Query 045903
Match_columns 385
No_of_seqs 224 out of 1238
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 06:43:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045903.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045903hhsearch_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 7.8E-54 1.7E-58 435.1 24.8 281 63-353 160-446 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 3.6E-47 7.8E-52 373.6 12.7 276 63-344 33-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.7E-41 3.7E-46 344.8 20.8 303 37-347 99-413 (487)
4 KOG1267 Mitochondrial transcri 100.0 2.1E-28 4.5E-33 246.1 15.1 277 36-319 65-411 (413)
5 PF02536 mTERF: mTERF; InterP 100.0 1.2E-28 2.7E-33 242.1 10.0 244 35-286 38-326 (345)
6 KOG1267 Mitochondrial transcri 99.8 6.2E-20 1.3E-24 184.7 12.2 234 72-313 68-336 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00032 7E-09 43.0 2.0 30 153-183 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.0 0.00063 1.4E-08 41.6 2.7 30 257-287 2-31 (31)
9 PF11955 PORR: Plant organelle 92.6 3.2 7E-05 40.8 13.7 31 240-271 262-293 (335)
10 cd04790 HTH_Cfa-like_unk Helix 92.3 0.23 5E-06 44.0 4.9 51 35-87 19-71 (172)
11 cd04790 HTH_Cfa-like_unk Helix 91.0 2.4 5.1E-05 37.6 9.9 54 66-123 17-72 (172)
12 PF04695 Pex14_N: Peroxisomal 75.9 4.9 0.00011 34.1 4.6 37 85-124 13-49 (136)
13 smart00165 UBA Ubiquitin assoc 65.3 11 0.00023 23.9 3.4 23 240-262 3-25 (37)
14 PF00627 UBA: UBA/TS-N domain; 65.2 9.5 0.00021 24.4 3.2 23 240-262 4-26 (37)
15 PF04695 Pex14_N: Peroxisomal 65.1 6.5 0.00014 33.4 3.0 31 236-266 21-51 (136)
16 PF14490 HHH_4: Helix-hairpin- 63.7 27 0.00058 27.4 6.2 9 212-220 64-72 (94)
17 cd00194 UBA Ubiquitin Associat 62.5 13 0.00028 23.7 3.4 23 240-262 3-25 (38)
18 PF11212 DUF2999: Protein of u 61.1 42 0.0009 25.2 6.1 58 65-129 3-63 (82)
19 PF11955 PORR: Plant organelle 60.6 31 0.00067 34.0 7.2 93 178-270 45-152 (335)
20 PF07499 RuvA_C: RuvA, C-termi 56.5 16 0.00035 24.8 3.2 24 64-87 4-27 (47)
21 PF08069 Ribosomal_S13_N: Ribo 55.9 8.5 0.00018 27.9 1.8 37 85-121 20-56 (60)
22 PF07499 RuvA_C: RuvA, C-termi 55.5 23 0.0005 24.0 3.9 25 238-262 3-27 (47)
23 cd04785 HTH_CadR-PbrR-like Hel 55.5 3.9 8.5E-05 34.1 0.0 50 35-86 18-69 (126)
24 KOG2561 Adaptor protein NUB1, 54.0 39 0.00085 34.4 6.6 133 61-220 301-445 (568)
25 TIGR01448 recD_rel helicase, p 53.3 83 0.0018 34.4 9.7 99 59-166 73-186 (720)
26 PRK13752 putative transcriptio 52.8 8.2 0.00018 33.1 1.6 50 35-86 25-76 (144)
27 cd04788 HTH_NolA-AlbR Helix-Tu 51.6 5.3 0.00012 31.6 0.2 51 35-87 18-70 (96)
28 TIGR00601 rad23 UV excision re 50.4 1.5E+02 0.0032 29.8 10.2 39 62-107 155-193 (378)
29 KOG0400 40S ribosomal protein 49.8 18 0.00038 30.4 3.0 64 84-148 19-82 (151)
30 PF14490 HHH_4: Helix-hairpin- 49.8 60 0.0013 25.4 6.0 22 65-86 10-31 (94)
31 cd04768 HTH_BmrR-like Helix-Tu 49.6 6.5 0.00014 31.1 0.4 51 35-87 18-70 (96)
32 cd04786 HTH_MerR-like_sg7 Heli 47.3 5.1 0.00011 33.8 -0.6 50 35-86 18-69 (131)
33 cd04782 HTH_BltR Helix-Turn-He 47.1 8.7 0.00019 30.4 0.8 50 35-86 18-69 (97)
34 PF02631 RecX: RecX family; I 46.5 1.4E+02 0.003 24.3 8.1 107 133-261 10-118 (121)
35 PRK10227 DNA-binding transcrip 46.2 11 0.00025 31.8 1.4 50 35-86 18-69 (135)
36 TIGR02047 CadR-PbrR Cd(II)/Pb( 46.0 8.9 0.00019 32.0 0.7 50 35-86 18-69 (127)
37 COG2511 GatE Archaeal Glu-tRNA 46.0 2.2E+02 0.0048 29.9 10.6 75 35-124 433-508 (631)
38 PF08004 DUF1699: Protein of u 45.8 55 0.0012 27.4 5.2 80 110-194 28-117 (131)
39 cd04784 HTH_CadR-PbrR Helix-Tu 45.7 9.8 0.00021 31.7 1.0 50 35-86 18-69 (127)
40 PRK08561 rps15p 30S ribosomal 44.2 62 0.0013 28.0 5.5 37 86-122 21-57 (151)
41 cd08319 Death_RAIDD Death doma 40.8 1.4E+02 0.003 23.0 6.6 19 106-124 21-39 (83)
42 TIGR00601 rad23 UV excision re 40.1 44 0.00096 33.5 4.7 44 235-287 153-196 (378)
43 PF11212 DUF2999: Protein of u 39.8 1.6E+02 0.0035 22.1 7.2 20 172-191 3-22 (82)
44 PRK00117 recX recombination re 38.5 2.2E+02 0.0047 24.3 8.4 73 100-194 80-153 (157)
45 PRK11613 folP dihydropteroate 37.6 71 0.0015 30.7 5.5 66 273-349 165-230 (282)
46 PF03960 ArsC: ArsC family; I 37.3 73 0.0016 25.5 4.9 21 109-129 70-90 (110)
47 PRK13749 transcriptional regul 37.1 13 0.00028 30.9 0.4 54 33-88 19-74 (121)
48 COG3620 Predicted transcriptio 34.2 38 0.00082 29.7 2.7 31 153-184 68-98 (187)
49 smart00657 RPOL4c DNA-directed 34.1 68 0.0015 26.4 4.2 57 93-155 52-108 (118)
50 COG1125 OpuBA ABC-type proline 31.0 55 0.0012 31.2 3.5 66 236-301 71-139 (309)
51 PTZ00072 40S ribosomal protein 30.6 1.2E+02 0.0026 26.1 5.1 49 73-122 6-54 (148)
52 PRK14135 recX recombination re 30.2 4.3E+02 0.0094 24.6 9.6 131 64-194 75-259 (263)
53 PF11181 YflT: Heat induced st 30.0 1.7E+02 0.0037 23.2 5.8 75 167-257 9-89 (103)
54 PF03960 ArsC: ArsC family; I 30.0 86 0.0019 25.1 4.2 21 181-201 70-90 (110)
55 PF03874 RNA_pol_Rpb4: RNA pol 29.1 39 0.00084 27.5 2.0 60 55-119 51-110 (117)
56 PF02787 CPSase_L_D3: Carbamoy 29.0 46 0.00099 27.7 2.4 60 59-119 9-82 (123)
57 TIGR02054 MerD mercuric resist 28.7 21 0.00045 29.6 0.3 50 35-86 21-72 (120)
58 cd08306 Death_FADD Fas-associa 28.1 1.6E+02 0.0036 22.6 5.2 18 106-123 21-38 (86)
59 PRK08561 rps15p 30S ribosomal 28.1 1.1E+02 0.0024 26.5 4.5 50 62-111 32-81 (151)
60 cd01108 HTH_CueR Helix-Turn-He 28.0 21 0.00046 29.7 0.2 19 67-85 50-68 (127)
61 TIGR02051 MerR Hg(II)-responsi 28.0 20 0.00043 29.8 0.0 19 67-85 49-67 (124)
62 PHA02591 hypothetical protein; 27.6 72 0.0016 24.4 2.9 27 58-84 43-69 (83)
63 PF10678 DUF2492: Protein of u 27.3 81 0.0018 24.1 3.2 60 310-375 7-69 (78)
64 TIGR02044 CueR Cu(I)-responsiv 27.0 23 0.0005 29.4 0.3 19 67-85 50-68 (127)
65 cd04783 HTH_MerR1 Helix-Turn-H 26.6 21 0.00046 29.6 -0.0 20 101-120 49-68 (126)
66 PF09288 UBA_3: Fungal ubiquit 26.6 84 0.0018 22.4 2.9 22 241-262 12-33 (55)
67 cd04787 HTH_HMRTR_unk Helix-Tu 26.5 24 0.00053 29.6 0.3 19 67-85 50-68 (133)
68 cd04780 HTH_MerR-like_sg5 Heli 26.3 50 0.0011 26.0 2.0 19 67-85 50-69 (95)
69 cd08316 Death_FAS_TNFRSF6 Deat 26.1 3.4E+02 0.0073 21.6 8.3 28 170-197 20-47 (97)
70 cd04770 HTH_HMRTR Helix-Turn-H 25.9 25 0.00053 28.9 0.2 19 67-85 50-68 (123)
71 PRK00117 recX recombination re 25.1 4.3E+02 0.0092 22.4 11.0 85 66-158 17-102 (157)
72 PF09999 DUF2240: Uncharacteri 25.1 1.6E+02 0.0035 25.2 5.1 39 214-261 72-111 (144)
73 PRK14136 recX recombination re 24.6 6.6E+02 0.014 24.5 12.0 25 238-262 278-302 (309)
74 TIGR01448 recD_rel helicase, p 24.3 5.5E+02 0.012 28.1 10.2 114 97-220 76-207 (720)
75 PRK09514 zntR zinc-responsive 24.2 29 0.00063 29.5 0.4 50 35-86 19-70 (140)
76 PF02022 Integrase_Zn: Integra 23.6 1.4E+02 0.003 19.7 3.4 30 236-265 6-36 (40)
77 cd01392 HTH_LacI Helix-turn-he 23.5 1.5E+02 0.0033 19.7 3.9 42 72-116 6-47 (52)
78 cd01109 HTH_YyaN Helix-Turn-He 23.2 30 0.00066 28.0 0.3 22 100-121 48-69 (113)
79 KOG3207 Beta-tubulin folding c 22.9 58 0.0013 33.3 2.2 45 70-114 204-257 (505)
80 PRK00116 ruvA Holliday junctio 22.8 1.4E+02 0.0031 26.7 4.6 26 237-262 148-173 (192)
81 cd01111 HTH_MerD Helix-Turn-He 22.7 31 0.00066 27.9 0.2 49 35-85 18-68 (107)
82 PF09278 MerR-DNA-bind: MerR, 22.6 1E+02 0.0022 21.9 3.0 20 241-260 6-25 (65)
83 PF08671 SinI: Anti-repressor 22.6 1.1E+02 0.0025 18.8 2.6 25 237-261 4-28 (30)
84 PF10440 WIYLD: Ubiquitin-bind 22.4 1.6E+02 0.0034 21.8 3.8 34 235-268 8-41 (65)
85 COG4669 EscJ Type III secretor 20.9 1.4E+02 0.003 27.9 4.0 96 61-166 31-129 (246)
86 cd08315 Death_TRAILR_DR4_DR5 D 20.9 2.7E+02 0.0058 22.0 5.3 21 104-124 25-45 (96)
87 cd04789 HTH_Cfa Helix-Turn-Hel 20.8 39 0.00085 26.9 0.5 48 35-85 19-68 (102)
88 cd04781 HTH_MerR-like_sg6 Heli 20.7 2.3E+02 0.0051 23.0 5.1 23 240-262 47-69 (120)
89 TIGR03853 matur_matur probable 20.6 1.3E+02 0.0027 23.0 3.1 60 310-375 5-67 (77)
90 KOG2629 Peroxisomal membrane a 20.6 1.7E+02 0.0036 28.2 4.6 26 236-261 20-45 (300)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=7.8e-54 Score=435.09 Aligned_cols=281 Identities=19% Similarity=0.328 Sum_probs=245.9
Q ss_pred chHHHHHHHhCCCChHHHHHHHHhCCCccccCcc-cHHHHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHH
Q 045903 63 PKNSTEVLKKWGCSDSDITKLFARRPTLQKADAL-NLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFL 141 (385)
Q Consensus 63 ~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e-~l~~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL 141 (385)
...+++||+++|+++++|++++.++|++|.++++ ++.++++||.++|++.++|++++.++|++|++++++++.|+++||
T Consensus 160 L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL 239 (487)
T PLN03196 160 LAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYL 239 (487)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHH
Confidence 3447888888888888888888888888888887 588888888888888888888888888888888888888888888
Q ss_pred HhhhcChhhHhhhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHHHhhCCcccccCC--CChhHHHHH-HhhCCCc
Q 045903 142 IKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTS--LNDQKMEYI-SRTQVSR 218 (385)
Q Consensus 142 ~~~g~~~~~v~~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~~--~~~~kv~~L-~~lG~~~ 218 (385)
+++|++.++|++++.++|++|++++|++++|++++|+++|++.+++..+++++|.+++.+. ...++++++ .++|+++
T Consensus 240 ~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~ 319 (487)
T PLN03196 240 ESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDP 319 (487)
T ss_pred HHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCH
Confidence 8888888888888888888888888878888888888888888888888888888887642 345566676 6789988
Q ss_pred ch--hhHHHHHHHHHhCcHHHHHHHHHHHHHcCCCHHHHHHHHHhCCCccccCHHHHHHHHHHHHHhcCCChhhHhhcCC
Q 045903 219 AS--KMYKYVVTLIAISRIETIREKVANLEKFGMSEDEIWSLFGRSPLLLTLSVDKVQRNMTFVVGTMKMPANVILEYPF 296 (385)
Q Consensus 219 ~~--~~~~~~p~il~~s~~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL~~s~e~l~~k~~fL~~~mg~~~~~i~~~P~ 296 (385)
++ .++...|+++++| +++|+++++||+++||+.++++.||+++|++|++|.++|+++++||+++||++.++|++||+
T Consensus 320 e~i~~~v~k~P~il~lS-e~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~ 398 (487)
T PLN03196 320 EDFGRVIEKLPQIVSLN-RNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPA 398 (487)
T ss_pred HHHHHHHHhcchhhccc-HHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChH
Confidence 87 4678889999987 58999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCcccccHHHHHHHHHHHHCCCCcccccCCcchhhhcccHHhHHHhhcccCCCC
Q 045903 297 LLFNNLEAVMKPRVLLAAKVQDMGLVPEIKGLPAILSALRMNEKRFLKVFIHCHPQD 353 (385)
Q Consensus 297 ~L~~Sle~rIkpR~~~l~~L~~~Gl~~~i~~~~~l~~~L~~Se~~F~~~~v~~~~~~ 353 (385)
||+||||+||+|||++ |+++|+. .++.++|+|||++|+++|+.+|.|.
