Query 020786
Match_columns 321
No_of_seqs 176 out of 1186
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 05:08:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020786hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 1.1E-58 2.4E-63 446.0 24.2 295 3-303 110-447 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 6.6E-51 1.4E-55 380.6 11.2 289 2-293 18-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 2.6E-45 5.7E-50 353.3 20.2 273 15-295 94-379 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 1.9E-38 4.1E-43 296.6 7.3 273 17-294 1-314 (345)
5 KOG1267 Mitochondrial transcri 100.0 3.2E-28 7E-33 232.2 15.5 256 10-271 88-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 1.9E-19 4.2E-24 171.9 11.2 211 48-264 90-335 (413)
7 smart00733 Mterf Mitochondrial 97.4 0.00015 3.1E-09 42.1 2.6 30 209-239 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.3 0.00026 5.6E-09 41.0 2.6 28 105-133 3-30 (31)
9 PF11955 PORR: Plant organelle 96.2 0.033 7.1E-07 51.7 9.2 224 22-249 46-317 (335)
10 cd04790 HTH_Cfa-like_unk Helix 92.7 0.65 1.4E-05 39.0 7.9 23 51-73 49-71 (172)
11 cd04790 HTH_Cfa-like_unk Helix 91.3 1 2.2E-05 37.8 7.4 114 16-141 50-167 (172)
12 PF04695 Pex14_N: Peroxisomal 83.0 1.5 3.2E-05 35.3 3.5 40 34-77 12-51 (136)
13 PF11955 PORR: Plant organelle 80.4 14 0.0003 34.5 9.4 219 29-256 22-294 (335)
14 PF04695 Pex14_N: Peroxisomal 79.7 3 6.5E-05 33.5 4.1 41 69-113 11-51 (136)
15 TIGR01448 recD_rel helicase, p 79.5 23 0.00051 36.7 11.5 94 5-108 69-166 (720)
16 PF14490 HHH_4: Helix-hairpin- 68.6 18 0.00038 26.9 5.7 64 13-101 8-72 (94)
17 PF03960 ArsC: ArsC family; I 67.0 12 0.00025 28.6 4.6 21 97-117 71-91 (110)
18 smart00165 UBA Ubiquitin assoc 66.8 8.8 0.00019 22.9 3.1 23 192-214 3-25 (37)
19 PF00627 UBA: UBA/TS-N domain; 66.5 8.4 0.00018 23.1 2.9 23 192-214 4-26 (37)
20 COG1378 Predicted transcriptio 65.1 39 0.00086 30.0 8.1 93 193-312 5-99 (247)
21 PF14490 HHH_4: Helix-hairpin- 63.2 20 0.00044 26.5 5.1 70 48-142 7-77 (94)
22 PF07499 RuvA_C: RuvA, C-termi 62.8 7.3 0.00016 24.9 2.3 26 190-215 3-28 (47)
23 PF07499 RuvA_C: RuvA, C-termi 62.6 11 0.00024 24.1 3.1 23 15-37 5-27 (47)
24 cd00194 UBA Ubiquitin Associat 62.3 12 0.00026 22.4 3.1 22 192-213 3-24 (38)
25 KOG2561 Adaptor protein NUB1, 61.2 23 0.00051 34.0 6.1 37 14-58 304-340 (568)
26 PF00356 LacI: Bacterial regul 58.0 25 0.00055 22.4 4.1 39 129-170 7-45 (46)
27 PF11181 YflT: Heat induced st 56.6 53 0.0011 24.7 6.5 79 118-209 9-89 (103)
28 PF11212 DUF2999: Protein of u 56.3 68 0.0015 22.6 6.2 47 87-141 3-49 (82)
29 PF07647 SAM_2: SAM domain (St 56.1 27 0.00059 23.6 4.5 52 10-66 3-54 (66)
30 KOG0400 40S ribosomal protein 55.2 19 0.00042 28.4 3.7 38 36-74 21-58 (151)
31 PF02022 Integrase_Zn: Integra 54.9 21 0.00046 22.1 3.3 30 188-217 6-36 (40)
32 COG1125 OpuBA ABC-type proline 52.9 26 0.00057 31.5 4.7 45 206-250 91-136 (309)
33 PHA01351 putative minor struct 51.5 2.1E+02 0.0045 29.5 11.0 65 11-75 641-717 (1070)
34 PF02787 CPSase_L_D3: Carbamoy 49.7 13 0.00028 29.3 2.1 21 22-42 21-41 (123)
35 PRK11613 folP dihydropteroate 46.9 44 0.00094 30.4 5.4 67 224-298 164-230 (282)
36 smart00354 HTH_LACI helix_turn 46.4 50 0.0011 22.8 4.6 40 129-171 8-47 (70)
37 COG3620 Predicted transcriptio 46.2 22 0.00048 29.4 2.9 12 58-69 16-27 (187)
38 PRK00116 ruvA Holliday junctio 45.0 96 0.0021 26.3 7.0 25 121-145 149-173 (192)
39 PF13331 DUF4093: Domain of un 42.0 1.4E+02 0.0029 22.0 6.4 21 191-211 66-86 (87)
40 PRK00116 ruvA Holliday junctio 41.6 56 0.0012 27.8 5.0 41 85-126 149-189 (192)
41 cd01392 HTH_LacI Helix-turn-he 41.5 58 0.0013 20.6 4.1 40 129-171 5-44 (52)
42 PRK08561 rps15p 30S ribosomal 40.5 1.8E+02 0.0038 23.8 7.3 36 108-144 21-56 (151)
43 cd08805 Death_ank1 Death domai 39.7 94 0.002 22.7 5.2 38 17-58 19-56 (84)
44 cd08306 Death_FADD Fas-associa 39.2 71 0.0015 23.3 4.5 21 18-38 18-38 (86)
45 KOG0400 40S ribosomal protein 38.9 32 0.0007 27.2 2.8 64 107-171 20-83 (151)
46 PRK10026 arsenate reductase; P 38.0 66 0.0014 26.0 4.6 45 97-146 76-120 (141)
47 cd00166 SAM Sterile alpha moti 37.9 1.1E+02 0.0023 20.0 5.1 24 12-37 3-26 (63)
48 PRK08561 rps15p 30S ribosomal 36.8 1.6E+02 0.0036 24.0 6.6 19 19-37 39-57 (151)
49 cd08306 Death_FADD Fas-associa 36.8 1E+02 0.0022 22.4 5.1 40 55-98 19-58 (86)
50 PF03960 ArsC: ArsC family; I 35.5 45 0.00098 25.3 3.2 22 131-152 69-90 (110)
51 cd08313 Death_TNFR1 Death doma 35.0 1.5E+02 0.0032 21.4 5.6 24 15-38 13-36 (80)
52 PF10440 WIYLD: Ubiquitin-bind 34.8 80 0.0017 21.9 3.9 40 187-226 8-47 (65)
53 PRK14136 recX recombination re 34.3 3.8E+02 0.0082 24.7 13.2 131 54-214 170-302 (309)
54 cd08319 Death_RAIDD Death doma 34.3 1.3E+02 0.0029 21.8 5.3 37 18-58 18-54 (83)
55 PF02631 RecX: RecX family; I 33.9 2.2E+02 0.0047 21.9 8.5 106 84-213 10-118 (121)
56 PF13720 Acetyltransf_11: Udp 31.5 66 0.0014 23.3 3.3 40 17-58 20-59 (83)
57 cd00739 DHPS DHPS subgroup of 31.3 1.2E+02 0.0026 27.1 5.7 68 225-301 152-220 (257)
58 PHA02591 hypothetical protein; 31.3 86 0.0019 22.6 3.6 22 188-209 46-67 (83)
59 cd02977 ArsC_family Arsenate R 31.1 1E+02 0.0023 22.9 4.6 21 97-117 74-94 (105)
60 PF08069 Ribosomal_S13_N: Ribo 30.7 37 0.0008 23.1 1.7 37 107-144 20-56 (60)
61 COG3620 Predicted transcriptio 30.6 70 0.0015 26.6 3.6 75 94-170 16-98 (187)
62 PF02631 RecX: RecX family; I 30.6 2.5E+02 0.0054 21.5 7.7 58 152-212 7-67 (121)
63 TIGR00601 rad23 UV excision re 30.2 77 0.0017 30.2 4.3 43 188-239 154-196 (378)
64 PF08671 SinI: Anti-repressor 30.0 80 0.0017 18.2 2.8 24 190-213 5-28 (30)
65 PF09288 UBA_3: Fungal ubiquit 29.8 67 0.0015 21.5 2.7 19 194-212 13-31 (55)
66 PHA00542 putative Cro-like pro 28.2 62 0.0013 23.3 2.7 32 5-36 12-43 (82)
67 smart00454 SAM Sterile alpha m 28.1 1.4E+02 0.0031 19.6 4.4 46 12-63 5-51 (68)
68 PRK00117 recX recombination re 28.0 3.2E+02 0.007 22.0 10.9 123 14-146 15-154 (157)
69 KOG2629 Peroxisomal membrane a 27.9 1E+02 0.0023 27.9 4.5 45 152-213 1-45 (300)
70 PF08069 Ribosomal_S13_N: Ribo 27.6 18 0.00039 24.6 -0.2 39 174-212 17-55 (60)
71 cd03032 ArsC_Spx Arsenate Redu 27.3 1.3E+02 0.0028 23.0 4.6 40 97-141 74-113 (115)
72 PRK13344 spxA transcriptional 26.4 1.3E+02 0.0029 23.8 4.6 41 97-142 74-114 (132)
73 COG5457 Uncharacterized conser 26.3 65 0.0014 22.2 2.3 19 18-36 41-59 (63)
74 PTZ00072 40S ribosomal protein 25.7 2.6E+02 0.0056 22.7 5.9 36 37-73 19-54 (148)
75 PRK10026 arsenate reductase; P 25.2 1.9E+02 0.004 23.4 5.2 22 132-153 75-96 (141)
76 cd08804 Death_ank2 Death domai 25.0 1.8E+02 0.0039 21.0 4.7 20 20-39 22-41 (84)
77 KOG2561 Adaptor protein NUB1, 24.8 2.6E+02 0.0056 27.3 6.7 131 79-213 259-398 (568)
78 COG0320 LipA Lipoate synthase 24.6 3.1E+02 0.0067 25.0 6.8 108 58-169 157-282 (306)
79 TIGR01617 arsC_related transcr 24.6 93 0.002 23.9 3.3 41 97-141 75-115 (117)
80 cd08319 Death_RAIDD Death doma 24.3 1.9E+02 0.004 21.0 4.6 39 56-98 20-58 (83)
81 cd08805 Death_ank1 Death domai 24.2 2.1E+02 0.0046 20.8 4.8 37 56-96 22-58 (84)
82 TIGR00014 arsC arsenate reduct 24.1 1.7E+02 0.0037 22.3 4.7 40 97-141 74-113 (114)
83 cd03034 ArsC_ArsC Arsenate Red 23.9 1.7E+02 0.0036 22.3 4.6 21 97-117 73-93 (112)
84 TIGR01448 recD_rel helicase, p 23.8 2.2E+02 0.0047 29.7 6.7 43 23-71 123-165 (720)
85 TIGR01496 DHPS dihydropteroate 23.0 1.7E+02 0.0038 26.0 5.1 67 225-299 150-216 (257)
86 PRK14487 cbb3-type cytochrome 23.0 2.2E+02 0.0049 24.7 5.5 63 141-203 134-209 (217)
87 PF09278 MerR-DNA-bind: MerR, 22.8 96 0.0021 20.8 2.7 18 194-211 7-24 (65)
88 TIGR01558 sm_term_P27 phage te 22.7 38 0.00082 26.1 0.7 9 198-206 87-95 (116)
89 COG1393 ArsC Arsenate reductas 22.4 64 0.0014 25.1 1.9 40 98-142 76-115 (117)
90 KOG3120 Predicted haloacid deh 22.1 1.9E+02 0.0041 25.5 4.8 43 48-96 58-100 (256)
91 PF09280 XPC-binding: XPC-bind 21.7 1.5E+02 0.0032 20.1 3.4 20 91-110 27-46 (59)
92 cd08779 Death_PIDD Death Domai 21.5 2.7E+02 0.0058 20.2 5.0 19 20-38 20-38 (86)
93 cd04768 HTH_BmrR-like Helix-Tu 21.4 1.8E+02 0.0039 21.4 4.2 24 192-215 48-71 (96)
94 PF01381 HTH_3: Helix-turn-hel 21.4 52 0.0011 21.1 1.1 18 21-38 6-23 (55)
95 cd08313 Death_TNFR1 Death doma 21.4 2.6E+02 0.0057 20.1 4.8 21 54-74 16-36 (80)
96 PF00536 SAM_1: SAM domain (St 21.2 1.3E+02 0.0028 20.0 3.1 21 12-34 4-24 (64)
97 TIGR01616 nitro_assoc nitrogen 21.1 1.3E+02 0.0029 23.6 3.5 46 97-147 73-118 (126)
98 cd04788 HTH_NolA-AlbR Helix-Tu 20.8 2.4E+02 0.0052 20.8 4.7 24 192-215 48-71 (96)
99 PF08004 DUF1699: Protein of u 20.5 2.5E+02 0.0055 22.2 4.8 28 117-144 89-116 (131)
100 PRK09875 putative hydrolase; P 20.3 95 0.0021 28.4 2.9 28 189-216 261-288 (292)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.1e-58 Score=446.00 Aligned_cols=295 Identities=14% Similarity=0.267 Sum_probs=238.1
Q ss_pred ccccccccCChH----HHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCcccc
Q 020786 3 NKEHRVLESDAY----ATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILE 78 (321)
Q Consensus 3 ~~~P~vL~~~~~----~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~ 78 (321)
.++|.+|+++++ ++++||+++|++.++|++++.++|.+|.+++++++.|+++||+++|+++++|++++.++|++|+
T Consensus 110 ~~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~ 189 (487)
T PLN03196 110 NEYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLG 189 (487)
T ss_pred ccCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhc
Confidence 467777777665 3677777777777777777777777777777777777777777777777777777777777777
Q ss_pred ccccccchhHHHHHHHhhcCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecch-hHH
Q 020786 79 RSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA-RLN 157 (321)
Q Consensus 79 ~s~~~~l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~-~~~ 157 (321)
+++++++.|+++||.++|++.+++++++.++|++|+++++++++|+++||+++|++.++|.+++.++|++++++.+ +++
T Consensus 190 ~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lk 269 (487)
T PLN03196 190 FKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVK 269 (487)
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHH
Confidence 7777777777777777777777777777777777777777777777777777777777777777777777777765 667
Q ss_pred HHHHHHHHcCCCCCchh--------------------------------------HHHHHHHHhhcCHHHHHHHHHHHHH
Q 020786 158 KIIDEVKKLGFDPTNLL--------------------------------------FVLAIRSMAVMSKALWEKKLEAYMN 199 (321)
Q Consensus 158 ~~v~~l~~lG~~~~~~~--------------------------------------~~~~~~~~~~~~~~~l~~~v~~l~~ 199 (321)
++++++.++|++++... +..+.+.+.+.++++++++++||++
T Consensus 270 p~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~ 349 (487)
T PLN03196 270 PNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRG 349 (487)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHH
Confidence 77777777776643211 2222344556788999999999999
Q ss_pred cCCCHHHHHHHhhccCccccccHHHHhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhHHHHHHHHHhCCCCCCCcc
Q 020786 200 FGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFS 279 (321)
Q Consensus 200 lG~~~~~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~~~ 279 (321)
+||+.++|..||.++|++|++|.++|++|++||+++||++.++|+++|++|+||+|+||+|||+++ +++|+ .++
T Consensus 350 ~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L---~~kGl---~~s 423 (487)
T PLN03196 350 RGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERV---AKKGI---KCS 423 (487)
T ss_pred cCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHH---HHcCC---CCC
