Query 048516
Match_columns 389
No_of_seqs 242 out of 1229
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 10:12:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048516.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048516hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 1.1E-58 2.5E-63 470.8 25.3 325 57-389 96-465 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 7.8E-51 1.7E-55 400.0 6.3 303 62-367 5-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 4.6E-44 1E-48 363.9 19.8 294 56-362 66-404 (487)
4 KOG1267 Mitochondrial transcri 100.0 6.3E-33 1.4E-37 279.1 15.4 278 53-337 59-370 (413)
5 PF02536 mTERF: mTERF; InterP 100.0 1.9E-29 4.1E-34 248.1 6.1 248 56-311 36-325 (345)
6 KOG1267 Mitochondrial transcri 99.6 7.2E-16 1.6E-20 155.4 10.6 280 56-345 94-411 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.0004 8.7E-09 42.5 2.4 30 283-313 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.0 0.00062 1.4E-08 41.6 2.5 28 179-207 3-30 (31)
9 PF11955 PORR: Plant organelle 91.2 1.1 2.4E-05 44.1 8.7 225 95-323 45-317 (335)
10 KOG0011 Nucleotide excision re 89.9 0.39 8.4E-06 46.3 4.2 111 56-185 138-262 (340)
11 cd04790 HTH_Cfa-like_unk Helix 88.7 1.3 2.8E-05 39.2 6.4 24 125-148 49-72 (172)
12 cd04790 HTH_Cfa-like_unk Helix 78.9 7.1 0.00015 34.6 6.7 22 90-111 50-71 (172)
13 PF04695 Pex14_N: Peroxisomal 74.7 5.7 0.00012 33.8 4.7 31 262-292 21-51 (136)
14 PF14490 HHH_4: Helix-hairpin- 72.0 11 0.00023 29.8 5.4 56 87-142 8-75 (94)
15 smart00165 UBA Ubiquitin assoc 71.6 6.3 0.00014 25.0 3.3 24 265-288 2-25 (37)
16 PF00627 UBA: UBA/TS-N domain; 71.5 5.9 0.00013 25.4 3.2 24 265-288 3-26 (37)
17 PF11181 YflT: Heat induced st 70.4 28 0.0006 27.9 7.6 79 192-283 9-89 (103)
18 PF04695 Pex14_N: Peroxisomal 69.4 5.9 0.00013 33.6 3.6 22 162-183 26-47 (136)
19 cd00194 UBA Ubiquitin Associat 67.7 8.4 0.00018 24.6 3.3 24 265-288 2-25 (38)
20 PF02787 CPSase_L_D3: Carbamoy 66.2 5.2 0.00011 33.4 2.6 60 85-145 11-83 (123)
21 PF11212 DUF2999: Protein of u 62.8 18 0.00038 27.1 4.4 58 88-153 2-62 (82)
22 PF14490 HHH_4: Helix-hairpin- 59.2 22 0.00047 28.0 4.9 47 122-193 7-53 (94)
23 PF00356 LacI: Bacterial regul 58.6 14 0.0003 25.1 3.2 40 203-245 7-46 (46)
24 PF02631 RecX: RecX family; I 57.9 13 0.00029 30.5 3.7 55 56-111 14-69 (121)
25 PF11212 DUF2999: Protein of u 56.7 41 0.00088 25.2 5.4 49 160-216 2-50 (82)
26 PF07499 RuvA_C: RuvA, C-termi 56.2 16 0.00034 24.9 3.1 24 88-111 4-27 (47)
27 PF03960 ArsC: ArsC family; I 54.9 29 0.00062 28.0 5.1 21 171-191 71-91 (110)
28 COG1125 OpuBA ABC-type proline 53.6 22 0.00049 33.8 4.6 66 260-325 69-137 (309)
29 TIGR01448 recD_rel helicase, p 53.5 35 0.00077 37.2 6.9 79 56-145 80-165 (720)
30 PRK08561 rps15p 30S ribosomal 52.8 30 0.00065 29.9 4.9 114 216-354 19-141 (151)
31 TIGR00601 rad23 UV excision re 51.6 24 0.00053 35.3 4.9 45 260-313 152-196 (378)
32 PF11955 PORR: Plant organelle 51.0 75 0.0016 31.3 8.2 93 204-296 46-152 (335)
33 PF07499 RuvA_C: RuvA, C-termi 49.4 31 0.00067 23.4 3.7 25 264-288 3-27 (47)
34 smart00657 RPOL4c DNA-directed 48.9 40 0.00087 27.8 5.1 27 86-112 56-82 (118)
35 COG3620 Predicted transcriptio 48.3 34 0.00073 30.0 4.5 49 195-244 50-98 (187)
36 PF02022 Integrase_Zn: Integra 48.2 33 0.00071 22.7 3.5 31 262-292 6-37 (40)
37 COG0320 LipA Lipoate synthase 45.4 33 0.00072 32.7 4.4 51 194-244 229-283 (306)
38 PF02787 CPSase_L_D3: Carbamoy 45.3 42 0.00091 28.0 4.7 67 195-285 13-82 (123)
39 COG1725 Predicted transcriptio 45.1 30 0.00064 29.0 3.7 65 224-288 46-119 (125)
40 KOG2561 Adaptor protein NUB1, 43.4 72 0.0016 32.5 6.6 136 86-246 302-445 (568)
41 PF03874 RNA_pol_Rpb4: RNA pol 42.3 37 0.00081 27.6 3.9 32 82-113 54-85 (117)
42 smart00354 HTH_LACI helix_turn 42.3 30 0.00066 25.4 3.1 40 203-245 8-47 (70)
43 PRK00116 ruvA Holliday junctio 39.0 72 0.0016 28.7 5.5 25 159-183 149-173 (192)
44 TIGR00601 rad23 UV excision re 38.0 44 0.00096 33.5 4.3 114 56-189 159-298 (378)
45 PF08069 Ribosomal_S13_N: Ribo 34.0 18 0.00038 26.2 0.6 36 109-145 20-55 (60)
46 PF13720 Acetyltransf_11: Udp 32.9 53 0.0012 25.3 3.2 38 93-132 22-59 (83)
47 KOG2629 Peroxisomal membrane a 32.8 82 0.0018 30.2 4.9 26 262-287 20-45 (300)
48 TIGR01448 recD_rel helicase, p 32.6 69 0.0015 35.0 5.1 76 64-142 123-210 (720)
49 COG0560 SerB Phosphoserine pho 31.9 1.5E+02 0.0032 27.0 6.5 86 113-207 6-94 (212)
50 cd08319 Death_RAIDD Death doma 31.7 1.9E+02 0.0042 22.2 6.1 35 131-169 21-55 (83)
51 PF08671 SinI: Anti-repressor 31.3 66 0.0014 19.9 2.7 25 263-287 4-28 (30)
52 PRK00116 ruvA Holliday junctio 31.2 60 0.0013 29.2 3.7 26 123-148 149-174 (192)
53 PRK11613 folP dihydropteroate 30.7 93 0.002 29.9 5.1 66 298-371 164-229 (282)
54 COG1386 scpB Chromosome segreg 29.9 56 0.0012 29.3 3.2 46 338-383 123-172 (184)
55 PF10440 WIYLD: Ubiquitin-bind 29.9 89 0.0019 23.0 3.7 28 261-288 8-35 (65)
56 cd08306 Death_FADD Fas-associa 29.6 98 0.0021 23.9 4.2 22 91-112 17-38 (86)
57 COG2137 OraA Uncharacterized p 29.4 2.7E+02 0.0059 24.7 7.5 24 86-109 86-109 (174)
58 cd01392 HTH_LacI Helix-turn-he 29.3 79 0.0017 21.2 3.3 40 203-245 5-44 (52)
59 cd08316 Death_FAS_TNFRSF6 Deat 29.3 1.8E+02 0.0038 23.2 5.7 27 87-113 20-46 (97)
60 KOG0400 40S ribosomal protein 28.4 85 0.0019 26.4 3.8 72 109-182 20-94 (151)
61 PRK10026 arsenate reductase; P 28.1 1.7E+02 0.0036 25.1 5.7 17 195-211 15-31 (141)
62 cd08315 Death_TRAILR_DR4_DR5 D 28.1 1.6E+02 0.0034 23.3 5.2 26 88-113 20-45 (96)
63 cd08306 Death_FADD Fas-associa 27.6 1.8E+02 0.0039 22.4 5.4 46 123-172 12-58 (86)
64 cd08313 Death_TNFR1 Death doma 27.4 87 0.0019 24.0 3.5 26 87-112 11-36 (80)
65 PF02631 RecX: RecX family; I 26.9 2.5E+02 0.0055 22.7 6.5 57 227-286 8-67 (121)
66 PRK09570 rpoH DNA-directed RNA 26.8 25 0.00054 27.0 0.3 48 86-149 19-66 (79)
67 PF10975 DUF2802: Protein of u 26.5 51 0.0011 24.6 2.0 21 56-76 46-66 (70)
68 PF13543 KSR1-SAM: SAM like do 26.0 1.1E+02 0.0023 25.8 4.1 53 57-110 70-124 (129)
69 cd08805 Death_ank1 Death domai 26.0 2.1E+02 0.0045 22.1 5.4 36 131-170 23-58 (84)
70 PF09288 UBA_3: Fungal ubiquit 25.7 90 0.0019 22.2 3.0 11 233-243 12-22 (55)
71 KOG0369 Pyruvate carboxylase [ 25.4 1.3E+02 0.0028 32.6 5.2 61 57-125 915-981 (1176)
72 PHA01351 putative minor struct 24.6 5.8E+02 0.013 27.8 9.8 62 86-147 642-715 (1070)
73 TIGR00281 segregation and cond 24.5 81 0.0017 28.3 3.3 47 337-383 117-167 (186)
74 PHA02591 hypothetical protein; 24.3 1.2E+02 0.0025 23.3 3.5 46 99-144 24-69 (83)
75 PF01191 RNA_pol_Rpb5_C: RNA p 24.2 27 0.00058 26.5 0.1 47 87-149 17-63 (74)
76 PF10440 WIYLD: Ubiquitin-bind 24.0 93 0.002 22.9 2.9 26 85-110 9-34 (65)
77 PRK14136 recX recombination re 23.8 6.8E+02 0.015 24.4 12.8 106 158-288 195-302 (309)
78 PF04079 DUF387: Putative tran 23.5 45 0.00097 29.1 1.4 44 337-380 112-159 (159)
79 PTZ00413 lipoate synthase; Pro 23.1 2.6E+02 0.0057 28.2 6.8 107 136-244 241-365 (398)
80 smart00354 HTH_LACI helix_turn 22.9 1.5E+02 0.0032 21.7 3.9 46 59-105 5-50 (70)
81 PRK00117 recX recombination re 22.7 2.3E+02 0.0051 24.1 5.8 57 87-144 78-150 (157)
82 PF03960 ArsC: ArsC family; I 22.7 74 0.0016 25.5 2.5 18 135-152 71-88 (110)
83 PF09278 MerR-DNA-bind: MerR, 22.3 87 0.0019 22.2 2.6 18 268-285 7-24 (65)
84 cd03032 ArsC_Spx Arsenate Redu 22.1 2.3E+02 0.005 22.8 5.4 21 275-295 73-93 (115)
85 PRK14134 recX recombination re 22.1 1.3E+02 0.0027 28.9 4.3 22 89-110 184-205 (283)
86 PRK10026 arsenate reductase; P 22.0 1.5E+02 0.0032 25.3 4.3 20 172-191 77-96 (141)
87 KOG3120 Predicted haloacid deh 21.5 2E+02 0.0043 26.8 5.1 45 85-135 57-101 (256)
88 cd08784 Death_DRs Death Domain 21.2 1.4E+02 0.0031 22.6 3.6 27 87-113 11-37 (79)
89 PRK14134 recX recombination re 21.1 7.3E+02 0.016 23.7 9.4 119 87-217 127-277 (283)
90 PF09280 XPC-binding: XPC-bind 21.1 1.2E+02 0.0025 21.8 2.9 20 165-184 27-46 (59)
91 smart00760 Bac_DnaA_C Bacteria 20.6 2.2E+02 0.0047 20.1 4.3 49 57-109 6-56 (60)
92 PF06896 DUF1268: Protein of u 20.6 3.5E+02 0.0077 22.2 6.0 55 256-317 47-103 (114)
93 cd02977 ArsC_family Arsenate R 20.3 2.5E+02 0.0054 22.0 5.1 22 274-295 72-93 (105)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.1e-58 Score=470.76 Aligned_cols=325 Identities=19% Similarity=0.290 Sum_probs=226.1
Q ss_pred HHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCC
Q 048516 57 ADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFS 136 (389)
Q Consensus 57 ~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s 136 (389)
++|| .+.|++.++..+ ....+...-..+..++++||+++|++.++|.++|.++|++|.++++++|.|+++||+++|++
T Consensus 96 l~~L-~s~G~~~~~i~~-~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs 173 (487)
T PLN03196 96 VEFL-HKLGLTIEDINE-YPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVK 173 (487)
T ss_pred HHHH-HHcCCChHHhcc-CcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCC
Confidence 3455 356666655541 11122222223455566666666666666666666666666666655666666666666666
Q ss_pred hhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhc
Q 048516 137 SSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYV 216 (389)
Q Consensus 137 ~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll 216 (389)
+++|++++.++|++|+++++++|.|+++||+++|++.+++.+++.++|++|+++++++++|+++||+++|++.++|.+++
T Consensus 174 ~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il 253 (487)
T PLN03196 174 RQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARIL 253 (487)
T ss_pred HHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 66666666666666666655556666666665555555556666666666665555555666666655666555555555
Q ss_pred ccCcEeeeecch-hHHHHHHHHHHhCCCC-------------------------------------Ccc-cHHHHHHHHh
Q 048516 217 YTYPTFFLYKPE-KVRCFVQRVDEIGFDR-------------------------------------NSK-MYLPAIRTMS 257 (389)
Q Consensus 217 ~~~P~il~~s~~-~~~~~v~~l~~lG~~~-------------------------------------~~~-~f~~a~~~~~ 257 (389)
.++|++|+++.+ +++++++++.++|+++ ++. .++.+.+.+.
