Query 048223
Match_columns 286
No_of_seqs 159 out of 1208
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 07:34:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048223.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048223hhsearch_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 6.9E-51 1.5E-55 384.5 18.7 268 1-276 148-459 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.4E-46 3E-51 344.2 7.0 255 1-257 21-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.1E-41 2.3E-46 321.9 16.8 256 1-261 112-414 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 4.9E-33 1.1E-37 254.6 4.8 240 17-261 2-317 (345)
5 KOG1267 Mitochondrial transcri 99.9 1E-22 2.2E-27 190.6 14.2 212 11-233 198-410 (413)
6 KOG1267 Mitochondrial transcri 99.9 2.5E-22 5.4E-27 188.0 10.9 225 1-237 115-342 (413)
7 smart00733 Mterf Mitochondrial 97.5 8.5E-05 1.8E-09 42.5 2.6 30 172-202 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.4 0.00013 2.8E-09 41.6 2.4 30 67-97 2-31 (31)
9 cd04790 HTH_Cfa-like_unk Helix 91.4 0.82 1.8E-05 37.6 6.9 114 50-173 49-167 (172)
10 cd04790 HTH_Cfa-like_unk Helix 89.8 1.2 2.6E-05 36.6 6.5 116 14-140 49-168 (172)
11 PF11955 PORR: Plant organelle 86.0 19 0.00042 32.9 12.4 198 19-220 44-295 (335)
12 PF04695 Pex14_N: Peroxisomal 85.5 1 2.2E-05 35.6 3.5 49 116-181 3-51 (136)
13 PF14490 HHH_4: Helix-hairpin- 77.9 10 0.00022 27.8 6.2 66 11-101 7-73 (94)
14 PF04695 Pex14_N: Peroxisomal 77.8 2.3 4.9E-05 33.6 2.9 30 11-40 22-51 (136)
15 COG1125 OpuBA ABC-type proline 70.0 11 0.00023 33.4 5.2 63 150-212 70-135 (309)
16 PF08069 Ribosomal_S13_N: Ribo 66.5 4 8.7E-05 27.4 1.6 34 2-35 23-56 (60)
17 PF11955 PORR: Plant organelle 66.2 37 0.0008 31.1 8.3 93 93-185 46-152 (335)
18 PF00627 UBA: UBA/TS-N domain; 66.0 9.3 0.0002 22.6 3.0 23 155-177 4-26 (37)
19 smart00165 UBA Ubiquitin assoc 65.4 9.9 0.00021 22.3 3.1 23 155-177 3-25 (37)
20 PF07499 RuvA_C: RuvA, C-termi 64.8 12 0.00026 23.5 3.5 25 153-177 3-27 (47)
21 cd00194 UBA Ubiquitin Associat 61.9 12 0.00027 21.9 3.1 23 155-177 3-25 (38)
22 KOG0400 40S ribosomal protein 60.2 12 0.00026 29.2 3.3 33 2-34 23-55 (151)
23 PRK14136 recX recombination re 59.5 1.4E+02 0.003 27.1 11.5 132 16-177 169-302 (309)
24 PF14490 HHH_4: Helix-hairpin- 57.8 20 0.00043 26.2 4.1 34 103-136 38-73 (94)
25 PF00356 LacI: Bacterial regul 56.9 14 0.00031 23.2 2.8 39 92-133 7-45 (46)
26 TIGR01448 recD_rel helicase, p 55.7 99 0.0021 31.5 10.0 116 11-136 76-208 (720)
27 PF08069 Ribosomal_S13_N: Ribo 55.4 4.4 9.4E-05 27.2 0.2 35 142-176 22-56 (60)
28 KOG0400 40S ribosomal protein 53.6 14 0.0003 28.8 2.7 64 70-134 20-83 (151)
29 PRK11613 folP dihydropteroate 53.0 34 0.00075 30.5 5.6 67 186-261 163-229 (282)
30 PF11212 DUF2999: Protein of u 52.4 77 0.0017 22.0 7.2 44 85-135 2-45 (82)
31 PRK08561 rps15p 30S ribosomal 52.3 52 0.0011 26.4 5.9 35 2-36 23-57 (151)
32 smart00354 HTH_LACI helix_turn 50.7 29 0.00062 23.7 3.8 39 93-134 9-47 (70)
33 PRK14487 cbb3-type cytochrome 48.1 49 0.0011 28.2 5.4 64 104-167 134-210 (217)
34 PF10440 WIYLD: Ubiquitin-bind 47.1 33 0.00072 23.4 3.5 34 149-182 7-40 (65)
35 PF11181 YflT: Heat induced st 46.6 1.1E+02 0.0023 22.6 6.6 21 81-101 9-29 (103)
36 PF02022 Integrase_Zn: Integra 43.1 53 0.0011 20.0 3.6 31 150-180 5-36 (40)
37 cd01392 HTH_LacI Helix-turn-he 41.5 86 0.0019 19.4 4.9 42 161-206 5-46 (52)
38 PF08671 SinI: Anti-repressor 39.5 37 0.0008 19.3 2.4 24 152-175 4-27 (30)
39 KOG2629 Peroxisomal membrane a 38.3 61 0.0013 28.9 4.7 43 117-176 3-45 (300)
40 PTZ00072 40S ribosomal protein 38.2 1.1E+02 0.0023 24.5 5.5 30 5-34 23-52 (148)
41 PF13720 Acetyltransf_11: Udp 37.8 43 0.00093 23.9 3.1 37 19-57 23-59 (83)
42 PRK08561 rps15p 30S ribosomal 37.8 52 0.0011 26.4 3.8 36 71-107 21-56 (151)
43 PF03960 ArsC: ArsC family; I 37.4 28 0.0006 26.0 2.2 21 60-80 71-91 (110)
44 cd08306 Death_FADD Fas-associa 35.6 83 0.0018 22.5 4.4 37 18-58 19-55 (86)
45 PF03960 ArsC: ArsC family; I 34.7 29 0.00063 25.9 1.9 22 94-115 69-90 (110)
46 COG0320 LipA Lipoate synthase 34.4 35 0.00076 30.3 2.6 110 58-167 158-283 (306)
47 cd04768 HTH_BmrR-like Helix-Tu 33.7 89 0.0019 22.7 4.4 23 155-177 48-70 (96)
48 smart00354 HTH_LACI helix_turn 33.2 1.3E+02 0.0029 20.3 5.0 41 161-205 8-48 (70)
49 PRK09875 putative hydrolase; P 32.2 40 0.00087 30.2 2.7 29 151-179 260-288 (292)
50 PF09278 MerR-DNA-bind: MerR, 32.2 45 0.00098 22.0 2.4 19 156-174 6-24 (65)
51 PF09288 UBA_3: Fungal ubiquit 32.2 60 0.0013 21.3 2.8 21 156-176 12-32 (55)
52 PRK00117 recX recombination re 31.7 2.6E+02 0.0056 22.1 9.9 137 16-179 18-155 (157)
53 cd04788 HTH_NolA-AlbR Helix-Tu 31.2 1.3E+02 0.0028 21.8 4.9 24 155-178 48-71 (96)
54 PF13331 DUF4093: Domain of un 30.8 2.1E+02 0.0045 20.7 5.7 18 157-174 69-86 (87)
55 COG5457 Uncharacterized conser 30.6 48 0.001 22.5 2.2 19 17-35 41-59 (63)
56 cd08784 Death_DRs Death Domain 30.3 1.2E+02 0.0025 21.3 4.4 46 15-65 14-59 (79)
57 PRK14134 recX recombination re 29.8 4E+02 0.0087 23.7 12.7 95 8-107 91-205 (283)
58 PRK14135 recX recombination re 29.5 3.4E+02 0.0073 23.6 8.1 82 87-176 63-148 (263)
59 PRK00116 ruvA Holliday junctio 29.2 1.1E+02 0.0024 25.5 4.7 25 84-108 149-173 (192)
60 PF11626 Rap1_C: TRF2-interact 28.9 1.1E+02 0.0024 21.8 4.1 25 166-196 62-86 (87)
61 PF06568 DUF1127: Domain of un 27.8 30 0.00064 20.9 0.8 13 18-30 27-39 (40)
62 COG3620 Predicted transcriptio 27.7 43 0.00094 27.3 1.9 76 92-167 15-98 (187)
63 cd04782 HTH_BltR Helix-Turn-He 27.4 1.4E+02 0.003 21.7 4.5 22 155-176 48-69 (97)
64 COG2137 OraA Uncharacterized p 26.8 3.6E+02 0.0078 22.2 7.2 18 53-70 92-109 (174)
65 PHA02591 hypothetical protein; 26.4 99 0.0021 21.9 3.2 27 7-33 43-69 (83)
66 COG0560 SerB Phosphoserine pho 26.4 2.3E+02 0.005 23.9 6.3 89 37-132 5-95 (212)
67 PF02787 CPSase_L_D3: Carbamoy 26.2 91 0.002 24.0 3.4 67 84-174 13-82 (123)
68 TIGR00601 rad23 UV excision re 25.9 1.2E+02 0.0026 28.4 4.7 44 150-202 153-196 (378)
69 PF13720 Acetyltransf_11: Udp 25.8 1.4E+02 0.0031 21.2 4.1 36 126-162 23-59 (83)
70 PRK14135 recX recombination re 25.4 4.5E+02 0.0097 22.8 10.2 23 154-176 236-258 (263)
71 cd08315 Death_TRAILR_DR4_DR5 D 24.9 1.9E+02 0.004 21.2 4.8 22 17-38 24-45 (96)
72 cd04774 HTH_YfmP Helix-Turn-He 24.8 2.2E+02 0.0049 20.6 5.2 26 155-180 47-73 (96)
73 KOG0062 ATPase component of AB 24.1 3.9E+02 0.0085 26.3 7.8 103 21-128 114-239 (582)
74 PTZ00072 40S ribosomal protein 23.7 48 0.001 26.4 1.4 32 146-177 23-54 (148)
75 PF12244 DUF3606: Protein of u 23.6 84 0.0018 20.6 2.4 20 157-176 23-43 (57)
76 TIGR03060 PS_II_psb29 photosys 23.3 3.7E+02 0.008 23.0 6.8 50 7-59 67-118 (214)
77 COG3797 Uncharacterized protei 23.1 1.9E+02 0.0041 23.9 4.8 67 11-79 20-96 (178)
78 cd01106 HTH_TipAL-Mta Helix-Tu 22.9 2.1E+02 0.0045 20.9 4.8 24 155-178 48-71 (103)
79 cd01107 HTH_BmrR Helix-Turn-He 22.6 2E+02 0.0043 21.3 4.6 25 155-179 49-73 (108)
80 COG2826 Tra8 Transposase and i 22.5 1.4E+02 0.0031 26.9 4.3 90 14-108 14-103 (318)
81 cd08316 Death_FAS_TNFRSF6 Deat 22.4 2.6E+02 0.0057 20.5 5.1 27 14-40 22-48 (97)
82 cd04775 HTH_Cfa-like Helix-Tur 22.3 2.3E+02 0.005 20.7 4.9 22 155-176 48-69 (102)
83 cd04769 HTH_MerR2 Helix-Turn-H 22.1 2.2E+02 0.0047 21.4 4.8 24 154-177 46-69 (116)
84 cd04770 HTH_HMRTR Helix-Turn-H 21.8 1.6E+02 0.0034 22.3 4.0 23 155-177 48-70 (123)
85 TIGR01616 nitro_assoc nitrogen 21.8 56 0.0012 25.3 1.5 45 60-109 73-117 (126)
86 KOG0871 Class 2 transcription 21.3 2.6E+02 0.0056 22.4 5.0 20 153-172 102-121 (156)
87 cd04777 HTH_MerR-like_sg1 Heli 21.1 1.3E+02 0.0029 22.2 3.4 23 154-176 45-67 (107)
88 cd01109 HTH_YyaN Helix-Turn-He 21.0 1.7E+02 0.0037 21.8 4.1 22 155-176 48-69 (113)
89 cd08804 Death_ank2 Death domai 20.7 1.9E+02 0.0042 20.5 4.0 35 20-58 23-57 (84)
90 cd08315 Death_TRAILR_DR4_DR5 D 20.4 3.5E+02 0.0076 19.7 5.8 43 87-133 22-65 (96)
91 cd08313 Death_TNFR1 Death doma 20.3 3.2E+02 0.0068 19.4 5.0 42 12-58 11-52 (80)
92 cd04784 HTH_CadR-PbrR Helix-Tu 20.2 1.8E+02 0.0039 22.2 4.1 21 155-175 48-68 (127)
93 PF08004 DUF1699: Protein of u 20.1 4.3E+02 0.0093 20.6 6.3 28 148-175 88-115 (131)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=6.9e-51 Score=384.47 Aligned_cols=268 Identities=21% Similarity=0.331 Sum_probs=234.3
Q ss_pred CCceeecCcc-cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccC
Q 048223 1 IPKVLLLSPE-TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHD 79 (286)
Q Consensus 1 ~P~lL~~~~~-~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s 79 (286)
||++|.++++ ++.|+++||+++|++.+++++++.++|.+|++++++++.|+++||.++|++.+++++++.++|.+|+++
T Consensus 148 ~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~s 227 (487)
T PLN03196 148 YPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMR 227 (487)
T ss_pred CCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcC
Confidence 6999999999 999999999999999999999999999999999988899999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHhcCCCchhHhhhhccCCeeEEecch-hHHHHHHHHHHcCCCCcchHHHH------------------
Q 048223 80 ADYYLLPNVKILRDSGVPESDIIKSIESWPKLFLRHPK-FFEKNVASVKEMGINPLRLKFVL------------------ 140 (286)
Q Consensus 80 ~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~-~l~~~v~~l~~lG~~~~~~~~~~------------------ 140 (286)
++++++|+++||+++|++.++|.+++.++|++|+++.+ ++++++++|+++|++++....+.
