Query 047553
Match_columns 377
No_of_seqs 203 out of 1243
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 12:07:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047553hhsearch_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 2.4E-58 5.3E-63 462.0 24.6 339 11-362 100-446 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.1E-50 2.4E-55 394.4 5.1 303 43-353 4-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 4.8E-45 1E-49 366.0 19.9 307 36-355 93-412 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.6E-37 1.2E-41 298.2 5.1 267 74-349 2-308 (345)
5 KOG1267 Mitochondrial transcri 100.0 7.7E-28 1.7E-32 239.1 16.8 288 36-331 59-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 3E-18 6.4E-23 170.5 11.4 186 104-294 90-310 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00038 8.2E-09 42.0 2.7 30 269-299 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.0 0.00044 9.6E-09 41.7 1.6 28 89-117 3-30 (31)
9 PF11955 PORR: Plant organelle 94.0 0.67 1.5E-05 44.9 11.3 202 77-283 45-293 (335)
10 cd04790 HTH_Cfa-like_unk Helix 89.8 1.6 3.5E-05 38.1 7.7 16 254-269 151-166 (172)
11 cd04790 HTH_Cfa-like_unk Helix 88.2 1.2 2.5E-05 39.0 5.7 117 107-238 49-169 (172)
12 PF04695 Pex14_N: Peroxisomal 79.9 3.5 7.5E-05 34.5 4.8 31 248-278 21-51 (136)
13 PF04695 Pex14_N: Peroxisomal 77.3 4.3 9.4E-05 33.9 4.6 35 60-95 15-49 (136)
14 COG1125 OpuBA ABC-type proline 69.7 15 0.00032 34.4 6.3 79 247-329 70-151 (309)
15 PF11955 PORR: Plant organelle 66.4 20 0.00044 34.8 7.0 220 85-315 22-293 (335)
16 PF14490 HHH_4: Helix-hairpin- 62.5 16 0.00034 28.3 4.6 23 105-127 8-30 (94)
17 PF11181 YflT: Heat induced st 60.9 38 0.00083 26.6 6.6 79 179-270 10-90 (103)
18 PF00627 UBA: UBA/TS-N domain; 60.9 14 0.0003 23.2 3.3 23 252-274 4-26 (37)
19 smart00165 UBA Ubiquitin assoc 60.8 15 0.00033 22.8 3.5 23 252-274 3-25 (37)
20 PF00356 LacI: Bacterial regul 59.4 17 0.00036 24.3 3.6 41 188-231 6-46 (46)
21 PF14490 HHH_4: Helix-hairpin- 58.7 33 0.00071 26.5 5.8 65 38-125 11-76 (94)
22 PF11212 DUF2999: Protein of u 58.1 28 0.00061 25.5 4.7 49 142-202 2-50 (82)
23 TIGR01448 recD_rel helicase, p 57.6 28 0.0006 37.6 6.9 84 37-127 79-165 (720)
24 KOG2561 Adaptor protein NUB1, 56.8 42 0.00092 33.6 7.2 60 47-114 281-340 (568)
25 cd00194 UBA Ubiquitin Associat 56.6 19 0.00042 22.4 3.5 23 252-274 3-25 (38)
26 TIGR00601 rad23 UV excision re 54.0 34 0.00074 33.8 6.3 134 38-205 159-361 (378)
27 COG3620 Predicted transcriptio 48.6 34 0.00073 29.5 4.5 30 201-230 69-98 (187)
28 KOG2875 8-oxoguanine DNA glyco 48.1 30 0.00066 32.4 4.5 98 16-132 117-226 (323)
29 PF07499 RuvA_C: RuvA, C-termi 46.6 31 0.00066 23.0 3.3 24 70-93 4-27 (47)
30 PRK11613 folP dihydropteroate 46.2 70 0.0015 30.3 6.8 67 284-358 164-230 (282)
31 PRK14136 recX recombination re 45.5 2.8E+02 0.0062 26.6 11.5 133 109-274 169-302 (309)
32 PF13543 KSR1-SAM: SAM like do 45.2 37 0.0008 28.1 4.2 56 36-92 67-124 (129)
33 PHA02591 hypothetical protein; 44.3 62 0.0013 24.3 4.8 27 206-232 38-64 (83)
34 smart00354 HTH_LACI helix_turn 39.7 53 0.0011 23.7 4.0 40 189-231 8-47 (70)
35 PRK14605 ruvA Holliday junctio 33.9 2.4E+02 0.0051 25.1 7.9 24 106-129 149-172 (194)
36 PRK00116 ruvA Holliday junctio 33.7 1.2E+02 0.0027 26.7 6.1 25 105-129 149-173 (192)
37 PRK14135 recX recombination re 32.4 4E+02 0.0087 24.5 16.7 78 182-273 179-258 (263)
38 cd01392 HTH_LacI Helix-turn-he 32.3 72 0.0016 21.0 3.5 40 189-231 5-44 (52)
39 PRK14601 ruvA Holliday junctio 32.0 2.3E+02 0.005 25.0 7.4 25 105-129 142-166 (183)
40 PF02022 Integrase_Zn: Integra 31.2 91 0.002 20.1 3.5 29 249-277 7-36 (40)
41 PF02787 CPSase_L_D3: Carbamoy 31.2 1.1E+02 0.0024 25.0 5.0 71 180-271 12-82 (123)
42 PF11212 DUF2999: Protein of u 31.0 2.2E+02 0.0047 21.0 5.8 39 44-87 9-47 (82)
43 PF14117 DUF4287: Domain of un 28.1 1.8E+02 0.0039 20.7 4.9 44 44-90 11-55 (61)
44 KOG0011 Nucleotide excision re 27.2 1.4E+02 0.0031 28.8 5.5 117 34-172 134-264 (340)
45 KOG2629 Peroxisomal membrane a 27.1 1.3E+02 0.0028 28.4 5.2 27 247-273 19-45 (300)
46 cd08306 Death_FADD Fas-associa 26.7 98 0.0021 23.5 3.7 37 74-114 18-54 (86)
47 PHA01351 putative minor struct 26.7 8.4E+02 0.018 26.4 11.6 54 39-93 647-715 (1070)
48 PF08671 SinI: Anti-repressor 25.9 1.1E+02 0.0024 18.5 3.0 17 257-273 12-28 (30)
49 PRK14606 ruvA Holliday junctio 25.7 3.7E+02 0.0081 23.7 7.7 25 105-129 143-167 (188)
50 cd08315 Death_TRAILR_DR4_DR5 D 25.7 1.8E+02 0.0039 22.6 5.0 40 70-114 20-59 (96)
51 TIGR03060 PS_II_psb29 photosys 25.7 2.3E+02 0.0051 25.6 6.4 67 16-82 50-120 (214)
52 PRK07562 ribonucleotide-diphos 24.8 1E+02 0.0022 35.1 4.7 82 40-124 717-821 (1220)
53 PRK00116 ruvA Holliday junctio 24.5 1.5E+02 0.0033 26.2 5.0 54 40-93 108-173 (192)
54 PF10440 WIYLD: Ubiquitin-bind 24.2 1.5E+02 0.0033 21.4 3.9 28 247-274 8-35 (65)
55 cd08313 Death_TNFR1 Death doma 24.1 2.1E+02 0.0045 21.5 4.9 25 70-94 12-36 (80)
56 KOG3120 Predicted haloacid deh 23.4 1.7E+02 0.0037 26.8 5.0 45 67-117 57-101 (256)
57 PRK08561 rps15p 30S ribosomal 23.1 1.3E+02 0.0028 25.7 3.9 111 227-342 10-143 (151)
58 PHA02415 DNA primase domain-co 22.6 1.4E+02 0.0029 32.6 4.9 81 2-92 43-144 (930)
59 PF02631 RecX: RecX family; I 22.6 4E+02 0.0086 21.2 8.3 111 138-273 8-118 (121)
60 PRK14136 recX recombination re 22.3 6.8E+02 0.015 24.0 9.1 81 39-127 169-250 (309)
61 PF03960 ArsC: ArsC family; I 22.2 2E+02 0.0044 22.6 4.9 83 180-281 8-90 (110)
62 PF08069 Ribosomal_S13_N: Ribo 21.6 34 0.00074 24.3 0.2 30 244-273 27-56 (60)
63 KOG0400 40S ribosomal protein 21.4 69 0.0015 26.5 1.9 64 166-231 20-83 (151)
64 COG1125 OpuBA ABC-type proline 20.7 1.1E+02 0.0023 28.9 3.3 45 105-150 73-119 (309)
65 PF01191 RNA_pol_Rpb5_C: RNA p 20.7 69 0.0015 23.8 1.7 48 68-131 16-63 (74)
66 PF11626 Rap1_C: TRF2-interact 20.7 3.1E+02 0.0066 20.7 5.4 17 188-204 4-20 (87)
67 PRK13753 dihydropteroate synth 20.0 2.1E+02 0.0046 27.0 5.2 16 341-356 204-219 (279)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2.4e-58 Score=461.96 Aligned_cols=339 Identities=19% Similarity=0.348 Sum_probs=306.0
Q ss_pred CCchhhhhhhhhhhhcccCCCCC-CCchhHHHhHhhCCCChhhHHHHHhhccCCCCC---CChHHHHHHHHhCCCChHHH
Q 047553 11 NSQNFAIKSLFSFFASLSKTPNS-TNFIFLNFLIKTLNIPKSRALPISNKFSRIKSL---EKPETVRQFLHNVGFSDTHI 86 (377)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~v~~L~~~~Gls~~~~~~i~~~~P~ll~~---~~~~~~l~~L~~lG~~~~~i 86 (377)
++.||.-.+++. ++.+-+++.. .-.+.++|| +++|++.+++.+++.++|.++.. .++.++++||+++|+++++|
T Consensus 100 ~s~G~~~~~i~~-~P~iL~~~v~~~l~Pvl~fL-~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i 177 (487)
T PLN03196 100 HKLGLTIEDINE-YPLVLGCSVKKNMIPVLDYL-EKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDI 177 (487)
T ss_pred HHcCCChHHhcc-CcHHhhcCHhhhhHHHHHHH-HHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHH
Confidence 345665555552 2444444333 335578999 89999999999999999999963 46889999999999999999
Q ss_pred HHHHHhCCCeeccCCCCchhhHHHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHH
Q 047553 87 QLTVTSRPTILFSDVDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFR 166 (377)
Q Consensus 87 ~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~ 166 (377)
++++.++|++|++++++++.|+++||+++|++.+++++++.++|++|+++++++++|+++||+++|++ .++|++++.
