l~~L~~l~G~s~~~i~~lv~~~P~ 190 (552)
.|-....+.+ .-...++.|++. |++. .+++..++.
T Consensus 153 ~pi~~Ht~~~~~g~e~l~il~e~-Gvd~---~rvvi~H~d 188 (292)
T PRK09875 153 RPISTHTSFSTMGLEQLALLQAH-GVDL---SRVTVGHCD 188 (292)
T ss_pred CcEEEcCCCccchHHHHHHHHHc-CcCc---ceEEEeCCC
Confidence 3555554554 334568899999 9974 445556655
No 23
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=42.69 E-value=64 Score=29.22 Aligned_cols=51 Identities=14% Similarity=0.245 Sum_probs=32.4
Q ss_pred HHHHhcCCCcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
.|||++|+=+.....---. =.|-..+-.....+..|++.||+-++|..++.
T Consensus 25 RyYE~~GLl~p~~r~~~gy-R~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~ 75 (144)
T PRK13752 25 RFYQRKGLLPEPDKPYGSI-RRYGEADVTRVRFVKSAQRLGFSLDEIAELLR 75 (144)
T ss_pred HHHHHCCCCCCCccCCCCC-eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4789999754321111000 11222344667888899999999999999884
No 24
>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=40.46 E-value=39 Score=22.64 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=15.3
Q ss_pred HHHHHHHHcCCchHHHHHHHhhc
Q 039791 433 ERFDCLLRNGVAFSKLCMMIRLT 455 (552)
Q Consensus 433 ~r~~~L~~~G~s~~~v~~mi~~~ 455 (552)
++++-|+++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45666777788777766665544
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=40.28 E-value=39 Score=22.48 Aligned_cols=23 Identities=26% Similarity=0.348 Sum_probs=15.1
Q ss_pred HHHHHHHHcCCchHHHHHHHhhc
Q 039791 433 ERFDCLLRNGVAFSKLCMMIRLT 455 (552)
Q Consensus 433 ~r~~~L~~~G~s~~~v~~mi~~~ 455 (552)
++++-|.++||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45566667777777776666554
No 26
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=38.64 E-value=88 Score=27.57 Aligned_cols=72 Identities=19% Similarity=0.140 Sum_probs=40.1
Q ss_pred hHHHHHHHHHhhcCCChhHHhhHhhcCccccccccccccccHHHHHHHHhhhhhcccccccccCCccchhh-HhHHHHHH
Q 039791 162 DLTAKLSRLKNYYGFSNVILVGICLGFPHVLAGNGDEWGTEIATLFDDLKTVFVDFGLMSSVEGNVEVWYD-ICRKIRVF 240 (552)
Q Consensus 162 ~l~~~l~~L~~l~G~s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~~l~~~~~~~~l~~~~~~s~~~-~~~~l~fl 240 (552)
.+-...++|+ . |++.++|..+-.-.|+.|.. +..+++.-+.+... +.. -...+.-.
T Consensus 12 Rlf~i~eAlr-r-G~sveeI~e~T~ID~wFL~~--------i~~Iv~~e~~L~~~-------------~~~~~~~~L~~a 68 (123)
T PF02787_consen 12 RLFAIAEALR-R-GYSVEEIHELTKIDPWFLEQ--------IKNIVDMEKELKEY-------------LNELDPELLRKA 68 (123)
T ss_dssp HHHHHHHHHH-T-TB-HHHHHHHH---HHHHHH--------HHHHHHHHHHHHHH-------------GGG--HHHHHHH
T ss_pred HHHHHHHHHH-c-CCCHHHHHHHHCccHHHHHH--------HHHHHHHHHHHHHh-------------hccchHHHHHHH
Confidence 4555666664 3 88999999998889999887 44444433322110 001 11245556
Q ss_pred hhCCCChhHHHHHHhh
Q 039791 241 YDFRFEKGKLGELMGR 256 (552)
Q Consensus 241 ~~lG~~~~~i~~li~~ 256 (552)
+.+||++.+|+++...
T Consensus 69 K~~GFsD~~IA~l~~~ 84 (123)
T PF02787_consen 69 KRLGFSDRQIARLWGV 84 (123)
T ss_dssp HHTT--HHHHHHHHTS
T ss_pred HHcCCCHHHHHhccCC
Confidence 7899999999998543
No 27
>PHA02591 hypothetical protein; Provisional
Probab=37.76 E-value=80 Score=25.43 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=20.7
Q ss_pred eeccccchHHHHHHHHhCCCChhhHHHHH
Q 039791 121 FLSEDSCLLNAACALSSFGFPWDKLGKLY 149 (552)
Q Consensus 121 ~ls~d~~l~~~~~~L~~~G~~~~~i~~~~ 149 (552)
|...++.+....+-|.+.|++.++|++.+
T Consensus 41 fi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 41 FVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 34445667777888888888888887755
No 28
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=36.61 E-value=2.6e+02 Score=26.29 Aligned_cols=19 Identities=21% Similarity=0.202 Sum_probs=11.8
Q ss_pred HHHhhcCCCHHHHHHHHHh
Q 039791 310 GLLNHLGLSAKELKSVSEM 328 (552)
Q Consensus 310 ~fL~~lG~s~~~i~~~l~~ 328 (552)
.+|..-|++.+.|..++..
T Consensus 145 r~L~~rGFs~~~i~~~l~~ 163 (174)
T COG2137 145 RFLLRRGFSYEVIKEALNE 163 (174)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5566667776666666543
No 29
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.92 E-value=96 Score=27.24 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=31.6
Q ss_pred HHHhcCCCcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 100 FFESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 100 f~eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
|+|..|+=+.....---. =.|-..+-.....+..|++.||+-++|..++.
T Consensus 19 ~Ye~~Gll~~~~r~~~g~-R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04785 19 YYESIGLLPEPARTAGGY-RLYGAAHVERLRFIRRARDLGFSLEEIRALLA 68 (126)
T ss_pred HHHHCCCCCCCCcCCCCc-cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 789999753321110000 11222344666788889999999999999884
No 30
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.84 E-value=47 Score=28.19 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=30.8
Q ss_pred HHHHhcCC-CcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGI-DHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl-~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
-|+|+.|+ .|..-.. . -.+-..+-.....+..|+++||+-++|..++.
T Consensus 18 RyYe~~GLl~p~~~~g---~-r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 66 (107)
T cd04777 18 RHYIDLGLLIPEKKGG---Q-YFFDEKCQDDLEFILELKGLGFSLIEIQKIFS 66 (107)
T ss_pred HHHHHCCCcCCccCCC---c-cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 47899997 4432111 0 11222344567788888999999999988774
No 31
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=34.49 E-value=1.1e+02 Score=26.82 Aligned_cols=49 Identities=18% Similarity=0.188 Sum_probs=30.8
Q ss_pred HHHHhcCCC-cccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGID-HAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
-|+|..|+= |..-.. .+- .+-.+|-.....+..|+++|||-++|..++.