T Consensus 399 ~LsySLEkRI~PR~~~---L~~kGl~------~sL~~~L~~sd~~F~~r~v~~y~e~ 446 (487)
T PLN03196 399 YFTYGLESRIKPRYER---VAKKGIK------CSLAWFLNCSDDKFEQRMSGDFIEG 446 (487)
T ss_pred HhccChhhhhHHHHHH---HHHcCCC------CCHHHHhccCHHHHHHHHhhhcccc
Confidence 9999999999999997 4899973 6899999999999999999999874
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=3.6e-47 Score=373.60 Aligned_cols=276 Identities=26% Similarity=0.435 Sum_probs=172.4
Q ss_pred chHHHHHHHhCCCChHHHHHHHHhCCCccccCcc-cHHHHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHH
Q 045903 63 PKNSTEVLKKWGCSDSDITKLFARRPTLQKADAL-NLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFL 141 (385)
Q Consensus 63 ~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e-~l~~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL 141 (385)
...+++||.+.|++.+++++++.++|.++..+.+ ++.|.++||+++|++++|+++++.++|++|..+.+.++.+++.||
T Consensus 33 l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L 112 (345)
T PF02536_consen 33 LLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFL 112 (345)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHH
T ss_pred hhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHH
Confidence 3345666666666666666666666666666533 466666666666666666666666666665555555566666666
Q ss_pred HhhhcChhhHhhhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHHHhhCCcccccC--CCChhHHHHHHhhCCCcc
Q 045903 142 IKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRT--SLNDQKMEYISRTQVSRA 219 (385)
Q Consensus 142 ~~~g~~~~~v~~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~--~~~~~kv~~L~~lG~~~~ 219 (385)
+++|++.+.+.+++..+|..+... +++.+.++++.++|++.+++.+++..+|+++..+ ....+++++++++|++.+
T Consensus 113 ~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~ 190 (345)
T PF02536_consen 113 RSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKE 190 (345)
T ss_dssp HHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GH
T ss_pred hhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccch
Confidence 666666554555555555543322 1233333333333333333333333333322221 134666777777777666
Q ss_pred h--hhHHHHHHHHHhCc--------------------------------HHHHHHHHHHHHHcCCCHHHHHHHHHhCCCc
Q 045903 220 S--KMYKYVVTLIAISR--------------------------------IETIREKVANLEKFGMSEDEIWSLFGRSPLL 265 (385)
Q Consensus 220 ~--~~~~~~p~il~~s~--------------------------------~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~l 265 (385)
+ .++...|.+++.+. .+++.+++++|.++|||.+|+++|+.++|++
T Consensus 191 ~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~i 270 (345)
T PF02536_consen 191 DIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQI 270 (345)
T ss_dssp HHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGG
T ss_pred hhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcch
Confidence 5 45555554444333 3589999999999999999999999999999
Q ss_pred cccCHHHHHHHHHHHHHhcCCChhhHhhcCCccccCcccccHHHHHHHHHHHHCCCCcccccCCcchhhhcccHHhHHH
Q 045903 266 LTLSVDKVQRNMTFVVGTMKMPANVILEYPFLLFNNLEAVMKPRVLLAAKVQDMGLVPEIKGLPAILSALRMNEKRFLK 344 (385)
Q Consensus 266 L~~s~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~rIkpR~~~l~~L~~~Gl~~~i~~~~~l~~~L~~Se~~F~~ 344 (385)
|++|.++++++++||+++||++.++|+++|++|+||+|+||+|||+++++|+++|+ . ..+++.++|++||++|++
T Consensus 271 L~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~---~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 271 LSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-I---INPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp GGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-G---GGGGS-HHHHHHHHHHT-
T ss_pred hhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-C---CCCCHHHHhhccHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999996 2 238999999999999975
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.7e-41 Score=344.80 Aligned_cols=303 Identities=17% Similarity=0.276 Sum_probs=267.6
Q ss_pred cccccchHHHHHhhchhccccCCC-CCchHHHHHHHhCCCChHHHHHHHHhCCCccccCcc-cHHHHHHHHHhCCCChHh
Q 045903 37 YSTICQAEAVVEEITQDQANNYSD-NHPKNSTEVLKKWGCSDSDITKLFARRPTLQKADAL-NLRFKLSVLNELGLNSDD 114 (385)
Q Consensus 37 ~~~~g~~~~~~~~~~~~~~~~~~~-~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e-~l~~~l~~L~~lG~~~~~ 114 (385)
..++|++..... .-|++.-.+. .+..++++||+++|++.++|++++.++|++|..+++ ++.|+++||+++|++.++
T Consensus 99 L~s~G~~~~~i~--~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~ 176 (487)
T PLN03196 99 LHKLGLTIEDIN--EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQD 176 (487)
T ss_pred HHHcCCChHHhc--cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHH
Confidence 345555554333 1222322233 467779999999999999999999999999999998 699999999999999999
Q ss_pred HHHHHHhCccccccccchhhHhHHHHHHhhhcChhhHhhhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHHHhhC
Q 045903 115 LVKIINCRPRFLSSRINICFEERVDFLIKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSR 194 (385)
Q Consensus 115 I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~~~v~~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~ 194 (385)
|++++.++|++|++++++++.|+++||.++|++.+++++++.++|++|+++++++++|+++||+++|++.++|++++.++
T Consensus 177 i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~ 256 (487)
T PLN03196 177 IPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKR 256 (487)
T ss_pred HHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCC--CChhHHHHHHhhCCCcch--hhHHHHHHHHHhCcHHHHHHHHHHHH-HcCCCHHHHHHHHHhCCCccccC
Q 045903 195 PTLIPRTS--LNDQKMEYISRTQVSRAS--KMYKYVVTLIAISRIETIREKVANLE-KFGMSEDEIWSLFGRSPLLLTLS 269 (385)
Q Consensus 195 P~il~~~~--~~~~kv~~L~~lG~~~~~--~~~~~~p~il~~s~~~~l~~kv~~L~-~~G~s~~ev~~mv~~~P~lL~~s 269 (385)
|++|+.+. ...+++++|.++|+++++ .++...|.+++++.++++.+++++|. ++||+.+++..++.++|+++++|
T Consensus 257 P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lS 336 (487)
T PLN03196 257 PYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLN 336 (487)
T ss_pred CceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhccc
Confidence 99999873 567889999999999987 56778889999887789999999996 79999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCChhhH----hhcCCccccCcccccHHHHHHHHHHHHCCCCcccccCCcchhhhccc-HHhHHH
Q 045903 270 VDKVQRNMTFVVGTMKMPANVI----LEYPFLLFNNLEAVMKPRVLLAAKVQDMGLVPEIKGLPAILSALRMN-EKRFLK 344 (385)
Q Consensus 270 ~e~l~~k~~fL~~~mg~~~~~i----~~~P~~L~~Sle~rIkpR~~~l~~L~~~Gl~~~i~~~~~l~~~L~~S-e~~F~~ 344 (385)
.++++++++||.+ +|++.++| .++|++|+||.+ .|++++.|+ ..++|+.. ........+|++| |++...
T Consensus 337 e~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~-~l~~k~dFl--vneMg~~~--~~Iv~fP~~LsySLEkRI~P 410 (487)
T PLN03196 337 RNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLE-IMKPSLEFF--KKEMKRPL--KELVEFPAYFTYGLESRIKP 410 (487)
T ss_pred HHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHH-HHHHHHHHH--HHHhCCCH--HHHHhChHHhccChhhhhHH
Confidence 9999999999997 99999887 699999999996 999999997 56778743 3446677888999 778888
Q ss_pred hhc
Q 045903 345 VFI 347 (385)
Q Consensus 345 ~~v 347 (385)
||-
T Consensus 411 R~~ 413 (487)
T PLN03196 411 RYE 413 (487)
T ss_pred HHH
Confidence 773
No 4
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.96 E-value=2.1e-28 Score=246.07 Aligned_cols=277 Identities=21% Similarity=0.395 Sum_probs=241.9
Q ss_pred ccccccchHHHHHhhchhccccCCCCCchHHHHHHHhCCCChHHHHHHHHhCCCccccCccc-HHHHHHHHHhCCCChHh
Q 045903 36 TYSTICQAEAVVEEITQDQANNYSDNHPKNSTEVLKKWGCSDSDITKLFARRPTLQKADALN-LRFKLSVLNELGLNSDD 114 (385)
Q Consensus 36 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~-l~~~l~~L~~lG~~~~~ 114 (385)
-.+++|+..+.+..+++. +.++...+|++++++|+++|+++.+|..++..+|.++..+.++ +.+++.+|.+.|++.++
T Consensus 65 ~~~s~~~~~~~~~~~~~~-~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~ 143 (413)
T KOG1267|consen 65 LVDSLGLSIKLARKLSRE-VSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSE 143 (413)
T ss_pred eccccccchhhHHHHHHH-HHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccc
Confidence 347788888888888776 8889999999999999999999999999999999999999985 88999899999999999
Q ss_pred HHHHHHhCccccccccchhhHhHHHHHHhhh--c---------------------------------ChhhHh-------
Q 045903 115 LVKIINCRPRFLSSRINICFEERVDFLIKLF--G---------------------------------SREMLC------- 152 (385)
Q Consensus 115 I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g--~---------------------------------~~~~v~------- 152 (385)
+++++...|.+|+.+.+.++.+.++|+++++ . ..+.+.