T Consensus 178 ~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~---~~~I~~il~ 254 (487)
T PLN03196 178 PRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLP---RLAVARILE 254 (487)
T ss_pred HHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCC---HHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred hccccccccccccchhhhHHHHHHcCCCchhHhhhhhhCCeeeEeeh-hhHHHHHHHHH-hcCCCCchh--hHHHHHHHH
Q 047553 167 RCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKE-LKIRHLVSRLL-DMGFSTNSR--MFVYGLVVL 242 (377)
Q Consensus 167 ~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~-~~l~~~v~~l~-~lG~~~~~~--~~~~~p~~l 242 (377)
++|++|+++++ ++++|++++|+++|++++++..+++++|.+++.+. ++++++++++. ++|+++++. ++.+.|.+
T Consensus 255 ~~P~iL~~sle-~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~i- 332 (487)
T PLN03196 255 KRPYILGFDLE-ETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQI- 332 (487)
T ss_pred hCCceeEcCHH-HhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchh-
Confidence 99999999998 78999999999999999999999999999999985 56999999985 799999986 34455554
Q ss_pred HhCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHHHHHHHHHHHHHhhCCChHHHhhCCccccccccccchhhH
Q 047553 243 SCLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEERLQLGLEFFLKEIECEKSVLVRIPICLACSIENRVIPRY 322 (377)
Q Consensus 243 ~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~~L~~k~~fL~~~~g~~~~~i~~~P~~L~~Sle~ri~pR~ 322 (377)
...+++++++|++||+++||+.++|..|+.++|++|++|+++|++|++||+++||++.++|+.+|++|+||+|+||+|||
T Consensus 333 l~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~ 412 (487)
T PLN03196 333 VSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRY 412 (487)
T ss_pred hcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHCCCCCCCCCccchhccchhhHHHHhcccCCCC
Q 047553 323 RVFQIIMSRGMFKKDCSFPSMLLLSEGNFLQKFVLSFGDD 362 (377)
Q Consensus 323 ~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~~~~~~~~ 362 (377)
+++ .++|+ ++++.++|++||++|+++|+..|.|+
T Consensus 413 ~~L---~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~ 446 (487)
T PLN03196 413 ERV---AKKGI---KCSLAWFLNCSDDKFEQRMSGDFIEG 446 (487)
T ss_pred HHH---HHcCC---CCCHHHHhccCHHHHHHHHhhhcccc
Confidence 975 58998 67999999999999999999999874
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=1.1e-50 Score=394.44 Aligned_cols=303 Identities=28% Similarity=0.471 Sum_probs=187.5
Q ss_pred HhhCCCChhhHHHHHhhccCCCCC---CChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCCCC
Q 047553 43 IKTLNIPKSRALPISNKFSRIKSL---EKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGLVG 119 (377)
Q Consensus 43 ~~~~Gls~~~~~~i~~~~P~ll~~---~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~s~ 119 (377)
++++|++++++.++++++|.++.. .++.++++||.++|++..|+++++.++|++|..+.+++|.|.++||+++|+++
T Consensus 4 ~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~ 83 (345)
T PF02536_consen 4 LKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSD 83 (345)
T ss_dssp HHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-H
T ss_pred HHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCH
Confidence 356666666666666666665521 34556666666666666666666666666666665556666666666666666
Q ss_pred chhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhhhHHHHHHcCCCchhHh
Q 047553 120 SDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLS 199 (377)
Q Consensus 120 ~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~ 199 (377)
+++.+++.++|++|..+.+.++.+++.||+++|++ .+.+.+++..+|.++... + ++.+.++++.++|++++++.
T Consensus 84 ~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~---~~~~~~~l~~~~~~~~~~-~--~~~~~v~~l~~lG~~~~~~~ 157 (345)
T PF02536_consen 84 EDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVP---PSQIISLLISRPPLFLSS-E--KIKERVEFLKELGFDPEKIG 157 (345)
T ss_dssp HHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT-----HHHHHHHHHH-CHHHHS--H--HHHCHHHHHCCCTSSHHHHC
T ss_pred HHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCc---HHHHHHHHHhcCccccch-h--HHHHHHHHHHHhCCCchhhc
Confidence 66666666666666665555666666666666665 444444444444433333 2 24555555555555555555
Q ss_pred hhhhhCCeeeEe-ehhhHHHHHHHHHhcCCCCchh--hHHH---------------------------------HHHHHH
Q 047553 200 MLLVWQPRLFCY-KELKIRHLVSRLLDMGFSTNSR--MFVY---------------------------------GLVVLS 243 (377)
Q Consensus 200 ~ll~~~P~il~~-s~~~l~~~v~~l~~lG~~~~~~--~~~~---------------------------------~p~~l~ 243 (377)
+++..+|+++.. +++.+++++++|+++|++.+++ ++.+ .|.++
T Consensus 158 ~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il- 236 (345)
T PF02536_consen 158 RVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQIL- 236 (345)
T ss_dssp CCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC----------------------------
T ss_pred ccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccccccccccccc-
Confidence 555555433322 2344555555555555544433 2232 34333
Q ss_pred hCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHHHHHHHHHHHHHhhCCChHHHhhCCccccccccccchhhHH
Q 047553 244 CLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEERLQLGLEFFLKEIECEKSVLVRIPICLACSIENRVIPRYR 323 (377)
Q Consensus 244 ~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~~L~~k~~fL~~~~g~~~~~i~~~P~~L~~Sle~ri~pR~~ 323 (377)
..+.+++.++++||.++||+.+|+++|+.++|+||++|.++|++|++||+++||++.++|+++|++|+||+|+||+|||+
T Consensus 237 ~~~~~~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 237 SLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYE 316 (345)
T ss_dssp THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHH
T ss_pred ccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHH
Confidence 33567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHCCCCCCCCCccchhccchhhHHH
Q 047553 324 VFQIIMSRGMFKKDCSFPSMLLLSEGNFLQ 353 (377)
Q Consensus 324 ~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~ 353 (377)
++++|+++|. +.++++.+++.+||++|++
T Consensus 317 ~~~~l~~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 317 VLKVLKSKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HHHTT--TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHHHCcC-CCCCCHHHHhhccHHHhcC
Confidence 9999999997 5689999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=4.8e-45 Score=366.02 Aligned_cols=307 Identities=18% Similarity=0.256 Sum_probs=275.8
Q ss_pred chhHHHhHhhCCCChhhHHHHHhhccCCCCC---CChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHH
Q 047553 36 FIFLNFLIKTLNIPKSRALPISNKFSRIKSL---EKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFF 112 (377)
Q Consensus 36 ~~~v~~L~~~~Gls~~~~~~i~~~~P~ll~~---~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL 112 (377)
...++|| +++|++.+++. ++|.++.. .++.++++||+++|+++.+|++++.++|++|.++++++|.|+++||
T Consensus 93 ~~~l~~L-~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL 167 (487)
T PLN03196 93 RERVEFL-HKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYL 167 (487)
T ss_pred HHHHHHH-HHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHH
Confidence 3456888 88999999986 68999863 5788999999999999999999999999999999999999999999
Q ss_pred HhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhhhHHHHHHcC
Q 047553 113 QHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCG 192 (377)
Q Consensus 113 ~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG 192 (377)
+++|++.+++++++.++|++|++++++++.|+++||+++|++ .+++++++.++|++|+++++ ++++|+++||+++|
T Consensus 168 ~~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 168 QGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVA---PRDIGPMLTRFPEILGMRVG-NNIKPKVDYLESLG 243 (487)
T ss_pred HHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCC---HHHHHHHHHhCcHHhhcChh-hhHHHHHHHHHHcC
Confidence 999999999999999999999999999999999999999999 99999999999999999999 88999999999999
Q ss_pred CCchhHhhhhhhCCeeeEeehh-hHHHHHHHHHhcCCCCchhh--HHHHHHHHHhCCHHHHHHHHHHHH-HcCCCHHHHH
Q 047553 193 IVGSQLSMLLVWQPRLFCYKEL-KIRHLVSRLLDMGFSTNSRM--FVYGLVVLSCLNEETFGRKLELFR-SYGFSKEEVL 268 (377)
Q Consensus 193 ~~~~~i~~ll~~~P~il~~s~~-~l~~~v~~l~~lG~~~~~~~--~~~~p~~l~~~s~~~l~~k~~~L~-~lG~s~~~v~ 268 (377)
++.++|.+++.++|++|+++.+ ++++++++|.++|++++++. +.+.|.++....++++.++++||. ++|++.+++.
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~ 323 (487)
T PLN03196 244 LPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFG 323 (487)
T ss_pred CCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHH
Confidence 9999999999999999999975 89999999999999999874 455677776666789999999996 9999999999
Q ss_pred HHHHhCCcccccCHHHHHHHHHHHHHhhCCChHHH----hhCCccccccccccchhhHHHHHHHHHCCCCC-CCCCccch
Q 047553 269 QMFRKAPLILKASEERLQLGLEFFLKEIECEKSVL----VRIPICLACSIENRVIPRYRVFQIIMSRGMFK-KDCSFPSM 343 (377)
Q Consensus 269 ~~i~~~P~iL~~s~~~L~~k~~fL~~~~g~~~~~i----~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~-~~~~l~~~ 343 (377)
.++.++|+++++|++++++|++||.+ +|++.++| .++|++|++|.+ .|+++++|+.. +.|... .-...+.+
T Consensus 324 ~~v~k~P~il~lSe~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~-~l~~k~dFlvn--eMg~~~~~Iv~fP~~ 399 (487)
T PLN03196 324 RVIEKLPQIVSLNRNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLE-IMKPSLEFFKK--EMKRPLKELVEFPAY 399 (487)
T ss_pred HHHHhcchhhcccHHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHH-HHHHHHHHHHH--HhCCCHHHHHhChHH
Confidence 99999999999999999999999986 99999987 699999999995 99999998753 455532 23456778
Q ss_pred hccc-hhhHHHHh
Q 047553 344 LLLS-EGNFLQKF 355 (377)
Q Consensus 344 l~~s-~~~F~~~~ 355 (377)
+++| |++..-||
T Consensus 400 LsySLEkRI~PR~ 412 (487)
T PLN03196 400 FTYGLESRIKPRY 412 (487)
T ss_pred hccChhhhhHHHH
Confidence 8887 44544444
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=5.6e-37 Score=298.20 Aligned_cols=267 Identities=34% Similarity=0.556 Sum_probs=218.1
Q ss_pred HHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhc
Q 047553 74 QFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILV 153 (377)
Q Consensus 74 ~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~ 153 (377)
++|+++||+++||.++++++|.+|.+++++++.|+++||+++|++..++++++.+||++|..++++++.|.++||+++|+
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 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchHHHHHHHhccccccccccccchhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCchh
Q 047553 154 DDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTNSR 233 (377)
Q Consensus 154 ~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~~~ 233 (377)
+ ++++.+++.++|++|+.+.+ .++.+++++|+++|++.+.+..++...|..+... +++++.++++.++|++++..
T Consensus 82 s---~~d~~~~l~r~p~~l~~~~~-~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~-~~~~~~v~~l~~lG~~~~~~ 156 (345)
T PF02536_consen 82 S---DEDIVKVLKRYPRILSFSVE-ENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS-EKIKERVEFLKELGFDPEKI 156 (345)
T ss_dssp ----HHHHHHHHHH-SHHHHS----HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS--HHHHCHHHHHCCCTSSHHHH
T ss_pred C---HHHHHHHHHhcchhhccchH-hhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch-hHHHHHHHHHHHhCCCchhh
Confidence 9 99999999999999999887 6899999999999999998889999999877666 88999999999999999987
Q ss_pred --hHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHH----------------------------
Q 047553 234 --MFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEE---------------------------- 283 (377)
Q Consensus 234 --~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~---------------------------- 283 (377)
+...+|..+...+++.++++++||+++|++.+++.+++.++|.++.+|.+
T Consensus 157 ~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il 236 (345)
T PF02536_consen 157 GRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQIL 236 (345)
T ss_dssp CCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------
T ss_pred cccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccccccccccccc
Confidence 67778888888999999999999999999999999999999999998875
Q ss_pred -----HHHHHHHHHHHhhCCChHHH----hhCCccccccccccchhhHHHHHHHHHCCCCCC-CCCccchhccchh
Q 047553 284 -----RLQLGLEFFLKEIECEKSVL----VRIPICLACSIENRVIPRYRVFQIIMSRGMFKK-DCSFPSMLLLSEG 349 (377)
Q Consensus 284 -----~L~~k~~fL~~~~g~~~~~i----~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~-~~~l~~~l~~s~~ 349 (377)
+++++++||.+ +|++.++| .++|++|++|.+ +++|+++|+. .+.|...+ -...+.++.+|=+
T Consensus 237 ~~~~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~--~~m~~~~~~i~~~P~~l~~sLe 308 (345)
T PF02536_consen 237 SLSEEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLV--KEMGLPLEEIVEFPQYLSYSLE 308 (345)
T ss_dssp THHHHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHH--HCCT--HHHHHHSCHHHCS-HH
T ss_pred ccchHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHH--HHhCcCHHHHhhCCceeEechh
Confidence 48899999987 99998885 679999999999 4999999874 35665422 2345667777753
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.95 E-value=7.7e-28 Score=239.11 Aligned_cols=288 Identities=26% Similarity=0.379 Sum_probs=246.5
Q ss_pred chhHHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHhc
Q 047553 36 FIFLNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHL 115 (377)
Q Consensus 36 ~~~v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~l 115 (377)
++.+.|++.++|++...+..+.+.. ......+++.++++|+++|+++.++..++..+|.++..+.++.+.|+..+|+..