T Consensus 18 RyYe~~GLl~p~~r~~---~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 18 RYYEKEGLLPAPARSA---NNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred HHHHHCCCCCCCCcCC---CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 368999964 332221 111 1112233445778889999999999999875
No 32
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=34.03 E-value=1.1e+02 Score=27.37 Aligned_cols=52 Identities=15% Similarity=0.184 Sum_probs=31.7
Q ss_pred HHHHhcCCCcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
.|+|..|+=++.-..--.. =.+-..|-.....+..|++.|++-++|..++..
T Consensus 18 RyYE~~GLl~p~~r~~~gy-R~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 18 RFYEEKGLVTPPMRSENGY-RTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred HHHHHCCCCCCcccCCCCc-ccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4789999743321110000 011123445667788889999999999998753
No 33
>PRK14136 recX recombination regulator RecX; Provisional
Probab=33.93 E-value=5.4e+02 Score=26.48 Aligned_cols=56 Identities=13% Similarity=0.109 Sum_probs=36.0
Q ss_pred cchHHHHHHHHhCC-CChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCCChhHHhhHhh
Q 039791 126 SCLLNAACALSSFG-FPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGFSNVILVGICL 186 (552)
Q Consensus 126 ~~l~~~~~~L~~~G-~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~s~~~i~~lv~ 186 (552)
+.+...++.|.+.| ++.......|.+. ..-.+.+..| -.-|... |++.+.|...+.
T Consensus 194 e~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp~rI---rqELrQK-GId~eLIEqALe 250 (309)
T PRK14136 194 DSVEPLLDALEREGWLSDARFAESLVHR-RASRVGSARI---VSELKRH-AVGDALVESVGA 250 (309)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhHHHH---HHHHHHc-CCCHHHHHHHHH
Confidence 45557888999888 5555677766543 2222222223 3567788 999988877776
No 34
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=33.59 E-value=1.4e+02 Score=26.38 Aligned_cols=20 Identities=20% Similarity=0.062 Sum_probs=16.2
Q ss_pred CCChhHHhhHhhcCcccccc
Q 039791 175 GFSNVILVGICLGFPHVLAG 194 (552)
Q Consensus 175 G~s~~~i~~lv~~~P~lL~~ 194 (552)
.=|+.++-.++.+||.+=..
T Consensus 27 RPSN~Dif~Lv~~CP~lk~i 46 (131)
T PF08004_consen 27 RPSNKDIFSLVERCPNLKAI 46 (131)
T ss_pred cCcchHHHHHHHhCCCCeEE
Confidence 34778999999999998654
No 35
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=32.18 E-value=1.2e+02 Score=26.61 Aligned_cols=49 Identities=18% Similarity=0.260 Sum_probs=31.8
Q ss_pred HHHHhcCCCc-ccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGIDH-AEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~~-~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
.|+|..|+=+ ..-.. .+- .|-.+|-.-...+..|++.|++-++|..++.
T Consensus 18 RyYe~~GLl~~~~r~~---~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 18 RYYEEIGLIPPPSRSD---NGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred HHHHHCCCCCCCCcCC---CCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3689999753 32211 111 1222344666788899999999999999874
No 36
>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=31.68 E-value=69 Score=22.36 Aligned_cols=29 Identities=14% Similarity=0.169 Sum_probs=21.4
Q ss_pred hHHHHHHHHH-HcCCchHHHHHHHhhcCcc
Q 039791 430 ELQERFDCLL-RNGVAFSKLCMMIRLTPKI 458 (552)
Q Consensus 430 ~L~~r~~~L~-~~G~s~~~v~~mi~~~P~i 458 (552)
+.-.....|. ++|++..+..+||..||..
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 4445667788 8999999999999999975
No 37
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.44 E-value=1.3e+02 Score=26.43 Aligned_cols=50 Identities=14% Similarity=0.211 Sum_probs=31.5
Q ss_pred HHHHhcCCCc-ccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGIDH-AEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~~-~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
.|+|..|+=+ ..-. +.+. .+-.+|-.....+..|+++||+-++|..++..
T Consensus 18 R~Ye~~GLl~~~~r~---~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04783 18 RYYQRRGLLPEPPRP---EGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred HHHHHCCCCCCCCcC---CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 4689999743 2221 1111 11122335557888999999999999998853
No 38
>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=31.42 E-value=1.3e+02 Score=25.90 Aligned_cols=24 Identities=17% Similarity=0.137 Sum_probs=14.6
Q ss_pred HhhHHHHHhhcCCCHHHHHHHHHh
Q 039791 305 VISVKGLLNHLGLSAKELKSVSEM 328 (552)
Q Consensus 305 L~~~v~fL~~lG~s~~~i~~~l~~ 328 (552)
....+.+|..-|++.+.|.+++..
T Consensus 95 ~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 95 KQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHhh
Confidence 444557777778777777776653
No 39
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=31.41 E-value=2e+02 Score=29.80 Aligned_cols=108 Identities=11% Similarity=0.150 Sum_probs=64.9
Q ss_pred HHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHHHHhhCCceecc------------c--
Q 039791 235 RKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSF------------D-- 300 (552)
Q Consensus 235 ~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~------------s-- 300 (552)
..+.-+.++|+..+++.+.++.. -++-.+.|+||.. |++...-.......|..-.. .
T Consensus 137 ~~V~~Im~MGy~re~V~~AlRAa--------fNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~ 207 (340)
T KOG0011|consen 137 QTVQQIMEMGYDREEVERALRAA--------FNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQGA 207 (340)
T ss_pred HHHHHHHHhCccHHHHHHHHHHh--------hCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCCccc
Confidence 35666678999999999888764 1455678899873 44432101111111111111 1
Q ss_pred ccccHhhHHHHHhhcCCCHHHHHHHHHhCCcccccccccchHHHHHhCCc-hHHHHHHHHc
Q 039791 301 LETQVISVKGLLNHLGLSAKELKSVSEMYPYVLGRNKMANLPYVIRAVDL-QDWFFNKITN 360 (552)
Q Consensus 301 ~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~~lk~~~~~L~~lGv-~~~l~~iI~~ 360 (552)
++..-...++||++.- .-.++..+|..+|.+|. ..|+.+|- ...+.+.|..