Confidence 999999999999999999999999999999999999999999999999999999999999999874 68998 689
Q ss_pred cccccccChhhHHHHHhhhccCCh
Q 020786 280 LTYMFKMTEKQFIERIVKKYEHKV 303 (321)
Q Consensus 280 l~~~l~~s~~~F~~~~~~~~~~~~ 303 (321)
+.++|+|||++|+++|+.+|.|.-
T Consensus 424 L~~~L~~sd~~F~~r~v~~y~e~~ 447 (487)
T PLN03196 424 LAWFLNCSDDKFEQRMSGDFIEGE 447 (487)
T ss_pred HHHHhccCHHHHHHHHhhhccccc
Confidence 999999999999999999998843
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=6.6e-51 Score=380.63 Aligned_cols=289 Identities=25% Similarity=0.420 Sum_probs=207.2
Q ss_pred cccccccccCChHH----HHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccc
Q 020786 2 LNKEHRVLESDAYA----TVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYIL 77 (321)
Q Consensus 2 v~~~P~vL~~~~~~----~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL 77 (321)
|+++|.+|.++++. .++||++.|++..|+++++.++|.+|..+.++++.|.++||+++|++++++.+++.++|++|
T Consensus 18 i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l 97 (345)
T PF02536_consen 18 IRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRIL 97 (345)
T ss_dssp HH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHH
T ss_pred HHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhh
Confidence 67899999998885 48999999999999999999999999999888999999999999999999999999999999
Q ss_pred cccccccchhHHHHHHHhhcCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeec-chhH
Q 020786 78 ERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQS-TARL 156 (321)
Q Consensus 78 ~~s~~~~l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~-~~~~ 156 (321)
..+.+.++.+++++|+++|++++.+.+.+..+|.++... +++++.++++.++|++++++.+++..+|+++... .+.+
T Consensus 98 ~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~ 175 (345)
T PF02536_consen 98 SFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESEL 175 (345)
T ss_dssp HS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCC
T ss_pred ccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHH
Confidence 998888899999999999998876777777777544333 2355555555555555555555555555333222 2344
Q ss_pred HHHHHHHHHcCCCCCc--h--------------------------------hHHHHHHHHhhcCHHHHHHHHHHHHHcCC
Q 020786 157 NKIIDEVKKLGFDPTN--L--------------------------------LFVLAIRSMAVMSKALWEKKLEAYMNFGL 202 (321)
Q Consensus 157 ~~~v~~l~~lG~~~~~--~--------------------------------~~~~~~~~~~~~~~~~l~~~v~~l~~lG~ 202 (321)
++++++++++|++.++ . .+....+.++..+.++++++++||.++||
T Consensus 176 ~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~ 255 (345)
T PF02536_consen 176 KPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGF 255 (345)
T ss_dssp HHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcC
Confidence 5555555555544332 1 22222333444567899999999999999
Q ss_pred CHHHHHHHhhccCccccccHHHHhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhHHHHHHHHHhCCCCCCCccccc
Q 020786 203 TKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFSLTY 282 (321)
Q Consensus 203 ~~~~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~~~l~~ 282 (321)
+++|+++|+.++|+||++|.+++++|++||.++||++.++|+++|++|+||+|+||+|||+++++|+++|. ...+++.+
T Consensus 256 s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~sl~~ 334 (345)
T PF02536_consen 256 SEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPSLSS 334 (345)
T ss_dssp -HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGGS-H
T ss_pred cHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999997 56899999
Q ss_pred ccccChhhHHH
Q 020786 283 MFKMTEKQFIE 293 (321)
Q Consensus 283 ~l~~s~~~F~~ 293 (321)
++.+||++|++
T Consensus 335 ~l~~s~~~F~~ 345 (345)
T PF02536_consen 335 MLSCSDEEFLK 345 (345)
T ss_dssp HHHHHHHHHT-
T ss_pred HhhccHHHhcC
Confidence 99999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2.6e-45 Score=353.25 Aligned_cols=273 Identities=16% Similarity=0.274 Sum_probs=221.5
Q ss_pred HHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHH
Q 020786 15 ATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRR 94 (321)
Q Consensus 15 ~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~ 94 (321)
++++||+++|++.+||. ++|.+|++++++++.|+++||.++|++..+|+++|.++|.+|..|+++++.|+++||++
T Consensus 94 ~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~ 169 (487)
T PLN03196 94 ERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQG 169 (487)
T ss_pred HHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHH
Confidence 46999999999999997 79999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecch-hHHHHHHHHHHcCCCCCc-
Q 020786 95 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTA-RLNKIIDEVKKLGFDPTN- 172 (321)
Q Consensus 95 ~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~-~~~~~v~~l~~lG~~~~~- 172 (321)
+|++++++.+++.++|++|++++++++.++++||.++|++.+++.+++.++|++|+++.+ ++.++++||.++|++.+.
T Consensus 170 lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I 249 (487)
T PLN03196 170 LDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAV 249 (487)
T ss_pred cCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHH
Confidence 999999999999999999999999999999999999999999999999999999999986 789999999999999886
Q ss_pred -hhHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHHH-HhhHHHHHHHhcCCChHHH----hhC
Q 020786 173 -LLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQK-ISKLMDCYVNKLSMEPLII----SKH 246 (321)
Q Consensus 173 -~~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~-l~~k~~fL~~~~g~~~~~i----~~~ 246 (321)
..+.++|.++....++++++++++|.++|++.+++..++.++|.+++++.+. ++++++|+.+++|++.+++ .++
T Consensus 250 ~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~ 329 (487)
T PLN03196 250 ARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKL 329 (487)
T ss_pred HHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhc
Confidence 3455567666655566888888888888888887777777777777777653 6666666665666665543 345
Q ss_pred CccccCCccCcchhHHHHHHHHHhCCCCCCCc-----ccccccccChhhHHHHH
Q 020786 247 PYLLLFSLEKRILPRCSVLQLLMSNKVITEDF-----SLTYMFKMTEKQFIERI 295 (321)
Q Consensus 247 P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~~-----~l~~~l~~s~~~F~~~~ 295 (321)
|+++++|.+ ++.+|..++ .+.|+..+++ ....++++|.+....++
T Consensus 330 P~il~lSe~-kl~~kvefL---~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~ 379 (487)
T PLN03196 330 PQIVSLNRN-VALKHVEFL---RGRGFSAQDVAKMVVRCPQILALNLEIMKPSL 379 (487)
T ss_pred chhhcccHH-HHHHHHHHH---HHcCCCHHHHHHHHHhCCceeeccHHHHHHHH
Confidence 666666654 455554433 3455543322 34445555555444433
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=1.9e-38 Score=296.57 Aligned_cols=273 Identities=29% Similarity=0.522 Sum_probs=218.6
Q ss_pred HHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhh
Q 020786 17 VEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVL 96 (321)
Q Consensus 17 l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g 96 (321)
.++|+++||+++||.++++++|.++.+++++++.|+++||.++|++..++++++++||.+|..++++++.|.++||+++|
T Consensus 1 ~~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~ 80 (345)
T PF02536_consen 1 EDLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIG 80 (345)
T ss_dssp -HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTS
T ss_pred ChHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHc
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCCc--hh
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTN--LL 174 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~~--~~ 174 (321)
++++++.+++.++|++|+.+.+.++.+++++|+++|++.+.+..++...|..+... +++.+.++++.++|++++. ..
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~-~~~~~~v~~l~~lG~~~~~~~~v 159 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS-EKIKERVEFLKELGFDPEKIGRV 159 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS--HHHHCHHHHHCCCTSSHHHHCCC
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch-hHHHHHHHHHHHhCCCchhhccc
Confidence 99999999999999999998887999999999999999998999999999877766 8999999999999999987 45
Q ss_pred HHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHHH------------------------------
Q 020786 175 FVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQK------------------------------ 224 (321)
Q Consensus 175 ~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~------------------------------ 224 (321)
...+|..+...++++++++++||+++|++.+++.+++.++|.++..|+++
T Consensus 160 i~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~ 239 (345)
T PF02536_consen 160 IAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLS 239 (345)
T ss_dssp HHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THH
T ss_pred ccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccc
Confidence 66678888888899999999999999999999999999999999888864
Q ss_pred ---HhhHHHHHHHhcCCChHHH----hhCCccccCCccCcchhHHHHHHHHHhCCCCCCC-cccccccccChh-hHHHH
Q 020786 225 ---ISKLMDCYVNKLSMEPLII----SKHPYLLLFSLEKRILPRCSVLQLLMSNKVITED-FSLTYMFKMTEK-QFIER 294 (321)
Q Consensus 225 ---l~~k~~fL~~~~g~~~~~i----~~~P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~-~~l~~~l~~s~~-~F~~~ 294 (321)
++++++||.+ +|++.++| .++|++|++|.++ ++|+++++. .+.|...++ ...+.++.+|=+ +-.-+
T Consensus 240 ~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~--~~m~~~~~~i~~~P~~l~~sLe~ri~PR 314 (345)
T PF02536_consen 240 EEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLV--KEMGLPLEEIVEFPQYLSYSLEKRIKPR 314 (345)
T ss_dssp HHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHH--HCCT--HHHHHHSCHHHCS-HHHHHHHH
T ss_pred hHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHH--HHhCcCHHHHhhCCceeEechhhhhhhH
Confidence 8889999988 89999886 5699999999995 999988764 345664322 234556776653 44434
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.96 E-value=3.2e-28 Score=232.25 Aligned_cols=256 Identities=23% Similarity=0.342 Sum_probs=221.2
Q ss_pred cCChHHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHH
Q 020786 10 ESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCI 89 (321)
Q Consensus 10 ~~~~~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v 89 (321)
..+|++++++|+++|+++++|..++..+|.++..+.++.+.++..+|...|++..++.++++..|.+|+.+...++.+.+
T Consensus 88 ~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~ 167 (413)
T KOG1267|consen 88 SVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFI 167 (413)
T ss_pred ccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHH
Confidence 45888999999999999999999999999999999999999999999999999999999999989998877777777777
Q ss_pred HHHHHhh-----------------------------------cCcHHHHHH-----------------------------
Q 020786 90 EILRRVL-----------------------------------DTDENVLKA----------------------------- 105 (321)
Q Consensus 90 ~~L~~~g-----------------------------------~~~~~v~~~----------------------------- 105 (321)
+|+.+++ ...+.+...
T Consensus 168 ~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~~l~~~~~~i~~~g~~p~ 247 (413)
T KOG1267|consen 168 EFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYLKLKARLPFLLTLGFDPK 247 (413)
T ss_pred HHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeehhhhhhhhhHHHhccCCc
Confidence 7777753 233333332
Q ss_pred ---HHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCCchhHHHHHHHH
Q 020786 106 ---IRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNLLFVLAIRSM 182 (321)
Q Consensus 106 ---l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~~~~~~~~~~~~ 182 (321)
+.++|.+++++.++++++++++|+++|++.++++.++.++|++++++.+++...++++.+. .++ +.+.|..
