Query 043018
Match_columns 300
No_of_seqs 191 out of 1141
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 12:00:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043018hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 7.7E-53 1.7E-57 403.5 19.6 261 1-267 148-447 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.6E-47 3.5E-52 355.2 7.1 256 1-257 21-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 9.8E-40 2.1E-44 313.2 15.8 255 1-259 112-412 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.6E-30 1.2E-34 237.7 4.3 237 18-258 2-314 (345)
5 KOG1267 Mitochondrial transcri 99.9 9.5E-24 2E-28 200.4 13.7 210 16-235 201-411 (413)
6 KOG1267 Mitochondrial transcri 99.9 9.2E-22 2E-26 186.8 13.0 226 1-238 115-342 (413)
7 smart00733 Mterf Mitochondrial 97.5 0.0001 2.3E-09 42.7 2.7 30 173-203 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.4 0.00014 3.1E-09 42.1 2.4 30 68-98 2-31 (31)
9 PF11955 PORR: Plant organelle 94.0 1 2.2E-05 41.8 11.9 195 22-220 46-294 (335)
10 cd04790 HTH_Cfa-like_unk Helix 91.4 1.1 2.5E-05 37.3 7.9 115 51-174 49-167 (172)
11 cd04790 HTH_Cfa-like_unk Helix 83.4 2 4.4E-05 35.9 4.5 113 15-140 49-167 (172)
12 PF04695 Pex14_N: Peroxisomal 82.0 2.3 5E-05 34.1 4.2 30 153-182 22-51 (136)
13 PF04695 Pex14_N: Peroxisomal 75.8 4.1 8.8E-05 32.6 3.9 40 70-113 12-51 (136)
14 PF11955 PORR: Plant organelle 74.0 19 0.00042 33.4 8.3 94 93-186 45-152 (335)
15 smart00165 UBA Ubiquitin assoc 64.3 12 0.00025 22.3 3.3 24 155-178 2-25 (37)
16 COG1125 OpuBA ABC-type proline 62.3 17 0.00036 32.7 5.1 55 151-205 70-126 (309)
17 PF00356 LacI: Bacterial regul 62.2 27 0.00059 22.3 4.8 41 92-135 6-46 (46)
18 PF00627 UBA: UBA/TS-N domain; 61.2 11 0.00025 22.5 2.8 24 155-178 3-26 (37)
19 cd00194 UBA Ubiquitin Associat 59.6 16 0.00034 21.8 3.3 23 156-178 3-25 (38)
20 PF08069 Ribosomal_S13_N: Ribo 55.3 9 0.0002 26.1 1.7 47 131-177 10-56 (60)
21 PF14490 HHH_4: Helix-hairpin- 54.7 37 0.00081 25.0 5.3 35 104-138 38-74 (94)
22 PRK14136 recX recombination re 53.0 1.9E+02 0.004 26.6 10.9 106 48-178 195-302 (309)
23 COG3620 Predicted transcriptio 51.8 21 0.00045 29.6 3.6 23 145-167 75-97 (187)
24 PRK11613 folP dihydropteroate 51.6 41 0.00088 30.5 5.9 68 189-264 165-232 (282)
25 PF14490 HHH_4: Helix-hairpin- 51.3 50 0.0011 24.3 5.5 71 11-106 6-77 (94)
26 smart00354 HTH_LACI helix_turn 47.8 42 0.00092 23.2 4.4 40 93-135 8-47 (70)
27 PF11212 DUF2999: Protein of u 47.3 78 0.0017 22.3 5.3 20 87-106 3-22 (82)
28 PF07499 RuvA_C: RuvA, C-termi 47.0 39 0.00085 21.5 3.7 26 154-179 3-28 (47)
29 PF02022 Integrase_Zn: Integra 44.6 35 0.00076 21.1 3.1 30 152-181 6-36 (40)
30 PF02787 CPSase_L_D3: Carbamoy 43.1 89 0.0019 24.4 6.0 88 85-204 13-100 (123)
31 PF02631 RecX: RecX family; I 35.9 1.7E+02 0.0036 22.4 6.6 106 48-177 10-118 (121)
32 cd01392 HTH_LacI Helix-turn-he 35.7 88 0.0019 19.6 4.2 40 93-135 5-44 (52)
33 PHA02591 hypothetical protein; 35.7 59 0.0013 23.4 3.4 22 151-172 45-66 (83)
34 PF11212 DUF2999: Protein of u 35.4 1.6E+02 0.0035 20.8 6.9 49 50-106 2-50 (82)
35 cd04781 HTH_MerR-like_sg6 Heli 35.1 1.3E+02 0.0029 23.1 5.9 25 154-178 45-69 (120)
36 PF09278 MerR-DNA-bind: MerR, 34.7 41 0.0009 22.6 2.6 18 158-175 7-24 (65)
37 PF03960 ArsC: ArsC family; I 34.3 47 0.001 25.1 3.1 22 95-116 69-90 (110)
38 PRK14487 cbb3-type cytochrome 32.7 99 0.0021 26.8 5.0 60 109-168 138-210 (217)
39 PF10440 WIYLD: Ubiquitin-bind 32.6 83 0.0018 21.8 3.7 36 150-185 7-42 (65)
40 PF11090 DUF2833: Protein of u 32.5 69 0.0015 23.5 3.5 57 73-132 21-79 (86)
41 PF08671 SinI: Anti-repressor 32.3 59 0.0013 18.8 2.5 23 154-176 5-27 (30)
42 PF09288 UBA_3: Fungal ubiquit 32.1 54 0.0012 21.9 2.6 21 157-177 12-32 (55)
43 KOG0400 40S ribosomal protein 31.5 34 0.00074 27.1 1.8 69 2-72 23-94 (151)
44 cd04788 HTH_NolA-AlbR Helix-Tu 30.1 1.6E+02 0.0034 21.7 5.3 25 155-179 47-71 (96)
45 PF11181 YflT: Heat induced st 30.0 1.7E+02 0.0037 21.8 5.5 21 82-102 9-29 (103)
46 KOG2629 Peroxisomal membrane a 29.8 1.1E+02 0.0023 27.8 4.9 25 153-177 21-45 (300)
47 cd08306 Death_FADD Fas-associa 29.5 52 0.0011 23.9 2.5 20 19-38 19-38 (86)
48 cd04768 HTH_BmrR-like Helix-Tu 29.0 1.1E+02 0.0024 22.5 4.3 26 154-179 46-71 (96)
49 PF14117 DUF4287: Domain of un 28.1 1.6E+02 0.0035 20.1 4.5 41 159-204 7-48 (61)
50 PRK08561 rps15p 30S ribosomal 27.1 67 0.0015 26.1 2.9 48 131-178 10-57 (151)
51 TIGR01448 recD_rel helicase, p 26.2 2.4E+02 0.0052 29.2 7.5 116 12-137 76-208 (720)
52 cd04774 HTH_YfmP Helix-Turn-He 24.9 2.6E+02 0.0056 20.6 5.6 28 154-181 45-73 (96)
53 PF08542 Rep_fac_C: Replicatio 24.0 1.1E+02 0.0025 21.7 3.5 58 169-232 6-65 (89)
54 cd08784 Death_DRs Death Domain 24.0 94 0.002 22.1 2.9 37 17-58 15-51 (79)
55 PTZ00072 40S ribosomal protein 23.9 85 0.0018 25.4 2.9 48 131-178 7-54 (148)
56 cd04777 HTH_MerR-like_sg1 Heli 23.7 1.2E+02 0.0026 22.7 3.7 24 154-177 44-67 (107)
57 cd04782 HTH_BltR Helix-Turn-He 23.7 1.7E+02 0.0036 21.6 4.4 24 154-177 46-69 (97)
58 TIGR01018 rpsD_arch ribosomal 23.6 1.2E+02 0.0026 25.1 3.8 40 220-259 65-105 (162)
59 cd00739 DHPS DHPS subgroup of 23.4 2.2E+02 0.0047 25.3 5.8 69 189-266 152-221 (257)
60 KOG2875 8-oxoguanine DNA glyco 22.3 4.3E+02 0.0094 24.0 7.2 24 158-181 202-226 (323)
61 COG0560 SerB Phosphoserine pho 22.2 3.5E+02 0.0076 23.1 6.7 87 39-132 6-94 (212)
62 PRK09875 putative hydrolase; P 22.1 69 0.0015 29.1 2.4 27 85-111 262-288 (292)
63 COG3769 Predicted hydrolase (H 22.1 91 0.002 27.4 2.9 48 2-63 7-64 (274)
64 PRK04051 rps4p 30S ribosomal p 22.1 1E+02 0.0022 25.8 3.2 38 221-258 66-103 (177)
65 PRK09875 putative hydrolase; P 21.7 88 0.0019 28.4 3.0 27 154-180 262-288 (292)
66 PF03800 Nuf2: Nuf2 family; I 21.7 3.9E+02 0.0084 21.2 6.5 92 154-257 14-117 (146)
67 cd04770 HTH_HMRTR Helix-Turn-H 21.0 2E+02 0.0043 22.1 4.5 25 154-178 46-70 (123)
68 PF06568 DUF1127: Domain of un 20.8 33 0.00071 21.1 -0.0 13 19-31 27-39 (40)
69 PRK08561 rps15p 30S ribosomal 20.7 2.2E+02 0.0049 23.2 4.7 35 72-107 21-55 (151)
70 COG0320 LipA Lipoate synthase 20.7 60 0.0013 29.3 1.6 111 58-168 157-283 (306)
71 TIGR01448 recD_rel helicase, p 20.5 4.3E+02 0.0094 27.3 8.0 141 49-201 77-223 (720)
72 TIGR01558 sm_term_P27 phage te 20.4 1.6E+02 0.0035 22.5 3.8 93 74-172 3-97 (116)
73 cd01106 HTH_TipAL-Mta Helix-Tu 20.2 2.8E+02 0.006 20.5 5.1 26 154-179 46-71 (103)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=7.7e-53 Score=403.55 Aligned_cols=261 Identities=17% Similarity=0.316 Sum_probs=233.6
Q ss_pred CCCceecCcCCChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccc
Q 043018 1 NPTLLLADPEKSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCN 80 (300)
Q Consensus 1 ~P~lL~~~~~~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s 80 (300)
+|++|.+++++++.|+++||+++|++.++|++++.++|++|++++++++.|+++||.++|++.+++++++.++|++|+++
T Consensus 148 ~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~s 227 (487)
T PLN03196 148 YPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMR 227 (487)
T ss_pred CCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcC
Confidence 68999999998899999999999999999999999999999999888899999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeechh-hHHHHHHHHHHhCCCCCChhH--------------------
Q 043018 81 IEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRD-LFKTMMDVIKKIGIEPTNFMF-------------------- 139 (300)
Q Consensus 81 ~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~-~l~~~v~~L~~lG~~~~~~~~-------------------- 139 (300)
++++++|+++||+++|++.++|++++.++|++|+.+.+ ++++++++|+++|++++...+
T Consensus 228 ve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~ 307 (487)
T PLN03196 228 VGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQ 307 (487)
T ss_pred hhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHH
Confidence 98889999999999999999999999999999988876 788899998888888653211
Q ss_pred ------------------HHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhC
Q 043018 140 ------------------ILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIG 201 (300)
Q Consensus 140 ------------------~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g 201 (300)
+.+.+.+++.++++|.++++||+++||+.++|..|++++|++|++|.++|++|++||+++||
T Consensus 308 ~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg 387 (487)
T PLN03196 308 QYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMK 387 (487)
T ss_pred HHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhC
Confidence 11233455678889999999999999999999999999999999999999999999999999
Q ss_pred CChhhhhhCCcccccCccccchhhHHHHHHHHHCCCCcCCCCchhhcccChhhHHHHhcccCcChH
Q 043018 202 LKPLDIVRCPNLLLISLKKRVLPRWSVLQVLMSKNLLKKDIDFIQALIVTKPVFERRFVTSYMDDS 267 (300)
Q Consensus 202 ~~~~~i~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~s~~~F~~~~v~~~~~~~ 267 (300)
++.++|+++|++|+||+|+||+|||++++ ++|+ ++++.++|+|||++|+++||.+|.|+.