T Consensus 254 ~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il 333 (487)
T PLN03196 254 EKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIV 333 (487)
T ss_pred HhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhh
Confidence 556666655554 5555555555555554 332 1233344567
Q ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHHcCCCccccCHHhHHHHHHHHhhccCCChhhHhhCCceeecCCCCccchHHH
Q 048516 258 SMTKEKWELKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFLCSIESNLKPRMR 337 (389)
Q Consensus 258 ~~s~~~~~~kv~~l~~~G~s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~~~~i~~~P~lL~~Sle~ri~PR~~ 337 (389)
.+++++|++|++||+++||+.+||..||+++|+||++|+++|+++++||+++||++.++|+++|++|+||||+||+|||.
T Consensus 334 ~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~ 413 (487)
T PLN03196 334 SLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYE 413 (487)
T ss_pred cccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred HHHHHHHcCcccCCCCchhhhcccHhhHHHhhccCCCC-cccccc-----ccCCCCCC
Q 048516 338 VYDMLKSKNLLRRKTGLATVCKLSKGKFLEKYVLPYQD-ELGDLS-----FLTMPQSQ 389 (389)
Q Consensus 338 vl~~L~~kGl~~~~~~l~~~l~~se~~F~~k~v~~~~e-~~p~l~-----~~~~~~~~ 389 (389)
+ |+++|+ ++++.+++.+||++|++|||.+|.| +..+-. .++|||++
T Consensus 414 ~---L~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~~~~~~~~~~~~~~~~~~~~ 465 (487)
T PLN03196 414 R---VAKKGI---KCSLAWFLNCSDDKFEQRMSGDFIEGEEMEPLFSMGGKLEMPGSE 465 (487)
T ss_pred H---HHHcCC---CCCHHHHhccCHHHHHHHHhhhcccccccCCCcccCCcccCCCCc
Confidence 6 569999 6899999999999999999999987 333332 26777763
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=7.8e-51 Score=400.03 Aligned_cols=303 Identities=24% Similarity=0.394 Sum_probs=205.1
Q ss_pred hccCCCHHHHHHhhcc--c-cCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChh
Q 048516 62 NRQHFSPESASEASSL--N-FSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSS 138 (389)
Q Consensus 62 ~s~Gls~~~a~~~s~~--~-~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~ 138 (389)
+++||+..+..++.++ . +..+...+..++++||.+.|++.+||.+++.++|.+|..+.++++.|.++||++.|++++
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 5666766666666442 1 222233446667777777777777777777777777777766667777777777777777
Q ss_pred hhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhccc
Q 048516 139 DIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYVYT 218 (389)
Q Consensus 139 ~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll~~ 218 (389)
|+++++.++|++|..+.++++.|+++||+++|++.+.+.+.+..+|.++... +.+++.++++.++|++++++.+++..
T Consensus 85 d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~ 162 (345)
T PF02536_consen 85 DIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAK 162 (345)
T ss_dssp HHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHH
T ss_pred HHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccc
Confidence 7777777777777666666677777777777777665666666666655444 34677777777777777777777777
Q ss_pred CcEeeeec-chhHHHHHHHHHHhCCCCCcc--cHHHHH--------------------------------HHHhcCCHHH
Q 048516 219 YPTFFLYK-PEKVRCFVQRVDEIGFDRNSK--MYLPAI--------------------------------RTMSSMTKEK 263 (389)
Q Consensus 219 ~P~il~~s-~~~~~~~v~~l~~lG~~~~~~--~f~~a~--------------------------------~~~~~~s~~~ 263 (389)
+|+++... .+.+++++++++++|++.++. ++.++| +.++..+.++
T Consensus 163 ~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~ 242 (345)
T PF02536_consen 163 NPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEK 242 (345)
T ss_dssp HHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHH
T ss_pred cchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHh
Confidence 77544444 456788888888888776431 222222 2233345678
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCccccCHHhHHHHHHHHhhccCCChhhHhhCCceeecCCCCccchHHHHHHHHH
Q 048516 264 WELKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASLFLCSIESNLKPRMRVYDMLK 343 (389)
Q Consensus 264 ~~~kv~~l~~~G~s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~~~~i~~~P~lL~~Sle~ri~PR~~vl~~L~ 343 (389)
+++++++|+++|||++||..|+.++|++|++|+++++++++||.++||++.++|+++|++|+||+|+||+|||+++++|+
T Consensus 243 l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~ 322 (345)
T PF02536_consen 243 LKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLK 322 (345)
T ss_dssp HHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCcccCCCCchhhhcccHhhHHH
Q 048516 344 SKNLLRRKTGLATVCKLSKGKFLE 367 (389)
Q Consensus 344 ~kGl~~~~~~l~~~l~~se~~F~~ 367 (389)
++|+ ..++++.+++.+||++|++
T Consensus 323 ~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 323 SKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp -TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred HCcC-CCCCCHHHHhhccHHHhcC
Confidence 9997 6689999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=4.6e-44 Score=363.86 Aligned_cols=294 Identities=14% Similarity=0.229 Sum_probs=242.0
Q ss_pred hHHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCC
Q 048516 56 LADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGF 135 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~ 135 (389)
+++||. +.|+++..+.+.-. -.+-+...++++||+++||+++||. ++|++|.+++++++.|+++||+++|+
T Consensus 66 ~~~~L~-~lgi~~~~l~~~~~----p~~~~~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~ 136 (487)
T PLN03196 66 VLDFLR-GIGIDPDELDGLEL----PSTVDVMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGV 136 (487)
T ss_pred HHHHHH-HcCCCchhhhccCC----CccHHHHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCC
Confidence 789995 79999988865321 1234567788999999999999997 79999999999999999999999999
Q ss_pred ChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhh
Q 048516 136 SSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKY 215 (389)
Q Consensus 136 s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~l 215 (389)
++++|+++|.++|.+|..|++++|.|+++||+++|++++++.+++.++|++|++++++++.|+++||+++|++.++|.++
T Consensus 137 s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~i 216 (487)
T PLN03196 137 TRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPM 216 (487)
T ss_pred CHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcEeeeecch-hHHHHHHHHHHhCCCCCc--ccHHHHHHHHhcC---------------------------------
Q 048516 216 VYTYPTFFLYKPE-KVRCFVQRVDEIGFDRNS--KMYLPAIRTMSSM--------------------------------- 259 (389)
Q Consensus 216 l~~~P~il~~s~~-~~~~~v~~l~~lG~~~~~--~~f~~a~~~~~~~--------------------------------- 259 (389)
+.++|++|+++.+ +++.+++++.++|++.+. ..+.++|..+...
T Consensus 217 l~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL 296 (487)
T PLN03196 217 LTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDIL 296 (487)
T ss_pred HHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCcee
Confidence 9999999999987 689999999999998764 1222222222211
Q ss_pred ---CHHHHHHHHHHHH-HcCCCHHHHHHHHHcCCCccccCHHhHHHHHHHHhhccCCChhhH----hhCCceeecCCCCc
Q 048516 260 ---TKEKWELKLKLFR-SLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDISSI----VNNASLFLCSIESN 331 (389)
Q Consensus 260 ---s~~~~~~kv~~l~-~~G~s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~~~~i----~~~P~lL~~Sle~r 331 (389)
.+++++++++++. ++||+.+++..++.++|+++++|+++++++++||.+ +||+.++| .++|++|+||.+ .
T Consensus 297 ~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~-~ 374 (487)
T PLN03196 297 GLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLE-I 374 (487)
T ss_pred EecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHH-H
Confidence 2345666666664 577777777778888888888888888888888886 88888887 588888888884 7
Q ss_pred cchHHHHHHHHHHcCcccC-CCCchhhhcccH
Q 048516 332 LKPRMRVYDMLKSKNLLRR-KTGLATVCKLSK 362 (389)
Q Consensus 332 i~PR~~vl~~L~~kGl~~~-~~~l~~~l~~se 362 (389)
|+|++.++. ...|+--. -..+..++.+|=
T Consensus 375 l~~k~dFlv--neMg~~~~~Iv~fP~~LsySL 404 (487)
T PLN03196 375 MKPSLEFFK--KEMKRPLKELVEFPAYFTYGL 404 (487)
T ss_pred HHHHHHHHH--HHhCCCHHHHHhChHHhccCh
Confidence 888886654 23354211 234566677763
No 4
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=100.00 E-value=6.3e-33 Score=279.06 Aligned_cols=278 Identities=25% Similarity=0.384 Sum_probs=242.9
Q ss_pred CcchHHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHH
Q 048516 53 KIDLADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHE 132 (389)
Q Consensus 53 ~f~~~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~s 132 (389)
+| .++|+++++|++...|..+++ .+......+|++++++|+++|+++++|.+++..+|+++..+.++.+.|++.+|++
T Consensus 59 ~f-~~s~~~~s~~~~~~~~~~~~~-~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~ 136 (413)
T KOG1267|consen 59 NF-ESSYLVDSLGLSIKLARKLSR-EVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDS 136 (413)
T ss_pred Cc-ceeeeccccccchhhHHHHHH-HHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhc
Confidence 39 999999999999999999888 7888889999999999999999999999999999999999999999999999999
Q ss_pred cCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhh--CChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCch
Q 048516 133 FGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVL--GSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSS 210 (389)
Q Consensus 133 lG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g--~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~ 210 (389)
.|++.++++++++..|.+|..+.+.++.+.++|+++++ .....+.+.+...|..... +..+. ++++++++|+.++
T Consensus 137 ~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~--~~~v~-~~~~~~~lg~~~~ 213 (413)
T KOG1267|consen 137 LGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLN--ENSVE-RLDIRRELGVKPR 213 (413)
T ss_pred cCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhcccccccccc--ccccc-cchhhHHhCCCHH
Confidence 99999999999999999999998889999999999986 4555555555444422222 12245 9999999999999
Q ss_pred hhhhhcccCcEeeeecchhHHHHHHHHHHhCCCCCcccHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHcCCC
Q 048516 211 QIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDRNSKMYLPAIRTMSSMTKEKWELKLKLFRSLGFSEDNILSMFRSMPP 290 (389)
Q Consensus 211 ~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~~~~~f~~a~~~~~~~s~~~~~~kv~~l~~~G~s~~~v~~~~~~~P~ 290 (389)
.+..++..+|+.+.... .+...+.++.++||+|.+.+|++|+..+...+++++++|+++|++.||+++||+.|+.++|+
T Consensus 214 ~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~ 292 (413)
T KOG1267|consen 214 LLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQ 292 (413)
T ss_pred HHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCch
Confidence 99999999999988754 78899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCHHh----------------------------HHHHHHHHhhccCCChhhHh----hCCceeecCCCCccchHHH
Q 048516 291 AFTVSERK----------------------------IRSVVETLLRRRDVDISSIV----NNASLFLCSIESNLKPRMR 337 (389)
Q Consensus 291 iL~~S~~~----------------------------l~~k~~fL~~~mg~~~~~i~----~~P~lL~~Sle~ri~PR~~ 337 (389)
+|++|+++ ++++++|+.. .|++..+++ ++|++++||+|+-+++.+.
T Consensus 293 ~l~~s~~~~~~~~~~~~~~~~~~~k~p~~l~~s~~~l~~~ie~l~~-~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~ 370 (413)
T KOG1267|consen 293 ILGYSVKKNLKTTEYLLKNPKHILKFPQLLRSSEDKLKPRIEFLLS-LGFSDVQILEMVKRFPQYLSFSLEKILKRKYE 370 (413)
T ss_pred heEeehhhhhHHHHHHHhcchhhhhhhhhhhccchhhhhhHHHHHH-cCCcHHHHHHHHhhccHHhhhhHHhhhhhhHH
Confidence 99999874 7788888887 687766653 4688888888873333333
No 5
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.95 E-value=1.9e-29 Score=248.14 Aligned_cols=248 Identities=21% Similarity=0.343 Sum_probs=196.0
Q ss_pred hHHHhhhccCCCHHHHHHhhc---cccCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHH
Q 048516 56 LADYLINRQHFSPESASEASS---LNFSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHE 132 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~---~~~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~s 132 (389)
.++||. +.|+|..+..++.. ...+....++..++++||+++|++++|+.+++.++|++|..+.+.++.|++++|++
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 KLEFLR-SLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRS 114 (345)
T ss_dssp HHHHHH-HTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHH
T ss_pred HHHHHH-HCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhh
Confidence 778995 89999988888733 12232235778999999999999999999999999999999888789999999999
Q ss_pred cCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhh
Q 048516 133 FGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQI 212 (389)
Q Consensus 133 lG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I 212 (389)
+|++.+++.+++..+|.++... +.+.+.++|+.++|++++++.+++.++|+++..+.+++++|+++||+++|++.+++
T Consensus 115 lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i 192 (345)
T PF02536_consen 115 LGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDI 192 (345)
T ss_dssp TT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHH
T ss_pred cCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhh
Confidence 9999998888888888776665 58999999999999999999999999998888888888999999999999999999
Q ss_pred hhhcccCcEeeeecchh---------------------------------HHHHHHHHHHhCCCCCcc-cHHHHHHHHhc
Q 048516 213 VKYVYTYPTFFLYKPEK---------------------------------VRCFVQRVDEIGFDRNSK-MYLPAIRTMSS 258 (389)
Q Consensus 213 ~~ll~~~P~il~~s~~~---------------------------------~~~~v~~l~~lG~~~~~~-~f~~a~~~~~~ 258 (389)
.+++.++|+++..+.++ +.++++++.++||+.++. .++..-+.++.