T Consensus 228 ve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~ 307 (487)
T PLN03196 228 VGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQ 307 (487)
T ss_pred hhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHH
Confidence 98889999999999999999999999999999999876 59999999999888875432111
Q ss_pred ---------------------HHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHhhcCCccccccHHHHHHHHHHHHhhc
Q 048223 141 ---------------------AIQAKCIMSESQWESKLHVYKKWGWSEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGM 199 (286)
Q Consensus 141 ---------------------~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~ 199 (286)
.|+ +...+++++.++++||+++||+.+++..|+.++|++|++|.+++++|++||+++|
T Consensus 308 ~~fL~~~lG~s~e~i~~~v~k~P~-il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneM 386 (487)
T PLN03196 308 QYWLTSKLKIDPEDFGRVIEKLPQ-IVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEM 386 (487)
T ss_pred HHHHHHhhCCCHHHHHHHHHhcch-hhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHh
Confidence 122 3345788999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHhhCCCceecCCCCccchHHHHHHHHHHCCCCCCCccccccccccChhhHHHHhcC-CC--ChhHHHHHHHhhc
Q 048223 200 GWEPAVIAKHPALTTFSMEKRIIPRGAVIQFLLSKGLVKSDTTYLTTLLSYPEKTFMLRLMN-YD--DAPKLLKLYQEKL 276 (286)
Q Consensus 200 g~~~~~i~~~P~~L~~Sle~~i~pR~~vl~~L~~~G~~~~~~~~l~~~l~~se~~F~~~~~~-~~--~~~~l~~~y~~~~ 276 (286)
|++.++|++||++|+||+|+||+|||. +|+++|+ .++ +.+++.+||++|+++|+. |. +..+..-.+.+..
T Consensus 387 g~~~~~Iv~fP~~LsySLEkRI~PR~~---~L~~kGl---~~s-L~~~L~~sd~~F~~r~v~~y~e~~~~~~~~~~~~~~ 459 (487)
T PLN03196 387 KRPLKELVEFPAYFTYGLESRIKPRYE---RVAKKGI---KCS-LAWFLNCSDDKFEQRMSGDFIEGEEMEPLFSMGGKL 459 (487)
T ss_pred CCCHHHHHhChHHhccChhhhhHHHHH---HHHHcCC---CCC-HHHHhccCHHHHHHHHhhhcccccccCCCcccCCcc
Confidence 999999999999999999999999995 5789999 467 999999999999999999 97 3444333333433
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=1.4e-46 Score=344.18 Aligned_cols=255 Identities=34% Similarity=0.547 Sum_probs=200.7
Q ss_pred CCceeecCcc-cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccC
Q 048223 1 IPKVLLLSPE-TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHD 79 (286)
Q Consensus 1 ~P~lL~~~~~-~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s 79 (286)
||.+|.++++ ++.|+++||.++|++.++++++++++|.++..++++++.|.++||+++|++++++.+++.++|++|..+
T Consensus 21 ~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~ 100 (345)
T PF02536_consen 21 YPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFS 100 (345)
T ss_dssp H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS-
T ss_pred CCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccc
Confidence 5999999999 999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cchhhhhHHHHHHhcCCCchhHhhhhccC----------------------------------CeeEEec-chhHHHHHH
Q 048223 80 ADYYLLPNVKILRDSGVPESDIIKSIESW----------------------------------PKLFLRH-PKFFEKNVA 124 (286)
Q Consensus 80 ~e~~l~~~v~~L~~~G~~~~~i~~~i~~~----------------------------------P~ll~~~-~~~l~~~v~ 124 (286)
.+.++.+++.+|+++|++.+.+.+++..+ |+++..+ .+.++++++
T Consensus 101 ~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~ 180 (345)
T PF02536_consen 101 VEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVE 180 (345)
T ss_dssp --HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHH
T ss_pred hHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHH
Confidence 87789999999999999988666554444 4333333 345888888
Q ss_pred HHHHcCCCCcch--HHHHHHHHHhc--------------------------------CCHHHHHHHHHHHHHcCCCHHHH
Q 048223 125 SVKEMGINPLRL--KFVLAIQAKCI--------------------------------MSESQWESKLHVYKKWGWSEQEW 170 (286)
Q Consensus 125 ~l~~lG~~~~~~--~~~~~~~~l~~--------------------------------~~~~~l~~~v~~l~~lG~s~~~i 170 (286)
+|+++|++.++. .+.+.|..+.. .+.+++.++++||+++||+.+|+
T Consensus 181 ~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei 260 (345)
T PF02536_consen 181 FLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEI 260 (345)
T ss_dssp HHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHH
T ss_pred HHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHH
Confidence 888888887653 23333333322 23568999999999999999999
Q ss_pred HHHhhcCCccccccHHHHHHHHHHHHhhcCCChHHHhhCCCceecCCCCccchHHHHHHHHHHCCCCCCCcccccccccc
Q 048223 171 LAAFLKCPWCMITSEDKITAIMDFFVNGMGWEPAVIAKHPALTTFSMEKRIIPRGAVIQFLLSKGLVKSDTTYLTTLLSY 250 (286)
Q Consensus 171 ~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~~~~i~~~P~~L~~Sle~~i~pR~~vl~~L~~~G~~~~~~~~l~~~l~~ 250 (286)
.+|+.++|++|++|.+++++|++||.++||++.++|+++|++|+||+|+||+|||+++++|+++|. ...++ +.+++.+
T Consensus 261 ~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~s-l~~~l~~ 338 (345)
T PF02536_consen 261 AKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPS-LSSMLSC 338 (345)
T ss_dssp HHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGG-S-HHHHH
T ss_pred HHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCC-HHHHhhc
Confidence 999999999999999999999999999999999999999999999999999999999999999997 55788 9999999
Q ss_pred ChhhHHH
Q 048223 251 PEKTFML 257 (286)
Q Consensus 251 se~~F~~ 257 (286)
||++|++
T Consensus 339 s~~~F~~ 345 (345)
T PF02536_consen 339 SDEEFLK 345 (345)
T ss_dssp HHHHHT-
T ss_pred cHHHhcC
Confidence 9999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.1e-41 Score=321.94 Aligned_cols=256 Identities=16% Similarity=0.236 Sum_probs=215.8
Q ss_pred CCceeecCcc-cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccC
Q 048223 1 IPKVLLLSPE-TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHD 79 (286)
Q Consensus 1 ~P~lL~~~~~-~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s 79 (286)
||++|+++++ ++.|+++||+++|++.++|++++.++|.+|..++++++.|+++||+++|+++++|++++.++|++|+++
T Consensus 112 ~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~ 191 (487)
T PLN03196 112 YPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFK 191 (487)
T ss_pred CcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCC
Confidence 7999999999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHhcCCCchhHhhhhccCCeeEEecchh-HHHHHHHHHHcCCCCcch--HHHHHHHHHhcCCHHHHHHH
Q 048223 80 ADYYLLPNVKILRDSGVPESDIIKSIESWPKLFLRHPKF-FEKNVASVKEMGINPLRL--KFVLAIQAKCIMSESQWESK 156 (286)
Q Consensus 80 ~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~-l~~~v~~l~~lG~~~~~~--~~~~~~~~l~~~~~~~l~~~ 156 (286)
+++++.|+++||+++|++++++.+++.++|++|+++.++ +.++++||+++|++.+.. .+.+.|+++++..+++++++
T Consensus 192 ~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~ 271 (487)
T PLN03196 192 LEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPN 271 (487)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHH
Confidence 999999999999999999999999999999999999875 999999999999998763 45556777766555677777
Q ss_pred HHHHHHcCCCHHHHHHHhhcCCc-------------------------------------cccccHHHHHHHHHHHHhhc
Q 048223 157 LHVYKKWGWSEQEWLAAFLKCPW-------------------------------------CMITSEDKITAIMDFFVNGM 199 (286)
Q Consensus 157 v~~l~~lG~s~~~i~~~i~~~P~-------------------------------------il~~s~~~l~~k~~fl~~~~ 199 (286)
+++++++|++.+++..++.++|. ++++|.++|++|++||.+ +
T Consensus 272 v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~-~ 350 (487)
T PLN03196 272 VECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRG-R 350 (487)
T ss_pred HHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHH-c
Confidence 77777777666666665555554 444555566778888876 8
Q ss_pred CCChHHH----hhCCCceecCCCCccchHHHHHHHHHH-CCCCCCCccccccccccC-hhhHHHHhcC
Q 048223 200 GWEPAVI----AKHPALTTFSMEKRIIPRGAVIQFLLS-KGLVKSDTTYLTTLLSYP-EKTFMLRLMN 261 (286)
Q Consensus 200 g~~~~~i----~~~P~~L~~Sle~~i~pR~~vl~~L~~-~G~~~~~~~~l~~~l~~s-e~~F~~~~~~ 261 (286)
||+.++| .++|++|+||.+ +|+++. +||.+ +|+..+++...|+++++| |+|..+||..
T Consensus 351 Gls~edI~~mv~k~P~lL~~S~~-~l~~k~---dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~ 414 (487)
T PLN03196 351 GFSAQDVAKMVVRCPQILALNLE-IMKPSL---EFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYER 414 (487)
T ss_pred CCCHHHHHHHHHhCCceeeccHH-HHHHHH---HHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHH
Confidence 8888877 588888888885 788874 56654 677654443378888888 7888888854
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.97 E-value=4.9e-33 Score=254.64 Aligned_cols=240 Identities=24% Similarity=0.448 Sum_probs=189.4
Q ss_pred HHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHHHHhcCC
Q 048223 17 EFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKILRDSGV 96 (286)
Q Consensus 17 ~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~~G~ 96 (286)
++|++.|++.++|.+++.++|.++.++.++++.|+++||.++|++..++++++.+||.+|..++++++.|+++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 68999999999999999999999999999999999999999999999999999999999999998899999999999999
Q ss_pred CchhHhhhhccCCeeEEecch-hHHHHHHHHHHcCCCCcch-H-----------------------------------HH
Q 048223 97 PESDIIKSIESWPKLFLRHPK-FFEKNVASVKEMGINPLRL-K-----------------------------------FV 139 (286)
Q Consensus 97 ~~~~i~~~i~~~P~ll~~~~~-~l~~~v~~l~~lG~~~~~~-~-----------------------------------~~ 139 (286)
+++++.+++.++|++|+.+.+ .+.+++.+|+++|++++.. . ..
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~ 161 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIA 161 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHH
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhccccc
Confidence 999999999999999988755 5999999999999987621 0 11
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHhhcCCccccccHH---------------------------------
Q 048223 140 LAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAAFLKCPWCMITSED--------------------------------- 186 (286)
Q Consensus 140 ~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~~P~il~~s~~--------------------------------- 186 (286)
.+|+.+...+++.|+++++||+++|++.+++.+++.++|+++++|.+
T Consensus 162 ~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~ 241 (345)
T PF02536_consen 162 KNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEE 241 (345)
T ss_dssp HHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHH
T ss_pred ccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchH
Confidence 22445566677889999999999999999999999999998888865
Q ss_pred HHHHHHHHHHhhcCCChHHH----hhCCCceecCCCCccchHHHHHHHHHH-CCCCCCCccccccccccC-hhhHHHHhc
Q 048223 187 KITAIMDFFVNGMGWEPAVI----AKHPALTTFSMEKRIIPRGAVIQFLLS-KGLVKSDTTYLTTLLSYP-EKTFMLRLM 260 (286)
Q Consensus 187 ~l~~k~~fl~~~~g~~~~~i----~~~P~~L~~Sle~~i~pR~~vl~~L~~-~G~~~~~~~~l~~~l~~s-e~~F~~~~~ 260 (286)
+++++++||.+ +|++.++| .++|++|++|.++ ++|+. +||.+ .|+..+++...|+++++| |++..+||.
T Consensus 242 ~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~---~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~ 316 (345)
T PF02536_consen 242 KLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKF---EFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYE 316 (345)
T ss_dssp HHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHH---HHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHH
T ss_pred hHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHH---HHHHHHhCcCHHHHhhCCceeEechhhhhhhHHH
Confidence 48999999999 99999987 5899999999995 99985 67754 788755544489999999 899999954
Q ss_pred C
Q 048223 261 N 261 (286)
Q Consensus 261 ~ 261 (286)
.