T Consensus 248 ~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~--~~~---~~k~p~~- 321 (413)
T KOG1267|consen 248 TREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN--PKH---ILKFPQL- 321 (413)
T ss_pred hhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc--chh---hhhhhhh-
Confidence 2334555555788899999999999999999999999999999999999999999998766 222 3334444
Q ss_pred hhcCHHHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHH-HHhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhH
Q 020786 183 AVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQ-KISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPR 261 (321)
Q Consensus 183 ~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~-~l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR 261 (321)
...++..+.++++|+..+|++..|+..|+.++|+++.+|++ .++.+.+|+.+.|+.+.++++.+|++++|++++|++||
T Consensus 322 l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr 401 (413)
T KOG1267|consen 322 LRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPR 401 (413)
T ss_pred hhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhH
Confidence 47889999999999999999999999999999999999999 69999999999999999999999999999999999999
Q ss_pred HHHHHHHHhC
Q 020786 262 CSVLQLLMSN 271 (321)
Q Consensus 262 ~~~l~~L~~~ 271 (321)
+.+..++..+
T Consensus 402 ~~~~~~~~~~ 411 (413)
T KOG1267|consen 402 FNVIKKLGVK 411 (413)
T ss_pred HHHHHHHhcc
Confidence 9998876543
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.80 E-value=1.9e-19 Score=171.92 Aligned_cols=211 Identities=26% Similarity=0.332 Sum_probs=167.9
Q ss_pred chhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhhcCcHHHHHHHHhCCccccccchhhhhhHHHH
Q 020786 48 CMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAI 127 (321)
Q Consensus 48 ~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~ 127 (321)
+-...+++|++.|++..++.+++..+|.++..+.++.+.|+..+|...|.+...+.+++..-|.+|+.+.+.++.+.++|
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~ 169 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEF 169 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHH
Confidence 57788899999999999999999999999999999999999999999999988888888887777775544445555555
Q ss_pred H-----------------------------------HHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCCc
Q 020786 128 L-----------------------------------VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTN 172 (321)
Q Consensus 128 L-----------------------------------~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~~ 172 (321)
+ .++|+.+..+..++...|..+.... .+...+.++..+|+++.+
T Consensus 170 l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~ 248 (413)
T KOG1267|consen 170 LKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKT 248 (413)
T ss_pred hhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCch
Confidence 4 4455566666666666777666554 677888899999999999
Q ss_pred hhHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHHHHhhHHHHHHHhcCCChHHHhhCCccccC
Q 020786 173 LLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLF 252 (321)
Q Consensus 173 ~~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~~~~i~~~P~~L~~ 252 (321)
.++++++..+.+.+++++++++++|+++||+.+||++|+.++|++|++|.+++..+++|+.+. .+++.++|+++.+
T Consensus 249 ~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p~~l~~ 324 (413)
T KOG1267|consen 249 REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFPQLLRS 324 (413)
T ss_pred hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhhhhhhc
Confidence 999999999999999999999999999999999999999999999999999765555555554 2225555555544
Q ss_pred CccCcchhHHHH
Q 020786 253 SLEKRILPRCSV 264 (321)
Q Consensus 253 sle~ri~pR~~~ 264 (321)
|.. .+.+|+++
T Consensus 325 s~~-~l~~~ie~ 335 (413)
T KOG1267|consen 325 SED-KLKPRIEF 335 (413)
T ss_pred cch-hhhhhHHH
Confidence 433 45555443
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=97.39 E-value=0.00015 Score=42.13 Aligned_cols=30 Identities=17% Similarity=0.321 Sum_probs=26.0
Q ss_pred HHhhccCccccccHHHHhhHHHHHHHhcCCC
Q 020786 209 SAFRRQPMFMIVSEQKISKLMDCYVNKLSME 239 (321)
Q Consensus 209 ~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~ 239 (321)
.++.++|.++++|.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4688999999999888999999999 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=97.25 E-value=0.00026 Score=41.02 Aligned_cols=28 Identities=29% Similarity=0.475 Sum_probs=15.6
Q ss_pred HHHhCCccccccchhhhhhHHHHHHHcCC
Q 020786 105 AIRAGCLVLEYDIEKVLEPNIAILVNHGV 133 (321)
Q Consensus 105 ~l~~~P~lL~~s~~~~l~~~v~~L~~lG~ 133 (321)
++.++|.+++++ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 455555555555 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=96.16 E-value=0.033 Score=51.74 Aligned_cols=224 Identities=15% Similarity=0.085 Sum_probs=120.5
Q ss_pred hCCCChHHHHHHHhhCCCccccCcc-------cchhhhHHHHHh--cCCChhHHHHHHhhCCccccccccccc-hhHHHH
Q 020786 22 TNGFSDSQIKSITVKRPKFYVYNLK-------KCMKPKLEFFKS--LGFAELQMAKFLSSQPYILERSLENHI-IPCIEI 91 (321)
Q Consensus 22 ~lG~s~~~i~~lv~~~P~lL~~~~~-------~~l~~~v~~L~~--lG~~~~~i~~il~~~P~iL~~s~~~~l-~~~v~~ 91 (321)
.+|+..-.+.+.+.+||.++..... -.+.+...-|.+ ..+-.+.-..++.+=-.+|.+|.++.| ..+++.
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~ 125 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAH 125 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHH
Confidence 6999778899999999998865321 113344433331 222111113334444456777766653 335666
Q ss_pred HH-HhhcCcHHHHHHHHhCCccccccc---hhhhhhHHHHHHHcCCChhhHHHhhh-------------hCCcce--eec
Q 020786 92 LR-RVLDTDENVLKAIRAGCLVLEYDI---EKVLEPNIAILVNHGVPKSLVVKLML-------------IQPRTL--LQS 152 (321)
Q Consensus 92 L~-~~g~~~~~v~~~l~~~P~lL~~s~---~~~l~~~v~~L~~lG~~~~~i~~ll~-------------~~P~il--~~~ 152 (321)
++ ++|++++-...++.++|..+.... +...-..+.|=.++.++.-+...... .+|--+ ++.
T Consensus 126 l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G~~ 205 (335)
T PF11955_consen 126 LRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPKGFR 205 (335)
T ss_pred HHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCCCcc
Confidence 66 799998888889999998876532 11122223332235554433332210 112111 111
Q ss_pred c-hhHHHHHHHHHHc----------CCCCCchhHH-HH---HHHHhhcC--HHHHHHHHHHHH-HcCCCHHHHHHHhhcc
Q 020786 153 T-ARLNKIIDEVKKL----------GFDPTNLLFV-LA---IRSMAVMS--KALWEKKLEAYM-NFGLTKDEVYSAFRRQ 214 (321)
Q Consensus 153 ~-~~~~~~v~~l~~l----------G~~~~~~~~~-~~---~~~~~~~~--~~~l~~~v~~l~-~lG~~~~~v~~~i~~~ 214 (321)
. .+..++++-++++ |+++++..+- ++ ...++.+. .....+++..|+ ++|++ ..+..++.+|
T Consensus 206 l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~rH 284 (335)
T PF11955_consen 206 LKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLLRH 284 (335)
T ss_pred ccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHHhC
Confidence 1 3566677777765 3344432222 22 23333332 223556666676 89998 5688899999
Q ss_pred CccccccHHHHhhHHHHHHHhcCCChHH-HhhCCcc
Q 020786 215 PMFMIVSEQKISKLMDCYVNKLSMEPLI-ISKHPYL 249 (321)
Q Consensus 215 P~iL~~s~~~l~~k~~fL~~~~g~~~~~-i~~~P~~ 249 (321)
|.|+..|.. -+.-.=||.+ ++...+ |.++|.+
T Consensus 285 PgIFYvS~k-g~~~TVfLrE--AY~~~~Liek~Pl~ 317 (335)
T PF11955_consen 285 PGIFYVSLK-GKRHTVFLRE--AYDGGELIEKHPLV 317 (335)
T ss_pred CCeEEEecc-CCceEEEEee--ccCCCCCCCCCchH
Confidence 999999864 2222334444 333333 5567776
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=92.74 E-value=0.65 Score=38.99 Aligned_cols=23 Identities=13% Similarity=0.271 Sum_probs=16.3
Q ss_pred hhHHHHHhcCCChhHHHHHHhhC
Q 020786 51 PKLEFFKSLGFAELQMAKFLSSQ 73 (321)
Q Consensus 51 ~~v~~L~~lG~~~~~i~~il~~~ 73 (321)
..+..|+++|++-++|..++...
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Confidence 55666777888888887777543
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=91.28 E-value=1 Score=37.84 Aligned_cols=114 Identities=13% Similarity=0.184 Sum_probs=59.1
Q ss_pred HHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHh----cCCChhHHHHHHhhCCccccccccccchhHHHH
Q 020786 16 TVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKS----LGFAELQMAKFLSSQPYILERSLENHIIPCIEI 91 (321)
Q Consensus 16 ~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~----lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~ 91 (321)
.+..|+++|++-++|..++..... +....+..+++.+.. +--....+..++...+.. ...-.-+....++.
T Consensus 50 ~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~-~~~~~V~~~~w~~l 124 (172)
T cd04790 50 QICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLL-KEQRLVTKEKWVAI 124 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-cccccCCHHHHHHH
Confidence 378889999999999999875542 111123333333331 222233444444333322 11100113445566
Q ss_pred HHHhhcCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHh
Q 020786 92 LRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKL 141 (321)
Q Consensus 92 L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~l 141 (321)
++..|+++++....=..+- ..+++ .-.+||.++|++.+++..+
T Consensus 125 ~~~~g~~~~~m~~wh~~fe---~~~p~----~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 125 LKAAGMDEADMRRWHIEFE---KMEPE----AHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHcCCChHHHHHHHHHHH---HhCcH----HHHHHHHHcCCCHHHHHHH
Confidence 6777777666433221110 12333 3567888888888877554
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=82.96 E-value=1.5 Score=35.29 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=25.7
Q ss_pred HhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccc
Q 020786 34 TVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYIL 77 (321)
Q Consensus 34 v~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL 77 (321)
+-.+|.+-... +..|++||++.|++.++|...+.+.+.--
T Consensus 12 FL~~p~V~~sp----~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 12 FLQDPKVRNSP----LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHCTTTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HhCCcccccCC----HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 44577765433 66788888888888888888887766544
No 13
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=80.44 E-value=14 Score=34.47 Aligned_cols=219 Identities=18% Similarity=0.252 Sum_probs=119.8
Q ss_pred HHHHHHhhCCCccccCcccchhhhHHHH-HhcCCChhHHHHHHhhCCccccccc---cc----cchhHHHHHHH--hhc-
Q 020786 29 QIKSITVKRPKFYVYNLKKCMKPKLEFF-KSLGFAELQMAKFLSSQPYILERSL---EN----HIIPCIEILRR--VLD- 97 (321)
Q Consensus 29 ~i~~lv~~~P~lL~~~~~~~l~~~v~~L-~~lG~~~~~i~~il~~~P~iL~~s~---~~----~l~~~v~~L~~--~g~- 97 (321)
.+..++.+.|.- .+ .+ ..+.-+ ..+|++...+.+.+.+||.++.... .. .+.+...-|.+ ..+
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--PL-RDLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVR 95 (335)
T ss_pred HHHHHHHcCCCC---cc--cH-HHHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHH
Confidence 456677777761 11 12 223333 3699977999999999999986543 11 14444444432 111
Q ss_pred --CcHHHHHHHHhCCccccccchhhh-hhHHHHHH-HcCCChhhHHHhhhhCCcceeecc----hhHHHHHHHHHHcCCC
Q 020786 98 --TDENVLKAIRAGCLVLEYDIEKVL-EPNIAILV-NHGVPKSLVVKLMLIQPRTLLQST----ARLNKIIDEVKKLGFD 169 (321)
Q Consensus 98 --~~~~v~~~l~~~P~lL~~s~~~~l-~~~v~~L~-~lG~~~~~i~~ll~~~P~il~~~~----~~~~~~v~~l~~lG~~ 169 (321)
...++..-++ .+|.+|.++.+ -.++..++ ++|+|.+-...++.++|..|.... ....+-+.|=.++.++
T Consensus 96 ~~~e~~~v~rL~---KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs 172 (335)
T PF11955_consen 96 EEMEPDLVERLR---KLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVS 172 (335)
T ss_pred HhChHHHHHHHH---HHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcC
Confidence 2334444444 36767766544 34566776 699999999999999999886532 0111111111112221
Q ss_pred CCchh--------------HHHHHHHHh--h-cCHHHHHHHHHHHHHc----------CCC---HHHHHHHhhccCcccc
Q 020786 170 PTNLL--------------FVLAIRSMA--V-MSKALWEKKLEAYMNF----------GLT---KDEVYSAFRRQPMFMI 219 (321)
Q Consensus 170 ~~~~~--------------~~~~~~~~~--~-~~~~~l~~~v~~l~~l----------G~~---~~~v~~~i~~~P~iL~ 219 (321)
.-+.. ...+++.-. + ......+++++-++++ |+. .+.=...+.-.=-+|+
T Consensus 173 ~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLS 252 (335)
T PF11955_consen 173 ALEKRAEKEYREKREDGFDRPLAFPVSFPKGFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLS 252 (335)
T ss_pred ccchhhhhccccccccccCCceeeeecCCCCccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHH
Confidence 11100 000111000 0 1123455555555532 111 1111112222234677
Q ss_pred ccHHH--HhhHHHHHHHhcCCChH---HHhhCCccccCCccC
Q 020786 220 VSEQK--ISKLMDCYVNKLSMEPL---IISKHPYLLLFSLEK 256 (321)
Q Consensus 220 ~s~~~--l~~k~~fL~~~~g~~~~---~i~~~P~~L~~sle~ 256 (321)
+.+++ ...++..+.+++|+|.. .+.++|.+|..|...
T Consensus 253 LTveKr~~~~~L~~fr~ef~lp~k~~~~l~rHPgIFYvS~kg 294 (335)
T PF11955_consen 253 LTVEKRTEVDHLTHFRKEFGLPQKFRRLLLRHPGIFYVSLKG 294 (335)
T ss_pred hhhhhhccHHHHHHHHHHhCCcHHHHHHHHhCCCeEEEeccC
Confidence 77776 56789999999999964 578999999999764
No 14
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=79.69 E-value=3 Score=33.53 Aligned_cols=41 Identities=15% Similarity=0.058 Sum_probs=25.6
Q ss_pred HHhhCCccccccccccchhHHHHHHHhhcCcHHHHHHHHhCCccc
Q 020786 69 FLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVL 113 (321)
Q Consensus 69 il~~~P~iL~~s~~~~l~~~v~~L~~~g~~~~~v~~~l~~~P~lL 113 (321)
-+..+|.+-..+ +..+++||++-|+++++|..++.+.+.--
T Consensus 11 ~FL~~p~V~~sp----~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 11 KFLQDPKVRNSP----LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHCTTTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHhCCcccccCC----HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 344567766654 45678888888888888888887766544
No 15
>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=79.46 E-value=23 Score=36.68 Aligned_cols=94 Identities=10% Similarity=0.059 Sum_probs=63.9
Q ss_pred ccccccCChHHHHHHHhh---CCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhc-CCChhHHHHHHhhCCcccccc
Q 020786 5 EHRVLESDAYATVEFFRT---NGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSL-GFAELQMAKFLSSQPYILERS 80 (321)
Q Consensus 5 ~P~vL~~~~~~~l~~L~~---lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~l-G~~~~~i~~il~~~P~iL~~s 80 (321)
+-.++..+.+..+.||.+ -|+.+....+++..++.=.. +.+...-+-|.++ |++...+..+...+..