T Consensus 193 ~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~ 272 (345)
T PF02536_consen 193 GKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILS 272 (345)
T ss_dssp HHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGG
T ss_pred hHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhh
Confidence 99999999888887764 888999999999998874 45555556677
Q ss_pred CCHHHHHHHHHHHH-HcCCCHHHHHHHHHcCCCccccCHH-hHHHH---HHHHhhccC
Q 048516 259 MTKEKWELKLKLFR-SLGFSEDNILSMFRSMPPAFTVSER-KIRSV---VETLLRRRD 311 (389)
Q Consensus 259 ~s~~~~~~kv~~l~-~~G~s~~~v~~~~~~~P~iL~~S~~-~l~~k---~~fL~~~mg 311 (389)
.+.+++++|++|+. ++|++.++| .++|++|++|.| +|+++ ++++.+ .|
T Consensus 273 ~s~e~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~ri~PR~~~~~~l~~-~g 325 (345)
T PF02536_consen 273 YSIEKLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKRIKPRYEVLKVLKS-KG 325 (345)
T ss_dssp S-HHHHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHHHHHHHHHHHTT---TT
T ss_pred cchhhhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhhhhhHHHHHHHHHH-Cc
Confidence 88888999999998 599999997 689999999965 69999 777776 46
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.64 E-value=7.2e-16 Score=155.40 Aligned_cols=280 Identities=21% Similarity=0.288 Sum_probs=225.2
Q ss_pred hHHHhhhccCCCHHHHHHhhcc--c-cCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHH
Q 048516 56 LADYLINRQHFSPESASEASSL--N-FSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHE 132 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~~--~-~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~s 132 (389)
+.+.| .+.|++..+..++... . ...+......+.+.+|++.|++.+.+.++++..|.+|...-+.++.+.++|+.+
T Consensus 94 ~~~~l-~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~ 172 (413)
T KOG1267|consen 94 VLSSL-RSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKS 172 (413)
T ss_pred HHHHH-HhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhc
Confidence 55655 6899999988876331 2 222333334566678899999999999999999999987767789999999998
Q ss_pred cC--CChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHH--------------------------------H
Q 048516 133 FG--FSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVC--------------------------------K 178 (389)
Q Consensus 133 lG--~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~--------------------------------~ 178 (389)
.+ ...+.+.++....|...... +.+. ++++++++|...+.+. +
T Consensus 173 ~~~~~~~s~~~~~~~~~~~~~~~~--~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~~l~~~~~~i~~~g~~p~~~ 249 (413)
T KOG1267|consen 173 IPPELLSSVVERLLTPVPSFLLNE--NSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYLKLKARLPFLLTLGFDPKTR 249 (413)
T ss_pred cchhhhhhHHHHhccccccccccc--cccc-cchhhHHhCCCHHHHHHHHhcCccceeeehhhhhhhhhHHHhccCCchh
Confidence 74 77777777777776433321 1222 5666666665555444 3
Q ss_pred HHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHHHHHHhCCCCCcccHHHHHHHHhc
Q 048516 179 AIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDRNSKMYLPAIRTMSS 258 (389)
Q Consensus 179 ~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~~~~~f~~a~~~~~~ 258 (389)
.+.+.|.+++++.++++++++++|+++|++.++|..++.++|++++++.+++...++++.+. .++ +...+.+..
T Consensus 250 ~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~--~~~----~~k~p~~l~ 323 (413)
T KOG1267|consen 250 EFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN--PKH----ILKFPQLLR 323 (413)
T ss_pred HHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc--chh----hhhhhhhhh
Confidence 34455666666789999999999999999999999999999999999999888888888766 222 334444458
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHHcCCCccccCHH-hHHHHHHHHhhccCCChhhHhhCCceeecCCCCccchHHH
Q 048516 259 MTKEKWELKLKLFRSLGFSEDNILSMFRSMPPAFTVSER-KIRSVVETLLRRRDVDISSIVNNASLFLCSIESNLKPRMR 337 (389)
Q Consensus 259 ~s~~~~~~kv~~l~~~G~s~~~v~~~~~~~P~iL~~S~~-~l~~k~~fL~~~mg~~~~~i~~~P~lL~~Sle~ri~PR~~ 337 (389)
.++.++.++++++...|++.+++..+++++|+++.+|.+ .++.+.+|+.+.|+++.+.++.+|.+++|++|+|+.||+.
T Consensus 324 ~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~ 403 (413)
T KOG1267|consen 324 SSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFN 403 (413)
T ss_pred ccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHH
Confidence 899999999999999999999999999999999999988 8999999999999999999999999999999999999999
Q ss_pred HHHHHHHc
Q 048516 338 VYDMLKSK 345 (389)
Q Consensus 338 vl~~L~~k 345 (389)
+.+.+..+
T Consensus 404 ~~~~~~~~ 411 (413)
T KOG1267|consen 404 VIKKLGVK 411 (413)
T ss_pred HHHHHhcc
Confidence 98876554
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=97.10 E-value=0.0004 Score=42.53 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=26.4
Q ss_pred HHHHcCCCccccCHHhHHHHHHHHhhccCCC
Q 048516 283 SMFRSMPPAFTVSERKIRSVVETLLRRRDVD 313 (389)
Q Consensus 283 ~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~ 313 (389)
.++.++|.+++.|+++|+++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4688999999999889999999999 58874
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.98 E-value=0.00062 Score=41.63 Aligned_cols=28 Identities=32% Similarity=0.449 Sum_probs=14.0
Q ss_pred HHHhcCcccccCchhhhhhHHHHHHHcCC
Q 048516 179 AIKATGWFLRRDLEKTLIPTIDILKNCGV 207 (389)
Q Consensus 179 ~l~~~P~lL~~sle~~l~p~v~~L~~lGv 207 (389)
++.++|++|+.+ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 344555555555 3335555555555554
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=91.25 E-value=1.1 Score=44.07 Aligned_cols=225 Identities=16% Similarity=0.140 Sum_probs=119.8
Q ss_pred HhCCCCHHHHHHHHhcCCccccccc-------ccchhhHHHHHHH--cCCChhhhhhHhhcCcccccccchhhh-HHHHH
Q 048516 95 RESGFSSTHIEKMVAKKPNILLINL-------HNTLKPKIKIFHE--FGFSSSDIVDIISSDPWLLHRSAENQF-QRSFL 164 (389)
Q Consensus 95 ~~lGls~~~i~~iv~~~P~lL~~~~-------~~~L~pkl~fL~s--lG~s~~~i~~iv~~~P~iL~~s~e~~L-~p~~~ 164 (389)
+.+|+..-.+.+.++++|.++..-. --.+.|...-|.+ ..+-.+.-..++.+--.+|-.|.++.| ..++.
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 5799977889999999999886422 1134455444432 222111112333333345555555442 33555
Q ss_pred HHH-HhhCChhHHHHHHHhcCcccccCc---hhhhhhHHHHHHHcCCCchhhhhh-------------c----ccCcEee
Q 048516 165 VLN-SVLGSNAGVCKAIKATGWFLRRDL---EKTLIPTIDILKNCGVSSSQIVKY-------------V----YTYPTFF 223 (389)
Q Consensus 165 fL~-~~g~s~~~v~~~l~~~P~lL~~sl---e~~l~p~v~~L~~lGv~~~~I~~l-------------l----~~~P~il 223 (389)
.++ ++|+.++-...++.++|..+...- ....-.-+.|=.++.++.-+.... - .++|.-+
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G~ 204 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPKGF 204 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCCCc
Confidence 555 688888887888889998886532 001111111111233333221111 1 1222222
Q ss_pred eecchhHHHHHHHHHHhC----------CCCCcccH-HHHH---HHHhcCCHH--HHHHHHHHHH-HcCCCHHHHHHHHH
Q 048516 224 LYKPEKVRCFVQRVDEIG----------FDRNSKMY-LPAI---RTMSSMTKE--KWELKLKLFR-SLGFSEDNILSMFR 286 (389)
Q Consensus 224 ~~s~~~~~~~v~~l~~lG----------~~~~~~~f-~~a~---~~~~~~s~~--~~~~kv~~l~-~~G~s~~~v~~~~~ 286 (389)
.. ..++.+.++.++++- +++++..+ .+|. +-+++++-+ ....++..|+ ++|++ +.+..++.
T Consensus 205 ~l-~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~ 282 (335)
T PF11955_consen 205 RL-KKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLL 282 (335)
T ss_pred cc-cHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHH
Confidence 21 135667777776653 34444333 2333 333443333 3467777788 69998 67789999
Q ss_pred cCCCccccCHHhHHHHHHHHhhccCCChhhHhhCCce
Q 048516 287 SMPPAFTVSERKIRSVVETLLRRRDVDISSIVNNASL 323 (389)
Q Consensus 287 ~~P~iL~~S~~~l~~k~~fL~~~mg~~~~~i~~~P~l 323 (389)
+||.|+.+|.. -+.-.=||.+...-+ .-|-++|.+
T Consensus 283 rHPgIFYvS~k-g~~~TVfLrEAY~~~-~Liek~Pl~ 317 (335)
T PF11955_consen 283 RHPGIFYVSLK-GKRHTVFLREAYDGG-ELIEKHPLV 317 (335)
T ss_pred hCCCeEEEecc-CCceEEEEeeccCCC-CCCCCCchH
Confidence 99999999964 333344666633222 335567766
No 10
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=89.92 E-value=0.39 Score=46.29 Aligned_cols=111 Identities=13% Similarity=0.165 Sum_probs=66.0
Q ss_pred hHHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHHHHhcCCccccc-----c---------ccc
Q 048516 56 LADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEKMVAKKPNILLI-----N---------LHN 121 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~-----~---------~~~ 121 (389)
+|.-++ ..|..+++...|.| ..-.|||..+.||-+ |+....-.......|..... . ++.
T Consensus 138 ~V~~Im-~MGy~re~V~~AlR-----AafNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~ 210 (340)
T KOG0011|consen 138 TVQQIM-EMGYDREEVERALR-----AAFNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQGAVEA 210 (340)
T ss_pred HHHHHH-HhCccHHHHHHHHH-----HhhCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCCccchhh
Confidence 455665 68999999888876 223689999999864 66653111111111111111 1 122
Q ss_pred chhhHHHHHHHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCc
Q 048516 122 TLKPKIKIFHEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGW 185 (389)
Q Consensus 122 ~L~pkl~fL~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~ 185 (389)
.-.+-++||++.- .-.++..+|..||.+|. ..|+.+|..+-.+.+.|..|+.
T Consensus 211 ~~~~~l~fLr~~~-qf~~lR~~iqqNP~ll~-----------~~Lqqlg~~nP~L~q~Iq~nqe 262 (340)
T KOG0011|consen 211 SGGDPLEFLRNQP-QFQQLRQMIQQNPELLH-----------PLLQQLGKQNPQLLQLIQENQE 262 (340)
T ss_pred hcCCchhhhhccH-HHHHHHHHHhhCHHHHH-----------HHHHHHhhhCHHHHHHHHHHHH
Confidence 2223477777431 12567888999998765 3456778777777777777654
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=88.66 E-value=1.3 Score=39.24 Aligned_cols=24 Identities=21% Similarity=0.319 Sum_probs=18.8
Q ss_pred hHHHHHHHcCCChhhhhhHhhcCc
Q 048516 125 PKIKIFHEFGFSSSDIVDIISSDP 148 (389)
Q Consensus 125 pkl~fL~slG~s~~~i~~iv~~~P 148 (389)
-.+..|++.|++-++|..++....
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPG 72 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCC
Confidence 457788899999999988887543
No 12
>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=78.86 E-value=7.1 Score=34.55 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=17.7
Q ss_pred HHHHHHhCCCCHHHHHHHHhcC
Q 048516 90 VLSFLRESGFSSTHIEKMVAKK 111 (389)
Q Consensus 90 vl~~L~~lGls~~~i~~iv~~~ 111 (389)
.+..++++||+-++|..++...
T Consensus 50 ~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 50 QICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHhcC
Confidence 4667789999999999888643
No 13
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=74.71 E-value=5.7 Score=33.76 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHcCCCcc
Q 048516 262 EKWELKLKLFRSLGFSEDNILSMFRSMPPAF 292 (389)
Q Consensus 262 ~~~~~kv~~l~~~G~s~~~v~~~~~~~P~iL 292 (389)
..++.|++||++=|++++||..++.+.+.--
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 4578999999999999999999999877544
No 14
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=72.00 E-value=11 Score=29.76 Aligned_cols=56 Identities=18% Similarity=0.286 Sum_probs=23.2
Q ss_pred hHHHHHHHHhCCCCHHHHHH-----------HHhcCCcccccccccchhhHHHHHH-HcCCChhhhhh
Q 048516 87 SDSVLSFLRESGFSSTHIEK-----------MVAKKPNILLINLHNTLKPKIKIFH-EFGFSSSDIVD 142 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~-----------iv~~~P~lL~~~~~~~L~pkl~fL~-slG~s~~~i~~ 142 (389)
...++.||..+|++...+.+ +|+.+|..|..++..-=-.+++.+. .+|+...+-.|
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~R 75 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPRR 75 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHHH
Confidence 34455556666666544444 4555666666654432223333333 45555544433
No 15
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=71.60 E-value=6.3 Score=25.02 Aligned_cols=24 Identities=29% Similarity=0.529 Sum_probs=18.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 265 ELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 265 ~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
+++++-+.++||+++++..++.++
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356777888888888888777654
No 16
>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=71.52 E-value=5.9 Score=25.38 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=17.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 265 ELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 265 ~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
+.+|+-++++||+++++..++..+
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 356777888888888888877654
No 17
>PF11181 YflT: Heat induced stress protein YflT
Probab=70.36 E-value=28 Score=27.86 Aligned_cols=79 Identities=20% Similarity=0.334 Sum_probs=47.0
Q ss_pred hhhhhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHHHH--HHhCCCCCcccHHHHHHHHhcCCHHHHHHHHH
Q 048516 192 EKTLIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRV--DEIGFDRNSKMYLPAIRTMSSMTKEKWELKLK 269 (389)
Q Consensus 192 e~~l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l--~~lG~~~~~~~f~~a~~~~~~~s~~~~~~kv~ 269 (389)
+..+...|+-|+.-|...++| .+++.+.++....-+.- ...|.. ...|.-.+..+.....+.++.+
T Consensus 9 ~~E~~~~I~~L~~~Gy~~ddI--------~Vva~d~~~~~~l~~~t~~~~~~~~--~~~~~d~~~~~f~~~~d~~~~~-- 76 (103)
T PF11181_consen 9 EEEALSAIEELKAQGYSEDDI--------YVVAKDKDRTERLADQTDTNTVGAS--EESFWDKIKNFFTSGGDELRSK-- 76 (103)
T ss_pred HHHHHHHHHHHHHcCCCcccE--------EEEEcCchHHHHHHHhcCCceeccc--cccHHHHHHHhccCCcHHHHHH--
Confidence 445888999999999999998 45555544443332221 112222 2345555555555455555544
Q ss_pred HHHHcCCCHHHHHH
Q 048516 270 LFRSLGFSEDNILS 283 (389)
Q Consensus 270 ~l~~~G~s~~~v~~ 283 (389)
|.++|++++++..
