Query 023027
Match_columns 288
No_of_seqs 178 out of 1286
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:54:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023027.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023027hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 1.9E-45 4.2E-50 351.7 16.2 248 34-284 159-449 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.7E-39 3.8E-44 300.2 2.0 241 31-272 29-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 7.3E-37 1.6E-41 292.7 14.9 248 29-279 86-349 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 9E-31 2E-35 242.0 3.1 239 40-281 2-325 (345)
5 KOG1267 Mitochondrial transcri 99.8 2.2E-20 4.7E-25 176.9 10.2 216 28-255 192-410 (413)
6 KOG1267 Mitochondrial transcri 99.7 1.5E-17 3.2E-22 157.6 11.5 209 37-255 93-341 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00033 7.1E-09 40.5 1.9 23 195-218 4-26 (31)
8 smart00733 Mterf Mitochondrial 96.9 0.00054 1.2E-08 39.5 1.8 28 158-186 3-30 (31)
9 PF14490 HHH_4: Helix-hairpin- 85.7 3.8 8.2E-05 30.4 6.5 42 85-126 37-78 (94)
10 cd04790 HTH_Cfa-like_unk Helix 81.1 3.6 7.9E-05 34.2 5.3 54 37-92 16-72 (172)
11 PF04695 Pex14_N: Peroxisomal 77.5 2.3 5E-05 34.0 2.9 38 55-95 14-51 (136)
12 PF00627 UBA: UBA/TS-N domain; 72.4 10 0.00023 22.7 4.3 23 69-91 4-26 (37)
13 PF11955 PORR: Plant organelle 70.9 11 0.00024 34.9 6.0 116 83-204 22-150 (335)
14 PF04695 Pex14_N: Peroxisomal 63.9 7.4 0.00016 31.1 3.0 30 173-202 22-51 (136)
15 smart00165 UBA Ubiquitin assoc 63.9 13 0.00028 22.1 3.4 24 175-198 2-25 (37)
16 PF07499 RuvA_C: RuvA, C-termi 62.0 13 0.00028 23.8 3.3 26 67-92 3-28 (47)
17 PF14490 HHH_4: Helix-hairpin- 58.0 30 0.00065 25.5 5.2 54 34-87 7-76 (94)
18 cd00194 UBA Ubiquitin Associat 57.5 19 0.00041 21.4 3.4 23 176-198 3-25 (38)
19 COG1125 OpuBA ABC-type proline 54.7 20 0.00042 32.2 4.2 85 32-135 70-160 (309)
20 COG3747 Phage terminase, small 54.1 2.9 6.2E-05 33.8 -0.9 96 16-121 36-135 (160)
21 COG1125 OpuBA ABC-type proline 46.5 25 0.00054 31.6 3.6 67 158-226 58-126 (309)
22 cd08315 Death_TRAILR_DR4_DR5 D 43.8 71 0.0015 23.8 5.3 43 68-115 20-62 (96)
23 PF11955 PORR: Plant organelle 42.3 34 0.00074 31.7 4.0 196 43-240 45-293 (335)
24 PRK11613 folP dihydropteroate 42.0 23 0.0005 32.0 2.8 63 210-276 165-229 (282)
25 cd08306 Death_FADD Fas-associa 38.3 69 0.0015 23.2 4.4 42 70-115 16-57 (86)
26 cd08313 Death_TNFR1 Death doma 37.7 1.2E+02 0.0025 21.9 5.4 52 67-123 11-62 (80)
27 PF08069 Ribosomal_S13_N: Ribo 36.9 18 0.00038 24.7 0.9 38 53-90 19-56 (60)
28 PHA02591 hypothetical protein; 35.8 55 0.0012 23.5 3.3 29 60-88 41-69 (83)
29 cd04790 HTH_Cfa-like_unk Helix 35.5 37 0.00081 28.2 2.9 51 66-124 117-167 (172)
30 smart00657 RPOL4c DNA-directed 34.6 60 0.0013 25.1 3.8 59 61-126 51-109 (118)
31 TIGR01558 sm_term_P27 phage te 33.8 3.4 7.4E-05 31.9 -3.4 96 20-125 2-100 (116)
32 TIGR01448 recD_rel helicase, p 33.4 29 0.00062 35.7 2.2 121 64-194 74-211 (720)
33 cd08805 Death_ank1 Death domai 31.6 1.3E+02 0.0028 21.9 4.8 40 72-115 20-59 (84)
34 cd08319 Death_RAIDD Death doma 31.3 1.1E+02 0.0023 22.3 4.3 47 73-124 19-65 (83)
35 PF12244 DUF3606: Protein of u 30.1 61 0.0013 21.7 2.7 22 177-198 22-44 (57)
36 PRK09875 putative hydrolase; P 29.9 54 0.0012 29.8 3.1 28 173-200 261-288 (292)
37 PF11212 DUF2999: Protein of u 28.1 1.2E+02 0.0026 21.4 3.9 48 68-124 2-49 (82)
38 PF09278 MerR-DNA-bind: MerR, 27.9 63 0.0014 21.6 2.6 20 178-197 7-26 (65)
39 PF14117 DUF4287: Domain of un 27.9 1.2E+02 0.0027 20.6 3.9 37 77-119 13-49 (61)
40 PRK09875 putative hydrolase; P 26.5 59 0.0013 29.5 2.8 27 67-93 262-288 (292)
41 PF10440 WIYLD: Ubiquitin-bind 25.7 1E+02 0.0022 21.4 3.2 36 172-207 9-44 (65)
42 cd08316 Death_FAS_TNFRSF6 Deat 25.4 99 0.0021 23.2 3.4 45 67-115 20-64 (97)
43 COG5457 Uncharacterized conser 25.2 71 0.0015 22.0 2.3 19 72-90 41-59 (63)
44 COG4669 EscJ Type III secretor 25.1 65 0.0014 28.3 2.6 80 63-149 29-111 (246)
45 PF13720 Acetyltransf_11: Udp 24.8 82 0.0018 22.7 2.8 42 71-114 20-61 (83)
46 PF08671 SinI: Anti-repressor 23.5 88 0.0019 18.1 2.2 24 67-90 5-28 (30)
47 PF09288 UBA_3: Fungal ubiquit 23.0 88 0.0019 20.9 2.4 23 69-91 11-33 (55)
48 PRK14487 cbb3-type cytochrome 22.8 87 0.0019 27.1 2.9 69 48-117 130-209 (217)
49 cd08784 Death_DRs Death Domain 22.8 2.5E+02 0.0055 19.8 5.0 43 68-115 12-54 (79)
50 PF03960 ArsC: ArsC family; I 22.5 1.2E+02 0.0026 22.7 3.5 23 77-99 69-91 (110)
51 cd01107 HTH_BmrR Helix-Turn-He 22.4 1.4E+02 0.0031 22.4 3.9 56 37-92 15-72 (108)
52 PF07223 DUF1421: Protein of u 22.2 87 0.0019 29.3 3.1 24 67-90 321-344 (358)
53 PF02022 Integrase_Zn: Integra 20.7 1.7E+02 0.0038 18.0 3.3 29 173-201 7-36 (40)
54 PRK00117 recX recombination re 20.5 2.3E+02 0.005 22.6 5.0 24 68-91 79-102 (157)
55 cd08777 Death_RIP1 Death Domai 20.4 2.6E+02 0.0056 20.3 4.7 52 71-125 17-68 (86)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.9e-45 Score=351.74 Aligned_cols=248 Identities=29% Similarity=0.534 Sum_probs=187.9
Q ss_pred chhHhHHHHhhCCCChh---hHhhhCCCCCCCCCC-ChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHH
Q 023027 34 LFRQKILHLQALNVNPQ---KALHQNPNFRCTPLS-SLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDF 109 (288)
Q Consensus 34 ~~~~~~~~L~~~G~~~~---~l~~~~P~ll~~s~~-~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~ 109 (288)
.+.++++||.++|++.+ +++.++|.+|+++.+ ++.++++||.++|++.+++++++.++|++|++++++++.++++|
T Consensus 159 ~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~f 238 (487)
T PLN03196 159 DLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDY 238 (487)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHH
Confidence 34455555555555543 345555555555554 35556666666666666666666666666666666666666666
Q ss_pred HhhhcCCCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccCCC--Cce-----------------------------
Q 023027 110 LLEEVLIPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFKGS--HKI----------------------------- 158 (288)
Q Consensus 110 L~~~lG~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~--~~l----------------------------- 158 (288)
|+ ++|++.++|++++.++|++|+++++++++|++++|+++|+++. ..+
T Consensus 239 L~-~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~ 317 (487)
T PLN03196 239 LE-SLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKI 317 (487)
T ss_pred HH-HcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCC
Confidence 66 4666666677777777777777666667777777766666542 122
Q ss_pred --------eecccceeeecchhcHHHHHHHHHHcCCCHHHHHHHHHhCCceeecCcccchhhHHHHHHHhhcCcHHHHhh
Q 023027 159 --------NCQTTVLLVSSVERTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKK 230 (288)
Q Consensus 159 --------i~~~P~lL~~~~~~~l~~kv~~L~~lG~s~~~v~~~l~~~P~iL~~s~e~~l~~k~~fL~~~~g~~~~~l~~ 230 (288)
+.++|.+++.+. +++.++++||+++||+.+++..|+.++|++|++|.+ +|++|++||.++||++.++|++
T Consensus 318 s~e~i~~~v~k~P~il~lSe-~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~-~l~~k~dFlvneMg~~~~~Iv~ 395 (487)
T PLN03196 318 DPEDFGRVIEKLPQIVSLNR-NVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLE-IMKPSLEFFKKEMKRPLKELVE 395 (487)
T ss_pred CHHHHHHHHHhcchhhcccH-HHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHH-HHHHHHHHHHHHhCCCHHHHHh
Confidence 334555555553 467889999999999999999999999999999997 9999999999999999999999
Q ss_pred CCcccccccccccHhhHHHHHHCCCCCChhhhcccCHHHHHHHHHHHHHhhhhh
Q 023027 231 FPQYFSFSLERKIKPRYRILVDHGFKLPLAQMLRVSDGEFNARLIEMRLKLAER 284 (288)
Q Consensus 231 ~P~~L~~sle~~l~pR~~~L~~~G~~~~l~~~l~~s~~~F~~~~~~~~~~~~~~ 284 (288)
+|.+|+||+|+||+|||++|+++|+++++.++|++||++|+++|+..+.++++.
