Query 044946
Match_columns 365
No_of_seqs 195 out of 1189
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:21:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044946.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044946hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 2.5E-55 5.4E-60 438.1 25.1 305 35-352 127-446 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 2.9E-48 6.2E-53 375.4 9.5 301 35-343 36-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1E-42 2.2E-47 347.6 20.3 297 35-345 95-412 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 3.8E-36 8.2E-41 290.8 5.7 290 41-344 5-314 (345)
5 KOG1267 Mitochondrial transcri 100.0 5.8E-28 1.3E-32 238.7 16.4 277 33-321 59-411 (413)
6 KOG1267 Mitochondrial transcri 99.7 1.6E-17 3.4E-22 164.5 10.2 204 101-315 90-336 (413)
7 smart00733 Mterf Mitochondrial 97.3 0.00018 3.8E-09 43.3 2.7 30 259-289 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.1 0.00037 8.1E-09 41.8 2.1 30 85-115 2-31 (31)
9 PF11955 PORR: Plant organelle 91.6 3 6.6E-05 40.2 12.0 218 74-299 45-317 (335)
10 cd04790 HTH_Cfa-like_unk Helix 90.2 1.8 3.9E-05 37.6 8.3 48 207-260 119-167 (172)
11 PF04695 Pex14_N: Peroxisomal 84.2 2.1 4.5E-05 35.7 5.0 30 239-268 22-51 (136)
12 PF04695 Pex14_N: Peroxisomal 75.0 5.1 0.00011 33.4 4.4 26 66-91 23-48 (136)
13 PRK14136 recX recombination re 72.9 73 0.0016 30.3 11.9 102 134-264 200-302 (309)
14 PF14490 HHH_4: Helix-hairpin- 72.3 15 0.00032 28.3 6.2 47 101-168 7-53 (94)
15 PRK14135 recX recombination re 70.5 89 0.0019 28.8 15.6 73 173-263 180-258 (263)
16 PF11955 PORR: Plant organelle 68.9 32 0.00069 33.3 8.9 95 178-272 44-152 (335)
17 PRK14136 recX recombination re 68.7 47 0.001 31.6 9.6 132 35-194 168-301 (309)
18 PF14490 HHH_4: Helix-hairpin- 64.0 21 0.00046 27.4 5.5 67 35-124 11-78 (94)
19 PF02631 RecX: RecX family; I 63.5 62 0.0013 25.9 8.5 70 174-263 48-118 (121)
20 PF00627 UBA: UBA/TS-N domain; 63.1 13 0.00029 23.1 3.5 24 241-264 3-26 (37)
21 PRK14134 recX recombination re 63.0 1.4E+02 0.0029 28.2 12.5 23 241-263 256-278 (283)
22 TIGR01448 recD_rel helicase, p 63.0 29 0.00062 37.3 8.1 106 34-167 79-187 (720)
23 PRK08561 rps15p 30S ribosomal 59.8 23 0.00051 29.9 5.3 98 228-330 21-141 (151)
24 smart00165 UBA Ubiquitin assoc 59.4 16 0.00034 22.6 3.4 23 242-264 3-25 (37)
25 COG2137 OraA Uncharacterized p 59.0 72 0.0016 27.8 8.4 133 35-194 26-163 (174)
26 cd04790 HTH_Cfa-like_unk Helix 58.2 18 0.00038 31.4 4.6 50 66-122 118-167 (172)
27 cd00194 UBA Ubiquitin Associat 55.5 20 0.00043 22.2 3.4 23 242-264 3-25 (38)
28 PF11264 ThylakoidFormat: Thyl 53.6 25 0.00055 31.7 4.9 74 2-75 30-111 (216)
29 PF07499 RuvA_C: RuvA, C-termi 52.3 28 0.00062 23.0 3.8 26 240-265 3-28 (47)
30 PF07499 RuvA_C: RuvA, C-termi 51.4 21 0.00046 23.6 3.1 24 67-90 4-27 (47)
31 PF08069 Ribosomal_S13_N: Ribo 48.3 10 0.00022 26.9 1.1 48 217-264 10-57 (60)
32 PF02631 RecX: RecX family; I 47.1 1.3E+02 0.0027 24.1 7.7 58 202-262 7-67 (121)
33 PF12244 DUF3606: Protein of u 45.6 36 0.00077 23.7 3.6 26 32-57 19-44 (57)
34 PHA02591 hypothetical protein; 45.1 29 0.00063 25.8 3.2 44 43-87 22-69 (83)
35 PRK13266 Thf1-like protein; Re 45.0 45 0.00097 30.3 5.1 75 3-77 36-118 (225)
36 PRK14137 recX recombination re 44.0 2.3E+02 0.005 25.1 9.8 128 37-194 48-178 (195)
37 TIGR03060 PS_II_psb29 photosys 43.2 76 0.0016 28.6 6.2 76 3-78 36-119 (214)
38 PF00356 LacI: Bacterial regul 40.6 62 0.0013 21.4 4.0 40 178-220 6-45 (46)
39 PF08671 SinI: Anti-repressor 40.5 42 0.00092 20.2 2.8 25 239-263 4-28 (30)
40 PF13543 KSR1-SAM: SAM like do 40.3 49 0.0011 27.3 4.2 52 37-89 71-124 (129)
41 smart00354 HTH_LACI helix_turn 40.2 52 0.0011 23.6 4.0 40 179-221 8-47 (70)
42 PRK00116 ruvA Holliday junctio 40.1 1E+02 0.0023 27.1 6.6 24 102-125 149-172 (192)
43 PF11181 YflT: Heat induced st 38.3 94 0.002 24.2 5.5 77 170-259 11-89 (103)
44 PRK00117 recX recombination re 38.2 1.8E+02 0.0039 24.4 7.7 56 35-91 31-103 (157)
45 PRK00116 ruvA Holliday junctio 37.9 50 0.0011 29.1 4.3 53 38-90 109-173 (192)
46 PRK11613 folP dihydropteroate 37.5 88 0.0019 29.5 6.0 65 275-347 165-229 (282)
47 PLN03060 inositol phosphatase- 37.3 33 0.00071 30.7 2.9 84 3-86 34-125 (206)
48 PF02022 Integrase_Zn: Integra 36.4 72 0.0016 20.5 3.7 29 239-267 7-36 (40)
49 PF11212 DUF2999: Protein of u 35.7 1.5E+02 0.0032 21.8 5.5 17 175-191 33-49 (82)
50 COG1125 OpuBA ABC-type proline 35.2 71 0.0015 29.9 4.8 63 238-300 71-136 (309)
51 PF03960 ArsC: ArsC family; I 34.8 84 0.0018 24.7 4.8 35 130-165 53-90 (110)
52 COG1393 ArsC Arsenate reductas 34.4 69 0.0015 25.9 4.2 52 134-192 62-115 (117)
53 KOG2629 Peroxisomal membrane a 32.9 91 0.002 29.3 5.1 25 239-263 21-45 (300)
54 cd08306 Death_FADD Fas-associa 32.8 1.4E+02 0.003 22.6 5.4 50 69-123 16-66 (86)
55 PF02787 CPSase_L_D3: Carbamoy 32.2 1.1E+02 0.0024 25.0 5.1 61 181-261 22-82 (123)
56 cd08315 Death_TRAILR_DR4_DR5 D 32.0 1.7E+02 0.0036 22.7 5.9 50 67-122 20-70 (96)
57 PF03874 RNA_pol_Rpb4: RNA pol 31.5 1E+02 0.0022 24.5 4.8 29 64-92 57-85 (117)
58 COG3620 Predicted transcriptio 31.2 1E+02 0.0022 26.6 4.7 50 170-220 49-98 (187)
59 cd01392 HTH_LacI Helix-turn-he 30.6 92 0.002 20.4 3.8 40 179-221 5-44 (52)
60 TIGR01616 nitro_assoc nitrogen 29.9 50 0.0011 27.0 2.7 42 147-197 75-118 (126)
61 PRK13344 spxA transcriptional 29.3 45 0.00097 27.5 2.3 37 147-192 76-114 (132)
62 PF11212 DUF2999: Protein of u 29.2 1.4E+02 0.003 21.9 4.4 47 67-121 2-48 (82)
63 smart00657 RPOL4c DNA-directed 29.0 71 0.0015 25.7 3.4 62 56-123 47-108 (118)
64 PF14117 DUF4287: Domain of un 28.5 1.6E+02 0.0035 20.9 4.7 45 41-88 11-56 (61)
65 PRK14137 recX recombination re 28.2 4.2E+02 0.0091 23.4 13.1 69 176-263 109-178 (195)
66 TIGR01448 recD_rel helicase, p 28.2 1.5E+02 0.0031 32.0 6.6 78 43-123 123-212 (720)
67 PF13331 DUF4093: Domain of un 28.1 2.5E+02 0.0055 21.3 6.1 53 33-87 30-86 (87)
68 COG3620 Predicted transcriptio 27.7 81 0.0018 27.2 3.6 73 181-254 17-98 (187)
69 PF03960 ArsC: ArsC family; I 27.4 1.2E+02 0.0027 23.7 4.6 22 250-271 69-90 (110)
70 cd08313 Death_TNFR1 Death doma 27.3 2.4E+02 0.0053 21.1 5.8 53 66-123 11-64 (80)
71 KOG2561 Adaptor protein NUB1, 27.1 1E+02 0.0023 30.8 4.7 30 63-92 300-329 (568)
72 cd03033 ArsC_15kD Arsenate Red 25.9 58 0.0013 26.0 2.4 15 147-161 74-88 (113)
73 TIGR00601 rad23 UV excision re 25.0 1.2E+02 0.0025 30.0 4.7 43 238-289 154-196 (378)
74 PRK14487 cbb3-type cytochrome 24.5 1.7E+02 0.0036 26.4 5.2 63 192-254 135-210 (217)
75 cd08319 Death_RAIDD Death doma 24.4 2.2E+02 0.0047 21.5 5.1 51 69-124 16-67 (83)
76 PRK14134 recX recombination re 24.0 6E+02 0.013 23.8 11.2 55 35-90 81-151 (283)
77 PRK09875 putative hydrolase; P 24.0 73 0.0016 30.2 3.0 28 239-266 261-288 (292)
78 PF09278 MerR-DNA-bind: MerR, 23.9 79 0.0017 22.0 2.6 19 243-261 6-24 (65)
79 PHA02591 hypothetical protein; 23.3 1.2E+02 0.0026 22.7 3.3 34 236-276 44-77 (83)
80 PRK12559 transcriptional regul 23.2 60 0.0013 26.7 2.1 37 147-192 76-114 (131)
81 KOG0400 40S ribosomal protein 23.2 64 0.0014 26.6 2.1 41 223-263 16-56 (151)
82 PF09288 UBA_3: Fungal ubiquit 23.1 1.3E+02 0.0028 20.9 3.3 22 242-263 11-32 (55)
83 PF13331 DUF4093: Domain of un 22.6 3.5E+02 0.0076 20.6 6.5 21 241-261 66-86 (87)
84 COG2137 OraA Uncharacterized p 22.4 5.2E+02 0.011 22.4 8.4 51 37-88 42-109 (174)
85 PF04891 NifQ: NifQ; InterPro 22.0 2.9E+02 0.0062 23.9 6.0 41 136-181 101-142 (167)
86 COG5457 Uncharacterized conser 21.9 90 0.002 22.3 2.4 19 71-89 41-59 (63)
87 PTZ00072 40S ribosomal protein 21.8 65 0.0014 27.1 1.9 48 217-264 7-54 (148)
88 cd08784 Death_DRs Death Domain 21.7 3.3E+02 0.0071 20.1 5.6 50 67-122 12-62 (79)
89 PF07647 SAM_2: SAM domain (St 21.7 1.1E+02 0.0023 21.3 2.9 12 107-118 42-53 (66)
90 PF03874 RNA_pol_Rpb4: RNA pol 21.7 96 0.0021 24.6 2.9 46 37-88 64-111 (117)
91 PRK07562 ribonucleotide-diphos 21.5 1.4E+02 0.003 33.9 4.9 84 37-121 717-821 (1220)
92 smart00354 HTH_LACI helix_turn 21.2 1.5E+02 0.0033 21.1 3.7 44 41-85 8-51 (70)
93 PRK00117 recX recombination re 21.2 4.9E+02 0.011 21.7 11.5 22 244-265 82-103 (157)
94 cd04781 HTH_MerR-like_sg6 Heli 20.7 1.6E+02 0.0036 23.5 4.1 23 242-264 47-69 (120)
95 cd04774 HTH_YfmP Helix-Turn-He 20.7 3E+02 0.0065 21.1 5.5 27 241-267 46-73 (96)
96 COG0320 LipA Lipoate synthase 20.6 1.4E+02 0.0029 28.2 3.9 78 139-220 157-244 (306)
97 PF06896 DUF1268: Protein of u 20.5 1.8E+02 0.0039 23.5 4.2 50 35-89 58-109 (114)
98 cd04788 HTH_NolA-AlbR Helix-Tu 20.3 2.5E+02 0.0054 21.5 4.9 24 242-265 48-71 (96)
99 cd08316 Death_FAS_TNFRSF6 Deat 20.1 1.2E+02 0.0027 23.6 3.1 28 66-93 20-47 (97)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2.5e-55 Score=438.11 Aligned_cols=305 Identities=20% Similarity=0.380 Sum_probs=256.4
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCC---CCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTL---EKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ 111 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~---~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~ 111 (365)
.++|| .++|++.+++.+++.++|.++.. .++.++++||+++|+++++|++++.++|.+|.+++++++.|+++||++
T Consensus 127 vl~fL-~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~ 205 (487)
T PLN03196 127 VLDYL-EKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVS 205 (487)
T ss_pred HHHHH-HHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHH
Confidence 34777 77888888888888888877643 356777888888888888888888888888888887778888888888
Q ss_pred cCCCCchHHHHHHH--------hccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCC
Q 044946 112 LGLVGSDLGKFISN--------LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGI 183 (365)
Q Consensus 112 lGl~~~~i~~ll~~--------~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~ 183 (365)
+|++.++|++++.+ +++++.|+++||.++|++ .+++++++.++|++| ++++++ +++|++++|+++|+
T Consensus 206 lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~---~~~I~~il~~~P~iL-~~sle~-~lkp~v~~L~elGv 280 (487)
T PLN03196 206 IGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLP---RLAVARILEKRPYIL-GFDLEE-TVKPNVECLLEFGV 280 (487)
T ss_pred cCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCC---HHHHHHHHHhCCcee-EcCHHH-hHHHHHHHHHHcCC
Confidence 88888888888777 567788888888888887 788888888888888 888876 78888888888888
Q ss_pred ChhhHHHHhhhcCccceecc-hhHHHHHHHHH-hccCCCch--hhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHH
Q 044946 184 VGSQLSMLLVRLPRLFCFND-LKLRQLVLRVL-DMGFTTDS--RMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIE 259 (365)
Q Consensus 184 ~~~~i~~ll~~~P~~l~~s~-~~i~~~v~~l~-~lG~~~~~--~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~ 259 (365)
+++.+..++.++|.+++.+. +++.+.++++. ++|+++++ .++.+.|. +.+.++++|+++++||+++||+.+++..