T Consensus 77 -l~~lGl~~~ea~~ 89 (103)
T PF11181_consen 77 -LESLGLSEDEAER 89 (103)
T ss_pred -HHHcCCCHHHHHH
Confidence 4678999888753
No 18
>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=69.43 E-value=5.9 Score=33.65 Aligned_cols=22 Identities=14% Similarity=0.054 Sum_probs=10.5
Q ss_pred HHHHHHHhhCChhHHHHHHHhc
Q 048516 162 SFLVLNSVLGSNAGVCKAIKAT 183 (389)
Q Consensus 162 ~~~fL~~~g~s~~~v~~~l~~~ 183 (389)
+++||++-|+++++|-.++.+.
T Consensus 26 k~~FL~sKGLt~~EI~~al~~a 47 (136)
T PF04695_consen 26 KIAFLESKGLTEEEIDEALGRA 47 (136)
T ss_dssp HHHHHHHCT--HHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHhc
Confidence 5555555555555555555443
No 19
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=67.74 E-value=8.4 Score=24.55 Aligned_cols=24 Identities=29% Similarity=0.470 Sum_probs=18.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 265 ELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 265 ~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
+++++-+.++||+++++..++..+
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356777888888888888777654
No 20
>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=66.19 E-value=5.2 Score=33.40 Aligned_cols=60 Identities=23% Similarity=0.377 Sum_probs=32.9
Q ss_pred cChHHHHHHHHhCCCCHHHHHHHHhcCCccccc-----ccccchhh--------HHHHHHHcCCChhhhhhHhh
Q 048516 85 ENSDSVLSFLRESGFSSTHIEKMVAKKPNILLI-----NLHNTLKP--------KIKIFHEFGFSSSDIVDIIS 145 (389)
Q Consensus 85 ~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~-----~~~~~L~p--------kl~fL~slG~s~~~i~~iv~ 145 (389)
+.+-.+.+.|+ .|+|.++|..+-.-+|++|.. +.++.|.. .+.-.+.+|||+.+|+++..
T Consensus 11 ~Rlf~i~eAlr-rG~sveeI~e~T~ID~wFL~~i~~Iv~~e~~L~~~~~~~~~~~L~~aK~~GFsD~~IA~l~~ 83 (123)
T PF02787_consen 11 ERLFAIAEALR-RGYSVEEIHELTKIDPWFLEQIKNIVDMEKELKEYLNELDPELLRKAKRLGFSDRQIARLWG 83 (123)
T ss_dssp THHHHHHHHHH-TTB-HHHHHHHH---HHHHHHHHHHHHHHHHHHHHGGG--HHHHHHHHHTT--HHHHHHHHT
T ss_pred cHHHHHHHHHH-cCCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHcCCCHHHHHhccC
Confidence 34455555554 488888888888888887742 22222222 34455578888888888853
No 21
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=62.75 E-value=18 Score=27.07 Aligned_cols=58 Identities=14% Similarity=0.373 Sum_probs=42.2
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChhhhhhH---hhcCcccccc
Q 048516 88 DSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDI---ISSDPWLLHR 153 (389)
Q Consensus 88 ~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~i---v~~~P~iL~~ 153 (389)
+++++.|+++.+|+++|..++... +.+ -.........+|++++.+..+ |-.+|.++.-
T Consensus 2 NPIia~LKehnvsd~qi~elFq~l----T~N----Pl~AMa~i~qLGip~eKLQ~lm~~VMqnP~Like 62 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQAL----TQN----PLAAMATIQQLGIPQEKLQQLMAQVMQNPALIKE 62 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHH----hhC----HHHHHHHHHHcCCCHHHHHHHHHHHhcChHHHHH
Confidence 467899999999999999887542 222 234567888999998876554 5578877653
No 22
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=59.25 E-value=22 Score=27.98 Aligned_cols=47 Identities=15% Similarity=0.289 Sum_probs=28.0
Q ss_pred chhhHHHHHHHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCcccccCchh
Q 048516 122 TLKPKIKIFHEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEK 193 (389)
Q Consensus 122 ~L~pkl~fL~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~ 193 (389)
.+...+.||...|++.....+|+..+- ++...+|+.+|+.|..++.+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg-------------------------~~ai~~l~~nPY~L~~~i~g 53 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYG-------------------------DDAIEILKENPYRLIEDIDG 53 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH--------------------------TTHHHHHHH-STCCCB-SSS
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHh-------------------------HHHHHHHHHChHHHHHHccC
Confidence 355667888899988877666654321 13467888999988886544
No 23
>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=58.58 E-value=14 Score=25.14 Aligned_cols=40 Identities=23% Similarity=0.442 Sum_probs=28.7
Q ss_pred HHcCCCchhhhhhcccCcEeeeecchhHHHHHHHHHHhCCCCC
Q 048516 203 KNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDRN 245 (389)
Q Consensus 203 ~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~~ 245 (389)
+.+|++..-+.+.|...+.+ +++.-+...+.++++|+.|+
T Consensus 7 ~~agvS~~TVSr~ln~~~~v---s~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPPRV---SEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHTSSHHHHHHHHTTCSSS---THHHHHHHHHHHHHHTB-SS
T ss_pred HHHCcCHHHHHHHHhCCCCC---CHHHHHHHHHHHHHHCCCCC
Confidence 55899999998888776533 55666667777888898764
No 24
>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=57.94 E-value=13 Score=30.46 Aligned_cols=55 Identities=15% Similarity=0.208 Sum_probs=30.5
Q ss_pred hHHHhhhccCCCHHHHHHhhccccCCC-CCcChHHHHHHHHhCCCCHHHHHHHHhcC
Q 048516 56 LADYLINRQHFSPESASEASSLNFSLK-DTENSDSVLSFLRESGFSSTHIEKMVAKK 111 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~~~~~l~-~~~~~~~vl~~L~~lGls~~~i~~iv~~~ 111 (389)
++++|. .+|+=.+..-..+.-..++. ....+..+.+-|+..|++...|..++...
T Consensus 14 vi~~l~-~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~~~ 69 (121)
T PF02631_consen 14 VIDRLK-ELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALEEY 69 (121)
T ss_dssp HHHHHH-HTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHTCS
T ss_pred HHHHHH-HcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHHHh
Confidence 677886 57875433321111011222 34557788888999999999888888743
No 25
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=56.69 E-value=41 Score=25.19 Aligned_cols=49 Identities=10% Similarity=0.257 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhc
Q 048516 160 QRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYV 216 (389)
Q Consensus 160 ~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll 216 (389)
.|.+..|++-.+||+++..++.. |+.+ --.-+..+.++|++++.+..++
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~N----Pl~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQN----PLAAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhC----HHHHHHHHHHcCCCHHHHHHHH
Confidence 36677778888888777666543 2222 3344566778888888776554
No 26
>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=56.22 E-value=16 Score=24.89 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhcC
Q 048516 88 DSVLSFLRESGFSSTHIEKMVAKK 111 (389)
Q Consensus 88 ~~vl~~L~~lGls~~~i~~iv~~~ 111 (389)
+.+++-|.++|++..++.+++.+-
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 456777888899988888888764
No 27
>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=54.91 E-value=29 Score=27.97 Aligned_cols=21 Identities=10% Similarity=0.166 Sum_probs=15.1
Q ss_pred CChhHHHHHHHhcCcccccCc
Q 048516 171 GSNAGVCKAIKATGWFLRRDL 191 (389)
Q Consensus 171 ~s~~~v~~~l~~~P~lL~~sl 191 (389)
.+++++..++..+|.++...+
T Consensus 71 ~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhHHHHHHHHhChhheeCCE
Confidence 577777888888888777764
No 28
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=53.56 E-value=22 Score=33.75 Aligned_cols=66 Identities=12% Similarity=0.142 Sum_probs=48.8
Q ss_pred CHHHHHHHHHHHH-HcCC-CHHHHHHHHHcCCCccccCHHhHHHHHHHHhhccCCChh-hHhhCCceee
Q 048516 260 TKEKWELKLKLFR-SLGF-SEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVDIS-SIVNNASLFL 325 (389)
Q Consensus 260 s~~~~~~kv~~l~-~~G~-s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~~~-~i~~~P~lL~ 325 (389)
..-++++++.|.- ..|+ +.-.|.+=+.-.|.+++++.++++.+.+-|.+-+|+++. +.-++|.=|+
T Consensus 69 d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLS 137 (309)
T COG1125 69 DPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELS 137 (309)
T ss_pred CHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcC
Confidence 3456778888765 5653 444566667788999999999999999999999999985 4445555443
No 29
>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=53.45 E-value=35 Score=37.25 Aligned_cols=79 Identities=18% Similarity=0.262 Sum_probs=50.4
Q ss_pred hHHHhhhc--cCCCHHHHHHhhccccCCCCC----cChHHHHHHHHh-CCCCHHHHHHHHhcCCcccccccccchhhHHH
Q 048516 56 LADYLINR--QHFSPESASEASSLNFSLKDT----ENSDSVLSFLRE-SGFSSTHIEKMVAKKPNILLINLHNTLKPKIK 128 (389)
Q Consensus 56 ~~~yLi~s--~Gls~~~a~~~s~~~~~l~~~----~~~~~vl~~L~~-lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~ 128 (389)
++.||-+. -|+-+..|.++.. .+--+.- ++|+ -|.. -|++...+.++...+.. .+.....+.
T Consensus 80 i~~yL~s~~~~GIG~~~A~~iv~-~fg~~~~~~i~~~~~----~L~~v~gi~~~~~~~i~~~~~~------~~~~~~~~~ 148 (720)
T TIGR01448 80 IVAYLSSRSIKGVGKKLAQRIVK-TFGEAAFDVLDDDPE----KLLEVPGISKANLEKFVSQWSQ------QGDERRLLA 148 (720)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHH-HhCHhHHHHHHhCHH----HHhcCCCCCHHHHHHHHHHHHH------hHHHHHHHH
Confidence 77888632 5778888888765 2221111 2233 2333 48998888888887622 123567788
Q ss_pred HHHHcCCChhhhhhHhh
Q 048516 129 IFHEFGFSSSDIVDIIS 145 (389)
Q Consensus 129 fL~slG~s~~~i~~iv~ 145 (389)
||.++|++.....+|..
T Consensus 149 ~L~~~gi~~~~a~ki~~ 165 (720)
T TIGR01448 149 GLQGLGIGIKLAQRIYK 165 (720)
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 99999999876666544
No 30
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=52.81 E-value=30 Score=29.87 Aligned_cols=114 Identities=15% Similarity=0.195 Sum_probs=66.0
Q ss_pred cccCcEeeeecchhHHHHHHHHHHhCCCCCcccHHHHHHHHhcCCHHHHHHHHHHHH-HcCCC------HHHHHHHHHcC
Q 048516 216 VYTYPTFFLYKPEKVRCFVQRVDEIGFDRNSKMYLPAIRTMSSMTKEKWELKLKLFR-SLGFS------EDNILSMFRSM 288 (389)
Q Consensus 216 l~~~P~il~~s~~~~~~~v~~l~~lG~~~~~~~f~~a~~~~~~~s~~~~~~kv~~l~-~~G~s------~~~v~~~~~~~ 288 (389)
-...|..+.++++.+++.+-.+.+-|++++.+..+ |+ +.|+. ...|.+++..+
T Consensus 19 ~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~--------------------LRD~~gip~Vk~vtG~ki~~iLk~~ 78 (151)
T PRK08561 19 RTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGII--------------------LRDQYGIPDVKLITGKKITEILEEN 78 (151)
T ss_pred CCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhh--------------------HhhccCCCceeeeccchHHHHHHHc
Confidence 34566677777777777777777777777553221 11 12221 23344444444
Q ss_pred CCccccCHH--hHHHHHHHHhhccCCChhhHhhCCceeecCCCCccchHHHHHHHHHHcCcccCCCCc
Q 048516 289 PPAFTVSER--KIRSVVETLLRRRDVDISSIVNNASLFLCSIESNLKPRMRVYDMLKSKNLLRRKTGL 354 (389)
Q Consensus 289 P~iL~~S~~--~l~~k~~fL~~~mg~~~~~i~~~P~lL~~Sle~ri~PR~~vl~~L~~kGl~~~~~~l 354 (389)
-.---+.+| .|..++.-|.+++.-...|....=.+ ..-+--|.+.++|++.++.+-.++.+
T Consensus 79 gl~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~skRgL-----~~~~skrrRLl~Yyk~~~~LP~~WkY 141 (151)
T PRK08561 79 GLAPEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGL-----QLIESKIRRLVKYYKRTGVLPADWRY 141 (151)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHhCCCcchhHHHH-----HHHHHHHHHHHHHHHhcCCCCCCCcC
Confidence 333334444 47777888888777777765432122 21233466888999999887656555
No 31
>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=51.63 E-value=24 Score=35.32 Aligned_cols=45 Identities=16% Similarity=0.286 Sum_probs=35.7
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHcCCCccccCHHhHHHHHHHHhhccCCC
Q 048516 260 TKEKWELKLKLFRSLGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRRDVD 313 (389)
Q Consensus 260 s~~~~~~kv~~l~~~G~s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~mg~~ 313 (389)
+.+..+..|+-+.+|||.+++|..+++. +-.+=.+.+|||.. |++
T Consensus 152 ~g~~~e~~I~~i~eMGf~R~qV~~ALRA-------afNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 152 VGSERETTIEEIMEMGYEREEVERALRA-------AFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred cchHHHHHHHHHHHhCCCHHHHHHHHHH-------HhCCHHHHHHHHHh--CCC
Confidence 3457788899999999999999888874 44455688999996 777
No 32
>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=51.05 E-value=75 Score=31.30 Aligned_cols=93 Identities=18% Similarity=0.324 Sum_probs=55.1
Q ss_pred HcCCCchhhhhhcccCcEeeeecch--------hHHHHHHHH--HHhCCCC-CcccHHHHHHHHhcCCHHH--HHHHHHH
Q 048516 204 NCGVSSSQIVKYVYTYPTFFLYKPE--------KVRCFVQRV--DEIGFDR-NSKMYLPAIRTMSSMTKEK--WELKLKL 270 (389)
Q Consensus 204 ~lGv~~~~I~~ll~~~P~il~~s~~--------~~~~~v~~l--~~lG~~~-~~~~f~~a~~~~~~~s~~~--~~~kv~~ 270 (389)
.+|++...+..++.++|.+|..... ++.+....+ +|..+-. .+...+..+.-++.+|.+. --.|++.