T Consensus 59 ~f~~s~~~~s~~~~~~~~~~~~~~~-~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~ 137 (413)
T KOG1267|consen 59 NFESSYLVDSLGLSIKLARKLSREV-SSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSL 137 (413)
T ss_pred CcceeeeccccccchhhHHHHHHHH-HhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhcc
Confidence 6788999999998888888777655 444457899999999999999999999999999999999999999999999999
Q ss_pred CCCCchhhhhhhcccccchhhhhccchhHHHHHHHHh--cCCC------------------------------CchHHH-
Q 047553 116 GLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKIL--VDDS------------------------------NNEDLT- 162 (377)
Q Consensus 116 G~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g--~~~~------------------------------~~~~i~- 162 (377)
|++...+++++...|.+|..+...++.+.++|+++++ ..++ ..+.+.
T Consensus 138 g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~ 217 (413)
T KOG1267|consen 138 GLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKS 217 (413)
T ss_pred CccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHH
Confidence 9999999999999999999887788999999998874 1100 022233
Q ss_pred -------------------------------HHHHhccccccccccccchhhhHHHHHHcCCCchhHhhhhhhCCeeeEe
Q 047553 163 -------------------------------RVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCY 211 (377)
Q Consensus 163 -------------------------------~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~ 211 (377)
+++.+.|.+++++.+ +++++++++|+++|++.+++..|+.++|+++++
T Consensus 218 ~l~~~~~~~~~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~-~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~ 296 (413)
T KOG1267|consen 218 LLESQPRPVLLYLKLKARLPFLLTLGFDPKTREFVKAPILLSYSSE-KTLEPKVEVLKSLGFSREEIWKMVKKCPQILGY 296 (413)
T ss_pred HHhcCccceeeehhhhhhhhhHHHhccCCchhHHHhhhhhhccccc-ccHHHHHHHHHHcCCCHHHHHHHHHhCchheEe
Confidence 223345555666677 789999999999999999999999999999999
Q ss_pred ehhhHHHHHHHHHhcCCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHH-HHHHHHH
Q 047553 212 KELKIRHLVSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEE-RLQLGLE 290 (377)
Q Consensus 212 s~~~l~~~v~~l~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~-~L~~k~~ 290 (377)
+.+++..+++++.+. .++ +.+.|.++ ..++..+.++++|+..+|++..|+..++.++|+++++|.+ .++.+.+
T Consensus 297 s~~~~~~~~~~~~~~---~~~--~~k~p~~l-~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~ 370 (413)
T KOG1267|consen 297 SVKKNLKTTEYLLKN---PKH--ILKFPQLL-RSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYE 370 (413)
T ss_pred ehhhhhHHHHHHHhc---chh--hhhhhhhh-hccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHH
Confidence 999888888888766 222 55566666 7789999999999999999999999999999999999998 8899999
Q ss_pred HHHHhhCCChHHHhhCCccccccccccchhhHHHHHHHHHC
Q 047553 291 FFLKEIECEKSVLVRIPICLACSIENRVIPRYRVFQIIMSR 331 (377)
Q Consensus 291 fL~~~~g~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~ 331 (377)
|+.+.|+++.+.++.+|++++|++|+|+.||+.+..++..+
T Consensus 371 ~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 371 YLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred HHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 99999999999999999999999999999999988766443
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.76 E-value=3e-18 Score=170.51 Aligned_cols=186 Identities=27% Similarity=0.396 Sum_probs=151.5
Q ss_pred chhhHHHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhh
Q 047553 104 TLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLR 183 (377)
Q Consensus 104 ~l~~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~ 183 (377)
+-...+++|+++|++..++..++..+|.++..+.++.+.|+..+|+..|.+ ...+..++...|.+|+.+.+ .++.+
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~---~s~l~~i~s~~~~il~~~~~-~~~~~ 165 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLP---SSELSSIVSVVPKILLKSKG-ESLST 165 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCcc---ccccchhhhccHHHHHhhcC-Cchhh
Confidence 466788999999999999999999999999999999999999999999998 66666666665655554333 23433
Q ss_pred -----------------------------------hHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCC
Q 047553 184 -----------------------------------NIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGF 228 (377)
Q Consensus 184 -----------------------------------~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~ 228 (377)
++++++++|+.+.++..++..+|+.+.... .+...+.++..+|+
T Consensus 166 ~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~ 244 (413)
T KOG1267|consen 166 FIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGF 244 (413)
T ss_pred HHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhcc
Confidence 455555566777777777777777766554 77888889999999
Q ss_pred CCchhhHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHHHHHHHHHHHHH
Q 047553 229 STNSRMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEERLQLGLEFFLK 294 (377)
Q Consensus 229 ~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~~L~~k~~fL~~ 294 (377)
++.+.++++++.++...+++++++|+++|+++||+.+||++|+.++|++|++|++++..++.|+.+
T Consensus 245 ~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~ 310 (413)
T KOG1267|consen 245 DPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLK 310 (413)
T ss_pred CCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999864433444333
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.15 E-value=0.00038 Score=41.97 Aligned_cols=30 Identities=33% Similarity=0.549 Sum_probs=26.5
Q ss_pred HHHHhCCcccccCHHHHHHHHHHHHHhhCCC
Q 047553 269 QMFRKAPLILKASEERLQLGLEFFLKEIECE 299 (377)
Q Consensus 269 ~~i~~~P~iL~~s~~~L~~k~~fL~~~~g~~ 299 (377)
+++.++|.+|++|+++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4788999999999999999999998 68874
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.95 E-value=0.00044 Score=41.66 Aligned_cols=28 Identities=43% Similarity=0.731 Sum_probs=14.7
Q ss_pred HHHhCCCeeccCCCCchhhHHHHHHhcCC
Q 047553 89 TVTSRPTILFSDVDKTLKPKIEFFQHLGL 117 (377)
Q Consensus 89 ii~~~P~lL~~~~~~~l~~~i~fL~~lG~ 117 (377)
++.++|++|..+ ++++.++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 445555555555 3345555555555554
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=94.02 E-value=0.67 Score=44.89 Aligned_cols=202 Identities=15% Similarity=0.182 Sum_probs=112.8
Q ss_pred HhCCCChHHHHHHHHhCCCeeccCCC---C----chhhHHHHHH--hcCCCCchhhhhhhcccccchhhhhccc-hhHHH
Q 047553 77 HNVGFSDTHIQLTVTSRPTILFSDVD---K----TLKPKIEFFQ--HLGLVGSDLGKFISKNPSLFAASLERKL-IPCVE 146 (377)
Q Consensus 77 ~~lG~~~~~i~~ii~~~P~lL~~~~~---~----~l~~~i~fL~--~lG~s~~~l~~ii~~~P~lL~~s~~~~l-~p~v~ 146 (377)
..+|+....+...+.++|.++....+ . .+-+...-|. +..+-.+.-..++.+=-.+|.++.++.| ..++.
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 46899778899999999999876431 1 1445555553 2222222224555555567777776553 23455
Q ss_pred HHH-HHhcCCCCchHHHHHHHhccccccccc-cc-cchhhhHHHHHHcCCCchhHhhhh-----------------hhCC
Q 047553 147 ILK-KILVDDSNNEDLTRVFRRCCWNLIMDT-EK-SGLLRNIEYLKSCGIVGSQLSMLL-----------------VWQP 206 (377)
Q Consensus 147 ~L~-~~g~~~~~~~~i~~~l~~~P~lL~~~~-~~-~~l~~~v~~L~~lG~~~~~i~~ll-----------------~~~P 206 (377)
.++ ++|++ ++-...++.+||..+.... ++ .....-+.|=.++.++.-+-.... ..+|
T Consensus 125 ~l~~dLGLP---~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp 201 (335)
T PF11955_consen 125 HLRRDLGLP---DDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFP 201 (335)
T ss_pred HHHHHcCCC---hhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCC
Confidence 565 68998 8888889999999886532 10 112222222122334333222221 1222
Q ss_pred eeeEeehhhHHHHHHHHHhcC----------CCCchh-hHHHHHHHHH---hC--CHHHHHHHHHHHH-HcCCCHHHHHH
Q 047553 207 RLFCYKELKIRHLVSRLLDMG----------FSTNSR-MFVYGLVVLS---CL--NEETFGRKLELFR-SYGFSKEEVLQ 269 (377)
Q Consensus 207 ~il~~s~~~l~~~v~~l~~lG----------~~~~~~-~~~~~p~~l~---~~--s~~~l~~k~~~L~-~lG~s~~~v~~ 269 (377)
.=+.. ..+..+.++-++++- +++++. +-.++..++. .. .......++..|+ ++|++. .+..
T Consensus 202 ~G~~l-~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~-k~~~ 279 (335)
T PF11955_consen 202 KGFRL-KKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQ-KFRR 279 (335)
T ss_pred CCccc-cHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcH-HHHH
Confidence 11111 134566666666653 333332 2334433321 21 2223456677776 899984 6888
Q ss_pred HHHhCCcccccCHH
Q 047553 270 MFRKAPLILKASEE 283 (377)
Q Consensus 270 ~i~~~P~iL~~s~~ 283 (377)
++.+||.||-.|..
T Consensus 280 ~l~rHPgIFYvS~k 293 (335)
T PF11955_consen 280 LLLRHPGIFYVSLK 293 (335)
T ss_pred HHHhCCCeEEEecc
Confidence 99999999998864
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=89.83 E-value=1.6 Score=38.09 Aligned_cols=16 Identities=25% Similarity=0.563 Sum_probs=11.9
Q ss_pred HHHHHHcCCCHHHHHH
Q 047553 254 LELFRSYGFSKEEVLQ 269 (377)
Q Consensus 254 ~~~L~~lG~s~~~v~~ 269 (377)
.+||.++|++.+++..
T Consensus 151 ~~~l~~~g~~~~~~~~ 166 (172)
T cd04790 151 QEFLQSLGIPEDEIER 166 (172)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 5677888888877764
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=88.24 E-value=1.2 Score=39.00 Aligned_cols=117 Identities=9% Similarity=0.072 Sum_probs=65.8
Q ss_pred hHHHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHH----HhcCCCCchHHHHHHHhccccccccccccchh
Q 047553 107 PKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKK----ILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLL 182 (377)
Q Consensus 107 ~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~----~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~ 182 (377)
..|..|+++|++-++|..++..... +....+..+.+.+.+ +--. .+.+..++...+..-.... -+..
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~---~~~l~~ll~~~~~~~~~~~--V~~~ 119 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQ---QRAIATLLKQPTLLKEQRL--VTKE 119 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhhcccccc--CCHH
Confidence 6777888999999999998876553 222234445544443 2233 3444554444333311111 1245
Q ss_pred hhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCchhhHHHH
Q 047553 183 RNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTNSRMFVYG 238 (377)
Q Consensus 183 ~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~~~~~~~~ 238 (377)
..++.++..|+++++..+.-..+- ...| +.=.+||..+|++++++.-.+.
T Consensus 120 ~w~~l~~~~g~~~~~m~~wh~~fe---~~~p---~~h~~~l~~~g~~~~~~~~ir~ 169 (172)
T cd04790 120 KWVAILKAAGMDEADMRRWHIEFE---KMEP---EAHQEFLQSLGIPEDEIERIRA 169 (172)
T ss_pred HHHHHHHHcCCChHHHHHHHHHHH---HhCc---HHHHHHHHHcCCCHHHHHHHHH
Confidence 566667778888877543322210 0111 1235789999999888754443
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=79.87 E-value=3.5 Score=34.54 Aligned_cols=31 Identities=19% Similarity=0.333 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCCccc
Q 047553 248 ETFGRKLELFRSYGFSKEEVLQMFRKAPLIL 278 (377)
Q Consensus 248 ~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL 278 (377)
..+..|++||++=|++.+||...+.+.+.--
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3578899999999999999999999877655
No 13
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=77.28 E-value=4.3 Score=33.95 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=18.9
Q ss_pred ccCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCCC
Q 047553 60 FSRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRPT 95 (377)
Q Consensus 60 ~P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P~ 95 (377)
.|.+.+ .-.+.+++||++.|++.+||..++.+.+.