T Consensus 281 ~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~-il~lSe~kl~~kvefL~~~Gls~edI~~ 359 (487)
T PLN03196 281 RKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQ-IVSLNRNVALKHVEFLRGRGFSAQDVAK 359 (487)
T ss_pred CHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcch-hhcccHHHHHHHHHHHHHcCCCHHHHHH
Confidence 88888888888888888774 45777788774 68888776 23444454 4577899999999999999999999999
Q ss_pred HHHhcCcccccCHHHHHHHHHHHHHhhCCChhhHhhcCcccccCCCCcchhHHHHHHHHHHhccccCCcCccchhccChH
Q 044946 260 MIRTAPRLLSASEERLKSGLDFFLKKIEFGKAVLVRMPCCMMYSIENRVIPRYRVFQIVMVRRMLKKDWSFPSVLVLSEE 339 (365)
Q Consensus 260 ~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~ 339 (365)
||+++|++|++|.++|++|++||+++||++.++|+++|++|+||+|+||+|||+++ +++|+ .+++.++|.+||+
T Consensus 360 mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L---~~kGl---~~sL~~~L~~sd~ 433 (487)
T PLN03196 360 MVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERV---AKKGI---KCSLAWFLNCSDD 433 (487)
T ss_pred HHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHH---HHcCC---CCCHHHHhccCHH
Confidence 99999999999999999999999999999999999999999999999999999985 58998 5899999999999
Q ss_pred hHHHHhhhcCCCC
Q 044946 340 NFLNKYVLSFGDD 352 (365)
Q Consensus 340 ~F~~~~v~~~~~~ 352 (365)
+|+++||.+|.|+
T Consensus 434 ~F~~r~v~~y~e~ 446 (487)
T PLN03196 434 KFEQRMSGDFIEG 446 (487)
T ss_pred HHHHHHhhhcccc
Confidence 9999999999884
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=2.9e-48 Score=375.42 Aligned_cols=301 Identities=30% Similarity=0.467 Sum_probs=235.5
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCC---CCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTL---EKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ 111 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~---~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~ 111 (365)
.++|| .+.|+|.+++.+++..+|.+... +++.++++||+++|.+++|+.+++.++|++|..+.+.++.++++||++
T Consensus 36 k~~fl-~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~ 114 (345)
T PF02536_consen 36 KLEFL-RSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRS 114 (345)
T ss_dssp HHHHH-HHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHH
T ss_pred HHHHH-HHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhh
Confidence 56999 88999999999999999988753 558899999999999999999999999999998887789999999999
Q ss_pred cCCCCchHHHHHHH------hccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCCCh
Q 044946 112 LGLVGSDLGKFISN------LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVG 185 (365)
Q Consensus 112 lGl~~~~i~~ll~~------~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~ 185 (365)
+|++.+.+.+++.. ..+++.+.++++.++|++ ++++.+++.++|+++ ..+.++ +++|+++||+++|++.
T Consensus 115 lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~---~~~~~~vi~~~P~~l-~~~~~~-~~~~~v~~L~~~G~~~ 189 (345)
T PF02536_consen 115 LGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFD---PEKIGRVIAKNPRLL-LSDSES-ELKPKVEFLRSLGFSK 189 (345)
T ss_dssp TT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSS---HHHHCCCHHHHHHHH-CGSCCC-CCHHHHHHHHHCTT-G
T ss_pred cCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCC---chhhcccccccchhh-ccccHH-HHHHHHHHHHhhcccc
Confidence 99999877777766 236899999999999999 999999999999888 777777 8999999999999999
Q ss_pred hhHHHHhhhcCccceecchhHHHHHHHHHhccCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044946 186 SQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTAP 265 (365)
Q Consensus 186 ~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P 265 (365)
+++.+++.++|+++..+.+++.+.+.++.+.|...+...+.+.|.++ ..+.+++.++++||+++|||.+|+.+|+.++|
T Consensus 190 ~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il-~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P 268 (345)
T PF02536_consen 190 EDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQIL-SLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFP 268 (345)
T ss_dssp HHHHHHHHHTTTGGGCGCHC----------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSG
T ss_pred hhhhHHhhcccceeccccccccccccccccccccccccccccccccc-ccchHhHHHHHHHHHHhcCcHHHHHHHHHhCc
Confidence 99999999999999999888666666665544444444444555554 56688999999999999999999999999999
Q ss_pred cccccCHHHHHHHHHHHHHhhCCChhhHhhcCcccccCCCCcchhHHHHHHHHHHhccccCCcCccchhccChHhHHH
Q 044946 266 RLLSASEERLKSGLDFFLKKIEFGKAVLVRMPCCMMYSIENRVIPRYRVFQIVMVRRMLKKDWSFPSVLVLSEENFLN 343 (365)
Q Consensus 266 ~iL~~s~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~ 343 (365)
++|++|+|++++|++||.++||++.++|+++|++|+||+|+||+|||+++++|+++|. ...+++.+++.+||++|++
T Consensus 269 ~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 269 QILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp GGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred chhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCCHHHHhhccHHHhcC
Confidence 9999999999999999999999999999999999999999999999999999999997 6689999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1e-42 Score=347.56 Aligned_cols=297 Identities=17% Similarity=0.272 Sum_probs=265.9
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCC---CCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTL---EKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ 111 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~---~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~ 111 (365)
.++|| .++|++.+++. ++|.+++. +++.++++||+++|+++++|+++|.++|++|.++++++|.|+++||++
T Consensus 95 ~l~~L-~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~ 169 (487)
T PLN03196 95 RVEFL-HKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQG 169 (487)
T ss_pred HHHHH-HHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHH
Confidence 34788 78999988886 57888753 578899999999999999999999999999999999999999999999
Q ss_pred cCCCCchHHHHHHH--------hccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCC
Q 044946 112 LGLVGSDLGKFISN--------LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGI 183 (365)
Q Consensus 112 lGl~~~~i~~ll~~--------~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~ 183 (365)
+|+++++|++++.+ ++++|.|+++||.++|.+ ++++++++.++|.+| ++++++ +++|+++||+++|+
T Consensus 170 lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs---~~~i~~il~~~P~iL-~~sve~-~i~P~v~fL~~lGv 244 (487)
T PLN03196 170 LDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVA---PRDIGPMLTRFPEIL-GMRVGN-NIKPKVDYLESLGL 244 (487)
T ss_pred cCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCC---HHHHHHHHHhCcHHh-hcChhh-hHHHHHHHHHHcCC
Confidence 99999999999988 678999999999999999 999999999999999 999999 99999999999999
Q ss_pred ChhhHHHHhhhcCccceecch-hHHHHHHHHHhccCCCch--hhHhHHHHHHhccChhhHHHHHHHHH-HhCCCHHHHHH
Q 044946 184 VGSQLSMLLVRLPRLFCFNDL-KLRQLVLRVLDMGFTTDS--RMFVHGLDALCRLSEKTFDRKLDLFR-SYGFSKEECIE 259 (365)
Q Consensus 184 ~~~~i~~ll~~~P~~l~~s~~-~i~~~v~~l~~lG~~~~~--~~~~~~~~~l~~~s~~~l~~~v~fL~-~~G~s~~ev~~ 259 (365)
+.++|.+++.++|++|+++.+ +++++++++.++|++++. .++.+.|.++....++++.++++||. ++||+.+++..
T Consensus 245 ~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~ 324 (487)
T PLN03196 245 PRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGR 324 (487)
T ss_pred CHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHH
Confidence 999999999999999999965 899999999999999986 34456677776556778999999997 99999999999
Q ss_pred HHHhcCcccccCHHHHHHHHHHHHHhhCCChhhH----hhcCcccccCCCCcchhHHHHHHHHHHhcccc-CCcCccchh
Q 044946 260 MIRTAPRLLSASEERLKSGLDFFLKKIEFGKAVL----VRMPCCMMYSIENRVIPRYRVFQIVMVRRMLK-KDWSFPSVL 334 (365)
Q Consensus 260 ~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~i----~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~-~~~~l~~~l 334 (365)
++.++|+++++|.+++++|++||.+ +|++.++| .++|++|+||.+ +|+++++|+. .+.|... ....++.++
T Consensus 325 ~v~k~P~il~lSe~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~-~l~~k~dFlv--neMg~~~~~Iv~fP~~L 400 (487)
T PLN03196 325 VIEKLPQIVSLNRNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLE-IMKPSLEFFK--KEMKRPLKELVEFPAYF 400 (487)
T ss_pred HHHhcchhhcccHHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHH-HHHHHHHHHH--HHhCCCHHHHHhChHHh
Confidence 9999999999999999999999996 89999886 699999999996 8999999985 4445542 246788999
Q ss_pred ccChH-hHHHHh
Q 044946 335 VLSEE-NFLNKY 345 (365)
Q Consensus 335 ~~s~~-~F~~~~ 345 (365)
++|-| +-.-||
T Consensus 401 sySLEkRI~PR~ 412 (487)
T PLN03196 401 TYGLESRIKPRY 412 (487)
T ss_pred ccChhhhhHHHH
Confidence 99965 655555
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=3.8e-36 Score=290.78 Aligned_cols=290 Identities=23% Similarity=0.387 Sum_probs=139.8
Q ss_pred HhcCCCHHHHHHHHhhcccCCC---CCCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcCCCCc
Q 044946 41 ETVNIPKSRALVISNQFSRIKT---LEKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLGLVGS 117 (365)
Q Consensus 41 ~~~Gls~~~~~~i~~~~p~l~~---~~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lGl~~~ 117 (365)
+++|++.+++.++++++|.+.. ..++.++++||.++|++.+++++++.+||.+|..+.++++.|.++||+++|++++
T Consensus 5 ~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~ 84 (345)
T PF02536_consen 5 KNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDE 84 (345)
T ss_dssp HHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HH
T ss_pred HHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHH
Confidence 4555555555555555554431 1334555555555555555555555555555555555555555555555555555
Q ss_pred hHHHHHHH--------hccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCCChhhHH
Q 044946 118 DLGKFISN--------LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLS 189 (365)
Q Consensus 118 ~i~~ll~~--------~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~ 189 (365)
++++++.+ .+.++.+++.||+++|++ ++.+.+++...|.++ ... + ++++.++++.++|++++++.
T Consensus 85 d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~---~~~~~~~l~~~~~~~-~~~-~--~~~~~v~~l~~lG~~~~~~~ 157 (345)
T PF02536_consen 85 DIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVP---PSQIISLLISRPPLF-LSS-E--KIKERVEFLKELGFDPEKIG 157 (345)
T ss_dssp HHHHHHHH-SHHHHS---HHHHHHHHHHHHTT-----HHHHHHHHHH-CHHH-HS--H--HHHCHHHHHCCCTSSHHHHC
T ss_pred HHHHHHHhcchhhccchHhhhhhhhhHHhhcCCc---HHHHHHHHHhcCccc-cch-h--HHHHHHHHHHHhCCCchhhc
Confidence 55555554 223455555555555555 444444444444443 222 2 35555555555555555555
Q ss_pred HHhhhcCccceec-chhHHHHHHHHHhccCCCch--hhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhcCc
Q 044946 190 MLLVRLPRLFCFN-DLKLRQLVLRVLDMGFTTDS--RMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTAPR 266 (365)
Q Consensus 190 ~ll~~~P~~l~~s-~~~i~~~v~~l~~lG~~~~~--~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P~ 266 (365)
+++..+|+++... ++.+++++++|+++|++.+. .++.+.|.++....++.++. +.++.+.|...++ .++.++|.
T Consensus 158 ~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~-~~~l~~~~~~~~~--~~i~~~p~ 234 (345)
T PF02536_consen 158 RVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEP-VLYLLSSGGVEEE--RVIKKFPQ 234 (345)
T ss_dssp CCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC----------------------------
T ss_pred ccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccc-ccccccccccccc--cccccccc
Confidence 5555555433332 34455555555555555543 34444444443322222322 2222322222222 44555555
Q ss_pred ccccCHHHHHHHHHHHHHhhCCChhhH----hhcCcccccCCCCcchhHHHHHHHHHHhccccC-CcCccchhccChHh-
Q 044946 267 LLSASEERLKSGLDFFLKKIEFGKAVL----VRMPCCMMYSIENRVIPRYRVFQIVMVRRMLKK-DWSFPSVLVLSEEN- 340 (365)
Q Consensus 267 iL~~s~e~l~~k~~fL~~~mg~~~~~i----~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~-~~~l~~~l~~s~~~- 340 (365)
++.++.++++++++||.+ +|++.++| .++|++|+||.|+ ++|+++|+. .+.|.... -...+.++.+|-++
T Consensus 235 il~~~~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~--~~m~~~~~~i~~~P~~l~~sLe~r 310 (345)
T PF02536_consen 235 ILSLSEEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLV--KEMGLPLEEIVEFPQYLSYSLEKR 310 (345)
T ss_dssp --THHHHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHH--HCCT--HHHHHHSCHHHCS-HHHH
T ss_pred ccccchHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHH--HHhCcCHHHHhhCCceeEechhhh
Confidence 555555679999999996 89998874 6899999999995 999999874 34565432 35678899999864
Q ss_pred HHHH
Q 044946 341 FLNK 344 (365)
Q Consensus 341 F~~~ 344 (365)
-.-+
T Consensus 311 i~PR 314 (345)
T PF02536_consen 311 IKPR 314 (345)
T ss_dssp HHHH
T ss_pred hhhH
Confidence 4444
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.95 E-value=5.8e-28 Score=238.74 Aligned_cols=277 Identities=26% Similarity=0.395 Sum_probs=236.4
Q ss_pred chhHHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHHc
Q 044946 33 SIFLNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQL 112 (365)
Q Consensus 33 ~~~v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~l 112 (365)
.+.+.|++.++|.+...+..+.+.. ......+++++.++|+++|+++.+|..++..+|.++..+.++.+.|++.+|++.
T Consensus 59 ~f~~s~~~~s~~~~~~~~~~~~~~~-~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~ 137 (413)
T KOG1267|consen 59 NFESSYLVDSLGLSIKLARKLSREV-SSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSL 137 (413)
T ss_pred CcceeeeccccccchhhHHHHHHHH-HhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhcc
Confidence 6788999999999999998888776 555668999999999999999999999999999999999999999999999999
Q ss_pred CCCCchHHHHHHH--------hccccchhHHHHHH-----------------------------------HhccCCCchH
Q 044946 113 GLVGSDLGKFISN--------LERKLIPCVEILKK-----------------------------------ILAEDSNNED 149 (365)
Q Consensus 113 Gl~~~~i~~ll~~--------~~~~l~p~v~fL~~-----------------------------------~g~~~~~~~~ 149 (365)
|++.++++.++.. ...++.+.++|+.+ +|.. +++
T Consensus 138 g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~---~~~ 214 (413)
T KOG1267|consen 138 GLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVK---PRL 214 (413)
T ss_pred CccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCC---HHH
Confidence 9999998887776 23444455555554 4443 444
Q ss_pred HHHH--------------------------------HHhccccccccCCCCcchhchHHHHHHcCCChhhHHHHhhhcCc
Q 044946 150 LIRV--------------------------------IRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLSMLLVRLPR 197 (365)
Q Consensus 150 v~~~--------------------------------l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~ 197 (365)
+... +.+.|.++ +++.++ +++|++++|+++|++.++|..++.++|+
T Consensus 215 L~~~l~~~~~~~~~~~~l~~~~~~i~~~g~~p~~~~~v~~~~~~-~~~~~~-~i~~kv~~l~~~Gf~~~di~~~~~k~P~ 292 (413)
T KOG1267|consen 215 LKSLLESQPRPVLLYLKLKARLPFLLTLGFDPKTREFVKAPILL-SYSSEK-TLEPKVEVLKSLGFSREEIWKMVKKCPQ 292 (413)
T ss_pred HHHHHhcCccceeeehhhhhhhhhHHHhccCCchhHHHhhhhhh-cccccc-cHHHHHHHHHHcCCCHHHHHHHHHhCch
Confidence 4432 22344444 456787 9999999999999999999999999999
Q ss_pred cceecchhHHHHHHHHHhccCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhcCcccccCHH-HHH
Q 044946 198 LFCFNDLKLRQLVLRVLDMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTAPRLLSASEE-RLK 276 (365)
Q Consensus 198 ~l~~s~~~i~~~v~~l~~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P~iL~~s~e-~l~ 276 (365)
+|+++.+++...++++.+. +++ +.+.|.++ +.++.++.++++|+..+|++..|+..|++++|+++.+|.+ .++
T Consensus 293 ~l~~s~~~~~~~~~~~~~~--~~~---~~k~p~~l-~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~ 366 (413)
T KOG1267|consen 293 ILGYSVKKNLKTTEYLLKN--PKH---ILKFPQLL-RSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILK 366 (413)
T ss_pred heEeehhhhhHHHHHHHhc--chh---hhhhhhhh-hccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhh
Confidence 9999999988888888776 332 55666666 8889999999999999999999999999999999999999 689
Q ss_pred HHHHHHHHhhCCChhhHhhcCcccccCCCCcchhHHHHHHHHHHh
Q 044946 277 SGLDFFLKKIEFGKAVLVRMPCCMMYSIENRVIPRYRVFQIVMVR 321 (365)
Q Consensus 277 ~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~ 321 (365)
.+.+|+.+.|+++.+.++.+|.+++|++|+|+.||+.+..++..+
T Consensus 367 ~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 367 RKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred hhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999876543
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.72 E-value=1.6e-17 Score=164.52 Aligned_cols=204 Identities=24% Similarity=0.370 Sum_probs=154.3
Q ss_pred cHHHHHHHHHHcCCCCchHHHHHHH--------hccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchh
Q 044946 101 TLKPKIAYFQQLGLVGSDLGKFISN--------LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLL 172 (365)
Q Consensus 101 ~l~p~l~fL~~lGl~~~~i~~ll~~--------~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~ 172 (365)
+-...+++|++.|+++.++..++.. .++.+.|+..+|...|.+ ..++.+++..-|.+| +.+.+. ++.
