Query 037691
Match_columns 337
No_of_seqs 182 out of 1270
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 03:28:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037691hhsearch_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 1.8E-45 3.9E-50 369.2 21.2 247 79-328 119-449 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 3.1E-39 6.8E-44 311.6 8.8 236 79-316 28-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.7E-34 3.6E-39 290.0 19.1 238 79-319 87-345 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 1.9E-29 4.1E-34 243.5 9.9 226 89-317 2-314 (345)
5 KOG1267 Mitochondrial transcri 99.8 6.6E-21 1.4E-25 188.9 11.6 161 135-299 249-410 (413)
6 KOG1267 Mitochondrial transcri 99.7 2.1E-17 4.5E-22 163.9 12.2 207 83-299 90-341 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00039 8.5E-09 42.2 2.5 30 237-268 2-31 (31)
8 smart00733 Mterf Mitochondrial 96.8 0.00089 1.9E-08 40.6 2.2 28 101-128 3-30 (31)
9 cd04790 HTH_Cfa-like_unk Helix 88.2 1.8 3.8E-05 38.0 6.8 141 86-237 16-166 (172)
10 PF04695 Pex14_N: Peroxisomal 67.5 5.1 0.00011 33.7 2.8 47 187-246 5-51 (136)
11 PF04695 Pex14_N: Peroxisomal 63.7 6.9 0.00015 32.9 2.9 38 104-144 14-51 (136)
12 PF11955 PORR: Plant organelle 60.6 19 0.00041 35.1 5.7 25 123-147 44-68 (335)
13 COG1125 OpuBA ABC-type proline 59.6 16 0.00035 34.5 4.7 21 302-322 219-239 (309)
14 PF00627 UBA: UBA/TS-N domain; 56.6 16 0.00035 23.2 3.1 23 220-242 4-26 (37)
15 PF11955 PORR: Plant organelle 56.0 26 0.00057 34.1 5.8 149 99-249 100-291 (335)
16 PRK14136 recX recombination re 55.8 1.4E+02 0.0031 28.7 10.5 110 111-242 191-302 (309)
17 smart00165 UBA Ubiquitin assoc 55.6 18 0.00039 22.7 3.2 24 219-242 2-25 (37)
18 COG1125 OpuBA ABC-type proline 55.6 19 0.00041 34.0 4.5 87 79-183 68-160 (309)
19 COG4669 EscJ Type III secretor 53.8 28 0.00061 32.2 5.2 101 79-185 28-130 (246)
20 PF07499 RuvA_C: RuvA, C-termi 53.3 11 0.00023 25.6 1.9 27 218-244 3-29 (47)
21 cd00194 UBA Ubiquitin Associat 52.2 22 0.00047 22.4 3.2 24 219-242 2-25 (38)
22 PRK14135 recX recombination re 51.6 1.5E+02 0.0033 27.3 10.1 58 80-140 87-149 (263)
23 PF02631 RecX: RecX family; I 48.2 47 0.001 26.8 5.4 27 215-241 92-118 (121)
24 PRK00117 recX recombination re 47.6 1.6E+02 0.0034 24.9 8.8 113 110-241 39-152 (157)
25 PF08069 Ribosomal_S13_N: Ribo 47.5 13 0.00029 26.8 1.7 38 103-140 20-57 (60)
26 PRK08561 rps15p 30S ribosomal 46.7 61 0.0013 27.9 5.8 37 104-140 21-57 (151)
27 PF12244 DUF3606: Protein of u 45.2 25 0.00053 25.0 2.8 24 153-176 21-44 (57)
28 PF14490 HHH_4: Helix-hairpin- 44.6 73 0.0016 24.7 5.7 17 81-97 5-21 (94)
29 PF02631 RecX: RecX family; I 44.2 27 0.00058 28.3 3.3 57 80-139 7-68 (121)
30 PF14490 HHH_4: Helix-hairpin- 42.8 1E+02 0.0022 23.9 6.3 25 115-139 7-31 (94)
31 PF07499 RuvA_C: RuvA, C-termi 42.2 41 0.00089 22.7 3.4 25 116-140 3-27 (47)
32 COG3620 Predicted transcriptio 41.1 65 0.0014 28.2 5.2 75 125-202 16-98 (187)
33 KOG0400 40S ribosomal protein 38.4 35 0.00077 28.5 3.1 39 104-142 21-59 (151)
34 PF10007 DUF2250: Uncharacteri 37.3 35 0.00076 26.8 2.8 52 85-139 10-61 (92)
35 PTZ00072 40S ribosomal protein 35.4 92 0.002 26.6 5.2 36 105-140 19-54 (148)
36 TIGR00601 rad23 UV excision re 31.9 5E+02 0.011 25.7 10.6 119 114-242 154-361 (378)
37 COG3620 Predicted transcriptio 30.4 51 0.0011 28.8 2.9 73 159-232 14-98 (187)
38 PF06757 Ins_allergen_rp: Inse 30.4 2.5E+02 0.0054 24.4 7.5 49 79-135 29-78 (179)
39 PF02022 Integrase_Zn: Integra 29.6 81 0.0018 20.8 3.1 30 216-245 6-36 (40)
40 cd08315 Death_TRAILR_DR4_DR5 D 29.4 1.9E+02 0.0041 22.7 5.9 43 117-163 20-62 (96)
41 PF08671 SinI: Anti-repressor 28.5 64 0.0014 19.9 2.3 25 217-241 4-28 (30)
42 cd08316 Death_FAS_TNFRSF6 Deat 28.4 2E+02 0.0044 22.7 5.9 46 116-164 20-65 (97)
43 PF03960 ArsC: ArsC family; I 27.1 55 0.0012 26.0 2.5 62 189-250 10-91 (110)
44 cd08306 Death_FADD Fas-associa 26.5 1.7E+02 0.0036 22.4 5.0 40 121-163 18-57 (86)
45 PF11212 DUF2999: Protein of u 26.2 1.7E+02 0.0038 21.9 4.7 57 117-181 2-61 (82)
46 PRK00117 recX recombination re 24.7 3.3E+02 0.0071 22.9 7.0 58 80-141 41-103 (157)
47 PF00356 LacI: Bacterial regul 24.6 2.3E+02 0.0049 19.1 4.9 39 226-269 7-45 (46)
48 PRK11613 folP dihydropteroate 24.4 92 0.002 29.6 3.8 64 252-319 163-228 (282)
49 PRK09875 putative hydrolase; P 24.0 68 0.0015 30.5 2.9 29 216-244 260-288 (292)
50 PRK14136 recX recombination re 23.8 3.3E+02 0.0072 26.2 7.4 55 80-139 192-251 (309)
51 cd04882 ACT_Bt0572_2 C-termina 23.6 1.1E+02 0.0025 20.9 3.4 50 80-129 9-63 (65)
52 PF03874 RNA_pol_Rpb4: RNA pol 23.5 65 0.0014 25.8 2.3 54 114-173 57-110 (117)
53 TIGR01448 recD_rel helicase, p 23.4 1.8E+02 0.0039 31.4 6.2 93 83-184 76-186 (720)
54 cd08313 Death_TNFR1 Death doma 23.1 3.1E+02 0.0066 20.8 5.8 45 116-164 11-55 (80)
55 cd04790 HTH_Cfa-like_unk Helix 22.5 1.1E+02 0.0023 26.7 3.6 51 115-172 117-167 (172)
56 cd04769 HTH_MerR2 Helix-Turn-H 22.4 1.1E+02 0.0023 24.7 3.4 52 86-140 15-69 (116)
57 PF13543 KSR1-SAM: SAM like do 22.4 2.1E+02 0.0045 23.9 5.1 53 119-175 69-124 (129)
58 PF08004 DUF1699: Protein of u 22.0 4.3E+02 0.0092 22.1 6.7 77 165-241 29-116 (131)
59 cd04788 HTH_NolA-AlbR Helix-Tu 22.0 2.5E+02 0.0055 21.6 5.3 39 219-261 47-85 (96)
60 PF09278 MerR-DNA-bind: MerR, 21.4 90 0.002 21.9 2.5 19 221-239 6-24 (65)
61 KOG0011 Nucleotide excision re 21.1 1.6E+02 0.0034 28.6 4.6 96 79-181 130-240 (340)
62 PHA02591 hypothetical protein; 20.6 1.4E+02 0.0031 22.7 3.4 30 108-137 40-69 (83)
63 COG1393 ArsC Arsenate reductas 20.4 1.6E+02 0.0034 24.1 3.9 15 83-97 13-27 (117)
64 cd04768 HTH_BmrR-like Helix-Tu 20.3 2.5E+02 0.0054 21.7 5.0 26 218-243 46-71 (96)
65 PF10440 WIYLD: Ubiquitin-bind 20.3 1.5E+02 0.0033 21.7 3.4 35 215-249 8-42 (65)
66 PF09288 UBA_3: Fungal ubiquit 20.3 1.3E+02 0.0027 21.4 2.8 21 221-241 12-32 (55)
67 cd08318 Death_NMPP84 Death dom 20.2 2.8E+02 0.0062 21.0 5.2 39 121-163 23-61 (86)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.8e-45 Score=369.18 Aligned_cols=247 Identities=25% Similarity=0.484 Sum_probs=181.8
Q ss_pred CCCccHHHHHHHHhhCCC---ChhhHhhhCCCcccCCcc-CHHHHHHHHHhCCCChHHHHHHHHhCcccccccc------
Q 037691 79 SPHSEFQEKMLYLDSIGV---DFFSLINDHPPIVSASLN-DIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRA------ 148 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~---di~~ii~~~P~lL~~s~e-~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~------ 148 (337)
.++.++.|+++||.++|+ +++++|.++|.+|..+++ ++.++++||+++|++.++|++++.++|++|+++.