T Consensus 317 ~ 317 (345)
T PF02536_consen 317 V 317 (345)
T ss_dssp H
T ss_pred H
Confidence 4
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.89 E-value=1e-22 Score=190.58 Aligned_cols=212 Identities=19% Similarity=0.235 Sum_probs=185.7
Q ss_pred cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHH
Q 048223 11 TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKI 90 (286)
Q Consensus 11 ~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~ 90 (286)
.+. .++++.++|....++...+.++|....... .+...+.++...|+.+.. +++.++|.++.++.++.+++++++
T Consensus 198 ~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~ 272 (413)
T KOG1267|consen 198 SVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEV 272 (413)
T ss_pred ccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHH
Confidence 344 788888888888888888888888776643 666777788888876666 788888999999999999999999
Q ss_pred HHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHH
Q 048223 91 LRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEW 170 (286)
Q Consensus 91 L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i 170 (286)
|+++|++.++|..++.++|++|+++.+++...++++.+. .++ ..+.|+.+ +.++..+.++++++..+|++..|+
T Consensus 273 l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~--~~~---~~k~p~~l-~~s~~~l~~~ie~l~~~g~~~~q~ 346 (413)
T KOG1267|consen 273 LKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN--PKH---ILKFPQLL-RSSEDKLKPRIEFLLSLGFSDVQI 346 (413)
T ss_pred HHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc--chh---hhhhhhhh-hccchhhhhhHHHHHHcCCcHHHH
Confidence 999999999999999999999999999988888888766 322 55556666 679999999999999999999999
Q ss_pred HHHhhcCCccccccHH-HHHHHHHHHHhhcCCChHHHhhCCCceecCCCCccchHHHHHHHHHH
Q 048223 171 LAAFLKCPWCMITSED-KITAIMDFFVNGMGWEPAVIAKHPALTTFSMEKRIIPRGAVIQFLLS 233 (286)
Q Consensus 171 ~~~i~~~P~il~~s~~-~l~~k~~fl~~~~g~~~~~i~~~P~~L~~Sle~~i~pR~~vl~~L~~ 233 (286)
..|+.++|+++.+|.+ .++.+.+|+.+.|+++.++++.+|.+++|++|+|+.||+.+...+..
T Consensus 347 ~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~ 410 (413)
T KOG1267|consen 347 LEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGV 410 (413)
T ss_pred HHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhc
Confidence 9999999999999988 89999999999999999999999999999999999999987766544
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.87 E-value=2.5e-22 Score=187.96 Aligned_cols=225 Identities=27% Similarity=0.350 Sum_probs=167.3
Q ss_pred CCceeecCcc-cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhh--cCchHHHHHHHhCCcccc
Q 048223 1 IPKVLLLSPE-TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLL--HSSEKTIALIIRFPYILY 77 (286)
Q Consensus 1 ~P~lL~~~~~-~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g--~~~~~i~~ii~~~P~iL~ 77 (286)
+|.+|.++.+ .+.|+..+|.+.|++.++++++++.-|.+++.+.+.++.+.++|+.+++ .....+.+.....|....
T Consensus 115 ~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~ 194 (413)
T KOG1267|consen 115 SPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLL 194 (413)
T ss_pred CchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccc
Confidence 3667777777 7777777777777777777777777777776665567777777777764 455555555554443222
Q ss_pred cCcchhhhhHHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHH
Q 048223 78 HDADYYLLPNVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKL 157 (286)
Q Consensus 78 ~s~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v 157 (286)
.. ..+. ++++++++|..+.++...+..+|..+.... .+...+.++.++|+++.+.++++++.++.+.++++++++|
T Consensus 195 ~~--~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv 270 (413)
T KOG1267|consen 195 NE--NSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKV 270 (413)
T ss_pred cc--cccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHH
Confidence 22 1244 777888888888888888888888887654 7888899999999999999999999999999999999999
Q ss_pred HHHHHcCCCHHHHHHHhhcCCccccccHHHHHHHHHHHHhhcCCChHHHhhCCCceecCCCCccchHHHHHHHHHHCCCC
Q 048223 158 HVYKKWGWSEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGMGWEPAVIAKHPALTTFSMEKRIIPRGAVIQFLLSKGLV 237 (286)
Q Consensus 158 ~~l~~lG~s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~~~~i~~~P~~L~~Sle~~i~pR~~vl~~L~~~G~~ 237 (286)
++|+++||+.+|++.|+.++|+++++|.+++..+++|+.+. .+++.++|+++.+|.. .+.+|+ +++...|+.
T Consensus 271 ~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p~~l~~s~~-~l~~~i---e~l~~~g~~ 342 (413)
T KOG1267|consen 271 EVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFPQLLRSSED-KLKPRI---EFLLSLGFS 342 (413)
T ss_pred HHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhhhhhhccch-hhhhhH---HHHHHcCCc
Confidence 99999999999999999999999999999766666666664 2226666666655554 566663 555555554
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=97.51 E-value=8.5e-05 Score=42.45 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=26.0
Q ss_pred HHhhcCCccccccHHHHHHHHHHHHhhcCCC
Q 048223 172 AAFLKCPWCMITSEDKITAIMDFFVNGMGWE 202 (286)
Q Consensus 172 ~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~ 202 (286)
.++.++|+++++|.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4678899999999889999999999 49875
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=97.39 E-value=0.00013 Score=41.64 Aligned_cols=30 Identities=30% Similarity=0.554 Sum_probs=19.4
Q ss_pred HHHHhCCcccccCcchhhhhHHHHHHhcCCC
Q 048223 67 ALIIRFPYILYHDADYYLLPNVKILRDSGVP 97 (286)
Q Consensus 67 ~ii~~~P~iL~~s~e~~l~~~v~~L~~~G~~ 97 (286)
+++.++|.+|+++ +++++++++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 4566677777777 44577777777766653
No 9
>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=91.39 E-value=0.82 Score=37.65 Aligned_cols=114 Identities=18% Similarity=0.071 Sum_probs=58.1
Q ss_pred hHHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHHHHh----cCCCchhHhhhhccCCeeEEecchhHHHHHHH
Q 048223 50 PTFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKILRD----SGVPESDIIKSIESWPKLFLRHPKFFEKNVAS 125 (286)
Q Consensus 50 ~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~----~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~ 125 (286)
..+..|+++|++-++|..++..... +....+...++.+.. +--....+..++...+..-....-+....++.
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~~~~~~V~~~~w~~l 124 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLLKEQRLVTKEKWVAI 124 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCHHHHHHH
Confidence 4566788899999999888775432 111123333333322 11112233333332222211111124556666
Q ss_pred HHHcCCCCcch-HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHH
Q 048223 126 VKEMGINPLRL-KFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAA 173 (286)
Q Consensus 126 l~~lG~~~~~~-~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~ 173 (286)
++.+|+++.+. ..... |-...+ ..-.+||.++|++.+++..|
T Consensus 125 ~~~~g~~~~~m~~wh~~---fe~~~p---~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 125 LKAAGMDEADMRRWHIE---FEKMEP---EAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHcCCChHHHHHHHHH---HHHhCc---HHHHHHHHHcCCCHHHHHHH
Confidence 77888877651 11111 111111 23458999999999998765
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=89.77 E-value=1.2 Score=36.65 Aligned_cols=116 Identities=15% Similarity=0.129 Sum_probs=65.8
Q ss_pred HHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHh----hhcCchHHHHHHHhCCcccccCcchhhhhHHH
Q 048223 14 RKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSH----LLHSSEKTIALIIRFPYILYHDADYYLLPNVK 89 (286)
Q Consensus 14 ~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~----~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~ 89 (286)
..|.+|++.|++-++|..++.....- ....+..+++.+.. +--..+.+..++...+..-.... -+....++
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~~----~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~~~~~~-V~~~~w~~ 123 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGDD----ATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLLKEQRL-VTKEKWVA 123 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCChh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc-CCHHHHHH
Confidence 57888999999999999998765431 11123333333322 11123344444443333321121 12566788
Q ss_pred HHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcchHHHH
Q 048223 90 ILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLRLKFVL 140 (286)
Q Consensus 90 ~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~~~~~~ 140 (286)
.++..|++++++.+.=..+ - ...=..=.+||..+|++++.+.-++
T Consensus 124 l~~~~g~~~~~m~~wh~~f----e--~~~p~~h~~~l~~~g~~~~~~~~ir 168 (172)
T cd04790 124 ILKAAGMDEADMRRWHIEF----E--KMEPEAHQEFLQSLGIPEDEIERIR 168 (172)
T ss_pred HHHHcCCChHHHHHHHHHH----H--HhCcHHHHHHHHHcCCCHHHHHHHH
Confidence 8889999998876542211 0 0112344689999999887654433
No 11
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=86.00 E-value=19 Score=32.93 Aligned_cols=198 Identities=16% Similarity=0.232 Sum_probs=106.5
Q ss_pred HhhCCCChhhHHHHHhhCCCceecccc-C------cchhHHHHhHh--hhc---CchHHHHHHHhCCcccccCcchhh-h
Q 048223 19 FHCEGISNPDTVKILSKYPGLLSRSLD-N------HLIPTFNSLSH--LLH---SSEKTIALIIRFPYILYHDADYYL-L 85 (286)
Q Consensus 19 L~~~G~~~~~i~~i~~~~P~il~~~~~-~------~l~~~~~~L~~--~g~---~~~~i~~ii~~~P~iL~~s~e~~l-~ 85 (286)
-..+|+....+.+++.+||.++..... . .+.|...-|.+ ..+ ...++..-+.| +|-++.++.| -
T Consensus 44 ~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~K---LLMMS~~~rlpL 120 (335)
T PF11955_consen 44 RRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRK---LLMMSKDRRLPL 120 (335)
T ss_pred HHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHH---HhccCCCCcccH
Confidence 335899778999999999999875431 1 33344433321 111 22333344444 5655554433 3
Q ss_pred hHHHHHH-hcCCCchhHhhhhccCCeeEEecc---h-hHHHHHHHHHHcCCCCcc------------------hHHHHHH
Q 048223 86 PNVKILR-DSGVPESDIIKSIESWPKLFLRHP---K-FFEKNVASVKEMGINPLR------------------LKFVLAI 142 (286)
Q Consensus 86 ~~v~~L~-~~G~~~~~i~~~i~~~P~ll~~~~---~-~l~~~v~~l~~lG~~~~~------------------~~~~~~~ 142 (286)
..+..++ ++|++.+-...++.++|..|.... + ..-+.+.|=.++.++.-. ..|...+
T Consensus 121 ~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~f 200 (335)
T PF11955_consen 121 SKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSF 200 (335)
T ss_pred HHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecC
Confidence 4677777 599999989999999999887632 0 111112221122221110 0011000
Q ss_pred HHHhcCCHHHHHHHHHHHHHc----------CCCH---HHHHHHhhcCCccccccHH--HHHHHHHHHHhhcCCChH---
Q 048223 143 QAKCIMSESQWESKLHVYKKW----------GWSE---QEWLAAFLKCPWCMITSED--KITAIMDFFVNGMGWEPA--- 204 (286)
Q Consensus 143 ~~l~~~~~~~l~~~v~~l~~l----------G~s~---~~i~~~i~~~P~il~~s~~--~l~~k~~fl~~~~g~~~~--- 204 (286)
+. .+.......+.++-++++ |++. +.=.+.+.-.=-+|++..+ ....++..|.+++|++..
T Consensus 201 p~-G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~k~~~ 279 (335)
T PF11955_consen 201 PK-GFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQKFRR 279 (335)
T ss_pred CC-CccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcHHHHH
Confidence 00 111234555555555522 2221 1111122212235666544 477889999999999964
Q ss_pred HHhhCCCceecCCCCc
Q 048223 205 VIAKHPALTTFSMEKR 220 (286)
Q Consensus 205 ~i~~~P~~L~~Sle~~ 220 (286)
-+.++|.+|..|....
T Consensus 280 ~l~rHPgIFYvS~kg~ 295 (335)
T PF11955_consen 280 LLLRHPGIFYVSLKGK 295 (335)
T ss_pred HHHhCCCeEEEeccCC
Confidence 4679999999997743
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=85.53 E-value=1 Score=35.56 Aligned_cols=49 Identities=18% Similarity=0.180 Sum_probs=33.7
Q ss_pred chhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHhhcCCccc
Q 048223 116 PKFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAAFLKCPWCM 181 (286)
Q Consensus 116 ~~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~~P~il 181 (286)
++.++..+.||++=-+. ...+..|++||++-|++.+||...+.+.+.--
T Consensus 3 e~li~~A~~FL~~p~V~-----------------~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 3 EDLIEQAVKFLQDPKVR-----------------NSPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHCTTTCC-----------------CS-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHhCCcccc-----------------cCCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 34577778888653332 23477899999999999999999998877644
No 13
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=77.91 E-value=10 Score=27.75 Aligned_cols=66 Identities=23% Similarity=0.328 Sum_probs=29.6
Q ss_pred cHHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHH
Q 048223 11 TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKI 90 (286)
Q Consensus 11 ~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~ 90 (286)
.+...+.||..+|++.....++...+-. +...+|..||+.|..++...==.+++.