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~---~s~l~~i~s~~~~il-~~~~~~-~~~ 164 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLP---SSELSSIVSVVPKIL-LKSKGE-SLS 164 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCcc---ccccchhhhccHHHH-HhhcCC-chh
Confidence 4566888999999999999988777 567778888899999998 888888888878887 654443 444
Q ss_pred chH-----------------------------------HHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhcc
Q 044946 173 RNI-----------------------------------EYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMG 217 (365)
Q Consensus 173 ~~v-----------------------------------~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG 217 (365)
+.+ ++++++|+.+..+..++...|+.+.... .+...+.++.++|
T Consensus 165 ~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g 243 (413)
T KOG1267|consen 165 TFIEFLKSIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLG 243 (413)
T ss_pred hHHHHhhccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhc
Confidence 444 4555555666666666666666665543 6778889999999
Q ss_pred CCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhcCcccccCHHHHHHHHHHHHHhhCCChhhHhhcC
Q 044946 218 FTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTAPRLLSASEERLKSGLDFFLKKIEFGKAVLVRMP 297 (365)
Q Consensus 218 ~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~i~~~P 297 (365)
+++.+.++++++.++.+.+++++++++++|+++||+.+|+.+|+.++|++|++|.+++..+++|+.+. .+++.++|
T Consensus 244 ~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p 319 (413)
T KOG1267|consen 244 FDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFP 319 (413)
T ss_pred cCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999755555555433 22244445
Q ss_pred cccccCCCCcchhHHHHH
Q 044946 298 CCMMYSIENRVIPRYRVF 315 (365)
Q Consensus 298 ~~L~~Sle~ri~pR~~~l 315 (365)
+++.+|.. .+.+|++++
T Consensus 320 ~~l~~s~~-~l~~~ie~l 336 (413)
T KOG1267|consen 320 QLLRSSED-KLKPRIEFL 336 (413)
T ss_pred hhhhccch-hhhhhHHHH
Confidence 44433333 344444443
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=97.35 E-value=0.00018 Score=43.31 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=26.4
Q ss_pred HHHHhcCcccccCHHHHHHHHHHHHHhhCCC
Q 044946 259 EMIRTAPRLLSASEERLKSGLDFFLKKIEFG 289 (365)
Q Consensus 259 ~~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~ 289 (365)
+++.++|.+++++.++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4788999999999888999999999 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=97.08 E-value=0.00037 Score=41.82 Aligned_cols=30 Identities=33% Similarity=0.580 Sum_probs=27.1
Q ss_pred HHHHhCCcceecCccCcHHHHHHHHHHcCCC
Q 044946 85 LAVHTKPTILFADVNKTLKPKIAYFQQLGLV 115 (365)
Q Consensus 85 ~li~~~P~lL~~~~~~~l~p~l~fL~~lGl~ 115 (365)
+++.++|.++..+ ++++.|+++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 5789999999999 66899999999999974
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=91.64 E-value=3 Score=40.23 Aligned_cols=218 Identities=14% Similarity=0.192 Sum_probs=112.9
Q ss_pred HhCCCChHHHHHHHHhCCcceecCc-------cCcHHHHHHHHH--HcCC---CCchHHHHHHH-----hcccc-chhHH
Q 044946 74 HSVGFSDTHIQLAVHTKPTILFADV-------NKTLKPKIAYFQ--QLGL---VGSDLGKFISN-----LERKL-IPCVE 135 (365)
Q Consensus 74 ~~lG~s~~~i~~li~~~P~lL~~~~-------~~~l~p~l~fL~--~lGl---~~~~i~~ll~~-----~~~~l-~p~v~ 135 (365)
..+|+....+...+.+||.++.... --.+-|...-|. +..+ ...++..-+.+ .++.| ..++.
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 3799977899999999999996532 112334333332 1222 22333333333 22322 34566
Q ss_pred HHH-HHhccCCCchHHHHHHHhccccccccCC-CC-cchhchHHHHHHcCCChhhHHHHh-------------hhcCccc
Q 044946 136 ILK-KILAEDSNNEDLIRVIRRMSWDLVVIDP-EK-SGLLRNIEYLKSCGIVGSQLSMLL-------------VRLPRLF 199 (365)
Q Consensus 136 fL~-~~g~~~~~~~~v~~~l~~~P~iL~~~s~-e~-~~l~~~v~~L~~lG~~~~~i~~ll-------------~~~P~~l 199 (365)
.++ ++|.+ ++-...++.+||..| .... ++ ...-.-+.|=.++.++.-+-.... -.+|--+
T Consensus 125 ~l~~dLGLP---~Df~~~lv~~yP~~F-rvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~f 200 (335)
T PF11955_consen 125 HLRRDLGLP---DDFRDSLVPKYPDYF-RVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSF 200 (335)
T ss_pred HHHHHcCCC---hhhccchhhhCCCCc-EEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecC
Confidence 666 68887 777778899999999 4321 11 011112222122333322222110 0122111
Q ss_pred e--ec-chhHHHHHHHHHhcc----------CCCch-hhHhHHHHH----HhccChh-hHHHHHHHHH-HhCCCHHHHHH
Q 044946 200 C--FN-DLKLRQLVLRVLDMG----------FTTDS-RMFVHGLDA----LCRLSEK-TFDRKLDLFR-SYGFSKEECIE 259 (365)
Q Consensus 200 ~--~s-~~~i~~~v~~l~~lG----------~~~~~-~~~~~~~~~----l~~~s~~-~l~~~v~fL~-~~G~s~~ev~~ 259 (365)
. +. ..+..+.++.++++- +++++ .+=.++..+ ++.+-++ ....++..|+ ++|++ +.+..
T Consensus 201 p~G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~ 279 (335)
T PF11955_consen 201 PKGFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRR 279 (335)
T ss_pred CCCccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHH
Confidence 1 11 235667777776644 33332 222233322 2222222 2456677777 88887 66888
Q ss_pred HHHhcCcccccCHHHHHHHHHHHHHhhCCChhh-HhhcCcc
Q 044946 260 MIRTAPRLLSASEERLKSGLDFFLKKIEFGKAV-LVRMPCC 299 (365)
Q Consensus 260 ~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~-i~~~P~~ 299 (365)
++.+||+|+.+|... +.-.=||++ ++..++ |-++|.+
T Consensus 280 ~l~rHPgIFYvS~kg-~~~TVfLrE--AY~~~~Liek~Pl~ 317 (335)
T PF11955_consen 280 LLLRHPGIFYVSLKG-KRHTVFLRE--AYDGGELIEKHPLV 317 (335)
T ss_pred HHHhCCCeEEEeccC-CceEEEEee--ccCCCCCCCCCchH
Confidence 888899998888642 222335664 455445 4467755
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=90.24 E-value=1.8 Score=37.61 Aligned_cols=48 Identities=13% Similarity=0.293 Sum_probs=28.6
Q ss_pred HHHHHHHHhccCCCch-hhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHH
Q 044946 207 RQLVLRVLDMGFTTDS-RMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEM 260 (365)
Q Consensus 207 ~~~v~~l~~lG~~~~~-~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~ 260 (365)
...++.++.+|+++.+ ......+. .. .=....+||.++|++.+|+..+
T Consensus 119 ~~w~~l~~~~g~~~~~m~~wh~~fe---~~---~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 119 EKWVAILKAAGMDEADMRRWHIEFE---KM---EPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHHH---Hh---CcHHHHHHHHHcCCCHHHHHHH
Confidence 4455566667777665 22222211 11 1245678999999999998754
No 11
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=84.23 E-value=2.1 Score=35.71 Aligned_cols=30 Identities=23% Similarity=0.355 Sum_probs=23.1
Q ss_pred hHHHHHHHHHHhCCCHHHHHHHHHhcCccc
Q 044946 239 TFDRKLDLFRSYGFSKEECIEMIRTAPRLL 268 (365)
Q Consensus 239 ~l~~~v~fL~~~G~s~~ev~~~i~~~P~iL 268 (365)
.+.+|++||++-|++.+||...+.+.+.--
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 478999999999999999999999877654
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=74.96 E-value=5.1 Score=33.35 Aligned_cols=26 Identities=23% Similarity=0.303 Sum_probs=14.4
Q ss_pred chhHHHHHHhCCCChHHHHHHHHhCC
Q 044946 66 PQTVSQFLHSVGFSDTHIQLAVHTKP 91 (365)
Q Consensus 66 ~~~~~~~L~~lG~s~~~i~~li~~~P 91 (365)
.+..++||++.|++++||..++.+.+
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~ 48 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAG 48 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcC
Confidence 45556666666666666666665544
No 13
>PRK14136 recX recombination regulator RecX; Provisional
Probab=72.94 E-value=73 Score=30.31 Aligned_cols=102 Identities=9% Similarity=0.129 Sum_probs=56.2
Q ss_pred HHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHH
Q 044946 134 VEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRV 213 (365)
Q Consensus 134 v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l 213 (365)
|++|++.|.-+ +...+....+. ..- ... -.....-|+.-||+.+.|...+... ..+.+......+
T Consensus 200 IerLke~gYLD--DeRFAesyVr~-R~~-kkG-----p~rIrqELrQKGId~eLIEqALeei------eEDE~E~A~~L~ 264 (309)
T PRK14136 200 LDALEREGWLS--DARFAESLVHR-RAS-RVG-----SARIVSELKRHAVGDALVESVGAQL------RETEFERAQAVW 264 (309)
T ss_pred HHHHHHcCCcC--HHHHHHHHHHH-Hhh-chh-----HHHHHHHHHHcCCCHHHHHHHHHhc------cHhHHHHHHHHH
Confidence 45555655542 66666555533 111 111 1223356888999999998877532 122233333333
Q ss_pred H-hccCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044946 214 L-DMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 214 ~-~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
+ +++-.+. ......+.+.||..-||+.+.|..++..+
T Consensus 265 eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 265 RKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 2 2221111 11234455899999999999999887654
No 14
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=72.32 E-value=15 Score=28.35 Aligned_cols=47 Identities=21% Similarity=0.381 Sum_probs=28.9
Q ss_pred cHHHHHHHHHHcCCCCchHHHHHHHhccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCC
Q 044946 101 TLKPKIAYFQQLGLVGSDLGKFISNLERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEK 168 (365)
Q Consensus 101 ~l~p~l~fL~~lGl~~~~i~~ll~~~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~ 168 (365)
.++..+.||.+.|++.....++... . .++...+|..+|+.| ..++.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~--------------y------g~~ai~~l~~nPY~L-~~~i~g 53 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKK--------------Y------GDDAIEILKENPYRL-IEDIDG 53 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHH--------------H-------TTHHHHHHH-STCC-CB-SSS
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH--------------H------hHHHHHHHHHChHHH-HHHccC
Confidence 4667788999999987766665432 2 235668999999999 765554
No 15
>PRK14135 recX recombination regulator RecX; Provisional
Probab=70.46 E-value=89 Score=28.77 Aligned_cols=73 Identities=14% Similarity=0.130 Sum_probs=41.2
Q ss_pred chHHHHHHcCCChhhHHHHhhhcCccceecch----hHHHHH-HHHHhccCCCchhhHhHHHHHHhccChhhH-HHHHHH
Q 044946 173 RNIEYLKSCGIVGSQLSMLLVRLPRLFCFNDL----KLRQLV-LRVLDMGFTTDSRMFVHGLDALCRLSEKTF-DRKLDL 246 (365)
Q Consensus 173 ~~v~~L~~lG~~~~~i~~ll~~~P~~l~~s~~----~i~~~v-~~l~~lG~~~~~~~~~~~~~~l~~~s~~~l-~~~v~f 246 (365)
....+|..-|++.+.|..++..... ....+ .+...+ ......+ ...+.+. ++.+.|
T Consensus 180 Ki~~~L~rkGf~~~~I~~~l~~~~~--e~d~~~e~e~l~~~~~k~~~k~~----------------~~~~~k~k~K~~~~ 241 (263)
T PRK14135 180 KIIQSLLTKGFSYEVIKAALEELDL--EQDEEEEQELLQKELEKAYRKYS----------------KYDGYELKQKLKQA 241 (263)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHccc--CCChHHHHHHHHHHHHHHHHHHh----------------cCCHHHHHHHHHHH
Confidence 3457899999999999988765310 00111 111111 1111121 1112233 455678
Q ss_pred HHHhCCCHHHHHHHHHh
Q 044946 247 FRSYGFSKEECIEMIRT 263 (365)
Q Consensus 247 L~~~G~s~~ev~~~i~~ 263 (365)
|..-||+.+.|..++..
T Consensus 242 L~rrGF~~~~I~~~l~~ 258 (263)
T PRK14135 242 LYRKGFSYDDIDSFLRE 258 (263)
T ss_pred HHHCCCCHHHHHHHHHH
Confidence 88999999999887764
No 16
>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=68.89 E-value=32 Score=33.29 Aligned_cols=95 Identities=15% Similarity=0.190 Sum_probs=58.3
Q ss_pred HHHcCCChhhHHHHhhhcCccceecc--h------hHHHHHHHH-H-hccCCC-chhhHhHHHHHHhccChhh--HHHHH
Q 044946 178 LKSCGIVGSQLSMLLVRLPRLFCFND--L------KLRQLVLRV-L-DMGFTT-DSRMFVHGLDALCRLSEKT--FDRKL 244 (365)
Q Consensus 178 L~~lG~~~~~i~~ll~~~P~~l~~s~--~------~i~~~v~~l-~-~lG~~~-~~~~~~~~~~~l~~~s~~~--l~~~v 244 (365)
-+.+|+++..+...+.++|.+|.... . ++.+....+ . +..+-. .....+..+.-+..+|.+. --.++
T Consensus 44 ~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki 123 (335)
T PF11955_consen 44 RRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKI 123 (335)
T ss_pred HHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHH
Confidence 34599977889999999999997532 0 122222222 1 111111 1133333444444555433 24678
Q ss_pred HHHH-HhCCCHHHHHHHHHhcCcccccCH
Q 044946 245 DLFR-SYGFSKEECIEMIRTAPRLLSASE 272 (365)
Q Consensus 245 ~fL~-~~G~s~~ev~~~i~~~P~iL~~s~ 272 (365)
..++ ++|+..+-...++.++|..+.+..