T Consensus 15 ~p~V~~-sp~~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 15 DPKVRN-SPLEKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp TTTCCC-S-HHHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred Cccccc-CCHHHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 444443 34556677777777777777766665543
No 14
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=69.66 E-value=15 Score=34.44 Aligned_cols=79 Identities=20% Similarity=0.217 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHH-HcC-CCHHHHHHHHHhCCcccccCHHHHHHHHHHHHHhhCCChH-HHhhCCccccccccccchhhHH
Q 047553 247 EETFGRKLELFR-SYG-FSKEEVLQMFRKAPLILKASEERLQLGLEFFLKEIECEKS-VLVRIPICLACSIENRVIPRYR 323 (377)
Q Consensus 247 ~~~l~~k~~~L~-~lG-~s~~~v~~~i~~~P~iL~~s~~~L~~k~~fL~~~~g~~~~-~i~~~P~~L~~Sle~ri~pR~~ 323 (377)
.-+|++++.|.. ..| |+.-.|.+=|...|.+++++.++++.|.+-|.+-+|+++. ..-+||.=|+- --..|.-
T Consensus 70 ~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLSG----GQQQRVG 145 (309)
T COG1125 70 PVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELSG----GQQQRVG 145 (309)
T ss_pred HHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcCc----chhhHHH
Confidence 346777787775 555 4555677778899999999999999999999999999885 45678876653 3445656
Q ss_pred HHHHHH
Q 047553 324 VFQIIM 329 (377)
Q Consensus 324 ~l~~L~ 329 (377)
+.++|.
T Consensus 146 v~RALA 151 (309)
T COG1125 146 VARALA 151 (309)
T ss_pred HHHHHh
Confidence 665553
No 15
>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=66.42 E-value=20 Score=34.76 Aligned_cols=220 Identities=21% Similarity=0.237 Sum_probs=119.9
Q ss_pred HHHHHHHhCCCeeccCCCCchhhHHHHH-HhcCCCCchhhhhhhcccccchhhh-h------ccchhHHHHHHH--HhcC
Q 047553 85 HIQLTVTSRPTILFSDVDKTLKPKIEFF-QHLGLVGSDLGKFISKNPSLFAASL-E------RKLIPCVEILKK--ILVD 154 (377)
Q Consensus 85 ~i~~ii~~~P~lL~~~~~~~l~~~i~fL-~~lG~s~~~l~~ii~~~P~lL~~s~-~------~~l~p~v~~L~~--~g~~ 154 (377)
.+..+|.+.|.= .+ .+. .+.-+ ..+|+.+..+...|.++|.++.... . =.+.+...-|.+ ..+-
T Consensus 22 ~l~~~i~~~p~~---~~--pl~-~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~ 95 (335)
T PF11955_consen 22 RLKDLILSQPSH---SL--PLR-DLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVR 95 (335)
T ss_pred HHHHHHHcCCCC---cc--cHH-HHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHH
Confidence 345667777751 11 122 22333 3699977999999999999987533 1 114444444322 1111
Q ss_pred CCCchHHHHHHHhccccccccccccchhhhHHHHH-HcCCCchhHhhhhhhCCeeeEeeh----hhHHHHHHHHHhcCCC
Q 047553 155 DSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLK-SCGIVGSQLSMLLVWQPRLFCYKE----LKIRHLVSRLLDMGFS 229 (377)
Q Consensus 155 ~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~-~lG~~~~~i~~ll~~~P~il~~s~----~~l~~~v~~l~~lG~~ 229 (377)
.+.-..++.+--.+|.++.+..--..+|..++ ++|+|.+-...++.++|..|.... ...-+.+.|=.++.++
T Consensus 96 ---~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs 172 (335)
T PF11955_consen 96 ---EEMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVS 172 (335)
T ss_pred ---HhChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcC
Confidence 11112333333447777777233356677787 599999999999999999987543 0011111111112222
Q ss_pred Cchh------------------hHHHH-HHHHHhCCHHHHHHHHHHHHHc----------CCC---HHHHHHHHHhCCcc
Q 047553 230 TNSR------------------MFVYG-LVVLSCLNEETFGRKLELFRSY----------GFS---KEEVLQMFRKAPLI 277 (377)
Q Consensus 230 ~~~~------------------~~~~~-p~~l~~~s~~~l~~k~~~L~~l----------G~s---~~~v~~~i~~~P~i 277 (377)
.-+. .|.-. |.- .......+.+++-++++ |++ .+.=...+.-.=.+
T Consensus 173 ~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G--~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHEl 250 (335)
T PF11955_consen 173 ALEKRAEKEYREKREDGFDRPLAFPVSFPKG--FRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHEL 250 (335)
T ss_pred ccchhhhhccccccccccCCceeeeecCCCC--ccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHH
Confidence 1111 11100 000 11234555555555543 111 11112233333346
Q ss_pred cccCHHH--HHHHHHHHHHhhCCChH---HHhhCCcccccccc
Q 047553 278 LKASEER--LQLGLEFFLKEIECEKS---VLVRIPICLACSIE 315 (377)
Q Consensus 278 L~~s~~~--L~~k~~fL~~~~g~~~~---~i~~~P~~L~~Sle 315 (377)
|++.+++ ...++..+.+++|++.+ -+.++|.++-.|..
T Consensus 251 LSLTveKr~~~~~L~~fr~ef~lp~k~~~~l~rHPgIFYvS~k 293 (335)
T PF11955_consen 251 LSLTVEKRTEVDHLTHFRKEFGLPQKFRRLLLRHPGIFYVSLK 293 (335)
T ss_pred HHhhhhhhccHHHHHHHHHHhCCcHHHHHHHHhCCCeEEEecc
Confidence 7777643 56889999999999975 47899999999864
No 16
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=62.45 E-value=16 Score=28.32 Aligned_cols=23 Identities=26% Similarity=0.330 Sum_probs=12.8
Q ss_pred hhhHHHHHHhcCCCCchhhhhhh
Q 047553 105 LKPKIEFFQHLGLVGSDLGKFIS 127 (377)
Q Consensus 105 l~~~i~fL~~lG~s~~~l~~ii~ 127 (377)
+...+.||.+.|++.....++..
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~ 30 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYK 30 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Confidence 55566777777777666665553
No 17
>PF11181 YflT: Heat induced stress protein YflT
Probab=60.95 E-value=38 Score=26.61 Aligned_cols=79 Identities=19% Similarity=0.226 Sum_probs=43.9
Q ss_pred cchhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHH--HhcCCCCchhhHHHHHHHHHhCCHHHHHHHHHH
Q 047553 179 SGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRL--LDMGFSTNSRMFVYGLVVLSCLNEETFGRKLEL 256 (377)
Q Consensus 179 ~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l--~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~ 256 (377)
..+...|+-|+.-|+..++| .+++.+.+..+..-+.- ...|.++. -|.....-+.....+.++.+
T Consensus 10 ~E~~~~I~~L~~~Gy~~ddI--------~Vva~d~~~~~~l~~~t~~~~~~~~~~--~~~d~~~~~f~~~~d~~~~~--- 76 (103)
T PF11181_consen 10 EEALSAIEELKAQGYSEDDI--------YVVAKDKDRTERLADQTDTNTVGASEE--SFWDKIKNFFTSGGDELRSK--- 76 (103)
T ss_pred HHHHHHHHHHHHcCCCcccE--------EEEEcCchHHHHHHHhcCCceeccccc--cHHHHHHHhccCCcHHHHHH---
Confidence 35888899999999999987 44554444333222211 11233232 23333333333345555544
Q ss_pred HHHcCCCHHHHHHH
Q 047553 257 FRSYGFSKEEVLQM 270 (377)
Q Consensus 257 L~~lG~s~~~v~~~ 270 (377)
|.++|++.+++.+.
T Consensus 77 l~~lGl~~~ea~~y 90 (103)
T PF11181_consen 77 LESLGLSEDEAERY 90 (103)
T ss_pred HHHcCCCHHHHHHH
Confidence 45899998877654
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=60.91 E-value=14 Score=23.19 Aligned_cols=23 Identities=26% Similarity=0.512 Sum_probs=16.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 047553 252 RKLELFRSYGFSKEEVLQMFRKA 274 (377)
Q Consensus 252 ~k~~~L~~lG~s~~~v~~~i~~~ 274 (377)
.+++-|.++||+.+++.+.+..+
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 45677778888888887777664
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=60.80 E-value=15 Score=22.77 Aligned_cols=23 Identities=39% Similarity=0.676 Sum_probs=17.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 047553 252 RKLELFRSYGFSKEEVLQMFRKA 274 (377)
Q Consensus 252 ~k~~~L~~lG~s~~~v~~~i~~~ 274 (377)
.+++-|.++||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45677778888888887777664
No 20
>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=59.41 E-value=17 Score=24.30 Aligned_cols=41 Identities=22% Similarity=0.372 Sum_probs=29.1
Q ss_pred HHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCc
Q 047553 188 LKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTN 231 (377)
Q Consensus 188 L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~ 231 (377)
-+.+|++...+.+++...|. .++++-+...+..+++|+.++
T Consensus 6 A~~agvS~~TVSr~ln~~~~---vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGPPR---VSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHTSSHHHHHHHHTTCSS---STHHHHHHHHHHHHHHTB-SS
T ss_pred HHHHCcCHHHHHHHHhCCCC---CCHHHHHHHHHHHHHHCCCCC
Confidence 35589999999998876653 366666666677788887653
No 21
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=58.72 E-value=33 Score=26.51 Aligned_cols=65 Identities=18% Similarity=0.321 Sum_probs=34.0
Q ss_pred hHHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHH-hcC
Q 047553 38 FLNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQ-HLG 116 (377)
Q Consensus 38 ~v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~-~lG 116 (377)
++.|| ..+|++...+.++.+.+ | ++...++..+|..|..++..-=-.+++.+. .+|
T Consensus 11 ~~~~L-~~~gl~~~~a~kl~~~y-------------------g---~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 11 LMAFL-QEYGLSPKLAMKLYKKY-------------------G---DDAIEILKENPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHH-HHTT--HHHHHHHHHHH-----------------------TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHH-HHcCCCHHHHHHHHHHH-------------------h---HHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence 45666 66777776666666544 1 133356778888888866543344555553 577
Q ss_pred CCCchhhhh
Q 047553 117 LVGSDLGKF 125 (377)
Q Consensus 117 ~s~~~l~~i 125 (377)
++..+-.++
T Consensus 68 ~~~~d~~Ri 76 (94)
T PF14490_consen 68 IEPDDPRRI 76 (94)
T ss_dssp --TT-HHHH
T ss_pred CCCCCHHHH
Confidence 776665544
No 22
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=58.11 E-value=28 Score=25.52 Aligned_cols=49 Identities=27% Similarity=0.449 Sum_probs=27.7
Q ss_pred hhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhhhHHHHHHcCCCchhHhhhh
Q 047553 142 IPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLL 202 (377)
Q Consensus 142 ~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll 202 (377)
.|.+..|++..++ ++.|..++.. |+ .+-...+..+..+|++++.+..++
T Consensus 2 NPIia~LKehnvs---d~qi~elFq~----lT-----~NPl~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 2 NPIIAILKEHNVS---DEQINELFQA----LT-----QNPLAAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred chHHHHHHHcCCC---HHHHHHHHHH----Hh-----hCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3556666777776 6666665543 11 123334555566777777665544
No 23
>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=57.65 E-value=28 Score=37.56 Aligned_cols=84 Identities=15% Similarity=0.156 Sum_probs=56.2
Q ss_pred hhHHHhHhh--CCCChhhHHHHHhhccCCCCCCChHHHHHHHHhC-CCChHHHHHHHHhCCCeeccCCCCchhhHHHHHH
Q 047553 37 IFLNFLIKT--LNIPKSRALPISNKFSRIKSLEKPETVRQFLHNV-GFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQ 113 (377)
Q Consensus 37 ~~v~~L~~~--~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~l-G~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~ 113 (377)
..+.||-+. -|+-+..+.+++..+..= ..+.++.-.+-|.++ |+++.....+...+.. .......+.||.