T Consensus 144 l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~ 223 (413)
T KOG1267|consen 144 LSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQP 223 (413)
T ss_pred cchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCc
Confidence 9999999999999888888999999999975 1 111111
Q ss_pred -------------------------hhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHHHhhCCcccccCC-CChh
Q 045903 153 -------------------------KAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTS-LNDQ 206 (385)
Q Consensus 153 -------------------------~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~~-~~~~ 206 (385)
+++.++|.+++++.++.+++++++|+++|++.++|..++.++|++++++. .+..
T Consensus 224 ~~~~~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~ 303 (413)
T KOG1267|consen 224 RPVLLYLKLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLK 303 (413)
T ss_pred cceeeehhhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhH
Confidence 33445677777789999999999999999999999999999999999875 3456
Q ss_pred HHHHHHhhCCCcchhhHHHHHHHHHhCcHHHHHHHHHHHHHcCCCHHHHHHHHHhCCCccccCHH-HHHHHHHHHHHhcC
Q 045903 207 KMEYISRTQVSRASKMYKYVVTLIAISRIETIREKVANLEKFGMSEDEIWSLFGRSPLLLTLSVD-KVQRNMTFVVGTMK 285 (385)
Q Consensus 207 kv~~L~~lG~~~~~~~~~~~p~il~~s~~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL~~s~e-~l~~k~~fL~~~mg 285 (385)
+++++.+. .++ +...|+++..+ +..+.++++++..+|++.+++..|++++|+++++|.+ .++.+.+|+.+.|+
T Consensus 304 ~~~~~~~~--~~~---~~k~p~~l~~s-~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~ 377 (413)
T KOG1267|consen 304 TTEYLLKN--PKH---ILKFPQLLRSS-EDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLL 377 (413)
T ss_pred HHHHHHhc--chh---hhhhhhhhhcc-chhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcC
Confidence 67777666 333 67788888554 6999999999999999999999999999999999999 78899999999999
Q ss_pred CChhhHhhcCCccccCcccccHHHHHHHHHHHHC
Q 045903 286 MPANVILEYPFLLFNNLEAVMKPRVLLAAKVQDM 319 (385)
Q Consensus 286 ~~~~~i~~~P~~L~~Sle~rIkpR~~~l~~L~~~ 319 (385)
++.++++.+|++++|++|+|+.||+.+..++..+
T Consensus 378 ~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 378 RPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred chHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 9999999999999999999999999998766544
No 5
>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=99.95 E-value=1.2e-28 Score=242.12 Aligned_cols=244 Identities=24% Similarity=0.373 Sum_probs=192.1
Q ss_pred cccccccchHHHHHhh--chhccccCC-CCCchHHHHHHHhCCCChHHHHHHHHhCCCccccCcc-cHHHHHHHHHhCCC
Q 045903 35 ATYSTICQAEAVVEEI--TQDQANNYS-DNHPKNSTEVLKKWGCSDSDITKLFARRPTLQKADAL-NLRFKLSVLNELGL 110 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~--~~~~~~~~~-~~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e-~l~~~l~~L~~lG~ 110 (385)
.+.-++|++.....++ .-|++...+ .++..+.+++|+++|++++|+.+++.++|+++..+.+ ++.+++++|+++|+
T Consensus 38 ~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv 117 (345)
T PF02536_consen 38 EFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGV 117 (345)
T ss_dssp HHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT-
T ss_pred HHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCC
Confidence 4557888885554433 222233344 4567789999999999999999999999999998877 79999999999999
Q ss_pred ChHhHHHHHHhCccccccccchhhHhHHHHHHhhhcChhhHhhhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHH
Q 045903 111 NSDDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPM 190 (385)
Q Consensus 111 ~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~~~v~~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~l 190 (385)
+.+.+.+++..+|.++... +++.+.++++.++|++++++.+++.++|+++..+.+++++++++||+++|++.+++.++
T Consensus 118 ~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~ 195 (345)
T PF02536_consen 118 PPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKL 195 (345)
T ss_dssp -HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHH
T ss_pred cHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHH
Confidence 9998999999988876655 58999999999999999999999999999998888889999999999999999999999
Q ss_pred HhhCCcccccCC----------------------------------CChhHHHHHHhhCCCcch--hhHHHHHHHHHhCc
Q 045903 191 LMSRPTLIPRTS----------------------------------LNDQKMEYISRTQVSRAS--KMYKYVVTLIAISR 234 (385)
Q Consensus 191 l~~~P~il~~~~----------------------------------~~~~kv~~L~~lG~~~~~--~~~~~~p~il~~s~ 234 (385)
+.++|.+++.+. ...++++++.++|+++++ .|+...|++++++.
T Consensus 196 l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~ 275 (345)
T PF02536_consen 196 LRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSI 275 (345)
T ss_dssp HHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-H
T ss_pred hhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcch
Confidence 999999998763 134567899999999988 79999999999986
Q ss_pred HHHHHHHHHHHH-HcCCCHHHHHHHHHhCCCccccCHHH-HHHH---HHHHHHhcCC
Q 045903 235 IETIREKVANLE-KFGMSEDEIWSLFGRSPLLLTLSVDK-VQRN---MTFVVGTMKM 286 (385)
Q Consensus 235 ~~~l~~kv~~L~-~~G~s~~ev~~mv~~~P~lL~~s~e~-l~~k---~~fL~~~mg~ 286 (385)
+.++++++||. ++|++.++| .++|.+|++|.|+ |+++ ++++.+ .|.
T Consensus 276 -e~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~ri~PR~~~~~~l~~-~g~ 326 (345)
T PF02536_consen 276 -EKLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKRIKPRYEVLKVLKS-KGL 326 (345)
T ss_dssp -HHHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHHHHHHHHHHHTT---TTT
T ss_pred -hhhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhhhhhHHHHHHHHHH-CcC
Confidence 66999999998 599999988 4899999999995 9999 777776 563
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.82 E-value=6.2e-20 Score=184.72 Aligned_cols=234 Identities=21% Similarity=0.329 Sum_probs=185.4
Q ss_pred hCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHHHhhhcChhhH
Q 045903 72 KWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSREML 151 (385)
Q Consensus 72 ~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~~~v 151 (385)
++|.+...+..+.. .+...+..+....+++|+++|++..+|.+++..+|.++..+.++.+.++..+|.+.|.+...+
T Consensus 68 s~~~~~~~~~~~~~---~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l 144 (413)
T KOG1267|consen 68 SLGLSIKLARKLSR---EVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSEL 144 (413)
T ss_pred ccccchhhHHHHHH---HHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCcccccc
Confidence 46655544444332 233345557889999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhCCcccccCccccHHHHHHHHHHc-----------------------------------CCChhhHHHHHhhCCc
Q 045903 152 CKAIVRNPSLLTYDLDKTIKPVVALYEQV-----------------------------------GISRHDLIPMLMSRPT 196 (385)
Q Consensus 152 ~~il~~~P~lL~~s~e~~l~~~v~~L~~l-----------------------------------Gl~~~~i~~ll~~~P~ 196 (385)
..++..-|.+|+.+.+.++.+.++|++++ |+..+.+..++..+|.
T Consensus 145 ~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~ 224 (413)
T KOG1267|consen 145 SSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPR 224 (413)
T ss_pred chhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCcc
Confidence 99998888888876666677777776665 3344444444444455
Q ss_pred ccccCCCChhHHHHHHhhCCCcchhhHHHHHHHHHhCcHHHHHHHHHHHHHcCCCHHHHHHHHHhCCCccccCHHHHHHH
Q 045903 197 LIPRTSLNDQKMEYISRTQVSRASKMYKYVVTLIAISRIETIREKVANLEKFGMSEDEIWSLFGRSPLLLTLSVDKVQRN 276 (385)
Q Consensus 197 il~~~~~~~~kv~~L~~lG~~~~~~~~~~~p~il~~s~~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL~~s~e~l~~k 276 (385)
.+.........+.++.++||++.+.++.+++.+++.+.++++++++++|+++||+.+|++.|++++|++|++|.+++..+
T Consensus 225 ~~~~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~ 304 (413)
T KOG1267|consen 225 PVLLYLKLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKT 304 (413)
T ss_pred ceeeehhhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHH
Confidence 44332234555678899999999999999999999999999999999999999999999999999999999999998888
Q ss_pred HHHHHHhcCCChhhHhhcCCccccCcccccHHHHHHH
Q 045903 277 MTFVVGTMKMPANVILEYPFLLFNNLEAVMKPRVLLA 313 (385)
Q Consensus 277 ~~fL~~~mg~~~~~i~~~P~~L~~Sle~rIkpR~~~l 313 (385)
++|+.+. .+++.++|+++.+|.. .+.+|++++
T Consensus 305 ~~~~~~~----~~~~~k~p~~l~~s~~-~l~~~ie~l 336 (413)
T KOG1267|consen 305 TEYLLKN----PKHILKFPQLLRSSED-KLKPRIEFL 336 (413)
T ss_pred HHHHHhc----chhhhhhhhhhhccch-hhhhhHHHH
Confidence 8888875 3347788888866654 788887765
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=97.10 E-value=0.00032 Score=42.95 Aligned_cols=30 Identities=33% Similarity=0.697 Sum_probs=19.7
Q ss_pred hhhhhCCcccccCccccHHHHHHHHHHcCCC
Q 045903 153 KAIVRNPSLLTYDLDKTIKPVVALYEQVGIS 183 (385)
Q Consensus 153 ~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~ 183 (385)
+++.++|.+|+++ +++++++++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 4566677777777 45577777777766653
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=97.01 E-value=0.00063 Score=41.61 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=25.4
Q ss_pred HHHHhCCCccccCHHHHHHHHHHHHHhcCCC
Q 045903 257 SLFGRSPLLLTLSVDKVQRNMTFVVGTMKMP 287 (385)
Q Consensus 257 ~mv~~~P~lL~~s~e~l~~k~~fL~~~mg~~ 287 (385)
+++.++|.++++|.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4678899999999888999999999 58874
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=3.2 Score=40.79 Aligned_cols=31 Identities=19% Similarity=0.507 Sum_probs=16.9
Q ss_pred HHHHHHH-HcCCCHHHHHHHHHhCCCccccCHH
Q 045903 240 EKVANLE-KFGMSEDEIWSLFGRSPLLLTLSVD 271 (385)
Q Consensus 240 ~kv~~L~-~~G~s~~ev~~mv~~~P~lL~~s~e 271 (385)
+++..|+ ++|++ ..+..++.+||.|+..|..
T Consensus 262 ~~L~~fr~ef~lp-~k~~~~l~rHPgIFYvS~k 293 (335)
T PF11955_consen 262 DHLTHFRKEFGLP-QKFRRLLLRHPGIFYVSLK 293 (335)
T ss_pred HHHHHHHHHhCCc-HHHHHHHHhCCCeEEEecc
Confidence 4444444 46665 4555566666666655544
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=92.27 E-value=0.23 Score=44.02 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=30.9
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHhC
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFARR 87 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~~ 87 (385)
+.|+..|+-..... ....-+.++.++... .+..|++.|++-++|..++...
T Consensus 19 RyYe~~GLl~p~~r--~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 19 LYYERIGLLSPSAR--SESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHCCCCCCCcc--CCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 67888886442111 122234555554443 4677888888888888877654
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=90.95 E-value=2.4 Score=37.59 Aligned_cols=54 Identities=6% Similarity=0.068 Sum_probs=32.2
Q ss_pred HHHHHHhCCCChHHHHHHHHhCCCccccCccc--HHHHHHHHHhCCCChHhHHHHHHhCc
Q 045903 66 STEVLKKWGCSDSDITKLFARRPTLQKADALN--LRFKLSVLNELGLNSDDLVKIINCRP 123 (385)
Q Consensus 66 ~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~--l~~~l~~L~~lG~~~~~I~~il~~~P 123 (385)
++.|....|+=... .+....--.++.+. -...+..|+++|++-++|..++....
T Consensus 17 tLRyYe~~GLl~p~----~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 17 TLLYYERIGLLSPS----ARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHCCCCCCC----ccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 66677777763211 01111222333332 23777888999999999999887543
No 12
>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=75.87 E-value=4.9 Score=34.12 Aligned_cols=37 Identities=16% Similarity=0.354 Sum_probs=22.2
Q ss_pred HhCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHhCcc
Q 045903 85 ARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCRPR 124 (385)
Q Consensus 85 ~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~P~ 124 (385)
..+|.|.... +..|++||++.|++.++|..++.+.+.