T Consensus 208 ~~~~~~~~l~fLr~~~-qf~~lR~~iqqNP~ll~--------~~Lqqlg~~nP~L~q~Iq~ 259 (340)
T KOG0011|consen 208 VEASGGDPLEFLRNQP-QFQQLRQMIQQNPELLH--------PLLQQLGKQNPQLLQLIQE 259 (340)
T ss_pred hhhhcCCchhhhhccH-HHHHHHHHHhhCHHHHH--------HHHHHHhhhCHHHHHHHHH
Confidence 2222335577777531 23467788888888775 46788887 7788888888
No 40
>PF10098 DUF2336: Uncharacterized protein conserved in bacteria (DUF2336); InterPro: IPR019285 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.79 E-value=2.7e+02 Score=27.59 Aligned_cols=151 Identities=16% Similarity=0.138 Sum_probs=92.9
Q ss_pred cCCCcchhHHHHHHHHHHHHHHHhcCCCChhhHHHHhhcChHHH--------------HHHHHhcCCCCChhhHHHHHHH
Q 039791 22 KIPTKYRPRAIKEAQQAVTEYLHYTKSIPFTYAEHISKHSLNTL--------------SKLIADLGVSYSAPSFSSTFQR 87 (552)
Q Consensus 22 ~~~~~~~~~~~~~a~~~~~~yL~~~~gl~~~~A~~is~~sp~~~--------------~~ll~~~~~~~~~~~~~~~~~r 87 (552)
.+|......-...+-+++.+++.+..+++...++.+.+.+-.-+ ..++. ...-....-...+.+
T Consensus 93 dLp~~~~~~L~~~v~~~lr~~l~~~~~~~~~~~~~~~~~a~~~a~~~~~~~~~~~~~a~~~v~--~l~~~g~L~~~lL~~ 170 (262)
T PF10098_consen 93 DLPPEVRRRLLWWVSEALRARLLSRFALDAERAQRLAAEARERAAAELAEDSRDRERARRLVR--HLRRRGRLTEALLLR 170 (262)
T ss_pred cCCHHHHHHHHhhccHHHHHHHHhccccchHHHHHHHHHHHHHHHhhhcccccchHHHHHHHH--HHHHcCCCCHHHHHH
Confidence 36677777777778888888887777788888777765533222 22222 111011122344445
Q ss_pred HHhhcCcchhHHHH-HhcCCCcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhhccccccChhhHHHH
Q 039791 88 FLRYHPINEFEFFF-ESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEEVSIFSQSSQDLTAK 166 (552)
Q Consensus 88 ~l~~~pi~~~e~f~-eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~~l~~~ 166 (552)
++...-...|..-+ +-.|+++..+..++- |..-.+....++..|+++.....+...-..-...+.+.+...
T Consensus 171 a~~~g~~~~f~aaLA~lsgl~~~~v~~il~--------d~~~~~L~~l~kaaGL~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (262)
T PF10098_consen 171 AACSGRLAFFAAALAELSGLPPARVRRILA--------DGGGEALAALCKAAGLPWATFPAFLAALAPWRRISRGDLEEA 242 (262)
T ss_pred HHHcCCHHHHHHHHHHHHCcCHHHHHHHHh--------CCCchHHHHHHHHcCCCHHHHHHHHHHHhhhcccCcchHHHH
Confidence 55544444444333 456788888887621 222335666777899999998888877777777777777777
Q ss_pred HHHHHhhcCCChhHHhhHh
Q 039791 167 LSRLKNYYGFSNVILVGIC 185 (552)
Q Consensus 167 l~~L~~l~G~s~~~i~~lv 185 (552)
+..|+.+ +.++-..++
T Consensus 243 ~~~y~~L---~~~~A~~~L 258 (262)
T PF10098_consen 243 LALYDRL---SPDAAQRVL 258 (262)
T ss_pred HHHHHcC---CHHHHHHHH
Confidence 7777776 454444444
No 41
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.90 E-value=1.4e+02 Score=26.28 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=30.5
Q ss_pred HHHHhcCCCc-ccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGIDH-AEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~~-~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
-|+|..|+=+ ..-.. .+- .+-.++-.-...+..|+++|++-++|..++.
T Consensus 18 R~Ye~~GLl~~~~r~~---~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 18 RFYEKQGLLPPPARTD---NNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred HHHHHCCCCCCCCcCC---CCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3689999743 22211 111 1112233456777889999999999999874
No 42
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=29.74 E-value=1.1e+02 Score=31.04 Aligned_cols=69 Identities=19% Similarity=0.302 Sum_probs=46.7
Q ss_pred hHHHHHHHHHHhhCCChHHHhhcCcccccccCCcchhHHHHHHHHHHCCCCCCccccccccccchhHHHHHhcccCC
Q 039791 465 TIEQKLDFLCQDLGSSLDYLYAFPTFLCFDLEYRIKPRYKFHMWLVENGLCTKNYSIASMVATSEKSFISRIYGIHP 541 (552)
Q Consensus 465 ~l~~k~~fL~~~mg~~~~~l~~~P~~L~ysle~rikpR~~~~~~L~~~G~~~~~~sl~~il~~sd~~F~~~~~~~~p 541 (552)
-++.+++.+.+ .|++.+.|+--|- ++|. +....-+++++.+..-. .+.+..++..|.|.|+..+.+..|
T Consensus 164 ~l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~----~lg~Pilvg~SRKsfig~~~~~~~ 232 (282)
T PRK11613 164 YFIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFH----HFNLPLLVGMSRKSMIGQLLNVGP 232 (282)
T ss_pred HHHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHH----hCCCCEEEEecccHHHHhhcCCCh
Confidence 45667777766 6999999998895 4553 45556677666554421 223345899999999998877533
No 43
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.29 E-value=1.5e+02 Score=25.73 Aligned_cols=51 Identities=18% Similarity=0.257 Sum_probs=32.7
Q ss_pred HHHHhcCCCc-ccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhhh
Q 039791 99 FFFESIGIDH-AEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKEE 152 (552)
Q Consensus 99 ~f~eslGl~~-~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~ 152 (552)
-|+|..|+=+ ..-.. .+- .+-.++-.....+..|++.|++-++|..++...
T Consensus 18 RyYe~~GLl~p~~r~~---~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 18 RYYERIGLLPPPQRSE---NGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHCCCCCCCCCCC---CCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 3689999743 33221 011 112234456678889999999999999988543
No 44
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=29.14 E-value=1.5e+02 Score=25.97 Aligned_cols=50 Identities=14% Similarity=0.127 Sum_probs=31.0
Q ss_pred HHHHhcCCC-cccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGID-HAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
-|+|+.|+= |..-..- -. =.+-.++-.-...+..|++.||+-++|..++.