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg~~-~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~~~~~L~ 151 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFGEA-AFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERRLLAGLQ 151 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhCHh-HHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHHHHHHHH
Confidence 456899332 388899999999877431 112222223345564 9999999988887732 123678889999
Q ss_pred hcCCCCchhhhhhh
Q 047553 114 HLGLVGSDLGKFIS 127 (377)
Q Consensus 114 ~lG~s~~~l~~ii~ 127 (377)
++|++.....++..
T Consensus 152 ~~gi~~~~a~ki~~ 165 (720)
T TIGR01448 152 GLGIGIKLAQRIYK 165 (720)
T ss_pred HcCCCHHHHHHHHH
Confidence 99999877666543
No 24
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=56.83 E-value=42 Score=33.63 Aligned_cols=60 Identities=12% Similarity=0.262 Sum_probs=40.4
Q ss_pred CCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHh
Q 047553 47 NIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQH 114 (377)
Q Consensus 47 Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~ 114 (377)
|...+....+-..+..+....-.+..+..+.++||.+++-+..++.|-. ++...++|+.+
T Consensus 281 g~~deAye~le~a~~~l~elki~d~~lsllv~mGfeesdaRlaLRsc~g--------~Vd~AvqfI~e 340 (568)
T KOG2561|consen 281 GQRDEAYEALESAHAKLLELKINDETLSLLVGMGFEESDARLALRSCNG--------DVDSAVQFIIE 340 (568)
T ss_pred CCcHHHHHHHHHHHHHHHHeeccchHHHHHHHcCCCchHHHHHHHhccc--------cHHHHHHHHHH
Confidence 5555555544433434444455677899999999999998888887754 35566777654
No 25
>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=56.57 E-value=19 Score=22.38 Aligned_cols=23 Identities=39% Similarity=0.590 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhC
Q 047553 252 RKLELFRSYGFSKEEVLQMFRKA 274 (377)
Q Consensus 252 ~k~~~L~~lG~s~~~v~~~i~~~ 274 (377)
.+++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45677778888888777776653
No 26
>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=53.98 E-value=34 Score=33.79 Aligned_cols=134 Identities=15% Similarity=0.186 Sum_probs=0.0
Q ss_pred hHHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCC-----------------------------------
Q 047553 38 FLNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFS----------------------------------- 82 (377)
Q Consensus 38 ~v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~----------------------------------- 82 (377)
+|+-+ -+.|+.++++.+.++.. ..|++..++|| --|+.
T Consensus 159 ~I~~i-~eMGf~R~qV~~ALRAa-----fNNPdRAVEYL-~tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~a~~ 231 (378)
T TIGR00601 159 TIEEI-MEMGYEREEVERALRAA-----FNNPDRAVEYL-LTGIPEDPEQPEPVQQTAASTAAATTETPQHGSVFEQAAQ 231 (378)
T ss_pred HHHHH-HHhCCCHHHHHHHHHHH-----hCCHHHHHHHH-HhCCCccccccccCCCcccccccccCCCCCCcchhhhhhc
Q ss_pred -------------------------hHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCCCCchhhhhhhcccccchhhh
Q 047553 83 -------------------------DTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASL 137 (377)
Q Consensus 83 -------------------------~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~ 137 (377)
-.+++.+|..+|++|- .+|+.+|-+..++..+|..+|.-|..-+
T Consensus 232 ~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~-----------~lLqql~~~nP~l~q~I~~n~e~Fl~ll 300 (378)
T TIGR00601 232 GGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLP-----------PLLQQIGQENPQLLQQISQHPEQFLQML 300 (378)
T ss_pred ccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHH-----------HHHHHHHhhCHHHHHHHHHCHHHHHHHh
Q ss_pred hccchhHHHHHHHHhc--CCCCchHHHHHHHhccc-------cccccccccchhhhHHHHHHcCCCchhHhhhhhhC
Q 047553 138 ERKLIPCVEILKKILV--DDSNNEDLTRVFRRCCW-------NLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQ 205 (377)
Q Consensus 138 ~~~l~p~v~~L~~~g~--~~~~~~~i~~~l~~~P~-------lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~ 205 (377)
.... |- . ..+......-.+. .+....+ + +..|+.|.+|||++..+......|
T Consensus 301 ~~~~----------~~~~~---~~~~~~~~~~~~~~~~~~~~~i~lT~e-E--~~AIeRL~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 301 NEPV----------GELAG---ESDMEGGVGAIAEAGLPQMNQIQVTPE-E--KEAIERLCALGFDRGLVIQAYFAC 361 (378)
T ss_pred cCcc----------ccccc---ccccccccccccccCcccccccccCHH-H--HHHHHHHHHcCCCHHHHHHHHHhc
No 27
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=48.57 E-value=34 Score=29.54 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=16.6
Q ss_pred hhhhCCeeeEeehhhHHHHHHHHHhcCCCC
Q 047553 201 LLVWQPRLFCYKELKIRHLVSRLLDMGFST 230 (377)
Q Consensus 201 ll~~~P~il~~s~~~l~~~v~~l~~lG~~~ 230 (377)
-+...|-+.+.+.+.+...++.+++-|+++
T Consensus 69 ~iM~spvv~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 69 TIMHSPVVSVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred hhccCCeeEECchhhHHHHHHHHHHcCCcc
Confidence 344455555555555666666666666553
No 28
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=48.06 E-value=30 Score=32.44 Aligned_cols=98 Identities=15% Similarity=0.235 Sum_probs=55.9
Q ss_pred hhhhhhhhhhcccCCCCCCC----chhHHHhHhhCCCChhhHHHHH-hhccCCCCCCChHHHHHHHHhCCCCh------H
Q 047553 16 AIKSLFSFFASLSKTPNSTN----FIFLNFLIKTLNIPKSRALPIS-NKFSRIKSLEKPETVRQFLHNVGFSD------T 84 (377)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~----~~~v~~L~~~~Gls~~~~~~i~-~~~P~ll~~~~~~~~l~~L~~lG~~~------~ 84 (377)
||+++++|- ||++-| +-||+++..++|--.-++..+- .-+|.+..... ..+-+-|+.+||-- +
T Consensus 117 P~E~lfSFi-----CSSNNNIaRIT~Mve~fc~~fG~~i~~~dg~~~h~FPsl~~L~g-~~~Ea~LR~~gfGYRAkYI~~ 190 (323)
T KOG2875|consen 117 PIECLFSFI-----CSSNNNIARITGMVERFCQAFGPRIIQLDGVDYHGFPSLQALAG-PEVEAELRKLGFGYRAKYISA 190 (323)
T ss_pred cHHHHHHHH-----hcCCCcHHHHHHHHHHHHHhhCcceEeecCcccccCccHHHhcC-cHhHHHHHHcCcchhHHHHHH
Confidence 566666665 555544 5678988899998877777663 34566543222 12445577777762 2
Q ss_pred HHHHHHHhCCCeeccCCCCchhhHHHHHHhc-CCCCchhhhhhhccccc
Q 047553 85 HIQLTVTSRPTILFSDVDKTLKPKIEFFQHL-GLVGSDLGKFISKNPSL 132 (377)
Q Consensus 85 ~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~l-G~s~~~l~~ii~~~P~l 132 (377)
..+.+....+. .+||+++ +.+-+++++.+..-|.+
T Consensus 191 ta~~l~~~~g~-------------~~wLqsl~~~~yeear~~L~~lpGV 226 (323)
T KOG2875|consen 191 TARALQEKQGG-------------LAWLQSLRKSSYEEAREALCSLPGV 226 (323)
T ss_pred HHHHHHHhccc-------------chHHHHHhcccHHHHHHHHhcCCCC
Confidence 22333333333 4566653 45556666666555543
No 29
>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=46.63 E-value=31 Score=22.99 Aligned_cols=24 Identities=25% Similarity=0.335 Sum_probs=16.1
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhC
Q 047553 70 ETVRQFLHNVGFSDTHIQLTVTSR 93 (377)
Q Consensus 70 ~~~l~~L~~lG~~~~~i~~ii~~~ 93 (377)
+.+++-|.++||++.++.+++..-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 345667777888888777777654
No 30
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=46.19 E-value=70 Score=30.29 Aligned_cols=67 Identities=9% Similarity=0.099 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHhhCCChHHHhhCCccccccccccchhhHHHHHHHHHCCCCCCCCCccchhccchhhHHHHhccc
Q 047553 284 RLQLGLEFFLKEIECEKSVLVRIPICLACSIENRVIPRYRVFQIIMSRGMFKKDCSFPSMLLLSEGNFLQKFVLS 358 (377)
Q Consensus 284 ~L~~k~~fL~~~~g~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~~~~ 358 (377)
-++.+++.+.+ .|++.+.|+-=|- +++ .+....-+++++.|..-. ...++.++..|.++|...+...
T Consensus 164 ~l~~~i~~a~~-~GI~~~~IilDPG-iGF--~k~~~~n~~ll~~l~~l~----~lg~Pilvg~SRKsfig~~~~~ 230 (282)
T PRK11613 164 YFIEQIARCEA-AGIAKEKLLLDPG-FGF--GKNLSHNYQLLARLAEFH----HFNLPLLVGMSRKSMIGQLLNV 230 (282)
T ss_pred HHHHHHHHHHH-cCCChhhEEEeCC-CCc--CCCHHHHHHHHHHHHHHH----hCCCCEEEEecccHHHHhhcCC
Confidence 45677887765 7999999888785 454 445566666666554421 2345678899999999877653
No 31
>PRK14136 recX recombination regulator RecX; Provisional
Probab=45.46 E-value=2.8e+02 Score=26.55 Aligned_cols=133 Identities=9% Similarity=0.144 Sum_probs=70.9
Q ss_pred HHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhhhHHHH
Q 047553 109 IEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYL 188 (377)
Q Consensus 109 i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L 188 (377)
+.+|..---+..+|.+-|.+. .++ ++.+...|++|++.|.-+ +...+....+. .. ... . -.....-|
T Consensus 169 L~lLSrReRSe~ELr~KL~kk----G~~-ee~IE~VIerLke~gYLD--DeRFAesyVr~-R~--~kk--G-p~rIrqEL 235 (309)
T PRK14136 169 LGYLSRREYSRAELARKLAPY----ADE-SDSVEPLLDALEREGWLS--DARFAESLVHR-RA--SRV--G-SARIVSEL 235 (309)
T ss_pred HHHhhcccccHHHHHHHHHHc----CCC-HHHHHHHHHHHHHcCCcC--HHHHHHHHHHH-Hh--hch--h-HHHHHHHH
Confidence 333333334555555555433 122 235677788888888764 66666665543 11 111 1 22334457
Q ss_pred HHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHH-hcCCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHH
Q 047553 189 KSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLL-DMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEV 267 (377)
Q Consensus 189 ~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~-~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v 267 (377)
+.-|++.+.|...+... .++.++.....++ .++-.+. ........+.||..-||+.+.|
T Consensus 236 rQKGId~eLIEqALeei------eEDE~E~A~~L~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I 295 (309)
T PRK14136 236 KRHAVGDALVESVGAQL------RETEFERAQAVWRKKFGALPQ--------------TPAERAKQARFLAARGFSSATI 295 (309)
T ss_pred HHcCCCHHHHHHHHHhc------cHhHHHHHHHHHHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHH
Confidence 77899988888776532 1111222222222 1221010 1122334478888999999999
Q ss_pred HHHHHhC
Q 047553 268 LQMFRKA 274 (377)
Q Consensus 268 ~~~i~~~ 274 (377)
.++|..+
T Consensus 296 ~~vLk~~ 302 (309)
T PRK14136 296 VKLLKVG 302 (309)
T ss_pred HHHHHhc
Confidence 8887654
No 32
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=45.17 E-value=37 Score=28.14 Aligned_cols=56 Identities=13% Similarity=0.228 Sum_probs=37.3
Q ss_pred chhHHHhHhhCCCChhhHHHHHhhccCCCCC--CChHHHHHHHHhCCCChHHHHHHHHh
Q 047553 36 FIFLNFLIKTLNIPKSRALPISNKFSRIKSL--EKPETVRQFLHNVGFSDTHIQLTVTS 92 (377)
Q Consensus 36 ~~~v~~L~~~~Gls~~~~~~i~~~~P~ll~~--~~~~~~l~~L~~lG~~~~~i~~ii~~ 92 (377)
|.--+|| +-.|++++.+..++.+.-.+... -+-+++-+.|..+|.+.++.+++...