T Consensus 13 L~~p~V~~sp---~~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 13 LQDPKVRNSP---LEKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp HCTTTCCCS----HHHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred hCCcccccCC---HHHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 3455554322 667888888888888888777776544
No 13
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=65.27 E-value=11 Score=23.90 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 045903 240 EKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 240 ~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
++++-|.++||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46677788888888888777765
No 14
>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=65.18 E-value=9.5 Score=24.38 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=16.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 045903 240 EKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 240 ~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
+.++-|.++||+.++..+++..+
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 45667777888888887777655
No 15
>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=65.05 E-value=6.5 Score=33.36 Aligned_cols=31 Identities=32% Similarity=0.425 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCCCcc
Q 045903 236 ETIREKVANLEKFGMSEDEIWSLFGRSPLLL 266 (385)
Q Consensus 236 ~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL 266 (385)
..+.+|++||++-|++.+||..++.+.+.--
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 5688999999999999999999999876544
No 16
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=63.68 E-value=27 Score=27.42 Aligned_cols=9 Identities=0% Similarity=0.036 Sum_probs=3.1
Q ss_pred HhhCCCcch
Q 045903 212 SRTQVSRAS 220 (385)
Q Consensus 212 ~~lG~~~~~ 220 (385)
.++|+++++
T Consensus 64 ~~~g~~~~d 72 (94)
T PF14490_consen 64 LKLGIEPDD 72 (94)
T ss_dssp HTTT--TT-
T ss_pred HHcCCCCCC
Confidence 445555554
No 17
>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=62.46 E-value=13 Score=23.67 Aligned_cols=23 Identities=26% Similarity=0.419 Sum_probs=17.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 045903 240 EKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 240 ~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
++++-|.++||+.+++..++..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777888888888888777655
No 18
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=61.05 E-value=42 Score=25.15 Aligned_cols=58 Identities=21% Similarity=0.384 Sum_probs=42.0
Q ss_pred HHHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChHhHHHHH---HhCccccccc
Q 045903 65 NSTEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKII---NCRPRFLSSR 129 (385)
Q Consensus 65 ~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il---~~~P~iL~~~ 129 (385)
..++.|+++.+|+++|..++... .+|.-........+|++++.+..++ -.+|.++..-
T Consensus 3 PIia~LKehnvsd~qi~elFq~l-------T~NPl~AMa~i~qLGip~eKLQ~lm~~VMqnP~LikeA 63 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQAL-------TQNPLAAMATIQQLGIPQEKLQQLMAQVMQNPALIKEA 63 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHH-------hhCHHHHHHHHHHcCCCHHHHHHHHHHHhcChHHHHHH
Confidence 47889999999999999887542 2455566777888999998876643 4567655433
No 19
>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=60.64 E-value=31 Score=33.97 Aligned_cols=93 Identities=17% Similarity=0.259 Sum_probs=56.1
Q ss_pred HHcCCChhhHHHHHhhCCcccccCC---------CChhHHHHH--HhhCCC-cc-hhhHHHHHHHHHhCcHHHH-HHHHH
Q 045903 178 EQVGISRHDLIPMLMSRPTLIPRTS---------LNDQKMEYI--SRTQVS-RA-SKMYKYVVTLIAISRIETI-REKVA 243 (385)
Q Consensus 178 ~~lGl~~~~i~~ll~~~P~il~~~~---------~~~~kv~~L--~~lG~~-~~-~~~~~~~p~il~~s~~~~l-~~kv~ 243 (385)
+.+|++...+...+.++|.+|.... ...+....| .+..+- .. ..+..+.--++.+|....+ -.+++
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 3578866788888888888875321 111222211 111111 11 1233444445555543333 36778
Q ss_pred HHH-HcCCCHHHHHHHHHhCCCccccCH
Q 045903 244 NLE-KFGMSEDEIWSLFGRSPLLLTLSV 270 (385)
Q Consensus 244 ~L~-~~G~s~~ev~~mv~~~P~lL~~s~ 270 (385)
.++ ++|++++-...++.+||..+....
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEEee
Confidence 887 899999999999999999987744
No 20
>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=56.46 E-value=16 Score=24.82 Aligned_cols=24 Identities=21% Similarity=0.331 Sum_probs=18.4
Q ss_pred hHHHHHHHhCCCChHHHHHHHHhC
Q 045903 64 KNSTEVLKKWGCSDSDITKLFARR 87 (385)
Q Consensus 64 ~~~l~~L~~~G~s~~~i~~iv~~~ 87 (385)
+.+++.|.++|++..++.+++.+-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 347888999999999888888763
No 21
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=55.91 E-value=8.5 Score=27.88 Aligned_cols=37 Identities=16% Similarity=0.170 Sum_probs=28.1
Q ss_pred HhCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHh
Q 045903 85 ARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINC 121 (385)
Q Consensus 85 ~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~ 121 (385)
+..|..+..+++++...+.-|..-|+++++|+-++..
T Consensus 20 ~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 20 RSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 4568888889999999999999999999999988764
No 22
>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=55.51 E-value=23 Score=24.02 Aligned_cols=25 Identities=16% Similarity=0.268 Sum_probs=19.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhC
Q 045903 238 IREKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 238 l~~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
+.+-++-|..+||+..++.+++.+.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4566778889999999888888764
No 23
>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=55.48 E-value=3.9 Score=34.11 Aligned_cols=50 Identities=20% Similarity=0.182 Sum_probs=32.8
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|+..|+-+.... .....+.++.++... .+..|++.||+-++|..++..
T Consensus 18 R~Ye~~Gll~~~~r--~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 18 RYYESIGLLPEPAR--TAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred HHHHHCCCCCCCCc--CCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 67888887542211 112234556655554 477889999999999998864
No 24
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=54.02 E-value=39 Score=34.35 Aligned_cols=133 Identities=12% Similarity=0.150 Sum_probs=65.7
Q ss_pred CCchHHHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhC-------C----CChHhH-HHHHHhCcccccc
Q 045903 61 NHPKNSTEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNEL-------G----LNSDDL-VKIINCRPRFLSS 128 (385)
Q Consensus 61 ~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~l-------G----~~~~~I-~~il~~~P~iL~~ 128 (385)
.-++..+..+.++||.+++.+..++.+.. ++...++|+.+- - -..+++ .+....+. .
T Consensus 301 ki~d~~lsllv~mGfeesdaRlaLRsc~g-------~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~k~~n~----~ 369 (568)
T KOG2561|consen 301 KINDETLSLLVGMGFEESDARLALRSCNG-------DVDSAVQFIIERREKLAQKREKDLAREREILERKKYGNT----P 369 (568)
T ss_pred eccchHHHHHHHcCCCchHHHHHHHhccc-------cHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC----C
Confidence 34555788888899998888888777654 233334443321 1 111122 11111110 0
Q ss_pred ccchhhHhHHHHHHhhhcChhhHhhhhhhCCcccccCccccHHHHHHHHHHcCCChhhHHHHHhhCCcccccCCCChhHH
Q 045903 129 RINICFEERVDFLIKLFGSREMLCKAIVRNPSLLTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTSLNDQKM 208 (385)
Q Consensus 129 ~~~~~l~p~v~fL~~~g~~~~~v~~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~~~~~~kv 208 (385)
.-.......+.+|.++|.+.+-...++.++ ++.+...++.|.. ..+++..-....|.-+ ...++
T Consensus 370 ~~~wvn~rs~~rL~~mGyer~la~eaL~r~--------~Ndi~~aldllq~---esdel~~n~~~~p~~v-----d~~~l 433 (568)
T KOG2561|consen 370 MKKWVNPRSLERLVSMGYERELAAEALRRN--------ENDIQKALDLLQD---ESDELESNKPKRPEQV-----DGISL 433 (568)
T ss_pred cccccCHHHHHHHHhcchHhHHHHHHHHhc--------cCcHHHHHHhcCC---cchhhhccCCCCCccc-----chhhH
Confidence 111123445677888887776666666553 2334444443321 1122222222222211 24566
Q ss_pred HHHHhhCCCcch
Q 045903 209 EYISRTQVSRAS 220 (385)
Q Consensus 209 ~~L~~lG~~~~~ 220 (385)
..|..|||++..
T Consensus 434 a~Lv~mGF~e~~ 445 (568)
T KOG2561|consen 434 AELVSMGFEEGK 445 (568)
T ss_pred HHHHHhccccch
Confidence 778888888765
No 25
>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=53.33 E-value=83 Score=34.38 Aligned_cols=99 Identities=14% Similarity=0.043 Sum_probs=61.8
Q ss_pred CCCCchHHHHHHHh---CCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhC-CCChHhHHHHHHhCccccccccchhh
Q 045903 59 SDNHPKNSTEVLKK---WGCSDSDITKLFARRPTLQKADALNLRFKLSVLNEL-GLNSDDLVKIINCRPRFLSSRINICF 134 (385)
Q Consensus 59 ~~~~~~~~l~~L~~---~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~l-G~~~~~I~~il~~~P~iL~~~~~~~l 134 (385)
.|...+.++.||.+ -|+-+....+++..+..= ..+.+...-+-|.++ |++...+..+...... ....
T Consensus 73 ~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~---~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~ 143 (720)
T TIGR01448 73 APTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEA---AFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDE 143 (720)
T ss_pred CCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHh---HHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHH
Confidence 34556678999986 477788888888776521 112333334456564 8887777777766521 1125
Q ss_pred HhHHHHHHhhhcChh-----------hHhhhhhhCCcccccCc
Q 045903 135 EERVDFLIKLFGSRE-----------MLCKAIVRNPSLLTYDL 166 (385)
Q Consensus 135 ~p~v~fL~~~g~~~~-----------~v~~il~~~P~lL~~s~ 166 (385)
...+.||.+.|++.. +...+|..||+.|..++
T Consensus 144 ~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i 186 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDV 186 (720)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhc
Confidence 556677777777653 34556777888776543
No 26
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=52.78 E-value=8.2 Score=33.11 Aligned_cols=50 Identities=12% Similarity=0.123 Sum_probs=33.8
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|+++|+-+.... ....-+.++.++... .+..|++.||+-++|..++..
T Consensus 25 RyYE~~GLl~p~~r--~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 25 RFYQRKGLLPEPDK--PYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL 76 (144)
T ss_pred HHHHHCCCCCCCcc--CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 78999997652111 111135566666554 478889999999999998864
No 27
>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=51.60 E-value=5.3 Score=31.60 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=30.7
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHhC
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFARR 87 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~~ 87 (385)
+.|++.|+-..... ....-+.++.++... .+..|++.|++-++|..++...
T Consensus 18 R~ye~~Gll~p~~r--~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 18 HHYDHIGLLSPSQR--TEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred HHHHHCCCCCCCcc--CCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 67788886542111 111123445544443 4777888899999988888654
No 28
>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=50.41 E-value=1.5e+02 Score=29.82 Aligned_cols=39 Identities=10% Similarity=0.117 Sum_probs=31.5
Q ss_pred CchHHHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHh
Q 045903 62 HPKNSTEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNE 107 (385)
Q Consensus 62 ~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~ 107 (385)
.-+..|+-+.++|++++++.+.++. ...|..+-|+||.+
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRA-------afNNPdRAVEYL~t 193 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRA-------AFNNPDRAVEYLLT 193 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHH-------HhCCHHHHHHHHHh
Confidence 4456899999999999999998764 45577888999874
No 29
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=49.81 E-value=18 Score=30.37 Aligned_cols=64 Identities=16% Similarity=0.035 Sum_probs=42.4
Q ss_pred HHhCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHHHhhhcCh
Q 045903 84 FARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSR 148 (385)
Q Consensus 84 v~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~ 148 (385)
.+..|..+..++|++.+-+--|..-|+++++|+-++...--+=..+.- +=..-+.+|++.|+.+
T Consensus 19 ~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v-~G~kI~Rilk~~Gl~P 82 (151)
T KOG0400|consen 19 RRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFV-TGNKILRILKSNGLAP 82 (151)
T ss_pred ccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhhee-chhHHHHHHHHcCCCC
Confidence 356788888889999988989999999999998766644333222211 1122345777777653
No 30
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=49.80 E-value=60 Score=25.42 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=11.0
Q ss_pred HHHHHHHhCCCChHHHHHHHHh
Q 045903 65 NSTEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 65 ~~l~~L~~~G~s~~~i~~iv~~ 86 (385)
.++.+|..+|++...+.++.+.