T Consensus 69 ~~~~~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~----~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~----- 139 (720)
T TIGR01448 69 MELEAPTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAF----DVLDDDPEKLLEVPGISKANLEKFVSQWSQ----- 139 (720)
T ss_pred EEEeCCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHH----HHHHhCHHHHhcCCCCCHHHHHHHHHHHHH-----
Confidence 334566677788999986 67888889999988874222 1233344566665 8988888888876632
Q ss_pred ccccchhHHHHHHHhhcCcHHHHHHHHh
Q 020786 81 LENHIIPCIEILRRVLDTDENVLKAIRA 108 (321)
Q Consensus 81 ~~~~l~~~v~~L~~~g~~~~~v~~~l~~ 108 (321)
.......+.||.++|++.....++...
T Consensus 140 -~~~~~~~~~~L~~~gi~~~~a~ki~~~ 166 (720)
T TIGR01448 140 -QGDERRLLAGLQGLGIGIKLAQRIYKF 166 (720)
T ss_pred -hHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 223566788999999887655555443
No 16
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=68.58 E-value=18 Score=26.90 Aligned_cols=64 Identities=13% Similarity=0.187 Sum_probs=32.6
Q ss_pred hHHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHH
Q 020786 13 AYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEIL 92 (321)
Q Consensus 13 ~~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L 92 (321)
...++.||..+|++...+.++...+-. +...+|..+|+.|..++..-=-..++.+
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~~yg~-------------------------~ai~~l~~nPY~L~~~i~gi~F~~aD~i 62 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYKKYGD-------------------------DAIEILKENPYRLIEDIDGIGFKTADKI 62 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHHHH-T-------------------------THHHHHHH-STCCCB-SSSSBHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhH-------------------------HHHHHHHHChHHHHHHccCCCHHHHHHH
Confidence 445788888888888877776654321 2235666777777665544433444444
Q ss_pred H-HhhcCcHH
Q 020786 93 R-RVLDTDEN 101 (321)
Q Consensus 93 ~-~~g~~~~~ 101 (321)
. ++|++..+
T Consensus 63 A~~~g~~~~d 72 (94)
T PF14490_consen 63 ALKLGIEPDD 72 (94)
T ss_dssp HHTTT--TT-
T ss_pred HHHcCCCCCC
Confidence 3 45554433
No 17
>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=67.01 E-value=12 Score=28.64 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=12.3
Q ss_pred cCcHHHHHHHHhCCccccccc
Q 020786 97 DTDENVLKAIRAGCLVLEYDI 117 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~ 117 (321)
.+.+++..++..+|.++...+
T Consensus 71 ~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhHHHHHHHHhChhheeCCE
Confidence 355666666666666665543
No 18
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=66.77 E-value=8.8 Score=22.86 Aligned_cols=23 Identities=22% Similarity=0.618 Sum_probs=16.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcc
Q 020786 192 KKLEAYMNFGLTKDEVYSAFRRQ 214 (321)
Q Consensus 192 ~~v~~l~~lG~~~~~v~~~i~~~ 214 (321)
++++-|.++||+++++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45667778888888777766544
No 19
>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=66.47 E-value=8.4 Score=23.15 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhhcc
Q 020786 192 KKLEAYMNFGLTKDEVYSAFRRQ 214 (321)
Q Consensus 192 ~~v~~l~~lG~~~~~v~~~i~~~ 214 (321)
+.++-|.++||+.++..+.+..+
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 45667778888888777766543
No 20
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=65.07 E-value=39 Score=30.03 Aligned_cols=93 Identities=16% Similarity=0.138 Sum_probs=53.7
Q ss_pred HHHHHHHcCCCHHHHHHHhhccCccccccHHHHhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhH-HHHHHHHHhC
Q 020786 193 KLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPR-CSVLQLLMSN 271 (321)
Q Consensus 193 ~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR-~~~l~~L~~~ 271 (321)
-++.|+++||+..|+. .+-.|+..-..++.+|.+.-.+ . +|| |.+++-|.++
T Consensus 5 ~~~~L~~lGlt~yEa~-------------------vY~aLl~~g~~tA~eis~~sgv---P-----~~kvY~vl~sLe~k 57 (247)
T COG1378 5 LEENLQKLGLTEYEAK-------------------VYLALLCLGEATAKEISEASGV---P-----RPKVYDVLRSLEKK 57 (247)
T ss_pred HHHHHHHcCCCHHHHH-------------------HHHHHHHhCCccHHHHHHHcCC---C-----chhHHHHHHHHHHC
Confidence 4678889999998875 3444555445666777654222 1 233 6789999999
Q ss_pred CCCCC-CcccccccccChhhHHHHHhhhccCChhHHHHHHhc
Q 020786 272 KVITE-DFSLTYMFKMTEKQFIERIVKKYEHKVPKVVKAHQG 312 (321)
Q Consensus 272 g~~~~-~~~l~~~l~~s~~~F~~~~~~~~~~~~~~~~~~~~~ 312 (321)
|++.. ..+...+-..+-+...++.-....+...++.+.++.
T Consensus 58 G~v~~~~g~P~~y~av~p~~~i~~~~~~~~~~~~~~~~~~~~ 99 (247)
T COG1378 58 GLVEVIEGRPKKYRAVPPEELIERIKEELQELLRELESELEE 99 (247)
T ss_pred CCEEeeCCCCceEEeCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99853 122222333344445555555554444444444443
No 21
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=63.18 E-value=20 Score=26.55 Aligned_cols=70 Identities=11% Similarity=0.179 Sum_probs=41.6
Q ss_pred chhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhhcCcHHHHHHHHhCCccccccchh-hhhhHHH
Q 020786 48 CMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEK-VLEPNIA 126 (321)
Q Consensus 48 ~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~-~l~~~v~ 126 (321)
.+...+.||.++|++.....++...+-. +...+|..+|+.|..++.. .++..=.
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~-------------------------~ai~~l~~nPY~L~~~i~gi~F~~aD~ 61 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGD-------------------------DAIEILKENPYRLIEDIDGIGFKTADK 61 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-T-------------------------THHHHHHH-STCCCB-SSSSBHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhH-------------------------HHHHHHHHChHHHHHHccCCCHHHHHH
Confidence 4667789999999999888888754322 2347789999999884432 3544333
Q ss_pred HHHHcCCChhhHHHhh
Q 020786 127 ILVNHGVPKSLVVKLM 142 (321)
Q Consensus 127 ~L~~lG~~~~~i~~ll 142 (321)
.-.++|++.++-.++-
T Consensus 62 iA~~~g~~~~d~~Ri~ 77 (94)
T PF14490_consen 62 IALKLGIEPDDPRRIR 77 (94)
T ss_dssp HHHTTT--TT-HHHHH
T ss_pred HHHHcCCCCCCHHHHH
Confidence 4466999988866654
No 22
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=62.75 E-value=7.3 Score=24.95 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=17.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhhccC
Q 020786 190 WEKKLEAYMNFGLTKDEVYSAFRRQP 215 (321)
Q Consensus 190 l~~~v~~l~~lG~~~~~v~~~i~~~P 215 (321)
+.+-++-|..+||+..++.+++.+-.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 34556677788888888887776543
No 23
>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=62.55 E-value=11 Score=24.08 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=16.3
Q ss_pred HHHHHHhhCCCChHHHHHHHhhC
Q 020786 15 ATVEFFRTNGFSDSQIKSITVKR 37 (321)
Q Consensus 15 ~~l~~L~~lG~s~~~i~~lv~~~ 37 (321)
.+++-|.++|+++.++.+++..-
T Consensus 5 d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 5 DALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777888888888888777654
No 24
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=62.27 E-value=12 Score=22.40 Aligned_cols=22 Identities=32% Similarity=0.653 Sum_probs=15.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhhc
Q 020786 192 KKLEAYMNFGLTKDEVYSAFRR 213 (321)
Q Consensus 192 ~~v~~l~~lG~~~~~v~~~i~~ 213 (321)
++++-|.++||+.+++...+..
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~ 24 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRA 24 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 4566777888888777766553
No 25
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=61.21 E-value=23 Score=34.04 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=22.6
Q ss_pred HHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHh
Q 020786 14 YATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKS 58 (321)
Q Consensus 14 ~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~ 58 (321)
+..++.+.++||.+.+....++.+-. ++...++|+..
T Consensus 304 d~~lsllv~mGfeesdaRlaLRsc~g--------~Vd~AvqfI~e 340 (568)
T KOG2561|consen 304 DETLSLLVGMGFEESDARLALRSCNG--------DVDSAVQFIIE 340 (568)
T ss_pred chHHHHHHHcCCCchHHHHHHHhccc--------cHHHHHHHHHH
Confidence 34567777777777777666665533 35555555553
No 26
>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=57.95 E-value=25 Score=22.41 Aligned_cols=39 Identities=28% Similarity=0.486 Sum_probs=25.1
Q ss_pred HHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCC
Q 020786 129 VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDP 170 (321)
Q Consensus 129 ~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~ 170 (321)
+..|++...+.+.+...| ..++++-+...+..+++|+.+
T Consensus 7 ~~agvS~~TVSr~ln~~~---~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPP---RVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHTSSHHHHHHHHTTCS---SSTHHHHHHHHHHHHHHTB-S
T ss_pred HHHCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHCCCC
Confidence 457888888888877664 334455555556667777765
No 27
>PF11181 YflT: Heat induced stress protein YflT
Probab=56.61 E-value=53 Score=24.75 Aligned_cols=79 Identities=16% Similarity=0.209 Sum_probs=41.1
Q ss_pred hhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecchhHHHHHHHH--HHcCCCCCchhHHHHHHHHhhcCHHHHHHHHH
Q 020786 118 EKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEV--KKLGFDPTNLLFVLAIRSMAVMSKALWEKKLE 195 (321)
Q Consensus 118 ~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l--~~lG~~~~~~~~~~~~~~~~~~~~~~l~~~v~ 195 (321)
+..+...|+-|+.-|++.++| .+++.+.+.....-+.- ...|... ..|.-....+.....+.++.
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI--------~Vva~d~~~~~~l~~~t~~~~~~~~~--~~~~d~~~~~f~~~~d~~~~--- 75 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI--------YVVAKDKDRTERLADQTDTNTVGASE--ESFWDKIKNFFTSGGDELRS--- 75 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE--------EEEEcCchHHHHHHHhcCCceecccc--ccHHHHHHHhccCCcHHHHH---
Confidence 345778888999999998887 34444433322211111 1123222 22222222222234455544
Q ss_pred HHHHcCCCHHHHHH
Q 020786 196 AYMNFGLTKDEVYS 209 (321)
Q Consensus 196 ~l~~lG~~~~~v~~ 209 (321)
-|.++|++.+++..
T Consensus 76 ~l~~lGl~~~ea~~ 89 (103)
T PF11181_consen 76 KLESLGLSEDEAER 89 (103)
T ss_pred HHHHcCCCHHHHHH
Confidence 45688999888754
No 28
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=56.29 E-value=68 Score=22.58 Aligned_cols=47 Identities=26% Similarity=0.396 Sum_probs=24.3
Q ss_pred hHHHHHHHhhcCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHh
Q 020786 87 PCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKL 141 (321)
Q Consensus 87 ~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~l 141 (321)
|-+..|++..+|++.+..++.. |+.+ --..+.....+|++++.+..+
T Consensus 3 PIia~LKehnvsd~qi~elFq~----lT~N----Pl~AMa~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQA----LTQN----PLAAMATIQQLGIPQEKLQQL 49 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHH----HhhC----HHHHHHHHHHcCCCHHHHHHH
Confidence 4556666666666666555432 1111 112345555666666665443
No 29
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=56.08 E-value=27 Score=23.57 Aligned_cols=52 Identities=15% Similarity=0.108 Sum_probs=30.0
Q ss_pred cCChHHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHH
Q 020786 10 ESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQM 66 (321)
Q Consensus 10 ~~~~~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i 66 (321)
.-+++.+.+||.++|+ .+....+..+----... -+.-.-+.|.++|++...-
T Consensus 3 ~w~~~~v~~WL~~~gl--~~y~~~f~~~~i~g~~~---L~~l~~~~L~~lGI~~~~~ 54 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGL--EQYADNFRENGIDGLED---LLQLTEEDLKELGITNLGH 54 (66)
T ss_dssp GHCHHHHHHHHHHTTC--GGGHHHHHHTTCSHHHH---HTTSCHHHHHHTTTTHHHH
T ss_pred CCCHHHHHHHHHHCCc--HHHHHHHHHcCCcHHHH---HhhCCHHHHHHcCCCCHHH
Confidence 3467888999999998 56666555442111000 0111235778888866544
No 30
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=55.18 E-value=19 Score=28.45 Aligned_cols=38 Identities=13% Similarity=0.190 Sum_probs=19.2
Q ss_pred hCCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhCC
Q 020786 36 KRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQP 74 (321)
Q Consensus 36 ~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~P 74 (321)
+.|..|..+++ ++..-+--+-.-|+++++|+-++...-
T Consensus 21 ~~PtWlK~~~d-dvkeqI~K~akKGltpsqIGviLRDsh 58 (151)
T KOG0400|consen 21 SVPTWLKLTAD-DVKEQIYKLAKKGLTPSQIGVILRDSH 58 (151)
T ss_pred CCcHHHhcCHH-HHHHHHHHHHHcCCChhHceeeeeccc
Confidence 44555555544 355555555555555555555444433
No 31
>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=54.87 E-value=21 Score=22.10 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=22.4
Q ss_pred HHHHHHHHHHH-HcCCCHHHHHHHhhccCcc
Q 020786 188 ALWEKKLEAYM-NFGLTKDEVYSAFRRQPMF 217 (321)
Q Consensus 188 ~~l~~~v~~l~-~lG~~~~~v~~~i~~~P~i 217 (321)
++.-.+...|. ++|++..+..+|+..||.+
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 45566677888 8999999999999999975
No 32
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=52.89 E-value=26 Score=31.53 Aligned_cols=45 Identities=18% Similarity=0.261 Sum_probs=27.1
Q ss_pred HHHHHhhccCccccccHHHHhhHHHHHHHhcCCChHH-HhhCCccc
Q 020786 206 EVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLI-ISKHPYLL 250 (321)
Q Consensus 206 ~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~~~~-i~~~P~~L 250 (321)
.|.+=+...|.+++++.++++.+.+-|.+-+|+++.+ .-+||.=|
T Consensus 91 Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eL 136 (309)
T COG1125 91 TVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHEL 136 (309)
T ss_pred cHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhc
Confidence 3444455667777777777777777777767776642 23444443
No 33
>PHA01351 putative minor structural protein
Probab=51.52 E-value=2.1e+02 Score=29.51 Aligned_cols=65 Identities=6% Similarity=0.014 Sum_probs=46.5
Q ss_pred CChHHHHHHHhhCCCChHHHHHHHhhC---CCccc-cCccc--------chhhhHHHHHhcCCChhHHHHHHhhCCc
Q 020786 11 SDAYATVEFFRTNGFSDSQIKSITVKR---PKFYV-YNLKK--------CMKPKLEFFKSLGFAELQMAKFLSSQPY 75 (321)
Q Consensus 11 ~~~~~~l~~L~~lG~s~~~i~~lv~~~---P~lL~-~~~~~--------~l~~~v~~L~~lG~~~~~i~~il~~~P~ 75 (321)
-+|+....-|+.+|++++=+..++..+ |.+-. .++-. +....-.-|+.+|++++.+.-+++.+-+
T Consensus 641 IspkeAitELKKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~yy~ 717 (1070)
T PHA01351 641 IDPKEAETELKKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKFYY 717 (1070)
T ss_pred cCHHHHHHHHHHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 477888999999999998888887776 43311 11111 2334457899999999999988887654
No 34
>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=49.69 E-value=13 Score=29.32 Aligned_cols=21 Identities=29% Similarity=0.449 Sum_probs=14.5
Q ss_pred hCCCChHHHHHHHhhCCCccc
Q 020786 22 TNGFSDSQIKSITVKRPKFYV 42 (321)
Q Consensus 22 ~lG~s~~~i~~lv~~~P~lL~ 42 (321)
..|+|-++|..+-.-.|.+|.