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~ 125 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAH 125 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHH
Confidence 3777667777777777777755320 122222221 1111111 1123444555555554443 3678888
Q ss_pred HH-HcCCCHHHHHHHHHcCCCccccCH
Q 048516 271 FR-SLGFSEDNILSMFRSMPPAFTVSE 296 (389)
Q Consensus 271 l~-~~G~s~~~v~~~~~~~P~iL~~S~ 296 (389)
++ .+|++++=...++.+||+.+....
T Consensus 126 l~~dLGLP~Df~~~lv~~yP~~Frvv~ 152 (335)
T PF11955_consen 126 LRRDLGLPDDFRDSLVPKYPDYFRVVD 152 (335)
T ss_pred HHHHcCCChhhccchhhhCCCCcEEee
Confidence 88 799999988899999999887754
No 33
>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=49.37 E-value=31 Score=23.38 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=19.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 264 WELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 264 ~~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
+++-++-|..+||++.++..++.+-
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4556778889999999998888765
No 34
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=48.94 E-value=40 Score=27.75 Aligned_cols=27 Identities=15% Similarity=0.256 Sum_probs=13.0
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHhcCC
Q 048516 86 NSDSVLSFLRESGFSSTHIEKMVAKKP 112 (389)
Q Consensus 86 ~~~~vl~~L~~lGls~~~i~~iv~~~P 112 (389)
....+...|+.+|++..++..++.-.|
T Consensus 56 ~i~~~~~~L~~~~L~k~E~~~i~Nl~P 82 (118)
T smart00657 56 IVRAVRTLLKSKKLHKFEIAQLGNLRP 82 (118)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCC
Confidence 333444444455555555555554444
No 35
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=48.25 E-value=34 Score=30.05 Aligned_cols=49 Identities=10% Similarity=0.188 Sum_probs=30.7
Q ss_pred hhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHHHHHHhCCCC
Q 048516 195 LIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDR 244 (389)
Q Consensus 195 l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~ 244 (389)
++..+++|.++-- ..-.++-+...|-+.+.+.+.+...++..++-|+++
T Consensus 50 ~k~Il~aL~e~e~-~~ita~~iM~spvv~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 50 VKRILEALEEAEK-TRITAKTIMHSPVVSVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred HHHHHHHHHHhhc-ceEeHhhhccCCeeEECchhhHHHHHHHHHHcCCcc
Confidence 5555666665422 222344556667777766677777777777778776
No 36
>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=48.16 E-value=33 Score=22.68 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=23.7
Q ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHHcCCCcc
Q 048516 262 EKWELKLKLFR-SLGFSEDNILSMFRSMPPAF 292 (389)
Q Consensus 262 ~~~~~kv~~l~-~~G~s~~~v~~~~~~~P~iL 292 (389)
+++-.....|+ ++|++.....++|..+|.|-
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~Cq 37 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKCQ 37 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCHH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHHh
Confidence 45667778888 79999999999999999873
No 37
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=45.36 E-value=33 Score=32.72 Aligned_cols=51 Identities=24% Similarity=0.342 Sum_probs=34.2
Q ss_pred hhhhHHHHHHHcCCCchhhhhhcccCcE----eeeecchhHHHHHHHHHHhCCCC
Q 048516 194 TLIPTIDILKNCGVSSSQIVKYVYTYPT----FFLYKPEKVRCFVQRVDEIGFDR 244 (389)
Q Consensus 194 ~l~p~v~~L~~lGv~~~~I~~ll~~~P~----il~~s~~~~~~~v~~l~~lG~~~ 244 (389)
.+...++=|++.|++-=-|.+.++-... .=...++.|+..-+...+|||..
T Consensus 229 Ev~e~m~DLr~~gvdilTiGQYlqPS~~HlpV~ryv~PeeF~~~~~~a~~~GF~~ 283 (306)
T COG0320 229 EVIEVMDDLRSAGVDILTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLH 283 (306)
T ss_pred HHHHHHHHHHHcCCCEEEeccccCCccccCCceeccCHHHHHHHHHHHHHccchh
Confidence 3666667777788887777776654322 22345777888777778888853
No 38
>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=45.30 E-value=42 Score=27.96 Aligned_cols=67 Identities=24% Similarity=0.336 Sum_probs=32.8
Q ss_pred hhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHH---HHHHhCCCCCcccHHHHHHHHhcCCHHHHHHHHHHH
Q 048516 195 LIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQ---RVDEIGFDRNSKMYLPAIRTMSSMTKEKWELKLKLF 271 (389)
Q Consensus 195 l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~---~l~~lG~~~~~~~f~~a~~~~~~~s~~~~~~kv~~l 271 (389)
+--..+.|+ -|++-++|..+-.-.|+.|. ++++.++ .+++.+ .+.-...+.-.
T Consensus 13 lf~i~eAlr-rG~sveeI~e~T~ID~wFL~----~i~~Iv~~e~~L~~~~-------------------~~~~~~~L~~a 68 (123)
T PF02787_consen 13 LFAIAEALR-RGYSVEEIHELTKIDPWFLE----QIKNIVDMEKELKEYL-------------------NELDPELLRKA 68 (123)
T ss_dssp HHHHHHHHH-TTB-HHHHHHHH---HHHHH----HHHHHHHHHHHHHHHG-------------------GG--HHHHHHH
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCccHHHHH----HHHHHHHHHHHHHHhh-------------------ccchHHHHHHH
Confidence 333444443 48888888877666666543 3444433 232221 11112344556
Q ss_pred HHcCCCHHHHHHHH
Q 048516 272 RSLGFSEDNILSMF 285 (389)
Q Consensus 272 ~~~G~s~~~v~~~~ 285 (389)
+++|||+.+|+.+.
T Consensus 69 K~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 69 KRLGFSDRQIARLW 82 (123)
T ss_dssp HHTT--HHHHHHHH
T ss_pred HHcCCCHHHHHhcc
Confidence 78999999998875
No 39
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=45.09 E-value=30 Score=29.03 Aligned_cols=65 Identities=17% Similarity=0.306 Sum_probs=41.0
Q ss_pred eecchhHHHHHHHHHHhCCCCC---cccHHHHH-H-H----HhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 224 LYKPEKVRCFVQRVDEIGFDRN---SKMYLPAI-R-T----MSSMTKEKWELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 224 ~~s~~~~~~~v~~l~~lG~~~~---~~~f~~a~-~-~----~~~~s~~~~~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
+.|+..+.+....|++.|+-.. ..+|+..- . . -.....+.+++-|+-.+.+|+|.+++..++...
T Consensus 46 ~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~s~eei~~~~~~~ 119 (125)
T COG1725 46 GVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLSLEEILELLKEI 119 (125)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3345667777777888787543 33454421 0 1 122234556667777788999999999888753
No 40
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=43.39 E-value=72 Score=32.53 Aligned_cols=136 Identities=14% Similarity=0.145 Sum_probs=69.4
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChhhhh-hHhhcCccc-----ccccch-hh
Q 048516 86 NSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSSDIV-DIISSDPWL-----LHRSAE-NQ 158 (389)
Q Consensus 86 ~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~-~iv~~~P~i-----L~~s~e-~~ 158 (389)
-+|..++.+-++||.+.+-+..++.+-. ++..-++|+.+.--..++.. +-..+--.+ +.-+.. +-
T Consensus 302 i~d~~lsllv~mGfeesdaRlaLRsc~g--------~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~k~~n~~~~~w 373 (568)
T KOG2561|consen 302 INDETLSLLVGMGFEESDARLALRSCNG--------DVDSAVQFIIERREKLAQKREKDLAREREILERKKYGNTPMKKW 373 (568)
T ss_pred ccchHHHHHHHcCCCchHHHHHHHhccc--------cHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCcccc
Confidence 3566788888899998888887776643 45556666664321111111 000000011 111000 11
Q ss_pred -hHHHHHHHHHhhCChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHHHH
Q 048516 159 -FQRSFLVLNSVLGSNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRV 237 (389)
Q Consensus 159 -L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l 237 (389)
....+.+|.+.|.+..-+..++.++ ++.+...++.|+. +.+++..-....|.- -....+..+
T Consensus 374 vn~rs~~rL~~mGyer~la~eaL~r~--------~Ndi~~aldllq~---esdel~~n~~~~p~~------vd~~~la~L 436 (568)
T KOG2561|consen 374 VNPRSLERLVSMGYERELAAEALRRN--------ENDIQKALDLLQD---ESDELESNKPKRPEQ------VDGISLAEL 436 (568)
T ss_pred cCHHHHHHHHhcchHhHHHHHHHHhc--------cCcHHHHHHhcCC---cchhhhccCCCCCcc------cchhhHHHH
Confidence 2336778888888777777777663 2224444444432 222232222222211 124567788
Q ss_pred HHhCCCCCc
Q 048516 238 DEIGFDRNS 246 (389)
Q Consensus 238 ~~lG~~~~~ 246 (389)
..|||+..+
T Consensus 437 v~mGF~e~~ 445 (568)
T KOG2561|consen 437 VSMGFEEGK 445 (568)
T ss_pred HHhccccch
Confidence 888888764
No 41
>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=42.34 E-value=37 Score=27.59 Aligned_cols=32 Identities=16% Similarity=0.349 Sum_probs=21.0
Q ss_pred CCCcChHHHHHHHHhCCCCHHHHHHHHhcCCc
Q 048516 82 KDTENSDSVLSFLRESGFSSTHIEKMVAKKPN 113 (389)
Q Consensus 82 ~~~~~~~~vl~~L~~lGls~~~i~~iv~~~P~ 113 (389)
.+++.....+..|..+|++..++..|+--.|.
T Consensus 54 ~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~ 85 (117)
T PF03874_consen 54 QNPESIKELREELKKFGLTEFEILQIINLRPT 85 (117)
T ss_dssp SSHHHHHHHHHHHTTSTS-HHHHHHHHHH--S
T ss_pred CCHHHHHHHHHHHhcccCCHHHHHHHhcCCCC
Confidence 34445666677777888888888888877774
No 42
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=42.26 E-value=30 Score=25.42 Aligned_cols=40 Identities=18% Similarity=0.293 Sum_probs=28.8
Q ss_pred HHcCCCchhhhhhcccCcEeeeecchhHHHHHHHHHHhCCCCC
Q 048516 203 KNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDRN 245 (389)
Q Consensus 203 ~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~~ 245 (389)
+.+|++..-|.+++...+.+ +++..+...+.++++|+.++
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 44788888888887766554 45666667777888888764
No 43
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=39.00 E-value=72 Score=28.65 Aligned_cols=25 Identities=12% Similarity=0.070 Sum_probs=14.8
Q ss_pred hHHHHHHHHHhhCChhHHHHHHHhc
Q 048516 159 FQRSFLVLNSVLGSNAGVCKAIKAT 183 (389)
Q Consensus 159 L~p~~~fL~~~g~s~~~v~~~l~~~ 183 (389)
+..-+.+|.++|.+..++.+++...
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3445566666666666666666554
No 44
>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=38.00 E-value=44 Score=33.50 Aligned_cols=114 Identities=11% Similarity=0.156 Sum_probs=67.4
Q ss_pred hHHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHH-----------H-----HhcCCccccccc
Q 048516 56 LADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEK-----------M-----VAKKPNILLINL 119 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~-----------i-----v~~~P~lL~~~~ 119 (389)
+|.-++ +.||.++++..|-| . .-.|||..++||-. |+... +.. . -...|.++-...
T Consensus 159 ~I~~i~-eMGf~R~qV~~ALR--A---afNNPdRAVEYL~t-GIP~~-~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~a~ 230 (378)
T TIGR00601 159 TIEEIM-EMGYEREEVERALR--A---AFNNPDRAVEYLLT-GIPED-PEQPEPVQQTAASTAAATTETPQHGSVFEQAA 230 (378)
T ss_pred HHHHHH-HhCCCHHHHHHHHH--H---HhCCHHHHHHHHHh-CCCcc-ccccccCCCcccccccccCCCCCCcchhhhhh
Confidence 566776 69999999988866 2 23689999999964 66632 100 0 000000000000
Q ss_pred --c--c------chhhHHHHHHHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCccccc
Q 048516 120 --H--N------TLKPKIKIFHEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRR 189 (389)
Q Consensus 120 --~--~------~L~pkl~fL~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~ 189 (389)
. . .=..-++||++.= .-.+++.+|..+|.+|-.= |+.+|.++-++..+|..||.-|..
T Consensus 231 ~~~~~~~~~~~~~g~~~l~~Lr~~p-qf~~lR~~vq~NP~~L~~l-----------Lqql~~~nP~l~q~I~~n~e~Fl~ 298 (378)
T TIGR00601 231 QGGTEQPATEAAQGGNPLEFLRNQP-QFQQLRQVVQQNPQLLPPL-----------LQQIGQENPQLLQQISQHPEQFLQ 298 (378)
T ss_pred cccccccccccccCCchHHHhhcCH-HHHHHHHHHHHCHHHHHHH-----------HHHHHhhCHHHHHHHHHCHHHHHH
Confidence 0 0 0011356666321 1256889999999998862 556777778888888888875543
No 45
>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=34.02 E-value=18 Score=26.24 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=0.0
Q ss_pred hcCCcccccccccchhhHHHHHHHcCCChhhhhhHhh
Q 048516 109 AKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDIIS 145 (389)
Q Consensus 109 ~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv~ 145 (389)
+..|.-+..+++ ++...+--|...|+++++|+-++.