T Consensus 119 ~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p 198 (487)
T PLN03196 119 SVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMST 198 (487)
T ss_pred CHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHH
Confidence 344566666666666666 356666666666666654 3555555555555555555555555555555442
Q ss_pred -------------------------------cchhHHHHHHHHHhcCChhHHHHHHHhCccccccchhhchhhHHHHHhh
Q 037691 149 -------------------------------SDILPVFTFLLREAKVNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQS 197 (337)
Q Consensus 149 -------------------------------~~l~~~v~fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~ 197 (337)
++++|+++||+ ++|++.++|.++|.++|++|+++++++++|++++|++
T Consensus 199 ~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~-~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~e 277 (487)
T PLN03196 199 SVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLE-SLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLE 277 (487)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHH-HcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHH
Confidence 34555555553 4555555666666666666666665556666666666
Q ss_pred hCCcc------ccc-------------------------------------ccceeeccchhhHHHHHHHHHHcCCCHHH
Q 037691 198 MGIAE------VNK-------------------------------------HTYLLSCSVEDKLIPRLQYFQKIGFSKRE 234 (337)
Q Consensus 198 lG~~~------i~k-------------------------------------~P~iL~~s~~~~l~~kv~fL~~lG~s~~~ 234 (337)
+|+++ +.+ +|++++++ +++|+++++||.++||+.++
T Consensus 278 lGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lS-e~kl~~kvefL~~~Gls~ed 356 (487)
T PLN03196 278 FGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLN-RNVALKHVEFLRGRGFSAQD 356 (487)
T ss_pred cCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhccc-HHHHHHHHHHHHHcCCCHHH
Confidence 66542 122 34444444 45788899999999999999
Q ss_pred HhHHHhcCCcccccChhhhHHHHHHHHHHhhCCChhHHhhcCcccccCccchhHHHHHHHHHcCCCCCchhhhccCHHHH
Q 037691 235 ATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKELKEFPQYFSFSLENRIKPRHQACVDKGVCFPLNVLLKTSEAQF 314 (337)
Q Consensus 235 i~~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~~~~I~~~P~~L~~Sle~rI~pR~~~L~~~Gl~~~l~~ll~~se~~F 314 (337)
|..|++++|++|++|+ ++|++|++||+++||++.++|+++|++|+||+|+||+|||++|+++|+.++|.++|.+||++|
T Consensus 357 I~~mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F 435 (487)
T PLN03196 357 VAKMVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKF 435 (487)
T ss_pred HHHHHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHH
Confidence 9999999999999995 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHchhcCCCCCC
Q 037691 315 HRRLDVCCNSSMPL 328 (337)
Q Consensus 315 ~e~~~~~~~~~~p~ 328 (337)
+++|+.+|.|--..
T Consensus 436 ~~r~v~~y~e~~~~ 449 (487)
T PLN03196 436 EQRMSGDFIEGEEM 449 (487)
T ss_pred HHHHhhhccccccc
Confidence 99999999774333
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=3.1e-39 Score=311.63 Aligned_cols=236 Identities=35% Similarity=0.661 Sum_probs=180.9
Q ss_pred CCCccHHHHHHHHhhCCC---ChhhHhhhCCCcccCCcc-CHHHHHHHHHhCCCChHHHHHHHHhCcccccccc-cchhH
Q 037691 79 SPHSEFQEKMLYLDSIGV---DFFSLINDHPPIVSASLN-DIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRA-SDILP 153 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~---di~~ii~~~P~lL~~s~e-~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~-~~l~~ 153 (337)
+++..+.|+++||.++|+ |+++++.++|.++..+++ ++.+.++||+++|++++|+.+++.++|++|..+. +++.+
T Consensus 28 ~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~ 107 (345)
T PF02536_consen 28 DPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSP 107 (345)
T ss_dssp -SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHH
T ss_pred cCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhh
Confidence 688999999999999999 699999999999999965 6999999999999999999999999999999985 48999
Q ss_pred HHHHHHHHhcCChhHHHHHHHhCc----------------------------------cccccchhhchhhHHHHHhhhC
Q 037691 154 VFTFLLREAKVNGSDLKRVISRRP----------------------------------RLLVSAVKTRLRPTLYFLQSMG 199 (337)
Q Consensus 154 ~v~fL~~~lGvs~~~v~~li~~~P----------------------------------~lL~~sv~~~l~~~v~~L~~lG 199 (337)
+++||+ ++|++.+.+.+++..+| +++..+.++.++++++||+++|
T Consensus 108 ~v~~L~-~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G 186 (345)
T PF02536_consen 108 NVAFLR-SLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLG 186 (345)
T ss_dssp HHHHHH-HTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCT
T ss_pred hhhHHh-hcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhc
Confidence 999995 67777664554444444 4444444456777777887777
Q ss_pred Ccc------cccccceeeccc--------------------------------hhhHHHHHHHHHHcCCCHHHHhHHHhc
Q 037691 200 IAE------VNKHTYLLSCSV--------------------------------EDKLIPRLQYFQKIGFSKREATAMFRR 241 (337)
Q Consensus 200 ~~~------i~k~P~iL~~s~--------------------------------~~~l~~kv~fL~~lG~s~~~i~~ml~~ 241 (337)
+++ +.++|.++.++. +++++++++||.++||+++|+++|+.+
T Consensus 187 ~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~ 266 (345)
T PF02536_consen 187 FSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRR 266 (345)
T ss_dssp T-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHH
T ss_pred ccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHh
Confidence 764 334454444433 347999999999999999999999999
Q ss_pred CCcccccChhhhHHHHHHHHHHhhCCChhHHhhcCcccccCccchhHHH---HHHHHHcC--CCCCchhhhccCHHHHHH
Q 037691 242 FPQLFNYSVKDNYERKLNYFVVGMGRDLKELKEFPQYFSFSLENRIKPR---HQACVDKG--VCFPLNVLLKTSEAQFHR 316 (337)
Q Consensus 242 ~P~IL~~sle~~L~~k~~fL~~~mG~~~~~I~~~P~~L~~Sle~rI~pR---~~~L~~~G--l~~~l~~ll~~se~~F~e 316 (337)
+|+||++|+ +++++|++||+++||++.++|+++|++|+||+|+||+|| +++|+++| ..+++.+++.+||++|++
T Consensus 267 ~P~iL~~s~-e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 267 FPQILSYSI-EKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp SGGGGGS-H-HHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred Ccchhhcch-hhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 999999995 679999999999999999999999999999999999999 66788999 668999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.7e-34 Score=290.02 Aligned_cols=238 Identities=16% Similarity=0.410 Sum_probs=207.9
Q ss_pred CCCccHHHHHHHHhhCCCChhhHhhhCCCcccCCcc-CHHHHHHHHHhCCCChHHHHHHHHhCcccccccc-cchhHHHH
Q 037691 79 SPHSEFQEKMLYLDSIGVDFFSLINDHPPIVSASLN-DIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRA-SDILPVFT 156 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~di~~ii~~~P~lL~~s~e-~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~-~~l~~~v~ 156 (337)
.+-+++.++++||+++|++-..+ .++|.+|.++++ ++.++++||+++|++..+|+++|.++|.+|..+. +++.|+++
T Consensus 87 ~~~~~~~~~l~~L~s~G~~~~~i-~~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~ 165 (487)
T PLN03196 87 STVDVMRERVEFLHKLGLTIEDI-NEYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVK 165 (487)
T ss_pred ccHHHHHHHHHHHHHcCCChHHh-ccCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHH
Confidence 57779999999999999976665 389999999997 6999999999999999999999999999999996 68999999
Q ss_pred HHHHHhcCChhHHHHHHHhCccccccchhhchhhHHHHHhhhCCcc------cccccceeeccchhhHHHHHHHHHHcCC
Q 037691 157 FLLREAKVNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIAE------VNKHTYLLSCSVEDKLIPRLQYFQKIGF 230 (337)
Q Consensus 157 fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~lG~~~------i~k~P~iL~~s~~~~l~~kv~fL~~lG~ 230 (337)
|| +.+|++.++|.+++.++|++|++++++++.++++||+++|+++ +.++|++|+++.+++|+++++||.++|+
T Consensus 166 fL-~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv 244 (487)
T PLN03196 166 YL-QGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGL 244 (487)
T ss_pred HH-HHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCC
Confidence 99 4899999999999999999999999988999999999999985 6789999999988899999999999999
Q ss_pred CHHHHhHHHhcCCcccccChhhhHHHHHHHHHHhhCCChhH----HhhcCcccccCccchhHHHHHHH-HHcCCC-----
Q 037691 231 SKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKE----LKEFPQYFSFSLENRIKPRHQAC-VDKGVC----- 300 (337)
Q Consensus 231 s~~~i~~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~~~~----I~~~P~~L~~Sle~rI~pR~~~L-~~~Gl~----- 300 (337)
+.++|++++.++|++|+++++++++++++||. ++|++.+. |.++|.+|++++++++.++..+| .+.|+.
T Consensus 245 ~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~-elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~ 323 (487)
T PLN03196 245 PRLAVARILEKRPYILGFDLEETVKPNVECLL-EFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFG 323 (487)
T ss_pred CHHHHHHHHHhCCceeEcCHHHhHHHHHHHHH-HcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHH
Confidence 99999999999999999998779999999987 78988765 47788888888888888888877 356664
Q ss_pred ---CCchhhhccCHHHHHHHHc
Q 037691 301 ---FPLNVLLKTSEAQFHRRLD 319 (337)
Q Consensus 301 ---~~l~~ll~~se~~F~e~~~ 319 (337)
...+.++.+|+++..+++.