T Consensus 388 ~~~~~Iv~fP~~LsySLEkRI~PR~~~L~---~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~~ 447 (487)
T PLN03196 388 RPLKELVEFPAYFTYGLESRIKPRYERVA---KKGI---KCSLAWFLNCSDDKFEQRMSGDFIEGE 447 (487)
T ss_pred CCHHHHHhChHHhccChhhhhHHHHHHHH---HcCC---CCCHHHHhccCHHHHHHHHhhhccccc
Confidence 99999999999999999999999998755 9998 589999999999999999999998853
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=1.6e-47 Score=355.21 Aligned_cols=256 Identities=33% Similarity=0.568 Sum_probs=201.5
Q ss_pred CCCceecCcCCChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccc
Q 043018 1 NPTLLLADPEKSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCN 80 (300)
Q Consensus 1 ~P~lL~~~~~~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s 80 (300)
+|.+|.+++++++.|+++||.++|++.+|++++++++|.+|..++++++.|.++||+++|++++++.+++.++|++|..+
T Consensus 21 ~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~ 100 (345)
T PF02536_consen 21 YPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFS 100 (345)
T ss_dssp H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS-
T ss_pred CCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred hhhhhhhHHHHHHhcCCChHHHHHHhhhCCccee-----------------------------------echhhHHHHHH
Q 043018 81 IEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLI-----------------------------------KRRDLFKTMMD 125 (300)
Q Consensus 81 ~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~-----------------------------------~~~~~l~~~v~ 125 (300)
.++++.+++++|+++|++.+.+.+++...|..+. .+.+.++++++
T Consensus 101 ~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~ 180 (345)
T PF02536_consen 101 VEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVE 180 (345)
T ss_dssp --HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHH
T ss_pred hHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHH
Confidence 7778999999999988888867776666666432 13457899999
Q ss_pred HHHHhCCCCCChh--HHHH--------------------------------HHHHhhccHHHHHHHHHHHHhCCCCHHHH
Q 043018 126 VIKKIGIEPTNFM--FILA--------------------------------VRSMSVLSKATWEKKKDALMSFSWSEDEF 171 (300)
Q Consensus 126 ~L~~lG~~~~~~~--~~~~--------------------------------~~~l~~~~~~~l~~kv~~l~~lG~s~~~i 171 (300)
+|+++|++.++.. +... .+.++..+.+++.++++||+++||+.+||
T Consensus 181 ~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei 260 (345)
T PF02536_consen 181 FLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEI 260 (345)
T ss_dssp HHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHH
T ss_pred HHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHH
Confidence 9999999876421 1111 22333445668999999999999999999
Q ss_pred HHHHHcCCcccccchhhHHHHHHHHHHHhCCChhhhhhCCcccccCccccchhhHHHHHHHHHCCCCcCCCCchhhcccC
Q 043018 172 YLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKPLDIVRCPNLLLISLKKRVLPRWSVLQVLMSKNLLKKDIDFIQALIVT 251 (300)
Q Consensus 172 ~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~~~i~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~s 251 (300)
.+|+.++|++|++|.+++++|++||.++||++.++|+++|++|+||+|+||+|||+++++|+++|+ ..++++.+++.+|
T Consensus 261 ~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~sl~~~l~~s 339 (345)
T PF02536_consen 261 AKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPSLSSMLSCS 339 (345)
T ss_dssp HHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGGS-HHHHHH
T ss_pred HHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCCHHHHhhcc
Confidence 999999999999999999999999999999999999999999999999999999999999999997 6689999999999
Q ss_pred hhhHHH
Q 043018 252 KPVFER 257 (300)
Q Consensus 252 ~~~F~~ 257 (300)
|++|++
T Consensus 340 ~~~F~~ 345 (345)
T PF02536_consen 340 DEEFLK 345 (345)
T ss_dssp HHHHT-
T ss_pred HHHhcC
Confidence 999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=9.8e-40 Score=313.18 Aligned_cols=255 Identities=18% Similarity=0.347 Sum_probs=197.4
Q ss_pred CCCceecCcCCChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccc
Q 043018 1 NPTLLLADPEKSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCN 80 (300)
Q Consensus 1 ~P~lL~~~~~~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s 80 (300)
+|++|++++++++.|+++||+++|++.++|+++|.++|.+|.+++++++.|+++||+++|++++++++++.++|++|+++
T Consensus 112 ~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~ 191 (487)
T PLN03196 112 YPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFK 191 (487)
T ss_pred CcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeechh-hHHHHHHHHHHhCCCCCChh--HHHHHHHHhhccHHHHHHH
Q 043018 81 IEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRD-LFKTMMDVIKKIGIEPTNFM--FILAVRSMSVLSKATWEKK 157 (300)
Q Consensus 81 ~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~-~l~~~v~~L~~lG~~~~~~~--~~~~~~~l~~~~~~~l~~k 157 (300)
+++++.|+++||+++|++.++|++++.++|++|+.+.+ +++++++||+++|++.+... +...|+++....+++++++
T Consensus 192 ~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~ 271 (487)
T PLN03196 192 LEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPN 271 (487)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHH
Confidence 99999999999999999999999999999999999986 68999999999999887532 2223333333223344444
Q ss_pred HHHHHh-------------------------------------CCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHh
Q 043018 158 KDALMS-------------------------------------FSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEI 200 (300)
Q Consensus 158 v~~l~~-------------------------------------lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~ 200 (300)
++++++ +|++.+++..++.++|+++++|.+++++|++||.+ +
T Consensus 272 v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~-~ 350 (487)
T PLN03196 272 VECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRG-R 350 (487)
T ss_pred HHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHH-c
Confidence 444444 55555555555556666666666666777777765 7
Q ss_pred CCChhhh----hhCCcccccCccccchhhHHHHHHHHHCCCCcCC-CCchhhcccCh-hhHHHHh
Q 043018 201 GLKPLDI----VRCPNLLLISLKKRVLPRWSVLQVLMSKNLLKKD-IDFIQALIVTK-PVFERRF 259 (300)
Q Consensus 201 g~~~~~i----~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~~~~-~~l~~~l~~s~-~~F~~~~ 259 (300)
||+.++| .++|++|++|. +.|+|++.++.. ..|+..+. ...+.++++|= ++-..||
T Consensus 351 Gls~edI~~mv~k~P~lL~~S~-~~l~~k~dFlvn--eMg~~~~~Iv~fP~~LsySLEkRI~PR~ 412 (487)
T PLN03196 351 GFSAQDVAKMVVRCPQILALNL-EIMKPSLEFFKK--EMKRPLKELVEFPAYFTYGLESRIKPRY 412 (487)
T ss_pred CCCHHHHHHHHHhCCceeeccH-HHHHHHHHHHHH--HhCCCHHHHHhChHHhccChhhhhHHHH
Confidence 7777766 47777777777 357776655441 23543322 34566677663 3544444
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.96 E-value=5.6e-30 Score=237.67 Aligned_cols=237 Identities=20% Similarity=0.387 Sum_probs=176.3
Q ss_pred HHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHHHHHhcCC
Q 043018 18 DYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAHGV 97 (300)
Q Consensus 18 ~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~lGl 97 (300)
++|++.|++++||.+++.++|.++.++.++++.|+++||.++|++..++++++.++|.+|..++++++.|.++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 58999999999999999999999999999999999999999999999999999999999999998999999999999999
Q ss_pred ChHHHHHHhhhCCcceeechh-hHHHHHHHHHHhCCCCCCh-hH-----------------------------------H
Q 043018 98 PEHLIAKLIMINPSSLIKRRD-LFKTMMDVIKKIGIEPTNF-MF-----------------------------------I 140 (300)
Q Consensus 98 ~~~~i~~ll~~~P~ll~~~~~-~l~~~v~~L~~lG~~~~~~-~~-----------------------------------~ 140 (300)
+++++.+++.++|++|+.+.+ .+.+++.+|.++|++++.. .. .