T Consensus 10 ~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 10 ELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp HHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 3555666666665555555444
No 31
>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=49.64 E-value=6.5 Score=31.10 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=31.1
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHhC
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFARR 87 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~~ 87 (385)
+.|++.|+-..... ....-+.++.++... .+..|++.|++-++|..++...
T Consensus 18 Ryye~~Gll~p~~~--~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 18 RHYDDIGLFKPAKI--AENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHCCCCCCCcc--CCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 67888886542111 111123444444443 4778889999999998888654
No 32
>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=47.28 E-value=5.1 Score=33.79 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=32.6
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|++.|+-..... .....+.++.++... .+..|++.||+-++|..++..
T Consensus 18 RyYE~~GLl~p~~r--~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 18 RFYEAEGLLSSVER--SANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred HHHHHCCCCCCCCc--CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 78999997542111 111234455555543 477889999999999998864
No 33
>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=47.15 E-value=8.7 Score=30.43 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=30.0
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|++.|+-..... ....-+.++.++... .+..|+++||+-++|..++..
T Consensus 18 R~ye~~Gll~p~~~--~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 18 FHYDKIGLFKPEIV--KENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHCCCCCCCcc--CCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 67888886431111 111134455554443 477888899998888887764
No 34
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=46.49 E-value=1.4e+02 Score=24.27 Aligned_cols=107 Identities=20% Similarity=0.114 Sum_probs=50.5
Q ss_pred hhHhHHHHHHhhhc-ChhhHhhhhhhCCcc-cccCccccHHHHHHHHHHcCCChhhHHHHHhhCCcccccCCCChhHHHH
Q 045903 133 CFEERVDFLIKLFG-SREMLCKAIVRNPSL-LTYDLDKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTSLNDQKMEY 210 (385)
Q Consensus 133 ~l~p~v~fL~~~g~-~~~~v~~il~~~P~l-L~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~~~~~~kv~~ 210 (385)
.+...+++|...|. ++...+....+.-.- =+++ -.....-|+.-|++.+.|...+...+.. +.-.+.
T Consensus 10 ~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G----~~~I~~~L~~kGi~~~~i~~~l~~~~~~-------e~a~~~ 78 (121)
T PF02631_consen 10 AIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKG----PRRIRQKLKQKGIDREIIEEALEEYDEE-------EEALEL 78 (121)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT------HHHHHHHHHHTT--HHHHHHHHTCS-HH-------HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHhccccccc----HHHHHHHHHHHCCChHHHHHHHHHhhHH-------HHHHHH
Confidence 45666677777764 444444433332111 1112 2223445778899988888877622210 110111
Q ss_pred HHhhCCCcchhhHHHHHHHHHhCcHHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 045903 211 ISRTQVSRASKMYKYVVTLIAISRIETIREKVANLEKFGMSEDEIWSLFGR 261 (385)
Q Consensus 211 L~~lG~~~~~~~~~~~p~il~~s~~~~l~~kv~~L~~~G~s~~ev~~mv~~ 261 (385)
+-+........+.....++.+.+|..-||+.+.|..++..
T Consensus 79 -----------~~kk~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 79 -----------AEKKYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp -----------HHHHHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred -----------HHHHHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 1111111111122345556678999999999999887754
No 35
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=46.16 E-value=11 Score=31.81 Aligned_cols=50 Identities=10% Similarity=0.139 Sum_probs=32.2
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|+..|+-+.... +..-.+.++.++... .+..|+.+||+-++|..++..
T Consensus 18 RyYE~~GLl~p~~r--~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 18 RFYEEKGLVTPPMR--SENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred HHHHHCCCCCCccc--CCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 77889987542211 112234455554443 477788999999999998864
No 36
>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=46.02 E-value=8.9 Score=32.04 Aligned_cols=50 Identities=14% Similarity=0.117 Sum_probs=32.3
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|++.|+-..... ....-+.++.++... .+..|+++|++-++|..++..
T Consensus 18 R~Ye~~GLl~~~~r--~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 18 RFYEKQGLLPPPAR--TDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred HHHHHCCCCCCCCc--CCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 77888887542111 122234455555443 477888999999999998863
No 37
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=45.97 E-value=2.2e+02 Score=29.89 Aligned_cols=75 Identities=19% Similarity=0.221 Sum_probs=45.0
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchHHHHHH-HhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChH
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKNSTEVL-KKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSD 113 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~L-~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~ 113 (385)
++.|.+-++.+..+.+.. ..|+.|...++-+ .++|++..=...++ ..|.+ ..++-|.+.|+.+.
T Consensus 433 TDIPpi~i~~~~l~~~~~-----~~Pe~~~ek~~r~~~eygLs~~LA~~~~-~~~~~---------~~FEel~e~~v~p~ 497 (631)
T COG2511 433 TDIPPIRIDEELLEKIKE-----NLPELPEEKVERYVKEYGLSKELAEQLA-SDPRV---------DLFEELVEKGVDPT 497 (631)
T ss_pred CCCCCcccCHHHHHHHhh-----hCCCCHHHHHHHHHHHhCCCHHHHHHHH-hhhhH---------HHHHHHHHcCCCHH
Confidence 344555555554443333 4888999988877 57999985555444 33322 22333334588888
Q ss_pred hHHHHHHhCcc
Q 045903 114 DLVKIINCRPR 124 (385)
Q Consensus 114 ~I~~il~~~P~ 124 (385)
.+++++..-..
T Consensus 498 ~~A~~L~~~~~ 508 (631)
T COG2511 498 LIASTLVNTLP 508 (631)
T ss_pred HHHHHHHHHHH
Confidence 88887765433
No 38
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=45.82 E-value=55 Score=27.37 Aligned_cols=80 Identities=11% Similarity=0.198 Sum_probs=46.3
Q ss_pred CChHhHHHHHHhCccc----cccccchhhHhHHH-HHHhhhcC--hhhHh---hhhhhCCcccccCccccHHHHHHHHHH
Q 045903 110 LNSDDLVKIINCRPRF----LSSRINICFEERVD-FLIKLFGS--REMLC---KAIVRNPSLLTYDLDKTIKPVVALYEQ 179 (385)
Q Consensus 110 ~~~~~I~~il~~~P~i----L~~~~~~~l~p~v~-fL~~~g~~--~~~v~---~il~~~P~lL~~s~e~~l~~~v~~L~~ 179 (385)
-|..||-+++.+||.+ +-.|.-+++....+ ||.--|+. +++|+ +=+.. -+.+...+..+++-|+.
T Consensus 28 PSN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinE-----Yy~i~~~vi~~I~el~~ 102 (131)
T PF08004_consen 28 PSNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINE-----YYEIPESVIERIKELKS 102 (131)
T ss_pred CcchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCcc-----cccCCHHHHHHHHHHHH
Confidence 3566788888888876 22333344544443 44444442 33433 11111 12344567888888888
Q ss_pred cCCChhhHHHHHhhC
Q 045903 180 VGISRHDLIPMLMSR 194 (385)
Q Consensus 180 lGl~~~~i~~ll~~~ 194 (385)
=|.+.+++..=+.+.
T Consensus 103 eG~s~eei~~ki~~e 117 (131)
T PF08004_consen 103 EGKSEEEIAEKISRE 117 (131)
T ss_pred cCCCHHHHHHHHHHh
Confidence 999988887655543
No 39
>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=45.73 E-value=9.8 Score=31.65 Aligned_cols=50 Identities=14% Similarity=0.127 Sum_probs=32.9
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|+..|+-..... ....-+.++.++... .+..|+++||+-++|..++..
T Consensus 18 RyYe~~GLl~p~~r--~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 18 RYYEKEGLLPAPAR--SANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHCCCCCCCCc--CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 78899996541111 112234556555553 577889999999999998864
No 40
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=44.24 E-value=62 Score=27.95 Aligned_cols=37 Identities=11% Similarity=0.089 Sum_probs=31.3
Q ss_pred hCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHhC
Q 045903 86 RRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCR 122 (385)
Q Consensus 86 ~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~ 122 (385)
..|..+..+++++...+.-|..-|.++++||-++...
T Consensus 21 ~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 21 EPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 4577788888899999999999999999999888754
No 41
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=40.84 E-value=1.4e+02 Score=23.03 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=13.8
Q ss_pred HhCCCChHhHHHHHHhCcc
Q 045903 106 NELGLNSDDLVKIINCRPR 124 (385)
Q Consensus 106 ~~lG~~~~~I~~il~~~P~ 124 (385)
+.+|++..+|..|-..||.
T Consensus 21 r~Lgls~~~I~~i~~~~p~ 39 (83)
T cd08319 21 LDLGLSQTDIYRCKENHPH 39 (83)
T ss_pred HHcCCCHHHHHHHHHhCCC
Confidence 4677777777777777774
No 42
>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=40.08 E-value=44 Score=33.46 Aligned_cols=44 Identities=9% Similarity=0.290 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCCCccccCHHHHHHHHHHHHHhcCCC
Q 045903 235 IETIREKVANLEKFGMSEDEIWSLFGRSPLLLTLSVDKVQRNMTFVVGTMKMP 287 (385)
Q Consensus 235 ~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL~~s~e~l~~k~~fL~~~mg~~ 287 (385)
.+.....|+-+.+|||++++|.++++. +-.+=.+.++||.. |++
T Consensus 153 g~~~e~~I~~i~eMGf~R~qV~~ALRA-------afNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 153 GSERETTIEEIMEMGYEREEVERALRA-------AFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred chHHHHHHHHHHHhCCCHHHHHHHHHH-------HhCCHHHHHHHHHh--CCC
Confidence 367888999999999999999988873 33345678999997 887
No 43
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=39.82 E-value=1.6e+02 Score=22.10 Aligned_cols=20 Identities=15% Similarity=0.516 Sum_probs=12.2
Q ss_pred HHHHHHHHcCCChhhHHHHH
Q 045903 172 PVVALYEQVGISRHDLIPML 191 (385)
Q Consensus 172 ~~v~~L~~lGl~~~~i~~ll 191 (385)
|.+..|++..++++.|..++
T Consensus 3 PIia~LKehnvsd~qi~elF 22 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELF 22 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHH
Confidence 55666666666666665544
No 44
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=38.47 E-value=2.2e+02 Score=24.28 Aligned_cols=73 Identities=14% Similarity=0.057 Sum_probs=41.6
Q ss_pred HHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHHHhhhcChhhHhhhhhh-CCcccccCccccHHHHHHHHH
Q 045903 100 FKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSREMLCKAIVR-NPSLLTYDLDKTIKPVVALYE 178 (385)
Q Consensus 100 ~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~~~v~~il~~-~P~lL~~s~e~~l~~~v~~L~ 178 (385)
...+-|...|++.+.|..++...+ .+ ... .+.+++.+ +...-..+. +.-...+.+|.
T Consensus 80 ~I~~~L~~kGi~~~~I~~~l~~~~----~d---~~e--------------~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~ 137 (157)
T PRK00117 80 RIRQELRQKGVDREIIEEALAELD----ID---WEE--------------LARELARKKFRRPLPDDA-KEKAKLVRFLA 137 (157)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHcC----cc---HHH--------------HHHHHHHHHcCCCCCCCH-HHHHHHHHHHH
Confidence 334567778888888877777643 11 111 11122221 222212222 23455677899
Q ss_pred HcCCChhhHHHHHhhC
Q 045903 179 QVGISRHDLIPMLMSR 194 (385)
Q Consensus 179 ~lGl~~~~i~~ll~~~ 194 (385)
.-|++.+.|..++...