T Consensus 324 ~~v~k~P~il~lSe~kl~~kve 345 (487)
T PLN03196 324 RVIEKLPQIVSLNRNVALKHVE 345 (487)
T ss_pred HHHHhcchhhcccHHHHHHHHH
Confidence 1355677777777666554
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.96 E-value=1.9e-29 Score=243.46 Aligned_cols=226 Identities=28% Similarity=0.571 Sum_probs=178.7
Q ss_pred HHHhhCCC---ChhhHhhhCCCcccCCccC-HHHHHHHHHhCCCChHHHHHHHHhCccccccc-ccchhHHHHHHHHHhc
Q 037691 89 LYLDSIGV---DFFSLINDHPPIVSASLND-IKSTVDLITSLDFAAAEFRRIVSMCPEILTSR-ASDILPVFTFLLREAK 163 (337)
Q Consensus 89 ~fL~slG~---di~~ii~~~P~lL~~s~e~-l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~-~~~l~~~v~fL~~~lG 163 (337)
++|+++|+ +|.+++.++|.++.++.++ +.++++||++.|++..++++++++||++|..+ .+++.++++|| +.+|
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L-~~~~ 80 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFL-KSIG 80 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHH-TTTS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHH-HHHc
Confidence 57899999 6999999999999999985 99999999999999999999999999999999 67999999999 5899
Q ss_pred CChhHHHHHHHhCccccccchhhchhhHHHHHhhhCCcc----------------------------------------c
Q 037691 164 VNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIAE----------------------------------------V 203 (337)
Q Consensus 164 vs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~lG~~~----------------------------------------i 203 (337)
++++++.+++.++|++|..+.++++.+++.+|+++|+++ +
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi 160 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVI 160 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCH
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccc
Confidence 999999999999999999988778999999999999874 1
Q ss_pred ccccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhcCCcccccChhh-------------------------------
Q 037691 204 NKHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKD------------------------------- 252 (337)
Q Consensus 204 ~k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~~P~IL~~sle~------------------------------- 252 (337)
.++|+++..+.++.++++++||+++|++.+++.+++.++|.++.+|+++
T Consensus 161 ~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~ 240 (345)
T PF02536_consen 161 AKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSE 240 (345)
T ss_dssp HHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHH
T ss_pred cccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccch
Confidence 2468777777788999999999999999999999999999999999754
Q ss_pred -hHHHHHHHHHHhhCCChhHH----hhcCcccccCccchhHHHHHHHHH-cCCC----CCchhhhccCHH-HHHHH
Q 037691 253 -NYERKLNYFVVGMGRDLKEL----KEFPQYFSFSLENRIKPRHQACVD-KGVC----FPLNVLLKTSEA-QFHRR 317 (337)
Q Consensus 253 -~L~~k~~fL~~~mG~~~~~I----~~~P~~L~~Sle~rI~pR~~~L~~-~Gl~----~~l~~ll~~se~-~F~e~ 317 (337)
+++++++||. ++|++.++| .++|++|++|.++ ++++++||.+ .|+. ...+.++.+|=+ +-.-|
T Consensus 241 ~~l~~~i~~L~-~lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR 314 (345)
T PF02536_consen 241 EKLKPKIEFLQ-SLGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPR 314 (345)
T ss_dssp HHHHHHHHHHH-TTT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHH
T ss_pred HhHHHHHHHHH-HhcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhH
Confidence 5899999997 699998774 8999999999995 9999999965 6775 355667776643 34434
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.84 E-value=6.6e-21 Score=188.90 Aligned_cols=161 Identities=30% Similarity=0.526 Sum_probs=138.2
Q ss_pred HHHHhCccccccc-ccchhHHHHHHHHHhcCChhHHHHHHHhCccccccchhhchhhHHHHHhhhCCcccccccceeecc
Q 037691 135 RIVSMCPEILTSR-ASDILPVFTFLLREAKVNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIAEVNKHTYLLSCS 213 (337)
Q Consensus 135 ~ii~~~P~iL~~~-~~~l~~~v~fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~lG~~~i~k~P~iL~~s 213 (337)
+++.+.|.++.++ .+.+.+++++|. .+|++.++|..++.++|++|+++.++ +..+++++.+. ..++.++|+++.++
T Consensus 249 ~~~v~~~~~~~~~~~~~i~~kv~~l~-~~Gf~~~di~~~~~k~P~~l~~s~~~-~~~~~~~~~~~-~~~~~k~p~~l~~s 325 (413)
T KOG1267|consen 249 REFVKAPILLSYSSEKTLEPKVEVLK-SLGFSREEIWKMVKKCPQILGYSVKK-NLKTTEYLLKN-PKHILKFPQLLRSS 325 (413)
T ss_pred hHHHhhhhhhcccccccHHHHHHHHH-HcCCCHHHHHHHHHhCchheEeehhh-hhHHHHHHHhc-chhhhhhhhhhhcc
Confidence 3444445555555 568999999994 78999999999999999999999984 55666666554 44588999999654
Q ss_pred chhhHHHHHHHHHHcCCCHHHHhHHHhcCCcccccChhhhHHHHHHHHHHhhCCChhHHhhcCcccccCccchhHHHHHH
Q 037691 214 VEDKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKELKEFPQYFSFSLENRIKPRHQA 293 (337)
Q Consensus 214 ~~~~l~~kv~fL~~lG~s~~~i~~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~~~~I~~~P~~L~~Sle~rI~pR~~~ 293 (337)
+..+.++++|+..+|++..|+.+|+.++|+++.+++++.++.+.+|+.+.|+++.++++.+|++++|++++|+.||+..
T Consensus 326 -~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~ 404 (413)
T KOG1267|consen 326 -EDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNV 404 (413)
T ss_pred -chhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHH
Confidence 7899999999999999999999999999999999985599999999999999999999999999999999999999998
Q ss_pred HHHcCC
Q 037691 294 CVDKGV 299 (337)
Q Consensus 294 L~~~Gl 299 (337)
...+|.
T Consensus 405 ~~~~~~ 410 (413)
T KOG1267|consen 405 IKKLGV 410 (413)
T ss_pred HHHHhc
Confidence 877664
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.73 E-value=2.1e-17 Score=163.91 Aligned_cols=207 Identities=26% Similarity=0.451 Sum_probs=150.3
Q ss_pred cHHHHHHHHhhCCC---ChhhHhhhCCCcccCCccC-HHHHHHHHHhCCCChHHHHHHHHhCccccccc-ccchhHHHHH
Q 037691 83 EFQEKMLYLDSIGV---DFFSLINDHPPIVSASLND-IKSTVDLITSLDFAAAEFRRIVSMCPEILTSR-ASDILPVFTF 157 (337)
Q Consensus 83 ~l~~~v~fL~slG~---di~~ii~~~P~lL~~s~e~-l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~-~~~l~~~v~f 157 (337)
+-....++|+++|+ ++.+++..+|.++..+.++ +.++..+|++.|++..+++.+++..|.+|..+ .+++.+.++|
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~ 169 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEF 169 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHH
Confidence 44556669999999 4889999999999888875 78888899999999999999999999999987 4689999999
Q ss_pred HHHHhc--CChhHHHHHHHhCccccccchhhchhhHHHHHhhhCCc----------------------------------
Q 037691 158 LLREAK--VNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIA---------------------------------- 201 (337)
Q Consensus 158 L~~~lG--vs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~lG~~---------------------------------- 201 (337)
+. .++ .....+.+++...|....... .+. ++++++++|..
T Consensus 170 l~-~~~~~~~~s~~~~~~~~~~~~~~~~~--~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~~l~~~~~~i~~~g~~ 245 (413)
T KOG1267|consen 170 LK-SIPPELLSSVVERLLTPVPSFLLNEN--SVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYLKLKARLPFLLTLGFD 245 (413)
T ss_pred hh-ccchhhhhhHHHHhcccccccccccc--ccc-cchhhHHhCCCHHHHHHHHhcCccceeeehhhhhhhhhHHHhccC
Confidence 85 553 455555555555552222211 122 34444444433
Q ss_pred c----cccccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhcCCcccccChhhhHHHHHHHHHHhhCCChhHHhhcCc
Q 037691 202 E----VNKHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDLKELKEFPQ 277 (337)
Q Consensus 202 ~----i~k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~~~~I~~~P~ 277 (337)
. +.+.|.++.++.++++++++++|.++||+.+||..|+.++|++|++|. +++..++.|+.+. .+++.++|+
T Consensus 246 p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~-~~~~~~~~~~~~~----~~~~~k~p~ 320 (413)
T KOG1267|consen 246 PKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSV-KKNLKTTEYLLKN----PKHILKFPQ 320 (413)
T ss_pred CchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeeh-hhhhHHHHHHHhc----chhhhhhhh
Confidence 1 234677777788999999999999999999999999999999999994 7666666666544 333666666
Q ss_pred ccccCccchhHHHHHHHHHcCC
Q 037691 278 YFSFSLENRIKPRHQACVDKGV 299 (337)
Q Consensus 278 ~L~~Sle~rI~pR~~~L~~~Gl 299 (337)
++.++.. .+.+|+++|...|.
T Consensus 321 ~l~~s~~-~l~~~ie~l~~~g~ 341 (413)
T KOG1267|consen 321 LLRSSED-KLKPRIEFLLSLGF 341 (413)
T ss_pred hhhccch-hhhhhHHHHHHcCC
Confidence 6655544 46666666666664
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=97.11 E-value=0.00039 Score=42.21 Aligned_cols=30 Identities=23% Similarity=0.689 Sum_probs=23.3
Q ss_pred HHHhcCCcccccChhhhHHHHHHHHHHhhCCC
Q 037691 237 AMFRRFPQLFNYSVKDNYERKLNYFVVGMGRD 268 (337)
Q Consensus 237 ~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~ 268 (337)
+++.++|+++.++ +++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHH-HcCCC
Confidence 4677888888888 688888888887 77764
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=96.82 E-value=0.00089 Score=40.56 Aligned_cols=28 Identities=25% Similarity=0.568 Sum_probs=13.9
Q ss_pred HhhhCCCcccCCccCHHHHHHHHHhCCC
Q 037691 101 LINDHPPIVSASLNDIKSTVDLITSLDF 128 (337)
Q Consensus 101 ii~~~P~lL~~s~e~l~~~v~~L~~lG~ 128 (337)
++.++|.++.++.++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYSEKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCcccccHHHhhHHHHHHHHcCC
Confidence 3445555555554445555555555544
No 9
>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=88.16 E-value=1.8 Score=37.98 Aligned_cols=141 Identities=12% Similarity=0.176 Sum_probs=66.7
Q ss_pred HHHHHHhhCCC-ChhhHhhhCC-CcccCCccCH--HHHHHHHHhCCCChHHHHHHHHhCcc----cccccccchhHHHHH
Q 037691 86 EKMLYLDSIGV-DFFSLINDHP-PIVSASLNDI--KSTVDLITSLDFAAAEFRRIVSMCPE----ILTSRASDILPVFTF 157 (337)
Q Consensus 86 ~~v~fL~slG~-di~~ii~~~P-~lL~~s~e~l--~~~v~~L~~lG~s~~~i~~ii~~~P~----iL~~~~~~l~~~v~f 157 (337)
.++.|..+.|+ .... +.+ .--.|+.+++ -..+..|+++|++-++|..++..... +|....+.+...++-
T Consensus 16 ~tLRyYe~~GLl~p~~---r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~~~~~~l~~ei~~ 92 (172)
T cd04790 16 STLLYYERIGLLSPSA---RSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRLAELNREIQR 92 (172)
T ss_pred HHHHHHHHCCCCCCCc---cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHH
Confidence 35667778887 2211 111 2233454432 26677889999999999999976542 111111223333333
Q ss_pred HHHHhcCChhHHHHHHHhCccccccchhhchhhHHHHHhhhCCcccc--cccceeeccchhhHHHHHHHHHHcCCCHHHH
Q 037691 158 LLREAKVNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQSMGIAEVN--KHTYLLSCSVEDKLIPRLQYFQKIGFSKREA 235 (337)
Q Consensus 158 L~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~~lG~~~i~--k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i 235 (337)
|++ ..+.+..++...+.. ...-.-+....++.++..|+++-. +-=.-|-. ..=..-.+||.++|++++++
T Consensus 93 L~~----~~~~l~~ll~~~~~~-~~~~~V~~~~w~~l~~~~g~~~~~m~~wh~~fe~---~~p~~h~~~l~~~g~~~~~~ 164 (172)
T cd04790 93 LRQ----QQRAIATLLKQPTLL-KEQRLVTKEKWVAILKAAGMDEADMRRWHIEFEK---MEPEAHQEFLQSLGIPEDEI 164 (172)
T ss_pred HHH----HHHHHHHHHHHHhhc-cccccCCHHHHHHHHHHcCCChHHHHHHHHHHHH---hCcHHHHHHHHHcCCCHHHH
Confidence 321 122344444332222 111001123445556667765411 00000000 01123467888888888887
Q ss_pred hH
Q 037691 236 TA 237 (337)
Q Consensus 236 ~~ 237 (337)
..