T Consensus 124 ~~l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 124 AHLRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHHHHcCCChhhccchhhhCCCCcEEee
Confidence 8888 899999988889999999877643
No 17
>PRK14136 recX recombination regulator RecX; Provisional
Probab=68.70 E-value=47 Score=31.60 Aligned_cols=132 Identities=13% Similarity=0.131 Sum_probs=76.3
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCC-ChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcC
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGF-SDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLG 113 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~-s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lG 113 (365)
++.|| ..---|..++..-+.+. .+ ..+.++.+++.|.+.|+ ++...++...+. ..-...+ .-.-.-|+.-|
T Consensus 168 AL~lL-SrReRSe~ELr~KL~kk-G~-~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp----~rIrqELrQKG 239 (309)
T PRK14136 168 ALGYL-SRREYSRAELARKLAPY-AD-ESDSVEPLLDALEREGWLSDARFAESLVHR-RASRVGS----ARIVSELKRHA 239 (309)
T ss_pred HHHHh-hcccccHHHHHHHHHHc-CC-CHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhH----HHHHHHHHHcC
Confidence 44677 66666777877655543 12 33568889999999887 677777665533 1111111 11234677889
Q ss_pred CCCchHHHHHHHhccccchhHHHHHHHhccCCCchHHHHHHHh-ccccccccCCCCcchhchHHHHHHcCCChhhHHHHh
Q 044946 114 LVGSDLGKFISNLERKLIPCVEILKKILAEDSNNEDLIRVIRR-MSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLSMLL 192 (365)
Q Consensus 114 l~~~~i~~ll~~~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~-~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~~ll 192 (365)
|+.+.|...+..++. ++ .+.+.+++.+ +.. + ..... .....+.||..-||+.+.|..+|
T Consensus 240 Id~eLIEqALeeieE------DE----------~E~A~~L~eKK~~~-~-~~d~k--ek~K~iRfL~rRGFS~D~I~~vL 299 (309)
T PRK14136 240 VGDALVESVGAQLRE------TE----------FERAQAVWRKKFGA-L-PQTPA--ERAKQARFLAARGFSSATIVKLL 299 (309)
T ss_pred CCHHHHHHHHHhccH------hH----------HHHHHHHHHHHhcc-c-CcCHH--HHHHHHHHHHHCCCCHHHHHHHH
Confidence 998877766543110 00 1222333333 222 2 21211 23455789999999999998877
Q ss_pred hh
Q 044946 193 VR 194 (365)
Q Consensus 193 ~~ 194 (365)
..
T Consensus 300 k~ 301 (309)
T PRK14136 300 KV 301 (309)
T ss_pred Hh
Confidence 54
No 18
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=64.01 E-value=21 Score=27.44 Aligned_cols=67 Identities=13% Similarity=0.262 Sum_probs=38.4
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHH-HcC
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQ-QLG 113 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~-~lG 113 (365)
++.|| ..+|+|...+.++.+.+ | ++...+|..+|-.|..++..-=-.+++-+- ++|
T Consensus 11 ~~~~L-~~~gl~~~~a~kl~~~y-------------------g---~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 11 LMAFL-QEYGLSPKLAMKLYKKY-------------------G---DDAIEILKENPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHH-HHTT--HHHHHHHHHHH-----------------------TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHH-HHcCCCHHHHHHHHHHH-------------------h---HHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence 45777 67888887777776654 2 134467899999998865543334455444 689
Q ss_pred CCCchHHHHHH
Q 044946 114 LVGSDLGKFIS 124 (365)
Q Consensus 114 l~~~~i~~ll~ 124 (365)
++..+-.++-.
T Consensus 68 ~~~~d~~Ri~A 78 (94)
T PF14490_consen 68 IEPDDPRRIRA 78 (94)
T ss_dssp --TT-HHHHHH
T ss_pred CCCCCHHHHHH
Confidence 88877666543
No 19
>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=63.54 E-value=62 Score=25.90 Aligned_cols=70 Identities=16% Similarity=0.097 Sum_probs=35.8
Q ss_pred hHHHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCCchhhHhHHHHHHhccC-hhhHHHHHHHHHHhCC
Q 044946 174 NIEYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTTDSRMFVHGLDALCRLS-EKTFDRKLDLFRSYGF 252 (365)
Q Consensus 174 ~v~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~~~~~~~~~~~~l~~~s-~~~l~~~v~fL~~~G~ 252 (365)
...-|+.-|++.+.|...+...+. .+. ..+.+.+ ........+ ....++.+.+|..-||
T Consensus 48 I~~~L~~kGi~~~~i~~~l~~~~~-----~e~---a~~~~~k------------k~~~~~~~~~~~~~~K~~~~L~rrGF 107 (121)
T PF02631_consen 48 IRQKLKQKGIDREIIEEALEEYDE-----EEE---ALELAEK------------KYRRYRKPSDRKRKQKLIRFLMRRGF 107 (121)
T ss_dssp HHHHHHHTT--HHHHHHHHTCS-H-----HHH---HHHHHHH------------HHHHTTTS-CHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHCCChHHHHHHHHHhhH-----HHH---HHHHHHH------------HHhcccCCCCHHHHHHHHHHHHHCCC
Confidence 446788899999999887761111 111 1111111 000000111 2334566788999999
Q ss_pred CHHHHHHHHHh
Q 044946 253 SKEECIEMIRT 263 (365)
Q Consensus 253 s~~ev~~~i~~ 263 (365)
+.+.|..++..
T Consensus 108 ~~~~i~~vi~~ 118 (121)
T PF02631_consen 108 SYDVIRRVISE 118 (121)
T ss_dssp -HHHHHHHCHH
T ss_pred CHHHHHHHHhh
Confidence 99999887654
No 20
>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=63.13 E-value=13 Score=23.14 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHhc
Q 044946 241 DRKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 241 ~~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
+..|+-|.++||+.++..+.+..+
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 356777888899998888776654
No 21
>PRK14134 recX recombination regulator RecX; Provisional
Probab=63.04 E-value=1.4e+02 Score=28.17 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=18.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHh
Q 044946 241 DRKLDLFRSYGFSKEECIEMIRT 263 (365)
Q Consensus 241 ~~~v~fL~~~G~s~~ev~~~i~~ 263 (365)
++...||.+-||+.+.|..++..
T Consensus 256 ~Kl~~~L~rkGf~~e~I~~vl~~ 278 (283)
T PRK14134 256 RRLSNYLLRRGYSWEEVKKSLNE 278 (283)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHH
Confidence 44568899999999999988753
No 22
>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=62.97 E-value=29 Score=37.27 Aligned_cols=106 Identities=16% Similarity=0.132 Sum_probs=69.5
Q ss_pred hhHHHHHH--hcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHh-CCCChHHHHHHHHhCCcceecCccCcHHHHHHHHH
Q 044946 34 IFLNYLIE--TVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHS-VGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQ 110 (365)
Q Consensus 34 ~~v~yL~~--~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~-lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~ 110 (365)
..+.||.+ --|+-+..+.+++..+. ..+.+.+..-.+-|.+ -|++...+..+...+.. .......+.||.
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg-~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~~~~~L~ 151 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFG-EAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERRLLAGLQ 151 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhC-HhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHHHHHHHH
Confidence 45699943 26788999999998873 2111122222334555 49999988888887621 224677889999
Q ss_pred HcCCCCchHHHHHHHhccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCC
Q 044946 111 QLGLVGSDLGKFISNLERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPE 167 (365)
Q Consensus 111 ~lGl~~~~i~~ll~~~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e 167 (365)
++|++.....++... + .++...+|..+|+.| ..++.
T Consensus 152 ~~gi~~~~a~ki~~~-----------y---------g~~~~~~i~~nPY~L-~~~i~ 187 (720)
T TIGR01448 152 GLGIGIKLAQRIYKF-----------Y---------QADTLDRVEKDPYLL-AEDVK 187 (720)
T ss_pred HcCCCHHHHHHHHHH-----------H---------hHHHHHHHHhCchhh-hhhcC
Confidence 999998766665432 1 235677888888888 55433
No 23
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=59.76 E-value=23 Score=29.88 Aligned_cols=98 Identities=13% Similarity=0.093 Sum_probs=46.5
Q ss_pred HHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhcCcc---------------------cccCHH--HHHHHHHHHHH
Q 044946 228 GLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTAPRL---------------------LSASEE--RLKSGLDFFLK 284 (365)
Q Consensus 228 ~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P~i---------------------L~~s~e--~l~~k~~fL~~ 284 (365)
.++.....+.+.+++.|--|.+-|++.++|+-+++..=.| -.+.+| .|-.++..|.+
T Consensus 21 ~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~~L~~ 100 (151)
T PRK08561 21 EPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRK 100 (151)
T ss_pred CCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHH
Confidence 3333334445555555555555566666665555443211 111112 23445555555
Q ss_pred hhCCChhhHhhcCcccccCCCCcchhHHHHHHHHHHhccccCCcCc
Q 044946 285 KIEFGKAVLVRMPCCMMYSIENRVIPRYRVFQIVMVRRMLKKDWSF 330 (365)
Q Consensus 285 ~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l 330 (365)
.+.....|.-..=. |-...--|.+.++|++..+....++.+
T Consensus 101 HL~~nkKD~~skRg-----L~~~~skrrRLl~Yyk~~~~LP~~WkY 141 (151)
T PRK08561 101 HLEENPKDLHNKRG-----LQLIESKIRRLVKYYKRTGVLPADWRY 141 (151)
T ss_pred HHHhCCCcchhHHH-----HHHHHHHHHHHHHHHHhcCCCCCCCcC
Confidence 55444443211101 111233566778888888776554444
No 24
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=59.44 E-value=16 Score=22.57 Aligned_cols=23 Identities=39% Similarity=0.715 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhc
Q 044946 242 RKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 242 ~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
++++-|.++||+++++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45677778888888887766654
No 25
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=59.03 E-value=72 Score=27.76 Aligned_cols=133 Identities=14% Similarity=0.033 Sum_probs=76.6
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCC-ChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcC
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGF-SDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLG 113 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~-s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lG 113 (365)
|+.|| +----|..++..-+.+. -.+.+-++.|+++|...|. ++...+....+.-.--+..|- ..-+-|...|
T Consensus 26 Al~~L-s~R~rse~ELr~kL~k~--~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g~G~~----rl~qeL~qkG 98 (174)
T COG2137 26 ALRLL-SRRDRSEKELRRKLAKK--EFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSRKGKGPA----RLKQELKQKG 98 (174)
T ss_pred HHHHH-HHHHHHHHHHHHHHHhc--cCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhcccChH----HHHHHHHHcC
Confidence 56666 54555677777655543 2233558899999998887 677777665544333333332 2335677889
Q ss_pred CCCchHHHHHHH--hccccchhHHHHHHHhccCCCchHHHHHHHhcccc-ccccCCCCcchhchH-HHHHHcCCChhhHH
Q 044946 114 LVGSDLGKFISN--LERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWD-LVVIDPEKSGLLRNI-EYLKSCGIVGSQLS 189 (365)
Q Consensus 114 l~~~~i~~ll~~--~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~i-L~~~s~e~~~l~~~v-~~L~~lG~~~~~i~ 189 (365)
++++.|..++.. -+... ......+..+++.- . . .+. ..+.++ .+|..-|++.+.|.
T Consensus 99 i~~~~Ie~aL~~~~~~~~~----------------~~a~~~~~kk~~~~~~-~--~~~-~~k~Ki~r~L~~rGFs~~~i~ 158 (174)
T COG2137 99 IDDEIIEEALELIDEEDEQ----------------ERARKVLRKKFKRENK-P--PDK-KEKAKIQRFLLRRGFSYEVIK 158 (174)
T ss_pred CCHHHHHHHHhccchHHHH----------------HHHHHHHHHHhCcccc-C--cch-hHHHHHHHHHHHcCCCHHHHH
Confidence 998888877653 00000 11112222323332 2 1 222 344444 57888999999998
Q ss_pred HHhhh
Q 044946 190 MLLVR 194 (365)
Q Consensus 190 ~ll~~ 194 (365)
.++..
T Consensus 159 ~~l~~ 163 (174)
T COG2137 159 EALNE 163 (174)
T ss_pred HHHHH
Confidence 87654
No 26
>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=58.21 E-value=18 Score=31.39 Aligned_cols=50 Identities=10% Similarity=0.203 Sum_probs=33.3
Q ss_pred chhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcCCCCchHHHH
Q 044946 66 PQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLGLVGSDLGKF 122 (365)
Q Consensus 66 ~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lGl~~~~i~~l 122 (365)
.+..++.++..|+++++..+.-..+ =...|+. ..+||.++|++..++..+
T Consensus 118 ~~~w~~l~~~~g~~~~~m~~wh~~f---e~~~p~~----h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 118 KEKWVAILKAAGMDEADMRRWHIEF---EKMEPEA----HQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHH---HHhCcHH----HHHHHHHcCCCHHHHHHH
Confidence 4567788888888888765543322 2335554 466888888888877654
No 27
>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=55.48 E-value=20 Score=22.22 Aligned_cols=23 Identities=35% Similarity=0.602 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhc
Q 044946 242 RKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 242 ~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
++++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46677788888888887766643
No 28
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=53.58 E-value=25 Score=31.65 Aligned_cols=74 Identities=9% Similarity=0.183 Sum_probs=44.6
Q ss_pred cccccccccccccccchhh--hcccc---CCC--CCCCchhH-HHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHH
Q 044946 2 QRLNSFRNSQNFAIKSFFS--FFSSV---SKT--PNTNSIFL-NYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFL 73 (365)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~--~~~~~---~~~--~~~~~~~v-~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L 73 (365)
.++|-+++.-.|.-...++ +.+.| -.+ |.....++ +-|+.++|+++++...-.++.-..........+.++|
T Consensus 30 Ve~HLl~~n~~F~yD~lfalG~vt~fd~fm~GY~p~~~~~~If~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l 109 (216)
T PF11264_consen 30 VELHLLSVNKDFQYDPLFALGLVTVFDRFMQGYPPEEDKDSIFNALCQALGFDPEQYRQDAEKLEEWAKGKSIEDLLSWL 109 (216)
T ss_pred HHHHHHHhccCceeCchHHhhHHHHHHHHhcCCCChhHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 4678888888887777664 33333 111 11122233 6677999999998887666543332335666777777
Q ss_pred Hh
Q 044946 74 HS 75 (365)
Q Consensus 74 ~~ 75 (365)
.+
T Consensus 110 ~~ 111 (216)
T PF11264_consen 110 SQ 111 (216)
T ss_pred hc
Confidence 64
No 29
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=52.28 E-value=28 Score=23.03 Aligned_cols=26 Identities=23% Similarity=0.393 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044946 240 FDRKLDLFRSYGFSKEECIEMIRTAP 265 (365)
Q Consensus 240 l~~~v~fL~~~G~s~~ev~~~i~~~P 265 (365)
+.+-++-|..+||++.++.+++.+-.
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 45667778899999999988877653
No 30
>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=51.43 E-value=21 Score=23.64 Aligned_cols=24 Identities=29% Similarity=0.331 Sum_probs=17.2
Q ss_pred hhHHHHHHhCCCChHHHHHHHHhC
Q 044946 67 QTVSQFLHSVGFSDTHIQLAVHTK 90 (365)
Q Consensus 67 ~~~~~~L~~lG~s~~~i~~li~~~ 90 (365)
+.+++-|.++|+++.++.+++.+-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 456777888888888888877654
No 31
>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=48.33 E-value=10 Score=26.88 Aligned_cols=48 Identities=10% Similarity=0.209 Sum_probs=26.4
Q ss_pred cCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044946 217 GFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 217 G~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
|.+...+-+.+.++.....+.+.+++.|--|.+-|++.++|+.+++..