T Consensus 21 rrG~sveeI~e~T~ID~wFL~ 41 (123)
T PF02787_consen 21 RRGYSVEEIHELTKIDPWFLE 41 (123)
T ss_dssp HTTB-HHHHHHHH---HHHHH
T ss_pred HcCCCHHHHHHHHCccHHHHH
Confidence 569999999999998988775
No 35
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=46.93 E-value=44 Score=30.42 Aligned_cols=67 Identities=15% Similarity=0.196 Sum_probs=44.9
Q ss_pred HHhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhHHHHHHHHHhCCCCCCCcccccccccChhhHHHHHhhh
Q 020786 224 KISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFSLTYMFKMTEKQFIERIVKK 298 (321)
Q Consensus 224 ~l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~~~~ 298 (321)
.++.+++.+.+ .|++.+.|.--|- ++++ +....-+.+++.+..-. ...+.-++..|.|+|...+.+.
T Consensus 164 ~l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~----~lg~Pilvg~SRKsfig~~~~~ 230 (282)
T PRK11613 164 YFIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFH----HFNLPLLVGMSRKSMIGQLLNV 230 (282)
T ss_pred HHHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHH----hCCCCEEEEecccHHHHhhcCC
Confidence 35677777776 6999999988885 4553 44555566665554311 2334558899999999887653
No 36
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=46.40 E-value=50 Score=22.84 Aligned_cols=40 Identities=25% Similarity=0.393 Sum_probs=25.7
Q ss_pred HHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCC
Q 020786 129 VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPT 171 (321)
Q Consensus 129 ~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~ 171 (321)
+..|++...|.+++...|.+ ++++.....+.++++|+.+.
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 34688888887777665544 44555555666677777654
No 37
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=46.23 E-value=22 Score=29.43 Aligned_cols=12 Identities=25% Similarity=0.490 Sum_probs=7.9
Q ss_pred hcCCChhHHHHH
Q 020786 58 SLGFAELQMAKF 69 (321)
Q Consensus 58 ~lG~~~~~i~~i 69 (321)
++|++.+++++.
T Consensus 16 ~LGitQ~dLA~~ 27 (187)
T COG3620 16 ELGITQKDLARR 27 (187)
T ss_pred HcCCCHHHHHHH
Confidence 467777776664
No 38
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=45.03 E-value=96 Score=26.34 Aligned_cols=25 Identities=24% Similarity=0.195 Sum_probs=20.2
Q ss_pred hhhHHHHHHHcCCChhhHHHhhhhC
Q 020786 121 LEPNIAILVNHGVPKSLVVKLMLIQ 145 (321)
Q Consensus 121 l~~~v~~L~~lG~~~~~i~~ll~~~ 145 (321)
+...+.+|.++|+++.++.+++...
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5667888888888888888887765
No 39
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=41.98 E-value=1.4e+02 Score=21.98 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=14.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHh
Q 020786 191 EKKLEAYMNFGLTKDEVYSAF 211 (321)
Q Consensus 191 ~~~v~~l~~lG~~~~~v~~~i 211 (321)
+.-+..|..+|+|.+|+.+++
T Consensus 66 KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 66 KQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred HHHHHHHHHcCCCHHHHHHHh
Confidence 333555667899999887765
No 40
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=41.56 E-value=56 Score=27.77 Aligned_cols=41 Identities=10% Similarity=0.072 Sum_probs=27.4
Q ss_pred chhHHHHHHHhhcCcHHHHHHHHhCCccccccchhhhhhHHH
Q 020786 85 IIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIA 126 (321)
Q Consensus 85 l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~ 126 (321)
+...+.+|.++|.+..++.+++.+.-.- ..++++-++..+.
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~~~-~~~~~~~i~~aL~ 189 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKILKE-AASVEELIREALK 189 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhcc-CCCHHHHHHHHHH
Confidence 5677888999999988888888776321 1355554554443
No 41
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=41.54 E-value=58 Score=20.59 Aligned_cols=40 Identities=20% Similarity=0.400 Sum_probs=22.5
Q ss_pred HHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCC
Q 020786 129 VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPT 171 (321)
Q Consensus 129 ~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~ 171 (321)
+.+|++...+.+++...| ..+.+......+.+.++|+.++
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 346777777777666554 2233344444455566666543
No 42
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=40.47 E-value=1.8e+02 Score=23.82 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=24.2
Q ss_pred hCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhh
Q 020786 108 AGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 144 (321)
Q Consensus 108 ~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~ 144 (321)
..|..+.++.++ ++..|--|..-|.++++|.-++.-
T Consensus 21 ~~P~W~~~~~ee-ve~~I~~lakkG~~pSqIG~~LRD 56 (151)
T PRK08561 21 EPPEWVDYSPEE-IEELVVELAKQGYSPSMIGIILRD 56 (151)
T ss_pred CCCccccCCHHH-HHHHHHHHHHCCCCHHHhhhhHhh
Confidence 456667777664 666777777777777777766644
No 43
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=39.74 E-value=94 Score=22.66 Aligned_cols=38 Identities=26% Similarity=0.328 Sum_probs=26.1
Q ss_pred HHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHh
Q 020786 17 VEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKS 58 (321)
Q Consensus 17 l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~ 58 (321)
-++-+.+|++.+||..+-..||.= +..+....+..+++
T Consensus 19 ~~Lar~L~vs~~dI~~I~~e~p~~----l~~Q~~~~L~~W~~ 56 (84)
T cd08805 19 AELARELQFSVEDINRIRVENPNS----LLEQSTALLNLWVD 56 (84)
T ss_pred HHHHHHcCCCHHHHHHHHHhCCCC----HHHHHHHHHHHHHH
Confidence 345568999999999999999962 22334444444443
No 44
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=39.16 E-value=71 Score=23.28 Aligned_cols=21 Identities=33% Similarity=0.578 Sum_probs=11.3
Q ss_pred HHHhhCCCChHHHHHHHhhCC
Q 020786 18 EFFRTNGFSDSQIKSITVKRP 38 (321)
Q Consensus 18 ~~L~~lG~s~~~i~~lv~~~P 38 (321)
++-+.+|+|..+|..+-..+|
T Consensus 18 ~laR~LGlse~~Id~i~~~~~ 38 (86)
T cd08306 18 KLARKLGLSETKIESIEEAHP 38 (86)
T ss_pred HHHHHcCCCHHHHHHHHHHCC
Confidence 344455555555555555555
No 45
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=38.92 E-value=32 Score=27.21 Aligned_cols=64 Identities=19% Similarity=0.156 Sum_probs=38.5
Q ss_pred HhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecchhHHHHHHHHHHcCCCCC
Q 020786 107 RAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPT 171 (321)
Q Consensus 107 ~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~lG~~~~ 171 (321)
+..|..+..+.++ +++-+--+..-|+++++|.-++...-.+=..+.-.=...+.++++-|+.++
T Consensus 20 r~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~Pe 83 (151)
T KOG0400|consen 20 RSVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPE 83 (151)
T ss_pred cCCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCC
Confidence 4567888888775 777777777788888888766654333222221111123455566666655
No 46
>PRK10026 arsenate reductase; Provisional
Probab=38.01 E-value=66 Score=25.98 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=25.7
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCC
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQP 146 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P 146 (321)
.+.+++..++..+|.++.-.+=.+ ... .-+|-+.+.+..++-+.|
T Consensus 76 ls~~e~l~ll~~~P~LIKRPIi~~-~~~----a~i~Rp~e~v~~~l~~~~ 120 (141)
T PRK10026 76 FTDDQLIDFMLQHPILINRPIVVT-PLG----TRLCRPSEVVLEILPDAQ 120 (141)
T ss_pred CCHHHHHHHHHhCccceeCcEEEc-CCC----eEEECCHHHHHHHhcccc
Confidence 466778888888888887654210 000 124556666666653333
No 47
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=37.86 E-value=1.1e+02 Score=19.97 Aligned_cols=24 Identities=13% Similarity=0.163 Sum_probs=17.1
Q ss_pred ChHHHHHHHhhCCCChHHHHHHHhhC
Q 020786 12 DAYATVEFFRTNGFSDSQIKSITVKR 37 (321)
Q Consensus 12 ~~~~~l~~L~~lG~s~~~i~~lv~~~ 37 (321)
+++.+.+||+++|+ .+....+..+
T Consensus 3 ~~~~V~~wL~~~~~--~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGL--GQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcCh--HHHHHHHHHc
Confidence 46778889988888 5566655554
No 48
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=36.85 E-value=1.6e+02 Score=24.00 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=9.7
Q ss_pred HHhhCCCChHHHHHHHhhC
Q 020786 19 FFRTNGFSDSQIKSITVKR 37 (321)
Q Consensus 19 ~L~~lG~s~~~i~~lv~~~ 37 (321)
-|..-|+++++|+-+++..
T Consensus 39 ~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 39 ELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred HHHHCCCCHHHhhhhHhhc
Confidence 3444555555555555443
No 49
>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=36.84 E-value=1e+02 Score=22.39 Aligned_cols=40 Identities=13% Similarity=0.367 Sum_probs=26.0
Q ss_pred HHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhhcC
Q 020786 55 FFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDT 98 (321)
Q Consensus 55 ~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g~~ 98 (321)
+-+.+|++..+|..+-..||. ++.......+..|+.-.+.
T Consensus 19 laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g~ 58 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKKK 58 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHCc
Confidence 444689999999999888884 2333455556555554443
No 50
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=35.55 E-value=45 Score=25.31 Aligned_cols=22 Identities=14% Similarity=0.412 Sum_probs=12.8
Q ss_pred cCCChhhHHHhhhhCCcceeec
Q 020786 131 HGVPKSLVVKLMLIQPRTLLQS 152 (321)
Q Consensus 131 lG~~~~~i~~ll~~~P~il~~~ 152 (321)
..++.+++..++..+|.++-+.