T Consensus 165 ~~ 166 (172)
T cd04790 165 ER 166 (172)
T ss_pred HH
Confidence 64
No 10
>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=67.54 E-value=5.1 Score=33.71 Aligned_cols=47 Identities=15% Similarity=0.258 Sum_probs=31.8
Q ss_pred chhhHHHHHhhhCCcccccccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhcCCccc
Q 037691 187 RLRPTLYFLQSMGIAEVNKHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRRFPQLF 246 (337)
Q Consensus 187 ~l~~~v~~L~~lG~~~i~k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~~P~IL 246 (337)
.|...+.||++ |.|-. ..+..|++||++-|++.+||..++.+.+.--
T Consensus 5 li~~A~~FL~~---------p~V~~----sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 5 LIEQAVKFLQD---------PKVRN----SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHCT---------TTCCC----S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHhCC---------ccccc----CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 45556677754 44433 3488999999999999999999999876654
No 11
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=63.65 E-value=6.9 Score=32.91 Aligned_cols=38 Identities=8% Similarity=0.211 Sum_probs=26.2
Q ss_pred hCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhCcccc
Q 037691 104 DHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMCPEIL 144 (337)
Q Consensus 104 ~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL 144 (337)
.+|.+-.. -+..+++||++.|++.++|...+.+.+.--
T Consensus 14 ~~p~V~~s---p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 14 QDPKVRNS---PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp CTTTCCCS----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCcccccC---CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 35665433 377999999999999999999998866533
No 12
>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=60.59 E-value=19 Score=35.07 Aligned_cols=25 Identities=16% Similarity=0.255 Sum_probs=18.0
Q ss_pred HHhCCCChHHHHHHHHhCccccccc
Q 037691 123 ITSLDFAAAEFRRIVSMCPEILTSR 147 (337)
Q Consensus 123 L~~lG~s~~~i~~ii~~~P~iL~~~ 147 (337)
-..+|+....+...+.+||.+|...
T Consensus 44 ~~~L~l~~~~~~~flrkyP~iF~~~ 68 (335)
T PF11955_consen 44 RRQLGLKPRKVSRFLRKYPSIFEVF 68 (335)
T ss_pred HHhcCCCcccHHHHHHhCCceEEEe
Confidence 3347776677888888888877764
No 13
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=59.57 E-value=16 Score=34.47 Aligned_cols=21 Identities=10% Similarity=0.040 Sum_probs=16.3
Q ss_pred CchhhhccCHHHHHHHHchhc
Q 037691 302 PLNVLLKTSEAQFHRRLDVCC 322 (337)
Q Consensus 302 ~l~~ll~~se~~F~e~~~~~~ 322 (337)
....++.....+|.+.|....
T Consensus 219 ~P~~il~~Pan~FV~~f~g~~ 239 (309)
T COG1125 219 TPDEILANPANDFVEDFFGES 239 (309)
T ss_pred CHHHHHhCccHHHHHHHhccc
Confidence 444678888899999988775
No 14
>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=56.56 E-value=16 Score=23.20 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCHHHHhHHHhcC
Q 037691 220 PRLQYFQKIGFSKREATAMFRRF 242 (337)
Q Consensus 220 ~kv~fL~~lG~s~~~i~~ml~~~ 242 (337)
..++-|.++||++++..+.+..+
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 56788889999999998887764
No 15
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=56.03 E-value=26 Score=34.08 Aligned_cols=149 Identities=18% Similarity=0.243 Sum_probs=79.5
Q ss_pred hhHhhhCCCcccCCccC--HHHHHHHHH-hCCCChHHHHHHHHhCcccccccc----cchhHHHHHHHHHhcCChhHHHH
Q 037691 99 FSLINDHPPIVSASLND--IKSTVDLIT-SLDFAAAEFRRIVSMCPEILTSRA----SDILPVFTFLLREAKVNGSDLKR 171 (337)
Q Consensus 99 ~~ii~~~P~lL~~s~e~--l~~~v~~L~-~lG~s~~~i~~ii~~~P~iL~~~~----~~l~~~v~fL~~~lGvs~~~v~~ 171 (337)
..++.+--.+|-++.+. .-.+++.++ ++|++.+=..+++.+||..|..-. ......+.|= .++.++.-+...
T Consensus 100 ~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd-~~LAvs~~E~~~ 178 (335)
T PF11955_consen 100 PDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWD-PELAVSALEKRA 178 (335)
T ss_pred HHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecC-CccCcCccchhh
Confidence 44455555567777764 345566665 699999999999999999887742 1233333332 345555433333
Q ss_pred HHH---------hCccccc------cchhhchhhHHHHHhhhCCc----cccc----c-----------cceeeccchh-
Q 037691 172 VIS---------RRPRLLV------SAVKTRLRPTLYFLQSMGIA----EVNK----H-----------TYLLSCSVED- 216 (337)
Q Consensus 172 li~---------~~P~lL~------~sv~~~l~~~v~~L~~lG~~----~i~k----~-----------P~iL~~s~~~- 216 (337)
.-. ..|.-+- +.+++..+..++-+|++-+. +... . =.+|++.+++
T Consensus 179 ~~~~~~~~~~~~~~~~~Fp~~fp~G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr 258 (335)
T PF11955_consen 179 EKEYREKREDGFDRPLAFPVSFPKGFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKR 258 (335)
T ss_pred hhccccccccccCCceeeeecCCCCccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhh
Confidence 311 0111111 12233445555555655432 1110 0 0133333332
Q ss_pred hHHHHHHHHH-HcCCCHHHHhHHHhcCCcccccC
Q 037691 217 KLIPRLQYFQ-KIGFSKREATAMFRRFPQLFNYS 249 (337)
Q Consensus 217 ~l~~kv~fL~-~lG~s~~~i~~ml~~~P~IL~~s 249 (337)
....++..|+ ++|++ +.+..++.++|.|+-.|
T Consensus 259 ~~~~~L~~fr~ef~lp-~k~~~~l~rHPgIFYvS 291 (335)
T PF11955_consen 259 TEVDHLTHFRKEFGLP-QKFRRLLLRHPGIFYVS 291 (335)
T ss_pred ccHHHHHHHHHHhCCc-HHHHHHHHhCCCeEEEe
Confidence 2345566666 57776 46677777777777777
No 16
>PRK14136 recX recombination regulator RecX; Provisional
Probab=55.83 E-value=1.4e+02 Score=28.72 Aligned_cols=110 Identities=10% Similarity=0.135 Sum_probs=64.1
Q ss_pred CCccCHHHHHHHHHhCC-CChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCChhHHHHHHHhCccccccchhhchh
Q 037691 111 ASLNDIKSTVDLITSLD-FAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVNGSDLKRVISRRPRLLVSAVKTRLR 189 (337)
Q Consensus 111 ~s~e~l~~~v~~L~~lG-~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~ 189 (337)
++.+.++..|+.|.+.| +++..++..+... +.=......| ..-| ..-||+.+.|..++... ..+ .+.
T Consensus 191 ~~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp~rI---rqEL-rQKGId~eLIEqALeei------eED-E~E 258 (309)
T PRK14136 191 DESDSVEPLLDALEREGWLSDARFAESLVHR-RASRVGSARI---VSEL-KRHAVGDALVESVGAQL------RET-EFE 258 (309)
T ss_pred CCHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhHHHH---HHHH-HHcCCCHHHHHHHHHhc------cHh-HHH
Confidence 45567899999999977 5667777766643 1111111122 2334 46799998888888743 111 122
Q ss_pred hHHHHHhh-hCCcccccccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhcC
Q 037691 190 PTLYFLQS-MGIAEVNKHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRRF 242 (337)
Q Consensus 190 ~~v~~L~~-lG~~~i~k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~~ 242 (337)
.....++. ++- .+ .. .......+.||..-||+.+.|..+|..+
T Consensus 259 ~A~~L~eKK~~~-----~~----~d-~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 259 RAQAVWRKKFGA-----LP----QT-PAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHHHHHHhcc-----cC----cC-HHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 22222322 211 11 11 2334566899999999999999888654
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=55.61 E-value=18 Score=22.72 Aligned_cols=24 Identities=25% Similarity=0.444 Sum_probs=19.5
Q ss_pred HHHHHHHHHcCCCHHHHhHHHhcC
Q 037691 219 IPRLQYFQKIGFSKREATAMFRRF 242 (337)
Q Consensus 219 ~~kv~fL~~lG~s~~~i~~ml~~~ 242 (337)
..+++-|..+||+++++...+..+
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356888889999999998877765
No 18
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=55.58 E-value=19 Score=34.02 Aligned_cols=87 Identities=18% Similarity=0.332 Sum_probs=64.5
Q ss_pred CCCccHHHHHHHH-hhCCC----ChhhHhhhCCCcccCCccCHHHHHHHHHh-CCCChHHHHHHHHhCcccccccccchh
Q 037691 79 SPHSEFQEKMLYL-DSIGV----DFFSLINDHPPIVSASLNDIKSTVDLITS-LDFAAAEFRRIVSMCPEILTSRASDIL 152 (337)
Q Consensus 79 ~~~~~l~~~v~fL-~slG~----di~~ii~~~P~lL~~s~e~l~~~v~~L~~-lG~s~~~i~~ii~~~P~iL~~~~~~l~ 152 (337)
-+...+...+-|. +++|+ .+.+=|.-.|.++.++-++++.+++.|.+ +|+++++. ..+||+=|+-.. +
T Consensus 68 ~d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~---~~RyP~eLSGGQ---Q 141 (309)
T COG1125 68 LDPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEY---ADRYPHELSGGQ---Q 141 (309)
T ss_pred CCHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHH---hhcCchhcCcch---h
Confidence 3455667777776 35787 46676788999999999999999987766 89998775 458998666531 1
Q ss_pred HHHHHHHHHhcCChhHHHHHHHhCccccccc
Q 037691 153 PVFTFLLREAKVNGSDLKRVISRRPRLLVSA 183 (337)
Q Consensus 153 ~~v~fL~~~lGvs~~~v~~li~~~P~lL~~s 183 (337)
+..| |.+.++..|.++.++
T Consensus 142 -------QRVG-----v~RALAadP~ilLMD 160 (309)
T COG1125 142 -------QRVG-----VARALAADPPILLMD 160 (309)
T ss_pred -------hHHH-----HHHHHhcCCCeEeec
Confidence 2345 678888999999876
No 19
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=53.78 E-value=28 Score=32.17 Aligned_cols=101 Identities=14% Similarity=0.214 Sum_probs=69.2
Q ss_pred CCCccHHHHHHHHhhCCCChhhHhhhCCCc-ccCCccCHHHHHHHHHhCCCChHHHHHHHHhCcc-cccccccchhHHHH
Q 037691 79 SPHSEFQEKMLYLDSIGVDFFSLINDHPPI-VSASLNDIKSTVDLITSLDFAAAEFRRIVSMCPE-ILTSRASDILPVFT 156 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~di~~ii~~~P~l-L~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~P~-iL~~~~~~l~~~v~ 156 (337)
=++.+-.+++..|.+.|++-.+...+.-.. +.-+.+++...+++|...|++......+-.-+|. =|-.++-.=+.++.