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~-------------------------~ai~~l~~nPY~L~~~i~gi~F~~aD~ 61 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGD-------------------------DAIEILKENPYRLIEDIDGIGFKTADK 61 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-T-------------------------THHHHHHH-STCCCB-SSSSBHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhH-------------------------HHHHHHHHChHHHHHHccCCCHHHHHH
Confidence 4556677777777776666555544311 233667778877776543311123333
Q ss_pred HH-hcCCCchhH
Q 048223 91 LR-DSGVPESDI 101 (286)
Q Consensus 91 L~-~~G~~~~~i 101 (286)
+. .+|++.++-
T Consensus 62 iA~~~g~~~~d~ 73 (94)
T PF14490_consen 62 IALKLGIEPDDP 73 (94)
T ss_dssp HHHTTT--TT-H
T ss_pred HHHHcCCCCCCH
Confidence 32 355554443
No 14
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=77.77 E-value=2.3 Score=33.60 Aligned_cols=30 Identities=17% Similarity=0.342 Sum_probs=21.6
Q ss_pred cHHHHHHHHhhCCCChhhHHHHHhhCCCce
Q 048223 11 TLLRKLEFFHCEGISNPDTVKILSKYPGLL 40 (286)
Q Consensus 11 ~l~~~l~fL~~~G~~~~~i~~i~~~~P~il 40 (286)
.+..+++||++.|++.+||...+.+.+.--
T Consensus 22 p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 22 PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp -HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 467899999999999999999988865443
No 15
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=70.00 E-value=11 Score=33.42 Aligned_cols=63 Identities=13% Similarity=0.153 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHH-HcCC-CHHHHHHHhhcCCccccccHHHHHHHHHHHHhhcCCChHHH-hhCCCc
Q 048223 150 ESQWESKLHVYK-KWGW-SEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGMGWEPAVI-AKHPAL 212 (286)
Q Consensus 150 ~~~l~~~v~~l~-~lG~-s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~~~~i-~~~P~~ 212 (286)
.-.++.++-|.- ..|+ +.-.+..=+.-.|.+++++.++++.+++-|.+-+|+++++. -+||.=
T Consensus 70 ~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~e 135 (309)
T COG1125 70 PVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHE 135 (309)
T ss_pred HHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchh
Confidence 455666666664 4554 44455566677899999999999999998888899987533 244443
No 16
>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=66.51 E-value=4 Score=27.36 Aligned_cols=34 Identities=24% Similarity=0.284 Sum_probs=24.9
Q ss_pred CceeecCcccHHHHHHHHhhCCCChhhHHHHHhh
Q 048223 2 PKVLLLSPETLLRKLEFFHCEGISNPDTVKILSK 35 (286)
Q Consensus 2 P~lL~~~~~~l~~~l~fL~~~G~~~~~i~~i~~~ 35 (286)
|.=+..++++++..|--|..-|+++++|+-++.-
T Consensus 23 P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 23 PSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp -TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 5567777788888888888899999999888753
No 17
>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=66.25 E-value=37 Score=31.13 Aligned_cols=93 Identities=13% Similarity=0.214 Sum_probs=51.3
Q ss_pred hcCCCchhHhhhhccCCeeEEecch--------hHHHHHHHH--HHcCCC-CcchHHHHHHHHHhcCC-HHHH-HHHHHH
Q 048223 93 DSGVPESDIIKSIESWPKLFLRHPK--------FFEKNVASV--KEMGIN-PLRLKFVLAIQAKCIMS-ESQW-ESKLHV 159 (286)
Q Consensus 93 ~~G~~~~~i~~~i~~~P~ll~~~~~--------~l~~~v~~l--~~lG~~-~~~~~~~~~~~~l~~~~-~~~l-~~~v~~ 159 (286)
.+|++...+...+.++|.+|..... ++.+....+ ++..+- ......+....-+..++ ...+ -.+|+.
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~ 125 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAH 125 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHH
Confidence 3677657777777777777754220 122222221 111110 01112233333333333 2233 577888
Q ss_pred HH-HcCCCHHHHHHHhhcCCccccccH
Q 048223 160 YK-KWGWSEQEWLAAFLKCPWCMITSE 185 (286)
Q Consensus 160 l~-~lG~s~~~i~~~i~~~P~il~~s~ 185 (286)
++ ++|++.+=...++.++|..+....
T Consensus 126 l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 126 LRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHHcCCChhhccchhhhCCCCcEEee
Confidence 87 899999988899999999887643
No 18
>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=65.99 E-value=9.3 Score=22.58 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=16.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
+.|+-|.++||+.++....+..+
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 56777888899988887776644
No 19
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=65.41 E-value=9.9 Score=22.25 Aligned_cols=23 Identities=26% Similarity=0.343 Sum_probs=16.9
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
++++-+.++||+++++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777788888888877776544
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=64.82 E-value=12 Score=23.54 Aligned_cols=25 Identities=28% Similarity=0.252 Sum_probs=19.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhhcC
Q 048223 153 WESKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 153 l~~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
+.+.++-|..+||++.++.+++.+.
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 4567788889999999999888754
No 21
>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=61.88 E-value=12 Score=21.94 Aligned_cols=23 Identities=26% Similarity=0.257 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
++++-|.++||+++++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777888888888877766543
No 22
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=60.17 E-value=12 Score=29.16 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=22.5
Q ss_pred CceeecCcccHHHHHHHHhhCCCChhhHHHHHh
Q 048223 2 PKVLLLSPETLLRKLEFFHCEGISNPDTVKILS 34 (286)
Q Consensus 2 P~lL~~~~~~l~~~l~fL~~~G~~~~~i~~i~~ 34 (286)
|.=|..++|++++-|--+...|++++||+-++.
T Consensus 23 PtWlK~~~ddvkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400|consen 23 PTWLKLTADDVKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred cHHHhcCHHHHHHHHHHHHHcCCChhHceeeee
Confidence 555666667777777777777777777765554
No 23
>PRK14136 recX recombination regulator RecX; Provisional
Probab=59.51 E-value=1.4e+02 Score=27.06 Aligned_cols=132 Identities=13% Similarity=0.152 Sum_probs=74.5
Q ss_pred HHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhc-CchHHHHHHHhCCcccccCcchhhhhHHHHHHhc
Q 048223 16 LEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLH-SSEKTIALIIRFPYILYHDADYYLLPNVKILRDS 94 (286)
Q Consensus 16 l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~-~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~~ 94 (286)
+.||..---+..+|.+=+.++ .++ +..+...|+.|.+.|. ++......+... ..-.... .....-|+..
T Consensus 169 L~lLSrReRSe~ELr~KL~kk----G~~-ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp----~rIrqELrQK 238 (309)
T PRK14136 169 LGYLSRREYSRAELARKLAPY----ADE-SDSVEPLLDALEREGWLSDARFAESLVHR-RASRVGS----ARIVSELKRH 238 (309)
T ss_pred HHHhhcccccHHHHHHHHHHc----CCC-HHHHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhH----HHHHHHHHHc
Confidence 344444455666666655544 222 1366778888888875 666666555543 1111221 1223558889
Q ss_pred CCCchhHhhhhccCCeeEEecchhHHHHHHHHH-HcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHH
Q 048223 95 GVPESDIIKSIESWPKLFLRHPKFFEKNVASVK-EMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAA 173 (286)
Q Consensus 95 G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~-~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~ 173 (286)
|++.+.|...+... ..+.++.....++ .++-.+ .........+.||..-||+.+.|..+
T Consensus 239 GId~eLIEqALeei------eEDE~E~A~~L~eKK~~~~~--------------~d~kek~K~iRfL~rRGFS~D~I~~v 298 (309)
T PRK14136 239 AVGDALVESVGAQL------RETEFERAQAVWRKKFGALP--------------QTPAERAKQARFLAARGFSSATIVKL 298 (309)
T ss_pred CCCHHHHHHHHHhc------cHhHHHHHHHHHHHHhcccC--------------cCHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 99999998887632 1222333333331 122111 01223345589999999999999988
Q ss_pred hhcC
Q 048223 174 FLKC 177 (286)
Q Consensus 174 i~~~ 177 (286)
+..+
T Consensus 299 Lk~~ 302 (309)
T PRK14136 299 LKVG 302 (309)
T ss_pred HHhc
Confidence 8654
No 24
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=57.83 E-value=20 Score=26.16 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=19.0
Q ss_pred hhhccCCeeEEecchh--HHHHHHHHHHcCCCCcch
Q 048223 103 KSIESWPKLFLRHPKF--FEKNVASVKEMGINPLRL 136 (286)
Q Consensus 103 ~~i~~~P~ll~~~~~~--l~~~v~~l~~lG~~~~~~ 136 (286)
.+|..+|+.|...... ++..=+..+++|++.++.
T Consensus 38 ~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~ 73 (94)
T PF14490_consen 38 EILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDP 73 (94)
T ss_dssp HHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-H
T ss_pred HHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCH
Confidence 4567789999875432 555545556789887753
No 25
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=56.90 E-value=14 Score=23.20 Aligned_cols=39 Identities=23% Similarity=0.435 Sum_probs=26.7
Q ss_pred HhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCC
Q 048223 92 RDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINP 133 (286)
Q Consensus 92 ~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~ 133 (286)
+..|++..-+.+++...| ..+++.-+...+..+++|+.+
T Consensus 7 ~~agvS~~TVSr~ln~~~---~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPP---RVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHTSSHHHHHHHHTTCS---SSTHHHHHHHHHHHHHHTB-S
T ss_pred HHHCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHCCCC
Confidence 447899999999887664 334555666666777788765
No 26
>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=55.68 E-value=99 Score=31.51 Aligned_cols=116 Identities=12% Similarity=0.053 Sum_probs=75.9
Q ss_pred cHHHHHHHHhh---CCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhh-hcCchHHHHHHHhCCcccccCcchhhhh
Q 048223 11 TLLRKLEFFHC---EGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHL-LHSSEKTIALIIRFPYILYHDADYYLLP 86 (286)
Q Consensus 11 ~l~~~l~fL~~---~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~-g~~~~~i~~ii~~~P~iL~~s~e~~l~~ 86 (286)
+-...+.||.+ -|+.+....+++.++..=.-. .|....+-|.++ |++.+.+.++..... ... ....
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~----~i~~~~~~L~~v~gi~~~~~~~i~~~~~-----~~~-~~~~ 145 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFD----VLDDDPEKLLEVPGISKANLEKFVSQWS-----QQG-DERR 145 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHH----HHHhCHHHHhcCCCCCHHHHHHHHHHHH-----HhH-HHHH
Confidence 45667889987 489888889999887643222 223334456665 888888877776641 111 2667
Q ss_pred HHHHHHhcCCCchhHh-----------hhhccCCeeEEecchh--HHHHHHHHHHcCCCCcch
Q 048223 87 NVKILRDSGVPESDII-----------KSIESWPKLFLRHPKF--FEKNVASVKEMGINPLRL 136 (286)
Q Consensus 87 ~v~~L~~~G~~~~~i~-----------~~i~~~P~ll~~~~~~--l~~~v~~l~~lG~~~~~~ 136 (286)
.+.||.++|++..... ..|..+|+.|..+... +...=...+.+|+++++.
T Consensus 146 ~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~~d~ 208 (720)
T TIGR01448 146 LLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDP 208 (720)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCCCCH
Confidence 8899999999975544 4578889988764331 332222336789987763
No 27
>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=55.39 E-value=4.4 Score=27.19 Aligned_cols=35 Identities=11% Similarity=-0.051 Sum_probs=24.8
Q ss_pred HHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHhhc
Q 048223 142 IQAKCIMSESQWESKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 142 ~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
++.+...+.+.+++.|--|.+-|++.++|+.+++.
T Consensus 22 ~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 22 PPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp --TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 34444467888888888888999999999988764
No 28
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=53.62 E-value=14 Score=28.77 Aligned_cols=64 Identities=19% Similarity=0.070 Sum_probs=42.6
Q ss_pred HhCCcccccCcchhhhhHHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCc
Q 048223 70 IRFPYILYHDADYYLLPNVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPL 134 (286)
Q Consensus 70 ~~~P~iL~~s~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~ 134 (286)
...|..|..+.++ ++.-|--|...|+++.+|+-++...-.+=-.+.-.=...+.+|+.-|+-++
T Consensus 20 r~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe 83 (151)
T KOG0400|consen 20 RSVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE 83 (151)
T ss_pred cCCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC
Confidence 4568888888886 888888899999999999876653321111111112234567888887765
No 29
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=52.99 E-value=34 Score=30.51 Aligned_cols=67 Identities=15% Similarity=0.150 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhhcCCChHHHhhCCCceecCCCCccchHHHHHHHHHHCCCCCCCccccccccccChhhHHHHhcC
Q 048223 186 DKITAIMDFFVNGMGWEPAVIAKHPALTTFSMEKRIIPRGAVIQFLLSKGLVKSDTTYLTTLLSYPEKTFMLRLMN 261 (286)
Q Consensus 186 ~~l~~k~~fl~~~~g~~~~~i~~~P~~L~~Sle~~i~pR~~vl~~L~~~G~~~~~~~~l~~~l~~se~~F~~~~~~ 261 (286)
+.++.+++.+.+ .|++.+.|+-=|. ++|. +.....+.+++.+.... ... +|-++..|.|+|+....+
T Consensus 163 ~~l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~----~lg-~Pilvg~SRKsfig~~~~ 229 (282)
T PRK11613 163 RYFIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFH----HFN-LPLLVGMSRKSMIGQLLN 229 (282)
T ss_pred HHHHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHH----hCC-CCEEEEecccHHHHhhcC
Confidence 356788888887 9999999887786 4553 34455554444443321 134 677899999999887765
No 30
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=52.35 E-value=77 Score=22.01 Aligned_cols=44 Identities=18% Similarity=0.347 Sum_probs=24.9
Q ss_pred hhHHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcc
Q 048223 85 LPNVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLR 135 (286)
Q Consensus 85 ~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~ 135 (286)
.|.++.|++.++|+++|..++.. |+ +.--..+..+.++|++++.