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 3456666666666666666544
No 51
>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=35.01 E-value=1.5e+02 Score=21.41 Aligned_cols=24 Identities=29% Similarity=0.480 Sum_probs=16.0
Q ss_pred HHHHHHhhCCCChHHHHHHHhhCC
Q 020786 15 ATVEFFRTNGFSDSQIKSITVKRP 38 (321)
Q Consensus 15 ~~l~~L~~lG~s~~~i~~lv~~~P 38 (321)
..-+|.+.+|+|+.+|..+-..+|
T Consensus 13 ~wk~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 13 RWKEFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCC
Confidence 345666677777777777766665
No 52
>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=34.76 E-value=80 Score=21.87 Aligned_cols=40 Identities=15% Similarity=0.177 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHHHHh
Q 020786 187 KALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKIS 226 (321)
Q Consensus 187 ~~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~l~ 226 (321)
.+++..-++.++.+||+.++|...+.+.=.+.+.+.+-|+
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~nW~lIE 47 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGNWELIE 47 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhhh
Confidence 4567777777778888888777666654444444433333
No 53
>PRK14136 recX recombination regulator RecX; Provisional
Probab=34.31 E-value=3.8e+02 Score=24.75 Aligned_cols=131 Identities=14% Similarity=0.162 Sum_probs=70.8
Q ss_pred HHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhhc-CcHHHHHHHHhCCccccccchhhhhhHHHHHHHcC
Q 020786 54 EFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLD-TDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHG 132 (321)
Q Consensus 54 ~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g~-~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG 132 (321)
.+|..---+..+|.+=|.+. +++ +..|...|++|.+.|. ++........+. ..-... -.....-|+.-|
T Consensus 170 ~lLSrReRSe~ELr~KL~kk----G~~-ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkG----p~rIrqELrQKG 239 (309)
T PRK14136 170 GYLSRREYSRAELARKLAPY----ADE-SDSVEPLLDALEREGWLSDARFAESLVHR-RASRVG----SARIVSELKRHA 239 (309)
T ss_pred HHhhcccccHHHHHHHHHHc----CCC-HHHHHHHHHHHHHcCCcCHHHHHHHHHHH-Hhhchh----HHHHHHHHHHcC
Confidence 44444445666666655543 233 2356777888888775 555666555543 111111 122335567789
Q ss_pred CChhhHHHhhhhCCcceeecchhHHHHHHHH-HHcCCCCCchhHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHh
Q 020786 133 VPKSLVVKLMLIQPRTLLQSTARLNKIIDEV-KKLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAF 211 (321)
Q Consensus 133 ~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l-~~lG~~~~~~~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i 211 (321)
|+.+.|...+... ..+.+......+ +.++-.+. ........+.||..-||+.+.|..++
T Consensus 240 Id~eLIEqALeei------eEDE~E~A~~L~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vL 299 (309)
T PRK14136 240 VGDALVESVGAQL------RETEFERAQAVWRKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLL 299 (309)
T ss_pred CCHHHHHHHHHhc------cHhHHHHHHHHHHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 9988888776532 112222222222 12221111 11234455789999999999998877
Q ss_pred hcc
Q 020786 212 RRQ 214 (321)
Q Consensus 212 ~~~ 214 (321)
..+
T Consensus 300 k~~ 302 (309)
T PRK14136 300 KVG 302 (309)
T ss_pred Hhc
Confidence 643
No 54
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=34.27 E-value=1.3e+02 Score=21.81 Aligned_cols=37 Identities=16% Similarity=0.282 Sum_probs=25.9
Q ss_pred HHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHh
Q 020786 18 EFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKS 58 (321)
Q Consensus 18 ~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~ 58 (321)
.+.+.+|+|.++|..+-..+|. ++...+...+.-|++
T Consensus 18 ~Lar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~ 54 (83)
T cd08319 18 QVLLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQ 54 (83)
T ss_pred HHHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHH
Confidence 4456899999999999999996 333345555545553
No 55
>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=33.94 E-value=2.2e+02 Score=21.86 Aligned_cols=106 Identities=11% Similarity=0.097 Sum_probs=54.3
Q ss_pred cchhHHHHHHHhhc-CcHHHHHHHHhCCcc-ccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecchhHHHHHH
Q 020786 84 HIIPCIEILRRVLD-TDENVLKAIRAGCLV-LEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIID 161 (321)
Q Consensus 84 ~l~~~v~~L~~~g~-~~~~v~~~l~~~P~l-L~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~~~~~~~v~ 161 (321)
.+...+++|.+.|. ++...+....+.-.- =+.+. .....-|+.-|++.+.|...+...+. .+.....+.
T Consensus 10 ~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~----~~I~~~L~~kGi~~~~i~~~l~~~~~-----~e~a~~~~~ 80 (121)
T PF02631_consen 10 AIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGP----RRIRQKLKQKGIDREIIEEALEEYDE-----EEEALELAE 80 (121)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--H----HHHHHHHHHTT--HHHHHHHHTCS-H-----HHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccH----HHHHHHHHHHCCChHHHHHHHHHhhH-----HHHHHHHHH
Confidence 46667788888885 555555544442111 12222 23456678899999998888762211 111111111
Q ss_pred -HHHHcCCCCCchhHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhhc
Q 020786 162 -EVKKLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRR 213 (321)
Q Consensus 162 -~l~~lG~~~~~~~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~ 213 (321)
.+.... . .......+.-+.+|..-||+.+.|..++..
T Consensus 81 kk~~~~~-~--------------~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 81 KKYRRYR-K--------------PSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHTT-T--------------S-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHhccc-C--------------CCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 111110 0 112355666678889999999999887753
No 56
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=31.48 E-value=66 Score=23.32 Aligned_cols=40 Identities=18% Similarity=0.264 Sum_probs=23.1
Q ss_pred HHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHh
Q 020786 17 VEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKS 58 (321)
Q Consensus 17 l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~ 58 (321)
+--|+..|+++++|..+=..+-.++... .++...++-+.+
T Consensus 20 ~vGLrR~Gfs~~~i~~l~~ayr~l~~~~--~~~~~a~~~l~~ 59 (83)
T PF13720_consen 20 LVGLRRRGFSKEEISALRRAYRILFRSG--LTLEEALEELEE 59 (83)
T ss_dssp HHHHHHTTS-HHHHHHHHHHHHHHHTSS--S-HHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHhCC--CCHHHHHHHHHH
Confidence 4456677777777776666665555433 246666666655
No 57
>cd00739 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS.
Probab=31.34 E-value=1.2e+02 Score=27.06 Aligned_cols=68 Identities=12% Similarity=0.112 Sum_probs=42.2
Q ss_pred HhhHHHHHHHhcCCChHHHhhCCcc-ccCCccCcchhHHHHHHHHHhCCCCCCCcccccccccChhhHHHHHhhhccC
Q 020786 225 ISKLMDCYVNKLSMEPLIISKHPYL-LLFSLEKRILPRCSVLQLLMSNKVITEDFSLTYMFKMTEKQFIERIVKKYEH 301 (321)
Q Consensus 225 l~~k~~fL~~~~g~~~~~i~~~P~~-L~~sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~~~~~~~ 301 (321)
++++++.+.+ .|++.++|.--|.+ ++.+. ...+..++.++.- + ...+..++..|.+.|...+....++
T Consensus 152 ~~~~i~~~~~-~Gi~~~~Ii~DPg~gf~ks~----~~~~~~l~~i~~l---~-~~~~pil~G~SrkSfig~~~~~~~~ 220 (257)
T cd00739 152 LEARLEAAES-AGVARNRIILDPGIGFGKTP----EHNLELLRRLDEL---K-QLGLPVLVGASRKSFIGALLGREPK 220 (257)
T ss_pred HHHHHHHHHH-cCCCHHHEEEecCCCcccCH----HHHHHHHHHHHHH---H-hCCCcEEEEecccHHHHHhcCCCcc
Confidence 6677787776 69999999888865 33331 2223333333210 0 1133557899999999988765443
No 58
>PHA02591 hypothetical protein; Provisional
Probab=31.30 E-value=86 Score=22.56 Aligned_cols=22 Identities=14% Similarity=0.040 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHH
Q 020786 188 ALWEKKLEAYMNFGLTKDEVYS 209 (321)
Q Consensus 188 ~~l~~~v~~l~~lG~~~~~v~~ 209 (321)
+.+..-..-|.+.|++.++|+.
T Consensus 46 dd~~~vA~eL~eqGlSqeqIA~ 67 (83)
T PHA02591 46 DDLISVTHELARKGFTVEKIAS 67 (83)
T ss_pred chHHHHHHHHHHcCCCHHHHHH
Confidence 4444445556677777777765
No 59
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=31.13 E-value=1e+02 Score=22.93 Aligned_cols=21 Identities=19% Similarity=0.214 Sum_probs=15.2
Q ss_pred cCcHHHHHHHHhCCccccccc
Q 020786 97 DTDENVLKAIRAGCLVLEYDI 117 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~ 117 (321)
.+.+++.+++.++|.++...+
T Consensus 74 ls~~e~~~~l~~~p~LikRPi 94 (105)
T cd02977 74 LSDEEALELMAEHPKLIKRPI 94 (105)
T ss_pred CCHHHHHHHHHhCcCeeeCCE
Confidence 466778888888888876553
No 60
>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=30.71 E-value=37 Score=23.12 Aligned_cols=37 Identities=24% Similarity=0.251 Sum_probs=22.4
Q ss_pred HhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhh
Q 020786 107 RAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 144 (321)
Q Consensus 107 ~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~ 144 (321)
...|..+.++.++ ++..|--|..-|+++++|.-+++.
T Consensus 20 ~~~P~W~~~~~~e-Ve~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 20 RSPPSWLKYSPEE-VEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp SS--TT--S-HHH-HHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCCCCCcCCCHHH-HHHHHHHHHHcCCCHHHhhhhhhh
Confidence 3457777777664 777777777778888887766653
No 61
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=30.59 E-value=70 Score=26.56 Aligned_cols=75 Identities=7% Similarity=0.168 Sum_probs=45.4
Q ss_pred HhhcCcHHHHHHH-HhCCccccccch------hhhhhHHHHHHHc-CCChhhHHHhhhhCCcceeecchhHHHHHHHHHH
Q 020786 94 RVLDTDENVLKAI-RAGCLVLEYDIE------KVLEPNIAILVNH-GVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKK 165 (321)
Q Consensus 94 ~~g~~~~~v~~~l-~~~P~lL~~s~~------~~l~~~v~~L~~l-G~~~~~i~~ll~~~P~il~~~~~~~~~~v~~l~~ 165 (321)
++|++++++++.. ...|.|-...-+ .+++..+++|.+. | ..-.++-+...|-+.+.+.+.+...++..++
T Consensus 16 ~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~--~~ita~~iM~spvv~v~pdDsi~~vv~lM~~ 93 (187)
T COG3620 16 ELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEK--TRITAKTIMHSPVVSVSPDDSISDVVNLMRD 93 (187)
T ss_pred HcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhc--ceEeHhhhccCCeeEECchhhHHHHHHHHHH
Confidence 4677777766543 233333221111 1456666777653 3 2233556667788888777888888888888
Q ss_pred cCCCC
Q 020786 166 LGFDP 170 (321)
Q Consensus 166 lG~~~ 170 (321)
-|++.
T Consensus 94 ~g~SQ 98 (187)
T COG3620 94 KGISQ 98 (187)
T ss_pred cCCcc
Confidence 88874
No 62
>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=30.59 E-value=2.5e+02 Score=21.52 Aligned_cols=58 Identities=16% Similarity=0.225 Sum_probs=30.3
Q ss_pred cchhHHHHHHHHHHcCCCCCch---hHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhh
Q 020786 152 STARLNKIIDEVKKLGFDPTNL---LFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFR 212 (321)
Q Consensus 152 ~~~~~~~~v~~l~~lG~~~~~~---~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~ 212 (321)
+.+.+...++.|.+.|+=.+.. .+++......+.++..++ .-|..-|++.+.|...+.
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~---~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIR---QKLKQKGIDREIIEEALE 67 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHH---HHHHHTT--HHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHH---HHHHHHCCChHHHHHHHH
Confidence 3455667777888888765432 233332222334444443 355678888888877666
No 63
>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=30.15 E-value=77 Score=30.16 Aligned_cols=43 Identities=19% Similarity=0.349 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhhccCccccccHHHHhhHHHHHHHhcCCC
Q 020786 188 ALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSME 239 (321)
Q Consensus 188 ~~l~~~v~~l~~lG~~~~~v~~~i~~~P~iL~~s~~~l~~k~~fL~~~~g~~ 239 (321)
+.....|+-+.+|||++++|.+.++ -+..+=.+-++||.. |+|
T Consensus 154 ~~~e~~I~~i~eMGf~R~qV~~ALR-------AafNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 154 SERETTIEEIMEMGYEREEVERALR-------AAFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHH-------HHhCCHHHHHHHHHh--CCC
Confidence 5788889999999999999987654 444556678999986 888
No 64
>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=30.04 E-value=80 Score=18.24 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=13.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhhc
Q 020786 190 WEKKLEAYMNFGLTKDEVYSAFRR 213 (321)
Q Consensus 190 l~~~v~~l~~lG~~~~~v~~~i~~ 213 (321)
|..-+.--++.|+|.+|++..+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 333344445788888888776543
No 65
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=29.78 E-value=67 Score=21.45 Aligned_cols=19 Identities=26% Similarity=0.688 Sum_probs=9.2
Q ss_pred HHHHHHcCCCHHHHHHHhh
Q 020786 194 LEAYMNFGLTKDEVYSAFR 212 (321)
Q Consensus 194 v~~l~~lG~~~~~v~~~i~ 212 (321)
|+-|.++||+.+.|...++
T Consensus 13 Vd~F~~mGF~~dkVvevlr 31 (55)
T PF09288_consen 13 VDQFENMGFERDKVVEVLR 31 (55)
T ss_dssp HHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHcCCcHHHHHHHHH
Confidence 4455566666665555443
No 66
>PHA00542 putative Cro-like protein
Probab=28.24 E-value=62 Score=23.30 Aligned_cols=32 Identities=19% Similarity=0.068 Sum_probs=23.7
Q ss_pred ccccccCChHHHHHHHhhCCCChHHHHHHHhh
Q 020786 5 EHRVLESDAYATVEFFRTNGFSDSQIKSITVK 36 (321)
Q Consensus 5 ~P~vL~~~~~~~l~~L~~lG~s~~~i~~lv~~ 36 (321)
.|.+...++......+...|++..++++.+..
T Consensus 12 Rp~~~~~~~~~l~~~l~~~glTq~elA~~lgI 43 (82)
T PHA00542 12 IPAAYTQRPDELVCALIRAGWSQEQIADATDV 43 (82)
T ss_pred CCcccCcCHHHHHHHHHHCCCCHHHHHHHHCc
Confidence 57777777777778888888888887755543
No 67
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=28.06 E-value=1.4e+02 Score=19.57 Aligned_cols=46 Identities=13% Similarity=0.118 Sum_probs=24.3
Q ss_pred ChHHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhh-HHHHHhcCCCh
Q 020786 12 DAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPK-LEFFKSLGFAE 63 (321)
Q Consensus 12 ~~~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~-v~~L~~lG~~~ 63 (321)
+++.+.+||..+|+.. ....+..+.- +...-+.-. -+.|.++|+..