T Consensus 28 L~e~eANemlAlL~~~gI~A~K~~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~eEkaR~~ 107 (246)
T COG4669 28 LSEKEANEMLALLMSHGINAEKKADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTEEKARLN 107 (246)
T ss_pred CCHhHHHHHHHHHHHcCCcceeeccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHHHHHHHH
Confidence 356677889999999999765554333222 2223346889999999999999888777777775 22223222334555
Q ss_pred HHHHHhcCChhHHHHHHHhCccccccchh
Q 037691 157 FLLREAKVNGSDLKRVISRRPRLLVSAVK 185 (337)
Q Consensus 157 fL~~~lGvs~~~v~~li~~~P~lL~~sv~ 185 (337)
|.. ++++.+.|++-..++..++.
T Consensus 108 ~~~------eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 108 YAK------EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHH------HHHHHHHHHhcCceEEEEEE
Confidence 553 46789999999999888775
No 20
>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=53.31 E-value=11 Score=25.60 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=20.6
Q ss_pred HHHHHHHHHHcCCCHHHHhHHHhcCCc
Q 037691 218 LIPRLQYFQKIGFSKREATAMFRRFPQ 244 (337)
Q Consensus 218 l~~kv~fL~~lG~s~~~i~~ml~~~P~ 244 (337)
+.+-++-|..+||++.++.+++.+-..
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 456688899999999999988876543
No 21
>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=52.19 E-value=22 Score=22.43 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=19.1
Q ss_pred HHHHHHHHHcCCCHHHHhHHHhcC
Q 037691 219 IPRLQYFQKIGFSKREATAMFRRF 242 (337)
Q Consensus 219 ~~kv~fL~~lG~s~~~i~~ml~~~ 242 (337)
..+++-|.++||+++++...+..+
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356888889999999988877654
No 22
>PRK14135 recX recombination regulator RecX; Provisional
Probab=51.56 E-value=1.5e+02 Score=27.29 Aligned_cols=58 Identities=9% Similarity=0.009 Sum_probs=33.9
Q ss_pred CCccHHHHHHHHhhCCC--Ch--h-hHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 80 PHSEFQEKMLYLDSIGV--DF--F-SLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 80 ~~~~l~~~v~fL~slG~--di--~-~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
+.+.++..|+.|...|. |. + ..+... +.....--......|+..|++.+.|..++...
T Consensus 87 ~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~---~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l 149 (263)
T PRK14135 87 SEEIISEVIDKLKEEKYIDDKEYAESYVRTN---INTGDKGPRVIKQKLLQKGIEDEIIEEALSEY 149 (263)
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH---HhccccchHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 55677888888888887 31 1 122211 11110112344567778899988888888764
No 23
>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=48.18 E-value=47 Score=26.83 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=19.1
Q ss_pred hhhHHHHHHHHHHcCCCHHHHhHHHhc
Q 037691 215 EDKLIPRLQYFQKIGFSKREATAMFRR 241 (337)
Q Consensus 215 ~~~l~~kv~fL~~lG~s~~~i~~ml~~ 241 (337)
....+..+.+|.+-||+.+.|..++..
T Consensus 92 ~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 92 RKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 345667788888999999998877653
No 24
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=47.59 E-value=1.6e+02 Score=24.86 Aligned_cols=113 Identities=12% Similarity=0.094 Sum_probs=60.3
Q ss_pred cCCccCHHHHHHHHHhCC-CChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCChhHHHHHHHhCccccccchhhch
Q 037691 110 SASLNDIKSTVDLITSLD-FAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVNGSDLKRVISRRPRLLVSAVKTRL 188 (337)
Q Consensus 110 ~~s~e~l~~~v~~L~~lG-~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l 188 (337)
+++.+.+...++.|...| +++...+....+.=.- ...--.....-| ..-|++.+.|..++.... .+ ..
T Consensus 39 g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~---~~~g~~~I~~~L-~~kGi~~~~I~~~l~~~~----~d---~~ 107 (157)
T PRK00117 39 GFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRAR---KGYGPRRIRQEL-RQKGVDREIIEEALAELD----ID---WE 107 (157)
T ss_pred CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh---CCchHHHHHHHH-HHcCCCHHHHHHHHHHcC----cc---HH
Confidence 345456778888888877 4555555554433111 101111223444 367999988888888653 11 11
Q ss_pred hhHHHHHhhhCCcccccccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhc
Q 037691 189 RPTLYFLQSMGIAEVNKHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRR 241 (337)
Q Consensus 189 ~~~v~~L~~lG~~~i~k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~ 241 (337)
......++. +....-..+. ..-+..+.+|.+-||+.+.|..++..
T Consensus 108 e~a~~~~~k-------~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 108 ELARELARK-------KFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHH-------HcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 111122211 0111111121 23456688899999999999887754
No 25
>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=47.53 E-value=13 Score=26.83 Aligned_cols=38 Identities=8% Similarity=0.141 Sum_probs=27.0
Q ss_pred hhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 103 NDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 103 ~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
...|.=+..+.++++..+--|..-|+++++|+.++...
T Consensus 20 ~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~ 57 (60)
T PF08069_consen 20 RSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQ 57 (60)
T ss_dssp SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHS
T ss_pred CCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhc
Confidence 34577777888888888888888999999999888653
No 26
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=46.72 E-value=61 Score=27.85 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=30.0
Q ss_pred hCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 104 DHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 104 ~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
..|.=+.++.|+++..+--|..-|+++++|+-++...
T Consensus 21 ~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 21 EPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 4455677788888888888899999999999888765
No 27
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=45.21 E-value=25 Score=24.99 Aligned_cols=24 Identities=8% Similarity=0.134 Sum_probs=20.1
Q ss_pred HHHHHHHHHhcCChhHHHHHHHhC
Q 037691 153 PVFTFLLREAKVNGSDLKRVISRR 176 (337)
Q Consensus 153 ~~v~fL~~~lGvs~~~v~~li~~~ 176 (337)
--+.||.+.+|++++++..+|...
T Consensus 21 ~ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHH
Confidence 357899889999999999998863
No 28
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=44.61 E-value=73 Score=24.68 Aligned_cols=17 Identities=24% Similarity=0.524 Sum_probs=7.9
Q ss_pred CccHHHHHHHHhhCCCC
Q 037691 81 HSEFQEKMLYLDSIGVD 97 (337)
Q Consensus 81 ~~~l~~~v~fL~slG~d 97 (337)
...+++.+.||..+|+.
T Consensus 5 ~~~~~~~~~~L~~~gl~ 21 (94)
T PF14490_consen 5 NRGLRELMAFLQEYGLS 21 (94)
T ss_dssp ----HHHHHHHHHTT--
T ss_pred HHHHHHHHHHHHHcCCC
Confidence 34556667777777774
No 29
>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=44.23 E-value=27 Score=28.31 Aligned_cols=57 Identities=9% Similarity=0.082 Sum_probs=33.8
Q ss_pred CCccHHHHHHHHhhCCC--Ch--h-hHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHh
Q 037691 80 PHSEFQEKMLYLDSIGV--DF--F-SLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSM 139 (337)
Q Consensus 80 ~~~~l~~~v~fL~slG~--di--~-~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~ 139 (337)
+.+.++..|+.|.+.|+ |- + ..+... +...-.--.....-|+..|++...|...+..
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~---~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~~ 68 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVRSR---LRRKGKGPRRIRQKLKQKGIDREIIEEALEE 68 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHHHH---HHHTT--HHHHHHHHHHTT--HHHHHHHHTC
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHh---cccccccHHHHHHHHHHHCCChHHHHHHHHH
Confidence 56788999999999999 32 2 222211 1001112334556888899999998888873
No 30
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=42.81 E-value=1e+02 Score=23.86 Aligned_cols=25 Identities=0% Similarity=0.138 Sum_probs=16.6
Q ss_pred CHHHHHHHHHhCCCChHHHHHHHHh
Q 037691 115 DIKSTVDLITSLDFAAAEFRRIVSM 139 (337)
Q Consensus 115 ~l~~~v~~L~~lG~s~~~i~~ii~~ 139 (337)
.+...+.||..+|++.....+++..
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4677889999999998777766543
No 31
>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=42.21 E-value=41 Score=22.65 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 116 IKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 116 l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
....++.|.++|++..++.+++.+-
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 3466777888888888887777664
No 32
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=41.10 E-value=65 Score=28.18 Aligned_cols=75 Identities=13% Similarity=0.245 Sum_probs=38.3
Q ss_pred hCCCChHHHHHHHHhCccccccc-ccchhHH-------HHHHHHHhcCChhHHHHHHHhCccccccchhhchhhHHHHHh
Q 037691 125 SLDFAAAEFRRIVSMCPEILTSR-ASDILPV-------FTFLLREAKVNGSDLKRVISRRPRLLVSAVKTRLRPTLYFLQ 196 (337)
Q Consensus 125 ~lG~s~~~i~~ii~~~P~iL~~~-~~~l~~~-------v~fL~~~lGvs~~~v~~li~~~P~lL~~sv~~~l~~~v~~L~ 196 (337)
++|++.+++++...-....+..= -.++.|+ +++|.+.-| ..-.++-|...| ++.++.+..+...++.++
T Consensus 16 ~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~--~~ita~~iM~sp-vv~v~pdDsi~~vv~lM~ 92 (187)
T COG3620 16 ELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEK--TRITAKTIMHSP-VVSVSPDDSISDVVNLMR 92 (187)
T ss_pred HcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhc--ceEeHhhhccCC-eeEECchhhHHHHHHHHH
Confidence 47777777776653322222221 1334443 444422111 111344555556 444444556777888888
Q ss_pred hhCCcc
Q 037691 197 SMGIAE 202 (337)
Q Consensus 197 ~lG~~~ 202 (337)
+.|+++
T Consensus 93 ~~g~SQ 98 (187)
T COG3620 93 DKGISQ 98 (187)
T ss_pred HcCCcc
Confidence 888876
No 33
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=38.36 E-value=35 Score=28.55 Aligned_cols=39 Identities=10% Similarity=0.198 Sum_probs=32.5
Q ss_pred hCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhCcc
Q 037691 104 DHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMCPE 142 (337)
Q Consensus 104 ~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~P~ 142 (337)
..|.-+..+.|++++.+--|...|+++.||+.++...-.
T Consensus 21 ~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshG 59 (151)
T KOG0400|consen 21 SVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHG 59 (151)
T ss_pred CCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccC
Confidence 467778888899999999999999999999988866543
No 34
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=37.32 E-value=35 Score=26.82 Aligned_cols=52 Identities=10% Similarity=0.229 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCCChhhHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHh
Q 037691 85 QEKMLYLDSIGVDFFSLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSM 139 (337)
Q Consensus 85 ~~~v~fL~slG~di~~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~ 139 (337)
-.++.+|...|.|-+..+.+. +..+++++...++-|.++|+=...=++++..
T Consensus 10 ~~IL~hl~~~~~Dy~k~ia~~---l~~~~~~v~~~l~~Le~~GLler~~g~~iK~ 61 (92)
T PF10007_consen 10 LKILQHLKKAGPDYAKSIARR---LKIPLEEVREALEKLEEMGLLERVEGKTIKR 61 (92)
T ss_pred HHHHHHHHHHCCCcHHHHHHH---HCCCHHHHHHHHHHHHHCCCeEEecCcccch
Confidence 457889999999988888876 5778889999999999999876655655544
No 35
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=35.41 E-value=92 Score=26.60 Aligned_cols=36 Identities=8% Similarity=0.187 Sum_probs=29.6
Q ss_pred CCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 105 HPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 105 ~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
.|.-+..+.++++..+--|..-|+++++||-++...