T Consensus 396 fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r~v~~y~e~~~~ 449 (487)
T PLN03196 396 FPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQRMSGDFIEGEEM 449 (487)
T ss_pred ChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHHHhhhccccccc
Confidence 999999999999999999999999999999999999999999999999887664
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=1.7e-39 Score=300.22 Aligned_cols=241 Identities=36% Similarity=0.639 Sum_probs=186.0
Q ss_pred cccchhHhHHHHhhCCCCh---hhHhhhCCCCCCCCC-CChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHH
Q 023027 31 AGLLFRQKILHLQALNVNP---QKALHQNPNFRCTPL-SSLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPI 106 (288)
Q Consensus 31 ~~~~~~~~~~~L~~~G~~~---~~l~~~~P~ll~~s~-~~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~ 106 (288)
....+.++++||.++|++. ++++.++|.++..+. +++.+.++||+++|++++++.+++.++|+++..+.+.++.++
T Consensus 29 ~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~ 108 (345)
T PF02536_consen 29 PEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPN 108 (345)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHH
T ss_pred CccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhh
Confidence 3345689999999999995 468999999999995 579999999999999999999999999999999876678888
Q ss_pred HHHHhh---------------------------------hcCCCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccC
Q 023027 107 IDFLLE---------------------------------EVLIPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFK 153 (288)
Q Consensus 107 l~~L~~---------------------------------~lG~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~ 153 (288)
+.||++ ++|++++++.+++.++|.++..+.+++++++++||+++|++
T Consensus 109 v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~ 188 (345)
T PF02536_consen 109 VAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFS 188 (345)
T ss_dssp HHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-
T ss_pred hhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhccc
Confidence 888874 35555666666677788777777777889999999998887
Q ss_pred CC--Cceeecccceeeecch--------------------------------hcHHHHHHHHHHcCCCHHHHHHHHHhCC
Q 023027 154 GS--HKINCQTTVLLVSSVE--------------------------------RTLKPKIDFLKNLGLSDEEVERMVIRSP 199 (288)
Q Consensus 154 ~~--~~li~~~P~lL~~~~~--------------------------------~~l~~kv~~L~~lG~s~~~v~~~l~~~P 199 (288)
+. .+++.++|.++..+.+ +++.++++||+++||+++|+.+|+.++|
T Consensus 189 ~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P 268 (345)
T PF02536_consen 189 KEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFP 268 (345)
T ss_dssp GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSG
T ss_pred chhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCc
Confidence 53 2344444444444433 3699999999999999999999999999
Q ss_pred ceeecCcccchhhHHHHHHHhhcCcHHHHhhCCcccccccccccHhh---HHHHHHCC--CCCChhhhcccCHHHHHH
Q 023027 200 GLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERKIKPR---YRILVDHG--FKLPLAQMLRVSDGEFNA 272 (288)
Q Consensus 200 ~iL~~s~e~~l~~k~~fL~~~~g~~~~~l~~~P~~L~~sle~~l~pR---~~~L~~~G--~~~~l~~~l~~s~~~F~~ 272 (288)
+||++|.+ ++++|++||.++||++.++|+++|.+|+||+|+||+|| +++|+++| ..+++.+++++||++|++
T Consensus 269 ~iL~~s~e-~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 269 QILSYSIE-KLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp GGGGS-HH-HHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred chhhcchh-hhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 99999999 69999999999999999999999999999999999999 55678899 678999999999999964
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=7.3e-37 Score=292.67 Aligned_cols=248 Identities=22% Similarity=0.397 Sum_probs=201.4
Q ss_pred CCcccchhHhHHHHhhCCCChhhHhhhCCCCCCCCCC-ChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHH
Q 023027 29 NDAGLLFRQKILHLQALNVNPQKALHQNPNFRCTPLS-SLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPII 107 (288)
Q Consensus 29 ~~~~~~~~~~~~~L~~~G~~~~~l~~~~P~ll~~s~~-~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l 107 (288)
|.++..++++++||.++|++.+++- ++|.+|.++++ ++.++++||.++|+++.+|++++.+||.+|+++++.++.|++
T Consensus 86 p~~~~~~~~~l~~L~s~G~~~~~i~-~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v 164 (487)
T PLN03196 86 PSTVDVMRERVEFLHKLGLTIEDIN-EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVV 164 (487)
T ss_pred CccHHHHHHHHHHHHHcCCChHHhc-cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHH
Confidence 5667777788888888888887764 78999888876 689999999999999999999999999999999888899999
Q ss_pred HHHhhhcCCCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccCCC--CceeecccceeeecchhcHHHHHHHHHHcC
Q 023027 108 DFLLEEVLIPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFKGS--HKINCQTTVLLVSSVERTLKPKIDFLKNLG 185 (288)
Q Consensus 108 ~~L~~~lG~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~--~~li~~~P~lL~~~~~~~l~~kv~~L~~lG 185 (288)
+||+ .+|+++++|.+++.++|.+|++++++++.++++||.++|+++. .+++.++|++|+++++++++++++||+++|
T Consensus 165 ~fL~-~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lG 243 (487)
T PLN03196 165 KYLQ-GLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLG 243 (487)
T ss_pred HHHH-HcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcC
Confidence 9998 5899999999999999999988888888888899888888865 578888888888888888888888888888
Q ss_pred CCHHHHHHHHHhCCceeecCcccchhhHHHHHHHhhcCcHHH----HhhCCcccccccccccHhhHHHH-HHCCCCC---
Q 023027 186 LSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDE----LKKFPQYFSFSLERKIKPRYRIL-VDHGFKL--- 257 (288)
Q Consensus 186 ~s~~~v~~~l~~~P~iL~~s~e~~l~~k~~fL~~~~g~~~~~----l~~~P~~L~~sle~~l~pR~~~L-~~~G~~~--- 257 (288)
++.+++.+++.++|++|++|++++++++++||. ++|++.+. +.++|.++++++++++.++..+| .+.|++.
T Consensus 244 v~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~-elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i 322 (487)
T PLN03196 244 LPRLAVARILEKRPYILGFDLEETVKPNVECLL-EFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDF 322 (487)
T ss_pred CCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHH-HcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHH
Confidence 888888888888888888888778888888887 67887654 35678888888777777777777 3566641
Q ss_pred -----ChhhhcccCHHHHHHHHHHHHH
Q 023027 258 -----PLAQMLRVSDGEFNARLIEMRL 279 (288)
Q Consensus 258 -----~l~~~l~~s~~~F~~~~~~~~~ 279 (288)
.++.++.+|++...+++..+..