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~ 161 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIA 161 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHH
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhccccc
Confidence 999999999999999987654 7999999999999986521 00 1
Q ss_pred HHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHcCCcccccchhh--------------------------------
Q 043018 141 LAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKRQPMLMLSSTKK-------------------------------- 188 (300)
Q Consensus 141 ~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~~P~iL~~S~~~-------------------------------- 188 (300)
..|..+...++++|+++++||+++|++.+++.+++.++|.++.+|.++
T Consensus 162 ~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~ 241 (345)
T PF02536_consen 162 KNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEE 241 (345)
T ss_dssp HHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHH
T ss_pred ccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchH
Confidence 122345556677889999999999999999999999999999888764
Q ss_pred -HHHHHHHHHHHhCCChhhh----hhCCcccccCccccchhhHHHHHHHHHCCCCcCC-CCchhhcccChh-hHHHH
Q 043018 189 -IRELMDFFVNEIGLKPLDI----VRCPNLLLISLKKRVLPRWSVLQVLMSKNLLKKD-IDFIQALIVTKP-VFERR 258 (300)
Q Consensus 189 -l~~ki~fl~~~~g~~~~~i----~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~~~~-~~l~~~l~~s~~-~F~~~ 258 (300)
++++++||.+ +|++.++| .++|++|++|.++ ++|++.++. .+.|+...+ ...+.++++|=+ +-..|
T Consensus 242 ~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 242 KLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLV--KEMGLPLEEIVEFPQYLSYSLEKRIKPR 314 (345)
T ss_dssp HHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHH--HCCT--HHHHHHSCHHHCS-HHHHHHHH
T ss_pred hHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHH--HHhCcCHHHHhhCCceeEechhhhhhhH
Confidence 7888888877 89998876 4789999999886 888766553 135665333 345677777764 34444
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.91 E-value=9.5e-24 Score=200.40 Aligned_cols=210 Identities=20% Similarity=0.261 Sum_probs=181.5
Q ss_pred HHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHHHHHhc
Q 043018 16 KIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAH 95 (300)
Q Consensus 16 ~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~l 95 (300)
.+++++++|....++...+..+|....... .+...+.++...|+.+.. +++.++|.+++++.++++++++++|+++
T Consensus 201 ~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~ 276 (413)
T KOG1267|consen 201 RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSL 276 (413)
T ss_pred cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHc
Confidence 677777777777777777777777665542 466667777777765555 7778888889888999999999999999
Q ss_pred CCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHH
Q 043018 96 GVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAF 175 (300)
Q Consensus 96 Gl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~ 175 (300)
|++.++|..++.++|++|+.+.+++..+++++.+. .++ +...|.++..++..+.++++|+..+|++..|+..|+
T Consensus 277 Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~--~~~----~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~ 350 (413)
T KOG1267|consen 277 GFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN--PKH----ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMV 350 (413)
T ss_pred CCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc--chh----hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHH
Confidence 99999999999999999999999999999998776 222 445555558899999999999999999999999999
Q ss_pred HcCCcccccchh-hHHHHHHHHHHHhCCChhhhhhCCcccccCccccchhhHHHHHHHHHC
Q 043018 176 KRQPMLMLSSTK-KIRELMDFFVNEIGLKPLDIVRCPNLLLISLKKRVLPRWSVLQVLMSK 235 (300)
Q Consensus 176 ~~~P~iL~~S~~-~l~~ki~fl~~~~g~~~~~i~~~P~ll~~sle~ri~pR~~~l~~L~~~ 235 (300)
+++|+++.+|.+ .++.+.+|+.+.|+++.++++.+|++++|++|+|+.||+.+...+..+
T Consensus 351 ~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 351 KRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred hhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 999999999999 699999999999999999999999999999999999999999876543
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.87 E-value=9.2e-22 Score=186.81 Aligned_cols=226 Identities=23% Similarity=0.373 Sum_probs=191.9
Q ss_pred CCCceecCcCCChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhc--cCChhHHHHHHhCCcccc
Q 043018 1 NPTLLLADPEKSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLV--QTNVNLVHAVKQSSRIIN 78 (300)
Q Consensus 1 ~P~lL~~~~~~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g--~~~~~v~~il~~~P~iL~ 78 (300)
+|.+|.+++++.+.|++.+|.+.|++.+.++++++..|.+|..+.+.++.+.++|+.+++ .....+.+.+...|....
T Consensus 115 ~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~ 194 (413)
T KOG1267|consen 115 SPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLL 194 (413)
T ss_pred CchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccc
Confidence 488999999999999999999999999999999999999988888889999999999985 555566666655553332
Q ss_pred cchhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCCChhHHHHHHHHhhccHHHHHHHH
Q 043018 79 CNIEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPTNFMFILAVRSMSVLSKATWEKKK 158 (300)
Q Consensus 79 ~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv 158 (300)
.. ..++ ++++++++|....++..++..+|+.+.... .+...+.++..+|+++.+.+++.++..+.+++++++++++
T Consensus 195 ~~--~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv 270 (413)
T KOG1267|consen 195 NE--NSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKV 270 (413)
T ss_pred cc--cccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHH
Confidence 22 2355 999999999999999999999999987755 7889999999999999999999999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhCCChhhhhhCCcccccCccccchhhHHHHHHHHHCCCC
Q 043018 159 DALMSFSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKPLDIVRCPNLLLISLKKRVLPRWSVLQVLMSKNLL 238 (300)
Q Consensus 159 ~~l~~lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~~~i~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~ 238 (300)
++|+++||+.+||+.|+.++|++|++|.+++..+++|+.+. .+++.++|+++.++.. .+.||+.++. ..|+.
T Consensus 271 ~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p~~l~~s~~-~l~~~ie~l~---~~g~~ 342 (413)
T KOG1267|consen 271 EVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFPQLLRSSED-KLKPRIEFLL---SLGFS 342 (413)
T ss_pred HHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhhhhhhccch-hhhhhHHHHH---HcCCc
Confidence 99999999999999999999999999999988888888886 3448888888866654 6888876554 55543
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=97.47 E-value=0.0001 Score=42.67 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=26.3
Q ss_pred HHHHcCCcccccchhhHHHHHHHHHHHhCCC
Q 043018 173 LAFKRQPMLMLSSTKKIRELMDFFVNEIGLK 203 (300)
Q Consensus 173 ~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~ 203 (300)
.++.++|+++++|.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4688999999999888999999998 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=97.38 E-value=0.00014 Score=42.08 Aligned_cols=30 Identities=30% Similarity=0.540 Sum_probs=18.5
Q ss_pred HHHHhCCcccccchhhhhhhHHHHHHhcCCC
Q 043018 68 HAVKQSSRIINCNIEKRLAPNVNTLRAHGVP 98 (300)
Q Consensus 68 ~il~~~P~iL~~s~e~~l~~~v~~L~~lGl~ 98 (300)
+++.++|.+|+++ +++++++++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 3556666666666 44566666666666653
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=93.98 E-value=1 Score=41.79 Aligned_cols=195 Identities=16% Similarity=0.258 Sum_probs=102.9
Q ss_pred hCCCCCCchhHHHhhcCccccccc-cC------cchhhhhHhhh--hcc---CChhHHHHHHhCCcccccchhhhh-hhH
Q 043018 22 SVGISGADLPKFLCSNKQLLVVSL-KS------NIIPIFEFLKG--LVQ---TNVNLVHAVKQSSRIINCNIEKRL-APN 88 (300)
Q Consensus 22 ~lG~s~~~i~~ii~~~P~lL~~s~-e~------~l~p~v~fL~~--~g~---~~~~v~~il~~~P~iL~~s~e~~l-~~~ 88 (300)
.+|++...+.+++.++|.++.... .. .+.|...-|.. ..+ ...+++.-+.+ +|-++.+++| -.+
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~K---LLMMS~~~rlpL~k 122 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRK---LLMMSKDRRLPLSK 122 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHH---HhccCCCCcccHHH
Confidence 589977899999999999887643 11 23333332221 111 22334444444 6766666544 345
Q ss_pred HHHHH-hcCCChHHHHHHhhhCCcceeech-h---hHHHHHHHHHHhCCCCC------------------ChhHHHHHHH
Q 043018 89 VNTLR-AHGVPEHLIAKLIMINPSSLIKRR-D---LFKTMMDVIKKIGIEPT------------------NFMFILAVRS 145 (300)
Q Consensus 89 v~~L~-~lGl~~~~i~~ll~~~P~ll~~~~-~---~l~~~v~~L~~lG~~~~------------------~~~~~~~~~~ 145 (300)
++.++ ++|++.+-...++.++|..|.... + ..-+.+.|=.++.++.- ...|...++.
T Consensus 123 i~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~ 202 (335)
T PF11955_consen 123 IAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPK 202 (335)
T ss_pred HHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCC
Confidence 66666 899999999999999999986422 0 01111111111111110 0111111110
Q ss_pred HhhccHHHHHHHHHHHHhC----------CCC---HHHHHHHHHcCCcccccchhh--HHHHHHHHHHHhCCChh---hh
Q 043018 146 MSVLSKATWEKKKDALMSF----------SWS---EDEFYLAFKRQPMLMLSSTKK--IRELMDFFVNEIGLKPL---DI 207 (300)
Q Consensus 146 l~~~~~~~l~~kv~~l~~l----------G~s---~~~i~~m~~~~P~iL~~S~~~--l~~ki~fl~~~~g~~~~---~i 207 (300)
.........++++-++++ |+. .+.=...+.-.=-+|++.+++ ...++.-|.+++|+|.. -+
T Consensus 203 -G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~k~~~~l 281 (335)
T PF11955_consen 203 -GFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQKFRRLL 281 (335)
T ss_pred -CccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcHHHHHHH
Confidence 001123445555555544 111 111111222222456666665 66788888888888863 35
Q ss_pred hhCCcccccCccc
Q 043018 208 VRCPNLLLISLKK 220 (300)
Q Consensus 208 ~~~P~ll~~sle~ 220 (300)
+++|.+|..|...
T Consensus 282 ~rHPgIFYvS~kg 294 (335)
T PF11955_consen 282 LRHPGIFYVSLKG 294 (335)
T ss_pred HhCCCeEEEeccC
Confidence 7888888888653
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=91.42 E-value=1.1 Score=37.32 Aligned_cols=115 Identities=13% Similarity=0.067 Sum_probs=57.0
Q ss_pred hhhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHHHHHh----cCCChHHHHHHhhhCCcceeechhhHHHHHHH
Q 043018 51 PIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRA----HGVPEHLIAKLIMINPSSLIKRRDLFKTMMDV 126 (300)
Q Consensus 51 p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~----lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~ 126 (300)
..+..|+++|++-++|..++..... +....+...++.+.+ +--....+..++...+..-....-.....++.