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~ 57 (60)
T PF08069_consen 10 GISGSTRPYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQ 57 (60)
T ss_dssp --------S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHS
T ss_pred CccCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhc
Confidence 333344444445555556677788888888888899999998877653
No 32
>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=47.06 E-value=1.3e+02 Score=24.09 Aligned_cols=58 Identities=14% Similarity=0.256 Sum_probs=30.8
Q ss_pred cchhHHHHHHHHHhccCCCch---hhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHH
Q 044946 202 NDLKLRQLVLRVLDMGFTTDS---RMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIR 262 (365)
Q Consensus 202 s~~~i~~~v~~l~~lG~~~~~---~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~ 262 (365)
+++.+..+++.|.+.|+-.+. ..+++.-......++. .-..-|+.-|++.+.+...+.
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~---~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPR---RIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HH---HHHHHHHHTT--HHHHHHHHT
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHH---HHHHHHHHHCCChHHHHHHHH
Confidence 455677888888888887553 3343332222223332 223456678888888877665
No 33
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=45.62 E-value=36 Score=23.73 Aligned_cols=26 Identities=4% Similarity=0.077 Sum_probs=22.7
Q ss_pred CchhHHHHHHhcCCCHHHHHHHHhhc
Q 044946 32 NSIFLNYLIETVNIPKSRALVISNQF 57 (365)
Q Consensus 32 ~~~~v~yL~~~~Gls~~~~~~i~~~~ 57 (365)
.+..|.|+.+.+|+|++++..+++.+
T Consensus 19 e~~ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 56678999999999999999998876
No 34
>PHA02591 hypothetical protein; Provisional
Probab=45.10 E-value=29 Score=25.85 Aligned_cols=44 Identities=14% Similarity=0.223 Sum_probs=32.3
Q ss_pred cCCCHHHHHHHHh----hcccCCCCCCchhHHHHHHhCCCChHHHHHHH
Q 044946 43 VNIPKSRALVISN----QFSRIKTLEKPQTVSQFLHSVGFSDTHIQLAV 87 (365)
Q Consensus 43 ~Gls~~~~~~i~~----~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~li 87 (365)
+.+++..+.+++. ++ .+.+.++..++..-|.+.|++..+|++.+
T Consensus 22 ~~~~~~~m~k~vqv~~~ry-fi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 22 CYIGEKKMQKVVQVGQTRY-FVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEhhhHhHHHhheeCCEEE-EEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 4556677777653 22 34456788889999999999999998765
No 35
>PRK13266 Thf1-like protein; Reviewed
Probab=45.02 E-value=45 Score=30.28 Aligned_cols=75 Identities=12% Similarity=0.215 Sum_probs=43.8
Q ss_pred ccccccccccccccchhh-----hccccCCC--CCCCchh-HHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHH
Q 044946 3 RLNSFRNSQNFAIKSFFS-----FFSSVSKT--PNTNSIF-LNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLH 74 (365)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~--~~~~~~~-v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~ 74 (365)
++|-+++.-.|.-...++ +|..|-.+ |.....+ .+-|+.++|+++++.....+..-......+...++++|.
T Consensus 36 ElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~ 115 (225)
T PRK13266 36 ELHLLSVNSDFKYDPLFALGLVTVFDRFMQGYRPEEHKDSIFNALCQAVGFDPEQLRQDAERLLELAKGKSLKEILSWLT 115 (225)
T ss_pred HHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence 467777777777766654 33333221 1112223 366778999999988877665422223356666777776
Q ss_pred hCC
Q 044946 75 SVG 77 (365)
Q Consensus 75 ~lG 77 (365)
+-|
T Consensus 116 ~~~ 118 (225)
T PRK13266 116 QKA 118 (225)
T ss_pred ccc
Confidence 443
No 36
>PRK14137 recX recombination regulator RecX; Provisional
Probab=43.98 E-value=2.3e+02 Score=25.08 Aligned_cols=128 Identities=9% Similarity=0.102 Sum_probs=65.7
Q ss_pred HHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCC-ChHHHHHHHHhCCcceecCccCcHHH--HHHHHHHcC
Q 044946 37 NYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGF-SDTHIQLAVHTKPTILFADVNKTLKP--KIAYFQQLG 113 (365)
Q Consensus 37 ~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~-s~~~i~~li~~~P~lL~~~~~~~l~p--~l~fL~~lG 113 (365)
.|| +.-.-|..++..-+.+. .. +.+.++.+++.|.+.|+ ++...++.... . +...| .-.-|+.-|
T Consensus 48 ~~L-s~R~rS~~ELr~KL~~k-g~-~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~-------~--k~~Gp~rI~~eL~qKG 115 (195)
T PRK14137 48 RAL-AARAMTAAELRAKLERR-SE-DEALVTEVLERVQELGYQDDAQVARAENS-------R--RGVGALRVRQTLRRRG 115 (195)
T ss_pred HHH-hcchhhHHHHHHHHHhc-CC-CHHHHHHHHHHHHHcCCCCHHHHHHHHHH-------h--cCchHHHHHHHHHHcC
Confidence 444 44444555555433332 11 22456777888888777 56666654311 1 11222 234677888
Q ss_pred CCCchHHHHHHHhccccchhHHHHHHHhccCCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCCChhhHHHHhh
Q 044946 114 LVGSDLGKFISNLERKLIPCVEILKKILAEDSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLSMLLV 193 (365)
Q Consensus 114 l~~~~i~~ll~~~~~~l~p~v~fL~~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~~ll~ 193 (365)
++.+.|...+...+.. -. .+.+.+++.+.-..+ .... . .-...+.||..-||+.+.|..++.
T Consensus 116 I~~~lI~~al~~~d~e------------de---~e~a~~l~~KK~~~~-~~~~-~-~k~K~~~~L~rRGFs~~~I~~al~ 177 (195)
T PRK14137 116 VEETLIEETLAARDPQ------------EE---QQEARNLLERRWSSF-ARKR-D-PRASAYAFLARRGFSGAVIWPAIR 177 (195)
T ss_pred CCHHHHHHHHHhcCch------------hH---HHHHHHHHHHhcccc-Ccch-h-HHHHHHHHHHHCCCCHHHHHHHHH
Confidence 8877776665431100 00 123334444432222 2111 1 224456788899999888877664
Q ss_pred h
Q 044946 194 R 194 (365)
Q Consensus 194 ~ 194 (365)
.
T Consensus 178 ~ 178 (195)
T PRK14137 178 E 178 (195)
T ss_pred H
Confidence 3
No 37
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=43.15 E-value=76 Score=28.59 Aligned_cols=76 Identities=11% Similarity=0.175 Sum_probs=48.6
Q ss_pred ccccccccccccccchhh-----hccccCCC--CCCCchh-HHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHH
Q 044946 3 RLNSFRNSQNFAIKSFFS-----FFSSVSKT--PNTNSIF-LNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLH 74 (365)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~--~~~~~~~-v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~ 74 (365)
++|-+++.-.|.-...++ +|..|-.+ |.....+ .+-|+.++|+++++.....+..-........+.+.+|+.
T Consensus 36 ElHLl~~n~~F~yDplfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~ 115 (214)
T TIGR03060 36 ELHLLSHQSDFKYDPLFALGLVTVFDRFMEGYRPEEHLDALFDALCNSNGFDPEQLREDAKQLLEQAKGKGLDEILSWLT 115 (214)
T ss_pred HHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence 578888888887776664 33333221 1112333 377779999999998887766433333457888899998
Q ss_pred hCCC
Q 044946 75 SVGF 78 (365)
Q Consensus 75 ~lG~ 78 (365)
.-|-
T Consensus 116 ~~~~ 119 (214)
T TIGR03060 116 QANL 119 (214)
T ss_pred cccc
Confidence 6553
No 38
>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=40.55 E-value=62 Score=21.45 Aligned_cols=40 Identities=18% Similarity=0.361 Sum_probs=26.5
Q ss_pred HHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCC
Q 044946 178 LKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTT 220 (365)
Q Consensus 178 L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~ 220 (365)
-+..|++...+.+++...|. .+++.-+.+.+..+++|+.+
T Consensus 6 A~~agvS~~TVSr~ln~~~~---vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGPPR---VSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHHTSSHHHHHHHHTTCSS---STHHHHHHHHHHHHHHTB-S
T ss_pred HHHHCcCHHHHHHHHhCCCC---CCHHHHHHHHHHHHHHCCCC
Confidence 35689999999998866543 24555555566667777654
No 39
>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=40.52 E-value=42 Score=20.21 Aligned_cols=25 Identities=24% Similarity=0.295 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHhCCCHHHHHHHHHh
Q 044946 239 TFDRKLDLFRSYGFSKEECIEMIRT 263 (365)
Q Consensus 239 ~l~~~v~fL~~~G~s~~ev~~~i~~ 263 (365)
.|..-+.-.++.|+|.+|+...+..
T Consensus 4 EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 4 EWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3445555566889999998876654
No 40
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=40.31 E-value=49 Score=27.30 Aligned_cols=52 Identities=10% Similarity=0.193 Sum_probs=33.0
Q ss_pred HHHHHhcCCCHHHHHHHHhhcccCCC--CCCchhHHHHHHhCCCChHHHHHHHHh
Q 044946 37 NYLIETVNIPKSRALVISNQFSRIKT--LEKPQTVSQFLHSVGFSDTHIQLAVHT 89 (365)
Q Consensus 37 ~yL~~~~Gls~~~~~~i~~~~p~l~~--~~~~~~~~~~L~~lG~s~~~i~~li~~ 89 (365)
.|| .-.|++++.+..+..+.-.|.. .-+-+++-+.+..+|.+.++.+++...
T Consensus 71 ~WL-~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~A 124 (129)
T PF13543_consen 71 QWL-RVVGLRPESIQAILSKVLTLEALLEMSDEELKEILNRCGAREEECRRLCRA 124 (129)
T ss_pred HHh-hhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 777 7788888888777654323321 123345666777778877777777653
No 41
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=40.18 E-value=52 Score=23.63 Aligned_cols=40 Identities=13% Similarity=0.307 Sum_probs=29.7
Q ss_pred HHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCCc
Q 044946 179 KSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTTD 221 (365)
Q Consensus 179 ~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~~ 221 (365)
+.+|++...|.+++...|.+ +++.-....+.++++|+.+.
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 45899999999988665554 45666667777788888665
No 42
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=40.07 E-value=1e+02 Score=27.07 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=16.8
Q ss_pred HHHHHHHHHHcCCCCchHHHHHHH
Q 044946 102 LKPKIAYFQQLGLVGSDLGKFISN 125 (365)
Q Consensus 102 l~p~l~fL~~lGl~~~~i~~ll~~ 125 (365)
+...+.+|.++|++..++.+++..
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~ 172 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAK 172 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 566777777777777777666654
No 43
>PF11181 YflT: Heat induced stress protein YflT
Probab=38.30 E-value=94 Score=24.23 Aligned_cols=77 Identities=17% Similarity=0.220 Sum_probs=41.2
Q ss_pred chhchHHHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHH--hccCCCchhhHhHHHHHHhccChhhHHHHHHHH
Q 044946 170 GLLRNIEYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVL--DMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLF 247 (365)
Q Consensus 170 ~l~~~v~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~--~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL 247 (365)
.+...|+-|+.-|+..++|. +++.+.++....-+.-. ..|..+ ..|...+..+.....+.++ +-|
T Consensus 11 E~~~~I~~L~~~Gy~~ddI~--------Vva~d~~~~~~l~~~t~~~~~~~~~--~~~~d~~~~~f~~~~d~~~---~~l 77 (103)
T PF11181_consen 11 EALSAIEELKAQGYSEDDIY--------VVAKDKDRTERLADQTDTNTVGASE--ESFWDKIKNFFTSGGDELR---SKL 77 (103)
T ss_pred HHHHHHHHHHHcCCCcccEE--------EEEcCchHHHHHHHhcCCceecccc--ccHHHHHHHhccCCcHHHH---HHH
Confidence 57778889999999999983 44444333322222211 123222 2222223333333344444 445
Q ss_pred HHhCCCHHHHHH
Q 044946 248 RSYGFSKEECIE 259 (365)
Q Consensus 248 ~~~G~s~~ev~~ 259 (365)
.++|++.+++.+
T Consensus 78 ~~lGl~~~ea~~ 89 (103)
T PF11181_consen 78 ESLGLSEDEAER 89 (103)
T ss_pred HHcCCCHHHHHH
Confidence 788999888754
No 44
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=38.22 E-value=1.8e+02 Score=24.37 Aligned_cols=56 Identities=13% Similarity=0.095 Sum_probs=35.2
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCC---C--------------CCCchhHHHHHHhCCCChHHHHHHHHhCC
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIK---T--------------LEKPQTVSQFLHSVGFSDTHIQLAVHTKP 91 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~---~--------------~~~~~~~~~~L~~lG~s~~~i~~li~~~P 91 (365)
...+| ...|++.+.+..++.++.... . ......+..-|...|++.+.|..++...+
T Consensus 31 l~~kL-~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~ 103 (157)
T PRK00117 31 LRRKL-AAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKGVDREIIEEALAELD 103 (157)
T ss_pred HHHHH-HhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence 34777 557888887777776654321 0 01233456677778888887777777653
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=37.94 E-value=50 Score=29.08 Aligned_cols=53 Identities=17% Similarity=0.155 Sum_probs=36.8
Q ss_pred HHHHhcCCCHHHHHHHHhhcc-cCC-----------CCCCchhHHHHHHhCCCChHHHHHHHHhC
Q 044946 38 YLIETVNIPKSRALVISNQFS-RIK-----------TLEKPQTVSQFLHSVGFSDTHIQLAVHTK 90 (365)
Q Consensus 38 yL~~~~Gls~~~~~~i~~~~p-~l~-----------~~~~~~~~~~~L~~lG~s~~~i~~li~~~ 90 (365)
-|..--|++...+.++...+- .+. .....+.++.+|.++|+++.++.+++..+
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 442334888888888765431 110 00125788999999999999999999877
No 46
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=37.53 E-value=88 Score=29.46 Aligned_cols=65 Identities=9% Similarity=0.192 Sum_probs=44.9
Q ss_pred HHHHHHHHHHhhCCChhhHhhcCcccccCCCCcchhHHHHHHHHHHhccccCCcCccchhccChHhHHHHhhh
Q 044946 275 LKSGLDFFLKKIEFGKAVLVRMPCCMMYSIENRVIPRYRVFQIVMVRRMLKKDWSFPSVLVLSEENFLNKYVL 347 (365)
Q Consensus 275 l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~g~~~~~~~l~~~l~~s~~~F~~~~v~ 347 (365)
++.+++.+.+ .|++.+.|+--|- +++ .++...-+.+++.+..-. ...++.++..|.++|......
T Consensus 165 l~~~i~~a~~-~GI~~~~IilDPG-iGF--~k~~~~n~~ll~~l~~l~----~lg~Pilvg~SRKsfig~~~~ 229 (282)
T PRK11613 165 FIEQIARCEA-AGIAKEKLLLDPG-FGF--GKNLSHNYQLLARLAEFH----HFNLPLLVGMSRKSMIGQLLN 229 (282)
T ss_pred HHHHHHHHHH-cCCChhhEEEeCC-CCc--CCCHHHHHHHHHHHHHHH----hCCCCEEEEecccHHHHhhcC
Confidence 5677888875 6999999888885 454 445556666665543321 246678899999999977654
No 47
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=37.25 E-value=33 Score=30.68 Aligned_cols=84 Identities=10% Similarity=0.134 Sum_probs=51.2
Q ss_pred ccccccccccccccchhh--hcccc---CCC--CCCCchh-HHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHH
Q 044946 3 RLNSFRNSQNFAIKSFFS--FFSSV---SKT--PNTNSIF-LNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLH 74 (365)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~--~~~~~---~~~--~~~~~~~-v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~ 74 (365)
++|-+++.-.|.-...++ +.++| -.+ |.....+ .+-|+.++|+++++..+..+..-......+...+.+|+.