T Consensus 323 ~~~v~k~P~il~lSe~kl~~kvefL~~ 349 (487)
T PLN03196 323 GRVIEKLPQIVSLNRNVALKHVEFLRG 349 (487)
T ss_pred HHHHHhcchhhcccHHHHHHHHHHHHH
Confidence 3456677777766666655443
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=99.96 E-value=9e-31 Score=242.04 Aligned_cols=239 Identities=31% Similarity=0.568 Sum_probs=187.9
Q ss_pred HHHhhCCCChh---hHhhhCCCCCCCCCC-ChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 40 LHLQALNVNPQ---KALHQNPNFRCTPLS-SLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 40 ~~L~~~G~~~~---~l~~~~P~ll~~s~~-~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
+.|.+.||+.+ ++++++|.++.++++ ++.++++||.+.|++..++++++++||.++..+.++++.+.++||+ ++|
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~-~~~ 80 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLK-SIG 80 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHT-TTS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHH-HHc
Confidence 45788899765 578999999988887 6999999999999999999999999999999998889999999999 699
Q ss_pred CCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccCCC------------------------------------Ccee
Q 023027 116 IPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFKGS------------------------------------HKIN 159 (288)
Q Consensus 116 ~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~------------------------------------~~li 159 (288)
++++++.+++.++|.+|..+.+.++.+++++|+++|+++. .+++
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi 160 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVI 160 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCH
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccc
Confidence 9999999999999999998887789999999999998752 2567
Q ss_pred ecccceeeecchhcHHHHHHHHHHcCCCHHHHHHHHHhCCceeecCccc-------------------------------
Q 023027 160 CQTTVLLVSSVERTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVEN------------------------------- 208 (288)
Q Consensus 160 ~~~P~lL~~~~~~~l~~kv~~L~~lG~s~~~v~~~l~~~P~iL~~s~e~------------------------------- 208 (288)
.++|.++..+.++.++++++||+++|++.+++.+++.++|.++..|.++
T Consensus 161 ~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~ 240 (345)
T PF02536_consen 161 AKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSE 240 (345)
T ss_dssp HHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHH
T ss_pred cccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccch
Confidence 8899888788788999999999999999999999999999999999985
Q ss_pred -chhhHHHHHHHhhcCcHHHH----hhCCcccccccccccHhhHHHHHH-CCCC----CChhhhcccCHH-HHHHH---H
Q 023027 209 -NLVPKVDFFIQEMKGDLDEL----KKFPQYFSFSLERKIKPRYRILVD-HGFK----LPLAQMLRVSDG-EFNAR---L 274 (288)
Q Consensus 209 -~l~~k~~fL~~~~g~~~~~l----~~~P~~L~~sle~~l~pR~~~L~~-~G~~----~~l~~~l~~s~~-~F~~~---~ 274 (288)
++.++++||. .+|++.+++ .++|.+|++|.++ ++++++||.+ +|++ ...++++++|=+ +-..| +
T Consensus 241 ~~l~~~i~~L~-~lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~ 318 (345)
T PF02536_consen 241 EKLKPKIEFLQ-SLGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVL 318 (345)
T ss_dssp HHHHHHHHHHH-TTT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHH
T ss_pred HhHHHHHHHHH-HhcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHH
Confidence 4889999998 599998775 6899999999995 9999999865 7876 346778888874 67777 4
Q ss_pred HHHHHhh
Q 023027 275 IEMRLKL 281 (288)
Q Consensus 275 ~~~~~~~ 281 (288)
..++.+|
T Consensus 319 ~~l~~~g 325 (345)
T PF02536_consen 319 KVLKSKG 325 (345)
T ss_dssp HTT--TT
T ss_pred HHHHHCc
Confidence 4444444
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.82 E-value=2.2e-20 Score=176.86 Aligned_cols=216 Identities=29% Similarity=0.454 Sum_probs=185.0
Q ss_pred CCCcccchhHhHHHHhhCCCChhh---HhhhCCCCCCCCCCChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChH
Q 023027 28 TNDAGLLFRQKILHLQALNVNPQK---ALHQNPNFRCTPLSSLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLE 104 (288)
Q Consensus 28 ~~~~~~~~~~~~~~L~~~G~~~~~---l~~~~P~ll~~s~~~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~ 104 (288)
.-..+..++ .++++.++|+.... .+..+|....... .+...+.++..+|+++.. +++.+.|.++.++.++++.
T Consensus 192 ~~~~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~ 267 (413)
T KOG1267|consen 192 FLLNENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLE 267 (413)
T ss_pred ccccccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHH
Confidence 344445555 78888899988764 4567777654333 677788888889987776 8888999999999999999
Q ss_pred HHHHHHhhhcCCCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccCCCCceeecccceeeecchhcHHHHHHHHHHc
Q 023027 105 PIIDFLLEEVLIPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFKGSHKINCQTTVLLVSSVERTLKPKIDFLKNL 184 (288)
Q Consensus 105 ~~l~~L~~~lG~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~~li~~~P~lL~~~~~~~l~~kv~~L~~l 184 (288)
+++++|+ .+||+.++|..++.++|++|+++.++ +...+.++.+. .+ . +.++|+++..+ +..+.++++|+...
T Consensus 268 ~kv~~l~-~~Gf~~~di~~~~~k~P~~l~~s~~~-~~~~~~~~~~~--~~--~-~~k~p~~l~~s-~~~l~~~ie~l~~~ 339 (413)
T KOG1267|consen 268 PKVEVLK-SLGFSREEIWKMVKKCPQILGYSVKK-NLKTTEYLLKN--PK--H-ILKFPQLLRSS-EDKLKPRIEFLLSL 339 (413)
T ss_pred HHHHHHH-HcCCCHHHHHHHHHhCchheEeehhh-hhHHHHHHHhc--ch--h-hhhhhhhhhcc-chhhhhhHHHHHHc
Confidence 9999999 58999999999999999999999886 55677777665 22 2 88999999555 67899999999999
Q ss_pred CCCHHHHHHHHHhCCceeecCcccchhhHHHHHHHhhcCcHHHHhhCCcccccccccccHhhHHHHHHCCC
Q 023027 185 GLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFSFSLERKIKPRYRILVDHGF 255 (288)
Q Consensus 185 G~s~~~v~~~l~~~P~iL~~s~e~~l~~k~~fL~~~~g~~~~~l~~~P~~L~~sle~~l~pR~~~L~~~G~ 255 (288)
|++..++..++.++|+++.+|.++.++.+.+|+.+.|+++.++++.+|.+++|++++|+.||+......|.
T Consensus 340 g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~ 410 (413)
T KOG1267|consen 340 GFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGV 410 (413)
T ss_pred CCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhc
Confidence 99999999999999999999999789999999999999999999999999999999999999999887664
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.73 E-value=1.5e-17 Score=157.63 Aligned_cols=209 Identities=27% Similarity=0.461 Sum_probs=146.5
Q ss_pred HhHHHHhhCCCChh---hHhhhCCCCCCCCCC-ChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhh
Q 023027 37 QKILHLQALNVNPQ---KALHQNPNFRCTPLS-SLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLE 112 (288)
Q Consensus 37 ~~~~~L~~~G~~~~---~l~~~~P~ll~~s~~-~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~ 112 (288)
...++|.+.|++.. .++..+|.++..+.+ .+.+...+|.+.|++..++..++...|.+++.....++...++|+++
T Consensus 93 s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~ 172 (413)
T KOG1267|consen 93 SVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKS 172 (413)
T ss_pred HHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhc
Confidence 34577899999865 467778888877766 47777788888999999999999988888887776788888888884
Q ss_pred hcC--CCCCCHhHHHhhCCccceeccccchhhHHHHHHHhccCC----------------------------------CC
Q 023027 113 EVL--IPFNDLPKSLTRCPRILVSDLKTQLRPSFKFLVEFGFKG----------------------------------SH 156 (288)
Q Consensus 113 ~lG--~s~~~i~~il~~~P~lL~~~~~~~l~~~v~~L~~lG~~~----------------------------------~~ 156 (288)
++ .....+.+.+...|...... ..+. ++++++++|..+ ..
T Consensus 173 -~~~~~~~s~~~~~~~~~~~~~~~~--~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~~l~~~~~~i~~~g~~p~~ 248 (413)
T KOG1267|consen 173 -IPPELLSSVVERLLTPVPSFLLNE--NSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYLKLKARLPFLLTLGFDPKT 248 (413)
T ss_pred -cchhhhhhHHHHhccccccccccc--cccc-cchhhHHhCCCHHHHHHHHhcCccceeeehhhhhhhhhHHHhccCCch
Confidence 53 56666666666665432221 1233 555555555432 22
Q ss_pred ceeecccceeeecchhcHHHHHHHHHHcCCCHHHHHHHHHhCCceeecCcccchhhHHHHHHHhhcCcHHHHhhCCcccc
Q 023027 157 KINCQTTVLLVSSVERTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLDELKKFPQYFS 236 (288)
Q Consensus 157 ~li~~~P~lL~~~~~~~l~~kv~~L~~lG~s~~~v~~~l~~~P~iL~~s~e~~l~~k~~fL~~~~g~~~~~l~~~P~~L~ 236 (288)
+++.+.|.++.++.++++++++++|+++||+.+|+.+|++++|++|++|.+ ++..+++|+.+. ..++.++|+++.