T Consensus 138 rkGF~~~~I~~~l~~~ 153 (157)
T PRK00117 138 RRGFSMDVIQRVLRNA 153 (157)
T ss_pred HCCCCHHHHHHHHHhh
Confidence 9999999998888654
No 45
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=37.64 E-value=71 Score=30.65 Aligned_cols=66 Identities=9% Similarity=0.067 Sum_probs=42.3
Q ss_pred HHHHHHHHHHhcCCChhhHhhcCCccccCcccccHHHHHHHHHHHHCCCCcccccCCcchhhhcccHHhHHHhhccc
Q 045903 273 VQRNMTFVVGTMKMPANVILEYPFLLFNNLEAVMKPRVLLAAKVQDMGLVPEIKGLPAILSALRMNEKRFLKVFIHC 349 (385)
Q Consensus 273 l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~rIkpR~~~l~~L~~~Gl~~~i~~~~~l~~~L~~Se~~F~~~~v~~ 349 (385)
+..+++.+.+ .|++.+.|+-.|. ++|+ +....-+++++.+..-.- ..+..++..|.|+|...+...
T Consensus 165 l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~~-------lg~Pilvg~SRKsfig~~~~~ 230 (282)
T PRK11613 165 FIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFHH-------FNLPLLVGMSRKSMIGQLLNV 230 (282)
T ss_pred HHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHHh-------CCCCEEEEecccHHHHhhcCC
Confidence 5667777776 8999999988896 4553 345555666555433210 122345667999999877654
No 46
>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=37.29 E-value=73 Score=25.52 Aligned_cols=21 Identities=14% Similarity=0.528 Sum_probs=11.2
Q ss_pred CCChHhHHHHHHhCccccccc
Q 045903 109 GLNSDDLVKIINCRPRFLSSR 129 (385)
Q Consensus 109 G~~~~~I~~il~~~P~iL~~~ 129 (385)
.++.+++..++..+|.++.+.
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 355555555555555555544
No 47
>PRK13749 transcriptional regulator MerD; Provisional
Probab=37.12 E-value=13 Score=30.92 Aligned_cols=54 Identities=11% Similarity=-0.008 Sum_probs=30.7
Q ss_pred cccccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHhCC
Q 045903 33 KSATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFARRP 88 (385)
Q Consensus 33 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~~P 88 (385)
|=+.|++.|+-+-... +..-.+.++.++... .+..++..||+-++|..++...+
T Consensus 19 tiR~YE~~GLl~p~~r--~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~ 74 (121)
T PRK13749 19 IVRDYLLRGLLRPVAC--TTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALD 74 (121)
T ss_pred HHHHHHHCCCCCCCCc--CCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 3377888886542211 111134444444443 36666778888888877776543
No 48
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=34.16 E-value=38 Score=29.74 Aligned_cols=31 Identities=35% Similarity=0.562 Sum_probs=21.7
Q ss_pred hhhhhCCcccccCccccHHHHHHHHHHcCCCh
Q 045903 153 KAIVRNPSLLTYDLDKTIKPVVALYEQVGISR 184 (385)
Q Consensus 153 ~il~~~P~lL~~s~e~~l~~~v~~L~~lGl~~ 184 (385)
+-+-..|-+ ..+.++.+...++.++..|+++
T Consensus 68 ~~iM~spvv-~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 68 KTIMHSPVV-SVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred hhhccCCee-EECchhhHHHHHHHHHHcCCcc
Confidence 344444544 4455777999999999999883
No 49
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=34.13 E-value=68 Score=26.37 Aligned_cols=57 Identities=16% Similarity=0.077 Sum_probs=35.0
Q ss_pred cCcccHHHHHHHHHhCCCChHhHHHHHHhCccccccccchhhHhHHHHHHhhhcChhhHhhhh
Q 045903 93 ADALNLRFKLSVLNELGLNSDDLVKIINCRPRFLSSRINICFEERVDFLIKLFGSREMLCKAI 155 (385)
Q Consensus 93 ~~~e~l~~~l~~L~~lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~g~~~~~v~~il 155 (385)
.+.+.+......|...|+.+.++..++.-+|.=. + .+...+.-+.+- .+++++-.++
T Consensus 52 ~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~----~-E~~~lI~sl~~r-~~ee~l~~iL 108 (118)
T smart00657 52 KNREIVRAVRTLLKSKKLHKFEIAQLGNLRPETA----E-EAQLLIPSLEER-IDEEELEELL 108 (118)
T ss_pred CCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCH----H-HHHHHhhhhhcc-CCHHHHHHHH
Confidence 3556677777788888888888888888888521 1 334444444332 3455554444
No 50
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=30.98 E-value=55 Score=31.21 Aligned_cols=66 Identities=14% Similarity=0.255 Sum_probs=43.3
Q ss_pred HHHHHHHHHHH-HcCC-CHHHHHHHHHhCCCccccCHHHHHHHHHHHHHhcCCChh-hHhhcCCccccC
Q 045903 236 ETIREKVANLE-KFGM-SEDEIWSLFGRSPLLLTLSVDKVQRNMTFVVGTMKMPAN-VILEYPFLLFNN 301 (385)
Q Consensus 236 ~~l~~kv~~L~-~~G~-s~~ev~~mv~~~P~lL~~s~e~l~~k~~fL~~~mg~~~~-~i~~~P~~L~~S 301 (385)
-.++.++.|.. ..|+ +.-.|.+=|.-.|.+++++.++++.+.+-|.+-+|++++ +.-+||.=|+-.
T Consensus 71 ~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLSGG 139 (309)
T COG1125 71 VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELSGG 139 (309)
T ss_pred HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcCcc
Confidence 45566666554 4443 334555556678888888888888888888888888764 455666665544
No 51
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=30.58 E-value=1.2e+02 Score=26.07 Aligned_cols=49 Identities=18% Similarity=0.235 Sum_probs=35.6
Q ss_pred CCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChHhHHHHHHhC
Q 045903 73 WGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKIINCR 122 (385)
Q Consensus 73 ~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~ 122 (385)
-|.|.+.+. .-+..|..+..+++++...+.-|..-|+++++||-++...
T Consensus 6 kG~S~S~~P-~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 6 KGISSSALP-YRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred CCCCCCCCC-CCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 344444333 1234577788888899999999999999999999888754
No 52
>PRK14135 recX recombination regulator RecX; Provisional
Probab=30.18 E-value=4.3e+02 Score=24.57 Aligned_cols=131 Identities=15% Similarity=0.096 Sum_probs=0.0
Q ss_pred hHHHHHHHhCCCChHHHHHHHHhCCCccccCcccH----------------HHHHHHHHhCCCChHhHHHHHHhCccccc
Q 045903 64 KNSTEVLKKWGCSDSDITKLFARRPTLQKADALNL----------------RFKLSVLNELGLNSDDLVKIINCRPRFLS 127 (385)
Q Consensus 64 ~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l----------------~~~l~~L~~lG~~~~~I~~il~~~P~iL~ 127 (385)
..+-+.|...|++++.|..++.+....-..+-... ...-+-|...|++.+.|..++.....-=.
T Consensus 75 ~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~~~~ 154 (263)
T PRK14135 75 KEVRDYLKKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTEEDQ 154 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCChhhH
Q ss_pred cccchhh-----------------HhHHHHHHhhhcChhhHhhhhh---------------------hCCcccccCcccc
Q 045903 128 SRINICF-----------------EERVDFLIKLFGSREMLCKAIV---------------------RNPSLLTYDLDKT 169 (385)
Q Consensus 128 ~~~~~~l-----------------~p~v~fL~~~g~~~~~v~~il~---------------------~~P~lL~~s~e~~ 169 (385)
.+....+ .....+|..-|++.+.|..++. +.+..=..+..+.
T Consensus 155 ~d~a~~~~~k~~~~~~~~~~~~~k~Ki~~~L~rkGf~~~~I~~~l~~~~~e~d~~~e~e~l~~~~~k~~~k~~~~~~~k~ 234 (263)
T PRK14135 155 IEVAQKLAEKLLKKYQKLPFKALKQKIIQSLLTKGFSYEVIKAALEELDLEQDEEEEQELLQKELEKAYRKYSKYDGYEL 234 (263)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHHHhcCCHHHH
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhhC
Q 045903 170 IKPVVALYEQVGISRHDLIPMLMSR 194 (385)
Q Consensus 170 l~~~v~~L~~lGl~~~~i~~ll~~~ 194 (385)
-.....||..-|++.+.|..++...
T Consensus 235 k~K~~~~L~rrGF~~~~I~~~l~~~ 259 (263)
T PRK14135 235 KQKLKQALYRKGFSYDDIDSFLREY 259 (263)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHh
No 53
>PF11181 YflT: Heat induced stress protein YflT
Probab=29.96 E-value=1.7e+02 Score=23.22 Aligned_cols=75 Identities=19% Similarity=0.359 Sum_probs=44.7
Q ss_pred cccHHHHHHHHHHcCCChhhHHHHHhhCCcccccCCCChhHHHHHHh------hCCCcchhhHHHHHHHHHhCcHHHHHH
Q 045903 167 DKTIKPVVALYEQVGISRHDLIPMLMSRPTLIPRTSLNDQKMEYISR------TQVSRASKMYKYVVTLIAISRIETIRE 240 (385)
Q Consensus 167 e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~il~~~~~~~~kv~~L~~------lG~~~~~~~~~~~p~il~~s~~~~l~~ 240 (385)
+..+...|+-|+.-|...++| .+++.+ ..+++.+.+ .|.++. .++..+..++. +.++.++
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI--------~Vva~d---~~~~~~l~~~t~~~~~~~~~~-~~~d~~~~~f~-~~~d~~~- 74 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI--------YVVAKD---KDRTERLADQTDTNTVGASEE-SFWDKIKNFFT-SGGDELR- 74 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE--------EEEEcC---chHHHHHHHhcCCceeccccc-cHHHHHHHhcc-CCcHHHH-
Confidence 445788899999999999888 556533 333433322 233332 34444555554 2334444
Q ss_pred HHHHHHHcCCCHHHHHH
Q 045903 241 KVANLEKFGMSEDEIWS 257 (385)
Q Consensus 241 kv~~L~~~G~s~~ev~~ 257 (385)
+-|.++|++.+++.+
T Consensus 75 --~~l~~lGl~~~ea~~ 89 (103)
T PF11181_consen 75 --SKLESLGLSEDEAER 89 (103)
T ss_pred --HHHHHcCCCHHHHHH
Confidence 445789999988764
No 54
>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=29.95 E-value=86 Score=25.09 Aligned_cols=21 Identities=38% Similarity=0.721 Sum_probs=17.7
Q ss_pred CCChhhHHHHHhhCCcccccC
Q 045903 181 GISRHDLIPMLMSRPTLIPRT 201 (385)
Q Consensus 181 Gl~~~~i~~ll~~~P~il~~~ 201 (385)
.++.+++..++..+|.++-+.
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 478899999999999998765
No 55
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=29.12 E-value=39 Score=27.48 Aligned_cols=60 Identities=28% Similarity=0.437 Sum_probs=0.0
Q ss_pred cccCCCCCchHHHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChHhHHHHH
Q 045903 55 ANNYSDNHPKNSTEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLVKII 119 (385)
Q Consensus 55 ~~~~~~~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~~il 119 (385)
..+.+++.....++.|.++|++..++..++.-.|. +++.+...+.-+.+ .++.++|..|+
T Consensus 51 ~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~----~~~El~~ii~~~~~-r~~ee~l~~iL 110 (117)
T PF03874_consen 51 SKFQNPESIKELREELKKFGLTEFEILQIINLRPT----TAVELRAIIESLES-RFSEEDLEEIL 110 (117)
T ss_dssp -SSSSHHHHHHHHHHHTTSTS-HHHHHHHHHH--S----SHHHHHHHSTTGTT-TSTHHHHHHHH
T ss_pred ccCCCHHHHHHHHHHHhcccCCHHHHHHHhcCCCC----CHHHHHHHHHHhcc-CCCHHHHHHHH
No 56
>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=28.97 E-value=46 Score=27.73 Aligned_cols=60 Identities=20% Similarity=0.229 Sum_probs=30.3
Q ss_pred CCCCchHHHHHHHhCCCChHHHHHHHHhCCCccccC-----cc-cH--------HHHHHHHHhCCCChHhHHHHH
Q 045903 59 SDNHPKNSTEVLKKWGCSDSDITKLFARRPTLQKAD-----AL-NL--------RFKLSVLNELGLNSDDLVKII 119 (385)
Q Consensus 59 ~~~~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~-----~e-~l--------~~~l~~L~~lG~~~~~I~~il 119 (385)
+++..-.+.+.|+ .|++.++|..+-.-+|+.|..= .+ .| ...+.-.+.+|+++..|+++.