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~~~~~~V~~~~w~~l 124 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLLKEQRLVTKEKWVAI 124 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCHHHHHHH
Confidence 4556678888888888877765432 111122223222221 22223334444432222211111123556666
Q ss_pred HHHhCCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHH
Q 043018 127 IKKIGIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLA 174 (300)
Q Consensus 127 L~~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m 174 (300)
++.+|+++++- ..-...|-. ..=....+||.++|++.+++..+
T Consensus 125 ~~~~g~~~~~m--~~wh~~fe~---~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 125 LKAAGMDEADM--RRWHIEFEK---MEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHcCCChHHH--HHHHHHHHH---hCcHHHHHHHHHcCCCHHHHHHH
Confidence 67778776641 111111111 12245678999999999998754
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=83.36 E-value=2 Score=35.85 Aligned_cols=113 Identities=17% Similarity=0.210 Sum_probs=62.2
Q ss_pred HHHHHHHhCCCCCCchhHHHhhcCc----cccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHH
Q 043018 15 PKIDYFESVGISGADLPKFLCSNKQ----LLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVN 90 (300)
Q Consensus 15 ~~l~~L~~lG~s~~~i~~ii~~~P~----lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~ 90 (300)
..|..|+++|++-++|..++..... ++....+ .|...++-|+. ....+..++...+..-....- +....++
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~~~~~-~l~~ei~~L~~---~~~~l~~ll~~~~~~~~~~~V-~~~~w~~ 123 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRLA-ELNREIQRLRQ---QQRAIATLLKQPTLLKEQRLV-TKEKWVA 123 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCChhHHHHHHHHHH-HHHHHHHHHHH---HHHHHHHHHHHHhhccccccC-CHHHHHH
Confidence 4577788999999999999875542 1111111 22222222222 123344444333332111111 2456778
Q ss_pred HHHhcCCChHHHHHHhhhCCcceeechhhH--HHHHHHHHHhCCCCCChhHH
Q 043018 91 TLRAHGVPEHLIAKLIMINPSSLIKRRDLF--KTMMDVIKKIGIEPTNFMFI 140 (300)
Q Consensus 91 ~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l--~~~v~~L~~lG~~~~~~~~~ 140 (300)
.++..|+++.++.+.=..+ ++. ..-.+||..+|++++.+.-+
T Consensus 124 l~~~~g~~~~~m~~wh~~f--------e~~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 124 ILKAAGMDEADMRRWHIEF--------EKMEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHcCCChHHHHHHHHHH--------HHhCcHHHHHHHHHcCCCHHHHHHH
Confidence 8888999988865432211 111 34578999999988765443
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=82.04 E-value=2.3 Score=34.08 Aligned_cols=30 Identities=30% Similarity=0.138 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHcCCccc
Q 043018 153 TWEKKKDALMSFSWSEDEFYLAFKRQPMLM 182 (300)
Q Consensus 153 ~l~~kv~~l~~lG~s~~~i~~m~~~~P~iL 182 (300)
.+..|++||++-|++.+||..++.+.+.--
T Consensus 22 p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 22 PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp -HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 488999999999999999999999887755
No 13
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=75.78 E-value=4.1 Score=32.64 Aligned_cols=40 Identities=20% Similarity=0.252 Sum_probs=27.0
Q ss_pred HHhCCcccccchhhhhhhHHHHHHhcCCChHHHHHHhhhCCcce
Q 043018 70 VKQSSRIINCNIEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSL 113 (300)
Q Consensus 70 l~~~P~iL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll 113 (300)
+..+|.+-....+ .+++||++-|++.++|..++.+.+.--
T Consensus 12 FL~~p~V~~sp~~----~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 12 FLQDPKVRNSPLE----KKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHCTTTCCCS-HH----HHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HhCCcccccCCHH----HHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3446777777754 489999999999999999988765543
No 14
>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=73.99 E-value=19 Score=33.41 Aligned_cols=94 Identities=11% Similarity=0.084 Sum_probs=55.3
Q ss_pred HhcCCChHHHHHHhhhCCcceeech------h--hHHHHHHHH--HHhCCCCC-ChhHHHHHHHHhhcc-HHH-HHHHHH
Q 043018 93 RAHGVPEHLIAKLIMINPSSLIKRR------D--LFKTMMDVI--KKIGIEPT-NFMFILAVRSMSVLS-KAT-WEKKKD 159 (300)
Q Consensus 93 ~~lGl~~~~i~~ll~~~P~ll~~~~------~--~l~~~v~~L--~~lG~~~~-~~~~~~~~~~l~~~~-~~~-l~~kv~ 159 (300)
+.+|++...+...+.++|.+|.... - ++.+....| ++..+-.+ ....+....-++.++ ... --.+++
T Consensus 45 ~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~ 124 (335)
T PF11955_consen 45 RQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIA 124 (335)
T ss_pred HhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHH
Confidence 3578866788888888888885422 0 233333332 12222111 112222233233233 223 367888
Q ss_pred HHH-hCCCCHHHHHHHHHcCCcccccch
Q 043018 160 ALM-SFSWSEDEFYLAFKRQPMLMLSST 186 (300)
Q Consensus 160 ~l~-~lG~s~~~i~~m~~~~P~iL~~S~ 186 (300)
.++ ++|++.+=...++.++|+.|.+..
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEEee
Confidence 888 899999988899999999986643
No 15
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=64.32 E-value=12 Score=22.26 Aligned_cols=24 Identities=29% Similarity=0.470 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 155 EKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 155 ~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
.++++-+.++||+.+++...+.++
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356777888899988888776654
No 16
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=62.29 E-value=17 Score=32.67 Aligned_cols=55 Identities=15% Similarity=0.239 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHH-hCC-CCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhCCChh
Q 043018 151 KATWEKKKDALM-SFS-WSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKPL 205 (300)
Q Consensus 151 ~~~l~~kv~~l~-~lG-~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~~ 205 (300)
.-.+++++-|.- ..| |++-.|.+=+.-.|.+++++.++++.+++-|.+-+|+++.
T Consensus 70 ~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~ 126 (309)
T COG1125 70 PVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPS 126 (309)
T ss_pred HHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHH
Confidence 446777777764 554 4555566777788999999999999999999998999875
No 17
>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=62.21 E-value=27 Score=22.26 Aligned_cols=41 Identities=15% Similarity=0.403 Sum_probs=29.1
Q ss_pred HHhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCC
Q 043018 92 LRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPT 135 (300)
Q Consensus 92 L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~ 135 (300)
=+.+|++..-+.+++...|.+ +.+.-+...+..+++|+.++
T Consensus 6 A~~agvS~~TVSr~ln~~~~v---s~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGPPRV---SEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHTSSHHHHHHHHTTCSSS---THHHHHHHHHHHHHHTB-SS
T ss_pred HHHHCcCHHHHHHHHhCCCCC---CHHHHHHHHHHHHHHCCCCC
Confidence 346899999999999776543 55566666777788887653
No 18
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=61.16 E-value=11 Score=22.54 Aligned_cols=24 Identities=25% Similarity=0.353 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 155 EKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 155 ~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
+.+|+-|.++||+.++..+.+..+
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHc
Confidence 356777777888888877666544
No 19
>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=59.63 E-value=16 Score=21.81 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCHHHHHHHHHcC
Q 043018 156 KKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 156 ~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
++++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777888899988887666544
No 20
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=55.29 E-value=9 Score=26.08 Aligned_cols=47 Identities=13% Similarity=0.027 Sum_probs=27.3
Q ss_pred CCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHc
Q 043018 131 GIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 131 G~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~ 177 (300)
|.+.+...+...+|.-+..+.+.+++.|--|.+-|++..+|..+++.
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 10 GISGSTRPYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp --------S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CccCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 44445455555444444577889999999999999999999988774
No 21
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=54.69 E-value=37 Score=25.02 Aligned_cols=35 Identities=37% Similarity=0.506 Sum_probs=18.3
Q ss_pred HHhhhCCcceeechh--hHHHHHHHHHHhCCCCCChh
Q 043018 104 KLIMINPSSLIKRRD--LFKTMMDVIKKIGIEPTNFM 138 (300)
Q Consensus 104 ~ll~~~P~ll~~~~~--~l~~~v~~L~~lG~~~~~~~ 138 (300)
..|..+|..|..... .++..=+.-+++|++.++..
T Consensus 38 ~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 38 EILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp HHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred HHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 466778888877443 34444444467888877643
No 22
>PRK14136 recX recombination regulator RecX; Provisional
Probab=53.05 E-value=1.9e+02 Score=26.61 Aligned_cols=106 Identities=19% Similarity=0.235 Sum_probs=61.6
Q ss_pred cchhhhhHhhhhcc-CChhHHHHHHhCCcccccchhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeechhhHHHHHHH
Q 043018 48 NIIPIFEFLKGLVQ-TNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDV 126 (300)
Q Consensus 48 ~l~p~v~fL~~~g~-~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~ 126 (300)
.+...|++|++.|. ++......+.+. ..-.... .....-|+.-|++.+.|...+... ..+.+......
T Consensus 195 ~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp----~rIrqELrQKGId~eLIEqALeei------eEDE~E~A~~L 263 (309)
T PRK14136 195 SVEPLLDALEREGWLSDARFAESLVHR-RASRVGS----ARIVSELKRHAVGDALVESVGAQL------RETEFERAQAV 263 (309)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhH----HHHHHHHHHcCCCHHHHHHHHHhc------cHhHHHHHHHH
Confidence 56677788888775 666666655543 1111111 122355888999999988887632 12223333333
Q ss_pred HH-HhCCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 127 IK-KIGIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 127 L~-~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
++ .++-.+. ........+.||..-||+.+.|..++..+
T Consensus 264 ~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 264 WRKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 32 2321111 12234455789999999999999888754
No 23
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=51.77 E-value=21 Score=29.56 Aligned_cols=23 Identities=13% Similarity=0.029 Sum_probs=12.4
Q ss_pred HHhhccHHHHHHHHHHHHhCCCC
Q 043018 145 SMSVLSKATWEKKKDALMSFSWS 167 (300)
Q Consensus 145 ~l~~~~~~~l~~kv~~l~~lG~s 167 (300)
++.+.+++.+..-++.++..|+|
T Consensus 75 vv~v~pdDsi~~vv~lM~~~g~S 97 (187)
T COG3620 75 VVSVSPDDSISDVVNLMRDKGIS 97 (187)
T ss_pred eeEECchhhHHHHHHHHHHcCCc
Confidence 33444555555555555555554
No 24
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=51.55 E-value=41 Score=30.47 Aligned_cols=68 Identities=9% Similarity=0.086 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhCCChhhhhhCCcccccCccccchhhHHHHHHHHHCCCCcCCCCchhhcccChhhHHHHhcccCc
Q 043018 189 IRELMDFFVNEIGLKPLDIVRCPNLLLISLKKRVLPRWSVLQVLMSKNLLKKDIDFIQALIVTKPVFERRFVTSYM 264 (300)
Q Consensus 189 l~~ki~fl~~~~g~~~~~i~~~P~ll~~sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~s~~~F~~~~v~~~~ 264 (300)
++.+++.+.+ .|++.+.|+--|- +++. +....-+.+++.|..- +...++-++..|.++|...+...-+
T Consensus 165 l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l----~~lg~Pilvg~SRKsfig~~~~~~~ 232 (282)
T PRK11613 165 FIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEF----HHFNLPLLVGMSRKSMIGQLLNVGP 232 (282)
T ss_pred HHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHH----HhCCCCEEEEecccHHHHhhcCCCh
Confidence 5667776655 8999999888885 4554 3444445555544331 1234566899999999988876433
No 25
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=51.30 E-value=50 Score=24.34 Aligned_cols=71 Identities=11% Similarity=0.122 Sum_probs=33.2
Q ss_pred CChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCChhHHHHHHhCCcccccchhh-hhhhHH
Q 043018 11 KSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEK-RLAPNV 89 (300)
Q Consensus 11 ~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~-~l~~~v 89 (300)
..++..+.||..+|++.....++...+ | ++...+|..+|+.|..++.+ ..+..=
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~y----------------------g---~~ai~~l~~nPY~L~~~i~gi~F~~aD 60 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKY----------------------G---DDAIEILKENPYRLIEDIDGIGFKTAD 60 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH--------------------------TTHHHHHHH-STCCCB-SSSSBHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH----------------------h---HHHHHHHHHChHHHHHHccCCCHHHHH
Confidence 356777889999998865554443221 1 13446777777777664332 122222
Q ss_pred HHHHhcCCChHHHHHHh
Q 043018 90 NTLRAHGVPEHLIAKLI 106 (300)
Q Consensus 90 ~~L~~lGl~~~~i~~ll 106 (300)
+.-+.+|++..+-.++.