T Consensus 249 ~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~-~~~~~~~~~~~~----~~~~~k~p~~l~ 323 (413)
T KOG1267|consen 249 REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVK-KNLKTTEYLLKN----PKHILKFPQLLR 323 (413)
T ss_pred hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehh-hhhHHHHHHHhc----chhhhhhhhhhh
Confidence 345567778888889999999999999999999999999999999999998 554555555433 222455555554
Q ss_pred cccccccHhhHHHHHHCCC
Q 023027 237 FSLERKIKPRYRILVDHGF 255 (288)
Q Consensus 237 ~sle~~l~pR~~~L~~~G~ 255 (288)
++.. .+.+|++++...|.
T Consensus 324 ~s~~-~l~~~ie~l~~~g~ 341 (413)
T KOG1267|consen 324 SSED-KLKPRIEFLLSLGF 341 (413)
T ss_pred ccch-hhhhhHHHHHHcCC
Confidence 4443 35555555555554
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=97.09 E-value=0.00033 Score=40.47 Aligned_cols=23 Identities=35% Similarity=0.658 Sum_probs=9.9
Q ss_pred HHhCCceeecCcccchhhHHHHHH
Q 023027 195 VIRSPGLLTFSVENNLVPKVDFFI 218 (288)
Q Consensus 195 l~~~P~iL~~s~e~~l~~k~~fL~ 218 (288)
+.++|.+|+++.+ +++++++||.
T Consensus 4 ~~~~P~il~~~~~-~l~~~~~~l~ 26 (31)
T smart00733 4 LKKFPQILGYSEK-KLKPKVEFLK 26 (31)
T ss_pred hhhCcCcccccHH-HhhHHHHHHH
Confidence 3444444444422 4444444444
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.93 E-value=0.00054 Score=39.52 Aligned_cols=28 Identities=46% Similarity=0.688 Sum_probs=16.2
Q ss_pred eeecccceeeecchhcHHHHHHHHHHcCC
Q 023027 158 INCQTTVLLVSSVERTLKPKIDFLKNLGL 186 (288)
Q Consensus 158 li~~~P~lL~~~~~~~l~~kv~~L~~lG~ 186 (288)
++.++|.++..+ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 455566666655 4456666666665555
No 9
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=85.74 E-value=3.8 Score=30.42 Aligned_cols=42 Identities=21% Similarity=0.040 Sum_probs=24.2
Q ss_pred HHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHHHh
Q 023027 85 GRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLT 126 (288)
Q Consensus 85 ~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~il~ 126 (288)
..+|..+|..|..++..---..++-+...+|++.++-.++..
T Consensus 37 i~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~Ri~A 78 (94)
T PF14490_consen 37 IEILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPRRIRA 78 (94)
T ss_dssp HHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HHHHHH
T ss_pred HHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHHHHHH
Confidence 356778888888866543445666666678888777665543
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=81.11 E-value=3.6 Score=34.24 Aligned_cols=54 Identities=15% Similarity=0.138 Sum_probs=33.0
Q ss_pred HhHHHHhhCCCChhhHhhhCC-CCCCCCCCC--hHHHHHHHHhCCCChhHHHHHHHhCC
Q 023027 37 QKILHLQALNVNPQKALHQNP-NFRCTPLSS--LLSLEHYLLSLGLSRPAVGRILDMHP 92 (288)
Q Consensus 37 ~~~~~L~~~G~~~~~l~~~~P-~ll~~s~~~--l~~~v~~L~~~Gls~~~i~~ii~~~P 92 (288)
.++.|....|+=... .+.+ +--.++.++ --..+..|++.|++-++|..++....
T Consensus 16 ~tLRyYe~~GLl~p~--~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 16 STLLYYERIGLLSPS--ARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHHCCCCCCC--ccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 456666667763211 1122 223455542 33577788999999999999887553
No 11
>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=77.52 E-value=2.3 Score=34.01 Aligned_cols=38 Identities=26% Similarity=0.333 Sum_probs=27.0
Q ss_pred hCCCCCCCCCCChHHHHHHHHhCCCChhHHHHHHHhCCccc
Q 023027 55 QNPNFRCTPLSSLLSLEHYLLSLGLSRPAVGRILDMHPKLL 95 (288)
Q Consensus 55 ~~P~ll~~s~~~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL 95 (288)
.+|.|-..+ +..+++||++.|++.+||..++.+.+.--
T Consensus 14 ~~p~V~~sp---~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 14 QDPKVRNSP---LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp CTTTCCCS----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCcccccCC---HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 356654443 78899999999999999999999876544
No 12
>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=72.44 E-value=10 Score=22.72 Aligned_cols=23 Identities=22% Similarity=0.302 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCChhHHHHHHHhC
Q 023027 69 SLEHYLLSLGLSRPAVGRILDMH 91 (288)
Q Consensus 69 ~~v~~L~~~Gls~~~i~~ii~~~ 91 (288)
..++-|.++||+.++..+.+..+
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 45677777788888777777666
No 13
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=70.87 E-value=11 Score=34.88 Aligned_cols=116 Identities=21% Similarity=0.277 Sum_probs=60.4
Q ss_pred HHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHHHhhCCccceecccc-c------hhhHHHHH-HH-hccC
Q 023027 83 AVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLTRCPRILVSDLKT-Q------LRPSFKFL-VE-FGFK 153 (288)
Q Consensus 83 ~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~il~~~P~lL~~~~~~-~------l~~~v~~L-~~-lG~~ 153 (288)
.+..+|.+.|. ..+ .+ ..++-++..+|++...+...+.+||.++..-... . +-+...-| .+ ..+-
T Consensus 22 ~l~~~i~~~p~---~~~--pl-~~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~ 95 (335)
T PF11955_consen 22 RLKDLILSQPS---HSL--PL-RDLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVR 95 (335)
T ss_pred HHHHHHHcCCC---Ccc--cH-HHHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHH
Confidence 34556666664 111 11 2344444467776677777888888877653310 0 00111111 10 0100
Q ss_pred --CCCceeecccceeeecchhcHH-HHHHHHH-HcCCCHHHHHHHHHhCCceeec
Q 023027 154 --GSHKINCQTTVLLVSSVERTLK-PKIDFLK-NLGLSDEEVERMVIRSPGLLTF 204 (288)
Q Consensus 154 --~~~~li~~~P~lL~~~~~~~l~-~kv~~L~-~lG~s~~~v~~~l~~~P~iL~~ 204 (288)
....++.+--.+|+.+.++.|- .+++.++ .+|++++-...++.++|..+..
T Consensus 96 ~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 96 EEMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HhChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 0012333334455555554443 6677774 7888887777788888887765
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=63.94 E-value=7.4 Score=31.06 Aligned_cols=30 Identities=33% Similarity=0.527 Sum_probs=22.8
Q ss_pred cHHHHHHHHHHcCCCHHHHHHHHHhCCcee
Q 023027 173 TLKPKIDFLKNLGLSDEEVERMVIRSPGLL 202 (288)
Q Consensus 173 ~l~~kv~~L~~lG~s~~~v~~~l~~~P~iL 202 (288)
.+..|++||++-|++++||...+.+.+.--
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 477999999999999999999999877654
No 15
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=63.92 E-value=13 Score=22.09 Aligned_cols=24 Identities=33% Similarity=0.452 Sum_probs=19.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhC
Q 023027 175 KPKIDFLKNLGLSDEEVERMVIRS 198 (288)
Q Consensus 175 ~~kv~~L~~lG~s~~~v~~~l~~~ 198 (288)
..+++-|.++||+.+++...+.++
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356788899999999988877776
No 16
>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=61.98 E-value=13 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=21.0
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHhCC
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDMHP 92 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~~P 92 (288)
..+.++-|.++|+++.++.+++.+-.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 46788899999999999999888764
No 17
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=57.98 E-value=30 Score=25.53 Aligned_cols=54 Identities=22% Similarity=0.337 Sum_probs=27.9
Q ss_pred chhHhHHHHhhCCCChh--------------hHhhhCCCCCCCCCCC-hHHHHHHH-HhCCCChhHHHHH
Q 023027 34 LFRQKILHLQALNVNPQ--------------KALHQNPNFRCTPLSS-LLSLEHYL-LSLGLSRPAVGRI 87 (288)
Q Consensus 34 ~~~~~~~~L~~~G~~~~--------------~l~~~~P~ll~~s~~~-l~~~v~~L-~~~Gls~~~i~~i 87 (288)
.+++.+.+|...|++.. ++++.+|..|..+..- --..++.+ +++|++.++-.++
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~Ri 76 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPRRI 76 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHHHH
Confidence 45667899999999963 3688999988775531 12223333 3466666554443
No 18
>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=57.54 E-value=19 Score=21.43 Aligned_cols=23 Identities=26% Similarity=0.460 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 023027 176 PKIDFLKNLGLSDEEVERMVIRS 198 (288)
Q Consensus 176 ~kv~~L~~lG~s~~~v~~~l~~~ 198 (288)
.+++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 56788889999999887777666
No 19
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=54.68 E-value=20 Score=32.23 Aligned_cols=85 Identities=21% Similarity=0.247 Sum_probs=63.5
Q ss_pred ccchhHhHHHH-hhCCCC----hhhHhhhCCCCCCCCCCChHHHHHHHHh-CCCChhHHHHHHHhCCcccccCCCCChHH
Q 023027 32 GLLFRQKILHL-QALNVN----PQKALHQNPNFRCTPLSSLLSLEHYLLS-LGLSRPAVGRILDMHPKLLTADIPRDLEP 105 (288)
Q Consensus 32 ~~~~~~~~~~L-~~~G~~----~~~l~~~~P~ll~~s~~~l~~~v~~L~~-~Gls~~~i~~ii~~~P~lL~~~~~~~l~~ 105 (288)
..+++.++.|- +..|+= +++=+.--|.++.++.++++.++.-|.+ +|+++++.. .|||+=|+-.- +.