T Consensus 18 RyYe~~GLl~p~~r~~~-gy-R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 18 RYYEEKGLIPPPLRSEG-GY-RTYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred HHHHHCCCCCCCCcCCC-CC-eecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 378999974 3222110 00 01112334555678889999999999999875
No 45
>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=28.95 E-value=88 Score=22.38 Aligned_cols=27 Identities=11% Similarity=0.186 Sum_probs=19.4
Q ss_pred HHHHHHHHHHcCCchHHHHHHHhhcCc
Q 039791 431 LQERFDCLLRNGVAFSKLCMMIRLTPK 457 (552)
Q Consensus 431 L~~r~~~L~~~G~s~~~v~~mi~~~P~ 457 (552)
+.+-++-|..+||+..++..++.+...
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 455667777889988888888877654
No 46
>PHA02591 hypothetical protein; Provisional
Probab=28.90 E-value=1e+02 Score=24.82 Aligned_cols=45 Identities=20% Similarity=0.268 Sum_probs=30.1
Q ss_pred CChhHHHHHHhhC-CcceecCchhhHHHHHHHHHhcCCChhHHHHHH
Q 039791 245 FEKGKLGELMGRN-KSIFLDYPEEVLVQKVEYFCRFGVGNEDVGLLL 290 (552)
Q Consensus 245 ~~~~~i~~li~~~-P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~il 290 (552)
+++..+.+++.-- -+-+ -.+++++.....-|.+.|++.++|++.+
T Consensus 24 ~~~~~m~k~vqv~~~ryf-i~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 24 IGEKKMQKVVQVGQTRYF-VESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred hhhHhHHHhheeCCEEEE-EeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3455555555432 2223 3456888888999999999998888764
No 47
>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=28.25 E-value=34 Score=23.86 Aligned_cols=25 Identities=20% Similarity=0.177 Sum_probs=20.0
Q ss_pred HHHHHhcCCCChhhHHHHhhcChHH
Q 039791 40 TEYLHYTKSIPFTYAEHISKHSLNT 64 (552)
Q Consensus 40 ~~yL~~~~gl~~~~A~~is~~sp~~ 64 (552)
..+|+.++|||-..|..|.+.+|..
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHHHHHHccCHHHHHHHHHHCHHH
Confidence 4689999999999999999998854
No 48
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=28.04 E-value=1.5e+02 Score=26.16 Aligned_cols=50 Identities=20% Similarity=0.315 Sum_probs=31.8
Q ss_pred HHHHhcCCCcccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHh
Q 039791 99 FFFESIGIDHAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYK 150 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~ 150 (552)
-|+|+.|+=+..... +.+- .+-.+|-.....+..|++.||+-++|..++.
T Consensus 19 R~Ye~~GLl~p~~r~--~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~ 69 (131)
T TIGR02043 19 RFYEKNGLIKPAGRT--DSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLS 69 (131)
T ss_pred HHHHHCCCCCCCCcC--CCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 368888974332111 1111 1222344666788889999999999999885
No 49
>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=27.77 E-value=73 Score=22.78 Aligned_cols=27 Identities=19% Similarity=0.175 Sum_probs=19.6
Q ss_pred HHHHHHHHHhhcCCChhHHhhHhhcCcc
Q 039791 163 LTAKLSRLKNYYGFSNVILVGICLGFPH 190 (552)
Q Consensus 163 l~~~l~~L~~l~G~s~~~i~~lv~~~P~ 190 (552)
....+.+|.++ |+++.++.+++.+-..
T Consensus 3 ~~d~~~AL~~L-Gy~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 3 LEDALEALISL-GYSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHHT-TS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHhhc
Confidence 45677788888 8888888888876544
No 50
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=27.58 E-value=56 Score=25.67 Aligned_cols=23 Identities=35% Similarity=0.585 Sum_probs=18.5
Q ss_pred HHHHHHHHhcCCCChhhHHHHhhc
Q 039791 37 QAVTEYLHYTKSIPFTYAEHISKH 60 (552)
Q Consensus 37 ~~~~~yL~~~~gl~~~~A~~is~~ 60 (552)
+-++|||... |+||-+|=+|..+
T Consensus 5 TdlAD~LVr~-GipFR~AH~iVg~ 27 (70)
T PF14698_consen 5 TDLADYLVRK-GIPFREAHHIVGR 27 (70)
T ss_dssp HHHHHHHHHT-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHH
Confidence 4588999966 9999999998765
No 51
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=26.48 E-value=1.3e+02 Score=32.58 Aligned_cols=137 Identities=15% Similarity=0.216 Sum_probs=80.1
Q ss_pred HHHHhCCCChhhHHHHHhhhccccccChhhHHH---HHHHHHhhcCCChhHHh-----hHhhcCccccccccccccccHH
Q 039791 133 CALSSFGFPWDKLGKLYKEEVSIFSQSSQDLTA---KLSRLKNYYGFSNVILV-----GICLGFPHVLAGNGDEWGTEIA 204 (552)
Q Consensus 133 ~~L~~~G~~~~~i~~~~~~~P~ll~~~~~~l~~---~l~~L~~l~G~s~~~i~-----~lv~~~P~lL~~s~~~~~~~l~ 204 (552)
++...+|.+.+....+...+..+=.+..|++.. .++-|++. -+....|. .....+|.+-.. |+
T Consensus 83 ry~e~~s~~sd~~~~~si~nK~vE~iGfDki~akQsn~kkL~~I-sLdn~~V~~~~~~~~~k~~~~v~~L---dL----- 153 (505)
T KOG3207|consen 83 RYYEKYSYSSDLESVLSISNKQVEFIGFDKIAAKQSNLKKLREI-SLDNYRVEDAGIEEYSKILPNVRDL---DL----- 153 (505)
T ss_pred HHHHhhcCCcchhhHhhhcCceeEEecHHHHHHHhhhHHhhhhe-eecCccccccchhhhhhhCCcceee---cc-----
Confidence 356778888887777778888888888887654 55555555 34333332 233334444333 22
Q ss_pred HHHHHHhhhhhcccccccccCCccchhhHhHHHHHHh---hCCCChhHHHHHHhhCCcceecCchhhHHHHHHHH--Hhc
Q 039791 205 TLFDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFY---DFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYF--CRF 279 (552)
Q Consensus 205 ~~~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~---~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL--~~l 279 (552)
+....++|..++...+.|. .+.++...+. +|. .+......+.+.-| .+.