T Consensus 61 ~iA~~~g~~~~d~~Ri~ 77 (94)
T PF14490_consen 61 KIALKLGIEPDDPRRIR 77 (94)
T ss_dssp HHHHTTT--TT-HHHHH
T ss_pred HHHHHcCCCCCCHHHHH
Confidence 23335677766655554
No 26
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=47.85 E-value=42 Score=23.15 Aligned_cols=40 Identities=15% Similarity=0.342 Sum_probs=29.4
Q ss_pred HhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCC
Q 043018 93 RAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPT 135 (300)
Q Consensus 93 ~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~ 135 (300)
+.+|++...|.+++...|.+ +++......+.++++|+.++
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 35789999998888766654 45566677777888888765
No 27
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=47.33 E-value=78 Score=22.33 Aligned_cols=20 Identities=30% Similarity=0.589 Sum_probs=11.2
Q ss_pred hHHHHHHhcCCChHHHHHHh
Q 043018 87 PNVNTLRAHGVPEHLIAKLI 106 (300)
Q Consensus 87 ~~v~~L~~lGl~~~~i~~ll 106 (300)
|.++.|++..+|.++|..++
T Consensus 3 PIia~LKehnvsd~qi~elF 22 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELF 22 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHH
Confidence 45555556666655555544
No 28
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=46.96 E-value=39 Score=21.45 Aligned_cols=26 Identities=27% Similarity=0.299 Sum_probs=18.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcCC
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQP 179 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~P 179 (300)
+.+-++-|.++||++.++.+++.+..
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 34556777889999999888877553
No 29
>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=44.64 E-value=35 Score=21.14 Aligned_cols=30 Identities=13% Similarity=0.100 Sum_probs=22.4
Q ss_pred HHHHHHHHHHH-hCCCCHHHHHHHHHcCCcc
Q 043018 152 ATWEKKKDALM-SFSWSEDEFYLAFKRQPML 181 (300)
Q Consensus 152 ~~l~~kv~~l~-~lG~s~~~i~~m~~~~P~i 181 (300)
+++-.+...|. ++|++.....+++..+|..
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 45666778888 8999999999999999974
No 30
>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=43.08 E-value=89 Score=24.45 Aligned_cols=88 Identities=20% Similarity=0.184 Sum_probs=40.5
Q ss_pred hhhHHHHHHhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhC
Q 043018 85 LAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPTNFMFILAVRSMSVLSKATWEKKKDALMSF 164 (300)
Q Consensus 85 l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~l 164 (300)
+--..+.|+ .|++.++|..+=.-.|+.|.. .+++...-+.|++.+ ...-...+.-.+++
T Consensus 13 lf~i~eAlr-rG~sveeI~e~T~ID~wFL~~-i~~Iv~~e~~L~~~~-------------------~~~~~~~L~~aK~~ 71 (123)
T PF02787_consen 13 LFAIAEALR-RGYSVEEIHELTKIDPWFLEQ-IKNIVDMEKELKEYL-------------------NELDPELLRKAKRL 71 (123)
T ss_dssp HHHHHHHHH-TTB-HHHHHHHH---HHHHHH-HHHHHHHHHHHHHHG-------------------GG--HHHHHHHHHT
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCccHHHHHH-HHHHHHHHHHHHHhh-------------------ccchHHHHHHHHHc
Confidence 434444443 499999999887777776622 122222222222210 01112234455689
Q ss_pred CCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhCCCh
Q 043018 165 SWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKP 204 (300)
Q Consensus 165 G~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~ 204 (300)
|||+.+|.++ .+.+.+.++. +.+..|+.+
T Consensus 72 GFsD~~IA~l-------~~~~e~~vr~----~R~~~~i~p 100 (123)
T PF02787_consen 72 GFSDRQIARL-------WGVSEEEVRE----LRKEHGIVP 100 (123)
T ss_dssp T--HHHHHHH-------HTS-HHHHHH----HHHHHT---
T ss_pred CCCHHHHHhc-------cCCCHHHHHH----HHHHcCCce
Confidence 9999999966 4556555544 444566554
No 31
>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=35.91 E-value=1.7e+02 Score=22.39 Aligned_cols=106 Identities=14% Similarity=0.093 Sum_probs=53.3
Q ss_pred cchhhhhHhhhhcc-CChhHHHHHHhCCcc-cccchhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeechhhHHHHHH
Q 043018 48 NIIPIFEFLKGLVQ-TNVNLVHAVKQSSRI-INCNIEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMD 125 (300)
Q Consensus 48 ~l~p~v~fL~~~g~-~~~~v~~il~~~P~i-L~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~ 125 (300)
.+...++.|...|. ++...+....+.-.- =+.+ -.....-|+.-|++.+.|...+...+. ......
T Consensus 10 ~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G----~~~I~~~L~~kGi~~~~i~~~l~~~~~--------~e~a~~ 77 (121)
T PF02631_consen 10 AIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKG----PRRIRQKLKQKGIDREIIEEALEEYDE--------EEEALE 77 (121)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT------HHHHHHHHHHTT--HHHHHHHHTCS-H--------HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHhccccccc----HHHHHHHHHHHCCChHHHHHHHHHhhH--------HHHHHH
Confidence 56677788888886 555555544442211 1222 223445688899999999888862211 111111
Q ss_pred HHHHhCCCCCChhHHHHHHHHh-hccHHHHHHHHHHHHhCCCCHHHHHHHHHc
Q 043018 126 VIKKIGIEPTNFMFILAVRSMS-VLSKATWEKKKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 126 ~L~~lG~~~~~~~~~~~~~~l~-~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~ 177 (300)
..+. ...... .......+.-+.+|..-||+.+.|..++..
T Consensus 78 ~~~k------------k~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 78 LAEK------------KYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHH------------HHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHH------------HHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 1111 000000 112334455568888999999999877653
No 32
>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=35.72 E-value=88 Score=19.65 Aligned_cols=40 Identities=18% Similarity=0.388 Sum_probs=27.4
Q ss_pred HhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCC
Q 043018 93 RAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPT 135 (300)
Q Consensus 93 ~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~ 135 (300)
+.+|++...|.+++...|. .+.+......+..+++|+.++
T Consensus 5 ~~~gvs~~tvs~~l~g~~~---vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 5 RAAGVSVATVSRVLNGKPR---VSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred HHHCcCHHHHHHHHcCCCC---CCHHHHHHHHHHHHHhCCCCC
Confidence 4578888888888876552 344455666666777887655
No 33
>PHA02591 hypothetical protein; Provisional
Probab=35.70 E-value=59 Score=23.37 Aligned_cols=22 Identities=5% Similarity=0.040 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHhCCCCHHHHH
Q 043018 151 KATWEKKKDALMSFSWSEDEFY 172 (300)
Q Consensus 151 ~~~l~~kv~~l~~lG~s~~~i~ 172 (300)
++.+..-..-|.+.|+|.++|+
T Consensus 45 ~dd~~~vA~eL~eqGlSqeqIA 66 (83)
T PHA02591 45 EDDLISVTHELARKGFTVEKIA 66 (83)
T ss_pred cchHHHHHHHHHHcCCCHHHHH
Confidence 3344444455556666666666
No 34
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=35.44 E-value=1.6e+02 Score=20.79 Aligned_cols=49 Identities=18% Similarity=0.344 Sum_probs=35.9
Q ss_pred hhhhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHHHHHhcCCChHHHHHHh
Q 043018 50 IPIFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAHGVPEHLIAKLI 106 (300)
Q Consensus 50 ~p~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll 106 (300)
.|.+..|++..+|++++..++.. |+.+ ---.+.....+|++.+.+..++
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~N----Pl~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQN----PLAAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhC----HHHHHHHHHHcCCCHHHHHHHH
Confidence 57888899999999888877654 3333 2245677888999998887664
No 35
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=35.12 E-value=1.3e+02 Score=23.05 Aligned_cols=25 Identities=12% Similarity=-0.065 Sum_probs=20.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
+-..+..++++||+-++|..++...
T Consensus 45 ~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 45 RLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 3456788889999999999888754
No 36
>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=34.70 E-value=41 Score=22.56 Aligned_cols=18 Identities=17% Similarity=0.158 Sum_probs=13.1
Q ss_pred HHHHHhCCCCHHHHHHHH
Q 043018 158 KDALMSFSWSEDEFYLAF 175 (300)
Q Consensus 158 v~~l~~lG~s~~~i~~m~ 175 (300)
|..++.+|||-+||..++
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 445668999999999988
No 37
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=34.30 E-value=47 Score=25.13 Aligned_cols=22 Identities=14% Similarity=0.380 Sum_probs=17.8
Q ss_pred cCCChHHHHHHhhhCCcceeec
Q 043018 95 HGVPEHLIAKLIMINPSSLIKR 116 (300)
Q Consensus 95 lGl~~~~i~~ll~~~P~ll~~~ 116 (300)
-.++.+++..++..+|.++.++
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 4489999999999999998654
No 38
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=32.71 E-value=99 Score=26.81 Aligned_cols=60 Identities=13% Similarity=-0.015 Sum_probs=35.8
Q ss_pred CCcceeechh--hHHHHHHHHHHhCCCCCChhHHHHHHHHhhc-----------cHHHHHHHHHHHHhCCCCH
Q 043018 109 NPSSLIKRRD--LFKTMMDVIKKIGIEPTNFMFILAVRSMSVL-----------SKATWEKKKDALMSFSWSE 168 (300)
Q Consensus 109 ~P~ll~~~~~--~l~~~v~~L~~lG~~~~~~~~~~~~~~l~~~-----------~~~~l~~kv~~l~~lG~s~ 168 (300)
+|+++....+ .+...+..++.+|++..+..+..+...+..- ....+..-|.||+.+|-..
T Consensus 138 y~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~~~ 210 (217)
T PRK14487 138 YPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGTAV 210 (217)
T ss_pred CcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhcccc
Confidence 4455444434 5677777778889988765554443322211 1245777788888887543
No 39
>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=32.57 E-value=83 Score=21.79 Aligned_cols=36 Identities=14% Similarity=0.154 Sum_probs=25.6
Q ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHHcCCcccccc
Q 043018 150 SKATWEKKKDALMSFSWSEDEFYLAFKRQPMLMLSS 185 (300)
Q Consensus 150 ~~~~l~~kv~~l~~lG~s~~~i~~m~~~~P~iL~~S 185 (300)
+.+.+..-++-++.+||+.++|...+.+.-.+.+.+
T Consensus 7 ~~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~n 42 (65)
T PF10440_consen 7 GNERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGN 42 (65)
T ss_pred CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCC
Confidence 346777888888899999988887776544444433
No 40
>PF11090 DUF2833: Protein of unknown function (DUF2833); InterPro: IPR020335 This entry contains proteins with no known function.