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT---~NPl~AMa~i~qLGip~eK 45 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LT---QNPLAAMATIQQLGIPQEK 45 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----Hh---hCHHHHHHHHHHcCCCHHH
Confidence 46677777777777777655432 11 1112234556667776654
No 31
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=52.35 E-value=52 Score=26.39 Aligned_cols=35 Identities=23% Similarity=0.163 Sum_probs=26.7
Q ss_pred CceeecCcccHHHHHHHHhhCCCChhhHHHHHhhC
Q 048223 2 PKVLLLSPETLLRKLEFFHCEGISNPDTVKILSKY 36 (286)
Q Consensus 2 P~lL~~~~~~l~~~l~fL~~~G~~~~~i~~i~~~~ 36 (286)
|.=+.+++++++..|--|..-|.++++|+-++.-.
T Consensus 23 P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 23 PEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 44566777788888888888888888888777643
No 32
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=50.74 E-value=29 Score=23.65 Aligned_cols=39 Identities=21% Similarity=0.327 Sum_probs=28.7
Q ss_pred hcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCc
Q 048223 93 DSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPL 134 (286)
Q Consensus 93 ~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~ 134 (286)
.+|++...|.+++...|.+ +++......+.++++|+.++
T Consensus 9 ~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 9 LAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPN 47 (70)
T ss_pred HHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCC
Confidence 3788888888888776654 45666667777888888664
No 33
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=48.10 E-value=49 Score=28.24 Aligned_cols=64 Identities=9% Similarity=0.049 Sum_probs=42.3
Q ss_pred hhccCCeeEEecch--hHHHHHHHHHHcCCCCcchHHHHHHHHHhcC-----------CHHHHHHHHHHHHHcCCCH
Q 048223 104 SIESWPKLFLRHPK--FFEKNVASVKEMGINPLRLKFVLAIQAKCIM-----------SESQWESKLHVYKKWGWSE 167 (286)
Q Consensus 104 ~i~~~P~ll~~~~~--~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~-----------~~~~l~~~v~~l~~lG~s~ 167 (286)
++-.+|+++....+ .+...+.-++.+|++=.+..+..+...+... ....+..-|+||+.||-..
T Consensus 134 ~MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~~~ 210 (217)
T PRK14487 134 NMPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGTAV 210 (217)
T ss_pred CCCCCcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhcccc
Confidence 45567787766655 5888888888899987665555554433211 1256777888888887654
No 34
>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=47.14 E-value=33 Score=23.40 Aligned_cols=34 Identities=9% Similarity=0.127 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHhhcCCcccc
Q 048223 149 SESQWESKLHVYKKWGWSEQEWLAAFLKCPWCMI 182 (286)
Q Consensus 149 ~~~~l~~~v~~l~~lG~s~~~i~~~i~~~P~il~ 182 (286)
+.+.+...++.++.+||+.+++...+.+--.+.+
T Consensus 7 ~~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~ 40 (65)
T PF10440_consen 7 GNERIDAALDAMRQLGFSKKQVRPVLKNLLKLYD 40 (65)
T ss_pred CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4567788888889999999888877764433433
No 35
>PF11181 YflT: Heat induced stress protein YflT
Probab=46.59 E-value=1.1e+02 Score=22.65 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=17.3
Q ss_pred chhhhhHHHHHHhcCCCchhH
Q 048223 81 DYYLLPNVKILRDSGVPESDI 101 (286)
Q Consensus 81 e~~l~~~v~~L~~~G~~~~~i 101 (286)
+..+...|+-|+.-|.++++|
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI 29 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI 29 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE
Confidence 344788899999999998887
No 36
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=43.08 E-value=53 Score=20.03 Aligned_cols=31 Identities=19% Similarity=0.428 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHH-HcCCCHHHHHHHhhcCCcc
Q 048223 150 ESQWESKLHVYK-KWGWSEQEWLAAFLKCPWC 180 (286)
Q Consensus 150 ~~~l~~~v~~l~-~lG~s~~~i~~~i~~~P~i 180 (286)
.+++-.+...|. ++|++......|+..+|..
T Consensus 5 H~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 5 HEKYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 345566777887 8999999999999999864
No 37
>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=41.46 E-value=86 Score=19.40 Aligned_cols=42 Identities=17% Similarity=0.191 Sum_probs=28.1
Q ss_pred HHcCCCHHHHHHHhhcCCccccccHHHHHHHHHHHHhhcCCChHHH
Q 048223 161 KKWGWSEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGMGWEPAVI 206 (286)
Q Consensus 161 ~~lG~s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~~~~i 206 (286)
+.+|++...+.+++...| +.+.++...-.+.... +|+.++.+
T Consensus 5 ~~~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~-l~~~~~~~ 46 (52)
T cd01392 5 RAAGVSVATVSRVLNGKP---RVSEETRERVLAAAEE-LGYRPNAA 46 (52)
T ss_pred HHHCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHH-hCCCCCHH
Confidence 467899999988887655 4455555555555554 88876554
No 38
>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=39.48 E-value=37 Score=19.35 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhh
Q 048223 152 QWESKLHVYKKWGWSEQEWLAAFL 175 (286)
Q Consensus 152 ~l~~~v~~l~~lG~s~~~i~~~i~ 175 (286)
.|..-|.-.++.|+|.+|+..-+.
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH
Confidence 345556666788999988877654
No 39
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=38.33 E-value=61 Score=28.91 Aligned_cols=43 Identities=21% Similarity=0.280 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHhhc
Q 048223 117 KFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 117 ~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
+-++..|+||++=-+ ....+..+.+||++-|++.+||...+++
T Consensus 3 dli~~AVkFL~~~kV-----------------r~aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 3 DLIENAVKFLQNPKV-----------------RDAPLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred HHHHHHHHHhcCccc-----------------ccchHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 346777888764322 2345778999999999999999988875
No 40
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=38.18 E-value=1.1e+02 Score=24.51 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=16.0
Q ss_pred eecCcccHHHHHHHHhhCCCChhhHHHHHh
Q 048223 5 LLLSPETLLRKLEFFHCEGISNPDTVKILS 34 (286)
Q Consensus 5 L~~~~~~l~~~l~fL~~~G~~~~~i~~i~~ 34 (286)
+..++++++..|--|..-|+++++|+-++.
T Consensus 23 ~~~~~eeVe~~I~klaKkG~~pSqIG~iLR 52 (148)
T PTZ00072 23 LKLSSSEVEDQICKLAKKGLTPSQIGVILR 52 (148)
T ss_pred hcCCHHHHHHHHHHHHHCCCCHhHhhhhhh
Confidence 444445555555555555555555555544
No 41
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=37.83 E-value=43 Score=23.89 Aligned_cols=37 Identities=16% Similarity=0.234 Sum_probs=16.0
Q ss_pred HhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHh
Q 048223 19 FHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSH 57 (286)
Q Consensus 19 L~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~ 57 (286)
|+..|++.+++..+=..|-.++... .++...++-+.+
T Consensus 23 LrR~Gfs~~~i~~l~~ayr~l~~~~--~~~~~a~~~l~~ 59 (83)
T PF13720_consen 23 LRRRGFSKEEISALRRAYRILFRSG--LTLEEALEELEE 59 (83)
T ss_dssp HHHTTS-HHHHHHHHHHHHHHHTSS--S-HHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHHHHHHhCC--CCHHHHHHHHHH
Confidence 4455555555555554444444332 144444444433
No 42
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=37.83 E-value=52 Score=26.40 Aligned_cols=36 Identities=17% Similarity=0.010 Sum_probs=24.6
Q ss_pred hCCcccccCcchhhhhHHHHHHhcCCCchhHhhhhcc
Q 048223 71 RFPYILYHDADYYLLPNVKILRDSGVPESDIIKSIES 107 (286)
Q Consensus 71 ~~P~iL~~s~e~~l~~~v~~L~~~G~~~~~i~~~i~~ 107 (286)
..|..+.++.++ ++..|.-|..-|+++++|+-++..
T Consensus 21 ~~P~W~~~~~ee-ve~~I~~lakkG~~pSqIG~~LRD 56 (151)
T PRK08561 21 EPPEWVDYSPEE-IEELVVELAKQGYSPSMIGIILRD 56 (151)
T ss_pred CCCccccCCHHH-HHHHHHHHHHCCCCHHHhhhhHhh
Confidence 446667777665 777777777777777777766643
No 43
>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=37.41 E-value=28 Score=26.02 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=14.3
Q ss_pred cCchHHHHHHHhCCcccccCc
Q 048223 60 HSSEKTIALIIRFPYILYHDA 80 (286)
Q Consensus 60 ~~~~~i~~ii~~~P~iL~~s~ 80 (286)
++.+++..++..+|.++...+
T Consensus 71 ~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhHHHHHHHHhChhheeCCE
Confidence 566777777777777777665
No 44
>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=35.63 E-value=83 Score=22.51 Aligned_cols=37 Identities=14% Similarity=0.179 Sum_probs=21.9
Q ss_pred HHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhh
Q 048223 18 FFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHL 58 (286)
Q Consensus 18 fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~ 58 (286)
+-+.+|++..+|..+-..+|.= +.......+..|+.-
T Consensus 19 laR~LGlse~~Id~i~~~~~~~----~~eq~~~mL~~W~~~ 55 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPRN----LREQVRQSLREWKKI 55 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCCC----HHHHHHHHHHHHHHh
Confidence 3445788888888888777732 222444555555543
No 45
>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=34.67 E-value=29 Score=25.90 Aligned_cols=22 Identities=23% Similarity=0.428 Sum_probs=17.9
Q ss_pred cCCCchhHhhhhccCCeeEEec
Q 048223 94 SGVPESDIIKSIESWPKLFLRH 115 (286)
Q Consensus 94 ~G~~~~~i~~~i~~~P~ll~~~ 115 (286)
..++.+++..++..+|.++...
T Consensus 69 ~~~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 69 DDLSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp TTSBHHHHHHHHHHSGGGB-SS
T ss_pred hhhhhHHHHHHHHhChhheeCC
Confidence 4588999999999999998764
No 46
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=34.42 E-value=35 Score=30.32 Aligned_cols=110 Identities=8% Similarity=0.043 Sum_probs=58.0
Q ss_pred hhcCchHHHHHHHhCCcccccCcch------hhhhHHHHHHhcCCC---chhHhhhhccCCeeEEecc--hhHHHHHHHH
Q 048223 58 LLHSSEKTIALIIRFPYILYHDADY------YLLPNVKILRDSGVP---ESDIIKSIESWPKLFLRHP--KFFEKNVASV 126 (286)
Q Consensus 58 ~g~~~~~i~~ii~~~P~iL~~s~e~------~l~~~v~~L~~~G~~---~~~i~~~i~~~P~ll~~~~--~~l~~~v~~l 126 (286)
+++.+..+..++...|.+|..|+|. .++|...|-+++.+= ++.-..++++.--+++..+ +.+.+.++-|
T Consensus 158 F~G~~~al~~v~~~~pdV~nHNvETVprL~~~VRp~A~Y~~SL~~L~~~k~~~P~i~TKSgiMlGLGEt~~Ev~e~m~DL 237 (306)
T COG0320 158 FRGNDDALEIVADAGPDVFNHNVETVPRLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIEVMDDL 237 (306)
T ss_pred ccCCHHHHHHHHhcCcchhhcccccchhcccccCCCCcHHHHHHHHHHHHHhCCCcccccceeeecCCcHHHHHHHHHHH
Confidence 4456677778888888999998875 233334444443221 1111234444444555543 3477777777
Q ss_pred HHcCCCCcchHHHHHH-----HHHhcCCHHHHHHHHHHHHHcCCCH
Q 048223 127 KEMGINPLRLKFVLAI-----QAKCIMSESQWESKLHVYKKWGWSE 167 (286)
Q Consensus 127 ~~lG~~~~~~~~~~~~-----~~l~~~~~~~l~~~v~~l~~lG~s~ 167 (286)
++.|++--++.=...| +..-+.+++.+..-=+.-.++||+.