T Consensus 154 ------------------S~NL~~nw~~v~~i~eqLp~Le~LNls~Nrl~-----~~~---~s~~~~~l~~lK~L~l~~C 207 (505)
T KOG3207|consen 154 ------------------SRNLFHNWFPVLKIAEQLPSLENLNLSSNRLS-----NFI---SSNTTLLLSHLKQLVLNSC 207 (505)
T ss_pred ------------------hhhhHHhHHHHHHHHHhcccchhccccccccc-----CCc---cccchhhhhhhheEEeccC
Confidence 2334567777776665553 4556554432 111 11111122222222 268
Q ss_pred CCChhHHHHHHhhCCceeccccccc
Q 039791 280 GVGNEDVGLLLLKSPEILSFDLETQ 304 (552)
Q Consensus 280 G~~~~~i~~il~~~P~iL~~s~e~~ 304 (552)
|++.++|.+++..+|.+....++.|
T Consensus 208 Gls~k~V~~~~~~fPsl~~L~L~~N 232 (505)
T KOG3207|consen 208 GLSWKDVQWILLTFPSLEVLYLEAN 232 (505)
T ss_pred CCCHHHHHHHHHhCCcHHHhhhhcc
Confidence 9999999999999998877666655
No 52
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=26.43 E-value=2e+02 Score=23.71 Aligned_cols=50 Identities=22% Similarity=0.289 Sum_probs=34.0
Q ss_pred HHHHHHhcCCCChhhHHHHhhcCh-----HHHHHHHHhcCCCCChhhHHHHHHHHHhhcCcchhHHHHHhcC
Q 039791 39 VTEYLHYTKSIPFTYAEHISKHSL-----NTLSKLIADLGVSYSAPSFSSTFQRFLRYHPINEFEFFFESIG 105 (552)
Q Consensus 39 ~~~yL~~~~gl~~~~A~~is~~sp-----~~~~~ll~~~~~~~~~~~~~~~~~r~l~~~pi~~~e~f~eslG 105 (552)
+++||++..=++.+|++.|.+..- .=+.+||. .|.-++-..|..|.+++.
T Consensus 21 l~d~L~q~~VLt~~d~EeI~~~~t~~~r~~ka~~LLd-----------------iL~~rG~~Af~~F~~aL~ 75 (86)
T cd08785 21 LTPYLRQCKVLDEQDEEEVLSSPRLPIRANRTGRLLD-----------------ILATRGKRGYVAFLESLE 75 (86)
T ss_pred HHHHHHhcCCCCHHHHHHHhCCCccccHHHHHHHHHH-----------------HHHhcCcchHHHHHHHHH
Confidence 999999888899999999977422 22233333 222356667777777764
No 53
>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=26.30 E-value=1.5e+02 Score=34.49 Aligned_cols=28 Identities=14% Similarity=0.128 Sum_probs=19.3
Q ss_pred hHHHHHHHHHhhc--CCChhHHhhHhhcCc
Q 039791 162 DLTAKLSRLKNYY--GFSNVILVGICLGFP 189 (552)
Q Consensus 162 ~l~~~l~~L~~l~--G~s~~~i~~lv~~~P 189 (552)
.....+.||.+-. |+.+..-.+|+..++
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg 105 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFG 105 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhC
Confidence 4567788888732 677777777777665
No 54
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.43 E-value=1.4e+02 Score=24.83 Aligned_cols=52 Identities=17% Similarity=0.339 Sum_probs=32.2
Q ss_pred HHHHhcCCCcccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhhh
Q 039791 99 FFFESIGIDHAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKEE 152 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~ 152 (552)
.|+|..|+=+..... +.+- .+-.+|-.....+..|++.|++-++|..++...
T Consensus 18 R~ye~~Gll~p~~r~--~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 18 HHYDHIGLLSPSQRT--EGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred HHHHHCCCCCCCccC--CCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 367888864332111 1111 122234456678888999999999999988543
No 55
>PHA01351 putative minor structural protein
Probab=25.27 E-value=4.7e+02 Score=30.00 Aligned_cols=105 Identities=12% Similarity=0.020 Sum_probs=52.8
Q ss_pred HHHHHHhCCCChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCC--ChhHHhhHhhcCcc---ccccccccccccHHH
Q 039791 131 AACALSSFGFPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGF--SNVILVGICLGFPH---VLAGNGDEWGTEIAT 205 (552)
Q Consensus 131 ~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~--s~~~i~~lv~~~P~---lL~~s~~~~~~~l~~ 205 (552)
...-|+++|+|.+.+..+..++-..- =..++.+--.-+.+. |. +.+.+.+.+..+-. ++.. ....+++-
T Consensus 694 ~~~ELKKL~IpdSqInil~t~yy~~~--~~~kls~~~~sl~~~-g~l~~~s~i~e~~~~y~~~~a~~~y---~~~~ei~y 767 (1070)
T PHA01351 694 LSGELKKIHKDKTALELYITKFYYEY--IYPKISNYHLQLARH-GILSDISKLPKEVNDYEYKPAVLTY---QTTLEIEY 767 (1070)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHH--HHHHHHHHHHHHHhc-CchhhHHHhhHHHHhccchhHHHhh---hHHHHHHH
Confidence 55668999999999887764432211 112233322333455 65 33445555555432 2222 11223333
Q ss_pred HHHHHhhhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHHhhC
Q 039791 206 LFDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELMGRN 257 (552)
Q Consensus 206 ~~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li~~~ 257 (552)
+-+-|+.+..+ ......-|+++|++++-..-++..+
T Consensus 768 i~~~lkdl~i~----------------~k~a~~el~kl~~s~~i~~~iv~~~ 803 (1070)
T PHA01351 768 IKESLKDLEIK----------------PKTAINELEKLGMQKDIAQLIVNTY 803 (1070)
T ss_pred HHHHHhhcccC----------------chhHHHHHHHcCchHHHHHHHHhhc
Confidence 33333332211 2345677889999876554445444
No 56
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.18 E-value=2.1e+02 Score=24.55 Aligned_cols=50 Identities=14% Similarity=0.222 Sum_probs=33.3
Q ss_pred HHHHhcCCC-cccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGID-HAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
.|+|+.|+= |.... +..=.+-..|-.....+..|++.|+|-++|..++..
T Consensus 18 ryYe~~GLi~p~~~~---~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 18 RLYEEKGLLPSPKRS---GNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred HHHHHCCCCCCCCCC---CCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 478999974 43322 110112234556677888999999999999998743
No 57
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=24.74 E-value=1.3e+02 Score=22.92 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=21.0
Q ss_pred HhcCCCChhhHHHHhhcChHHHHHHHHh
Q 039791 44 HYTKSIPFTYAEHISKHSLNTLSKLIAD 71 (552)
Q Consensus 44 ~~~~gl~~~~A~~is~~sp~~~~~ll~~ 71 (552)
+..+|+|..+.+...+=++.++.++=.+
T Consensus 6 R~~~glsl~~va~~t~I~~~~l~aiE~~ 33 (62)
T PF13413_consen 6 REAKGLSLEDVAEETKISVSYLEAIENG 33 (62)
T ss_dssp HHCTT--HHHHHHHCS--HHHHHHHHCT
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHCc
Confidence 4589999999999999999999998764
No 58
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=24.62 E-value=2.1e+02 Score=24.95 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=31.5
Q ss_pred HHHHhcCCCcccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGIDHAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
-|+|..|+=+..... +.+- .+-.++-.-...+..|++.||+-++|..++..