T Consensus 70 ~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~---~RyP~eLSGGQ----QQ 142 (309)
T COG1125 70 PVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYA---DRYPHELSGGQ----QQ 142 (309)
T ss_pred HHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHh---hcCchhcCcch----hh
Confidence 45788889998 789983 3455677899999999998888888766 799987665 49998887762 23
Q ss_pred HHHHHhhhcCCCCCCHhHHHhhCCccceec
Q 023027 106 IIDFLLEEVLIPFNDLPKSLTRCPRILVSD 135 (288)
Q Consensus 106 ~l~~L~~~lG~s~~~i~~il~~~P~lL~~~ 135 (288)
+ .| |.+.+...|.++.++
T Consensus 143 R-------VG-----v~RALAadP~ilLMD 160 (309)
T COG1125 143 R-------VG-----VARALAADPPILLMD 160 (309)
T ss_pred H-------HH-----HHHHHhcCCCeEeec
Confidence 3 44 566677788877665
No 20
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=54.11 E-value=2.9 Score=33.75 Aligned_cols=96 Identities=17% Similarity=0.138 Sum_probs=46.1
Q ss_pred CCCCCCCCCcCCCCCcccchhHhHHHHhhCCCC-hhh--HhhhCCCCCCCCCCChHHHHHHHHhCCCChhHHHHH-HHhC
Q 023027 16 TSVQPPSHISASTNDAGLLFRQKILHLQALNVN-PQK--ALHQNPNFRCTPLSSLLSLEHYLLSLGLSRPAVGRI-LDMH 91 (288)
Q Consensus 16 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~G~~-~~~--l~~~~P~ll~~s~~~l~~~v~~L~~~Gls~~~i~~i-i~~~ 91 (288)
.+..+|.||.+. |..+.++++-+|..++.= +++ +++.+ |..-+.....++-++..|+.-..-... +.++
T Consensus 36 ~~pkaPdwLd~~---A~~~Wrrvvp~L~e~~ll~~~D~~~Le~Y----C~~ysiY~~av~~lkk~G~ii~~~~~g~~krN 108 (160)
T COG3747 36 LAPKAPDWLDPT---AKKEWRRVVPFLEELKLLKPADLTLLELY----CVAYSIYRNAVAHLKKHGFIITNQFSGRVKRN 108 (160)
T ss_pred cCCCCccccCHH---HHHHHHHHHHHHHHhccCCHHHHHHHHHH----HHHHHHHHHHHHHHHHcceeeeccccceecCC
Confidence 445556666543 333445666666666542 222 22221 111123444555566666655433233 5666
Q ss_pred CcccccCCCCChHHHHHHHhhhcCCCCCCH
Q 023027 92 PKLLTADIPRDLEPIIDFLLEEVLIPFNDL 121 (288)
Q Consensus 92 P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i 121 (288)
|.+-.++ +....+--|.+++|+++..=
T Consensus 109 Pav~~~s---dA~~~l~klaSeLGltP~ar 135 (160)
T COG3747 109 PAVQAAS---DAIRNLLKLASELGLTPSAR 135 (160)
T ss_pred hHHHHHH---HHHHHHHHHHHHhCCChHHH
Confidence 6655554 23444445555666665543
No 21
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=46.48 E-value=25 Score=31.56 Aligned_cols=67 Identities=18% Similarity=0.245 Sum_probs=42.3
Q ss_pred eeecccceeeecchhcHHHHHHHH-HHcC-CCHHHHHHHHHhCCceeecCcccchhhHHHHHHHhhcCcHH
Q 023027 158 INCQTTVLLVSSVERTLKPKIDFL-KNLG-LSDEEVERMVIRSPGLLTFSVENNLVPKVDFFIQEMKGDLD 226 (288)
Q Consensus 158 li~~~P~lL~~~~~~~l~~kv~~L-~~lG-~s~~~v~~~l~~~P~iL~~s~e~~l~~k~~fL~~~~g~~~~ 226 (288)
+....-.+-..+. -.++.++.|. +..| |++-.+..=+.-.|.++..+.+ +++.|.+-|.+-+|++..
T Consensus 58 I~i~g~~i~~~d~-~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~-~i~~r~~ELl~lvgL~p~ 126 (309)
T COG1125 58 ILIDGEDISDLDP-VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKE-RIKKRADELLDLVGLDPS 126 (309)
T ss_pred EEECCeecccCCH-HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHH-HHHHHHHHHHHHhCCCHH
Confidence 3333333433443 3577777776 5555 4444555566777888887776 788888777777777654
No 22
>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=43.85 E-value=71 Score=23.80 Aligned_cols=43 Identities=14% Similarity=0.063 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 68 LSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 68 ~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
...-.+.+.+|++..+|..+-..+|.- .+.....+.-|+...|
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~-----~eq~~qmL~~W~~~~G 62 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVT-----REQLYQMLLTWVNKTG 62 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCC-----HHHHHHHHHHHHHhhC
Confidence 455667889999999999999999852 2356777777876666
No 23
>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=42.30 E-value=34 Score=31.70 Aligned_cols=196 Identities=17% Similarity=0.159 Sum_probs=105.1
Q ss_pred hhCCCC---hhhHhhhCCCCCCCCC---C-----ChHHHHHHHHh--CCCChhHHHHHHHhCCcccccCCCCChH-HHHH
Q 023027 43 QALNVN---PQKALHQNPNFRCTPL---S-----SLLSLEHYLLS--LGLSRPAVGRILDMHPKLLTADIPRDLE-PIID 108 (288)
Q Consensus 43 ~~~G~~---~~~l~~~~P~ll~~s~---~-----~l~~~v~~L~~--~Gls~~~i~~ii~~~P~lL~~~~~~~l~-~~l~ 108 (288)
..+|+. ....+.++|.++.... . .+.+...-|.+ ..+-.+.-..++.+--.+|..+.++.|. .+++
T Consensus 45 ~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~ 124 (335)
T PF11955_consen 45 RQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIA 124 (335)
T ss_pred HhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHH
Confidence 567774 2368999999863221 1 23333333221 1121111133444445566666655543 5778
Q ss_pred HHhhhcCCCCCCHhHHHhhCCccceecc---ccchhhHHHHHHHhccCCCC-------------------ceeeccccee
Q 023027 109 FLLEEVLIPFNDLPKSLTRCPRILVSDL---KTQLRPSFKFLVEFGFKGSH-------------------KINCQTTVLL 166 (288)
Q Consensus 109 ~L~~~lG~s~~~i~~il~~~P~lL~~~~---~~~l~~~v~~L~~lG~~~~~-------------------~li~~~P~lL 166 (288)
.++.++|++++-..+++.+||..+.... +......+.|=.++.++..+ ..=.++|.-+
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G~ 204 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPKGF 204 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCCCc
Confidence 8887999999999999999999887532 11122223332234443221 0112333333
Q ss_pred eecchhcHHHHHHHHHHcCC----------C---HHHHHHHHHhCCceeecCccc-chhhHHHHHHHhhcCcH---HHHh
Q 023027 167 VSSVERTLKPKIDFLKNLGL----------S---DEEVERMVIRSPGLLTFSVEN-NLVPKVDFFIQEMKGDL---DELK 229 (288)
Q Consensus 167 ~~~~~~~l~~kv~~L~~lG~----------s---~~~v~~~l~~~P~iL~~s~e~-~l~~k~~fL~~~~g~~~---~~l~ 229 (288)
. ..+..+.+++-++++-+ . .+.=...+.-.=-+|+..++| ....++..|.+++|++. +.+.