T Consensus 238 r~~gvdilTiGQYlqPS~~HlpV~ryv~PeeF~~~~~~a~~~GF~~ 283 (306)
T COG0320 238 RSAGVDILTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLH 283 (306)
T ss_pred HHcCCCEEEeccccCCccccCCceeccCHHHHHHHHHHHHHccchh
Confidence 7777764332211111 2223345565555445555677754
No 47
>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=33.66 E-value=89 Score=22.70 Aligned_cols=23 Identities=13% Similarity=0.062 Sum_probs=19.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
..|.+++++||+-++|..++...
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 48 QFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Confidence 56778899999999999998754
No 48
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=33.19 E-value=1.3e+02 Score=20.27 Aligned_cols=41 Identities=15% Similarity=0.144 Sum_probs=30.2
Q ss_pred HHcCCCHHHHHHHhhcCCccccccHHHHHHHHHHHHhhcCCChHH
Q 048223 161 KKWGWSEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGMGWEPAV 205 (286)
Q Consensus 161 ~~lG~s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~~~~ 205 (286)
+.+|+|...|.+++...|.+ +.++-+.-.+.+.+ +|+.+..
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~-~gy~~~~ 48 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV---SEETREKVLAAMEE-LGYIPNR 48 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHH-hCCCCCH
Confidence 46799999999888766665 66666666677776 8886554
No 49
>PRK09875 putative hydrolase; Provisional
Probab=32.20 E-value=40 Score=30.24 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhhcCCc
Q 048223 151 SQWESKLHVYKKWGWSEQEWLAAFLKCPW 179 (286)
Q Consensus 151 ~~l~~~v~~l~~lG~s~~~i~~~i~~~P~ 179 (286)
.-+..-+-.|++.|+++++|.+|+..+|.
T Consensus 260 ~i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 260 YLLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 34566777888999999999999999997
No 50
>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=32.17 E-value=45 Score=22.02 Aligned_cols=19 Identities=16% Similarity=0.230 Sum_probs=14.0
Q ss_pred HHHHHHHcCCCHHHHHHHh
Q 048223 156 KLHVYKKWGWSEQEWLAAF 174 (286)
Q Consensus 156 ~v~~l~~lG~s~~~i~~~i 174 (286)
-|..++++|||-++|..++
T Consensus 6 ~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3556679999999999998
No 51
>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=32.15 E-value=60 Score=21.34 Aligned_cols=21 Identities=5% Similarity=0.310 Sum_probs=12.9
Q ss_pred HHHHHHHcCCCHHHHHHHhhc
Q 048223 156 KLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 156 ~v~~l~~lG~s~~~i~~~i~~ 176 (286)
-|+-|.++||+.+.+-..+++
T Consensus 12 lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHcCCcHHHHHHHHHH
Confidence 456677777777777776653
No 52
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=31.70 E-value=2.6e+02 Score=22.09 Aligned_cols=137 Identities=11% Similarity=0.010 Sum_probs=0.0
Q ss_pred HHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhh-cCchHHHHHHHhCCcccccCcchhhhhHHHHHHhc
Q 048223 16 LEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLL-HSSEKTIALIIRFPYILYHDADYYLLPNVKILRDS 94 (286)
Q Consensus 16 l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g-~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~~ 94 (286)
+.+|..-.-+..+|..-+.+. +.+-+ .+...++.|.+.| +++........+.- ...... -.....-|...
T Consensus 18 l~~L~~r~~s~~el~~kL~~k----g~~~~-~i~~vl~~l~~~~~ldD~~~a~~~~~~~---~~~~~g-~~~I~~~L~~k 88 (157)
T PRK00117 18 LRLLARREHSRAELRRKLAAK----GFSEE-VIEAVLDRLKEEGLLDDERFAESFVRSR---ARKGYG-PRRIRQELRQK 88 (157)
T ss_pred HHHHccchhHHHHHHHHHHhc----CCCHH-HHHHHHHHHHHcCCCCHHHHHHHHHHHH---HhCCch-HHHHHHHHHHc
Q ss_pred CCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHh
Q 048223 95 GVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKWGWSEQEWLAAF 174 (286)
Q Consensus 95 G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~lG~s~~~i~~~i 174 (286)
|++.+.|..++...+ .+..+.....+. +............-+..+.+|..-||+.+.|..++
T Consensus 89 Gi~~~~I~~~l~~~~------~d~~e~a~~~~~------------k~~~~~~~~~~~~k~Ki~~~L~rkGF~~~~I~~~l 150 (157)
T PRK00117 89 GVDREIIEEALAELD------IDWEELARELAR------------KKFRRPLPDDAKEKAKLVRFLARRGFSMDVIQRVL 150 (157)
T ss_pred CCCHHHHHHHHHHcC------ccHHHHHHHHHH------------HHcCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_pred hcCCc
Q 048223 175 LKCPW 179 (286)
Q Consensus 175 ~~~P~ 179 (286)
.....
T Consensus 151 ~~~~~ 155 (157)
T PRK00117 151 RNALD 155 (157)
T ss_pred Hhhhc
No 53
>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=31.16 E-value=1.3e+02 Score=21.81 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=20.0
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcCC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKCP 178 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~P 178 (286)
..|..++++||+-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 48 HQIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhCCC
Confidence 567888899999999999987543
No 54
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=30.79 E-value=2.1e+02 Score=20.66 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=12.6
Q ss_pred HHHHHHcCCCHHHHHHHh
Q 048223 157 LHVYKKWGWSEQEWLAAF 174 (286)
Q Consensus 157 v~~l~~lG~s~~~i~~~i 174 (286)
++.|..+|+|++|+..++
T Consensus 69 lkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 69 LKRLNMFGITREEFEEAL 86 (87)
T ss_pred HHHHHHcCCCHHHHHHHh
Confidence 344556788888887765
No 55
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=30.63 E-value=48 Score=22.48 Aligned_cols=19 Identities=26% Similarity=0.246 Sum_probs=14.9
Q ss_pred HHHhhCCCChhhHHHHHhh
Q 048223 17 EFFHCEGISNPDTVKILSK 35 (286)
Q Consensus 17 ~fL~~~G~~~~~i~~i~~~ 35 (286)
..|.++|++..|+...+.+
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 4577889999888887766
No 56
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=30.34 E-value=1.2e+02 Score=21.31 Aligned_cols=46 Identities=11% Similarity=0.094 Sum_probs=29.5
Q ss_pred HHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHH
Q 048223 15 KLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKT 65 (286)
Q Consensus 15 ~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i 65 (286)
.-++.+.+|++..+|..+-..+|. .. ....+.+.-|+.-.+....+
T Consensus 14 Wk~laR~LGls~~~I~~ie~~~~~-~~----eq~~~mL~~W~~k~G~~At~ 59 (79)
T cd08784 14 HKRFFRKLGLSDNEIKVAELDNPQ-HR----DRVYELLRIWRNKEGRKATL 59 (79)
T ss_pred HHHHHHHcCCCHHHHHHHHHcCCc-hH----HHHHHHHHHHHhccCcCcHH
Confidence 345677889999999888888887 32 24556666555543333333
No 57
>PRK14134 recX recombination regulator RecX; Provisional
Probab=29.77 E-value=4e+02 Score=23.67 Aligned_cols=95 Identities=9% Similarity=-0.023 Sum_probs=50.2
Q ss_pred CcccHHHHHHHHhhCC-CChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCc------------
Q 048223 8 SPETLLRKLEFFHCEG-ISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPY------------ 74 (286)
Q Consensus 8 ~~~~l~~~l~fL~~~G-~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~------------ 74 (286)
+.+.+..+|++|.+.| ++....+....+.- +-..+ -...-.-|..-|++++.|..++...+.
T Consensus 91 ~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~-~~~~G----~~~I~~eL~qKGI~~~iIe~al~~~~~e~e~e~a~~l~~ 165 (283)
T PRK14134 91 DEDAVNRVIRFLKEYNFIDDDKYCDMYIREK-INSYG----RNKIKYTLLNKGIKENIIIEKINNIDEEKEKKVAYKLAE 165 (283)
T ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-HHhhh----HHHHHHHHHHCCCCHHHHHHHHHhCChhhHHHHHHHHHH
Confidence 3335666677777666 34444444433321 00111 011224577788887777777654321
Q ss_pred -----cccc--CcchhhhhHHHHHHhcCCCchhHhhhhcc
Q 048223 75 -----ILYH--DADYYLLPNVKILRDSGVPESDIIKSIES 107 (286)
Q Consensus 75 -----iL~~--s~e~~l~~~v~~L~~~G~~~~~i~~~i~~ 107 (286)
.-.. +..+.-...+.||..-|++.+.|..++..
T Consensus 166 Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~ 205 (283)
T PRK14134 166 KKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNE 205 (283)
T ss_pred HhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 1001 11112345668888899998888877653
No 58
>PRK14135 recX recombination regulator RecX; Provisional
Probab=29.46 E-value=3.4e+02 Score=23.56 Aligned_cols=82 Identities=7% Similarity=-0.047 Sum_probs=41.5
Q ss_pred HHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHHHHHcCCCCcchHHHHHH--HHHh--cCCHHHHHHHHHHHHH
Q 048223 87 NVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVASVKEMGINPLRLKFVLAI--QAKC--IMSESQWESKLHVYKK 162 (286)
Q Consensus 87 ~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~l~~lG~~~~~~~~~~~~--~~l~--~~~~~~l~~~v~~l~~ 162 (286)
.+.+|..-.-+..++.+=+.+. +.+.+.+...++.|.+.|+-.+ ..+.... ..+. ..+... -..-|..
T Consensus 63 Al~~L~~r~~s~~el~~kL~~k----g~~~~~Ie~vl~~l~~~~~ldD-~~~a~~~~~~~~~~~~~g~~~---I~~kL~~ 134 (263)
T PRK14135 63 ALYYLSYQMRTEKEVRDYLKKH----EISEEIISEVIDKLKEEKYIDD-KEYAESYVRTNINTGDKGPRV---IKQKLLQ 134 (263)
T ss_pred HHHHhhhccccHHHHHHHHHHC----CCCHHHHHHHHHHHHHcCCCCH-HHHHHHHHHHHHhccccchHH---HHHHHHH
Confidence 3455555555555555444432 3345567777788888886433 2222221 1111 012222 2234456
Q ss_pred cCCCHHHHHHHhhc
Q 048223 163 WGWSEQEWLAAFLK 176 (286)
Q Consensus 163 lG~s~~~i~~~i~~ 176 (286)
-|++.+.|...+..
T Consensus 135 kGi~~~~Ie~~l~~ 148 (263)
T PRK14135 135 KGIEDEIIEEALSE 148 (263)
T ss_pred cCCCHHHHHHHHHh
Confidence 77777777776654
No 59
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=29.24 E-value=1.1e+02 Score=25.49 Aligned_cols=25 Identities=20% Similarity=0.175 Sum_probs=22.0
Q ss_pred hhhHHHHHHhcCCCchhHhhhhccC
Q 048223 84 LLPNVKILRDSGVPESDIIKSIESW 108 (286)
Q Consensus 84 l~~~v~~L~~~G~~~~~i~~~i~~~ 108 (286)
+...+.+|.++|+++.++.+++...
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 6778899999999999999988766
No 60
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=28.85 E-value=1.1e+02 Score=21.81 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=13.7
Q ss_pred CHHHHHHHhhcCCccccccHHHHHHHHHHHH
Q 048223 166 SEQEWLAAFLKCPWCMITSEDKITAIMDFFV 196 (286)
Q Consensus 166 s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~ 196 (286)
+.+++.+++.+| +.+.+..+.+||.
T Consensus 62 ~~~~~~~L~~kh------G~~~i~~R~~FL~ 86 (87)
T PF11626_consen 62 DKDDIERLIKKH------GEERIERRKEFLE 86 (87)
T ss_dssp -HHHHHHHHHHH-------HHHHHHHHHHHT
T ss_pred CHHHHHHHHHHh------CHHHHHHHHHHHh
Confidence 445555555544 5666666666664
No 61
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=27.84 E-value=30 Score=20.95 Aligned_cols=13 Identities=15% Similarity=0.166 Sum_probs=10.5
Q ss_pred HHhhCCCChhhHH
Q 048223 18 FFHCEGISNPDTV 30 (286)
Q Consensus 18 fL~~~G~~~~~i~ 30 (286)
-|.++|++.+|+.
T Consensus 27 ~L~DIGl~R~di~ 39 (40)
T PF06568_consen 27 QLADIGLTRSDIR 39 (40)
T ss_pred HHHHcCCCHHHhc
Confidence 4778999998874
No 62
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=27.66 E-value=43 Score=27.31 Aligned_cols=76 Identities=11% Similarity=0.200 Sum_probs=0.0
Q ss_pred HhcCCCchhHhhhh-ccCCeeEEe-------cchhHHHHHHHHHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 048223 92 RDSGVPESDIIKSI-ESWPKLFLR-------HPKFFEKNVASVKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVYKKW 163 (286)
Q Consensus 92 ~~~G~~~~~i~~~i-~~~P~ll~~-------~~~~l~~~v~~l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l~~l 163 (286)
+++|++.+++++.. ...|.+-.. ..+++...++.|.+.-=..-...-.-.-+.+..++++.+...++.++..