T Consensus 17 R~Ye~~GLl~~~~r~--~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~ 68 (124)
T TIGR02051 17 RYYERKGLLPEPDRP--EGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL 68 (124)
T ss_pred HHHHHCCCCCCCccC--CCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhc
Confidence 468999974321111 1111 12223345557888899999999999998854
No 59
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=24.27 E-value=5.3e+02 Score=23.23 Aligned_cols=59 Identities=8% Similarity=0.064 Sum_probs=33.1
Q ss_pred chHHHHHHHHhCC-CChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCCChhHHhhHhhcCc
Q 039791 127 CLLNAACALSSFG-FPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGFSNVILVGICLGFP 189 (552)
Q Consensus 127 ~l~~~~~~L~~~G-~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~s~~~i~~lv~~~P 189 (552)
.+...++.|...| ++....+..+.+.-.--..+.. ..-.-|... |++.+.|..++...+
T Consensus 44 ~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~---~I~~~L~~k-Gi~~~~I~~~l~~~~ 103 (157)
T PRK00117 44 VIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPR---RIRQELRQK-GVDREIIEEALAELD 103 (157)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHH---HHHHHHHHc-CCCHHHHHHHHHHcC
Confidence 3345667777777 4444555544333222222222 234466778 999888888777654
No 60
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=23.87 E-value=2.8e+02 Score=21.98 Aligned_cols=55 Identities=11% Similarity=0.271 Sum_probs=34.1
Q ss_pred HHHHHHhhCCCChhHHHHHHhhCCcceecCchhhHHHHHHHHHhcCCChhHHHH---HHhhCCcee
Q 039791 235 RKIRVFYDFRFEKGKLGELMGRNKSIFLDYPEEVLVQKVEYFCRFGVGNEDVGL---LLLKSPEIL 297 (552)
Q Consensus 235 ~~l~fl~~lG~~~~~i~~li~~~P~lL~~~~~~~l~~~v~fL~~lG~~~~~i~~---il~~~P~iL 297 (552)
+.++.|++..+|+++|..++... +. +-...+.....+|++++.+.. .+..+|.++
T Consensus 3 PIia~LKehnvsd~qi~elFq~l----T~----NPl~AMa~i~qLGip~eKLQ~lm~~VMqnP~Li 60 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQAL----TQ----NPLAAMATIQQLGIPQEKLQQLMAQVMQNPALI 60 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHH----hh----CHHHHHHHHHHcCCCHHHHHHHHHHHhcChHHH
Confidence 34566778888888888776542 22 223455667778888776543 344556543
No 61
>PRK14134 recX recombination regulator RecX; Provisional
Probab=23.23 E-value=7.9e+02 Score=24.87 Aligned_cols=172 Identities=12% Similarity=0.033 Sum_probs=90.9
Q ss_pred cchHHHHHHHHhCC-CChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCCChhHHhhHhhcCccccccccccccccHH
Q 039791 126 SCLLNAACALSSFG-FPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGFSNVILVGICLGFPHVLAGNGDEWGTEIA 204 (552)
Q Consensus 126 ~~l~~~~~~L~~~G-~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~s~~~i~~lv~~~P~lL~~s~~~~~~~l~ 204 (552)
+.+-..++.|.++| ++....+..+.+.-. -..++..|. .-|... |++.+.|...+...+. +.+..
T Consensus 93 ~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~-~~~G~~~I~---~eL~qK-GI~~~iIe~al~~~~~---------e~e~e 158 (283)
T PRK14134 93 DAVNRVIRFLKEYNFIDDDKYCDMYIREKI-NSYGRNKIK---YTLLNK-GIKENIIIEKINNIDE---------EKEKK 158 (283)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HhhhHHHHH---HHHHHC-CCCHHHHHHHHHhCCh---------hhHHH
Confidence 45557888999988 555566666655422 233333333 466788 9999988888874321 11222
Q ss_pred HHHHHHhhhhhcccccccccC--CccchhhH-hHHHHHHhhCCCChhHHHHHHhhCCcceecC---ch---hhHHHHHHH
Q 039791 205 TLFDDLKTVFVDFGLMSSVEG--NVEVWYDI-CRKIRVFYDFRFEKGKLGELMGRNKSIFLDY---PE---EVLVQKVEY 275 (552)
Q Consensus 205 ~~~~~L~~l~~~~~~~~l~~~--~~~s~~~~-~~~l~fl~~lG~~~~~i~~li~~~P~lL~~~---~~---~~l~~~v~f 275 (552)
.....++. -+... ...+..+. ....++|..-||+.+.|..++... +... -+ +++..
T Consensus 159 ~a~~l~~K--------k~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~---~~~~~~~~~~~~~~~~~---- 223 (283)
T PRK14134 159 VAYKLAEK--------KYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNEL---IKNEALYKDNNSQNIEN---- 223 (283)
T ss_pred HHHHHHHH--------hhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHH---HhHhhhhhhccccchhh----
Confidence 22222211 01000 11122233 345689999999999998888763 1100 00 01111
Q ss_pred HHhcCCChhHHHHHH--hhCCceeccccc--ccHhhHHHHHhhcCCCHHHHHHHHHh
Q 039791 276 FCRFGVGNEDVGLLL--LKSPEILSFDLE--TQVISVKGLLNHLGLSAKELKSVSEM 328 (552)
Q Consensus 276 L~~lG~~~~~i~~il--~~~P~iL~~s~e--~~L~~~v~fL~~lG~s~~~i~~~l~~ 328 (552)
....+.-+....+ .+++.+....-+ +--+..+.||..-|++.+.|..++..