T Consensus 67 P~l~~WL-~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~A 124 (129)
T PF13543_consen 67 PSLRQWL-RVVGLRPESIQAILSKVLTLEALLEMSDEELKEILNRCGAREEECRRLCRA 124 (129)
T ss_pred CcHHHHh-hhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3344788 88899999888887543222211 23345677777888888888887653
No 33
>PHA02591 hypothetical protein; Provisional
Probab=44.33 E-value=62 Score=24.25 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=17.5
Q ss_pred CeeeEeehhhHHHHHHHHHhcCCCCch
Q 047553 206 PRLFCYKELKIRHLVSRLLDMGFSTNS 232 (377)
Q Consensus 206 P~il~~s~~~l~~~v~~l~~lG~~~~~ 232 (377)
-+-|..|++.+.....-|.+.|++..+
T Consensus 38 ~ryfi~~~dd~~~vA~eL~eqGlSqeq 64 (83)
T PHA02591 38 TRYFVESEDDLISVTHELARKGFTVEK 64 (83)
T ss_pred EEEEEeccchHHHHHHHHHHcCCCHHH
Confidence 355566666666666777777776554
No 34
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=39.69 E-value=53 Score=23.70 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=29.3
Q ss_pred HHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCc
Q 047553 189 KSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTN 231 (377)
Q Consensus 189 ~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~ 231 (377)
+.+|++...|.+++...+.+ ++++.+...+.++++|+.++
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPN 47 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCC
Confidence 44788888888888766654 56666777777888888665
No 35
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.86 E-value=2.4e+02 Score=25.06 Aligned_cols=24 Identities=25% Similarity=0.245 Sum_probs=13.0
Q ss_pred hhHHHHHHhcCCCCchhhhhhhcc
Q 047553 106 KPKIEFFQHLGLVGSDLGKFISKN 129 (377)
Q Consensus 106 ~~~i~fL~~lG~s~~~l~~ii~~~ 129 (377)
...+..|.++|++..++.+++...
T Consensus 149 ~e~~~aL~~LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 149 SDILATLTALGYSSSEAAKAISSL 172 (194)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 445555555555555555555443
No 36
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.69 E-value=1.2e+02 Score=26.74 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=15.2
Q ss_pred hhhHHHHHHhcCCCCchhhhhhhcc
Q 047553 105 LKPKIEFFQHLGLVGSDLGKFISKN 129 (377)
Q Consensus 105 l~~~i~fL~~lG~s~~~l~~ii~~~ 129 (377)
+...+.+|.++|++..++.+++...
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556666666666666666665544
No 37
>PRK14135 recX recombination regulator RecX; Provisional
Probab=32.36 E-value=4e+02 Score=24.49 Aligned_cols=78 Identities=15% Similarity=0.098 Sum_probs=39.7
Q ss_pred hhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhh-HHHHHHHHHhcCCCCchhhHHHHHHHHHhCCHHHHHHH-HHHHHH
Q 047553 182 LRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELK-IRHLVSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRK-LELFRS 259 (377)
Q Consensus 182 ~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~-l~~~v~~l~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k-~~~L~~ 259 (377)
.....+|..-||+.+.|..++.... .....+. ++..... ..+....+....+...+.| ..||.+
T Consensus 179 ~Ki~~~L~rkGf~~~~I~~~l~~~~--~e~d~~~e~e~l~~~------------~~k~~~k~~~~~~~k~k~K~~~~L~r 244 (263)
T PRK14135 179 QKIIQSLLTKGFSYEVIKAALEELD--LEQDEEEEQELLQKE------------LEKAYRKYSKYDGYELKQKLKQALYR 244 (263)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHcc--cCCChHHHHHHHHHH------------HHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 3446778888999888887775431 0001111 1110000 0001111111122344444 567779
Q ss_pred cCCCHHHHHHHHHh
Q 047553 260 YGFSKEEVLQMFRK 273 (377)
Q Consensus 260 lG~s~~~v~~~i~~ 273 (377)
-||+.+.|..++..
T Consensus 245 rGF~~~~I~~~l~~ 258 (263)
T PRK14135 245 KGFSYDDIDSFLRE 258 (263)
T ss_pred CCCCHHHHHHHHHH
Confidence 99999988887765
No 38
>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=32.30 E-value=72 Score=21.02 Aligned_cols=40 Identities=18% Similarity=0.327 Sum_probs=26.9
Q ss_pred HHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCc
Q 047553 189 KSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTN 231 (377)
Q Consensus 189 ~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~ 231 (377)
+.+|++...+.+++...+ ..+.+......+...++|+.++
T Consensus 5 ~~~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 5 RAAGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred HHHCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCC
Confidence 457888888888876655 2345556666666777777655
No 39
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.01 E-value=2.3e+02 Score=24.95 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=15.4
Q ss_pred hhhHHHHHHhcCCCCchhhhhhhcc
Q 047553 105 LKPKIEFFQHLGLVGSDLGKFISKN 129 (377)
Q Consensus 105 l~~~i~fL~~lG~s~~~l~~ii~~~ 129 (377)
....++-|.++|+++.++.+++..-
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 3455666666666666666666554
No 40
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=31.20 E-value=91 Score=20.15 Aligned_cols=29 Identities=14% Similarity=0.359 Sum_probs=21.0
Q ss_pred HHHHHHHHHH-HcCCCHHHHHHHHHhCCcc
Q 047553 249 TFGRKLELFR-SYGFSKEEVLQMFRKAPLI 277 (377)
Q Consensus 249 ~l~~k~~~L~-~lG~s~~~v~~~i~~~P~i 277 (377)
++-.....|. ++|++..+..+++..+|..
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 3445567787 8999999999999999975
No 41
>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=31.18 E-value=1.1e+02 Score=24.97 Aligned_cols=71 Identities=18% Similarity=0.251 Sum_probs=31.8
Q ss_pred chhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHH
Q 047553 180 GLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFRS 259 (377)
Q Consensus 180 ~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~ 259 (377)
++--..+.|+ -|++.++|..+=.-.|++| .++++.++.=+++. .. ..+.-...+.-.++
T Consensus 12 Rlf~i~eAlr-rG~sveeI~e~T~ID~wFL----~~i~~Iv~~e~~L~-------------~~---~~~~~~~~L~~aK~ 70 (123)
T PF02787_consen 12 RLFAIAEALR-RGYSVEEIHELTKIDPWFL----EQIKNIVDMEKELK-------------EY---LNELDPELLRKAKR 70 (123)
T ss_dssp HHHHHHHHHH-TTB-HHHHHHHH---HHHH----HHHHHHHHHHHHHH-------------HH---GGG--HHHHHHHHH
T ss_pred HHHHHHHHHH-cCCCHHHHHHHHCccHHHH----HHHHHHHHHHHHHH-------------Hh---hccchHHHHHHHHH
Confidence 3444444443 4888888887766666655 23333333211110 00 00111122334458
Q ss_pred cCCCHHHHHHHH
Q 047553 260 YGFSKEEVLQMF 271 (377)
Q Consensus 260 lG~s~~~v~~~i 271 (377)
+|||..+|+++.
T Consensus 71 ~GFsD~~IA~l~ 82 (123)
T PF02787_consen 71 LGFSDRQIARLW 82 (123)
T ss_dssp TT--HHHHHHHH
T ss_pred cCCCHHHHHhcc
Confidence 999999888763
No 42
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=31.02 E-value=2.2e+02 Score=21.00 Aligned_cols=39 Identities=13% Similarity=0.281 Sum_probs=17.3
Q ss_pred hhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCChHHHH
Q 047553 44 KTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFSDTHIQ 87 (377)
Q Consensus 44 ~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~~~~i~ 87 (377)
+...+|++++..+.... .+++-........+|+..+.+.
T Consensus 9 Kehnvsd~qi~elFq~l-----T~NPl~AMa~i~qLGip~eKLQ 47 (82)
T PF11212_consen 9 KEHNVSDEQINELFQAL-----TQNPLAAMATIQQLGIPQEKLQ 47 (82)
T ss_pred HHcCCCHHHHHHHHHHH-----hhCHHHHHHHHHHcCCCHHHHH
Confidence 44555555554444322 1344444444445555544433
No 43
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=28.06 E-value=1.8e+02 Score=20.75 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=29.8
Q ss_pred hhCCCChhhHHHHHhhccCCCCCCChHHHHHHHH-hCCCChHHHHHHH
Q 047553 44 KTLNIPKSRALPISNKFSRIKSLEKPETVRQFLH-NVGFSDTHIQLTV 90 (377)
Q Consensus 44 ~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~-~lG~~~~~i~~ii 90 (377)
+..|-+.++...++...| ...+..++++||+ ++|+...+-..|+
T Consensus 11 ~kTGk~~~~W~~~~~~~~---~~~k~~e~v~WLK~ehgLghGhA~Aiv 55 (61)
T PF14117_consen 11 KKTGKTLDEWLALAREGG---PLTKHGEIVAWLKDEHGLGHGHANAIV 55 (61)
T ss_pred HHHCcCHHHHHHHHHHhC---CCCcHHHHHHHHHHHHCCChHHHHHHH
Confidence 456778888777777776 2246777788886 4777766655544
No 44
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=27.18 E-value=1.4e+02 Score=28.75 Aligned_cols=117 Identities=13% Similarity=0.167 Sum_probs=67.6
Q ss_pred CCchhHHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCCCeecc------------C-
Q 047553 34 TNFIFLNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRPTILFS------------D- 100 (377)
Q Consensus 34 ~~~~~v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~------------~- 100 (377)
+...+|.-+ -..|..++++.++++.. ..+++..++||- .|+....-.......|..... .
T Consensus 134 ~~e~~V~~I-m~MGy~re~V~~AlRAa-----fNNPeRAVEYLl-~GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~ 206 (340)
T KOG0011|consen 134 EYEQTVQQI-MEMGYDREEVERALRAA-----FNNPERAVEYLL-NGIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQG 206 (340)
T ss_pred hhHHHHHHH-HHhCccHHHHHHHHHHh-----hCChhhhHHHHh-cCCcccccCCcccCCcccCCCCCCCCChhhcCCcc
Confidence 444566666 36888888888777532 368888899885 244432100011111111111 1
Q ss_pred -CCCchhhHHHHHHhcCCCCchhhhhhhcccccchhhhhccchhHHHHHHHHhcCCCCchHHHHHHHhccccc
Q 047553 101 -VDKTLKPKIEFFQHLGLVGSDLGKFISKNPSLFAASLERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNL 172 (377)
Q Consensus 101 -~~~~l~~~i~fL~~lG~s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL 172 (377)
++..-..-++||++. -.-.+++.+|..||.+|.- .|+.+|-. .-.+.+.|..|+.-|
T Consensus 207 ~~~~~~~~~l~fLr~~-~qf~~lR~~iqqNP~ll~~-----------~Lqqlg~~---nP~L~q~Iq~nqe~F 264 (340)
T KOG0011|consen 207 AVEASGGDPLEFLRNQ-PQFQQLRQMIQQNPELLHP-----------LLQQLGKQ---NPQLLQLIQENQEAF 264 (340)
T ss_pred chhhhcCCchhhhhcc-HHHHHHHHHHhhCHHHHHH-----------HHHHHhhh---CHHHHHHHHHHHHHH
Confidence 111222447777753 1234678889999988652 56778887 778888888777533
No 45
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.13 E-value=1.3e+02 Score=28.42 Aligned_cols=27 Identities=26% Similarity=0.591 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 047553 247 EETFGRKLELFRSYGFSKEEVLQMFRK 273 (377)
Q Consensus 247 ~~~l~~k~~~L~~lG~s~~~v~~~i~~ 273 (377)
+..+..|.+||++-|++.+||...+.+
T Consensus 19 ~aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 19 DAPLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred cchHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 346777899999999999999877776
No 46
>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=26.71 E-value=98 Score=23.49 Aligned_cols=37 Identities=14% Similarity=0.420 Sum_probs=21.3
Q ss_pred HHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHh
Q 047553 74 QFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQH 114 (377)
Q Consensus 74 ~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~ 114 (377)
++-+.+|++..+|..+-..+|. +..+.....+..++.