T Consensus 15 k~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~spvv~v~pdDsi~~vv~lM~~~ 94 (187)
T COG3620 15 KELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHSPVVSVSPDDSISDVVNLMRDK 94 (187)
T ss_pred HHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccCCeeEECchhhHHHHHHHHHHc
Q ss_pred CCCH
Q 048223 164 GWSE 167 (286)
Q Consensus 164 G~s~ 167 (286)
|+|.
T Consensus 95 g~SQ 98 (187)
T COG3620 95 GISQ 98 (187)
T ss_pred CCcc
No 63
>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=27.39 E-value=1.4e+02 Score=21.74 Aligned_cols=22 Identities=18% Similarity=0.101 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhhc
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
..|.+++++||+-++|..++..
T Consensus 48 ~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 48 DIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHHHHcCCCHHHHHHHHhc
Confidence 4678889999999999998764
No 64
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=26.83 E-value=3.6e+02 Score=22.20 Aligned_cols=18 Identities=11% Similarity=-0.079 Sum_probs=9.6
Q ss_pred HHhHhhhcCchHHHHHHH
Q 048223 53 NSLSHLLHSSEKTIALII 70 (286)
Q Consensus 53 ~~L~~~g~~~~~i~~ii~ 70 (286)
+-|...|++++.|..++.
T Consensus 92 qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 92 QELKQKGIDDEIIEEALE 109 (174)
T ss_pred HHHHHcCCCHHHHHHHHh
Confidence 345555666555555543
No 65
>PHA02591 hypothetical protein; Provisional
Probab=26.42 E-value=99 Score=21.91 Aligned_cols=27 Identities=15% Similarity=0.190 Sum_probs=22.0
Q ss_pred cCcccHHHHHHHHhhCCCChhhHHHHH
Q 048223 7 LSPETLLRKLEFFHCEGISNPDTVKIL 33 (286)
Q Consensus 7 ~~~~~l~~~l~fL~~~G~~~~~i~~i~ 33 (286)
.+.|++.....-|.+.|++.++|++.+
T Consensus 43 ~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 43 ESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred eccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 344478888889999999999998875
No 66
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=26.36 E-value=2.3e+02 Score=23.91 Aligned_cols=89 Identities=25% Similarity=0.216 Sum_probs=53.8
Q ss_pred CCceeccccCcchh--HHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHHHHhcCCCchhHhhhhccCCeeEEe
Q 048223 37 PGLLSRSLDNHLIP--TFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKILRDSGVPESDIIKSIESWPKLFLR 114 (286)
Q Consensus 37 P~il~~~~~~~l~~--~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~ 114 (286)
..++..++|.++.. .++++...-+...++.++..+...... +.+..++.++..|+ |.+.+.+..+...++.+.
T Consensus 5 ~~L~vFD~D~TLi~~~~~~~~~~~~g~~~~v~~~t~~~~~~~~-~~~~~~~~~v~~l~--g~~~~~v~~~~~~~~~l~-- 79 (212)
T COG0560 5 KKLAVFDLDGTLINAELIDELARGAGVGEEVLAITERAMRGEL-DFEESLRLRVALLK--GLPVEVLEEVREEFLRLT-- 79 (212)
T ss_pred cceEEEecccchhhHHHHHHHHHHhCCHHHHHHHHHHHhcccc-cHHHHHHHHHHHhC--CCCHHHHHHHHHhcCcCC--
Confidence 35677788887777 334455444455667666666554433 44444556666554 667778877777653332
Q ss_pred cchhHHHHHHHHHHcCCC
Q 048223 115 HPKFFEKNVASVKEMGIN 132 (286)
Q Consensus 115 ~~~~l~~~v~~l~~lG~~ 132 (286)
....+.+.++++.|..
T Consensus 80 --~ga~elv~~lk~~G~~ 95 (212)
T COG0560 80 --PGAEELVAALKAAGAK 95 (212)
T ss_pred --ccHHHHHHHHHHCCCE
Confidence 2356677778877754
No 67
>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=26.18 E-value=91 Score=24.04 Aligned_cols=67 Identities=19% Similarity=0.188 Sum_probs=33.1
Q ss_pred hhhHHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHHHH---HHHcCCCCcchHHHHHHHHHhcCCHHHHHHHHHHH
Q 048223 84 LLPNVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNVAS---VKEMGINPLRLKFVLAIQAKCIMSESQWESKLHVY 160 (286)
Q Consensus 84 l~~~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v~~---l~~lG~~~~~~~~~~~~~~l~~~~~~~l~~~v~~l 160 (286)
+-...+.|+ .|++-++|..+-.-.|+.|. +++..++. +++.+ ...-.+.+.-.
T Consensus 13 lf~i~eAlr-rG~sveeI~e~T~ID~wFL~----~i~~Iv~~e~~L~~~~-------------------~~~~~~~L~~a 68 (123)
T PF02787_consen 13 LFAIAEALR-RGYSVEEIHELTKIDPWFLE----QIKNIVDMEKELKEYL-------------------NELDPELLRKA 68 (123)
T ss_dssp HHHHHHHHH-TTB-HHHHHHHH---HHHHH----HHHHHHHHHHHHHHHG-------------------GG--HHHHHHH
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCccHHHHH----HHHHHHHHHHHHHHhh-------------------ccchHHHHHHH
Confidence 444444454 48888888877666666653 33333322 22210 00111244556
Q ss_pred HHcCCCHHHHHHHh
Q 048223 161 KKWGWSEQEWLAAF 174 (286)
Q Consensus 161 ~~lG~s~~~i~~~i 174 (286)
+++|||..+|+.+.
T Consensus 69 K~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 69 KRLGFSDRQIARLW 82 (123)
T ss_dssp HHTT--HHHHHHHH
T ss_pred HHcCCCHHHHHhcc
Confidence 79999999999874
No 68
>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=25.92 E-value=1.2e+02 Score=28.35 Aligned_cols=44 Identities=14% Similarity=0.257 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhhcCCccccccHHHHHHHHHHHHhhcCCC
Q 048223 150 ESQWESKLHVYKKWGWSEQEWLAAFLKCPWCMITSEDKITAIMDFFVNGMGWE 202 (286)
Q Consensus 150 ~~~l~~~v~~l~~lG~s~~~i~~~i~~~P~il~~s~~~l~~k~~fl~~~~g~~ 202 (286)
.+..+..|+-+.++||.+++|.+.++ .+-.+=++-+|||.. |++
T Consensus 153 g~~~e~~I~~i~eMGf~R~qV~~ALR-------AafNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 153 GSERETTIEEIMEMGYEREEVERALR-------AAFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred chHHHHHHHHHHHhCCCHHHHHHHHH-------HHhCCHHHHHHHHHh--CCC
Confidence 45788899999999999999998775 244566788999995 787
No 69
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=25.81 E-value=1.4e+02 Score=21.18 Aligned_cols=36 Identities=14% Similarity=0.087 Sum_probs=15.9
Q ss_pred HHHcCCCCcchHH-HHHHHHHhcCCHHHHHHHHHHHHH
Q 048223 126 VKEMGINPLRLKF-VLAIQAKCIMSESQWESKLHVYKK 162 (286)
Q Consensus 126 l~~lG~~~~~~~~-~~~~~~l~~~~~~~l~~~v~~l~~ 162 (286)
|+.-|++++++.. ..+...+.. +..++++.++-+++
T Consensus 23 LrR~Gfs~~~i~~l~~ayr~l~~-~~~~~~~a~~~l~~ 59 (83)
T PF13720_consen 23 LRRRGFSKEEISALRRAYRILFR-SGLTLEEALEELEE 59 (83)
T ss_dssp HHHTTS-HHHHHHHHHHHHHHHT-SSS-HHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHHHHHHh-CCCCHHHHHHHHHH
Confidence 4455565555432 233444332 33455555555554
No 70
>PRK14135 recX recombination regulator RecX; Provisional
Probab=25.44 E-value=4.5e+02 Score=22.77 Aligned_cols=23 Identities=9% Similarity=0.050 Sum_probs=18.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHhhc
Q 048223 154 ESKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 154 ~~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
+..+.||..-||+.+.|..++..
T Consensus 236 ~K~~~~L~rrGF~~~~I~~~l~~ 258 (263)
T PRK14135 236 QKLKQALYRKGFSYDDIDSFLRE 258 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHH
Confidence 45567888999999999887754
No 71
>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=24.88 E-value=1.9e+02 Score=21.21 Aligned_cols=22 Identities=9% Similarity=0.012 Sum_probs=14.2
Q ss_pred HHHhhCCCChhhHHHHHhhCCC
Q 048223 17 EFFHCEGISNPDTVKILSKYPG 38 (286)
Q Consensus 17 ~fL~~~G~~~~~i~~i~~~~P~ 38 (286)
++.+.+|++..+|..+-..+|.
T Consensus 24 ~laR~LGLse~~I~~i~~~~~~ 45 (96)
T cd08315 24 RLMRQLGLSENEIDVAKANERV 45 (96)
T ss_pred HHHHHcCCCHHHHHHHHHHCCC
Confidence 3555667777777666666665
No 72
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.81 E-value=2.2e+02 Score=20.63 Aligned_cols=26 Identities=15% Similarity=0.041 Sum_probs=21.2
Q ss_pred HHHHHHHH-cCCCHHHHHHHhhcCCcc
Q 048223 155 SKLHVYKK-WGWSEQEWLAAFLKCPWC 180 (286)
Q Consensus 155 ~~v~~l~~-lG~s~~~i~~~i~~~P~i 180 (286)
..|..+++ +|++.+++..++...+..
T Consensus 47 ~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 47 ERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 45677787 999999999999877765
No 73
>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]
Probab=24.12 E-value=3.9e+02 Score=26.25 Aligned_cols=103 Identities=14% Similarity=0.166 Sum_probs=68.2
Q ss_pred hCCCChhhHHHHHhhCCCceeccccCcchh-HHHHhHhhhcCchHHHHHHHhCCccccc-CcchhhhhHHH-HHHhcCCC
Q 048223 21 CEGISNPDTVKILSKYPGLLSRSLDNHLIP-TFNSLSHLLHSSEKTIALIIRFPYILYH-DADYYLLPNVK-ILRDSGVP 97 (286)
Q Consensus 21 ~~G~~~~~i~~i~~~~P~il~~~~~~~l~~-~~~~L~~~g~~~~~i~~ii~~~P~iL~~-s~e~~l~~~v~-~L~~~G~~ 97 (286)
..|+.++-+-+.+.+ -.+=...+++.+.. .+.-+.+.--++.....++...+.++.. ..++ ... .|.++||+
T Consensus 114 rNG~GKsTLLRaia~-~~v~~f~veqE~~g~~t~~~~~~l~~D~~~~dfl~~e~~l~~~~~l~e----i~~~~L~glGFt 188 (582)
T KOG0062|consen 114 RNGIGKSTLLRAIAN-GQVSGFHVEQEVRGDDTEALQSVLESDTERLDFLAEEKELLAGLTLEE----IYDKILAGLGFT 188 (582)
T ss_pred CCCCcHHHHHHHHHh-cCcCccCchhheeccchHHHhhhhhccHHHHHHHHhhhhhhccchHHH----HHHHHHHhCCCC
Confidence 368888888888887 23444444544433 3445556556777888888888888877 4433 333 89999999
Q ss_pred chhHh-----------------hhhccCCeeEEecch--h-HHHHHHHHHH
Q 048223 98 ESDII-----------------KSIESWPKLFLRHPK--F-FEKNVASVKE 128 (286)
Q Consensus 98 ~~~i~-----------------~~i~~~P~ll~~~~~--~-l~~~v~~l~~ 128 (286)
++... +.+-..|-+|-.++- . =...|.||.+
T Consensus 189 ~emq~~pt~slSGGWrMrlaLARAlf~~pDlLLLDEPTNhLDv~av~WLe~ 239 (582)
T KOG0062|consen 189 PEMQLQPTKSLSGGWRMRLALARALFAKPDLLLLDEPTNHLDVVAVAWLEN 239 (582)
T ss_pred HHHHhccccccCcchhhHHHHHHHHhcCCCEEeecCCcccchhHHHHHHHH
Confidence 87654 556677999988743 2 2345666643
No 74
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=23.69 E-value=48 Score=26.40 Aligned_cols=32 Identities=16% Similarity=0.105 Sum_probs=22.7
Q ss_pred hcCCHHHHHHHHHHHHHcCCCHHHHHHHhhcC
Q 048223 146 CIMSESQWESKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 146 ~~~~~~~l~~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
...+.+.+++.|--|..-|.+.+||+.+++..