T Consensus 205 ~--l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~k~~~~l~ 282 (335)
T PF11955_consen 205 R--LKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQKFRRLLL 282 (335)
T ss_pred c--ccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcHHHHHHHH
Confidence 2 23456677766653321 1 110001111111245555554 35677788888999985 3578
Q ss_pred hCCcccccccc
Q 023027 230 KFPQYFSFSLE 240 (288)
Q Consensus 230 ~~P~~L~~sle 240 (288)
++|.+|..|..
T Consensus 283 rHPgIFYvS~k 293 (335)
T PF11955_consen 283 RHPGIFYVSLK 293 (335)
T ss_pred hCCCeEEEecc
Confidence 99999999864
No 24
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=41.96 E-value=23 Score=31.98 Aligned_cols=63 Identities=14% Similarity=0.263 Sum_probs=34.2
Q ss_pred hhhHHHHHHHhhcCcHHHHhhCCcccccccccccHhhHHHHHHCCC--CCChhhhcccCHHHHHHHHHH
Q 023027 210 LVPKVDFFIQEMKGDLDELKKFPQYFSFSLERKIKPRYRILVDHGF--KLPLAQMLRVSDGEFNARLIE 276 (288)
Q Consensus 210 l~~k~~fL~~~~g~~~~~l~~~P~~L~~sle~~l~pR~~~L~~~G~--~~~l~~~l~~s~~~F~~~~~~ 276 (288)
++.+++.+. ..|++.+.|+--|. +++. +.....++.|+.... ...++.++..|.|+|...+..
T Consensus 165 l~~~i~~a~-~~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~~lg~Pilvg~SRKsfig~~~~ 229 (282)
T PRK11613 165 FIEQIARCE-AAGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFHHFNLPLLVGMSRKSMIGQLLN 229 (282)
T ss_pred HHHHHHHHH-HcCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHHhCCCCEEEEecccHHHHhhcC
Confidence 344455554 46777777777775 3443 334445554433111 123455677777777766543
No 25
>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=38.27 E-value=69 Score=23.23 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=29.1
Q ss_pred HHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 70 LEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 70 ~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
.-.+-+.+|++..+|..+-..||. ++.+.....+..|+..-|
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g 57 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHC
Confidence 344557789999999999999983 332345666777765455
No 26
>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=37.68 E-value=1.2e+02 Score=21.92 Aligned_cols=52 Identities=17% Similarity=0.195 Sum_probs=34.6
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhH
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPK 123 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~ 123 (288)
+...-+|.+.+|+|+.+|..+=..|| +..+.....+.-|+...|-..+.+..
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~-----~~~Eq~yqmL~~W~~~~g~~~At~~~ 62 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR-----RCRDAQYQMLKVWKERGPRPYATLQH 62 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC-----ChHHHHHHHHHHHHHhcCCCcchHHH
Confidence 45667788999999999999988887 22234556677776555532343433
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=36.88 E-value=18 Score=24.69 Aligned_cols=38 Identities=21% Similarity=0.198 Sum_probs=27.4
Q ss_pred hhhCCCCCCCCCCChHHHHHHHHhCCCChhHHHHHHHh
Q 023027 53 LHQNPNFRCTPLSSLLSLEHYLLSLGLSRPAVGRILDM 90 (288)
Q Consensus 53 ~~~~P~ll~~s~~~l~~~v~~L~~~Gls~~~i~~ii~~ 90 (288)
-...|.=+..+.+++++.+--|...|+++++|+-++.-
T Consensus 19 ~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 19 RRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp -SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 34457777888889999999999999999999988753
No 28
>PHA02591 hypothetical protein; Provisional
Probab=35.83 E-value=55 Score=23.55 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=25.5
Q ss_pred CCCCCCChHHHHHHHHhCCCChhHHHHHH
Q 023027 60 RCTPLSSLLSLEHYLLSLGLSRPAVGRIL 88 (288)
Q Consensus 60 l~~s~~~l~~~v~~L~~~Gls~~~i~~ii 88 (288)
+..|.|++.++..-|.+.|++.++|+..+
T Consensus 41 fi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 41 FVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 56778899999999999999999998754
No 29
>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=35.52 E-value=37 Score=28.16 Aligned_cols=51 Identities=16% Similarity=0.165 Sum_probs=30.6
Q ss_pred ChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHH
Q 023027 66 SLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKS 124 (288)
Q Consensus 66 ~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~i 124 (288)
+....++.++..|+++++..+.=..+- ... -..-.+||. .+|++.+++..+
T Consensus 117 ~~~~w~~l~~~~g~~~~~m~~wh~~fe---~~~----p~~h~~~l~-~~g~~~~~~~~i 167 (172)
T cd04790 117 TKEKWVAILKAAGMDEADMRRWHIEFE---KME----PEAHQEFLQ-SLGIPEDEIERI 167 (172)
T ss_pred CHHHHHHHHHHcCCChHHHHHHHHHHH---HhC----cHHHHHHHH-HcCCCHHHHHHH
Confidence 356677777788888777543322221 122 235567887 488888777554
No 30
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=34.55 E-value=60 Score=25.08 Aligned_cols=59 Identities=17% Similarity=0.207 Sum_probs=41.5
Q ss_pred CCCCCChHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHHHh
Q 023027 61 CTPLSSLLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLT 126 (288)
Q Consensus 61 ~~s~~~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~il~ 126 (288)
..+.+.+....+.|...|+.+.++..++.-+|. +.+ .+...+.-+.+. ++++++..++.
T Consensus 51 ~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~----s~~-E~~~lI~sl~~r--~~ee~l~~iL~ 109 (118)
T smart00657 51 FKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPE----TAE-EAQLLIPSLEER--IDEEELEELLD 109 (118)
T ss_pred CCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC----CHH-HHHHHhhhhhcc--CCHHHHHHHHH
Confidence 345667888999999999999999999999984 222 355555555421 56777766654
No 31
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=33.79 E-value=3.4 Score=31.91 Aligned_cols=96 Identities=9% Similarity=0.143 Sum_probs=49.9
Q ss_pred CCCCCcCCCCCcccchhHhHHHHhhCCC-Chhh--HhhhCCCCCCCCCCChHHHHHHHHhCCCChhHHHHHHHhCCcccc
Q 023027 20 PPSHISASTNDAGLLFRQKILHLQALNV-NPQK--ALHQNPNFRCTPLSSLLSLEHYLLSLGLSRPAVGRILDMHPKLLT 96 (288)
Q Consensus 20 ~~~~l~~~~~~~~~~~~~~~~~L~~~G~-~~~~--l~~~~P~ll~~s~~~l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~ 96 (288)
+|.||++ .+..+.++.+..|...|+ +..+ ++..+ +...+......+.+...|+..+.-......||.+-.
T Consensus 2 ~P~~L~~---~ak~~w~ri~~~L~~~~~l~~~D~~~l~~y----c~a~~~~~~a~~~i~~~G~~~~~~~g~~k~nPa~~i 74 (116)
T TIGR01558 2 APDWLGK---EGKDEWKRVAPELKGSGILTNLDRDALLRY----CEAYDRYREATDDLEATGITATVEDGSPKANPALTV 74 (116)
T ss_pred CchhHhH---HHHHHHHHHHHHHHHcCCchHHHHHHHHHH----HHHHHHHHHHHHHHHHcCeeEEeCCCCeecChHHHH
Confidence 6778874 345555777788888884 4332 33332 222334455555566666543322222345665544
Q ss_pred cCCCCChHHHHHHHhhhcCCCCCCHhHHH
Q 023027 97 ADIPRDLEPIIDFLLEEVLIPFNDLPKSL 125 (288)
Q Consensus 97 ~~~~~~l~~~l~~L~~~lG~s~~~i~~il 125 (288)
.+ +.......+.. ++|+++..=.++.
T Consensus 75 ~~--~a~~~~~~l~~-elGLtP~sR~kl~ 100 (116)
T TIGR01558 75 VE--DAFKQLRSIGS-ALGLTPSSRSRLV 100 (116)
T ss_pred HH--HHHHHHHHHHH-HcCCCHHHHHHhc
Confidence 43 12333334444 6888876655554
No 32
>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=33.43 E-value=29 Score=35.72 Aligned_cols=121 Identities=21% Similarity=0.143 Sum_probs=0.0
Q ss_pred CCChHHHHHHHHh---CCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHHHhhCCccceeccccch
Q 023027 64 LSSLLSLEHYLLS---LGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKSLTRCPRILVSDLKTQL 140 (288)
Q Consensus 64 ~~~l~~~v~~L~~---~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~il~~~P~lL~~~~~~~l 140 (288)
+...+..+.||.+ -|+.+....+|+..+ +.+.-+.+....+-|.+--|++......+.... .-....