T Consensus 34 E~HLl~~n~~f~yD~lfAlGlvt~fd~fm~GY~Pee~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~ 113 (206)
T PLN03060 34 QQHLMRYNATYKYDPIFALGFVTVYDQLMDGYPNATDRDAIFKAYIEALGEDPDQYRKDAKKLEEWASSQSASGIADFNS 113 (206)
T ss_pred HHHHHHhccCceeCchHHhhHHHHHHHHHcCCCChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence 567888888887776664 33333 221 1112223 377779999999988887765433333456777888887
Q ss_pred hCCCChHHHHHH
Q 044946 75 SVGFSDTHIQLA 86 (365)
Q Consensus 75 ~lG~s~~~i~~l 86 (365)
.-|-.+..+..+
T Consensus 114 ~~~~~~~~l~~~ 125 (206)
T PLN03060 114 GDGEVEAVLKDI 125 (206)
T ss_pred cccccchHHHHH
Confidence 666444444444
No 48
>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=36.39 E-value=72 Score=20.54 Aligned_cols=29 Identities=10% Similarity=0.432 Sum_probs=22.0
Q ss_pred hHHHHHHHHH-HhCCCHHHHHHHHHhcCcc
Q 044946 239 TFDRKLDLFR-SYGFSKEECIEMIRTAPRL 267 (365)
Q Consensus 239 ~l~~~v~fL~-~~G~s~~ev~~~i~~~P~i 267 (365)
++=.+...|. +.|++..+...|+..||.+
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 4556678888 8999999999999999975
No 49
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=35.67 E-value=1.5e+02 Score=21.79 Aligned_cols=17 Identities=24% Similarity=0.399 Sum_probs=9.7
Q ss_pred HHHHHHcCCChhhHHHH
Q 044946 175 IEYLKSCGIVGSQLSML 191 (365)
Q Consensus 175 v~~L~~lG~~~~~i~~l 191 (365)
+....++|++++.+..+
T Consensus 33 Ma~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 33 MATIQQLGIPQEKLQQL 49 (82)
T ss_pred HHHHHHcCCCHHHHHHH
Confidence 44555666666665544
No 50
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=35.20 E-value=71 Score=29.90 Aligned_cols=63 Identities=25% Similarity=0.322 Sum_probs=43.6
Q ss_pred hhHHHHHHHHH-HhCCCH-HHHHHHHHhcCcccccCHHHHHHHHHHHHHhhCCChhh-HhhcCccc
Q 044946 238 KTFDRKLDLFR-SYGFSK-EECIEMIRTAPRLLSASEERLKSGLDFFLKKIEFGKAV-LVRMPCCM 300 (365)
Q Consensus 238 ~~l~~~v~fL~-~~G~s~-~ev~~~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~~~~-i~~~P~~L 300 (365)
-++++++.|-. ..|+=+ -.|..=|.-.|.+++++.++++.+++-|.+.+|+++.+ .-+||.=|
T Consensus 71 ~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eL 136 (309)
T COG1125 71 VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHEL 136 (309)
T ss_pred HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhc
Confidence 45677777755 666433 23444456789999999999999999999888998753 33455433
No 51
>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=34.76 E-value=84 Score=24.67 Aligned_cols=35 Identities=14% Similarity=0.133 Sum_probs=22.1
Q ss_pred cchhHHHHHHHh-c--cCCCchHHHHHHHhccccccccC
Q 044946 130 LIPCVEILKKIL-A--EDSNNEDLIRVIRRMSWDLVVID 165 (365)
Q Consensus 130 l~p~v~fL~~~g-~--~~~~~~~v~~~l~~~P~iL~~~s 165 (365)
+.++-..+++++ . .+.+++++..++..+|.++ ...
T Consensus 53 in~~~~~~k~l~~~~~~~~s~~e~i~~l~~~p~Li-kRP 90 (110)
T PF03960_consen 53 INTRSKTYKELGKLKKDDLSDEELIELLLENPKLI-KRP 90 (110)
T ss_dssp B-TTSHHHHHTTHHHCTTSBHHHHHHHHHHSGGGB--SS
T ss_pred hcCccchHhhhhhhhhhhhhhHHHHHHHHhChhhe-eCC
Confidence 334445566655 1 1223899999999999999 544
No 52
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=34.36 E-value=69 Score=25.88 Aligned_cols=52 Identities=12% Similarity=0.105 Sum_probs=27.3
Q ss_pred HHHHHHHhcc--CCCchHHHHHHHhccccccccCCCCcchhchHHHHHHcCCChhhHHHHh
Q 044946 134 VEILKKILAE--DSNNEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLKSCGIVGSQLSMLL 192 (365)
Q Consensus 134 v~fL~~~g~~--~~~~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~~lG~~~~~i~~ll 192 (365)
-..++.++.. +..++++...+..+|.++ -..+= +.+.- ..+|++++++..++
T Consensus 62 ~~~~r~L~~~~~~~~~~~~~~~i~~~~~Li-kRPiv---v~~~~---~~iG~~~e~~~~~l 115 (117)
T COG1393 62 GTTYRELNLDKEDLSDEELIEALLENPSLI-KRPIV---VDNKK---LRVGFNEEEIRAFL 115 (117)
T ss_pred cchHHHcCCcccccChHHHHHHHHhChhhc-cCCeE---EeCCc---eEecCCHHHHHHHh
Confidence 3444554422 233777788888888555 32211 11110 24677777776544
No 53
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=32.92 E-value=91 Score=29.32 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHhCCCHHHHHHHHHh
Q 044946 239 TFDRKLDLFRSYGFSKEECIEMIRT 263 (365)
Q Consensus 239 ~l~~~v~fL~~~G~s~~ev~~~i~~ 263 (365)
-+..|.+||++-|++.+||...+++
T Consensus 21 Pli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 21 PLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred hHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 4788999999999999999888776
No 54
>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=32.79 E-value=1.4e+02 Score=22.55 Aligned_cols=50 Identities=12% Similarity=0.329 Sum_probs=31.9
Q ss_pred HHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH-cCCCCchHHHHH
Q 044946 69 VSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ-LGLVGSDLGKFI 123 (365)
Q Consensus 69 ~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~-lGl~~~~i~~ll 123 (365)
.-.+-+.+|+++.+|..+-..||. ++.......+..++. -| ..+.+..++
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g-~~At~~~L~ 66 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKK-KEAKVADLI 66 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHC-cchHHHHHH
Confidence 456667889999999999998883 333345555654443 45 444444443
No 55
>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=32.24 E-value=1.1e+02 Score=24.95 Aligned_cols=61 Identities=13% Similarity=0.110 Sum_probs=31.3
Q ss_pred cCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHH
Q 044946 181 CGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEM 260 (365)
Q Consensus 181 lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~ 260 (365)
.|++.++|..+-.-+|++|. +++..++.=+++.- ...+.-...+.-.+++|||+.+|+++
T Consensus 22 rG~sveeI~e~T~ID~wFL~----~i~~Iv~~e~~L~~----------------~~~~~~~~~L~~aK~~GFsD~~IA~l 81 (123)
T PF02787_consen 22 RGYSVEEIHELTKIDPWFLE----QIKNIVDMEKELKE----------------YLNELDPELLRKAKRLGFSDRQIARL 81 (123)
T ss_dssp TTB-HHHHHHHH---HHHHH----HHHHHHHHHHHHHH----------------HGGG--HHHHHHHHHTT--HHHHHHH
T ss_pred cCCCHHHHHHHHCccHHHHH----HHHHHHHHHHHHHH----------------hhccchHHHHHHHHHcCCCHHHHHhc
Confidence 49999999887777888763 34444433322110 00111123455567899999999987
Q ss_pred H
Q 044946 261 I 261 (365)
Q Consensus 261 i 261 (365)
.
T Consensus 82 ~ 82 (123)
T PF02787_consen 82 W 82 (123)
T ss_dssp H
T ss_pred c
Confidence 4
No 56
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.01 E-value=1.7e+02 Score=22.71 Aligned_cols=50 Identities=12% Similarity=0.294 Sum_probs=33.7
Q ss_pred hhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHH-HcCCCCchHHHH
Q 044946 67 QTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQ-QLGLVGSDLGKF 122 (365)
Q Consensus 67 ~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~-~lGl~~~~i~~l 122 (365)
..+-.+.+.+|+|+.+|..+-..+|.- .......+.-++ .-|- .+.+..+
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~-----~eq~~qmL~~W~~~~G~-~At~~~L 70 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVT-----REQLYQMLLTWVNKTGR-KASVNTL 70 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCC-----HHHHHHHHHHHHHhhCC-CcHHHHH
Confidence 457778889999999999999999863 224555565555 3554 3334444
No 57
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=31.47 E-value=1e+02 Score=24.49 Aligned_cols=29 Identities=21% Similarity=0.386 Sum_probs=17.2
Q ss_pred CCchhHHHHHHhCCCChHHHHHHHHhCCc
Q 044946 64 EKPQTVSQFLHSVGFSDTHIQLAVHTKPT 92 (365)
Q Consensus 64 ~~~~~~~~~L~~lG~s~~~i~~li~~~P~ 92 (365)
+.+...++.|.+.|+++.++..++--.|.
T Consensus 57 e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~ 85 (117)
T PF03874_consen 57 ESIKELREELKKFGLTEFEILQIINLRPT 85 (117)
T ss_dssp HHHHHHHHHHTTSTS-HHHHHHHHHH--S
T ss_pred HHHHHHHHHHhcccCCHHHHHHHhcCCCC
Confidence 34555666666777777777777776664
No 58
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=31.18 E-value=1e+02 Score=26.59 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=29.5
Q ss_pred chhchHHHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCC
Q 044946 170 GLLRNIEYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTT 220 (365)
Q Consensus 170 ~l~~~v~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~ 220 (365)
+++..+++|.++.= ..-.++-+...|-+.+.+.+++...++.+++-|++.
T Consensus 49 t~k~Il~aL~e~e~-~~ita~~iM~spvv~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 49 TVKRILEALEEAEK-TRITAKTIMHSPVVSVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred HHHHHHHHHHHhhc-ceEeHhhhccCCeeEECchhhHHHHHHHHHHcCCcc
Confidence 45555566655321 222344555667666666677777777777777654
No 59
>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=30.63 E-value=92 Score=20.39 Aligned_cols=40 Identities=13% Similarity=0.319 Sum_probs=27.3
Q ss_pred HHcCCChhhHHHHhhhcCccceecchhHHHHHHHHHhccCCCc
Q 044946 179 KSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVLDMGFTTD 221 (365)
Q Consensus 179 ~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~~lG~~~~ 221 (365)
+.+|++...|.+++...| ..+++......+...++|+.++
T Consensus 5 ~~~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 5 RAAGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred HHHCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCC
Confidence 458999999998886555 2344555566666777777654
No 60
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=29.87 E-value=50 Score=27.02 Aligned_cols=42 Identities=2% Similarity=0.017 Sum_probs=26.4
Q ss_pred chHHHHHHHhccccccccCCCCcchhchHHH--HHHcCCChhhHHHHhhhcCc
Q 044946 147 NEDLIRVIRRMSWDLVVIDPEKSGLLRNIEY--LKSCGIVGSQLSMLLVRLPR 197 (365)
Q Consensus 147 ~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~--L~~lG~~~~~i~~ll~~~P~ 197 (365)
.+++..++..+|.++ -.. .+.. =.-+|++.+.+..++...|.
T Consensus 75 ~~e~i~lm~~~P~LI-KRP--------Ii~~~~~~~iGf~~e~~~~~l~~~~~ 118 (126)
T TIGR01616 75 EASALALMVSDPLLI-RRP--------LMDLGGIRCAGFDREPVLSWIGLQTQ 118 (126)
T ss_pred HHHHHHHHHhCcCeE-eCC--------EEEECCEEEEcCCHHHHHHHhCCCCC
Confidence 677888888888888 433 2211 01268888877776655443
No 61
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=29.26 E-value=45 Score=27.51 Aligned_cols=37 Identities=16% Similarity=0.127 Sum_probs=23.4
Q ss_pred chHHHHHHHhccccccccCCCCcchhchHHHHH--HcCCChhhHHHHh
Q 044946 147 NEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYLK--SCGIVGSQLSMLL 192 (365)
Q Consensus 147 ~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L~--~lG~~~~~i~~ll 192 (365)
.+++..++..+|.++ ... .|..=. -+|++++.+..++
T Consensus 76 ~~e~i~ll~~~P~Li-kRP--------Iv~~~~~~~iG~~~e~~~~~l 114 (132)
T PRK13344 76 VNEVIDLIQENPRIL-KSP--------ILIDDKRLQVGYKEDDIRAFL 114 (132)
T ss_pred HHHHHHHHHhCccce-eCc--------EEEeCCEEEeCCCHHHHHHHc
Confidence 677888888888888 433 221101 1688887777655
No 62
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=29.20 E-value=1.4e+02 Score=21.95 Aligned_cols=47 Identities=23% Similarity=0.298 Sum_probs=26.7
Q ss_pred hhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcCCCCchHHH
Q 044946 67 QTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLGLVGSDLGK 121 (365)
Q Consensus 67 ~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lGl~~~~i~~ 121 (365)
.+++..|.+..+|+++|..++.. |+.+| --.......+|++.+.+..
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~NP----l~AMa~i~qLGip~eKLQ~ 48 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQNP----LAAMATIQQLGIPQEKLQQ 48 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhCH----HHHHHHHHHcCCCHHHHHH
Confidence 45677777777777777766542 22222 2234566667776554433
No 63
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=28.96 E-value=71 Score=25.74 Aligned_cols=62 Identities=18% Similarity=0.266 Sum_probs=37.4
Q ss_pred hcccCCCCCCchhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHHcCCCCchHHHHH
Q 044946 56 QFSRIKTLEKPQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQLGLVGSDLGKFI 123 (365)
Q Consensus 56 ~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~lGl~~~~i~~ll 123 (365)
++|...+++.+.++.+.|...|+.+.++..++.-+|.= ++ .++..+.-+.+- ++.+++..++
T Consensus 47 ~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s----~~-E~~~lI~sl~~r-~~ee~l~~iL 108 (118)
T smart00657 47 KFARFKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPET----AE-EAQLLIPSLEER-IDEEELEELL 108 (118)
T ss_pred HcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC----HH-HHHHHhhhhhcc-CCHHHHHHHH
Confidence 44444455667777888888899999988888777752 22 233333333322 4555555443
No 64
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=28.47 E-value=1.6e+02 Score=20.85 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=31.2
Q ss_pred HhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHH-hCCCChHHHHHHHH
Q 044946 41 ETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLH-SVGFSDTHIQLAVH 88 (365)
Q Consensus 41 ~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~-~lG~s~~~i~~li~ 88 (365)
...|-+.++-..+++.-| ...+..+++++|+ ++|+.......++.