T Consensus 23 ~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 23 LKLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred hcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 33567777777777777888788887777643
No 75
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=23.64 E-value=84 Score=20.65 Aligned_cols=20 Identities=20% Similarity=0.408 Sum_probs=15.6
Q ss_pred HHHH-HHcCCCHHHHHHHhhc
Q 048223 157 LHVY-KKWGWSEQEWLAAFLK 176 (286)
Q Consensus 157 v~~l-~~lG~s~~~i~~~i~~ 176 (286)
|.|+ +++|+|.+++..+|.+
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~ 43 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRA 43 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 4455 4899999999998874
No 76
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=23.34 E-value=3.7e+02 Score=22.97 Aligned_cols=50 Identities=12% Similarity=0.063 Sum_probs=26.9
Q ss_pred cCcc-cHHHHHHHHh-hCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhh
Q 048223 7 LSPE-TLLRKLEFFH-CEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLL 59 (286)
Q Consensus 7 ~~~~-~l~~~l~fL~-~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g 59 (286)
|.|+ +.....+-|. ++|+++.++.....+.-.... ..+......|+..-|
T Consensus 67 Y~Pee~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~---~~s~~~i~~~l~~~~ 118 (214)
T TIGR03060 67 YRPEEHLDALFDALCNSNGFDPEQLREDAKQLLEQAK---GKGLDEILSWLTQAN 118 (214)
T ss_pred CCChHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh---cCCHHHHHHHHhccc
Confidence 4455 5555665555 478887777666554322222 124445556665443
No 77
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.13 E-value=1.9e+02 Score=23.88 Aligned_cols=67 Identities=7% Similarity=-0.011 Sum_probs=48.0
Q ss_pred cHHHHHHHHhhCCCChhhHHHHHhhCCCceecccc-CcchhHHH--HhHhhhc-------CchHHHHHHHhCCcccccC
Q 048223 11 TLLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLD-NHLIPTFN--SLSHLLH-------SSEKTIALIIRFPYILYHD 79 (286)
Q Consensus 11 ~l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~-~~l~~~~~--~L~~~g~-------~~~~i~~ii~~~P~iL~~s 79 (286)
.+...-.++.++||. ++..++.+-.-+|+.... ..+..+++ |-..+|. |.++..+++..||+--...
T Consensus 20 ~MAdLka~~~dlGf~--~v~T~iaSGNlvf~s~~~~~el~~klE~afe~~fg~~~dilVrs~~~~~~i~a~nPf~~~~~ 96 (178)
T COG3797 20 VMADLKAALTDLGFA--NVRTYIASGNLVFESEAGAAELEAKLEAAFEKRFGRHVDILVRSAEDWETIAAANPFPEEAA 96 (178)
T ss_pred eHHHHHHHHHHcCcc--hhhHhhhcCCEEEEcCCChHHHHHHHHHHHHHHcCCCccEEEeeHHHHHHHHhcCCCchhhc
Confidence 566777899999997 678888888777765432 35566664 3344664 6788899999999876654
No 78
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=22.88 E-value=2.1e+02 Score=20.91 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=19.3
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcCC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKCP 178 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~P 178 (286)
..+.++++.|++-+++..++....
T Consensus 48 ~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 48 QQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCc
Confidence 456778899999999999887553
No 79
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.58 E-value=2e+02 Score=21.32 Aligned_cols=25 Identities=8% Similarity=0.070 Sum_probs=20.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcCCc
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKCPW 179 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~P~ 179 (286)
..|..++.+||+-+++..++...+.
T Consensus 49 ~~I~~lr~~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 49 NRIKYLRDLGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCH
Confidence 4677788999999999999877653
No 80
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=22.51 E-value=1.4e+02 Score=26.90 Aligned_cols=90 Identities=19% Similarity=0.087 Sum_probs=57.1
Q ss_pred HHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhhhcCchHHHHHHHhCCcccccCcchhhhhHHHHHHh
Q 048223 14 RKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHLLHSSEKTIALIIRFPYILYHDADYYLLPNVKILRD 93 (286)
Q Consensus 14 ~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~g~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~ 93 (286)
-.|+.|.+-|+|..+|++.+.++|.-+...+.++-..- .+... ...+.....-.+...-+..+++ |...|.-.-.
T Consensus 14 ~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~--~Y~a~-~A~~~~~~~rrr~~~k~~~~~e--L~~~V~e~L~ 88 (318)
T COG2826 14 YEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRD--IYSAV-KAQERYRMLRRRRIRKLKLNPE--LRELVLEKLK 88 (318)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccc--eeeHH-HHHHHHHHhhcccCCcccCCHH--HHHHHHHHHH
Confidence 35788999999999999999999988776554322111 22211 1112244444455555666654 6665555555
Q ss_pred cCCCchhHhhhhccC
Q 048223 94 SGVPESDIIKSIESW 108 (286)
Q Consensus 94 ~G~~~~~i~~~i~~~ 108 (286)
.-.|+++|+..+...
T Consensus 89 ~~wSPEQI~g~l~~~ 103 (318)
T COG2826 89 SKWSPEQIIGRLKKS 103 (318)
T ss_pred hhCCHHHHHHHHHhc
Confidence 558999998877665
No 81
>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=22.40 E-value=2.6e+02 Score=20.55 Aligned_cols=27 Identities=22% Similarity=0.257 Sum_probs=19.3
Q ss_pred HHHHHHhhCCCChhhHHHHHhhCCCce
Q 048223 14 RKLEFFHCEGISNPDTVKILSKYPGLL 40 (286)
Q Consensus 14 ~~l~fL~~~G~~~~~i~~i~~~~P~il 40 (286)
..-+|-+.+|++..+|..+-..+|.=.
T Consensus 22 ~wK~faR~lglse~~Id~I~~~~~~d~ 48 (97)
T cd08316 22 DVKKFVRKSGLSEPKIDEIKLDNPQDT 48 (97)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCCCCh
Confidence 344566778888888888888877643
No 82
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 dissimil
Probab=22.26 E-value=2.3e+02 Score=20.73 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCHHHHHHHhhc
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
..|..+++.||+-+++..++..
T Consensus 48 ~~I~~l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 48 EKIVFLQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred HHHHHHHHCCCCHHHHHHHHcC
Confidence 5667778999999999998764
No 83
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.11 E-value=2.2e+02 Score=21.40 Aligned_cols=24 Identities=17% Similarity=0.155 Sum_probs=19.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHhhcC
Q 048223 154 ESKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 154 ~~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
-..|.+++++||+-++|..++..+
T Consensus 46 l~~I~~lr~~G~sl~eI~~~l~~~ 69 (116)
T cd04769 46 LRFIKEARQLGFTLAELKAIFAGH 69 (116)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhcc
Confidence 356788899999999999988654
No 84
>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=21.80 E-value=1.6e+02 Score=22.32 Aligned_cols=23 Identities=13% Similarity=-0.005 Sum_probs=19.1
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcC
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLKC 177 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~~ 177 (286)
..|.+++++||+-++|..++...
T Consensus 48 ~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 48 RFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHCCCCHHHHHHHHHhh
Confidence 57788889999999999988643
No 85
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=21.76 E-value=56 Score=25.31 Aligned_cols=45 Identities=16% Similarity=0.139 Sum_probs=26.9
Q ss_pred cCchHHHHHHHhCCcccccCcchhhhhHHHHHHhcCCCchhHhhhhccCC
Q 048223 60 HSSEKTIALIIRFPYILYHDADYYLLPNVKILRDSGVPESDIIKSIESWP 109 (286)
Q Consensus 60 ~~~~~i~~ii~~~P~iL~~s~e~~l~~~v~~L~~~G~~~~~i~~~i~~~P 109 (286)
++.+++..++..+|.++...+-. -..+ .-+|++.+.+..++...|
T Consensus 73 ls~~e~i~lm~~~P~LIKRPIi~-~~~~----~~iGf~~e~~~~~l~~~~ 117 (126)
T TIGR01616 73 IDEASALALMVSDPLLIRRPLMD-LGGI----RCAGFDREPVLSWIGLQT 117 (126)
T ss_pred CCHHHHHHHHHhCcCeEeCCEEE-ECCE----EEEcCCHHHHHHHhCCCC
Confidence 34566777778888877777522 1111 126777777776665444
No 86
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=21.30 E-value=2.6e+02 Score=22.42 Aligned_cols=20 Identities=30% Similarity=0.348 Sum_probs=11.8
Q ss_pred HHHHHHHHHHcCCCHHHHHH
Q 048223 153 WESKLHVYKKWGWSEQEWLA 172 (286)
Q Consensus 153 l~~~v~~l~~lG~s~~~i~~ 172 (286)
-+.+..-|...|++.+++.+
T Consensus 102 ~~~kssk~e~~Gi~eEEL~~ 121 (156)
T KOG0871|consen 102 RRRKSSKFEKSGIPEEELLR 121 (156)
T ss_pred hhhhhhhHHhcCCCHHHHHH
Confidence 34455556667777766543
No 87
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.14 E-value=1.3e+02 Score=22.17 Aligned_cols=23 Identities=22% Similarity=0.060 Sum_probs=19.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHhhc
Q 048223 154 ESKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 154 ~~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
-..|..++++|||-++|..++..
T Consensus 45 l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 45 LEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHh
Confidence 45677888999999999998853
No 88
>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=20.95 E-value=1.7e+02 Score=21.78 Aligned_cols=22 Identities=9% Similarity=-0.053 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCCHHHHHHHhhc
Q 048223 155 SKLHVYKKWGWSEQEWLAAFLK 176 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~~ 176 (286)
..|..++++||+-++|..++..
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 48 EFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 4667788999999999988763
No 89
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. 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
Probab=20.71 E-value=1.9e+02 Score=20.49 Aligned_cols=35 Identities=9% Similarity=0.021 Sum_probs=20.9
Q ss_pred hhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhh
Q 048223 20 HCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHL 58 (286)
Q Consensus 20 ~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~ 58 (286)
+.+||+..+|.++-..||.=+. ......+..|+.-
T Consensus 23 r~Lg~se~dI~~i~~~~~~~~~----eq~~~mL~~W~~r 57 (84)
T cd08804 23 RELDFTEEQIHQIRIENPNSLQ----DQSHALLKYWLER 57 (84)
T ss_pred HHcCCCHHHHHHHHHHCcccHH----HHHHHHHHHHHHc
Confidence 4678888888777777774332 2344455555543
No 90
>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=20.36 E-value=3.5e+02 Score=19.73 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=25.6
Q ss_pred HHHHHHhcCCCchhHhhhhccCCeeEEecchhHHHHH-HHHHHcCCCC
Q 048223 87 NVKILRDSGVPESDIIKSIESWPKLFLRHPKFFEKNV-ASVKEMGINP 133 (286)
Q Consensus 87 ~v~~L~~~G~~~~~i~~~i~~~P~ll~~~~~~l~~~v-~~l~~lG~~~ 133 (286)
.-.+.+.+|++..+|-.+-..+|.- .+.....+ .|.+..|-..
T Consensus 22 Wk~laR~LGLse~~I~~i~~~~~~~----~eq~~qmL~~W~~~~G~~A 65 (96)
T cd08315 22 WNRLMRQLGLSENEIDVAKANERVT----REQLYQMLLTWVNKTGRKA 65 (96)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCC----HHHHHHHHHHHHHhhCCCc
Confidence 3346677888888888887777752 34433333 3444555543
No 91
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=20.30 E-value=3.2e+02 Score=19.35 Aligned_cols=42 Identities=12% Similarity=0.051 Sum_probs=25.9
Q ss_pred HHHHHHHHhhCCCChhhHHHHHhhCCCceeccccCcchhHHHHhHhh
Q 048223 12 LLRKLEFFHCEGISNPDTVKILSKYPGLLSRSLDNHLIPTFNSLSHL 58 (286)
Q Consensus 12 l~~~l~fL~~~G~~~~~i~~i~~~~P~il~~~~~~~l~~~~~~L~~~ 58 (286)
+...-+|-+.+|++..+|..+-..+| =+. ......+.-|+.-
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~-~~~----Eq~yqmL~~W~~~ 52 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR-RCR----DAQYQMLKVWKER 52 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC-ChH----HHHHHHHHHHHHh
Confidence 34455677788888888888877777 222 2444555555443
No 92
>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=20.25 E-value=1.8e+02 Score=22.17 Aligned_cols=21 Identities=10% Similarity=-0.054 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCCHHHHHHHhh
Q 048223 155 SKLHVYKKWGWSEQEWLAAFL 175 (286)
Q Consensus 155 ~~v~~l~~lG~s~~~i~~~i~ 175 (286)
..|..++++||+-++|..++.
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 48 LFIRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred HHHHHHHHcCCCHHHHHHHHH
Confidence 567888899999999999886
No 93
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=20.14 E-value=4.3e+02 Score=20.61 Aligned_cols=28 Identities=18% Similarity=0.049 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHhh
Q 048223 148 MSESQWESKLHVYKKWGWSEQEWLAAFL 175 (286)
Q Consensus 148 ~~~~~l~~~v~~l~~lG~s~~~i~~~i~ 175 (286)
..++.+-+++.-|++-|.+.+++..=+.
T Consensus 88 ~i~~~vi~~I~el~~eG~s~eei~~ki~ 115 (131)
T PF08004_consen 88 EIPESVIERIKELKSEGKSEEEIAEKIS 115 (131)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3467788899999999999998877554
Done!