T Consensus 5 ~~~~v~~wL~~~g~~~--y~~~f~~~~i----~g~~ll~~~~~~~l~~lgi~~ 51 (68)
T smart00454 5 SPESVADWLESIGLEQ--YADNFRKNGI----DGALLLLLTSEEDLKELGITK 51 (68)
T ss_pred CHHHHHHHHHHCChHH--HHHHHHHCCC----CHHHHHhcChHHHHHHcCCCc
Confidence 4566788888888754 5555544421 111111111 35677788744
No 68
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=27.99 E-value=3.2e+02 Score=21.98 Aligned_cols=123 Identities=11% Similarity=0.079 Sum_probs=0.0
Q ss_pred HHHHHHHhhCCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcC-CChhHHHHHHhhCCccccccccccchhHHHHH
Q 020786 14 YATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLG-FAELQMAKFLSSQPYILERSLENHIIPCIEIL 92 (321)
Q Consensus 14 ~~~l~~L~~lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG-~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L 92 (321)
+.++.+|..-.-|..++.+-+... +.+.+ .+...|+.|...| +++...+....+.-.--..+ -......|
T Consensus 15 ~~al~~L~~r~~s~~el~~kL~~k----g~~~~-~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g----~~~I~~~L 85 (157)
T PRK00117 15 ARALRLLARREHSRAELRRKLAAK----GFSEE-VIEAVLDRLKEEGLLDDERFAESFVRSRARKGYG----PRRIRQEL 85 (157)
T ss_pred HHHHHHHccchhHHHHHHHHHHhc----CCCHH-HHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCch----HHHHHHHH
Q ss_pred HHhhcCcHHHHHHHHhCC----------------ccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCC
Q 020786 93 RRVLDTDENVLKAIRAGC----------------LVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQP 146 (321)
Q Consensus 93 ~~~g~~~~~v~~~l~~~P----------------~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P 146 (321)
..-|++.+.|..++...+ ..-..+. ..-...+.+|..-||+.+.|...+....
T Consensus 86 ~~kGi~~~~I~~~l~~~~~d~~e~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~l~~~~ 154 (157)
T PRK00117 86 RQKGVDREIIEEALAELDIDWEELARELARKKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRVLRNAL 154 (157)
T ss_pred HHcCCCHHHHHHHHHHcCccHHHHHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHHHHhhh
No 69
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.93 E-value=1e+02 Score=27.94 Aligned_cols=45 Identities=24% Similarity=0.282 Sum_probs=0.0
Q ss_pred cchhHHHHHHHHHHcCCCCCchhHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhhc
Q 020786 152 STARLNKIIDEVKKLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRR 213 (321)
Q Consensus 152 ~~~~~~~~v~~l~~lG~~~~~~~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~~ 213 (321)
.++-+...|.||+.=-+-. ..+..|.+||++-|++.+||...+.+
T Consensus 1 Redli~~AVkFL~~~kVr~-----------------aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 1 REDLIENAVKFLQNPKVRD-----------------APLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred CcHHHHHHHHHhcCccccc-----------------chHHHHHHHHHhcCCCHHHHHHHHHh
No 70
>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=27.57 E-value=18 Score=24.63 Aligned_cols=39 Identities=18% Similarity=0.081 Sum_probs=21.0
Q ss_pred hHHHHHHHHhhcCHHHHHHHHHHHHHcCCCHHHHHHHhh
Q 020786 174 LFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFR 212 (321)
Q Consensus 174 ~~~~~~~~~~~~~~~~l~~~v~~l~~lG~~~~~v~~~i~ 212 (321)
.+.+.+|.-+..+.+.+.+.+--|.+-|++..+|..+++
T Consensus 17 P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLR 55 (60)
T PF08069_consen 17 PYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_dssp -S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHH
T ss_pred CCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhh
Confidence 333333333345566777777777777777777776654
No 71
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=27.32 E-value=1.3e+02 Score=22.95 Aligned_cols=40 Identities=10% Similarity=0.086 Sum_probs=24.8
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHh
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKL 141 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~l 141 (321)
.+.+++..++..+|.++...+=. ... =.-.|++.+.+..+
T Consensus 74 ls~~e~i~~l~~~p~LikRPii~--~~~---~~~vG~~~e~~~~~ 113 (115)
T cd03032 74 LSLSELIRLISEHPSLLRRPIII--DEK---RLQIGYNEDEIRQF 113 (115)
T ss_pred CCHHHHHHHHHhChhheeCCEEE--eCC---EEEeCCCHHHHHHh
Confidence 36677888888999888776431 111 01267777766554
No 72
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=26.43 E-value=1.3e+02 Score=23.75 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=27.6
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhh
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLM 142 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll 142 (321)
.+.+++..++..+|.++...+=. ... . --.|++.+++..++
T Consensus 74 ls~~e~i~ll~~~P~LikRPIv~--~~~--~-~~iG~~~e~~~~~l 114 (132)
T PRK13344 74 LSVNEVIDLIQENPRILKSPILI--DDK--R-LQVGYKEDDIRAFL 114 (132)
T ss_pred CCHHHHHHHHHhCccceeCcEEE--eCC--E-EEeCCCHHHHHHHc
Confidence 35677888999999998876531 111 0 12788888887765
No 73
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=26.33 E-value=65 Score=22.18 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=14.7
Q ss_pred HHHhhCCCChHHHHHHHhh
Q 020786 18 EFFRTNGFSDSQIKSITVK 36 (321)
Q Consensus 18 ~~L~~lG~s~~~i~~lv~~ 36 (321)
..|.++|+|..|+...+.+
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5667888888888877665
No 74
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=25.71 E-value=2.6e+02 Score=22.73 Aligned_cols=36 Identities=11% Similarity=0.191 Sum_probs=20.6
Q ss_pred CCCccccCcccchhhhHHHHHhcCCChhHHHHHHhhC
Q 020786 37 RPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQ 73 (321)
Q Consensus 37 ~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~~~ 73 (321)
.|..+..+.+ ++...|.-|..-|+++++|+-++...
T Consensus 19 ~P~w~~~~~e-eVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 19 PPSWLKLSSS-EVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred CCchhcCCHH-HHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 4444555554 36666666666666666666655543
No 75
>PRK10026 arsenate reductase; Provisional
Probab=25.18 E-value=1.9e+02 Score=23.38 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=16.7
Q ss_pred CCChhhHHHhhhhCCcceeecc
Q 020786 132 GVPKSLVVKLMLIQPRTLLQST 153 (321)
Q Consensus 132 G~~~~~i~~ll~~~P~il~~~~ 153 (321)
+++.+++..++..+|.++-+..
T Consensus 75 ~ls~~e~l~ll~~~P~LIKRPI 96 (141)
T PRK10026 75 KFTDDQLIDFMLQHPILINRPI 96 (141)
T ss_pred CCCHHHHHHHHHhCccceeCcE
Confidence 3566778889999998887653
No 76
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=24.96 E-value=1.8e+02 Score=21.04 Aligned_cols=20 Identities=30% Similarity=0.586 Sum_probs=11.3
Q ss_pred HhhCCCChHHHHHHHhhCCC
Q 020786 20 FRTNGFSDSQIKSITVKRPK 39 (321)
Q Consensus 20 L~~lG~s~~~i~~lv~~~P~ 39 (321)
-+.+||+..+|.++-..||.
T Consensus 22 Ar~Lg~se~dI~~i~~~~~~ 41 (84)
T cd08804 22 ARELDFTEEQIHQIRIENPN 41 (84)
T ss_pred HHHcCCCHHHHHHHHHHCcc
Confidence 34566666666665555553
No 77
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=24.79 E-value=2.6e+02 Score=27.27 Aligned_cols=131 Identities=16% Similarity=0.187 Sum_probs=66.5
Q ss_pred ccccccchhHHHHHHHhhc----CcHHHHHHH-HhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCcceeecc
Q 020786 79 RSLENHIIPCIEILRRVLD----TDENVLKAI-RAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQST 153 (321)
Q Consensus 79 ~s~~~~l~~~v~~L~~~g~----~~~~v~~~l-~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~il~~~~ 153 (321)
.+.|+.|.-++..|+.+.. .+.+.-..+ ..+..+..+-+.+ ..+..+-++|+.+++-...++.|-+-+-...
T Consensus 259 ~spEraL~lRL~LLQGV~~yHqg~~deAye~le~a~~~l~elki~d---~~lsllv~mGfeesdaRlaLRsc~g~Vd~Av 335 (568)
T KOG2561|consen 259 QSPERALILRLELLQGVVAYHQGQRDEAYEALESAHAKLLELKIND---ETLSLLVGMGFEESDARLALRSCNGDVDSAV 335 (568)
T ss_pred CChhHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHeeccc---hHHHHHHHcCCCchHHHHHHHhccccHHHHH
Confidence 4456666667777776432 222333333 3333344444332 4677888899999988888877765333332
Q ss_pred hhHHHHHHHHHHcCC--CCCchhHHHHHHHHhhcCHH--HHHHHHHHHHHcCCCHHHHHHHhhc
Q 020786 154 ARLNKIIDEVKKLGF--DPTNLLFVLAIRSMAVMSKA--LWEKKLEAYMNFGLTKDEVYSAFRR 213 (321)
Q Consensus 154 ~~~~~~v~~l~~lG~--~~~~~~~~~~~~~~~~~~~~--~l~~~v~~l~~lG~~~~~v~~~i~~ 213 (321)
..+.+.-+.+.+... ...++.+.+. ..+..+... -....+.+|.++|++.+-+...+.+
T Consensus 336 qfI~erre~laq~R~k~~a~Ere~~~r-~k~~n~~~~~wvn~rs~~rL~~mGyer~la~eaL~r 398 (568)
T KOG2561|consen 336 QFIIERREKLAQKREKDLAREREILER-KKYGNTPMKKWVNPRSLERLVSMGYERELAAEALRR 398 (568)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHH-HHhcCCCcccccCHHHHHHHHhcchHhHHHHHHHHh
Confidence 222222222211110 0011111000 001111111 1345678889999999988888887
No 78
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=24.60 E-value=3.1e+02 Score=24.98 Aligned_cols=108 Identities=11% Similarity=0.126 Sum_probs=56.4
Q ss_pred hcCCChhHHHHHHhhCCcccccccccc------chhHHHHHHHhhcCcHHHHHHHHhCCcccccc--------chhhhhh
Q 020786 58 SLGFAELQMAKFLSSQPYILERSLENH------IIPCIEILRRVLDTDENVLKAIRAGCLVLEYD--------IEKVLEP 123 (321)
Q Consensus 58 ~lG~~~~~i~~il~~~P~iL~~s~~~~------l~~~v~~L~~~g~~~~~v~~~l~~~P~lL~~s--------~~~~l~~ 123 (321)
+++-..+.+..++..-|.++..++|.. ++|.-.|-+++.+ +..+=...|.+.+.| -++.+..
T Consensus 157 DF~G~~~al~~v~~~~pdV~nHNvETVprL~~~VRp~A~Y~~SL~~----L~~~k~~~P~i~TKSgiMlGLGEt~~Ev~e 232 (306)
T COG0320 157 DFRGNDDALEIVADAGPDVFNHNVETVPRLYPRVRPGATYERSLSL----LERAKELGPDIPTKSGLMVGLGETDEEVIE 232 (306)
T ss_pred cccCCHHHHHHHHhcCcchhhcccccchhcccccCCCCcHHHHHHH----HHHHHHhCCCcccccceeeecCCcHHHHHH
Confidence 343366777778888888888887643 4444555555532 222233344444422 1223455
Q ss_pred HHHHHHHcCCChhhHHHhhhhC----CcceeecchhHHHHHHHHHHcCCC
Q 020786 124 NIAILVNHGVPKSLVVKLMLIQ----PRTLLQSTARLNKIIDEVKKLGFD 169 (321)
Q Consensus 124 ~v~~L~~lG~~~~~i~~ll~~~----P~il~~~~~~~~~~v~~l~~lG~~ 169 (321)
.+.-|++.|++-=.|.+.+.-. |-.=..+++.++..-+.-.++||.
T Consensus 233 ~m~DLr~~gvdilTiGQYlqPS~~HlpV~ryv~PeeF~~~~~~a~~~GF~ 282 (306)
T COG0320 233 VMDDLRSAGVDILTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFL 282 (306)
T ss_pred HHHHHHHcCCCEEEeccccCCccccCCceeccCHHHHHHHHHHHHHccch
Confidence 5555566777655555544211 111123455555555555566664
No 79
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=24.56 E-value=93 Score=23.86 Aligned_cols=41 Identities=12% Similarity=0.111 Sum_probs=24.1
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHh
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKL 141 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~l 141 (321)
.+.+++..++..+|.++...+=.+ ... . --.|++.+++..+
T Consensus 75 ls~~e~~~~i~~~p~LikRPIi~~-~~~-~--~~vG~~~e~~~~~ 115 (117)
T TIGR01617 75 LSDKEALELLAEDPALLRRPLIVD-TKN-R--LLIGFKSESIEEF 115 (117)
T ss_pred CCHHHHHHHHHhCcceEecCEEEe-CCc-e--EEecCCHHHHHHh
Confidence 366778888888888887664310 000 0 0267776666543
No 80
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=24.30 E-value=1.9e+02 Score=21.04 Aligned_cols=39 Identities=13% Similarity=0.323 Sum_probs=25.8
Q ss_pred HHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhhcC
Q 020786 56 FKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDT 98 (321)
Q Consensus 56 L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g~~ 98 (321)
...+|++.++|.++=..||.= +..++...+.-|++-.+.
T Consensus 20 ar~Lgls~~~I~~i~~~~p~~----l~eQv~~mL~~W~~r~G~ 58 (83)
T cd08319 20 LLDLGLSQTDIYRCKENHPHN----VQSQIVEALVKWRQRFGK 58 (83)
T ss_pred HHHcCCCHHHHHHHHHhCCCC----HHHHHHHHHHHHHHhcCC
Confidence 346899999999998888863 333455555555554333
No 81
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=24.21 E-value=2.1e+02 Score=20.82 Aligned_cols=37 Identities=11% Similarity=0.131 Sum_probs=23.8
Q ss_pred HHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhh
Q 020786 56 FKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVL 96 (321)
Q Consensus 56 L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g 96 (321)
-..+|++.++|..+-..||.= +..+....+..|.+-.