T Consensus 19 ~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 19 PPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred CCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 455577788888888888999999999999888765
No 36
>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=31.86 E-value=5e+02 Score=25.73 Aligned_cols=119 Identities=13% Similarity=0.219 Sum_probs=0.0
Q ss_pred cCHHHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCC----------------------------
Q 037691 114 NDIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVN---------------------------- 165 (337)
Q Consensus 114 e~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs---------------------------- 165 (337)
++.+..|+-+.++|++++++.+.++. .+ ++-..-|+|| .-|+.
T Consensus 154 ~~~e~~I~~i~eMGf~R~qV~~ALRA-----af--NNPdRAVEYL--~tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (378)
T TIGR00601 154 SERETTIEEIMEMGYEREEVERALRA-----AF--NNPDRAVEYL--LTGIPEDPEQPEPVQQTAASTAAATTETPQHGS 224 (378)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHH-----Hh--CCHHHHHHHH--HhCCCccccccccCCCcccccccccCCCCCCcc
Q ss_pred --------------------------------hhHHHHHHHhCccccccchhhchhhH------------HHHHhhhCCc
Q 037691 166 --------------------------------GSDLKRVISRRPRLLVSAVKTRLRPT------------LYFLQSMGIA 201 (337)
Q Consensus 166 --------------------------------~~~v~~li~~~P~lL~~sv~~~l~~~------------v~~L~~lG~~ 201 (337)
-.+++.+|..+|++|--=++ .|... =+||+=++-.
T Consensus 225 lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~lLq-ql~~~nP~l~q~I~~n~e~Fl~ll~~~ 303 (378)
T TIGR00601 225 VFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPPLLQ-QIGQENPQLLQQISQHPEQFLQMLNEP 303 (378)
T ss_pred hhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHHHHH-HHHhhCHHHHHHHHHCHHHHHHHhcCc
Q ss_pred ccc-----------------cccceeeccchhhHHHHHHHHHHcCCCHHHHhHHHhcC
Q 037691 202 EVN-----------------KHTYLLSCSVEDKLIPRLQYFQKIGFSKREATAMFRRF 242 (337)
Q Consensus 202 ~i~-----------------k~P~iL~~s~~~~l~~kv~fL~~lG~s~~~i~~ml~~~ 242 (337)
.-. -.+......+...=+..|+-|+.+||+++.+.+....|
T Consensus 304 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lT~eE~~AIeRL~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 304 VGELAGESDMEGGVGAIAEAGLPQMNQIQVTPEEKEAIERLCALGFDRGLVIQAYFAC 361 (378)
T ss_pred ccccccccccccccccccccCcccccccccCHHHHHHHHHHHHcCCCHHHHHHHHHhc
No 37
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=30.42 E-value=51 Score=28.84 Aligned_cols=73 Identities=16% Similarity=0.235 Sum_probs=43.7
Q ss_pred HHHhcCChhHHHHHHH-hCccccccchh------hchhhHHHHHhhhCCcc-----cccccceeeccchhhHHHHHHHHH
Q 037691 159 LREAKVNGSDLKRVIS-RRPRLLVSAVK------TRLRPTLYFLQSMGIAE-----VNKHTYLLSCSVEDKLIPRLQYFQ 226 (337)
Q Consensus 159 ~~~lGvs~~~v~~li~-~~P~lL~~sv~------~~l~~~v~~L~~lG~~~-----i~k~P~iL~~s~~~~l~~kv~fL~ 226 (337)
++++|++.+++++..- .+|.|=...-. ..++..+++|.+..-.. +...|- +.++.++.+...++.++
T Consensus 14 Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~spv-v~v~pdDsi~~vv~lM~ 92 (187)
T COG3620 14 RKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHSPV-VSVSPDDSISDVVNLMR 92 (187)
T ss_pred HHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcceEeHhhhccCCe-eEECchhhHHHHHHHHH
Confidence 4678888888877643 33433322221 12344455555432121 444554 45566899999999999
Q ss_pred HcCCCH
Q 037691 227 KIGFSK 232 (337)
Q Consensus 227 ~lG~s~ 232 (337)
..|+|.
T Consensus 93 ~~g~SQ 98 (187)
T COG3620 93 DKGISQ 98 (187)
T ss_pred HcCCcc
Confidence 999974
No 38
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=30.35 E-value=2.5e+02 Score=24.38 Aligned_cols=49 Identities=20% Similarity=0.396 Sum_probs=33.1
Q ss_pred CCCccHHHHHHHHhhCCC-ChhhHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHH
Q 037691 79 SPHSEFQEKMLYLDSIGV-DFFSLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRR 135 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~-di~~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ 135 (337)
..|.+++..++||.+-++ ++-.-+...| +++..++||++.|++...+-.
T Consensus 29 ~~D~efq~~~~yl~s~~f~~l~~~l~~~p--------E~~~l~~yL~~~gldv~~~i~ 78 (179)
T PF06757_consen 29 LEDAEFQAAVRYLNSSEFKQLWQQLEALP--------EVKALLDYLESAGLDVYYYIN 78 (179)
T ss_pred HcCHHHHHHHHHHcChHHHHHHHHHHcCH--------HHHHHHHHHHHCCCCHHHHHH
Confidence 356778888888888776 4443333343 456888899999998766433
No 39
>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=29.61 E-value=81 Score=20.75 Aligned_cols=30 Identities=17% Similarity=0.338 Sum_probs=22.4
Q ss_pred hhHHHHHHHHH-HcCCCHHHHhHHHhcCCcc
Q 037691 216 DKLIPRLQYFQ-KIGFSKREATAMFRRFPQL 245 (337)
Q Consensus 216 ~~l~~kv~fL~-~lG~s~~~i~~ml~~~P~I 245 (337)
+++-.+...|. ++|++..+..++|..+|..
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 35566788888 8999999999999999864
No 40
>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=29.37 E-value=1.9e+02 Score=22.66 Aligned_cols=43 Identities=9% Similarity=0.062 Sum_probs=31.6
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhc
Q 037691 117 KSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAK 163 (337)
Q Consensus 117 ~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lG 163 (337)
...-++.+.+|++..+|..+-..+|.- .+.....+.-|++..|
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~----~eq~~qmL~~W~~~~G 62 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVT----REQLYQMLLTWVNKTG 62 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCC----HHHHHHHHHHHHHhhC
Confidence 345567788999999999999998852 3566666777766666
No 41
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=28.54 E-value=64 Score=19.92 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=16.0
Q ss_pred hHHHHHHHHHHcCCCHHHHhHHHhc
Q 037691 217 KLIPRLQYFQKIGFSKREATAMFRR 241 (337)
Q Consensus 217 ~l~~kv~fL~~lG~s~~~i~~ml~~ 241 (337)
.|..-+.-..+.|++.+|++..+..
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 4555566666889999998877653
No 42
>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=28.42 E-value=2e+02 Score=22.67 Aligned_cols=46 Identities=9% Similarity=0.113 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcC
Q 037691 116 IKSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKV 164 (337)
Q Consensus 116 l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGv 164 (337)
+...-+|-+.+|+++.+|..+-..+|.=+ .+.....+.-|.+..|-
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d~---~Eq~~qmL~~W~~~~G~ 65 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQDT---AEQKVQLLRAWYQSHGK 65 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCCh---HHHHHHHHHHHHHHhCC
Confidence 44566788999999999999999988532 24455556666555563
No 43
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=27.08 E-value=55 Score=25.98 Aligned_cols=62 Identities=23% Similarity=0.410 Sum_probs=0.0
Q ss_pred hhHHHHHhhhCCc----cccccc----------ceeeccchhhHHHHHHHHHHcC------CCHHHHhHHHhcCCccccc
Q 037691 189 RPTLYFLQSMGIA----EVNKHT----------YLLSCSVEDKLIPRLQYFQKIG------FSKREATAMFRRFPQLFNY 248 (337)
Q Consensus 189 ~~~v~~L~~lG~~----~i~k~P----------~iL~~s~~~~l~~kv~fL~~lG------~s~~~i~~ml~~~P~IL~~ 248 (337)
+..++||++.|+. ++.+.| ..+..+.++-+..+=..++++| ++.+++..++..+|.++..
T Consensus 10 rka~~~L~~~gi~~~~~d~~k~p~s~~el~~~l~~~~~~~~~lin~~~~~~k~l~~~~~~~~s~~e~i~~l~~~p~LikR 89 (110)
T PF03960_consen 10 RKALKWLEENGIEYEFIDYKKEPLSREELRELLSKLGNGPDDLINTRSKTYKELGKLKKDDLSDEELIELLLENPKLIKR 89 (110)
T ss_dssp HHHHHHHHHTT--EEEEETTTS---HHHHHHHHHHHTSSGGGGB-TTSHHHHHTTHHHCTTSBHHHHHHHHHHSGGGB-S
T ss_pred HHHHHHHHHcCCCeEeehhhhCCCCHHHHHHHHHHhcccHHHHhcCccchHhhhhhhhhhhhhhHHHHHHHHhChhheeC
Q ss_pred Ch
Q 037691 249 SV 250 (337)
Q Consensus 249 sl 250 (337)
.|
T Consensus 90 PI 91 (110)
T PF03960_consen 90 PI 91 (110)
T ss_dssp SE
T ss_pred CE
No 44
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=26.50 E-value=1.7e+02 Score=22.39 Aligned_cols=40 Identities=13% Similarity=0.160 Sum_probs=28.0
Q ss_pred HHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhc
Q 037691 121 DLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAK 163 (337)
Q Consensus 121 ~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lG 163 (337)
++-+.+|++..+|..+-..+|. .-.+.....+..|++.-|
T Consensus 18 ~laR~LGlse~~Id~i~~~~~~---~~~eq~~~mL~~W~~~~g 57 (86)
T cd08306 18 KLARKLGLSETKIESIEEAHPR---NLREQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHHcCCCHHHHHHHHHHCCC---CHHHHHHHHHHHHHHhHC
Confidence 4667789999999999998883 112556666766655555
No 45
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=26.18 E-value=1.7e+02 Score=21.91 Aligned_cols=57 Identities=11% Similarity=0.292 Sum_probs=33.8
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCChhHHH---HHHHhCccccc
Q 037691 117 KSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVNGSDLK---RVISRRPRLLV 181 (337)
Q Consensus 117 ~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs~~~v~---~li~~~P~lL~ 181 (337)
.|.+..|.+..+|+++|..++.. |+.+ -.-....+ ..+|+.++.+- ..+..+|.++.