T Consensus 74 p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~f----g~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~------~~~~~~ 143 (720)
T TIGR01448 74 PTSKEGIVAYLSSRSIKGVGKKLAQRIVKTF----GEAAFDVLDDDPEKLLEVPGISKANLEKFVSQW------SQQGDE 143 (720)
T ss_pred CCCHHHHHHHHhcCCCCCcCHHHHHHHHHHh----CHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH------HHhHHH
Q ss_pred hhHHHHHHHhccCCC-------------CceeecccceeeecchhcHHHHHHHH-HHcCCCHHHHHHH
Q 023027 141 RPSFKFLVEFGFKGS-------------HKINCQTTVLLVSSVERTLKPKIDFL-KNLGLSDEEVERM 194 (288)
Q Consensus 141 ~~~v~~L~~lG~~~~-------------~~li~~~P~lL~~~~~~~l~~kv~~L-~~lG~s~~~v~~~ 194 (288)
...+.||.++|++.. -.++..+|..|..++..-==.++|.+ +.+|+..++-.++
T Consensus 144 ~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~~d~~Ri 211 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDPRRI 211 (720)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCCCCHHHH
No 33
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) 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-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=31.58 E-value=1.3e+02 Score=21.86 Aligned_cols=40 Identities=13% Similarity=0.184 Sum_probs=27.3
Q ss_pred HHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 72 HYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 72 ~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
..-+.+|++.++|..+-..||.= +..+....+..|++.-|
T Consensus 20 ~Lar~L~vs~~dI~~I~~e~p~~----l~~Q~~~~L~~W~~r~g 59 (84)
T cd08805 20 ELARELQFSVEDINRIRVENPNS----LLEQSTALLNLWVDREG 59 (84)
T ss_pred HHHHHcCCCHHHHHHHHHhCCCC----HHHHHHHHHHHHHHhcC
Confidence 44567999999999999999952 22234555666664344
No 34
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=31.31 E-value=1.1e+02 Score=22.25 Aligned_cols=47 Identities=19% Similarity=0.236 Sum_probs=31.0
Q ss_pred HHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHH
Q 023027 73 YLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKS 124 (288)
Q Consensus 73 ~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~i 124 (288)
..+.+|++..+|..+-..||. ++.+.+...+.-|+...| ..+-+.++
T Consensus 19 Lar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~r~G-~~ATv~~L 65 (83)
T cd08319 19 VLLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQRFG-KKATVQSL 65 (83)
T ss_pred HHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhcC-CCCcHHHH
Confidence 346799999999999999885 233355666666765556 44444333
No 35
>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=30.10 E-value=61 Score=21.67 Aligned_cols=22 Identities=18% Similarity=0.502 Sum_probs=17.8
Q ss_pred HHHHH-HHcCCCHHHHHHHHHhC
Q 023027 177 KIDFL-KNLGLSDEEVERMVIRS 198 (288)
Q Consensus 177 kv~~L-~~lG~s~~~v~~~l~~~ 198 (288)
-+.|+ +.+|+|.+++...|.+.
T Consensus 22 ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHH
Confidence 35666 78999999999888765
No 36
>PRK09875 putative hydrolase; Provisional
Probab=29.86 E-value=54 Score=29.77 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHcCCCHHHHHHHHHhCCc
Q 023027 173 TLKPKIDFLKNLGLSDEEVERMVIRSPG 200 (288)
Q Consensus 173 ~l~~kv~~L~~lG~s~~~v~~~l~~~P~ 200 (288)
.+..-+..|++.|+++++|.+|+..||.
T Consensus 261 i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 261 LLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 4566667788999999999999999996
No 37
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=28.11 E-value=1.2e+02 Score=21.41 Aligned_cols=48 Identities=13% Similarity=0.137 Sum_probs=31.6
Q ss_pred HHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHH
Q 023027 68 LSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKS 124 (288)
Q Consensus 68 ~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~i 124 (288)
.|.++.|++..+|+++|..++... +.+ -......+. .+|++.+.+..+
T Consensus 2 NPIia~LKehnvsd~qi~elFq~l----T~N----Pl~AMa~i~-qLGip~eKLQ~l 49 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQAL----TQN----PLAAMATIQ-QLGIPQEKLQQL 49 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHH----hhC----HHHHHHHHH-HcCCCHHHHHHH
Confidence 466788888888888888776543 222 234455666 588887776544
No 38
>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=27.89 E-value=63 Score=21.60 Aligned_cols=20 Identities=35% Similarity=0.496 Sum_probs=14.0
Q ss_pred HHHHHHcCCCHHHHHHHHHh
Q 023027 178 IDFLKNLGLSDEEVERMVIR 197 (288)
Q Consensus 178 v~~L~~lG~s~~~v~~~l~~ 197 (288)
|..++.+|||-+||+.++.-
T Consensus 7 I~~~r~lGfsL~eI~~~l~l 26 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELLEL 26 (65)
T ss_dssp HHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHhc
Confidence 45567899999999999833
No 39
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=27.88 E-value=1.2e+02 Score=20.61 Aligned_cols=37 Identities=11% Similarity=0.033 Sum_probs=27.0
Q ss_pred CCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCC
Q 023027 77 LGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFN 119 (288)
Q Consensus 77 ~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~ 119 (288)
.|-+.++...++...| +. ..-.+++.+|++++|+...
T Consensus 13 TGk~~~~W~~~~~~~~-----~~-~k~~e~v~WLK~ehgLghG 49 (61)
T PF14117_consen 13 TGKTLDEWLALAREGG-----PL-TKHGEIVAWLKDEHGLGHG 49 (61)
T ss_pred HCcCHHHHHHHHHHhC-----CC-CcHHHHHHHHHHHHCCChH
Confidence 6888888888888887 22 2345788888888887754
No 40
>PRK09875 putative hydrolase; Provisional
Probab=26.53 E-value=59 Score=29.51 Aligned_cols=27 Identities=26% Similarity=0.341 Sum_probs=18.5
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHhCCc
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDMHPK 93 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~~P~ 93 (288)
+...+-.|+..|+++++|.+++..||.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 455566677777777777777777763
No 41
>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=25.72 E-value=1e+02 Score=21.36 Aligned_cols=36 Identities=19% Similarity=0.304 Sum_probs=27.1
Q ss_pred hcHHHHHHHHHHcCCCHHHHHHHHHhCCceeecCcc
Q 023027 172 RTLKPKIDFLKNLGLSDEEVERMVIRSPGLLTFSVE 207 (288)
Q Consensus 172 ~~l~~kv~~L~~lG~s~~~v~~~l~~~P~iL~~s~e 207 (288)
..+..-++.++.+||+.++|...+.+-=.+...+++
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~nW~ 44 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGNWE 44 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCch
Confidence 467788888999999999988777766555555554
No 42
>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=25.45 E-value=99 Score=23.16 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=32.6
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
+..+-+|-+.+|++..+|..+-..+|+=. .+.....+.-|....|
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d~----~Eq~~qmL~~W~~~~G 64 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQDT----AEQKVQLLRAWYQSHG 64 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCCh----HHHHHHHHHHHHHHhC
Confidence 45677888999999999999999998532 1244556666665556
No 43
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=25.18 E-value=71 Score=21.98 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=15.5
Q ss_pred HHHHhCCCChhHHHHHHHh
Q 023027 72 HYLLSLGLSRPAVGRILDM 90 (288)
Q Consensus 72 ~~L~~~Gls~~~i~~ii~~ 90 (288)
+.|.++|+++.|+...+.+
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5677899999998887776
No 44
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=25.05 E-value=65 Score=28.34 Aligned_cols=80 Identities=14% Similarity=0.203 Sum_probs=39.4
Q ss_pred CCCChHHHHHHHHhCCCChhHHHHHHHhCCcc-cccCCCCChHHHHHHHhhhcCCCCCCHhHHHhhCCc--cceeccccc
Q 023027 63 PLSSLLSLEHYLLSLGLSRPAVGRILDMHPKL-LTADIPRDLEPIIDFLLEEVLIPFNDLPKSLTRCPR--ILVSDLKTQ 139 (288)
Q Consensus 63 s~~~l~~~v~~L~~~Gls~~~i~~ii~~~P~l-L~~~~~~~l~~~l~~L~~~lG~s~~~i~~il~~~P~--lL~~~~~~~ 139 (288)
+..+..+.+..|.+.|++.+... .+.-.. +.-+ +.++...+++|+ ..|+++.....+-..+|. +..+..++
T Consensus 29 ~e~eANemlAlL~~~gI~A~K~~---~~~g~~~l~Ve-~~~fa~Av~iL~-~~GlPr~~f~~l~d~Fp~dgLVsSP~eE- 102 (246)
T COG4669 29 SEKEANEMLALLMSHGINAEKKA---DKDGGTSLLVE-ESDFAEAVEILN-QNGLPRKKFTTLGDIFPKDGLVSSPTEE- 102 (246)
T ss_pred CHhHHHHHHHHHHHcCCcceeec---cCCCceEEEEc-HHHHHHHHHHHH-hcCCCCCCCCcHHHhCCcccccCCcHHH-
Confidence 33455666666666666554331 111111 2222 234556666666 366666666666555655 44444332
Q ss_pred hhhHHHHHHH
Q 023027 140 LRPSFKFLVE 149 (288)
Q Consensus 140 l~~~v~~L~~ 149 (288)
+.++.|..+
T Consensus 103 -kaR~~~~~e 111 (246)
T COG4669 103 -KARLNYAKE 111 (246)
T ss_pred -HHHHHHHHH
Confidence 445555544
No 45
>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=24.78 E-value=82 Score=22.73 Aligned_cols=42 Identities=21% Similarity=0.168 Sum_probs=27.8
Q ss_pred HHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhc
Q 023027 71 EHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEV 114 (288)
Q Consensus 71 v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~l 114 (288)
.--|+..|++++++..+=..|-.+...+ .++...++-+.++.