T Consensus 20 ~~~P~W~~~~~~-eVe~~I~klakkG~tpSqIG~iLR 55 (60)
T PF08069_consen 20 RSPPSWLKYSPE-EVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_dssp SS--TT--S-HH-HHHHHHHHHCCTTHCHHHHHHHHH
T ss_pred CCCCCCcCCCHH-HHHHHHHHHHHcCCCHHHhhhhhh
No 46
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=32.92 E-value=53 Score=25.26 Aligned_cols=38 Identities=24% Similarity=0.265 Sum_probs=19.2
Q ss_pred HHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHH
Q 048516 93 FLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHE 132 (389)
Q Consensus 93 ~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~s 132 (389)
-|+..||+.++|..+=..+-.+.... .++...++.+.+
T Consensus 22 GLrR~Gfs~~~i~~l~~ayr~l~~~~--~~~~~a~~~l~~ 59 (83)
T PF13720_consen 22 GLRRRGFSKEEISALRRAYRILFRSG--LTLEEALEELEE 59 (83)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHHHTSS--S-HHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhCC--CCHHHHHHHHHH
Confidence 35666777766666555554333332 245555555554
No 47
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=32.77 E-value=82 Score=30.20 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHc
Q 048516 262 EKWELKLKLFRSLGFSEDNILSMFRS 287 (389)
Q Consensus 262 ~~~~~kv~~l~~~G~s~~~v~~~~~~ 287 (389)
.-+..|.+||++=|++++||..++++
T Consensus 20 aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 20 APLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred chHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 45789999999999999999999987
No 48
>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=32.64 E-value=69 Score=35.03 Aligned_cols=76 Identities=14% Similarity=0.123 Sum_probs=42.4
Q ss_pred cCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHHH-----------HHhcCCcccccccccchhhHHHHHH-
Q 048516 64 QHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIEK-----------MVAKKPNILLINLHNTLKPKIKIFH- 131 (389)
Q Consensus 64 ~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~~-----------iv~~~P~lL~~~~~~~L~pkl~fL~- 131 (389)
-|++++.+.++...+ ........++.||.++|++...+.+ +++.+|..|..++..-=-..++.+.
T Consensus 123 ~gi~~~~~~~i~~~~---~~~~~~~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~ 199 (720)
T TIGR01448 123 PGISKANLEKFVSQW---SQQGDERRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQ 199 (720)
T ss_pred CCCCHHHHHHHHHHH---HHhHHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHH
Confidence 355555555554312 1122356778999999999765544 5667888777654421112233332
Q ss_pred HcCCChhhhhh
Q 048516 132 EFGFSSSDIVD 142 (389)
Q Consensus 132 slG~s~~~i~~ 142 (389)
.+|+.+.+-.|
T Consensus 200 ~~g~~~~d~~R 210 (720)
T TIGR01448 200 ALGIALNDPRR 210 (720)
T ss_pred HcCCCCCCHHH
Confidence 56666554444
No 49
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=31.94 E-value=1.5e+02 Score=27.01 Aligned_cols=86 Identities=13% Similarity=0.062 Sum_probs=38.6
Q ss_pred cccccccccchhhH--HHHHH-HcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHHHhcCccccc
Q 048516 113 NILLINLHNTLKPK--IKIFH-EFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAIKATGWFLRR 189 (389)
Q Consensus 113 ~lL~~~~~~~L~pk--l~fL~-slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l~~~P~lL~~ 189 (389)
.++..|.|.||... ++++. ..|. ..++..+..+...... +.+..+..++.+|+ |.+.+.+..+...++.+...
T Consensus 6 ~L~vFD~D~TLi~~~~~~~~~~~~g~-~~~v~~~t~~~~~~~~-~~~~~~~~~v~~l~--g~~~~~v~~~~~~~~~l~~g 81 (212)
T COG0560 6 KLAVFDLDGTLINAELIDELARGAGV-GEEVLAITERAMRGEL-DFEESLRLRVALLK--GLPVEVLEEVREEFLRLTPG 81 (212)
T ss_pred ceEEEecccchhhHHHHHHHHHHhCC-HHHHHHHHHHHhcccc-cHHHHHHHHHHHhC--CCCHHHHHHHHHhcCcCCcc
Confidence 45556666666661 23333 2332 3344444444433322 33444444444443 23344444444444332221
Q ss_pred CchhhhhhHHHHHHHcCC
Q 048516 190 DLEKTLIPTIDILKNCGV 207 (389)
Q Consensus 190 sle~~l~p~v~~L~~lGv 207 (389)
....++++++.|.
T Consensus 82 -----a~elv~~lk~~G~ 94 (212)
T COG0560 82 -----AEELVAALKAAGA 94 (212)
T ss_pred -----HHHHHHHHHHCCC
Confidence 3455666666654
No 50
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=31.73 E-value=1.9e+02 Score=22.21 Aligned_cols=35 Identities=17% Similarity=0.334 Sum_probs=18.3
Q ss_pred HHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHh
Q 048516 131 HEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSV 169 (389)
Q Consensus 131 ~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~ 169 (389)
+.+|+|.++|.+|-..+|. ++..++...+.-|+.-
T Consensus 21 r~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~r 55 (83)
T cd08319 21 LDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQR 55 (83)
T ss_pred HHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHh
Confidence 3566666666666666553 2333444444445443
No 51
>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=31.26 E-value=66 Score=19.87 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHc
Q 048516 263 KWELKLKLFRSLGFSEDNILSMFRS 287 (389)
Q Consensus 263 ~~~~kv~~l~~~G~s~~~v~~~~~~ 287 (389)
.|..=+.--++.|+|.+||+..+..
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 4555555566789999998776543
No 52
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=31.16 E-value=60 Score=29.18 Aligned_cols=26 Identities=8% Similarity=0.256 Sum_probs=22.0
Q ss_pred hhhHHHHHHHcCCChhhhhhHhhcCc
Q 048516 123 LKPKIKIFHEFGFSSSDIVDIISSDP 148 (389)
Q Consensus 123 L~pkl~fL~slG~s~~~i~~iv~~~P 148 (389)
+...+.+|.++|+++.++.+++...-
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~~ 174 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKIL 174 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 56778899999999999999988763
No 53
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=30.72 E-value=93 Score=29.87 Aligned_cols=66 Identities=9% Similarity=0.144 Sum_probs=44.2
Q ss_pred hHHHHHHHHhhccCCChhhHhhCCceeecCCCCccchHHHHHHHHHHcCcccCCCCchhhhcccHhhHHHhhcc
Q 048516 298 KIRSVVETLLRRRDVDISSIVNNASLFLCSIESNLKPRMRVYDMLKSKNLLRRKTGLATVCKLSKGKFLEKYVL 371 (389)
Q Consensus 298 ~l~~k~~fL~~~mg~~~~~i~~~P~lL~~Sle~ri~PR~~vl~~L~~kGl~~~~~~l~~~l~~se~~F~~k~v~ 371 (389)
-++.+++.+.+ .|++.+.|+--|. +++. |....-+.+++.+.. ++ ...+.-++..|.|.|...+..
T Consensus 164 ~l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~---l~-~lg~Pilvg~SRKsfig~~~~ 229 (282)
T PRK11613 164 YFIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAE---FH-HFNLPLLVGMSRKSMIGQLLN 229 (282)
T ss_pred HHHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHH---HH-hCCCCEEEEecccHHHHhhcC
Confidence 45667777776 7999999888885 4553 455555666554433 11 234556789999999987764
No 54
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=29.91 E-value=56 Score=29.30 Aligned_cols=46 Identities=30% Similarity=0.278 Sum_probs=35.7
Q ss_pred HHHHHHHcCcccCCC----CchhhhcccHhhHHHhhccCCCCcccccccc
Q 048516 338 VYDMLKSKNLLRRKT----GLATVCKLSKGKFLEKYVLPYQDELGDLSFL 383 (389)
Q Consensus 338 vl~~L~~kGl~~~~~----~l~~~l~~se~~F~~k~v~~~~e~~p~l~~~ 383 (389)
+++-|+.+|+++... .=...+..+-+.|++.|....-++.|.+.++
T Consensus 123 ~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~Fl~~fGl~sl~eLp~~~~~ 172 (184)
T COG1386 123 VISTLLERGLIREVGRRDTPGRPYLYGTTEKFLDYFGLDSLDELPDLEEL 172 (184)
T ss_pred HHHHHHHCCCeEecCCCCCCCCceeeeccHHHHHHhCccccccccCcchh
Confidence 567788999986422 3335667778999999999999999998874
No 55
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.87 E-value=89 Score=23.04 Aligned_cols=28 Identities=25% Similarity=0.592 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 261 KEKWELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 261 ~~~~~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
.+.+..-++.++.+||++++|...+.+-
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~L 35 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNL 35 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4556666777778888888876666543
No 56
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=29.64 E-value=98 Score=23.89 Aligned_cols=22 Identities=32% Similarity=0.496 Sum_probs=14.0
Q ss_pred HHHHHhCCCCHHHHHHHHhcCC
Q 048516 91 LSFLRESGFSSTHIEKMVAKKP 112 (389)
Q Consensus 91 l~~L~~lGls~~~i~~iv~~~P 112 (389)
-.+-+.+|+++.+|..+-..+|
T Consensus 17 k~laR~LGlse~~Id~i~~~~~ 38 (86)
T cd08306 17 RKLARKLGLSETKIESIEEAHP 38 (86)
T ss_pred HHHHHHcCCCHHHHHHHHHHCC
Confidence 3444666777777766666666
No 57
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=29.38 E-value=2.7e+02 Score=24.65 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=15.0
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHh
Q 048516 86 NSDSVLSFLRESGFSSTHIEKMVA 109 (389)
Q Consensus 86 ~~~~vl~~L~~lGls~~~i~~iv~ 109 (389)
.|..+.+=|...|++++.|..++.
T Consensus 86 G~~rl~qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 86 GPARLKQELKQKGIDDEIIEEALE 109 (174)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHHh
Confidence 355555666666777666666665
No 58
>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=29.33 E-value=79 Score=21.19 Aligned_cols=40 Identities=20% Similarity=0.372 Sum_probs=25.7
Q ss_pred HHcCCCchhhhhhcccCcEeeeecchhHHHHHHHHHHhCCCCC
Q 048516 203 KNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQRVDEIGFDRN 245 (389)
Q Consensus 203 ~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~l~~lG~~~~ 245 (389)
+.+|++...|.+++...+ ..+.+......+.+.++|+.++
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 347888888887776655 2234455556666777777654
No 59
>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=29.31 E-value=1.8e+02 Score=23.19 Aligned_cols=27 Identities=30% Similarity=0.569 Sum_probs=21.0
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCCc
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKPN 113 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P~ 113 (389)
+..+-.|-+.+|+|+.+|..+...+|.
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~ 46 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQ 46 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCC
Confidence 445677778888888888888888775
No 60
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=28.41 E-value=85 Score=26.41 Aligned_cols=72 Identities=17% Similarity=0.098 Sum_probs=0.0
Q ss_pred hcCCcccccccccchhhHHHHHHHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhC---ChhHHHHHHHh
Q 048516 109 AKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLG---SNAGVCKAIKA 182 (389)
Q Consensus 109 ~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~---s~~~v~~~l~~ 182 (389)
+..|.-|..++| ++..-+--|...|++++||+-++.-.-.|=..+.- +=...+.+|++-|+ -.+++-.++++
T Consensus 20 r~~PtWlK~~~d-dvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v-~G~kI~Rilk~~Gl~PeiPeDLy~likk 94 (151)
T KOG0400|consen 20 RSVPTWLKLTAD-DVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFV-TGNKILRILKSNGLAPEIPEDLYHLIKK 94 (151)
T ss_pred cCCcHHHhcCHH-HHHHHHHHHHHcCCChhHceeeeecccCcchhhee-chhHHHHHHHHcCCCCCCcHHHHHHHHH
No 61
>PRK10026 arsenate reductase; Provisional
Probab=28.09 E-value=1.7e+02 Score=25.05 Aligned_cols=17 Identities=18% Similarity=0.419 Sum_probs=11.2
Q ss_pred hhhHHHHHHHcCCCchh
Q 048516 195 LIPTIDILKNCGVSSSQ 211 (389)
Q Consensus 195 l~p~v~~L~~lGv~~~~ 211 (389)
.+.-++||++.|++-+.
T Consensus 15 ~RKA~~wL~~~gi~~~~ 31 (141)
T PRK10026 15 SRNTLEMIRNSGTEPTI 31 (141)
T ss_pred HHHHHHHHHHCCCCcEE
Confidence 56667777777776543
No 62
>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=28.08 E-value=1.6e+02 Score=23.35 Aligned_cols=26 Identities=27% Similarity=0.335 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhcCCc
Q 048516 88 DSVLSFLRESGFSSTHIEKMVAKKPN 113 (389)
Q Consensus 88 ~~vl~~L~~lGls~~~i~~iv~~~P~ 113 (389)
+.+-.+.+.+|+|+.+|..+-..+|.
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~ 45 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERV 45 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCC
Confidence 55666778888888888888888875
No 63
>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=27.64 E-value=1.8e+02 Score=22.40 Aligned_cols=46 Identities=15% Similarity=0.271 Sum_probs=31.9
Q ss_pred hhhHHH-HHHHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCC
Q 048516 123 LKPKIK-IFHEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGS 172 (389)
Q Consensus 123 L~pkl~-fL~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s 172 (389)
+.+.-. +-+.+|+|..+|-.+-..+|. ++.......+..|+.-.+.
T Consensus 12 lG~~Wk~laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g~ 58 (86)
T cd08306 12 VGRDWRKLARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKKK 58 (86)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHCc
Confidence 444433 445899999999999999983 4445667777777765553
No 64
>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=27.41 E-value=87 Score=24.02 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=21.7
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCC
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKP 112 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P 112 (389)
+..+-.|.+.+|+|+.+|..|-..+|
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 45677888999999999998888776
No 65
>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=26.87 E-value=2.5e+02 Score=22.72 Aligned_cols=57 Identities=12% Similarity=0.283 Sum_probs=26.7
Q ss_pred chhHHHHHHHHHHhCCCCCcc---cHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHH
Q 048516 227 PEKVRCFVQRVDEIGFDRNSK---MYLPAIRTMSSMTKEKWELKLKLFRSLGFSEDNILSMFR 286 (389)
Q Consensus 227 ~~~~~~~v~~l~~lG~~~~~~---~f~~a~~~~~~~s~~~~~~kv~~l~~~G~s~~~v~~~~~ 286 (389)
.+.+...++.+.+.|+-.+.. .|+..-......++..+. .-|+.-|++.+.|..++.