Probab=32.53 E-value=69 Score=23.49 Aligned_cols=57 Identities=14% Similarity=0.083 Sum_probs=38.4
Q ss_pred CCcccccchhhhhh--hHHHHHHhcCCChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCC
Q 043018 73 SSRIINCNIEKRLA--PNVNTLRAHGVPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGI 132 (300)
Q Consensus 73 ~P~iL~~s~e~~l~--~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~ 132 (300)
++++++.+.-..+. .+++|.+.+ .+.+..++..+|++...--.....-+.||+.+|.
T Consensus 21 ~~Wfvtt~~v~~~~~~~~~eF~k~i---~~~~d~~l~~Y~~l~N~V~~~N~~HIRfLk~lGA 79 (86)
T PF11090_consen 21 CLWFVTTNKVKSLTKKERREFRKLI---KEYLDKMLKQYPVLWNFVWVGNKSHIRFLKSLGA 79 (86)
T ss_pred eEEEEECcHHhhcCHhhhHHHHHHH---HHHHHHHHHHhhheeEEEEeCCHHHHHHHHhcCc
Confidence 46777766433333 347777754 3456667778888877666667788888888886
No 41
>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=32.28 E-value=59 Score=18.81 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=13.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHH
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFK 176 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~ 176 (300)
|..=+.-.++.|+|.+||.+.+.
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Confidence 44444455678888888886654
No 42
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=32.06 E-value=54 Score=21.91 Aligned_cols=21 Identities=14% Similarity=0.309 Sum_probs=13.5
Q ss_pred HHHHHHhCCCCHHHHHHHHHc
Q 043018 157 KKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 157 kv~~l~~lG~s~~~i~~m~~~ 177 (300)
-|+-|.++||+.+.|...+++
T Consensus 12 lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHcCCcHHHHHHHHHH
Confidence 366677788888877777664
No 43
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=31.50 E-value=34 Score=27.06 Aligned_cols=69 Identities=19% Similarity=0.232 Sum_probs=0.0
Q ss_pred CCceecCcCCChhHHHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhcc---CChhHHHHHHh
Q 043018 2 PTLLLADPEKSLRPKIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQ---TNVNLVHAVKQ 72 (300)
Q Consensus 2 P~lL~~~~~~~l~~~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~---~~~~v~~il~~ 72 (300)
|.-|..++|+ +..-|--|..-|++++||+-++...--+=..+.- +=...+.+|++.|+ -++|+-.+|.+
T Consensus 23 PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLRDshGi~q~r~v-~G~kI~Rilk~~Gl~PeiPeDLy~likk 94 (151)
T KOG0400|consen 23 PTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFV-TGNKILRILKSNGLAPEIPEDLYHLIKK 94 (151)
T ss_pred cHHHhcCHHH-HHHHHHHHHHcCCChhHceeeeecccCcchhhee-chhHHHHHHHHcCCCCCCcHHHHHHHHH
No 44
>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=30.08 E-value=1.6e+02 Score=21.69 Aligned_cols=25 Identities=20% Similarity=0.061 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHcCC
Q 043018 155 EKKKDALMSFSWSEDEFYLAFKRQP 179 (300)
Q Consensus 155 ~~kv~~l~~lG~s~~~i~~m~~~~P 179 (300)
-..+..++++||+.++|..++....
T Consensus 47 l~~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 47 LHQIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhCCC
Confidence 4567788899999999999987654
No 45
>PF11181 YflT: Heat induced stress protein YflT
Probab=29.96 E-value=1.7e+02 Score=21.81 Aligned_cols=21 Identities=29% Similarity=0.430 Sum_probs=15.5
Q ss_pred hhhhhhHHHHHHhcCCChHHH
Q 043018 82 EKRLAPNVNTLRAHGVPEHLI 102 (300)
Q Consensus 82 e~~l~~~v~~L~~lGl~~~~i 102 (300)
+..+...|+-|+.-|.+.++|
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI 29 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI 29 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE
Confidence 344777788888888888776
No 46
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.79 E-value=1.1e+02 Score=27.78 Aligned_cols=25 Identities=40% Similarity=0.436 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHc
Q 043018 153 TWEKKKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 153 ~l~~kv~~l~~lG~s~~~i~~m~~~ 177 (300)
.+..|.+||++-|++.+||...+++
T Consensus 21 Pli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 21 PLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred hHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 5788999999999999999988886
No 47
>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=29.49 E-value=52 Score=23.93 Aligned_cols=20 Identities=10% Similarity=0.189 Sum_probs=13.8
Q ss_pred HHHhCCCCCCchhHHHhhcC
Q 043018 19 YFESVGISGADLPKFLCSNK 38 (300)
Q Consensus 19 ~L~~lG~s~~~i~~ii~~~P 38 (300)
+-+.+|+|..+|..+-..+|
T Consensus 19 laR~LGlse~~Id~i~~~~~ 38 (86)
T cd08306 19 LARKLGLSETKIESIEEAHP 38 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCC
Confidence 34467777777777777777
No 48
>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=29.02 E-value=1.1e+02 Score=22.53 Aligned_cols=26 Identities=12% Similarity=-0.100 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcCC
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQP 179 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~P 179 (300)
.-..+.+++++|++.++|..++....
T Consensus 46 ~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 46 QLQFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCc
Confidence 34567788899999999999887643
No 49
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=28.09 E-value=1.6e+02 Score=20.07 Aligned_cols=41 Identities=17% Similarity=0.196 Sum_probs=32.1
Q ss_pred HHHH-hCCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhCCCh
Q 043018 159 DALM-SFSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKP 204 (300)
Q Consensus 159 ~~l~-~lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~ 204 (300)
+-+. +.|-+.++...++...| +..+-...+.+|.++.|+..
T Consensus 7 ~~Ie~kTGk~~~~W~~~~~~~~-----~~~k~~e~v~WLK~ehgLgh 48 (61)
T PF14117_consen 7 PNIEKKTGKTLDEWLALAREGG-----PLTKHGEIVAWLKDEHGLGH 48 (61)
T ss_pred hHhHHHHCcCHHHHHHHHHHhC-----CCCcHHHHHHHHHHHHCCCh
Confidence 3344 67888899888888888 55667788899998888875
No 50
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=27.13 E-value=67 Score=26.15 Aligned_cols=48 Identities=13% Similarity=-0.029 Sum_probs=33.8
Q ss_pred CCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 131 GIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 131 G~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
|.+.+...+...+|.-+..+++.+++.|--|.+-|.+.++|+-+++..
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 10 GKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 555555555555543345678888888888888888888888777654
No 51
>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=26.17 E-value=2.4e+02 Score=29.15 Aligned_cols=116 Identities=18% Similarity=0.119 Sum_probs=70.2
Q ss_pred ChhHHHHHHHh---CCCCCCchhHHHhhcCccccccccCcchhhhhHhhhh-ccCChhHHHHHHhCCcccccchhhhhhh
Q 043018 12 SLRPKIDYFES---VGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGL-VQTNVNLVHAVKQSSRIINCNIEKRLAP 87 (300)
Q Consensus 12 ~l~~~l~~L~~---lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~-g~~~~~v~~il~~~P~iL~~s~e~~l~~ 87 (300)
+....+.||.+ -|+.+....+|+..+..=...-++ ...+-|.++ |++++.+.++...... ....+.
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~----~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~ 145 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLD----DDPEKLLEVPGISKANLEKFVSQWSQ------QGDERR 145 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHH----hCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHH
Confidence 45677889986 377777777788777643222222 223445554 6777777666665311 123667
Q ss_pred HHHHHHhcCCChHHHH-----------HHhhhCCcceeechh--hHHHHHHHHHHhCCCCCCh
Q 043018 88 NVNTLRAHGVPEHLIA-----------KLIMINPSSLIKRRD--LFKTMMDVIKKIGIEPTNF 137 (300)
Q Consensus 88 ~v~~L~~lGl~~~~i~-----------~ll~~~P~ll~~~~~--~l~~~v~~L~~lG~~~~~~ 137 (300)
.+.||.++|++..... ..+..+|+.|..... .++..=+.-+.+|+++++.
T Consensus 146 ~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~~d~ 208 (720)
T TIGR01448 146 LLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDP 208 (720)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCCCCH
Confidence 7889999999875544 467788887765322 2322222235688887764
No 52
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.89 E-value=2.6e+02 Score=20.62 Aligned_cols=28 Identities=14% Similarity=0.006 Sum_probs=22.6
Q ss_pred HHHHHHHHHh-CCCCHHHHHHHHHcCCcc
Q 043018 154 WEKKKDALMS-FSWSEDEFYLAFKRQPML 181 (300)
Q Consensus 154 l~~kv~~l~~-lG~s~~~i~~m~~~~P~i 181 (300)
.-..+..+++ +|++.+++..++...+..
T Consensus 45 ~l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 45 RLERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 3455677887 999999999999887775
No 53
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=24.04 E-value=1.1e+02 Score=21.71 Aligned_cols=58 Identities=16% Similarity=0.197 Sum_probs=32.5
Q ss_pred HHHHHHHHcCCcccccchhhHHHHHHHHHHHhCCChhhhhh--CCcccccCccccchhhHHHHHHH
Q 043018 169 DEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIGLKPLDIVR--CPNLLLISLKKRVLPRWSVLQVL 232 (300)
Q Consensus 169 ~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g~~~~~i~~--~P~ll~~sle~ri~pR~~~l~~L 232 (300)
+++.+++. .++.-+.+.++.+++=+..+ |++..+|++ +..++...++...++ .+++.+
T Consensus 6 ~~i~~i~~---~~~~~~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~~~~~~~k~--~i~~~l 65 (89)
T PF08542_consen 6 EVIEEILE---SCLNGDFKEARKKLYELLVE-GYSASDILKQLHEVLVESDIPDSQKA--EILKIL 65 (89)
T ss_dssp HHHHHHHH---HHHHTCHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTSTSSHHHHH--HHHHHH
T ss_pred HHHHHHHH---HHHhCCHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHhhccHHHHH--HHHHHH
Confidence 44444444 33444667777888877776 888888764 455555555544443 344444
No 54
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.98 E-value=94 Score=22.13 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=25.1
Q ss_pred HHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhh
Q 043018 17 IDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKG 58 (300)
Q Consensus 17 l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~ 58 (300)
-++.+.+|++..+|..+-..+|. .. ......+.-|+.