T Consensus 9 td~Rlf~i~eAlr-rG~sveeI~e~T~ID~wFL~~i~~Iv~~e~~L~~~~~~~~~~~L~~aK~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 9 TDERLFAIAEALR-RGYSVEEIHELTKIDPWFLEQIKNIVDMEKELKEYLNELDPELLRKAKRLGFSDRQIARLW 82 (123)
T ss_dssp BTTHHHHHHHHHH-TTB-HHHHHHHH---HHHHHHHHHHHHHHHHHHHHGGG--HHHHHHHHHTT--HHHHHHHH
T ss_pred CCcHHHHHHHHHH-cCCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHcCCCHHHHHhcc
Confidence 3333334555554 4999999999988888876431 11 11 123333445677777777664
No 57
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=28.71 E-value=21 Score=29.65 Aligned_cols=50 Identities=12% Similarity=0.067 Sum_probs=25.2
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|++.|+.+-... +..--+.++.++... .+..|+..|++-++|..++..
T Consensus 21 R~Ye~~GLL~p~~r--~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~ 72 (120)
T TIGR02054 21 RDYLLRGLLHPVRR--TTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRA 72 (120)
T ss_pred HHHHHCCCCCCCcc--CCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 66777775441111 111123344444433 355666677777777666653
No 58
>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=28.12 E-value=1.6e+02 Score=22.61 Aligned_cols=18 Identities=28% Similarity=0.549 Sum_probs=12.1
Q ss_pred HhCCCChHhHHHHHHhCc
Q 045903 106 NELGLNSDDLVKIINCRP 123 (385)
Q Consensus 106 ~~lG~~~~~I~~il~~~P 123 (385)
+.+|++..+|..+-..+|
T Consensus 21 R~LGlse~~Id~i~~~~~ 38 (86)
T cd08306 21 RKLGLSETKIESIEEAHP 38 (86)
T ss_pred HHcCCCHHHHHHHHHHCC
Confidence 456777777777666666
No 59
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=28.06 E-value=1.1e+02 Score=26.46 Aligned_cols=50 Identities=20% Similarity=0.158 Sum_probs=31.1
Q ss_pred CchHHHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCC
Q 045903 62 HPKNSTEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLN 111 (385)
Q Consensus 62 ~~~~~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~ 111 (385)
+....+.-|..-|.+++||+-+++..-.|=....-+=....+.|++-|+.
T Consensus 32 eve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~ 81 (151)
T PRK08561 32 EIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLA 81 (151)
T ss_pred HHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCC
Confidence 33346777889999999999988765333221221223445666777764
No 60
>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=28.02 E-value=21 Score=29.67 Aligned_cols=19 Identities=26% Similarity=0.342 Sum_probs=10.3
Q ss_pred HHHHHhCCCChHHHHHHHH
Q 045903 67 TEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~~G~s~~~i~~iv~ 85 (385)
+..|++.||+-++|..++.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 50 IRRARDLGFSLEEIRELLA 68 (127)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 4455555555555555543
No 61
>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=28.00 E-value=20 Score=29.76 Aligned_cols=19 Identities=21% Similarity=0.258 Sum_probs=10.7
Q ss_pred HHHHHhCCCChHHHHHHHH
Q 045903 67 TEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~~G~s~~~i~~iv~ 85 (385)
+..|+..||+-++|..++.
T Consensus 49 I~~l~~~G~sl~eI~~~l~ 67 (124)
T TIGR02051 49 IKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred HHHHHHCCCCHHHHHHHHh
Confidence 4455556666666555554
No 62
>PHA02591 hypothetical protein; Provisional
Probab=27.58 E-value=72 Score=24.38 Aligned_cols=27 Identities=22% Similarity=0.247 Sum_probs=22.6
Q ss_pred CCCCCchHHHHHHHhCCCChHHHHHHH
Q 045903 58 YSDNHPKNSTEVLKKWGCSDSDITKLF 84 (385)
Q Consensus 58 ~~~~~~~~~l~~L~~~G~s~~~i~~iv 84 (385)
++.++..++..-|.+.|++.++|++.+
T Consensus 43 ~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 43 ESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred eccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 466777788999999999999998754
No 63
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=27.34 E-value=81 Score=24.13 Aligned_cols=60 Identities=13% Similarity=0.049 Sum_probs=40.5
Q ss_pred HHHHHHHHHCCCCcccccCCcchhhhcccHHhHHH--hhcccCCCCc-hHHHHHHHHhhcCccccchhh
Q 045903 310 VLLAAKVQDMGLVPEIKGLPAILSALRMNEKRFLK--VFIHCHPQDA-ADELMAVYKTAKGIKRLAATS 375 (385)
Q Consensus 310 ~~~l~~L~~~Gl~~~i~~~~~l~~~L~~Se~~F~~--~~v~~~~~~~-~~~l~~~y~~~~~~~~~~~~~ 375 (385)
|++|..|.+.|-. .+-.++...=.++|-+ ||..|..+++ +++|.++..++.+....+.++
T Consensus 7 HeVL~mmi~~~~~------~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~rgKfi~~~~g~ 69 (78)
T PF10678_consen 7 HEVLNMMIESGNP------YTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEERGKFIPSDDGF 69 (78)
T ss_pred HHHHHHHHHcCCC------cCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHcCCEeecCCCE
Confidence 6777766566621 2333333344567765 8889998875 789999999998887665443
No 64
>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=26.99 E-value=23 Score=29.43 Aligned_cols=19 Identities=16% Similarity=0.191 Sum_probs=11.0
Q ss_pred HHHHHhCCCChHHHHHHHH
Q 045903 67 TEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~~G~s~~~i~~iv~ 85 (385)
+..|++.||+-++|..++.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 50 ISRARQVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHCCCCHHHHHHHHH
Confidence 4455566666666665554
No 65
>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=26.63 E-value=21 Score=29.56 Aligned_cols=20 Identities=20% Similarity=0.496 Sum_probs=9.4
Q ss_pred HHHHHHhCCCChHhHHHHHH
Q 045903 101 KLSVLNELGLNSDDLVKIIN 120 (385)
Q Consensus 101 ~l~~L~~lG~~~~~I~~il~ 120 (385)
.+..|+++|++-++|..++.
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04783 49 FIKRAQELGFTLDEIAELLE 68 (126)
T ss_pred HHHHHHHcCCCHHHHHHHHh
Confidence 34444444444444444443
No 66
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=26.57 E-value=84 Score=22.36 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=13.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHhC
Q 045903 241 KVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 241 kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
-|+-|..+||+.+.|..++++.
T Consensus 12 lVd~F~~mGF~~dkVvevlrrl 33 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRRL 33 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHHS
T ss_pred HHHHHHHcCCcHHHHHHHHHHh
Confidence 4566677788887777777653
No 67
>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=26.54 E-value=24 Score=29.59 Aligned_cols=19 Identities=21% Similarity=0.316 Sum_probs=9.7
Q ss_pred HHHHHhCCCChHHHHHHHH
Q 045903 67 TEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~~G~s~~~i~~iv~ 85 (385)
+..|+++||+-++|..++.
T Consensus 50 I~~lr~~G~sL~eI~~~l~ 68 (133)
T cd04787 50 ILSARQLGFSLKDIKEILS 68 (133)
T ss_pred HHHHHHcCCCHHHHHHHHh
Confidence 4445555555555555443
No 68
>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=26.33 E-value=50 Score=26.04 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=9.8
Q ss_pred HHHHHh-CCCChHHHHHHHH
Q 045903 67 TEVLKK-WGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~-~G~s~~~i~~iv~ 85 (385)
+..|++ +|++-++|..++.
T Consensus 50 I~~L~~~~G~~l~~I~~~l~ 69 (95)
T cd04780 50 IRALQQEGGLPISQIKEVLD 69 (95)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 344443 5555555555554
No 69
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=26.11 E-value=3.4e+02 Score=21.58 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=23.0
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhhCCcc
Q 045903 170 IKPVVALYEQVGISRHDLIPMLMSRPTL 197 (385)
Q Consensus 170 l~~~v~~L~~lGl~~~~i~~ll~~~P~i 197 (385)
++..-+|-+++|+++.+|..+-..+|+-
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d 47 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQD 47 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCC
Confidence 4445667789999999999999999884
No 70
>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=25.87 E-value=25 Score=28.95 Aligned_cols=19 Identities=21% Similarity=0.298 Sum_probs=10.1
Q ss_pred HHHHHhCCCChHHHHHHHH
Q 045903 67 TEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 67 l~~L~~~G~s~~~i~~iv~ 85 (385)
+..|++.||+-++|..++.
T Consensus 50 I~~lr~~G~sl~eI~~~l~ 68 (123)
T cd04770 50 IRRAQALGFSLAEIRELLS 68 (123)
T ss_pred HHHHHHCCCCHHHHHHHHH
Confidence 4455555555555555543
No 71
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=25.12 E-value=4.3e+02 Score=22.43 Aligned_cols=85 Identities=14% Similarity=0.084 Sum_probs=46.2
Q ss_pred HHHHHHhCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCC-ChHhHHHHHHhCccccccccchhhHhHHHHHHhh
Q 045903 66 STEVLKKWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGL-NSDDLVKIINCRPRFLSSRINICFEERVDFLIKL 144 (385)
Q Consensus 66 ~l~~L~~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~-~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~ 144 (385)
.+.+|..-.-|..+|..-+.+. +.+.+.+...|+.|.+.|. +....+....+.=.--+.+ -.....-|..-
T Consensus 17 al~~L~~r~~s~~el~~kL~~k----g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g----~~~I~~~L~~k 88 (157)
T PRK00117 17 ALRLLARREHSRAELRRKLAAK----GFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYG----PRRIRQELRQK 88 (157)
T ss_pred HHHHHccchhHHHHHHHHHHhc----CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCch----HHHHHHHHHHc
Confidence 4555555555555555555443 3344456666777777664 3434444333221111111 12224578888
Q ss_pred hcChhhHhhhhhhC
Q 045903 145 FGSREMLCKAIVRN 158 (385)
Q Consensus 145 g~~~~~v~~il~~~ 158 (385)
|++.+.|..++...
T Consensus 89 Gi~~~~I~~~l~~~ 102 (157)
T PRK00117 89 GVDREIIEEALAEL 102 (157)
T ss_pred CCCHHHHHHHHHHc
Confidence 99988888887654
No 72
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=25.07 E-value=1.6e+02 Score=25.25 Aligned_cols=39 Identities=5% Similarity=0.160 Sum_probs=28.7
Q ss_pred hCCCcchhhHHHHHHHHHhCcHHHHHHHHHHHHH-cCCCHHHHHHHHHh
Q 045903 214 TQVSRASKMYKYVVTLIAISRIETIREKVANLEK-FGMSEDEIWSLFGR 261 (385)
Q Consensus 214 lG~~~~~~~~~~~p~il~~s~~~~l~~kv~~L~~-~G~s~~ev~~mv~~ 261 (385)
.||.|++.+++ ..+.+.+-++++.+ .|++..++..++.+
T Consensus 72 ~~FkP~~~~l~---------e~~~fe~ild~ia~~~g~~~~evv~~in~ 111 (144)
T PF09999_consen 72 LGFKPDEEILQ---------ERDPFERILDYIAAKTGIEKQEVVAEINE 111 (144)
T ss_pred CCCCCcHHHHh---------cccHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 57777664432 34678888888886 99999998887765
No 73
>PRK14136 recX recombination regulator RecX; Provisional
Probab=24.55 E-value=6.6e+02 Score=24.46 Aligned_cols=25 Identities=20% Similarity=0.155 Sum_probs=20.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhC
Q 045903 238 IREKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 238 l~~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
..+.+.||..-||+.+.|..++..+
T Consensus 278 k~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 278 RAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 4455789999999999999888754
No 74
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=24.27 E-value=5.5e+02 Score=28.11 Aligned_cols=114 Identities=11% Similarity=0.103 Sum_probs=68.8
Q ss_pred cHHHHHHHHHh---CCCChHhHHHHHHhCccccccccchhhHhHHHHHHhh-hcChhhHhhhhhhCCcccccCccccHHH
Q 045903 97 NLRFKLSVLNE---LGLNSDDLVKIINCRPRFLSSRINICFEERVDFLIKL-FGSREMLCKAIVRNPSLLTYDLDKTIKP 172 (385)
Q Consensus 97 ~l~~~l~~L~~---lG~~~~~I~~il~~~P~iL~~~~~~~l~p~v~fL~~~-g~~~~~v~~il~~~P~lL~~s~e~~l~~ 172 (385)
+....+.||.+ -|+.+..-.+|+..+.. +.-+.|....+-|.++ |++++.+..+...+.. ......