T Consensus 8 ~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~---~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 8 EEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIR---QKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHH---HHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHH---HHHHHHCCChHHHHHHHH
Confidence 445666777777777763322 222222211222333332 234556888777777665
No 66
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=26.78 E-value=25 Score=26.99 Aligned_cols=48 Identities=19% Similarity=0.436 Sum_probs=35.3
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChhhhhhHhhcCcc
Q 048516 86 NSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDIISSDPW 149 (389)
Q Consensus 86 ~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv~~~P~ 149 (389)
+.+..-++|+.+++...|+ |+++..||- + +.+|+.+.|+.+|+...+.
T Consensus 19 s~eE~~~lL~~y~i~~~qL-------P~I~~~DPv------~---r~~g~k~GdVvkI~R~S~t 66 (79)
T PRK09570 19 SEEEAKKLLKEYGIKPEQL-------PKIKASDPV------V---KAIGAKPGDVIKIVRKSPT 66 (79)
T ss_pred CHHHHHHHHHHcCCCHHHC-------CceeccChh------h---hhcCCCCCCEEEEEECCCC
Confidence 4677888999999999985 555555542 1 3458888899888877654
No 67
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=26.46 E-value=51 Score=24.57 Aligned_cols=21 Identities=19% Similarity=0.069 Sum_probs=17.1
Q ss_pred hHHHhhhccCCCHHHHHHhhc
Q 048516 56 LADYLINRQHFSPESASEASS 76 (389)
Q Consensus 56 ~~~yLi~s~Gls~~~a~~~s~ 76 (389)
.++=|+++||||.++|.-+.+
T Consensus 46 ~~~el~~~CgL~~aEAeLl~~ 66 (70)
T PF10975_consen 46 SVEELMEECGLSRAEAELLLS 66 (70)
T ss_pred CHHHHHHHcCCCHHHHHHHHH
Confidence 578889999999999986543
No 68
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=26.05 E-value=1.1e+02 Score=25.82 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=31.1
Q ss_pred HHHhhhccCCCHHHHHHhhccccCCCCC--cChHHHHHHHHhCCCCHHHHHHHHhc
Q 048516 57 ADYLINRQHFSPESASEASSLNFSLKDT--ENSDSVLSFLRESGFSSTHIEKMVAK 110 (389)
Q Consensus 57 ~~yLi~s~Gls~~~a~~~s~~~~~l~~~--~~~~~vl~~L~~lGls~~~i~~iv~~ 110 (389)
-.|| .-.|++++.+..+..+...|+.- -+-+.+-+.|..+|.+.++.+++.+.
T Consensus 70 ~~WL-~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~~~g~~~EE~rRL~~A 124 (129)
T PF13543_consen 70 RQWL-RVVGLRPESIQAILSKVLTLEALLEMSDEELKEILNRCGAREEECRRLCRA 124 (129)
T ss_pred HHHh-hhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 4566 46777777777664423344321 22345666677777777777766543
No 69
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=25.99 E-value=2.1e+02 Score=22.12 Aligned_cols=36 Identities=25% Similarity=0.157 Sum_probs=19.7
Q ss_pred HHcCCChhhhhhHhhcCcccccccchhhhHHHHHHHHHhh
Q 048516 131 HEFGFSSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVL 170 (389)
Q Consensus 131 ~slG~s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g 170 (389)
+.+|+|.++|-.|-..||. ++.++..-.+..|++-.
T Consensus 23 r~L~vs~~dI~~I~~e~p~----~l~~Q~~~~L~~W~~r~ 58 (84)
T cd08805 23 RELQFSVEDINRIRVENPN----SLLEQSTALLNLWVDRE 58 (84)
T ss_pred HHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhc
Confidence 3566666666666666663 22334444555555543
No 70
>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=25.75 E-value=90 Score=22.20 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=4.4
Q ss_pred HHHHHHHhCCC
Q 048516 233 FVQRVDEIGFD 243 (389)
Q Consensus 233 ~v~~l~~lG~~ 243 (389)
.|+.+..|||+
T Consensus 12 lVd~F~~mGF~ 22 (55)
T PF09288_consen 12 LVDQFENMGFE 22 (55)
T ss_dssp HHHHHHHHT--
T ss_pred HHHHHHHcCCc
Confidence 34445555554
No 71
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=25.38 E-value=1.3e+02 Score=32.56 Aligned_cols=61 Identities=20% Similarity=0.411 Sum_probs=44.5
Q ss_pred HHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHh------CCCCHHHHHHHHhcCCcccccccccchhh
Q 048516 57 ADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRE------SGFSSTHIEKMVAKKPNILLINLHNTLKP 125 (389)
Q Consensus 57 ~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~------lGls~~~i~~iv~~~P~lL~~~~~~~L~p 125 (389)
..|.+ .-+||.+++..-+. .+ +-|++|++||++ -||.+.-=.++++..|+ +...|...+.|
T Consensus 915 AQFMV-qN~Lt~~~~~~rA~-~L-----sFP~SVvdf~qG~iGqP~gGFPEPlRs~VLk~~~r-~~gRPG~~l~p 981 (1176)
T KOG0369|consen 915 AQFMV-QNKLTRDDVERRAE-EL-----SFPKSVVDFFQGLIGQPYGGFPEPLRSKVLKGKPR-LTGRPGAELPP 981 (1176)
T ss_pred HHHHH-hcCCCHHHHHHHhh-hc-----CCcHHHHHHHhcccCCCCCCCCchhHHHHhcCCCc-cCCCCCCcCCc
Confidence 45666 57888888876544 22 348999999986 47877766788888898 66667766666
No 72
>PHA01351 putative minor structural protein
Probab=24.65 E-value=5.8e+02 Score=27.85 Aligned_cols=62 Identities=5% Similarity=0.030 Sum_probs=39.8
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHhcC---Ccccc-ccccc--------chhhHHHHHHHcCCChhhhhhHhhcC
Q 048516 86 NSDSVLSFLRESGFSSTHIEKMVAKK---PNILL-INLHN--------TLKPKIKIFHEFGFSSSDIVDIISSD 147 (389)
Q Consensus 86 ~~~~vl~~L~~lGls~~~i~~iv~~~---P~lL~-~~~~~--------~L~pkl~fL~slG~s~~~i~~iv~~~ 147 (389)
+|+....=|+.+|++++=+..++..+ |.+-. .++-. +..-....|+.+|++++++.-+++.+
T Consensus 642 spkeAitELKKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~y 715 (1070)
T PHA01351 642 DPKEAETELKKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKF 715 (1070)
T ss_pred CHHHHHHHHHHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 35566677888999987666677666 43311 11111 12224568899999999988877765
No 73
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=24.55 E-value=81 Score=28.33 Aligned_cols=47 Identities=23% Similarity=0.207 Sum_probs=36.3
Q ss_pred HHHHHHHHcCcccCC----CCchhhhcccHhhHHHhhccCCCCcccccccc
Q 048516 337 RVYDMLKSKNLLRRK----TGLATVCKLSKGKFLEKYVLPYQDELGDLSFL 383 (389)
Q Consensus 337 ~vl~~L~~kGl~~~~----~~l~~~l~~se~~F~~k~v~~~~e~~p~l~~~ 383 (389)
.+++-|.++|+++.. ..-...+..+-++|++-|....-++.|.+.++
T Consensus 117 ~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~Fl~~FGL~sl~dLP~~~~~ 167 (186)
T TIGR00281 117 QIVDDLVEKGLVVELGRKDTPGRSFIYETTPKFYDYFGIDSLDELPKLEDF 167 (186)
T ss_pred HHHHHHHHCCCeEecCcCCCCCCCeeehhhHHHHHHhCCCCHhhCCCchhh
Confidence 567888999998532 22245677888999999999999999988764
No 74
>PHA02591 hypothetical protein; Provisional
Probab=24.33 E-value=1.2e+02 Score=23.29 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=0.0
Q ss_pred CCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChhhhhhHh
Q 048516 99 FSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDII 144 (389)
Q Consensus 99 ls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv 144 (389)
++.....+++.-.-.--.-..++++.....-|.+.|+|.++|++.+
T Consensus 24 ~~~~~m~k~vqv~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 24 IGEKKMQKVVQVGQTRYFVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred hhhHhHHHhheeCCEEEEEeccchHHHHHHHHHHcCCCHHHHHHHh
No 75
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=24.19 E-value=27 Score=26.46 Aligned_cols=47 Identities=19% Similarity=0.280 Sum_probs=32.0
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCCChhhhhhHhhcCcc
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGFSSSDIVDIISSDPW 149 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv~~~P~ 149 (389)
.+.+-++|+.+|+++.| -|+++..||- + +-+|+.+.|+.+|+...|.
T Consensus 17 ~eE~~~lL~~y~i~~~q-------LP~I~~~DPv------~---r~~g~k~GdVvkI~R~S~t 63 (74)
T PF01191_consen 17 EEEKKELLKKYNIKPEQ-------LPKILSSDPV------A---RYLGAKPGDVVKIIRKSET 63 (74)
T ss_dssp HHHHHHHHHHTT--TTC-------SSEEETTSHH------H---HHTT--TTSEEEEEEEETT
T ss_pred HHHHHHHHHHhCCChhh-------CCcccccChh------h---hhcCCCCCCEEEEEecCCC
Confidence 56677888999998876 6888877753 2 3458999999988887664
No 76
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=23.99 E-value=93 Score=22.92 Aligned_cols=26 Identities=27% Similarity=0.529 Sum_probs=20.8
Q ss_pred cChHHHHHHHHhCCCCHHHHHHHHhc
Q 048516 85 ENSDSVLSFLRESGFSSTHIEKMVAK 110 (389)
Q Consensus 85 ~~~~~vl~~L~~lGls~~~i~~iv~~ 110 (389)
...|+.+.-++.+||+..+|..++.+
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45777888889999999988877754
No 77
>PRK14136 recX recombination regulator RecX; Provisional
Probab=23.85 E-value=6.8e+02 Score=24.37 Aligned_cols=106 Identities=11% Similarity=0.063 Sum_probs=60.7
Q ss_pred hhHHHHHHHHHhhC-ChhHHHHHHHhcCcccccCchhhhhhHHHHHHHcCCCchhhhhhcccCcEeeeecchhHHHHHHH
Q 048516 158 QFQRSFLVLNSVLG-SNAGVCKAIKATGWFLRRDLEKTLIPTIDILKNCGVSSSQIVKYVYTYPTFFLYKPEKVRCFVQR 236 (389)
Q Consensus 158 ~L~p~~~fL~~~g~-s~~~v~~~l~~~P~lL~~sle~~l~p~v~~L~~lGv~~~~I~~ll~~~P~il~~s~~~~~~~v~~ 236 (389)
.|...|++|++.|. +|........+. .. . . .. -.....-|++-||+.+.|...+... ..+.+....+.
T Consensus 195 ~IE~VIerLke~gYLDDeRFAesyVr~-R~-~-k-kG-p~rIrqELrQKGId~eLIEqALeei------eEDE~E~A~~L 263 (309)
T PRK14136 195 SVEPLLDALEREGWLSDARFAESLVHR-RA-S-R-VG-SARIVSELKRHAVGDALVESVGAQL------RETEFERAQAV 263 (309)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHHHH-Hh-h-c-hh-HHHHHHHHHHcCCCHHHHHHHHHhc------cHhHHHHHHHH
Confidence 56677788888875 666666655543 11 1 1 11 2223455788999999988877532 11223222222
Q ss_pred HH-HhCCCCCcccHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Q 048516 237 VD-EIGFDRNSKMYLPAIRTMSSMTKEKWELKLKLFRSLGFSEDNILSMFRSM 288 (389)
Q Consensus 237 l~-~lG~~~~~~~f~~a~~~~~~~s~~~~~~kv~~l~~~G~s~~~v~~~~~~~ 288 (389)
++ .++-.+. ........+.||..=||+.+.|..++..+
T Consensus 264 ~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 264 WRKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 22 2221111 12233445778889999999999888754
No 78
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=23.50 E-value=45 Score=29.13 Aligned_cols=44 Identities=27% Similarity=0.289 Sum_probs=23.3
Q ss_pred HHHHHHHHcCcccC----CCCchhhhcccHhhHHHhhccCCCCccccc
Q 048516 337 RVYDMLKSKNLLRR----KTGLATVCKLSKGKFLEKYVLPYQDELGDL 380 (389)
Q Consensus 337 ~vl~~L~~kGl~~~----~~~l~~~l~~se~~F~~k~v~~~~e~~p~l 380 (389)
.+++-|..+|+++. +..-..++..+-++|++-|...--++.|.|
T Consensus 112 ~~i~~L~e~glI~~~gr~~~~Grp~ly~tT~~Fl~~Fgl~sl~eLP~l 159 (159)
T PF04079_consen 112 SVIKTLLERGLIEEVGRKDTPGRPILYGTTDKFLEYFGLESLEELPPL 159 (159)
T ss_dssp CHHHHHHHTTSEEEEEE-TTTT--EEEEE-HHHHHHCT----------
T ss_pred HHHHHHHHCCCEEecCcCCCCCCCeEeehhHHHHHHcCCCCHHHCcCC
Confidence 34677889999863 223346777888999999998888888765
No 79
>PTZ00413 lipoate synthase; Provisional
Probab=23.12 E-value=2.6e+02 Score=28.17 Aligned_cols=107 Identities=17% Similarity=0.177 Sum_probs=59.0
Q ss_pred ChhhhhhHhhcCcccccccchhhhHHHHHHHHHhhCChhHHHHHH---H---------hcCcccc--cCchhhhhhHHHH
Q 048516 136 SSSDIVDIISSDPWLLHRSAENQFQRSFLVLNSVLGSNAGVCKAI---K---------ATGWFLR--RDLEKTLIPTIDI 201 (389)
Q Consensus 136 s~~~i~~iv~~~P~iL~~s~e~~L~p~~~fL~~~g~s~~~v~~~l---~---------~~P~lL~--~sle~~l~p~v~~ 201 (389)
..+.+.++...-|.++..++|. ....+.-.+.-+.+-++-.++| + +..-|++ -+.+ .+...+..