T Consensus 15 k~laR~LGls~~~I~~ie~~~~~-~~----eq~~~mL~~W~~ 51 (79)
T cd08784 15 KRFFRKLGLSDNEIKVAELDNPQ-HR----DRVYELLRIWRN 51 (79)
T ss_pred HHHHHHcCCCHHHHHHHHHcCCc-hH----HHHHHHHHHHHh
Confidence 45667888888888888888887 32 245555554444
No 55
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=23.92 E-value=85 Score=25.39 Aligned_cols=48 Identities=15% Similarity=0.120 Sum_probs=35.1
Q ss_pred CCCCCChhHHHHHHHHhhccHHHHHHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 131 GIEPTNFMFILAVRSMSVLSKATWEKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 131 G~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
|.+.+...+...+|.-+..+++.+++.|--|.+-|.+.++|+.+++..
T Consensus 7 G~S~S~~P~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 7 GISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred CCCCCCCCCCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 555555556555554345678889999988999999999999777743
No 56
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.74 E-value=1.2e+02 Score=22.75 Aligned_cols=24 Identities=17% Similarity=-0.085 Sum_probs=19.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHc
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~ 177 (300)
+-..|..++++|||-++|..++.-
T Consensus 44 ~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 44 DLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHh
Confidence 455667778999999999998864
No 57
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.71 E-value=1.7e+02 Score=21.58 Aligned_cols=24 Identities=13% Similarity=-0.164 Sum_probs=19.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHc
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKR 177 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~ 177 (300)
.-..+.+++++||+.++|..++..
T Consensus 46 ~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 46 QLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhc
Confidence 345577889999999999988764
No 58
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=23.65 E-value=1.2e+02 Score=25.07 Aligned_cols=40 Identities=20% Similarity=0.239 Sum_probs=31.9
Q ss_pred ccchhhHHHHHHHHHCCCCc-CCCCchhhcccChhhHHHHh
Q 043018 220 KRVLPRWSVLQVLMSKNLLK-KDIDFIQALIVTKPVFERRF 259 (300)
Q Consensus 220 ~ri~pR~~~l~~L~~~Gl~~-~~~~l~~~l~~s~~~F~~~~ 259 (300)
.|+...-..+..|...|++. ...++..++..+-+.|+++=
T Consensus 65 ~r~~~~~~LL~kL~~~Gll~e~~~~Ld~vl~Ltv~~~leRR 105 (162)
T TIGR01018 65 QRLFEGNQLLRRLVRLGILDEENAKLDDVLGLTVEDFLERR 105 (162)
T ss_pred HHHHHHHHHHHHHHHcCCCccccCCHHHHHhccHHHHHHHh
Confidence 34544557888888999996 45789999999999999974
No 59
>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=23.43 E-value=2.2e+02 Score=25.31 Aligned_cols=69 Identities=13% Similarity=0.152 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHhCCChhhhhhCCcc-cccCccccchhhHHHHHHHHHCCCCcCCCCchhhcccChhhHHHHhcccCcCh
Q 043018 189 IRELMDFFVNEIGLKPLDIVRCPNL-LLISLKKRVLPRWSVLQVLMSKNLLKKDIDFIQALIVTKPVFERRFVTSYMDD 266 (300)
Q Consensus 189 l~~ki~fl~~~~g~~~~~i~~~P~l-l~~sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~s~~~F~~~~v~~~~~~ 266 (300)
++.+++.+.+ .|++.+.|.--|.+ +.-+.+ ..+.+++.+.. .++ ..++.++..|++.|........+++
T Consensus 152 ~~~~i~~~~~-~Gi~~~~Ii~DPg~gf~ks~~----~~~~~l~~i~~---l~~-~~~pil~G~SrkSfig~~~~~~~~~ 221 (257)
T cd00739 152 LEARLEAAES-AGVARNRIILDPGIGFGKTPE----HNLELLRRLDE---LKQ-LGLPVLVGASRKSFIGALLGREPKD 221 (257)
T ss_pred HHHHHHHHHH-cCCCHHHEEEecCCCcccCHH----HHHHHHHHHHH---HHh-CCCcEEEEecccHHHHHhcCCCccc
Confidence 5667776665 89999999888865 333321 12233332222 111 1345678999999999988765544
No 60
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=22.30 E-value=4.3e+02 Score=24.02 Aligned_cols=24 Identities=25% Similarity=-0.034 Sum_probs=17.9
Q ss_pred HHHHHh-CCCCHHHHHHHHHcCCcc
Q 043018 158 KDALMS-FSWSEDEFYLAFKRQPML 181 (300)
Q Consensus 158 v~~l~~-lG~s~~~i~~m~~~~P~i 181 (300)
.++|++ .+.+-+++.+++...|.+
T Consensus 202 ~~wLqsl~~~~yeear~~L~~lpGV 226 (323)
T KOG2875|consen 202 LAWLQSLRKSSYEEAREALCSLPGV 226 (323)
T ss_pred chHHHHHhcccHHHHHHHHhcCCCC
Confidence 567774 567888888888887764
No 61
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=22.23 E-value=3.5e+02 Score=23.12 Aligned_cols=87 Identities=16% Similarity=0.186 Sum_probs=50.0
Q ss_pred ccccccccCcchh--hhhHhhhhccCChhHHHHHHhCCcccccchhhhhhhHHHHHHhcCCChHHHHHHhhhCCcceeec
Q 043018 39 QLLVVSLKSNIIP--IFEFLKGLVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAHGVPEHLIAKLIMINPSSLIKR 116 (300)
Q Consensus 39 ~lL~~s~e~~l~p--~v~fL~~~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~~~P~ll~~~ 116 (300)
.++..+++.+|.. .++++...-+...++..+..+.....- +.+..++.+++.|+ |.+.+.+..+...++.+.-
T Consensus 6 ~L~vFD~D~TLi~~~~~~~~~~~~g~~~~v~~~t~~~~~~~~-~~~~~~~~~v~~l~--g~~~~~v~~~~~~~~~l~~-- 80 (212)
T COG0560 6 KLAVFDLDGTLINAELIDELARGAGVGEEVLAITERAMRGEL-DFEESLRLRVALLK--GLPVEVLEEVREEFLRLTP-- 80 (212)
T ss_pred ceEEEecccchhhHHHHHHHHHHhCCHHHHHHHHHHHhcccc-cHHHHHHHHHHHhC--CCCHHHHHHHHHhcCcCCc--
Confidence 3555666666666 334555544555667666666555433 44445555655554 4577777777766533321
Q ss_pred hhhHHHHHHHHHHhCC
Q 043018 117 RDLFKTMMDVIKKIGI 132 (300)
Q Consensus 117 ~~~l~~~v~~L~~lG~ 132 (300)
...+.+.++++.|.
T Consensus 81 --ga~elv~~lk~~G~ 94 (212)
T COG0560 81 --GAEELVAALKAAGA 94 (212)
T ss_pred --cHHHHHHHHHHCCC
Confidence 24566677777664
No 62
>PRK09875 putative hydrolase; Provisional
Probab=22.15 E-value=69 Score=29.11 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=23.9
Q ss_pred hhhHHHHHHhcCCChHHHHHHhhhCCc
Q 043018 85 LAPNVNTLRAHGVPEHLIAKLIMINPS 111 (300)
Q Consensus 85 l~~~v~~L~~lGl~~~~i~~ll~~~P~ 111 (300)
++..+..|++.|+++++|.+++..+|.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 566677899999999999999999996
No 63
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=22.14 E-value=91 Score=27.36 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=34.6
Q ss_pred CCceecCcCCChhH----------HHHHHHhCCCCCCchhHHHhhcCccccccccCcchhhhhHhhhhccCC
Q 043018 2 PTLLLADPEKSLRP----------KIDYFESVGISGADLPKFLCSNKQLLVVSLKSNIIPIFEFLKGLVQTN 63 (300)
Q Consensus 2 P~lL~~~~~~~l~~----------~l~~L~~lG~s~~~i~~ii~~~P~lL~~s~e~~l~p~v~fL~~~g~~~ 63 (300)
|.++..|.|+++.+ .+.-|++.|+ |-++++| ++....+.+..++|+.+
T Consensus 7 ~~lIFtDlD~TLl~~~ye~~pA~pv~~el~d~G~------------~Vi~~SS--KT~aE~~~l~~~l~v~~ 64 (274)
T COG3769 7 PLLIFTDLDGTLLPHSYEWQPAAPVLLELKDAGV------------PVILCSS--KTRAEMLYLQKSLGVQG 64 (274)
T ss_pred ceEEEEcccCcccCCCCCCCccchHHHHHHHcCC------------eEEEecc--chHHHHHHHHHhcCCCC
Confidence 56666777776544 6666777774 5677776 67888888888999874
No 64
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=22.10 E-value=1e+02 Score=25.83 Aligned_cols=38 Identities=21% Similarity=0.167 Sum_probs=31.7
Q ss_pred cchhhHHHHHHHHHCCCCcCCCCchhhcccChhhHHHH
Q 043018 221 RVLPRWSVLQVLMSKNLLKKDIDFIQALIVTKPVFERR 258 (300)
Q Consensus 221 ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~s~~~F~~~ 258 (300)
++.-.-.++..|...|++..+.++.+++..+-+.||++
T Consensus 66 r~~~~~~Ll~kL~~~Gil~~~~~L~~vl~L~v~~~ler 103 (177)
T PRK04051 66 RAKEEEQLLGKLKRYGILKENATLDDVLSLTVEDILER 103 (177)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCCHHHHHhccHHHHHHh
Confidence 34444567888889999988889999999999999997
No 65
>PRK09875 putative hydrolase; Provisional
Probab=21.73 E-value=88 Score=28.43 Aligned_cols=27 Identities=11% Similarity=0.167 Sum_probs=23.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcCCc
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQPM 180 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~P~ 180 (300)
+..-+..|++.|+++++|.+|+..+|.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 455566788899999999999999996
No 66
>PF03800 Nuf2: Nuf2 family; InterPro: IPR005549 Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Q9C953 from SWISSPROT. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.; GO: 0007067 mitosis, 0000775 chromosome, centromeric region; PDB: 2VE7_D 3IZ0_D.
Probab=21.71 E-value=3.9e+02 Score=21.18 Aligned_cols=92 Identities=20% Similarity=0.245 Sum_probs=40.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHH-HhCCChhhh----------hhCCcccccCccccc
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVN-EIGLKPLDI----------VRCPNLLLISLKKRV 222 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~-~~g~~~~~i----------~~~P~ll~~sle~ri 222 (300)
..+-+++|.++|++..+ . -+. .|+ .+.++.-++.+.+ -+|.+.+++ +.+|.+..-++...