T Consensus 11 ~kTGk~~~~W~~~~~~~~---~~~k~~e~v~WLK~ehgLghGhA~Aiv~ 56 (61)
T PF14117_consen 11 KKTGKTLDEWLALAREGG---PLTKHGEIVAWLKDEHGLGHGHANAIVA 56 (61)
T ss_pred HHHCcCHHHHHHHHHHhC---CCCcHHHHHHHHHHHHCCChHHHHHHHH
Confidence 457888888888877765 2256777888887 67777766555543
No 65
>PRK14137 recX recombination regulator RecX; Provisional
Probab=28.25 E-value=4.2e+02 Score=23.41 Aligned_cols=69 Identities=12% Similarity=0.041 Sum_probs=40.4
Q ss_pred HHHHHcCCChhhHHHHhhhcCccceecchhHHHHHHHHH-hccCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCH
Q 044946 176 EYLKSCGIVGSQLSMLLVRLPRLFCFNDLKLRQLVLRVL-DMGFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSK 254 (365)
Q Consensus 176 ~~L~~lG~~~~~i~~ll~~~P~~l~~s~~~i~~~v~~l~-~lG~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~ 254 (365)
.-|+.-|++.+.|...+... -..+.+......+. .++-.... ...-++.+.||..-||+.
T Consensus 109 ~eL~qKGI~~~lI~~al~~~-----d~ede~e~a~~l~~KK~~~~~~~--------------~~~k~K~~~~L~rRGFs~ 169 (195)
T PRK14137 109 QTLRRRGVEETLIEETLAAR-----DPQEEQQEARNLLERRWSSFARK--------------RDPRASAYAFLARRGFSG 169 (195)
T ss_pred HHHHHcCCCHHHHHHHHHhc-----CchhHHHHHHHHHHHhccccCcc--------------hhHHHHHHHHHHHCCCCH
Confidence 56888999999998877532 11222333333443 22211100 111245578999999999
Q ss_pred HHHHHHHHh
Q 044946 255 EECIEMIRT 263 (365)
Q Consensus 255 ~ev~~~i~~ 263 (365)
+.|..++..
T Consensus 170 ~~I~~al~~ 178 (195)
T PRK14137 170 AVIWPAIRE 178 (195)
T ss_pred HHHHHHHHH
Confidence 988877663
No 66
>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=28.22 E-value=1.5e+02 Score=31.99 Aligned_cols=78 Identities=21% Similarity=0.186 Sum_probs=49.6
Q ss_pred cCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCCChHHHHH-----------HHHhCCcceecCccCcHHHHHHHH-H
Q 044946 43 VNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGFSDTHIQL-----------AVHTKPTILFADVNKTLKPKIAYF-Q 110 (365)
Q Consensus 43 ~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~-----------li~~~P~lL~~~~~~~l~p~l~fL-~ 110 (365)
-|++...+.++...+.. ......++.||.++|++...+.+ +|..+|..|..++..-=....+-+ +
T Consensus 123 ~gi~~~~~~~i~~~~~~---~~~~~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~ 199 (720)
T TIGR01448 123 PGISKANLEKFVSQWSQ---QGDERRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQ 199 (720)
T ss_pred CCCCHHHHHHHHHHHHH---hHHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHH
Confidence 36777777776665411 13367789999999999765544 678899888765432112233333 4
Q ss_pred HcCCCCchHHHHH
Q 044946 111 QLGLVGSDLGKFI 123 (365)
Q Consensus 111 ~lGl~~~~i~~ll 123 (365)
.+|+...+-.++-
T Consensus 200 ~~g~~~~d~~Ri~ 212 (720)
T TIGR01448 200 ALGIALNDPRRIT 212 (720)
T ss_pred HcCCCCCCHHHHH
Confidence 6888877766543
No 67
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=28.13 E-value=2.5e+02 Score=21.33 Aligned_cols=53 Identities=11% Similarity=0.114 Sum_probs=31.2
Q ss_pred chhHHHHHHhcCCCHH----HHHHHHhhcccCCCCCCchhHHHHHHhCCCChHHHHHHH
Q 044946 33 SIFLNYLIETVNIPKS----RALVISNQFSRIKTLEKPQTVSQFLHSVGFSDTHIQLAV 87 (365)
Q Consensus 33 ~~~v~yL~~~~Gls~~----~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~li 87 (365)
.++.+.| -.+|++-. .-+..+...-.+ .+.+..+.+.-|..+|+|.+++..++
T Consensus 30 ~it~~dL-~~~GL~g~~~s~~rR~~l~~~L~i-Gy~N~KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 30 EITWEDL-IELGLIGGPDSKERREKLGEYLGI-GYGNAKQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred cCCHHHH-HHCCCCCCccHHHHHHHHHHHHCC-CCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 4677666 34777422 222222221144 44677777888888888888887765
No 68
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=27.65 E-value=81 Score=27.17 Aligned_cols=73 Identities=14% Similarity=0.191 Sum_probs=39.7
Q ss_pred cCCChhhHHHHhh-hcCccce-------ecchhHHHHHHHHHhccCCC-chhhHhHHHHHHhccChhhHHHHHHHHHHhC
Q 044946 181 CGIVGSQLSMLLV-RLPRLFC-------FNDLKLRQLVLRVLDMGFTT-DSRMFVHGLDALCRLSEKTFDRKLDLFRSYG 251 (365)
Q Consensus 181 lG~~~~~i~~ll~-~~P~~l~-------~s~~~i~~~v~~l~~lG~~~-~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G 251 (365)
+|++++++++..- ..|.+=. -..++++..++.|.+.--.. ....+.++| .+...+++.+...++.++..|
T Consensus 17 LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~sp-vv~v~pdDsi~~vv~lM~~~g 95 (187)
T COG3620 17 LGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHSP-VVSVSPDDSISDVVNLMRDKG 95 (187)
T ss_pred cCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccCC-eeEECchhhHHHHHHHHHHcC
Confidence 7777777765431 2222211 11356777777776532111 112222222 334567788888888888888
Q ss_pred CCH
Q 044946 252 FSK 254 (365)
Q Consensus 252 ~s~ 254 (365)
+|.
T Consensus 96 ~SQ 98 (187)
T COG3620 96 ISQ 98 (187)
T ss_pred Ccc
Confidence 874
No 69
>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=27.42 E-value=1.2e+02 Score=23.71 Aligned_cols=22 Identities=32% Similarity=0.536 Sum_probs=17.4
Q ss_pred hCCCHHHHHHHHHhcCcccccC
Q 044946 250 YGFSKEECIEMIRTAPRLLSAS 271 (365)
Q Consensus 250 ~G~s~~ev~~~i~~~P~iL~~s 271 (365)
..++.+++..++..+|.++...
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 4588899999999999887655
No 70
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=27.28 E-value=2.4e+02 Score=21.07 Aligned_cols=53 Identities=13% Similarity=0.217 Sum_probs=31.6
Q ss_pred chhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHH-HcCCCCchHHHHH
Q 044946 66 PQTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQ-QLGLVGSDLGKFI 123 (365)
Q Consensus 66 ~~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~-~lGl~~~~i~~ll 123 (365)
+..+-.|-+.+|+|+.+|..+-..|| +........+.-++ .-|-..+.+..++
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~-----~~~Eq~yqmL~~W~~~~g~~~At~~~L~ 64 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR-----RCRDAQYQMLKVWKERGPRPYATLQHLL 64 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC-----ChHHHHHHHHHHHHHhcCCCcchHHHHH
Confidence 34567788888999998888887776 11123444444333 3455444444443
No 71
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=27.08 E-value=1e+02 Score=30.84 Aligned_cols=30 Identities=20% Similarity=0.354 Sum_probs=19.6
Q ss_pred CCCchhHHHHHHhCCCChHHHHHHHHhCCc
Q 044946 63 LEKPQTVSQFLHSVGFSDTHIQLAVHTKPT 92 (365)
Q Consensus 63 ~~~~~~~~~~L~~lG~s~~~i~~li~~~P~ 92 (365)
..-.+..+..+-++||.+.+.+..++.|-.
T Consensus 300 lki~d~~lsllv~mGfeesdaRlaLRsc~g 329 (568)
T KOG2561|consen 300 LKINDETLSLLVGMGFEESDARLALRSCNG 329 (568)
T ss_pred eeccchHHHHHHHcCCCchHHHHHHHhccc
Confidence 344556677777777777777766666643
No 72
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=25.91 E-value=58 Score=26.02 Aligned_cols=15 Identities=7% Similarity=0.113 Sum_probs=11.8
Q ss_pred chHHHHHHHhccccc
Q 044946 147 NEDLIRVIRRMSWDL 161 (365)
Q Consensus 147 ~~~v~~~l~~~P~iL 161 (365)
++++..++..+|.++
T Consensus 74 ~~e~~~ll~~~P~Li 88 (113)
T cd03033 74 EEEALALMIADPLLI 88 (113)
T ss_pred HHHHHHHHHhCccee
Confidence 677778888888887
No 73
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.95 E-value=1.2e+02 Score=29.95 Aligned_cols=43 Identities=14% Similarity=0.322 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHhCCCHHHHHHHHHhcCcccccCHHHHHHHHHHHHHhhCCC
Q 044946 238 KTFDRKLDLFRSYGFSKEECIEMIRTAPRLLSASEERLKSGLDFFLKKIEFG 289 (365)
Q Consensus 238 ~~l~~~v~fL~~~G~s~~ev~~~i~~~P~iL~~s~e~l~~k~~fL~~~mg~~ 289 (365)
...+..|+-+.++||.+++|.+.++ .+-.+=.+-++||.. |++
T Consensus 154 ~~~e~~I~~i~eMGf~R~qV~~ALR-------AafNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 154 SERETTIEEIMEMGYEREEVERALR-------AAFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHH-------HHhCCHHHHHHHHHh--CCC
Confidence 4678889999999999999988766 333445678999993 888
No 74
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=24.48 E-value=1.7e+02 Score=26.44 Aligned_cols=63 Identities=11% Similarity=0.026 Sum_probs=36.2
Q ss_pred hhhcCccceecch--hHHHHHHHHHhccCCCchhhHhHHHHHHhcc-----------ChhhHHHHHHHHHHhCCCH
Q 044946 192 LVRLPRLFCFNDL--KLRQLVLRVLDMGFTTDSRMFVHGLDALCRL-----------SEKTFDRKLDLFRSYGFSK 254 (365)
Q Consensus 192 l~~~P~~l~~s~~--~i~~~v~~l~~lG~~~~~~~~~~~~~~l~~~-----------s~~~l~~~v~fL~~~G~s~ 254 (365)
.-.+|+++....+ .+...+..++.+|++-....+..+...+... ...++..-|.||+.+|-..
T Consensus 135 MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt~~~i~~a~~~~~~~a~~~~~~~~~~~~te~~AliAYLq~LG~~~ 210 (217)
T PRK14487 135 MPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAKAAVKGKADPIADDGDPGEITEMDALIAYLQSLGTAV 210 (217)
T ss_pred CCCCcccccccCCHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHhhccccccccCCCccHHHHHHHHHHHhcccc
Confidence 3345555544322 5666677777788887765555555443221 1134666677777777543
No 75
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=24.43 E-value=2.2e+02 Score=21.50 Aligned_cols=51 Identities=22% Similarity=0.369 Sum_probs=33.3
Q ss_pred HHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH-cCCCCchHHHHHH
Q 044946 69 VSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ-LGLVGSDLGKFIS 124 (365)
Q Consensus 69 ~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~-lGl~~~~i~~ll~ 124 (365)
.-.+.+.+|++.++|.++-..||. +....+...+.-+++ -| ..+-+..++.
T Consensus 16 W~~Lar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~r~G-~~ATv~~L~~ 67 (83)
T cd08319 16 WEQVLLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQRFG-KKATVQSLIQ 67 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhcC-CCCcHHHHHH
Confidence 345567899999999999998885 333345555555554 45 5555555543
No 76
>PRK14134 recX recombination regulator RecX; Provisional
Probab=24.01 E-value=6e+02 Score=23.79 Aligned_cols=55 Identities=7% Similarity=-0.008 Sum_probs=31.0
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCC--C--------------CCCchhHHHHHHhCCCChHHHHHHHHhC
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIK--T--------------LEKPQTVSQFLHSVGFSDTHIQLAVHTK 90 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~--~--------------~~~~~~~~~~L~~lG~s~~~i~~li~~~ 90 (365)
..++| ...|++++.+..++.++-... + ...+..+..-|+..|++++.|...+...
T Consensus 81 lr~KL-~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~~~G~~~I~~eL~qKGI~~~iIe~al~~~ 151 (283)
T PRK14134 81 IKEKL-YLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKINSYGRNKIKYTLLNKGIKENIIIEKINNI 151 (283)
T ss_pred HHHHH-HhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhhHHHHHHHHHHCCCCHHHHHHHHHhC
Confidence 34666 445777777777665542211 0 0123334566677777777777666543
No 77
>PRK09875 putative hydrolase; Provisional
Probab=23.99 E-value=73 Score=30.16 Aligned_cols=28 Identities=25% Similarity=0.427 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHhCCCHHHHHHHHHhcCc
Q 044946 239 TFDRKLDLFRSYGFSKEECIEMIRTAPR 266 (365)
Q Consensus 239 ~l~~~v~fL~~~G~s~~ev~~~i~~~P~ 266 (365)
-+..-+-.|++.|+++++|.+|+..+|.
T Consensus 261 i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 261 LLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 3566677888999999999999999996
No 78
>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=23.91 E-value=79 Score=22.00 Aligned_cols=19 Identities=37% Similarity=0.536 Sum_probs=14.0
Q ss_pred HHHHHHHhCCCHHHHHHHH
Q 044946 243 KLDLFRSYGFSKEECIEMI 261 (365)
Q Consensus 243 ~v~fL~~~G~s~~ev~~~i 261 (365)
-|..++++|||-+||..++
T Consensus 6 ~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3556779999999999998
No 79
>PHA02591 hypothetical protein; Provisional
Probab=23.34 E-value=1.2e+02 Score=22.69 Aligned_cols=34 Identities=24% Similarity=0.304 Sum_probs=22.1
Q ss_pred ChhhHHHHHHHHHHhCCCHHHHHHHHHhcCcccccCHHHHH
Q 044946 236 SEKTFDRKLDLFRSYGFSKEECIEMIRTAPRLLSASEERLK 276 (365)
Q Consensus 236 s~~~l~~~v~fL~~~G~s~~ev~~~i~~~P~iL~~s~e~l~ 276 (365)
+++.+..-..-|.+.|+|.++|+. .|+++.+.++
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~-------~LGVsqetVr 77 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIAS-------LLGVSVRKVR 77 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHH-------HhCCCHHHHH
Confidence 345566666777788888888875 3555555443
No 80
>PRK12559 transcriptional regulator Spx; Provisional
Probab=23.22 E-value=60 Score=26.68 Aligned_cols=37 Identities=11% Similarity=0.053 Sum_probs=21.9
Q ss_pred chHHHHHHHhccccccccCCCCcchhchHHHH--HHcCCChhhHHHHh
Q 044946 147 NEDLIRVIRRMSWDLVVIDPEKSGLLRNIEYL--KSCGIVGSQLSMLL 192 (365)
Q Consensus 147 ~~~v~~~l~~~P~iL~~~s~e~~~l~~~v~~L--~~lG~~~~~i~~ll 192 (365)
.+++..++..+|.++ -.. .+..= .-+|++++.+..++
T Consensus 76 ~~e~i~ll~~~P~Li-kRP--------Ii~~~~~~~iGf~~e~~~~~l 114 (131)
T PRK12559 76 LNEFYKLIIEHPLML-RRP--------IMLDEKRLQIGFNDEEIRKFL 114 (131)
T ss_pred HHHHHHHHHhCcceE-eCC--------EEEeCCEEEEcCCHHHHHHHh
Confidence 577788888888888 332 22110 12677777766554
No 81
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=23.15 E-value=64 Score=26.57 Aligned_cols=41 Identities=7% Similarity=0.176 Sum_probs=23.9
Q ss_pred hhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044946 223 RMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRT 263 (365)
Q Consensus 223 ~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~ 263 (365)
.-++++++..+.++.+.+++-|--|..-|++..||+-+++.