T Consensus 224 --~~~~~~~~~~~~~a~kr~~~~~~~e~d~~k~~~Kl~~~L~rkGf~~e~I~~vl~~ 278 (283)
T PRK14134 224 --NIKDENIEELHNLARKRYDIIIKSEDDKNKIYRRLSNYLLRRGYSWEEVKKSLNE 278 (283)
T ss_pred --ccccChHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 1122222222222 234444322111 22355569999999999999998865
No 62
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=23.04 E-value=1.9e+02 Score=23.95 Aligned_cols=59 Identities=14% Similarity=0.196 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhcCCChhHHHHHHhhCCceecccccccHhhHHHHHhhcCCCHHHHHHHHHhCCccccccc----ccchH
Q 039791 267 EVLVQKVEYFCRFGVGNEDVGLLLLKSPEILSFDLETQVISVKGLLNHLGLSAKELKSVSEMYPYVLGRNK----MANLP 342 (552)
Q Consensus 267 ~~l~~~v~fL~~lG~~~~~i~~il~~~P~iL~~s~e~~L~~~v~fL~~lG~s~~~i~~~l~~~P~iL~~~~----lk~~~ 342 (552)
..+...+.||.+.|++...+.++...+ | ++...+|+.+|..|..+. .+..-
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~y----------------------g---~~ai~~l~~nPY~L~~~i~gi~F~~aD 60 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKY----------------------G---DDAIEILKENPYRLIEDIDGIGFKTAD 60 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH--------------------------TTHHHHHHH-STCCCB-SSSSBHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH----------------------h---HHHHHHHHHChHHHHHHccCCCHHHHH
Confidence 456778899999999987766665432 2 134466788888888742 33444
Q ss_pred HHHHhCCc
Q 039791 343 YVIRAVDL 350 (552)
Q Consensus 343 ~~L~~lGv 350 (552)
.+-+.+|+
T Consensus 61 ~iA~~~g~ 68 (94)
T PF14490_consen 61 KIALKLGI 68 (94)
T ss_dssp HHHHTTT-
T ss_pred HHHHHcCC
Confidence 56667887
No 63
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=23.04 E-value=1.4e+02 Score=26.48 Aligned_cols=51 Identities=14% Similarity=0.259 Sum_probs=33.4
Q ss_pred HHHHhcCCCcccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGIDHAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
.|||++|+=++.-.. +.+- .|-.++-.....+..|++.||+-++|..++..
T Consensus 18 RyYE~~GLl~p~r~~--~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (133)
T cd04787 18 RFYTRIGLLRPTRDP--VNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred HHHHHCCCCCCCcCC--CCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 468999975433211 0111 12234556678888999999999999998853
No 64
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.88 E-value=1.5e+02 Score=24.57 Aligned_cols=50 Identities=16% Similarity=0.293 Sum_probs=30.8
Q ss_pred HHHHhcCCC-cccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGID-HAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
-|+|+.|+= |..-.. .+- .+-..|-.-...+..|++.|+|-++|..++..
T Consensus 18 Ryye~~Gll~p~~~~~---~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (96)
T cd04768 18 RHYDDIGLFKPAKIAE---NGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT 69 (96)
T ss_pred HHHHHCCCCCCCccCC---CCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 367888864 322211 111 11122345557788899999999999998854
No 65
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=22.56 E-value=2.5e+02 Score=28.42 Aligned_cols=64 Identities=16% Similarity=0.283 Sum_probs=46.9
Q ss_pred hHHHHHH-HHhCC-CChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCCChhHHhhHhhcCcccccc
Q 039791 128 LLNAACA-LSSFG-FPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGFSNVILVGICLGFPHVLAG 194 (552)
Q Consensus 128 l~~~~~~-L~~~G-~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~s~~~i~~lv~~~P~lL~~ 194 (552)
++-.+-| ++..| ||.-.+..=+.-.|.+.+++-++++.+..-|-+++|+++.+. ..+||+=|++
T Consensus 73 LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~---~~RyP~eLSG 138 (309)
T COG1125 73 LRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEY---ADRYPHELSG 138 (309)
T ss_pred HHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHH---hhcCchhcCc
Confidence 3444433 45566 555566666667799999999999988887776669987654 5799999998
No 66
>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=22.34 E-value=1.3e+02 Score=25.45 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=10.2
Q ss_pred CCChhHHHHHHhhCCceeccc
Q 039791 280 GVGNEDVGLLLLKSPEILSFD 300 (552)
Q Consensus 280 G~~~~~i~~il~~~P~iL~~s 300 (552)
.++.+++..++..+|.++...
T Consensus 70 ~~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 70 DLSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp TSBHHHHHHHHHHSGGGB-SS
T ss_pred hhhhHHHHHHHHhChhheeCC
Confidence 344555555555555554443
No 67
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=21.82 E-value=2.5e+02 Score=31.21 Aligned_cols=112 Identities=18% Similarity=0.156 Sum_probs=63.1
Q ss_pred cCCCcccccccCCCcceeeccc----cchHHHHHHHHhCCCChhhHHHHHhhhccccccChhhHHHHHHHHHhhcCCChh
Q 039791 104 IGIDHAEVSCFLPANKFFLSED----SCLLNAACALSSFGFPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKNYYGFSNV 179 (552)
Q Consensus 104 lGl~~~~~~~~~P~~l~~ls~d----~~l~~~~~~L~~~G~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~l~G~s~~ 179 (552)
+|+.+...+...|+.+ +|. ..+...++||...|++.. ++.=....| +..+....+.||...+ ++.
T Consensus 51 ~~~~~~~~s~~dpRpl---~dk~~~s~c~~~I~~fL~engf~~~-iS~k~l~~P-----S~KdF~~iFkfLY~~L--dp~ 119 (581)
T KOG0995|consen 51 LSSFNTSNSIRDPRPL---SDKRYRSQCIRQIYNFLVENGFSHP-ISIKLLMKP-----SVKDFIAIFKFLYGFL--DPD 119 (581)
T ss_pred ccccCchhccCCCCCc---ccHHHHHHHHHHHHHHHHHcCCCCC-hhhhhcCCC-----ccccHHHHHHHHHhcc--CCC
Confidence 6666777777778744 443 467788999999999832 222122222 3335666777776542 110
Q ss_pred HHhhHhhcCccccccccccccccHHHHHHHHhhhhhc---ccccccccCCccchhhHhHHHHHHhh
Q 039791 180 ILVGICLGFPHVLAGNGDEWGTEIATLFDDLKTVFVD---FGLMSSVEGNVEVWYDICRKIRVFYD 242 (552)
Q Consensus 180 ~i~~lv~~~P~lL~~s~~~~~~~l~~~~~~L~~l~~~---~~~~~l~~~~~~s~~~~~~~l~fl~~ 242 (552)
..+| . ..+.+ ++..||+++.. -+..+.+.+.+.+|+++...+-+|-+
T Consensus 120 ------y~f~----~---r~EeE---V~~ilK~L~YPf~~siSs~~a~gspH~WP~iL~mlhWlvd 169 (581)
T KOG0995|consen 120 ------YEFP----E---RIEEE---VVQILKNLKYPFLLSISSLQAAGSPHNWPHILGMLHWLVD 169 (581)
T ss_pred ------cccc----h---hHHHH---HHHHHHhCCCCcccchhhhccCCCCCccHHHHHHHHHHHH
Confidence 0111 1 22222 22333332222 12245567788999999999888875
No 68
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=21.73 E-value=2.3e+02 Score=25.08 Aligned_cols=50 Identities=22% Similarity=0.321 Sum_probs=32.1
Q ss_pred HHHHhcCCC-cccccccCCCcc-eeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGID-HAEVSCFLPANK-FFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l-~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
-|+|+.|+= |..-.. .+- .+-..|-.....+..|++.||+-++|..++..