T Consensus 20 ~vGLrR~Gfs~~~i~~l~~ayr~l~~~~--~~~~~a~~~l~~~~ 61 (83)
T PF13720_consen 20 LVGLRRRGFSKEEISALRRAYRILFRSG--LTLEEALEELEEEY 61 (83)
T ss_dssp HHHHHHTTS-HHHHHHHHHHHHHHHTSS--S-HHHHHHHHHHHT
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhCC--CCHHHHHHHHHHhc
Confidence 4457888999998888777776655554 36777777776433
No 46
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=23.48 E-value=88 Score=18.13 Aligned_cols=24 Identities=21% Similarity=0.309 Sum_probs=14.9
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHh
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDM 90 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~ 90 (288)
+...+.--++.|++.+++...+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 444555556789999988877654
No 47
>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=23.05 E-value=88 Score=20.92 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=11.8
Q ss_pred HHHHHHHhCCCChhHHHHHHHhC
Q 023027 69 SLEHYLLSLGLSRPAVGRILDMH 91 (288)
Q Consensus 69 ~~v~~L~~~Gls~~~i~~ii~~~ 91 (288)
..++-|.++||+.+.+-.++.+-
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrrl 33 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRRL 33 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHS
T ss_pred HHHHHHHHcCCcHHHHHHHHHHh
Confidence 34555666666666655555443
No 48
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=22.83 E-value=87 Score=27.13 Aligned_cols=69 Identities=12% Similarity=0.146 Sum_probs=33.1
Q ss_pred ChhhHhhhCCCCCCCCCC--ChHHHHHHHHhCCC--ChhHHHHHHH----h-CCcc--cccCCCCChHHHHHHHhhhcCC
Q 023027 48 NPQKALHQNPNFRCTPLS--SLLSLEHYLLSLGL--SRPAVGRILD----M-HPKL--LTADIPRDLEPIIDFLLEEVLI 116 (288)
Q Consensus 48 ~~~~l~~~~P~ll~~s~~--~l~~~v~~L~~~Gl--s~~~i~~ii~----~-~P~l--L~~~~~~~l~~~l~~L~~~lG~ 116 (288)
.++.+.-.+|.+.....+ .+...+.-|+.+|+ ++++|...-. + .|.. ....-...+...+.||+ .+|-
T Consensus 130 ~PgS~MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq-~LG~ 208 (217)
T PRK14487 130 VPESNMPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQ-SLGT 208 (217)
T ss_pred CCCCCCCCCcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHH-Hhcc
Confidence 344444445555544444 45666666666666 3445544222 1 0000 00011134677778887 4774
Q ss_pred C
Q 023027 117 P 117 (288)
Q Consensus 117 s 117 (288)
.
T Consensus 209 ~ 209 (217)
T PRK14487 209 A 209 (217)
T ss_pred c
Confidence 3
No 49
>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=22.81 E-value=2.5e+02 Score=19.82 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcC
Q 023027 68 LSLEHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVL 115 (288)
Q Consensus 68 ~~~v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG 115 (288)
...-.+.+.+|++..+|..+=..+|. .. +.....+.-|+...|
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~-~~----eq~~~mL~~W~~k~G 54 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQ-HR----DRVYELLRIWRNKEG 54 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCc-hH----HHHHHHHHHHHhccC
Confidence 44556778899999999999999997 21 245677777775556
No 50
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=22.47 E-value=1.2e+02 Score=22.72 Aligned_cols=23 Identities=30% Similarity=0.314 Sum_probs=13.0
Q ss_pred CCCChhHHHHHHHhCCcccccCC
Q 023027 77 LGLSRPAVGRILDMHPKLLTADI 99 (288)
Q Consensus 77 ~Gls~~~i~~ii~~~P~lL~~~~ 99 (288)
..++.+++..++..+|.++.+.+
T Consensus 69 ~~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 69 DDLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp TTSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhhHHHHHHHHhChhheeCCE
Confidence 34566666666666666665553
No 51
>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=22.38 E-value=1.4e+02 Score=22.42 Aligned_cols=56 Identities=16% Similarity=0.258 Sum_probs=34.0
Q ss_pred HhHHHHhhCCCChhhHhhhCCCCCCCCCCC--hHHHHHHHHhCCCChhHHHHHHHhCC
Q 023027 37 QKILHLQALNVNPQKALHQNPNFRCTPLSS--LLSLEHYLLSLGLSRPAVGRILDMHP 92 (288)
Q Consensus 37 ~~~~~L~~~G~~~~~l~~~~P~ll~~s~~~--l~~~v~~L~~~Gls~~~i~~ii~~~P 92 (288)
.++.|....|+=+..-....-.--.++.++ .-..+..|++.|++-+++..++....
T Consensus 15 ~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 15 KALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADN 72 (108)
T ss_pred HHHHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 456677777764321111101233455543 44577888999999999999887765
No 52
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=22.24 E-value=87 Score=29.34 Aligned_cols=24 Identities=17% Similarity=0.178 Sum_probs=22.0
Q ss_pred hHHHHHHHHhCCCChhHHHHHHHh
Q 023027 67 LLSLEHYLLSLGLSRPAVGRILDM 90 (288)
Q Consensus 67 l~~~v~~L~~~Gls~~~i~~ii~~ 90 (288)
++++|+-+.++||.+|.|+.+|.|
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v~r 344 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATVRR 344 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHH
Confidence 789999999999999999988876
No 53
>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=20.68 E-value=1.7e+02 Score=18.03 Aligned_cols=29 Identities=14% Similarity=0.301 Sum_probs=20.2
Q ss_pred cHHHHHHHHH-HcCCCHHHHHHHHHhCCce
Q 023027 173 TLKPKIDFLK-NLGLSDEEVERMVIRSPGL 201 (288)
Q Consensus 173 ~l~~kv~~L~-~lG~s~~~v~~~l~~~P~i 201 (288)
....+...|. ++|++....+.|+..||..
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 3455667784 8899999999999999863
No 54
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=20.47 E-value=2.3e+02 Score=22.65 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=15.2
Q ss_pred HHHHHHHHhCCCChhHHHHHHHhC
Q 023027 68 LSLEHYLLSLGLSRPAVGRILDMH 91 (288)
Q Consensus 68 ~~~v~~L~~~Gls~~~i~~ii~~~ 91 (288)
......|...|++.+.|..++...
T Consensus 79 ~~I~~~L~~kGi~~~~I~~~l~~~ 102 (157)
T PRK00117 79 RRIRQELRQKGVDREIIEEALAEL 102 (157)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHc
Confidence 344556667777777777666654
No 55
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=20.39 E-value=2.6e+02 Score=20.27 Aligned_cols=52 Identities=8% Similarity=0.019 Sum_probs=29.8
Q ss_pred HHHHHhCCCChhHHHHHHHhCCcccccCCCCChHHHHHHHhhhcCCCCCCHhHHH
Q 023027 71 EHYLLSLGLSRPAVGRILDMHPKLLTADIPRDLEPIIDFLLEEVLIPFNDLPKSL 125 (288)
Q Consensus 71 v~~L~~~Gls~~~i~~ii~~~P~lL~~~~~~~l~~~l~~L~~~lG~s~~~i~~il 125 (288)
-.+-+.+|++..+|..+-..|+. .++.+.....+..|+..-|-..+.+.+++
T Consensus 17 k~lar~LG~s~~eI~~ie~~~~r---~~~~eq~~~mL~~W~~r~g~~~ATv~~L~ 68 (86)
T cd08777 17 KRCARKLGFTESEIEEIDHDYER---DGLKEKVHQMLHKWKMKEGSKGATVGKLA 68 (86)
T ss_pred HHHHHHcCCCHHHHHHHHHhccc---CCHHHHHHHHHHHHHHccCCCCcHHHHHH
Confidence 34557799999999887655532 11222355666667654553344444443
Done!