T Consensus 22 ar~L~vs~~dI~~I~~e~p~~----l~~Q~~~~L~~W~~r~ 58 (84)
T cd08805 22 ARELQFSVEDINRIRVENPNS----LLEQSTALLNLWVDRE 58 (84)
T ss_pred HHHcCCCHHHHHHHHHhCCCC----HHHHHHHHHHHHHHhc
Confidence 346889999999998888853 2234444555555443
No 82
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=24.06 E-value=1.7e+02 Score=22.34 Aligned_cols=40 Identities=25% Similarity=0.282 Sum_probs=24.7
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHh
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKL 141 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~l 141 (321)
.+.+++..++.++|.++...+=. ... . .-+|++++.+..+
T Consensus 74 ls~~e~i~~l~~~P~LikRPIi~--~~~--~-~~vG~~~e~i~~~ 113 (114)
T TIGR00014 74 LSDQELLDAMVAHPILLERPIVV--AGD--G-ARIGRPPENVLDI 113 (114)
T ss_pred CCHHHHHHHHHHCcCcccCCeEE--ECC--E-EEEcCCHHHHHHh
Confidence 35677888888888888766421 111 0 1267777776654
No 83
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=23.86 E-value=1.7e+02 Score=22.31 Aligned_cols=21 Identities=29% Similarity=0.422 Sum_probs=15.9
Q ss_pred cCcHHHHHHHHhCCccccccc
Q 020786 97 DTDENVLKAIRAGCLVLEYDI 117 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~ 117 (321)
.+.+++..++..+|.++...+
T Consensus 73 ls~~e~i~ll~~~P~LikRPI 93 (112)
T cd03034 73 LSDEELIDAMAAHPILIERPI 93 (112)
T ss_pred CCHHHHHHHHHhCcCcccCCE
Confidence 466778888888888887664
No 84
>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=23.78 E-value=2.2e+02 Score=29.66 Aligned_cols=43 Identities=12% Similarity=0.183 Sum_probs=29.4
Q ss_pred CCCChHHHHHHHhhCCCccccCcccchhhhHHHHHhcCCChhHHHHHHh
Q 020786 23 NGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLS 71 (321)
Q Consensus 23 lG~s~~~i~~lv~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~i~~il~ 71 (321)
-|+++..+..+...+.. .......+.||.++|++.+...++..
T Consensus 123 ~gi~~~~~~~i~~~~~~------~~~~~~~~~~L~~~gi~~~~a~ki~~ 165 (720)
T TIGR01448 123 PGISKANLEKFVSQWSQ------QGDERRLLAGLQGLGIGIKLAQRIYK 165 (720)
T ss_pred CCCCHHHHHHHHHHHHH------hHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 37777777777776622 12367778999999999866655443
No 85
>TIGR01496 DHPS dihydropteroate synthase. This model represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (pfam00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of pfam00809 and COG0294 are represented by TIGR00284.
Probab=23.00 E-value=1.7e+02 Score=26.03 Aligned_cols=67 Identities=13% Similarity=0.110 Sum_probs=39.4
Q ss_pred HhhHHHHHHHhcCCChHHHhhCCccccCCccCcchhHHHHHHHHHhCCCCCCCcccccccccChhhHHHHHhhhc
Q 020786 225 ISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFSLTYMFKMTEKQFIERIVKKY 299 (321)
Q Consensus 225 l~~k~~fL~~~~g~~~~~i~~~P~~L~~sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~~~~~ 299 (321)
++++++.+.+ .|++.++|.--|.+ ++.- ....=+++++.++.- + ...+..++..|.++|.......-
T Consensus 150 ~~~~i~~~~~-~Gi~~~~iilDPg~-gf~k--s~~~~~~~l~~i~~l---~-~~~~p~l~G~SrkSfig~v~~~~ 216 (257)
T TIGR01496 150 LEARAEELVA-AGVAAERIILDPGI-GFGK--TPEHNLELLKHLEEF---V-ALGYPLLVGASRKSFIGALLGTP 216 (257)
T ss_pred HHHHHHHHHH-cCCCHHHEEEECCC-Cccc--CHHHHHHHHHHHHHH---H-hCCCcEEEEecccHHHHhhcCCC
Confidence 5667777766 69998998888844 3421 122222333332210 0 12245688999999998886543
No 86
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=23.00 E-value=2.2e+02 Score=24.73 Aligned_cols=63 Identities=10% Similarity=-0.001 Sum_probs=38.3
Q ss_pred hhhhCCcceeecch--hHHHHHHHHHHcCCCCCchhHHHHHHHHhhc-----------CHHHHHHHHHHHHHcCCC
Q 020786 141 LMLIQPRTLLQSTA--RLNKIIDEVKKLGFDPTNLLFVLAIRSMAVM-----------SKALWEKKLEAYMNFGLT 203 (321)
Q Consensus 141 ll~~~P~il~~~~~--~~~~~v~~l~~lG~~~~~~~~~~~~~~~~~~-----------~~~~l~~~v~~l~~lG~~ 203 (321)
++-.+|+++....+ .+..++..++.+|++=.+..+..|...+... ....+..-+.||+.+|-.
T Consensus 134 ~MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~~ 209 (217)
T PRK14487 134 NMPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGTA 209 (217)
T ss_pred CCCCCcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhccc
Confidence 34456666655544 6778888888889886665555554443321 124566667777776643
No 87
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.83 E-value=96 Score=20.76 Aligned_cols=18 Identities=11% Similarity=0.379 Sum_probs=12.8
Q ss_pred HHHHHHcCCCHHHHHHHh
Q 020786 194 LEAYMNFGLTKDEVYSAF 211 (321)
Q Consensus 194 v~~l~~lG~~~~~v~~~i 211 (321)
+..++.+|||-++|..++
T Consensus 7 I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 345568999999999988
No 88
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=22.73 E-value=38 Score=26.14 Aligned_cols=9 Identities=33% Similarity=0.501 Sum_probs=4.2
Q ss_pred HHcCCCHHH
Q 020786 198 MNFGLTKDE 206 (321)
Q Consensus 198 ~~lG~~~~~ 206 (321)
.++|+|...
T Consensus 87 ~elGLtP~s 95 (116)
T TIGR01558 87 SALGLTPSS 95 (116)
T ss_pred HHcCCCHHH
Confidence 345555443
No 89
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=22.40 E-value=64 Score=25.13 Aligned_cols=40 Identities=13% Similarity=0.272 Sum_probs=24.3
Q ss_pred CcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhh
Q 020786 98 TDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLM 142 (321)
Q Consensus 98 ~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll 142 (321)
+.+++...+..+|.++...+= +.+.- ...|++.+++..++
T Consensus 76 ~~~~~~~~i~~~~~LikRPiv--v~~~~---~~iG~~~e~~~~~l 115 (117)
T COG1393 76 SDEELIEALLENPSLIKRPIV--VDNKK---LRVGFNEEEIRAFL 115 (117)
T ss_pred ChHHHHHHHHhChhhccCCeE--EeCCc---eEecCCHHHHHHHh
Confidence 566778888888866655431 11110 34788888777654
No 90
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=22.06 E-value=1.9e+02 Score=25.47 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=28.9
Q ss_pred chhhhHHHHHhcCCChhHHHHHHhhCCccccccccccchhHHHHHHHhh
Q 020786 48 CMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVL 96 (321)
Q Consensus 48 ~l~~~v~~L~~lG~~~~~i~~il~~~P~iL~~s~~~~l~~~v~~L~~~g 96 (321)
-+...+.+|.+-|.+.++|.+++..-|..=+ +.+.+.++.+.|
T Consensus 58 ~M~rv~k~Lheqgv~~~~ik~~~r~iP~~Pg------mv~lik~~ak~g 100 (256)
T KOG3120|consen 58 LMDRVFKELHEQGVRIAEIKQVLRSIPIVPG------MVRLIKSAAKLG 100 (256)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHhcCCCCcc------HHHHHHHHHhCC
Confidence 3666677777888888888888777776554 334555666555
No 91
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=21.75 E-value=1.5e+02 Score=20.06 Aligned_cols=20 Identities=15% Similarity=0.346 Sum_probs=9.6
Q ss_pred HHHHhhcCcHHHHHHHHhCC
Q 020786 91 ILRRVLDTDENVLKAIRAGC 110 (321)
Q Consensus 91 ~L~~~g~~~~~v~~~l~~~P 110 (321)
.|..++-+.-++...|..+|
T Consensus 27 lLqql~~~nP~l~q~I~~n~ 46 (59)
T PF09280_consen 27 LLQQLGQSNPQLLQLIQQNP 46 (59)
T ss_dssp HHHHHHCCSHHHHHHHHHTH
T ss_pred HHHHHhccCHHHHHHHHHCH
Confidence 34444444455555544444
No 92
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=21.51 E-value=2.7e+02 Score=20.19 Aligned_cols=19 Identities=16% Similarity=0.109 Sum_probs=10.6
Q ss_pred HhhCCCChHHHHHHHhhCC
Q 020786 20 FRTNGFSDSQIKSITVKRP 38 (321)
Q Consensus 20 L~~lG~s~~~i~~lv~~~P 38 (321)
-+.+|+|.++|..+-..||
T Consensus 20 ar~LGlse~~Id~Ie~~~~ 38 (86)
T cd08779 20 GLHLGLSYRELQRIKYNNR 38 (86)
T ss_pred HHHcCCCHHHHHHHHHHCc
Confidence 3355555555555555555
No 93
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.45 E-value=1.8e+02 Score=21.45 Aligned_cols=24 Identities=8% Similarity=0.130 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhhccC
Q 020786 192 KKLEAYMNFGLTKDEVYSAFRRQP 215 (321)
Q Consensus 192 ~~v~~l~~lG~~~~~v~~~i~~~P 215 (321)
..+.+|+++|++-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 48 QFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCc
Confidence 345677899999999999887543
No 94
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=21.43 E-value=52 Score=21.07 Aligned_cols=18 Identities=11% Similarity=0.180 Sum_probs=8.2
Q ss_pred hhCCCChHHHHHHHhhCC
Q 020786 21 RTNGFSDSQIKSITVKRP 38 (321)
Q Consensus 21 ~~lG~s~~~i~~lv~~~P 38 (321)
...|+|..|+++.+...|
T Consensus 6 ~~~gls~~~la~~~gis~ 23 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISR 23 (55)
T ss_dssp HHTTS-HHHHHHHHTS-H
T ss_pred HHcCCCHHHHHHHhCCCc
Confidence 345555555555554333
No 95
>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=21.42 E-value=2.6e+02 Score=20.10 Aligned_cols=21 Identities=19% Similarity=0.469 Sum_probs=16.5
Q ss_pred HHHHhcCCChhHHHHHHhhCC
Q 020786 54 EFFKSLGFAELQMAKFLSSQP 74 (321)
Q Consensus 54 ~~L~~lG~~~~~i~~il~~~P 74 (321)
+|-+.+|+|..+|-.+=..||
T Consensus 16 ~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 16 EFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHcCCCHHHHHHHHHhCC
Confidence 566678888888888877777
No 96
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=21.18 E-value=1.3e+02 Score=19.98 Aligned_cols=21 Identities=14% Similarity=0.202 Sum_probs=14.3
Q ss_pred ChHHHHHHHhhCCCChHHHHHHH
Q 020786 12 DAYATVEFFRTNGFSDSQIKSIT 34 (321)
Q Consensus 12 ~~~~~l~~L~~lG~s~~~i~~lv 34 (321)
+++.|.+||.++|+ ++....+
T Consensus 4 ~~~~V~~WL~~~~l--~~y~~~F 24 (64)
T PF00536_consen 4 SVEDVSEWLKSLGL--EQYAENF 24 (64)
T ss_dssp SHHHHHHHHHHTTG--GGGHHHH
T ss_pred CHHHHHHHHHHCCC--HHHHHHH
Confidence 56778888888888 3444444
No 97
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=21.14 E-value=1.3e+02 Score=23.63 Aligned_cols=46 Identities=11% Similarity=0.126 Sum_probs=29.7
Q ss_pred cCcHHHHHHHHhCCccccccchhhhhhHHHHHHHcCCChhhHHHhhhhCCc
Q 020786 97 DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPR 147 (321)
Q Consensus 97 ~~~~~v~~~l~~~P~lL~~s~~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~ 147 (321)
.+.+++..++..+|.++.-.+=.. ... .-+|++.+.+..++...|.
T Consensus 73 ls~~e~i~lm~~~P~LIKRPIi~~-~~~----~~iGf~~e~~~~~l~~~~~ 118 (126)
T TIGR01616 73 IDEASALALMVSDPLLIRRPLMDL-GGI----RCAGFDREPVLSWIGLQTQ 118 (126)
T ss_pred CCHHHHHHHHHhCcCeEeCCEEEE-CCE----EEEcCCHHHHHHHhCCCCC
Confidence 466778888888888887664210 111 1268888888777765553
No 98
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.75 E-value=2.4e+02 Score=20.78 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhhccC
Q 020786 192 KKLEAYMNFGLTKDEVYSAFRRQP 215 (321)
Q Consensus 192 ~~v~~l~~lG~~~~~v~~~i~~~P 215 (321)
..+..++++|++-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 48 HQIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhCCC
Confidence 446677899999999999886543
No 99
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=20.53 E-value=2.5e+02 Score=22.19 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=17.4
Q ss_pred chhhhhhHHHHHHHcCCChhhHHHhhhh
Q 020786 117 IEKVLEPNIAILVNHGVPKSLVVKLMLI 144 (321)
Q Consensus 117 ~~~~l~~~v~~L~~lG~~~~~i~~ll~~ 144 (321)
+...+..++.-|++-|.+.+++..-+.+
T Consensus 89 i~~~vi~~I~el~~eG~s~eei~~ki~~ 116 (131)
T PF08004_consen 89 IPESVIERIKELKSEGKSEEEIAEKISR 116 (131)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3445666677777777777776654433
No 100
>PRK09875 putative hydrolase; Provisional
Probab=20.31 E-value=95 Score=28.37 Aligned_cols=28 Identities=18% Similarity=0.302 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhhccCc
Q 020786 189 LWEKKLEAYMNFGLTKDEVYSAFRRQPM 216 (321)
Q Consensus 189 ~l~~~v~~l~~lG~~~~~v~~~i~~~P~ 216 (321)
-+..-+-.|++.|+++++|.+|+..+|.
T Consensus 261 i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 261 LLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 3555566788999999999999999996
Done!