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~----~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~ 145 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGE----AAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERR 145 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCH----hHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHH
Confidence 45666778875 37777777777766553 2222233333445554 6776666666554411 122667
Q ss_pred HHHHHHHcCCChh-----------hHHHHHhhCCcccccCC--CChhHHHHH-HhhCCCcch
Q 045903 173 VVALYEQVGISRH-----------DLIPMLMSRPTLIPRTS--LNDQKMEYI-SRTQVSRAS 220 (385)
Q Consensus 173 ~v~~L~~lGl~~~-----------~i~~ll~~~P~il~~~~--~~~~kv~~L-~~lG~~~~~ 220 (385)
.+.+|.++|++.. +...++..+|+.|..+. ..-.+.+.+ ..+|+++++
T Consensus 146 ~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~~d 207 (720)
T TIGR01448 146 LLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALND 207 (720)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCCCC
Confidence 7888999999864 34457788899887532 123444443 668998876
No 75
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.24 E-value=29 Score=29.49 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=30.3
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHHh
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFAR 86 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~~ 86 (385)
+.|++.|+-..... ...--+.++.++... .+..|++.||+-++|..++..
T Consensus 19 R~Ye~~GLl~p~~r--~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 19 RFYEKQGLMDPEVR--TEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred HHHHHCCCCCCccc--CCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 67888886432111 111134455555544 366788889998888888754
No 76
>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=23.57 E-value=1.4e+02 Score=19.70 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=21.6
Q ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHHhCCCc
Q 045903 236 ETIREKVANLE-KFGMSEDEIWSLFGRSPLL 265 (385)
Q Consensus 236 ~~l~~kv~~L~-~~G~s~~ev~~mv~~~P~l 265 (385)
+.+-.....|. ++|++.....++|..||.+
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 34455667777 7999999999999999975
No 77
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.48 E-value=1.5e+02 Score=19.69 Aligned_cols=42 Identities=17% Similarity=0.280 Sum_probs=25.8
Q ss_pred hCCCChHHHHHHHHhCCCccccCcccHHHHHHHHHhCCCChHhHH
Q 045903 72 KWGCSDSDITKLFARRPTLQKADALNLRFKLSVLNELGLNSDDLV 116 (385)
Q Consensus 72 ~~G~s~~~i~~iv~~~P~lL~~~~e~l~~~l~~L~~lG~~~~~I~ 116 (385)
.+|++.+.|.+++...+. .+.+......+....+|.....+.
T Consensus 6 ~~gvs~~tvs~~l~g~~~---vs~~~~~~i~~~~~~l~~~~~~~~ 47 (52)
T cd01392 6 AAGVSVATVSRVLNGKPR---VSEETRERVLAAAEELGYRPNAAA 47 (52)
T ss_pred HHCcCHHHHHHHHcCCCC---CCHHHHHHHHHHHHHhCCCCCHHH
Confidence 467777777777765552 244455555666666777655543
No 78
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=23.15 E-value=30 Score=28.00 Aligned_cols=22 Identities=14% Similarity=0.206 Sum_probs=12.1
Q ss_pred HHHHHHHhCCCChHhHHHHHHh
Q 045903 100 FKLSVLNELGLNSDDLVKIINC 121 (385)
Q Consensus 100 ~~l~~L~~lG~~~~~I~~il~~ 121 (385)
..+..|+++|++-++|..++..
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 48 EFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 4445555566666666555543
No 79
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=22.87 E-value=58 Score=33.26 Aligned_cols=45 Identities=27% Similarity=0.287 Sum_probs=34.2
Q ss_pred HHhCCCChHHHHHHHHhCCCccccCcc-c--------HHHHHHHHHhCCCChHh
Q 045903 70 LKKWGCSDSDITKLFARRPTLQKADAL-N--------LRFKLSVLNELGLNSDD 114 (385)
Q Consensus 70 L~~~G~s~~~i~~iv~~~P~lL~~~~e-~--------l~~~l~~L~~lG~~~~~ 114 (385)
|.+||+++++|..++..+|.+.....+ + -...++.|+++.++...
T Consensus 204 l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~ 257 (505)
T KOG3207|consen 204 LNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNN 257 (505)
T ss_pred eccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCc
Confidence 458999999999999999998665543 2 24667788888776543
No 80
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=22.78 E-value=1.4e+02 Score=26.66 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhC
Q 045903 237 TIREKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 237 ~l~~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
.+.+-+.+|..+|++..++.+++..+
T Consensus 148 ~~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 148 ALEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 36788899999999999999998876
No 81
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=22.67 E-value=31 Score=27.91 Aligned_cols=49 Identities=12% Similarity=0.081 Sum_probs=23.1
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHH
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~ 85 (385)
+.|++.|+-+.... +..--+.++.++... .+..|+..|++-++|..++.
T Consensus 18 R~ye~~GLl~p~~r--~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~ 68 (107)
T cd01111 18 RDYLLRGLLHPVAR--TEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCR 68 (107)
T ss_pred HHHHHCCCCCCCCc--CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 56666665431111 111123334433332 34556666666666666654
No 82
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.59 E-value=1e+02 Score=21.90 Aligned_cols=20 Identities=30% Similarity=0.481 Sum_probs=14.2
Q ss_pred HHHHHHHcCCCHHHHHHHHH
Q 045903 241 KVANLEKFGMSEDEIWSLFG 260 (385)
Q Consensus 241 kv~~L~~~G~s~~ev~~mv~ 260 (385)
.+..++.+|||-+|+..++.
T Consensus 6 ~I~~~r~lGfsL~eI~~~l~ 25 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELLE 25 (65)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHh
Confidence 34566789999999999983
No 83
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=22.57 E-value=1.1e+02 Score=18.84 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Q 045903 237 TIREKVANLEKFGMSEDEIWSLFGR 261 (385)
Q Consensus 237 ~l~~kv~~L~~~G~s~~ev~~mv~~ 261 (385)
.|..-+.--++.|+|.+|++..+..
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3444455556789999998876653
No 84
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=22.44 E-value=1.6e+02 Score=21.76 Aligned_cols=34 Identities=15% Similarity=0.233 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhCCCcccc
Q 045903 235 IETIREKVANLEKFGMSEDEIWSLFGRSPLLLTL 268 (385)
Q Consensus 235 ~~~l~~kv~~L~~~G~s~~ev~~mv~~~P~lL~~ 268 (385)
.+.+..-++.++.+||+.++|...+.+.=.+.+.
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~ 41 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDG 41 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcC
Confidence 3677888888899999999888777654433333
No 85
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=20.92 E-value=1.4e+02 Score=27.93 Aligned_cols=96 Identities=11% Similarity=0.213 Sum_probs=60.3
Q ss_pred CCchHHHHHHHhCCCChHHHHHHHHhCCCc-cccCcccHHHHHHHHHhCCCChHhHHHHHHhCcc--ccccccchhhHhH
Q 045903 61 NHPKNSTEVLKKWGCSDSDITKLFARRPTL-QKADALNLRFKLSVLNELGLNSDDLVKIINCRPR--FLSSRINICFEER 137 (385)
Q Consensus 61 ~~~~~~l~~L~~~G~s~~~i~~iv~~~P~l-L~~~~e~l~~~l~~L~~lG~~~~~I~~il~~~P~--iL~~~~~~~l~p~ 137 (385)
++.+.++++|.++|++.+.. ..+.-.. +..+...+...+++|+..|+++..-..+-.-+|. +.....++ +.+
T Consensus 31 ~eANemlAlL~~~gI~A~K~---~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~eE--kaR 105 (246)
T COG4669 31 KEANEMLALLMSHGINAEKK---ADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTEE--KAR 105 (246)
T ss_pred hHHHHHHHHHHHcCCcceee---ccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHHH--HHH
Confidence 35667899999999976543 1111111 2233336889999999999998877777777775 44444332 445
Q ss_pred HHHHHhhhcChhhHhhhhhhCCcccccCc
Q 045903 138 VDFLIKLFGSREMLCKAIVRNPSLLTYDL 166 (385)
Q Consensus 138 v~fL~~~g~~~~~v~~il~~~P~lL~~s~ 166 (385)
+.|.++ +++.+.+.+-..++..++
T Consensus 106 ~~~~~e-----Q~le~tLs~mDGVi~ArV 129 (246)
T COG4669 106 LNYAKE-----QQLEQTLSKMDGVISARV 129 (246)
T ss_pred HHHHHH-----HHHHHHHHhcCceEEEEE
Confidence 666654 566666666666665443
No 86
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.91 E-value=2.7e+02 Score=21.97 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=10.8
Q ss_pred HHHhCCCChHhHHHHHHhCcc
Q 045903 104 VLNELGLNSDDLVKIINCRPR 124 (385)
Q Consensus 104 ~L~~lG~~~~~I~~il~~~P~ 124 (385)
+.+.+|++..+|..+-..+|.
T Consensus 25 laR~LGLse~~I~~i~~~~~~ 45 (96)
T cd08315 25 LMRQLGLSENEIDVAKANERV 45 (96)
T ss_pred HHHHcCCCHHHHHHHHHHCCC
Confidence 334555555555555555553
No 87
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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 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=20.83 E-value=39 Score=26.93 Aligned_cols=48 Identities=13% Similarity=0.118 Sum_probs=26.4
Q ss_pred cccccccchHHHHHhhchhccccCCCCCchH--HHHHHHhCCCChHHHHHHHH
Q 045903 35 ATYSTICQAEAVVEEITQDQANNYSDNHPKN--STEVLKKWGCSDSDITKLFA 85 (385)
Q Consensus 35 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~--~l~~L~~~G~s~~~i~~iv~ 85 (385)
+.|++.|+-+.. . ...--+.++.++... .+..|++.|++-++|..++.
T Consensus 19 R~ye~~Gll~~~-r--~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 19 LYYEKLGLITGT-R--NANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred HHHHHCCCCCCC-c--CCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 567777755421 1 111123344444433 46677788888888777654
No 88
>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=20.73 E-value=2.3e+02 Score=23.04 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=19.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 045903 240 EKVANLEKFGMSEDEIWSLFGRS 262 (385)
Q Consensus 240 ~kv~~L~~~G~s~~ev~~mv~~~ 262 (385)
..+..|+++||+-+++..++...
T Consensus 47 ~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 47 ALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcc
Confidence 46788889999999999988754
No 89
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=20.64 E-value=1.3e+02 Score=23.02 Aligned_cols=60 Identities=17% Similarity=0.080 Sum_probs=39.7
Q ss_pred HHHHHHHHHCCCCcccccCCcchhhhcccHHhHHH--hhcccCCCCc-hHHHHHHHHhhcCccccchhh
Q 045903 310 VLLAAKVQDMGLVPEIKGLPAILSALRMNEKRFLK--VFIHCHPQDA-ADELMAVYKTAKGIKRLAATS 375 (385)
Q Consensus 310 ~~~l~~L~~~Gl~~~i~~~~~l~~~L~~Se~~F~~--~~v~~~~~~~-~~~l~~~y~~~~~~~~~~~~~ 375 (385)
|.+|..|.+.|-. .+-.+....=.++|-+ ||-.|..+++ +++|.++..++.+....+..+
T Consensus 5 HeVL~mml~~~~~------~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~kgKfi~~~~gf 67 (77)
T TIGR03853 5 HEVLNLMLASGEP------YTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKKGKFIESDGGF 67 (77)
T ss_pred HHHHHHHHHcCCC------cCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHCCCEeecCCcE
Confidence 5677777666631 2222333334566765 8888888875 789999999998877665443
No 90
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.57 E-value=1.7e+02 Score=28.17 Aligned_cols=26 Identities=31% Similarity=0.431 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHh
Q 045903 236 ETIREKVANLEKFGMSEDEIWSLFGR 261 (385)
Q Consensus 236 ~~l~~kv~~L~~~G~s~~ev~~mv~~ 261 (385)
..+..|.+||++-|++.+||..++++
T Consensus 20 aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 20 APLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred chHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 67889999999999999999998886
Done!