T Consensus 18 ~laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~ 54 (86)
T cd08306 18 KLARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKK 54 (86)
T ss_pred HHHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHH
Confidence 3445677777777777777762 333334455544443
No 47
>PHA01351 putative minor structural protein
Probab=26.70 E-value=8.4e+02 Score=26.36 Aligned_cols=54 Identities=22% Similarity=0.119 Sum_probs=37.0
Q ss_pred HHHhHhhCCCChhhHHHHHhhc---cCCCC------------CCChHHHHHHHHhCCCChHHHHHHHHhC
Q 047553 39 LNFLIKTLNIPKSRALPISNKF---SRIKS------------LEKPETVRQFLHNVGFSDTHIQLTVTSR 93 (377)
Q Consensus 39 v~~L~~~~Gls~~~~~~i~~~~---P~ll~------------~~~~~~~l~~L~~lG~~~~~i~~ii~~~ 93 (377)
..-| +.+|++++=+..++... |.+.+ +-+.+..-.-|+.+|++++++.-++..+
T Consensus 647 itEL-KKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~y 715 (1070)
T PHA01351 647 ETEL-KKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKF 715 (1070)
T ss_pred HHHH-HHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556 77888888777666543 44432 1344556778889999999988887765
No 48
>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=25.88 E-value=1.1e+02 Score=18.47 Aligned_cols=17 Identities=29% Similarity=0.456 Sum_probs=10.2
Q ss_pred HHHcCCCHHHHHHHHHh
Q 047553 257 FRSYGFSKEEVLQMFRK 273 (377)
Q Consensus 257 L~~lG~s~~~v~~~i~~ 273 (377)
-+++|+|.+|++..+..
T Consensus 12 A~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 12 AKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHTT--HHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHh
Confidence 34688888888776654
No 49
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.71 E-value=3.7e+02 Score=23.70 Aligned_cols=25 Identities=12% Similarity=0.161 Sum_probs=16.8
Q ss_pred hhhHHHHHHhcCCCCchhhhhhhcc
Q 047553 105 LKPKIEFFQHLGLVGSDLGKFISKN 129 (377)
Q Consensus 105 l~~~i~fL~~lG~s~~~l~~ii~~~ 129 (377)
....++-|.++|+++.++.+++.+-
T Consensus 143 ~~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 143 YHESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556667777777777777776544
No 50
>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=25.68 E-value=1.8e+02 Score=22.64 Aligned_cols=40 Identities=10% Similarity=0.285 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHh
Q 047553 70 ETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQH 114 (377)
Q Consensus 70 ~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~ 114 (377)
+..-.+.+.+|++..+|..+-..+|.- .+.....+..++.
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~-----~eq~~qmL~~W~~ 59 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVT-----REQLYQMLLTWVN 59 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCC-----HHHHHHHHHHHHH
Confidence 445667778888888888888888762 2345566666654
No 51
>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=25.67 E-value=2.3e+02 Score=25.62 Aligned_cols=67 Identities=6% Similarity=0.019 Sum_probs=42.7
Q ss_pred hhhhhhhhh--hcc-cCCCCCCCch-hHHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCC
Q 047553 16 AIKSLFSFF--ASL-SKTPNSTNFI-FLNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFS 82 (377)
Q Consensus 16 ~~~~~~~~~--~~~-~~~~~~~~~~-~v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~ 82 (377)
|+..+|..+ -.+ -|=+.+++.. ..+.|++++|++++++.....+.-........+.++.|+..-|-.
T Consensus 50 plfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~ 120 (214)
T TIGR03060 50 PLFALGLVTVFDRFMEGYRPEEHLDALFDALCNSNGFDPEQLREDAKQLLEQAKGKGLDEILSWLTQANLS 120 (214)
T ss_pred chHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccC
Confidence 566666655 223 4444455543 448888999999999887776552222335677888888766533
No 52
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=24.79 E-value=1e+02 Score=35.08 Aligned_cols=82 Identities=21% Similarity=0.296 Sum_probs=50.7
Q ss_pred HHhHhhCCCChhhHHHHHhhc---cCCCCCCChHHHHHHHHhCCCChHHHHHHHHhCC-----------CeeccCC----
Q 047553 40 NFLIKTLNIPKSRALPISNKF---SRIKSLEKPETVRQFLHNVGFSDTHIQLTVTSRP-----------TILFSDV---- 101 (377)
Q Consensus 40 ~~L~~~~Gls~~~~~~i~~~~---P~ll~~~~~~~~l~~L~~lG~~~~~i~~ii~~~P-----------~lL~~~~---- 101 (377)
.-| +.+|++.+++..+.... -++.....+ -.+.|...||++.+|.++-..-| +.|..+.
T Consensus 717 ~~L-~~lG~~~~~i~~i~~~~~~~Gsl~~~~~i--~~~~l~~~Gf~~~~~~~~~~~l~~~fdi~~~fn~~~lg~~f~~~~ 793 (1220)
T PRK07562 717 EAL-RTLGYSESQIAEIEAYAVGHGTLNQAPGI--NHSTLKAKGFTDEKIEKVEAALKSAFDIKFAFNKWTLGEDFCKDT 793 (1220)
T ss_pred HHH-HHcCCCHHHHHHHHHHhhcCCCccCCCCC--CHHHHhhcCCcHHHHHHHHHHhhhhhhhhhhhcccccchhhhhhc
Confidence 445 78999999998887643 223221111 24578899999999887444333 3333222
Q ss_pred -----CCchhhHHHHHHhcCCCCchhhh
Q 047553 102 -----DKTLKPKIEFFQHLGLVGSDLGK 124 (377)
Q Consensus 102 -----~~~l~~~i~fL~~lG~s~~~l~~ 124 (377)
+.--.|-++.|..+|++.++|..
T Consensus 794 lg~~~~~~~~~~f~ll~~~g~t~~~i~a 821 (1220)
T PRK07562 794 LGIPAEQLNDPSFDLLEHLGFSKKDIEA 821 (1220)
T ss_pred ccCcHhhhccccchhhhhcccchhhHHH
Confidence 22224677788888988766644
No 53
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.47 E-value=1.5e+02 Score=26.16 Aligned_cols=54 Identities=19% Similarity=0.106 Sum_probs=37.7
Q ss_pred HHhHhhCCCChhhHHHHHhhccCCCC------------CCChHHHHHHHHhCCCChHHHHHHHHhC
Q 047553 40 NFLIKTLNIPKSRALPISNKFSRIKS------------LEKPETVRQFLHNVGFSDTHIQLTVTSR 93 (377)
Q Consensus 40 ~~L~~~~Gls~~~~~~i~~~~P~ll~------------~~~~~~~l~~L~~lG~~~~~i~~ii~~~ 93 (377)
+.|.+--|+++..+.+++..+-.-.. ....+.++.+|.++|+++.++.+++...
T Consensus 108 ~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 108 KALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34533348888888888754311110 0125789999999999999999999876
No 54
>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=24.18 E-value=1.5e+02 Score=21.43 Aligned_cols=28 Identities=29% Similarity=0.539 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhC
Q 047553 247 EETFGRKLELFRSYGFSKEEVLQMFRKA 274 (377)
Q Consensus 247 ~~~l~~k~~~L~~lG~s~~~v~~~i~~~ 274 (377)
.+.+..-++.++.+||+.++|..++.+-
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~L 35 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNL 35 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4455666677777888887777666653
No 55
>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=24.12 E-value=2.1e+02 Score=21.55 Aligned_cols=25 Identities=20% Similarity=0.407 Sum_probs=15.8
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhCC
Q 047553 70 ETVRQFLHNVGFSDTHIQLTVTSRP 94 (377)
Q Consensus 70 ~~~l~~L~~lG~~~~~i~~ii~~~P 94 (377)
...-+|.+.+|+++.+|..+-..+|
T Consensus 12 ~~wk~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 12 RRWKEFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 3445566667777777776666665
No 56
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=23.40 E-value=1.7e+02 Score=26.77 Aligned_cols=45 Identities=24% Similarity=0.244 Sum_probs=37.9
Q ss_pred CChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCC
Q 047553 67 EKPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGL 117 (377)
Q Consensus 67 ~~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~ 117 (377)
+-++.+...|.+.|.+.++|.++++.-|.. + .+.+.++++.+.|-
T Consensus 57 e~M~rv~k~Lheqgv~~~~ik~~~r~iP~~----P--gmv~lik~~ak~g~ 101 (256)
T KOG3120|consen 57 ELMDRVFKELHEQGVRIAEIKQVLRSIPIV----P--GMVRLIKSAAKLGC 101 (256)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHhcCCCC----c--cHHHHHHHHHhCCC
Confidence 457788999999999999999999998865 3 37888999988874
No 57
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=23.14 E-value=1.3e+02 Score=25.65 Aligned_cols=111 Identities=14% Similarity=-0.003 Sum_probs=0.0
Q ss_pred CCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCCcccccCHH-----------------------
Q 047553 227 GFSTNSRMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMFRKAPLILKASEE----------------------- 283 (377)
Q Consensus 227 G~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~~P~iL~~s~~----------------------- 283 (377)
|.+....-+.+.++.-...+.+.++..+--|.+-|.+..+|.-+++..=.|=....-
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~ 89 (151)
T PRK08561 10 GKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLR 89 (151)
T ss_pred CCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHH
Q ss_pred HHHHHHHHHHHhhCCChHHHhhCCccccccccccchhhHHHHHHHHHCCCCCCCCCccc
Q 047553 284 RLQLGLEFFLKEIECEKSVLVRIPICLACSIENRVIPRYRVFQIIMSRGMFKKDCSFPS 342 (377)
Q Consensus 284 ~L~~k~~fL~~~~g~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l~~ 342 (377)
.|-.|+.-|.+++....+|....=.++. -+-.|.+.++++++.+.+..+.....
T Consensus 90 ~L~~ri~~L~~HL~~nkKD~~skRgL~~-----~~skrrRLl~Yyk~~~~LP~~WkY~~ 143 (151)
T PRK08561 90 NLIKKAVNLRKHLEENPKDLHNKRGLQL-----IESKIRRLVKYYKRTGVLPADWRYSP 143 (151)
T ss_pred HHHHHHHHHHHHHHhCCCcchhHHHHHH-----HHHHHHHHHHHHHhcCCCCCCCcCCH
No 58
>PHA02415 DNA primase domain-containing protein
Probab=22.64 E-value=1.4e+02 Score=32.60 Aligned_cols=81 Identities=14% Similarity=0.174 Sum_probs=48.5
Q ss_pred CccccCCCCCCchhhhhhhhhhhhcccCCCCCCCchhHHHhHhhCCCChhhHHHHHhhc---cCCC--------------
Q 047553 2 QRLKLNPFPNSQNFAIKSLFSFFASLSKTPNSTNFIFLNFLIKTLNIPKSRALPISNKF---SRIK-------------- 64 (377)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~L~~~~Gls~~~~~~i~~~~---P~ll-------------- 64 (377)
|||++++.++.-++-|+| ++|-...|. ++|+.+-.|++..++.+.+... |...