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~N---Pl~AMa~i-~qLGip~eKLQ~lm~~VMqnP~Lik 61 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQN---PLAAMATI-QQLGIPQEKLQQLMAQVMQNPALIK 61 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhC---HHHHHHHH-HHcCCCHHHHHHHHHHHhcChHHHH
Confidence 36677888888888888877654 2222 12223444 46788876644 34445665543
No 46
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=24.69 E-value=3.3e+02 Score=22.86 Aligned_cols=58 Identities=9% Similarity=0.052 Sum_probs=35.4
Q ss_pred CCccHHHHHHHHhhCCC-C---h-hhHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhCc
Q 037691 80 PHSEFQEKMLYLDSIGV-D---F-FSLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMCP 141 (337)
Q Consensus 80 ~~~~l~~~v~fL~slG~-d---i-~~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~P 141 (337)
+.+.++..|+.|...|. | . ...+... .- .-.--......|+..|++.+.|..++....
T Consensus 41 ~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~-~~---~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~ 103 (157)
T PRK00117 41 SEEVIEAVLDRLKEEGLLDDERFAESFVRSR-AR---KGYGPRRIRQELRQKGVDREIIEEALAELD 103 (157)
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-Hh---CCchHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence 45677777778887777 2 1 1222222 11 101133445688899999999998888754
No 47
>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=24.63 E-value=2.3e+02 Score=19.07 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=28.0
Q ss_pred HHcCCCHHHHhHHHhcCCcccccChhhhHHHHHHHHHHhhCCCh
Q 037691 226 QKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYFVVGMGRDL 269 (337)
Q Consensus 226 ~~lG~s~~~i~~ml~~~P~IL~~sle~~L~~k~~fL~~~mG~~~ 269 (337)
+..|+|...|.+++...|.+ + ...+.|+.-..+++|+.+
T Consensus 7 ~~agvS~~TVSr~ln~~~~v---s--~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPPRV---S--EETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHTSSHHHHHHHHTTCSSS---T--HHHHHHHHHHHHHHTB-S
T ss_pred HHHCcCHHHHHHHHhCCCCC---C--HHHHHHHHHHHHHHCCCC
Confidence 47899999999999887644 4 456666666667888753
No 48
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=24.38 E-value=92 Score=29.55 Aligned_cols=64 Identities=17% Similarity=0.179 Sum_probs=38.7
Q ss_pred hhHHHHHHHHHHhhCCChhHHhhcCcccccCccchhHHHHHHHHHcCC--CCCchhhhccCHHHHHHHHc
Q 037691 252 DNYERKLNYFVVGMGRDLKELKEFPQYFSFSLENRIKPRHQACVDKGV--CFPLNVLLKTSEAQFHRRLD 319 (337)
Q Consensus 252 ~~L~~k~~fL~~~mG~~~~~I~~~P~~L~~Sle~rI~pR~~~L~~~Gl--~~~l~~ll~~se~~F~e~~~ 319 (337)
+-++.+++.+. ..|++.+.|+--|- +++. +.....++.|+.... ...++-++-.|.+.|...+.
T Consensus 163 ~~l~~~i~~a~-~~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~~lg~Pilvg~SRKsfig~~~ 228 (282)
T PRK11613 163 RYFIEQIARCE-AAGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFHHFNLPLLVGMSRKSMIGQLL 228 (282)
T ss_pred HHHHHHHHHHH-HcCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHHhCCCCEEEEecccHHHHhhc
Confidence 34566677665 68999888888884 4543 334445554433211 13445567778888886654
No 49
>PRK09875 putative hydrolase; Provisional
Probab=24.01 E-value=68 Score=30.53 Aligned_cols=29 Identities=24% Similarity=0.406 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHhHHHhcCCc
Q 037691 216 DKLIPRLQYFQKIGFSKREATAMFRRFPQ 244 (337)
Q Consensus 216 ~~l~~kv~fL~~lG~s~~~i~~ml~~~P~ 244 (337)
.-+..-+..|++.|+++++|.+|+..+|+
T Consensus 260 ~i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 260 YLLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 34666677888999999999999999996
No 50
>PRK14136 recX recombination regulator RecX; Provisional
Probab=23.81 E-value=3.3e+02 Score=26.22 Aligned_cols=55 Identities=16% Similarity=0.112 Sum_probs=31.1
Q ss_pred CCccHHHHHHHHhhCCC--C--hh-hHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHh
Q 037691 80 PHSEFQEKMLYLDSIGV--D--FF-SLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSM 139 (337)
Q Consensus 80 ~~~~l~~~v~fL~slG~--d--i~-~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~ 139 (337)
+.+.++..|++|.+.|+ | .. ..|.. .. .-.--.....-|+..|++.+-|...+..
T Consensus 192 ~ee~IE~VIerLke~gYLDDeRFAesyVr~--R~---~kkGp~rIrqELrQKGId~eLIEqALee 251 (309)
T PRK14136 192 ESDSVEPLLDALEREGWLSDARFAESLVHR--RA---SRVGSARIVSELKRHAVGDALVESVGAQ 251 (309)
T ss_pred CHHHHHHHHHHHHHcCCcCHHHHHHHHHHH--Hh---hchhHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 44566677777777777 2 22 22211 01 1011223346788899999888888764
No 51
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.64 E-value=1.1e+02 Score=20.85 Aligned_cols=50 Identities=10% Similarity=0.177 Sum_probs=34.4
Q ss_pred CCccHHHHHHHHhhCCCChhhHhhhC-----CCcccCCccCHHHHHHHHHhCCCC
Q 037691 80 PHSEFQEKMLYLDSIGVDFFSLINDH-----PPIVSASLNDIKSTVDLITSLDFA 129 (337)
Q Consensus 80 ~~~~l~~~v~fL~slG~di~~ii~~~-----P~lL~~s~e~l~~~v~~L~~lG~s 129 (337)
-.+.+.+.++.|.+.|+.+..+.... -..+...++......+.|++.|+.
T Consensus 9 ~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~~~~~~~~L~~~G~~ 63 (65)
T cd04882 9 KPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTEDIEKAIEVLQERGVE 63 (65)
T ss_pred CCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCCHHHHHHHHHHCCce
Confidence 34588899999999999876553211 123444556677888888888874
No 52
>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=23.50 E-value=65 Score=25.82 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=30.9
Q ss_pred cCHHHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCChhHHHHHH
Q 037691 114 NDIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVNGSDLKRVI 173 (337)
Q Consensus 114 e~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs~~~v~~li 173 (337)
+.++..++.|...|++..++..|+.-+|. +...+...+.-+ +-.++++++.++|
T Consensus 57 e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~----~~~El~~ii~~~--~~r~~ee~l~~iL 110 (117)
T PF03874_consen 57 ESIKELREELKKFGLTEFEILQIINLRPT----TAVELRAIIESL--ESRFSEEDLEEIL 110 (117)
T ss_dssp HHHHHHHHHHTTSTS-HHHHHHHHHH--S----SHHHHHHHSTTG--TTTSTHHHHHHHH
T ss_pred HHHHHHHHHHhcccCCHHHHHHHhcCCCC----CHHHHHHHHHHh--ccCCCHHHHHHHH
Confidence 45777788888888888888888888883 222333333222 1125555555554
No 53
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=23.42 E-value=1.8e+02 Score=31.36 Aligned_cols=93 Identities=15% Similarity=0.214 Sum_probs=58.7
Q ss_pred cHHHHHHHHhhC---CC--C-hhhHhhhCCCcccCCccCHHHHHHHHHhC-CCChHHHHHHHHhCcccccccccchhHHH
Q 037691 83 EFQEKMLYLDSI---GV--D-FFSLINDHPPIVSASLNDIKSTVDLITSL-DFAAAEFRRIVSMCPEILTSRASDILPVF 155 (337)
Q Consensus 83 ~l~~~v~fL~sl---G~--d-i~~ii~~~P~lL~~s~e~l~~~v~~L~~l-G~s~~~i~~ii~~~P~iL~~~~~~l~~~v 155 (337)
..+..+.||.+- |+ . -.+|+.++..= .++.+....+-|.++ |++.+....+....- ........+
T Consensus 76 ~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~---~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~-----~~~~~~~~~ 147 (720)
T TIGR01448 76 SKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEA---AFDVLDDDPEKLLEVPGISKANLEKFVSQWS-----QQGDERRLL 147 (720)
T ss_pred CHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHh---HHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH-----HhHHHHHHH
Confidence 456677899863 33 1 34566555321 124455556677774 999999998887752 112366778
Q ss_pred HHHHHHhcCChhHHH-----------HHHHhCccccccch
Q 037691 156 TFLLREAKVNGSDLK-----------RVISRRPRLLVSAV 184 (337)
Q Consensus 156 ~fL~~~lGvs~~~v~-----------~li~~~P~lL~~sv 184 (337)
.|| ..+|++.+... .+|..+|+.|..++
T Consensus 148 ~~L-~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i 186 (720)
T TIGR01448 148 AGL-QGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDV 186 (720)
T ss_pred HHH-HHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhc
Confidence 888 58999976444 45566676666543
No 54
>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=23.13 E-value=3.1e+02 Score=20.84 Aligned_cols=45 Identities=7% Similarity=0.072 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcC
Q 037691 116 IKSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKV 164 (337)
Q Consensus 116 l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGv 164 (337)
+...-+|.+.+|+++.+|..+=..+| .. .+.....+.-|++.-|-
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~---~~-~Eq~yqmL~~W~~~~g~ 55 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR---RC-RDAQYQMLKVWKERGPR 55 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC---Ch-HHHHHHHHHHHHHhcCC
Confidence 45566788999999999999988886 22 24455556666554553
No 55
>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=22.47 E-value=1.1e+02 Score=26.68 Aligned_cols=51 Identities=14% Similarity=0.207 Sum_probs=35.0
Q ss_pred CHHHHHHHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhcCChhHHHHH
Q 037691 115 DIKSTVDLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAKVNGSDLKRV 172 (337)
Q Consensus 115 ~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lGvs~~~v~~l 172 (337)
+....++.++..|++++++.+.=..+= . ..=..-.+|| +.+|++.+++..+
T Consensus 117 ~~~~w~~l~~~~g~~~~~m~~wh~~fe----~--~~p~~h~~~l-~~~g~~~~~~~~i 167 (172)
T cd04790 117 TKEKWVAILKAAGMDEADMRRWHIEFE----K--MEPEAHQEFL-QSLGIPEDEIERI 167 (172)
T ss_pred CHHHHHHHHHHcCCChHHHHHHHHHHH----H--hCcHHHHHHH-HHcCCCHHHHHHH
Confidence 456778888999999988755543321 1 2233456888 5899999887665
No 56
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.42 E-value=1.1e+02 Score=24.67 Aligned_cols=52 Identities=12% Similarity=0.066 Sum_probs=35.9
Q ss_pred HHHHHHhhCCC-ChhhHhhhCCCcccCCccC--HHHHHHHHHhCCCChHHHHHHHHhC
Q 037691 86 EKMLYLDSIGV-DFFSLINDHPPIVSASLND--IKSTVDLITSLDFAAAEFRRIVSMC 140 (337)
Q Consensus 86 ~~v~fL~slG~-di~~ii~~~P~lL~~s~e~--l~~~v~~L~~lG~s~~~i~~ii~~~ 140 (337)
.++.|..+.|+ .... +.+..-.++.++ .-..+..|+++|++-++|..++..+
T Consensus 15 ~tLryYe~~GLi~p~~---~~~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (116)
T cd04769 15 KAIRLYEEKGLLPSPK---RSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGH 69 (116)
T ss_pred HHHHHHHHCCCCCCCC---CCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 46668888888 3322 233444456554 3456888999999999999998764
No 57
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=22.35 E-value=2.1e+02 Score=23.95 Aligned_cols=53 Identities=9% Similarity=0.192 Sum_probs=31.9
Q ss_pred HHHHHHhCCCChHHHHHHHHhCc---ccccccccchhHHHHHHHHHhcCChhHHHHHHHh
Q 037691 119 TVDLITSLDFAAAEFRRIVSMCP---EILTSRASDILPVFTFLLREAKVNGSDLKRVISR 175 (337)
Q Consensus 119 ~v~~L~~lG~s~~~i~~ii~~~P---~iL~~~~~~l~~~v~fL~~~lGvs~~~v~~li~~ 175 (337)
.-+||+=+|++++.|..++.+-- .++..+.+++. +.+ +.+|.++++.+++.+.