T Consensus 18 RyYE~~GLl~p~~r~~---~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 18 RFYEAEGLLSSVERSA---NGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred HHHHHCCCCCCCCcCC---CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 478999974 322111 011 11223446667888899999999999998853
No 69
>KOG1411 consensus Aspartate aminotransferase/Glutamic oxaloacetic transaminase AAT1/GOT2 [Amino acid transport and metabolism]
Probab=21.64 E-value=1.4e+02 Score=31.35 Aligned_cols=120 Identities=16% Similarity=0.247 Sum_probs=72.7
Q ss_pred HHHhCCCChhhHHHHHhhhccccccChhh---HHHHHHHHH-hhc---CCChhHHhhHhhcCccccccccccccccHHHH
Q 039791 134 ALSSFGFPWDKLGKLYKEEVSIFSQSSQD---LTAKLSRLK-NYY---GFSNVILVGICLGFPHVLAGNGDEWGTEIATL 206 (552)
Q Consensus 134 ~L~~~G~~~~~i~~~~~~~P~ll~~~~~~---l~~~l~~L~-~l~---G~s~~~i~~lv~~~P~lL~~s~~~~~~~l~~~ 206 (552)
|=+++|+=.+.+|.+- |...+.+. +.+-+..+- -+| .+-.+.|...|...|.+-.. .-.+++-+
T Consensus 271 yAKNMGLYgERvGa~s-----vvc~~ad~A~rV~SQlk~liRpmYSnPP~hGArIv~~Il~d~~l~~~----W~~evk~M 341 (427)
T KOG1411|consen 271 YAKNMGLYGERVGALS-----VVCKDADEAKRVESQLKILIRPMYSNPPLHGARIVATILSDPDLKNQ----WLGEVKGM 341 (427)
T ss_pred hhhhcchhhhccceeE-----EEecCHHHHHHHHHHHHHHhcccccCCCccchhhhhhccCChHHHHH----HHHHHHHH
Confidence 4567788888888753 56666653 444444332 222 33335566666666655332 22233334
Q ss_pred HHHHhhhhhcccccccccCCccchhhHhHHHHHHhhCCCChhHHHHHHhhCCccee
Q 039791 207 FDDLKTVFVDFGLMSSVEGNVEVWYDICRKIRVFYDFRFEKGKLGELMGRNKSIFL 262 (552)
Q Consensus 207 ~~~L~~l~~~~~~~~l~~~~~~s~~~~~~~l~fl~~lG~~~~~i~~li~~~P~lL~ 262 (552)
.+.+.++.-.....+-.+..+-+|+++-.-+..|.--|++++|+..+...+---++
T Consensus 342 adRi~~mR~~L~d~L~~~gs~~~W~hI~~QIGMF~fTgl~peQv~~l~ke~~iYmT 397 (427)
T KOG1411|consen 342 ADRIISMRQQLFDALEKEGSPGNWSHITKQIGMFCFTGLNPEQVDWLTKEYHIYLT 397 (427)
T ss_pred HHhhhhhHHHHhHHhhcCCCCccHHHHHHhhheeeecCCCHHHHHHHHhhheeeec
Confidence 44444333222233344556779999999999999999999999999888755454
No 70
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.44 E-value=1.7e+02 Score=24.25 Aligned_cols=51 Identities=16% Similarity=0.269 Sum_probs=30.6
Q ss_pred HHHHhcCCC-cccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhh
Q 039791 99 FFFESIGID-HAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKE 151 (552)
Q Consensus 99 ~f~eslGl~-~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~ 151 (552)
-|+|+.|+= |.....- -. -.+-..|-.-...+..|++.|++-++|..++..
T Consensus 18 R~ye~~Gll~p~~~~~~-gy-R~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 18 FHYDKIGLFKPEIVKEN-GY-RYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHCCCCCCCccCCC-CC-ccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 367888973 3322210 00 011122334556788899999999999998743
No 71
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=20.98 E-value=1.8e+02 Score=25.27 Aligned_cols=52 Identities=12% Similarity=0.089 Sum_probs=33.2
Q ss_pred HHHHhcCCCcccccccCCCcceeeccccchHHHHHHHHhCCCChhhHHHHHhhh
Q 039791 99 FFFESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSSFGFPWDKLGKLYKEE 152 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~~G~~~~~i~~~~~~~ 152 (552)
-|+|+.|+=++.-.. -.. =.+-..+-.....+..|++.|+|-++|..++...
T Consensus 18 RyYe~~GLl~p~~~~-~gy-R~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 18 RYYEEKGLIASIGRR-GLR-RQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHCCCCCCCcCC-CCc-eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 478999974432221 111 1122234455678899999999999999988553
No 72
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.19 E-value=3.1e+02 Score=22.72 Aligned_cols=67 Identities=15% Similarity=0.157 Sum_probs=38.7
Q ss_pred HHHHhcCCCcccccccCCCcceeeccccchHHHHHHHHh-CCCChhhHHHHHhhhccccccChhhHHHHHHHHHh
Q 039791 99 FFFESIGIDHAEVSCFLPANKFFLSEDSCLLNAACALSS-FGFPWDKLGKLYKEEVSIFSQSSQDLTAKLSRLKN 172 (552)
Q Consensus 99 ~f~eslGl~~~~~~~~~P~~l~~ls~d~~l~~~~~~L~~-~G~~~~~i~~~~~~~P~ll~~~~~~l~~~l~~L~~ 172 (552)
.|+|+.|+=+..-..= +..-.|-.++-.....+..|++ +|++.++|..++.. .+-+.+..+++.+..
T Consensus 18 R~Ye~~GLl~p~~r~~-~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~------~~~~~~~~~~~~~~~ 85 (95)
T cd04780 18 KYYLREGLLPEGRRLA-PNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA------IADASLPSTLLALAV 85 (95)
T ss_pred HHHHHCCCCCCCcCCC-CCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh------cCcccHHHHHHHHHH
Confidence 4688888744321110 1011222334455667777875 99999999998743 233346666666654
No 73
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=20.12 E-value=94 Score=27.65 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=17.4
Q ss_pred CCChhHHhhHhhcCccccccc
Q 039791 175 GFSNVILVGICLGFPHVLAGN 195 (552)
Q Consensus 175 G~s~~~i~~lv~~~P~lL~~s 195 (552)
.++.+++..++..+|.++-.+
T Consensus 73 ~ls~~e~i~ll~~~P~LikRP 93 (132)
T PRK13344 73 ELSVNEVIDLIQENPRILKSP 93 (132)
T ss_pred cCCHHHHHHHHHhCccceeCc
Confidence 346688899999999999885
Done!