T Consensus 43 PSFsVn~~~~~k~NiWyC--------FGCG~GGDa--IDFVmkieglSF~EAVe~Lae~~GI~lp~ps~s~kekK~Ka~F 112 (930)
T PHA02415 43 PSLSIYVNHPKHGTGWRD--------HSADAGGSC--IDLVIHARGGTVADAVRYLHDAYGIPLDRPAPAERREKSTVEY 112 (930)
T ss_pred CceEEeecccccCcEEEE--------eCCCCCCCH--HHHHHHHhCCCHHHHHHHHHHHcCCCCCCccccccchhhhhhh
Confidence 677777665555556777 565555544 7777666677777766555431 1110
Q ss_pred --C--CCChHHHHHHHHhCCCChHHHHHHHHh
Q 047553 65 --S--LEKPETVRQFLHNVGFSDTHIQLTVTS 92 (377)
Q Consensus 65 --~--~~~~~~~l~~L~~lG~~~~~i~~ii~~ 92 (377)
. ..+..++++||.+-|++++-|...+..
T Consensus 113 l~~r~~ad~rrA~AYLK~RGIS~EVI~~cIk~ 144 (930)
T PHA02415 113 IADRCLAERERVREYLGGRGISAAAIDAAFAA 144 (930)
T ss_pred hHhhhccchHHHHHHHHhcCCCHHHHHHHHHc
Confidence 0 012334677888888887777765554
No 59
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=22.63 E-value=4e+02 Score=21.20 Aligned_cols=111 Identities=14% Similarity=0.125 Sum_probs=0.0
Q ss_pred hccchhHHHHHHHHhcCCCCchHHHHHHHhccccccccccccchhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHH
Q 047553 138 ERKLIPCVEILKKILVDDSNNEDLTRVFRRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIR 217 (377)
Q Consensus 138 ~~~l~p~v~~L~~~g~~~~~~~~i~~~l~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~ 217 (377)
+..+...+++|.+.|.-+ +...+....+.-.-...- + -.....-|+.-|++.+.|...+. -......-.+
T Consensus 8 ~e~I~~vi~~l~~~gyid--D~~ya~~~v~~~~~~~~~---G-~~~I~~~L~~kGi~~~~i~~~l~----~~~~~e~a~~ 77 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYID--DERYAESYVRSRLRRKGK---G-PRRIRQKLKQKGIDREIIEEALE----EYDEEEEALE 77 (121)
T ss_dssp HHHHHHHHHHHHHTTSS---HHHHHHHHHHHHHHHTT------HHHHHHHHHHTT--HHHHHHHHT----CS-HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCC--HHHHHHHHHHHhcccccc---c-HHHHHHHHHHHCCChHHHHHHHH----HhhHHHHHHH
Q ss_pred HHHHHHHhcCCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 047553 218 HLVSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFRSYGFSKEEVLQMFRK 273 (377)
Q Consensus 218 ~~v~~l~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~ 273 (377)
-.-+.+....-... ....+.-+.+|.+-||+.+.|..++..
T Consensus 78 ~~~kk~~~~~~~~~---------------~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 78 LAEKKYRRYRKPSD---------------RKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHTTTS-C---------------HHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHhcccCCCC---------------HHHHHHHHHHHHHCCCCHHHHHHHHhh
No 60
>PRK14136 recX recombination regulator RecX; Provisional
Probab=22.33 E-value=6.8e+02 Score=24.03 Aligned_cols=81 Identities=11% Similarity=0.111 Sum_probs=39.1
Q ss_pred HHHhHhhCCCChhhHHHHHhhccCCCCCCChHHHHHHHHhCCCC-hHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCC
Q 047553 39 LNFLIKTLNIPKSRALPISNKFSRIKSLEKPETVRQFLHNVGFS-DTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGL 117 (377)
Q Consensus 39 v~~L~~~~Gls~~~~~~i~~~~P~ll~~~~~~~~l~~L~~lG~~-~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~ 117 (377)
+.|| ..---+..++..-+.+. .+ ..+.++.+|+.|.+.|+= +...++.+... .. .... -...-.-|+..|+
T Consensus 169 L~lL-SrReRSe~ELr~KL~kk-G~-~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~--~kkG--p~rIrqELrQKGI 240 (309)
T PRK14136 169 LGYL-SRREYSRAELARKLAPY-AD-ESDSVEPLLDALEREGWLSDARFAESLVHR-RA--SRVG--SARIVSELKRHAV 240 (309)
T ss_pred HHHh-hcccccHHHHHHHHHHc-CC-CHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-Hh--hchh--HHHHHHHHHHcCC
Confidence 3444 55555566665444433 11 124566677777776654 33344443322 11 1111 1122345566777
Q ss_pred CCchhhhhhh
Q 047553 118 VGSDLGKFIS 127 (377)
Q Consensus 118 s~~~l~~ii~ 127 (377)
+.+.|..++.
T Consensus 241 d~eLIEqALe 250 (309)
T PRK14136 241 GDALVESVGA 250 (309)
T ss_pred CHHHHHHHHH
Confidence 7766666554
No 61
>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=22.24 E-value=2e+02 Score=22.55 Aligned_cols=83 Identities=18% Similarity=0.309 Sum_probs=43.0
Q ss_pred chhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCchhhHHHHHHHHHhCCHHHHHHHHHHHHH
Q 047553 180 GLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTNSRMFVYGLVVLSCLNEETFGRKLELFRS 259 (377)
Q Consensus 180 ~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~~~~~~~~p~~l~~~s~~~l~~k~~~L~~ 259 (377)
+-+...+||++.|+..+.+. +. +.| -+-++..+++..+|.+.++..- .....++. ..-+..
T Consensus 8 t~rka~~~L~~~gi~~~~~d-~~-k~p-------~s~~el~~~l~~~~~~~~~lin---------~~~~~~k~-l~~~~~ 68 (110)
T PF03960_consen 8 TCRKALKWLEENGIEYEFID-YK-KEP-------LSREELRELLSKLGNGPDDLIN---------TRSKTYKE-LGKLKK 68 (110)
T ss_dssp HHHHHHHHHHHTT--EEEEE-TT-TS----------HHHHHHHHHHHTSSGGGGB----------TTSHHHHH-TTHHHC
T ss_pred HHHHHHHHHHHcCCCeEeeh-hh-hCC-------CCHHHHHHHHHHhcccHHHHhc---------CccchHhh-hhhhhh
Confidence 35677888998888765431 11 222 1223344556666654443211 11111111 111223
Q ss_pred cCCCHHHHHHHHHhCCcccccC
Q 047553 260 YGFSKEEVLQMFRKAPLILKAS 281 (377)
Q Consensus 260 lG~s~~~v~~~i~~~P~iL~~s 281 (377)
-.++.+++.+++.++|.++...
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 4589999999999999998866
No 62
>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=21.55 E-value=34 Score=24.32 Aligned_cols=30 Identities=10% Similarity=0.171 Sum_probs=20.4
Q ss_pred hCCHHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 047553 244 CLNEETFGRKLELFRSYGFSKEEVLQMFRK 273 (377)
Q Consensus 244 ~~s~~~l~~k~~~L~~lG~s~~~v~~~i~~ 273 (377)
..+.+.++..+--|.+-|++..+|.-+++.
T Consensus 27 ~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 27 KYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp -S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 445667777777777778888888866654
No 63
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.37 E-value=69 Score=26.49 Aligned_cols=64 Identities=16% Similarity=0.122 Sum_probs=35.2
Q ss_pred HhccccccccccccchhhhHHHHHHcCCCchhHhhhhhhCCeeeEeehhhHHHHHHHHHhcCCCCc
Q 047553 166 RRCCWNLIMDTEKSGLLRNIEYLKSCGIVGSQLSMLLVWQPRLFCYKELKIRHLVSRLLDMGFSTN 231 (377)
Q Consensus 166 ~~~P~lL~~~~~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~s~~~l~~~v~~l~~lG~~~~ 231 (377)
++.|..|..+.+ + +..-|--+-.-|+++.+|.-+++-.-.+=-.+.-.=...+.+|++-|+-++
T Consensus 20 r~~PtWlK~~~d-d-vkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe 83 (151)
T KOG0400|consen 20 RSVPTWLKLTAD-D-VKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE 83 (151)
T ss_pred cCCcHHHhcCHH-H-HHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC
Confidence 456777777776 4 666666677778888887665543322211111111123455566666554
No 64
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=20.71 E-value=1.1e+02 Score=28.85 Aligned_cols=45 Identities=22% Similarity=0.327 Sum_probs=19.6
Q ss_pred hhhHHHHHH-hcCC-CCchhhhhhhcccccchhhhhccchhHHHHHHH
Q 047553 105 LKPKIEFFQ-HLGL-VGSDLGKFISKNPSLFAASLERKLIPCVEILKK 150 (377)
Q Consensus 105 l~~~i~fL~-~lG~-s~~~l~~ii~~~P~lL~~s~~~~l~p~v~~L~~ 150 (377)
|+.++.|-. .+|+ +.-.+..=|.-.|.++..+-+ .++.+++-|..
T Consensus 73 LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~-~i~~r~~ELl~ 119 (309)
T COG1125 73 LRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKE-RIKKRADELLD 119 (309)
T ss_pred HHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHH-HHHHHHHHHHH
Confidence 444444432 3332 334444445555555554432 44444444443
No 65
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=20.71 E-value=69 Score=23.80 Aligned_cols=48 Identities=27% Similarity=0.329 Sum_probs=31.8
Q ss_pred ChHHHHHHHHhCCCChHHHHHHHHhCCCeeccCCCCchhhHHHHHHhcCCCCchhhhhhhcccc
Q 047553 68 KPETVRQFLHNVGFSDTHIQLTVTSRPTILFSDVDKTLKPKIEFFQHLGLVGSDLGKFISKNPS 131 (377)
Q Consensus 68 ~~~~~l~~L~~lG~~~~~i~~ii~~~P~lL~~~~~~~l~~~i~fL~~lG~s~~~l~~ii~~~P~ 131 (377)
..+++-++|..++++..| -|+|+..|+- +. .+|+.+.++.+|+...|.
T Consensus 16 s~eE~~~lL~~y~i~~~q-------LP~I~~~DPv------~r---~~g~k~GdVvkI~R~S~t 63 (74)
T PF01191_consen 16 SEEEKKELLKKYNIKPEQ-------LPKILSSDPV------AR---YLGAKPGDVVKIIRKSET 63 (74)
T ss_dssp -HHHHHHHHHHTT--TTC-------SSEEETTSHH------HH---HTT--TTSEEEEEEEETT
T ss_pred CHHHHHHHHHHhCCChhh-------CCcccccChh------hh---hcCCCCCCEEEEEecCCC
Confidence 345677788888888774 7888887743 33 458999999998887774
No 66
>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=20.66 E-value=3.1e+02 Score=20.73 Aligned_cols=17 Identities=12% Similarity=0.032 Sum_probs=7.9
Q ss_pred HHHcCCCchhHhhhhhh
Q 047553 188 LKSCGIVGSQLSMLLVW 204 (377)
Q Consensus 188 L~~lG~~~~~i~~ll~~ 204 (377)
+.++|++...+...+..
T Consensus 4 ~~~~g~~~~~v~~aL~~ 20 (87)
T PF11626_consen 4 YEELGYSREFVTHALYA 20 (87)
T ss_dssp HHHHTB-HHHHHHHHHH
T ss_pred HHHhCCCHHHHHHHHHH
Confidence 34455555555555443
No 67
>PRK13753 dihydropteroate synthase; Provisional
Probab=20.03 E-value=2.1e+02 Score=27.03 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=7.9
Q ss_pred cchhccchhhHHHHhc
Q 047553 341 PSMLLLSEGNFLQKFV 356 (377)
Q Consensus 341 ~~~l~~s~~~F~~~~~ 356 (377)
+-++..|.|+|..++.
T Consensus 204 PvLvg~SRKsfig~~~ 219 (279)
T PRK13753 204 PLLVSVSRKSFLGATV 219 (279)
T ss_pred ceEEEccHhHHHHHHc
Confidence 3445555555555444
Done!