T Consensus 16 lPY~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRD 56 (151)
T KOG0400|consen 16 LPYRRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRD 56 (151)
T ss_pred cccccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeec
Confidence 33444444445555666666666666667777777655444
No 82
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=23.14 E-value=1.3e+02 Score=20.93 Aligned_cols=22 Identities=27% Similarity=0.706 Sum_probs=13.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHh
Q 044946 242 RKLDLFRSYGFSKEECIEMIRT 263 (365)
Q Consensus 242 ~~v~fL~~~G~s~~ev~~~i~~ 263 (365)
.-|+-|.++||+.+.+...+++
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCcHHHHHHHHHH
Confidence 3456677778887777766664
No 83
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=22.59 E-value=3.5e+02 Score=20.55 Aligned_cols=21 Identities=24% Similarity=0.468 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCCHHHHHHHH
Q 044946 241 DRKLDLFRSYGFSKEECIEMI 261 (365)
Q Consensus 241 ~~~v~fL~~~G~s~~ev~~~i 261 (365)
+.-++.|..+|+|.+|+.+++
T Consensus 66 KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 66 KQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred HHHHHHHHHcCCCHHHHHHHh
Confidence 333455567788888887665
No 84
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=22.44 E-value=5.2e+02 Score=22.45 Aligned_cols=51 Identities=16% Similarity=0.203 Sum_probs=35.6
Q ss_pred HHHHHhcCCCHHHHHHHHhhcc---cCC--------------CCCCchhHHHHHHhCCCChHHHHHHHH
Q 044946 37 NYLIETVNIPKSRALVISNQFS---RIK--------------TLEKPQTVSQFLHSVGFSDTHIQLAVH 88 (365)
Q Consensus 37 ~yL~~~~Gls~~~~~~i~~~~p---~l~--------------~~~~~~~~~~~L~~lG~s~~~i~~li~ 88 (365)
.|| ...|++...+..++.++- .+. +...+..+.+-|...|++++.|..++.
T Consensus 42 ~kL-~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g~G~~rl~qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 42 RKL-AKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSRKGKGPARLKQELKQKGIDDEIIEEALE 109 (174)
T ss_pred HHH-HhccCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhcccChHHHHHHHHHcCCCHHHHHHHHh
Confidence 777 668888877777766542 111 113356667888899999999998886
No 85
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=22.00 E-value=2.9e+02 Score=23.89 Aligned_cols=41 Identities=7% Similarity=0.114 Sum_probs=27.4
Q ss_pred HHHHHhccCCCchHHHHHHHh-ccccccccCCCCcchhchHHHHHHc
Q 044946 136 ILKKILAEDSNNEDLIRVIRR-MSWDLVVIDPEKSGLLRNIEYLKSC 181 (365)
Q Consensus 136 fL~~~g~~~~~~~~v~~~l~~-~P~iL~~~s~e~~~l~~~v~~L~~l 181 (365)
.|+++|..+ ++++..++.+ +|.+- ..+..+ ++=+=-|++++
T Consensus 101 LWqDLGL~~--R~eLs~Lm~r~Fp~La-a~N~~~--MrWKKFfYrql 142 (167)
T PF04891_consen 101 LWQDLGLRS--RAELSALMRRHFPPLA-ARNTRN--MRWKKFFYRQL 142 (167)
T ss_pred cHHhcCCCC--HHHHHHHHHHHhHHHH-HhccCC--CcHHHHHHHHH
Confidence 477777765 8899998887 57777 766663 55443344444
No 86
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=21.90 E-value=90 Score=22.33 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=16.3
Q ss_pred HHHHhCCCChHHHHHHHHh
Q 044946 71 QFLHSVGFSDTHIQLAVHT 89 (365)
Q Consensus 71 ~~L~~lG~s~~~i~~li~~ 89 (365)
..|.++|+|..|+...+.+
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 6678999999999888776
No 87
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=21.78 E-value=65 Score=27.08 Aligned_cols=48 Identities=10% Similarity=0.218 Sum_probs=32.5
Q ss_pred cCCCchhhHhHHHHHHhccChhhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044946 217 GFTTDSRMFVHGLDALCRLSEKTFDRKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 217 G~~~~~~~~~~~~~~l~~~s~~~l~~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
|.+....-+.+.++.....+.+.+++.|--|.+-|.+.++|+-+++..
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 444444444444455445667788888888888888888888877754
No 88
>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=21.72 E-value=3.3e+02 Score=20.08 Aligned_cols=50 Identities=18% Similarity=0.361 Sum_probs=32.5
Q ss_pred hhHHHHHHhCCCChHHHHHHHHhCCcceecCccCcHHHHHHHHHH-cCCCCchHHHH
Q 044946 67 QTVSQFLHSVGFSDTHIQLAVHTKPTILFADVNKTLKPKIAYFQQ-LGLVGSDLGKF 122 (365)
Q Consensus 67 ~~~~~~L~~lG~s~~~i~~li~~~P~lL~~~~~~~l~p~l~fL~~-lGl~~~~i~~l 122 (365)
...-++.+.+|+++.+|..+-..+|. . .....+.+.-++. -|- .+.+..+
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~-~----~eq~~~mL~~W~~k~G~-~At~~~L 62 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQ-H----RDRVYELLRIWRNKEGR-KATLNTL 62 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCc-h----HHHHHHHHHHHHhccCc-CcHHHHH
Confidence 44567788999999999999999987 2 1245555554443 454 3333333
No 89
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=21.71 E-value=1.1e+02 Score=21.29 Aligned_cols=12 Identities=17% Similarity=0.396 Sum_probs=6.9
Q ss_pred HHHHHcCCCCch
Q 044946 107 AYFQQLGLVGSD 118 (365)
Q Consensus 107 ~fL~~lGl~~~~ 118 (365)
+.|.++|++...
T Consensus 42 ~~L~~lGI~~~~ 53 (66)
T PF07647_consen 42 EDLKELGITNLG 53 (66)
T ss_dssp HHHHHTTTTHHH
T ss_pred HHHHHcCCCCHH
Confidence 355667775443
No 90
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=21.66 E-value=96 Score=24.62 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=28.3
Q ss_pred HHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCC--CChHHHHHHHH
Q 044946 37 NYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVG--FSDTHIQLAVH 88 (365)
Q Consensus 37 ~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG--~s~~~i~~li~ 88 (365)
+.| ..+|++..++..+++-.| .++..+-..+.+++ ++++++.+++.
T Consensus 64 ~~L-~~~~L~~~E~~qi~Nl~P-----~~~~El~~ii~~~~~r~~ee~l~~iL~ 111 (117)
T PF03874_consen 64 EEL-KKFGLTEFEILQIINLRP-----TTAVELRAIIESLESRFSEEDLEEILD 111 (117)
T ss_dssp HHH-TTSTS-HHHHHHHHHH-------SSHHHHHHHSTTGTTTSTHHHHHHHHH
T ss_pred HHH-hcccCCHHHHHHHhcCCC-----CCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 666 567777777777776653 45555555555555 67777777654
No 91
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=21.47 E-value=1.4e+02 Score=33.93 Aligned_cols=84 Identities=18% Similarity=0.219 Sum_probs=50.2
Q ss_pred HHHHHhcCCCHHHHHHHHhhcccCCCCCCchh-HHHHHHhCCCChHHHHHHHHhCCcce-----------e---------
Q 044946 37 NYLIETVNIPKSRALVISNQFSRIKTLEKPQT-VSQFLHSVGFSDTHIQLAVHTKPTIL-----------F--------- 95 (365)
Q Consensus 37 ~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~-~~~~L~~lG~s~~~i~~li~~~P~lL-----------~--------- 95 (365)
.-| ..+|++.+++..+....-.-.+..++.. -.+.|...||++++|.++=..-|..+ .
T Consensus 717 ~~L-~~lG~~~~~i~~i~~~~~~~Gsl~~~~~i~~~~l~~~Gf~~~~~~~~~~~l~~~fdi~~~fn~~~lg~~f~~~~lg 795 (1220)
T PRK07562 717 EAL-RTLGYSESQIAEIEAYAVGHGTLNQAPGINHSTLKAKGFTDEKIEKVEAALKSAFDIKFAFNKWTLGEDFCKDTLG 795 (1220)
T ss_pred HHH-HHcCCCHHHHHHHHHHhhcCCCccCCCCCCHHHHhhcCCcHHHHHHHHHHhhhhhhhhhhhcccccchhhhhhccc
Confidence 555 7899999999888864311112222222 25678899999999987555544444 1
Q ss_pred cCccCcHHHHHHHHHHcCCCCchHHH
Q 044946 96 ADVNKTLKPKIAYFQQLGLVGSDLGK 121 (365)
Q Consensus 96 ~~~~~~l~p~l~fL~~lGl~~~~i~~ 121 (365)
.+.+.--.|-++.|..+|++.++|..
T Consensus 796 ~~~~~~~~~~f~ll~~~g~t~~~i~a 821 (1220)
T PRK07562 796 IPAEQLNDPSFDLLEHLGFSKKDIEA 821 (1220)
T ss_pred CcHhhhccccchhhhhcccchhhHHH
Confidence 12222223455667777777666654
No 92
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=21.24 E-value=1.5e+02 Score=21.11 Aligned_cols=44 Identities=14% Similarity=0.232 Sum_probs=24.4
Q ss_pred HhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHhCCCChHHHHH
Q 044946 41 ETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHSVGFSDTHIQL 85 (365)
Q Consensus 41 ~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~lG~s~~~i~~ 85 (365)
+..|+|.+-+.++++.-+.+ +++..+.+.+.++++|..+....+
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v-~~~t~~~i~~~~~~~gy~~~~~~~ 51 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV-SEETREKVLAAMEELGYIPNRVAR 51 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC-CHHHHHHHHHHHHHhCCCCCHHHH
Confidence 44566666666665544333 334455566666666665554443
No 93
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=21.17 E-value=4.9e+02 Score=21.66 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=16.9
Q ss_pred HHHHHHhCCCHHHHHHHHHhcC
Q 044946 244 LDLFRSYGFSKEECIEMIRTAP 265 (365)
Q Consensus 244 v~fL~~~G~s~~ev~~~i~~~P 265 (365)
..-|..-|++.+.|...+...+
T Consensus 82 ~~~L~~kGi~~~~I~~~l~~~~ 103 (157)
T PRK00117 82 RQELRQKGVDREIIEEALAELD 103 (157)
T ss_pred HHHHHHcCCCHHHHHHHHHHcC
Confidence 3457788999999888877654
No 94
>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=20.71 E-value=1.6e+02 Score=23.50 Aligned_cols=23 Identities=30% Similarity=0.371 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhc
Q 044946 242 RKLDLFRSYGFSKEECIEMIRTA 264 (365)
Q Consensus 242 ~~v~fL~~~G~s~~ev~~~i~~~ 264 (365)
..+..++++||+-++|..++...
T Consensus 47 ~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 47 ALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcc
Confidence 46788889999999999888754
No 95
>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=20.70 E-value=3e+02 Score=21.10 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=22.1
Q ss_pred HHHHHHHHH-hCCCHHHHHHHHHhcCcc
Q 044946 241 DRKLDLFRS-YGFSKEECIEMIRTAPRL 267 (365)
Q Consensus 241 ~~~v~fL~~-~G~s~~ev~~~i~~~P~i 267 (365)
-..+..|++ .|++.+++..++...+..
T Consensus 46 l~~I~~L~~~~G~~l~ei~~~l~~~~~~ 73 (96)
T cd04774 46 LERILRLREVLGFSLQEVTHFLERPLEP 73 (96)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 355778887 999999999999887775
No 96
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=20.59 E-value=1.4e+02 Score=28.17 Aligned_cols=78 Identities=9% Similarity=0.035 Sum_probs=43.7
Q ss_pred HHhccCCCchHHHHHHHhccccccccCCCC-----cchhchHHHHHHcCCCh---hhHHHHhhhcCccceec--chhHHH
Q 044946 139 KILAEDSNNEDLIRVIRRMSWDLVVIDPEK-----SGLLRNIEYLKSCGIVG---SQLSMLLVRLPRLFCFN--DLKLRQ 208 (365)
Q Consensus 139 ~~g~~~~~~~~v~~~l~~~P~iL~~~s~e~-----~~l~~~v~~L~~lG~~~---~~i~~ll~~~P~~l~~s--~~~i~~ 208 (365)
++.+. ++.+..++...|.+| .+++|. -.++|...|-+++.+=+ +.-..++++..-+++.. .+.+.+
T Consensus 157 DF~G~---~~al~~v~~~~pdV~-nHNvETVprL~~~VRp~A~Y~~SL~~L~~~k~~~P~i~TKSgiMlGLGEt~~Ev~e 232 (306)
T COG0320 157 DFRGN---DDALEIVADAGPDVF-NHNVETVPRLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIE 232 (306)
T ss_pred cccCC---HHHHHHHHhcCcchh-hcccccchhcccccCCCCcHHHHHHHHHHHHHhCCCcccccceeeecCCcHHHHHH
Confidence 35555 777888888899999 998884 12233444544443211 01111333333334443 355777
Q ss_pred HHHHHHhccCCC
Q 044946 209 LVLRVLDMGFTT 220 (365)
Q Consensus 209 ~v~~l~~lG~~~ 220 (365)
.++.|++.|++-
T Consensus 233 ~m~DLr~~gvdi 244 (306)
T COG0320 233 VMDDLRSAGVDI 244 (306)
T ss_pred HHHHHHHcCCCE
Confidence 777777777664
No 97
>PF06896 DUF1268: Protein of unknown function (DUF1268); InterPro: IPR009681 This entry is represented by Bacteriophage bIL286, Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=20.49 E-value=1.8e+02 Score=23.45 Aligned_cols=50 Identities=20% Similarity=0.415 Sum_probs=0.0
Q ss_pred hHHHHHHhcCCCHHHHHHHHhhcccCCCCCCchhHHHHHHh--CCCChHHHHHHHHh
Q 044946 35 FLNYLIETVNIPKSRALVISNQFSRIKTLEKPQTVSQFLHS--VGFSDTHIQLAVHT 89 (365)
Q Consensus 35 ~v~yL~~~~Gls~~~~~~i~~~~p~l~~~~~~~~~~~~L~~--lG~s~~~i~~li~~ 89 (365)
+..|+..-+|++.++..++ ... +.++....+.++.. .|++++|+......
T Consensus 58 ~~~Fi~~iL~L~dkq~ekl-~~i----D~~~~~e~~~yl~~rl~G~sD~~i~~~~~~ 109 (114)
T PF06896_consen 58 MLKFIQDILKLNDKQVEKL-EDI----DFEDLQEIVSYLVMRLQGMSDEQIELAEKE 109 (114)
T ss_pred HHHHHHHHHCCCHHHHHHH-hcC----CHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
No 98
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.30 E-value=2.5e+02 Score=21.46 Aligned_cols=24 Identities=21% Similarity=0.268 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCHHHHHHHHHhcC
Q 044946 242 RKLDLFRSYGFSKEECIEMIRTAP 265 (365)
Q Consensus 242 ~~v~fL~~~G~s~~ev~~~i~~~P 265 (365)
..|..|+++||+-++|..++....
T Consensus 48 ~~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 48 HQIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhCCC
Confidence 567888999999999999987543
No 99
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=20.12 E-value=1.2e+02 Score=23.55 Aligned_cols=28 Identities=21% Similarity=0.349 Sum_probs=24.0
Q ss_pred chhHHHHHHhCCCChHHHHHHHHhCCcc
Q 044946 66 PQTVSQFLHSVGFSDTHIQLAVHTKPTI 93 (365)
Q Consensus 66 ~~~~~~~L~~lG~s~~~i~~li~~~P~l 93 (365)
+..+-+|-+.+|+|+.+|..+-..+|.=
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d 47 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQD 47 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCC
Confidence 3457888899999999999999999864
Done!