T Consensus 69 l~~WL~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~---~~l-~~~g~~~EE~rRL~~A 124 (129)
T PF13543_consen 69 LRQWLRVVGLRPESIQAILSKVLTLEALLEMSDEELK---EIL-NRCGAREEECRRLCRA 124 (129)
T ss_pred HHHHhhhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHH---HHH-HHhCCCHHHHHHHHHH
Confidence 34688889999998888865421 12223322232 233 4577777777777653
No 58
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=21.98 E-value=4.3e+02 Score=22.10 Aligned_cols=77 Identities=22% Similarity=0.377 Sum_probs=44.3
Q ss_pred ChhHHHHHHHhCccccccchh----hchhhHH-HHHhhhCCc----ccccccc-e-eeccchhhHHHHHHHHHHcCCCHH
Q 037691 165 NGSDLKRVISRRPRLLVSAVK----TRLRPTL-YFLQSMGIA----EVNKHTY-L-LSCSVEDKLIPRLQYFQKIGFSKR 233 (337)
Q Consensus 165 s~~~v~~li~~~P~lL~~sv~----~~l~~~v-~~L~~lG~~----~i~k~P~-i-L~~s~~~~l~~kv~fL~~lG~s~~ 233 (337)
+..++-.++.+||++=...+- +++...+ -||.-.|+. ++--+-. + =.+.+++.+-+++.-|..-|.+.+
T Consensus 29 SN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinEYy~i~~~vi~~I~el~~eG~s~e 108 (131)
T PF08004_consen 29 SNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINEYYEIPESVIERIKELKSEGKSEE 108 (131)
T ss_pred cchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCcccccCCHHHHHHHHHHHHcCCCHH
Confidence 556778888888876553322 2333333 234434554 1211000 0 001245678899999999999999
Q ss_pred HHhHHHhc
Q 037691 234 EATAMFRR 241 (337)
Q Consensus 234 ~i~~ml~~ 241 (337)
++..-+.+
T Consensus 109 ei~~ki~~ 116 (131)
T PF08004_consen 109 EIAEKISR 116 (131)
T ss_pred HHHHHHHH
Confidence 99765554
No 59
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.98 E-value=2.5e+02 Score=21.64 Aligned_cols=39 Identities=18% Similarity=0.259 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCCHHHHhHHHhcCCcccccChhhhHHHHHHHH
Q 037691 219 IPRLQYFQKIGFSKREATAMFRRFPQLFNYSVKDNYERKLNYF 261 (337)
Q Consensus 219 ~~kv~fL~~lG~s~~~i~~ml~~~P~IL~~sle~~L~~k~~fL 261 (337)
-..+..|+.+||+-++|..++..... ...+.++.+.+-+
T Consensus 47 l~~I~~lr~~G~~l~eI~~~l~~~~~----~~~~~l~~~~~~l 85 (96)
T cd04788 47 LHQIIALRRLGFSLREIGRALDGPDF----DPLELLRRQLARL 85 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhCCCh----hHHHHHHHHHHHH
Confidence 36678888999999999999875442 2224455554444
No 60
>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=21.43 E-value=90 Score=21.94 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=14.0
Q ss_pred HHHHHHHcCCCHHHHhHHH
Q 037691 221 RLQYFQKIGFSKREATAMF 239 (337)
Q Consensus 221 kv~fL~~lG~s~~~i~~ml 239 (337)
-|..++.+|||-++|..++
T Consensus 6 ~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3556678999999999998
No 61
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=21.12 E-value=1.6e+02 Score=28.63 Aligned_cols=96 Identities=15% Similarity=0.185 Sum_probs=53.1
Q ss_pred CCCccHHHHHHHHhhCCCChhhHhhhCCCcccCCccCHHHHHHHHHhCCCChHHHHHHHHhCcccccc------------
Q 037691 79 SPHSEFQEKMLYLDSIGVDFFSLINDHPPIVSASLNDIKSTVDLITSLDFAAAEFRRIVSMCPEILTS------------ 146 (337)
Q Consensus 79 ~~~~~l~~~v~fL~slG~di~~ii~~~P~lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii~~~P~iL~~------------ 146 (337)
..+.+.+..|.-+.++|-+...++.. |..+..+-+..|+||.. |++...-.......|..-..
T Consensus 130 v~G~~~e~~V~~Im~MGy~re~V~~A----lRAafNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~ 204 (340)
T KOG0011|consen 130 VVGSEYEQTVQQIMEMGYDREEVERA----LRAAFNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFP 204 (340)
T ss_pred hccchhHHHHHHHHHhCccHHHHHHH----HHHhhCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCC
Confidence 44557788888888999876655432 33455677788888875 45542111111111111111
Q ss_pred c--c-cchhHHHHHHHHHhcCChhHHHHHHHhCccccc
Q 037691 147 R--A-SDILPVFTFLLREAKVNGSDLKRVISRRPRLLV 181 (337)
Q Consensus 147 ~--~-~~l~~~v~fL~~~lGvs~~~v~~li~~~P~lL~ 181 (337)
. + ..-..-++||+..- .-.+++.+|..+|.+|.
T Consensus 205 ~~~~~~~~~~~l~fLr~~~--qf~~lR~~iqqNP~ll~ 240 (340)
T KOG0011|consen 205 QGAVEASGGDPLEFLRNQP--QFQQLRQMIQQNPELLH 240 (340)
T ss_pred ccchhhhcCCchhhhhccH--HHHHHHHHHhhCHHHHH
Confidence 1 0 11123477885322 23568888999987765
No 62
>PHA02591 hypothetical protein; Provisional
Probab=20.62 E-value=1.4e+02 Score=22.74 Aligned_cols=30 Identities=13% Similarity=0.225 Sum_probs=24.4
Q ss_pred cccCCccCHHHHHHHHHhCCCChHHHHHHH
Q 037691 108 IVSASLNDIKSTVDLITSLDFAAAEFRRIV 137 (337)
Q Consensus 108 lL~~s~e~l~~~v~~L~~lG~s~~~i~~ii 137 (337)
-+-.+.|++.....-|.+.|++..+|++.+
T Consensus 40 yfi~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 40 YFVESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EEEeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 344566789999999999999999998654
No 63
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=20.40 E-value=1.6e+02 Score=24.07 Aligned_cols=15 Identities=13% Similarity=0.539 Sum_probs=10.4
Q ss_pred cHHHHHHHHhhCCCC
Q 037691 83 EFQEKMLYLDSIGVD 97 (337)
Q Consensus 83 ~l~~~v~fL~slG~d 97 (337)
..+...+||+..|++
T Consensus 13 t~rka~~~L~~~gi~ 27 (117)
T COG1393 13 TCRKALAWLEEHGIE 27 (117)
T ss_pred HHHHHHHHHHHcCCC
Confidence 345566788888885
No 64
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.34 E-value=2.5e+02 Score=21.69 Aligned_cols=26 Identities=15% Similarity=0.329 Sum_probs=20.8
Q ss_pred HHHHHHHHHHcCCCHHHHhHHHhcCC
Q 037691 218 LIPRLQYFQKIGFSKREATAMFRRFP 243 (337)
Q Consensus 218 l~~kv~fL~~lG~s~~~i~~ml~~~P 243 (337)
.-..+.+|+.+|++-++|..++....
T Consensus 46 ~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 46 QLQFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCc
Confidence 33567888899999999999887643
No 65
>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=20.31 E-value=1.5e+02 Score=21.73 Aligned_cols=35 Identities=17% Similarity=0.522 Sum_probs=25.9
Q ss_pred hhhHHHHHHHHHHcCCCHHHHhHHHhcCCcccccC
Q 037691 215 EDKLIPRLQYFQKIGFSKREATAMFRRFPQLFNYS 249 (337)
Q Consensus 215 ~~~l~~kv~fL~~lG~s~~~i~~ml~~~P~IL~~s 249 (337)
...++..++.++.+||+.++|...|.+-=.+.+.+
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~n 42 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGN 42 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCC
Confidence 45788889999999999999887776544444433
No 66
>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=20.26 E-value=1.3e+02 Score=21.42 Aligned_cols=21 Identities=24% Similarity=0.656 Sum_probs=14.8
Q ss_pred HHHHHHHcCCCHHHHhHHHhc
Q 037691 221 RLQYFQKIGFSKREATAMFRR 241 (337)
Q Consensus 221 kv~fL~~lG~s~~~i~~ml~~ 241 (337)
-|+-|..+||+.+.|...+++
T Consensus 12 lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHcCCcHHHHHHHHHH
Confidence 477788889988888877765
No 67
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. 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 (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=20.17 E-value=2.8e+02 Score=21.05 Aligned_cols=39 Identities=18% Similarity=0.180 Sum_probs=25.6
Q ss_pred HHHHhCCCChHHHHHHHHhCcccccccccchhHHHHHHHHHhc
Q 037691 121 DLITSLDFAAAEFRRIVSMCPEILTSRASDILPVFTFLLREAK 163 (337)
Q Consensus 121 ~~L~~lG~s~~~i~~ii~~~P~iL~~~~~~l~~~v~fL~~~lG 163 (337)
++-+.+|++..+|..|-..++.+ .+.....+..|++.-|
T Consensus 23 ~Lar~LGls~~dI~~i~~~~~~~----~eq~~~mL~~W~~r~g 61 (86)
T cd08318 23 TLAPHLEMKDKEIRAIESDSEDI----KMQAKQLLVAWQDREG 61 (86)
T ss_pred HHHHHcCCCHHHHHHHHhcCCCH----HHHHHHHHHHHHHhcC
Confidence 35567999999998887766531 2455666666654445
Done!