T Consensus 241 ~~e~l~~L~eAG~dvynHNLET-v~rLyp~VRt~~atYe~sLe~Lr~AKe~f~~gi~tcSGiIVGLGET~e-Evie~m~d 318 (398)
T PTZ00413 241 DLKSVEKLANSPLSVYAHNIEC-VERITPYVRDRRASYRQSLKVLEHVKEFTNGAMLTKSSIMLGLGETEE-EVRQTLRD 318 (398)
T ss_pred CHHHHHHHHhcCCCEEeccccc-CHhHHHHHccCcCCHHHHHHHHHHHHHHhcCCceEeeeeEecCCCCHH-HHHHHHHH
Confidence 3456666777777777777663 2222222221111222222222 1 2222333 2333 37777778
Q ss_pred HHHcCCCchhhhhhcccCcE----eeeecchhHHHHHHHHHHhCCCC
Q 048516 202 LKNCGVSSSQIVKYVYTYPT----FFLYKPEKVRCFVQRVDEIGFDR 244 (389)
Q Consensus 202 L~~lGv~~~~I~~ll~~~P~----il~~s~~~~~~~v~~l~~lG~~~ 244 (389)
|+++|++.--|.+.|.-.+. .=...++.|+..-+...+|||..
T Consensus 319 LrelGVDivtIGQYL~Ps~~h~~V~~yv~P~~F~~~~~~a~~~Gf~~ 365 (398)
T PTZ00413 319 LRTAGVSAVTLGQYLQPTKTRLKVSRYAHPKEFEMWEEEAMKMGFLY 365 (398)
T ss_pred HHHcCCcEEeeccccCCCcccCCceeccCHHHHHHHHHHHHHcCCce
Confidence 88899988888776654332 22345777887777778889865
No 80
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.88 E-value=1.5e+02 Score=21.66 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=22.4
Q ss_pred HhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHHhCCCCHHHHH
Q 048516 59 YLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLRESGFSSTHIE 105 (389)
Q Consensus 59 yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~~lGls~~~i~ 105 (389)
-+-+.+|+|...+..+....... +++..+.+.+.++.+|.......
T Consensus 5 ~iA~~~gvS~~TVSr~ln~~~~v-~~~t~~~i~~~~~~~gy~~~~~~ 50 (70)
T smart00354 5 DVARLAGVSKATVSRVLNGNGRV-SEETREKVLAAMEELGYIPNRVA 50 (70)
T ss_pred HHHHHHCCCHHHHHHHHCCCCCC-CHHHHHHHHHHHHHhCCCCCHHH
Confidence 34445566665555443311111 33445556666666666544433
No 81
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=22.73 E-value=2.3e+02 Score=24.10 Aligned_cols=57 Identities=19% Similarity=0.238 Sum_probs=0.0
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCC----------------cccccccccchhhHHHHHHHcCCChhhhhhHh
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKP----------------NILLINLHNTLKPKIKIFHEFGFSSSDIVDII 144 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P----------------~lL~~~~~~~L~pkl~fL~slG~s~~~i~~iv 144 (389)
+..+.+-|..-|++.+.|..++...+ ..-..+. +.-.-..++|...||+.+.|.+++
T Consensus 78 ~~~I~~~L~~kGi~~~~I~~~l~~~~~d~~e~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~l 150 (157)
T PRK00117 78 PRRIRQELRQKGVDREIIEEALAELDIDWEELARELARKKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRVL 150 (157)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCccHHHHHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHHH
No 82
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=22.71 E-value=74 Score=25.51 Aligned_cols=18 Identities=17% Similarity=0.623 Sum_probs=7.1
Q ss_pred CChhhhhhHhhcCccccc
Q 048516 135 FSSSDIVDIISSDPWLLH 152 (389)
Q Consensus 135 ~s~~~i~~iv~~~P~iL~ 152 (389)
++.+++..++..+|.++.
T Consensus 71 ~s~~e~i~~l~~~p~Lik 88 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIK 88 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-
T ss_pred hhhHHHHHHHHhChhhee
Confidence 333444444444444433
No 83
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.29 E-value=87 Score=22.25 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=13.4
Q ss_pred HHHHHHcCCCHHHHHHHH
Q 048516 268 LKLFRSLGFSEDNILSMF 285 (389)
Q Consensus 268 v~~l~~~G~s~~~v~~~~ 285 (389)
|..++.+|||-+||..++
T Consensus 7 I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 456678999999999998
No 84
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=22.09 E-value=2.3e+02 Score=22.82 Aligned_cols=21 Identities=10% Similarity=0.270 Sum_probs=17.0
Q ss_pred CCCHHHHHHHHHcCCCccccC
Q 048516 275 GFSEDNILSMFRSMPPAFTVS 295 (389)
Q Consensus 275 G~s~~~v~~~~~~~P~iL~~S 295 (389)
.+|++|+.+++..+|.++...
T Consensus 73 ~ls~~e~i~~l~~~p~LikRP 93 (115)
T cd03032 73 ELSLSELIRLISEHPSLLRRP 93 (115)
T ss_pred cCCHHHHHHHHHhChhheeCC
Confidence 467888999999999887655
No 85
>PRK14134 recX recombination regulator RecX; Provisional
Probab=22.09 E-value=1.3e+02 Score=28.94 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=11.5
Q ss_pred HHHHHHHhCCCCHHHHHHHHhc
Q 048516 89 SVLSFLRESGFSSTHIEKMVAK 110 (389)
Q Consensus 89 ~vl~~L~~lGls~~~i~~iv~~ 110 (389)
.+..||..-||+.+.|..++..
T Consensus 184 Kl~~~L~rrGFs~~~I~~vl~~ 205 (283)
T PRK14134 184 KLGPYLISRGYSSNIAEWILNE 205 (283)
T ss_pred HHHHHHHHCCCCHHHHHHHHHH
Confidence 3455555555555555555443
No 86
>PRK10026 arsenate reductase; Provisional
Probab=22.04 E-value=1.5e+02 Score=25.34 Aligned_cols=20 Identities=5% Similarity=0.164 Sum_probs=10.9
Q ss_pred ChhHHHHHHHhcCcccccCc
Q 048516 172 SNAGVCKAIKATGWFLRRDL 191 (389)
Q Consensus 172 s~~~v~~~l~~~P~lL~~sl 191 (389)
+++++..++..+|.++...+
T Consensus 77 s~~e~l~ll~~~P~LIKRPI 96 (141)
T PRK10026 77 TDDQLIDFMLQHPILINRPI 96 (141)
T ss_pred CHHHHHHHHHhCccceeCcE
Confidence 44555555555555555543
No 87
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=21.49 E-value=2e+02 Score=26.81 Aligned_cols=45 Identities=24% Similarity=0.265 Sum_probs=34.2
Q ss_pred cChHHHHHHHHhCCCCHHHHHHHHhcCCcccccccccchhhHHHHHHHcCC
Q 048516 85 ENSDSVLSFLRESGFSSTHIEKMVAKKPNILLINLHNTLKPKIKIFHEFGF 135 (389)
Q Consensus 85 ~~~~~vl~~L~~lGls~~~i~~iv~~~P~lL~~~~~~~L~pkl~fL~slG~ 135 (389)
+=.+.|...|.+.|.+.++|.++++.-|. .| .+.+.++++.+.|-
T Consensus 57 e~M~rv~k~Lheqgv~~~~ik~~~r~iP~----~P--gmv~lik~~ak~g~ 101 (256)
T KOG3120|consen 57 ELMDRVFKELHEQGVRIAEIKQVLRSIPI----VP--GMVRLIKSAAKLGC 101 (256)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHhcCCC----Cc--cHHHHHHHHHhCCC
Confidence 34678888888888888888888888774 23 37777888887774
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=21.23 E-value=1.4e+02 Score=22.55 Aligned_cols=27 Identities=26% Similarity=0.397 Sum_probs=20.8
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCCc
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKPN 113 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P~ 113 (389)
++..-.+.+.+||++.+|..+-..+|.
T Consensus 11 ~~~Wk~laR~LGls~~~I~~ie~~~~~ 37 (79)
T cd08784 11 FDQHKRFFRKLGLSDNEIKVAELDNPQ 37 (79)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCc
Confidence 344566778888888888888888876
No 89
>PRK14134 recX recombination regulator RecX; Provisional
Probab=21.14 E-value=7.3e+02 Score=23.68 Aligned_cols=119 Identities=12% Similarity=0.039 Sum_probs=62.9
Q ss_pred hHHHHHHHHhCCCCHHHHHHHHhcCCcc---------c----ccc--cc---cchhh-HHHHHHHcCCChhhhhhHhhcC
Q 048516 87 SDSVLSFLRESGFSSTHIEKMVAKKPNI---------L----LIN--LH---NTLKP-KIKIFHEFGFSSSDIVDIISSD 147 (389)
Q Consensus 87 ~~~vl~~L~~lGls~~~i~~iv~~~P~l---------L----~~~--~~---~~L~p-kl~fL~slG~s~~~i~~iv~~~ 147 (389)
|..+-.=|+..|++.+-|..++...+.- + ... .+ ..... ..+||...||+.+.|..++...
T Consensus 127 ~~~I~~eL~qKGI~~~iIe~al~~~~~e~e~e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~ 206 (283)
T PRK14134 127 RNKIKYTLLNKGIKENIIIEKINNIDEEKEKKVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNEL 206 (283)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhCChhhHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence 5566677889999999888887754311 0 000 00 01122 3578888888888887776431
Q ss_pred cccccccchhhhHHHHHHHHH---------hhCC-hhHHHHH-HHhcCcccccCch--hhhhhHHHHHHHcCCCchhhhh
Q 048516 148 PWLLHRSAENQFQRSFLVLNS---------VLGS-NAGVCKA-IKATGWFLRRDLE--KTLIPTIDILKNCGVSSSQIVK 214 (389)
Q Consensus 148 P~iL~~s~e~~L~p~~~fL~~---------~g~s-~~~v~~~-l~~~P~lL~~sle--~~l~p~v~~L~~lGv~~~~I~~ 214 (389)
+ ..-+|-.+ .... -+.+..+ -++++.+....-+ +.-...+.||..-|++-+.|..
T Consensus 207 ---~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~kr~~~~~~~e~d~~k~~~Kl~~~L~rkGf~~e~I~~ 274 (283)
T PRK14134 207 ---I---------KNEALYKDNNSQNIENNIKDENIEELHNLARKRYDIIIKSEDDKNKIYRRLSNYLLRRGYSWEEVKK 274 (283)
T ss_pred ---H---------hHhhhhhhccccchhhccccChHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 1 11111111 1111 1222222 2334444322211 2245667788888888888877
Q ss_pred hcc
Q 048516 215 YVY 217 (389)
Q Consensus 215 ll~ 217 (389)
++.
T Consensus 275 vl~ 277 (283)
T PRK14134 275 SLN 277 (283)
T ss_pred HHH
Confidence 653
No 90
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=21.13 E-value=1.2e+02 Score=21.85 Aligned_cols=20 Identities=20% Similarity=0.222 Sum_probs=10.1
Q ss_pred HHHHhhCChhHHHHHHHhcC
Q 048516 165 VLNSVLGSNAGVCKAIKATG 184 (389)
Q Consensus 165 fL~~~g~s~~~v~~~l~~~P 184 (389)
++..++.++-++...+..+|
T Consensus 27 lLqql~~~nP~l~q~I~~n~ 46 (59)
T PF09280_consen 27 LLQQLGQSNPQLLQLIQQNP 46 (59)
T ss_dssp HHHHHHCCSHHHHHHHHHTH
T ss_pred HHHHHhccCHHHHHHHHHCH
Confidence 34445555555555555444
No 91
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=20.63 E-value=2.2e+02 Score=20.08 Aligned_cols=49 Identities=14% Similarity=0.186 Sum_probs=31.1
Q ss_pred HHHhhhccCCCHHHHHHhhccccCCCCCcChHHHHHHHH--hCCCCHHHHHHHHh
Q 048516 57 ADYLINRQHFSPESASEASSLNFSLKDTENSDSVLSFLR--ESGFSSTHIEKMVA 109 (389)
Q Consensus 57 ~~yLi~s~Gls~~~a~~~s~~~~~l~~~~~~~~vl~~L~--~lGls~~~i~~iv~ 109 (389)
++-.-+.+|++.++...-++ -.....+..+..||. .+|+|-++|++.+.
T Consensus 6 ~~~Va~~~~i~~~~i~s~~R----~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 6 IEAVAEYFGVKPEDLKSKSR----KREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHHhCCCHHHHhcCCC----CcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 34444567888877655443 112234667777773 58888888888764
No 92
>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=20.59 E-value=3.5e+02 Score=22.20 Aligned_cols=55 Identities=13% Similarity=0.287 Sum_probs=0.0
Q ss_pred HhcCCHHHHHHHHHHHHH-cCCCHHHHHHHHHcCCCccccCHHhHHHHHHHHhhcc-CCChhhH
Q 048516 256 MSSMTKEKWELKLKLFRS-LGFSEDNILSMFRSMPPAFTVSERKIRSVVETLLRRR-DVDISSI 317 (389)
Q Consensus 256 ~~~~s~~~~~~kv~~l~~-~G~s~~~v~~~~~~~P~iL~~S~~~l~~k~~fL~~~m-g~~~~~i 317 (389)
+...+...++.-++|++. +|++.+++..+ -. .+.+.++.-+.|+...| |.+-+++
T Consensus 47 ~~~~~~~~~~~~~~Fi~~iL~L~dkq~ekl-~~------iD~~~~~e~~~yl~~rl~G~sD~~i 103 (114)
T PF06896_consen 47 IDEASRNILKEMLKFIQDILKLNDKQVEKL-ED------IDFEDLQEIVSYLVMRLQGMSDEQI 103 (114)
T ss_pred HHHhHHHHHHHHHHHHHHHHCCCHHHHHHH-hc------CCHHHHHHHHHHHHHHHcCCCHHHH
No 93
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=20.31 E-value=2.5e+02 Score=22.03 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=17.9
Q ss_pred cCCCHHHHHHHHHcCCCccccC
Q 048516 274 LGFSEDNILSMFRSMPPAFTVS 295 (389)
Q Consensus 274 ~G~s~~~v~~~~~~~P~iL~~S 295 (389)
-+++++|+.+++..+|.+|...
T Consensus 72 ~~ls~~e~~~~l~~~p~LikRP 93 (105)
T cd02977 72 DELSDEEALELMAEHPKLIKRP 93 (105)
T ss_pred cCCCHHHHHHHHHhCcCeeeCC
Confidence 4678999999999999887643
Done!