T Consensus 14 ~~eIv~~L~~~~~~~t~-~-dl~-kPt-----~e~v~~ly~~~L~~~~g~~~e~~~~~~~~~~~~~~~pe~~~~~i~~l- 84 (146)
T PF03800_consen 14 PDEIVNCLQECGIPVTE-E-DLK-KPT-----PEFVQKLYERFLETFLGISPEDIEQPMFEALESLEYPELHEESIPLL- 84 (146)
T ss_dssp HHHHHHHHHHHT--HHH-H-C---G-------HHHHHHHHHHHHHHHHT--CGGG--C---TT---S-GGGGTTTHHHH-
T ss_pred HHHHHHHHHHCCCCcCH-H-HHc-CCC-----HHHHHHHHHHHHHHHHCcCHHHHhhhhHHHHhcccchhhHHHHHHHH-
Confidence 34456666666665221 1 111 133 4566666666663 578877776 34555555454321
Q ss_pred hhhHHHH-HHHHHCCCCcCCCCchhhcccChhhHHH
Q 043018 223 LPRWSVL-QVLMSKNLLKKDIDFIQALIVTKPVFER 257 (300)
Q Consensus 223 ~pR~~~l-~~L~~~Gl~~~~~~l~~~l~~s~~~F~~ 257 (300)
--++.+ +++...|+. +.++.+++....+|+..
T Consensus 85 -~l~~~~~~~~~~~gv~--DF~l~Dl~~P~~~R~~~ 117 (146)
T PF03800_consen 85 -NLFRHLQKFLKDCGVP--DFSLSDLLKPDPKRTRR 117 (146)
T ss_dssp -HHHHHHHHHHHHTT-------HHHHHS--HHHHHH
T ss_pred -HHHHHHHHHHHHcCCC--CCCHHHhcCCcHHHHHH
Confidence 112222 334456774 78888999888876644
No 67
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.99 E-value=2e+02 Score=22.07 Aligned_cols=25 Identities=8% Similarity=-0.048 Sum_probs=20.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcC
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQ 178 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~ 178 (300)
.-..+.+++++|||.++|..++...
T Consensus 46 ~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 46 RLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 3466788889999999999888654
No 68
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=20.80 E-value=33 Score=21.09 Aligned_cols=13 Identities=15% Similarity=0.552 Sum_probs=10.5
Q ss_pred HHHhCCCCCCchh
Q 043018 19 YFESVGISGADLP 31 (300)
Q Consensus 19 ~L~~lG~s~~~i~ 31 (300)
-|.++|++.+||.
T Consensus 27 ~L~DIGl~R~di~ 39 (40)
T PF06568_consen 27 QLADIGLTRSDIR 39 (40)
T ss_pred HHHHcCCCHHHhc
Confidence 5788999988874
No 69
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=20.75 E-value=2.2e+02 Score=23.17 Aligned_cols=35 Identities=14% Similarity=0.267 Sum_probs=26.2
Q ss_pred hCCcccccchhhhhhhHHHHHHhcCCChHHHHHHhh
Q 043018 72 QSSRIINCNIEKRLAPNVNTLRAHGVPEHLIAKLIM 107 (300)
Q Consensus 72 ~~P~iL~~s~e~~l~~~v~~L~~lGl~~~~i~~ll~ 107 (300)
..|..+.++.++ ++..|--|..-|++.++|+-++.
T Consensus 21 ~~P~W~~~~~ee-ve~~I~~lakkG~~pSqIG~~LR 55 (151)
T PRK08561 21 EPPEWVDYSPEE-IEELVVELAKQGYSPSMIGIILR 55 (151)
T ss_pred CCCccccCCHHH-HHHHHHHHHHCCCCHHHhhhhHh
Confidence 456677777765 77777778888888888887765
No 70
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=20.71 E-value=60 Score=29.33 Aligned_cols=111 Identities=11% Similarity=0.133 Sum_probs=0.0
Q ss_pred hhccCChhHHHHHHhCCcccccchh------hhhhhHHHHHHhcCC---ChHHHHHHhhhCCcceeechh--hHHHHHHH
Q 043018 58 GLVQTNVNLVHAVKQSSRIINCNIE------KRLAPNVNTLRAHGV---PEHLIAKLIMINPSSLIKRRD--LFKTMMDV 126 (300)
Q Consensus 58 ~~g~~~~~v~~il~~~P~iL~~s~e------~~l~~~v~~L~~lGl---~~~~i~~ll~~~P~ll~~~~~--~l~~~v~~ 126 (300)
++++.++.+..++...|.+|..++| ..++|...|-+++.+ -++.-..++++.--+++..+. .+.+.++-
T Consensus 157 DF~G~~~al~~v~~~~pdV~nHNvETVprL~~~VRp~A~Y~~SL~~L~~~k~~~P~i~TKSgiMlGLGEt~~Ev~e~m~D 236 (306)
T COG0320 157 DFRGNDDALEIVADAGPDVFNHNVETVPRLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIEVMDD 236 (306)
T ss_pred cccCCHHHHHHHHhcCcchhhcccccchhcccccCCCCcHHHHHHHHHHHHHhCCCcccccceeeecCCcHHHHHHHHHH
Q ss_pred HHHhCCCCCChhHHHHH-----HHHhhccHHHHHHHHHHHHhCCCCH
Q 043018 127 IKKIGIEPTNFMFILAV-----RSMSVLSKATWEKKKDALMSFSWSE 168 (300)
Q Consensus 127 L~~lG~~~~~~~~~~~~-----~~l~~~~~~~l~~kv~~l~~lG~s~ 168 (300)
|.+.|++-=++..-..| ++.-..+++.++.-=+.-.++||+.
T Consensus 237 Lr~~gvdilTiGQYlqPS~~HlpV~ryv~PeeF~~~~~~a~~~GF~~ 283 (306)
T COG0320 237 LRSAGVDILTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLH 283 (306)
T ss_pred HHHcCCCEEEeccccCCccccCCceeccCHHHHHHHHHHHHHccchh
No 71
>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=20.51 E-value=4.3e+02 Score=27.31 Aligned_cols=141 Identities=11% Similarity=-0.009 Sum_probs=74.8
Q ss_pred chhhhhHhhh---hccCChhHHHHHHhCCcccccchhhhhhhHHHHHHhc-CCChHHHHHHhhhCCcceeechhhHHHHH
Q 043018 49 IIPIFEFLKG---LVQTNVNLVHAVKQSSRIINCNIEKRLAPNVNTLRAH-GVPEHLIAKLIMINPSSLIKRRDLFKTMM 124 (300)
Q Consensus 49 l~p~v~fL~~---~g~~~~~v~~il~~~P~iL~~s~e~~l~~~v~~L~~l-Gl~~~~i~~ll~~~P~ll~~~~~~l~~~v 124 (300)
....+.||.+ -|+.++...+++..++ .+.-+.+....+.|.+. |++.+...++..... ........+
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv~~fg----~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~-----~~~~~~~~~ 147 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIVKTFG----EAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS-----QQGDERRLL 147 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHhC----HhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH-----HhHHHHHHH
Confidence 3456678875 2334556667776654 33223455556677775 999988888776531 122367888
Q ss_pred HHHHHhCCCCCChhHHHHHHHHhhccHHHHHHHHHHHH-h-CCCCHHHHHHHHHcCCcccccchhhHHHHHHHHHHHhC
Q 043018 125 DVIKKIGIEPTNFMFILAVRSMSVLSKATWEKKKDALM-S-FSWSEDEFYLAFKRQPMLMLSSTKKIRELMDFFVNEIG 201 (300)
Q Consensus 125 ~~L~~lG~~~~~~~~~~~~~~l~~~~~~~l~~kv~~l~-~-lG~s~~~i~~m~~~~P~iL~~S~~~l~~ki~fl~~~~g 201 (300)
.||.++|++++....+.. .......+.++++==.|. + .|++-..+-++-.+ -.+=.-++..++.-+.|..++..
T Consensus 148 ~~L~~~gi~~~~a~ki~~--~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~-~g~~~~d~~Ri~a~i~~~L~~~~ 223 (720)
T TIGR01448 148 AGLQGLGIGIKLAQRIYK--FYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQA-LGIALNDPRRITAGLVYSLQQAC 223 (720)
T ss_pred HHHHHcCCCHHHHHHHHH--HHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHh
Confidence 999999998763222211 111111122222221122 1 33333333333333 23333455667777777776544
No 72
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=20.36 E-value=1.6e+02 Score=22.49 Aligned_cols=93 Identities=10% Similarity=0.072 Sum_probs=45.1
Q ss_pred CcccccchhhhhhhHHHHHHhcC-CChHHHHHHhhhCCcceeechhhHHHHHHHHHHhCCCCCCh-hHHHHHHHHhhccH
Q 043018 74 SRIINCNIEKRLAPNVNTLRAHG-VPEHLIAKLIMINPSSLIKRRDLFKTMMDVIKKIGIEPTNF-MFILAVRSMSVLSK 151 (300)
Q Consensus 74 P~iL~~s~e~~l~~~v~~L~~lG-l~~~~i~~ll~~~P~ll~~~~~~l~~~v~~L~~lG~~~~~~-~~~~~~~~l~~~~~ 151 (300)
|.-|+-.-...++..+..|.+.| ++..++..+-. +|..-+......+.+++-|+..+.. ......|.+. ...
T Consensus 3 P~~L~~~ak~~w~ri~~~L~~~~~l~~~D~~~l~~-----yc~a~~~~~~a~~~i~~~G~~~~~~~g~~k~nPa~~-i~~ 76 (116)
T TIGR01558 3 PDWLGKEGKDEWKRVAPELKGSGILTNLDRDALLR-----YCEAYDRYREATDDLEATGITATVEDGSPKANPALT-VVE 76 (116)
T ss_pred chhHhHHHHHHHHHHHHHHHHcCCchHHHHHHHHH-----HHHHHHHHHHHHHHHHHcCeeEEeCCCCeecChHHH-HHH
Confidence 44444333445677777777777 46666555432 2233345556666666666543210 1111111111 112
Q ss_pred HHHHHHHHHHHhCCCCHHHHH
Q 043018 152 ATWEKKKDALMSFSWSEDEFY 172 (300)
Q Consensus 152 ~~l~~kv~~l~~lG~s~~~i~ 172 (300)
+..+.-..+..++|+|+..=.
T Consensus 77 ~a~~~~~~l~~elGLtP~sR~ 97 (116)
T TIGR01558 77 DAFKQLRSIGSALGLTPSSRS 97 (116)
T ss_pred HHHHHHHHHHHHcCCCHHHHH
Confidence 234444455557888876533
No 73
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=20.22 E-value=2.8e+02 Score=20.51 Aligned_cols=26 Identities=15% Similarity=0.035 Sum_probs=20.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHcCC
Q 043018 154 WEKKKDALMSFSWSEDEFYLAFKRQP 179 (300)
Q Consensus 154 l~~kv~~l~~lG~s~~~i~~m~~~~P 179 (300)
.-..+.+++..|++.+++..++....
T Consensus 46 ~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 46 RLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 34557778899999999999887654
Done!