Query 035716
Match_columns 308
No_of_seqs 221 out of 1306
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 05:41:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 2.7E-49 5.9E-54 384.7 18.4 263 36-303 135-441 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 3.7E-43 8E-48 330.2 2.3 257 39-299 12-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 5E-38 1.1E-42 305.9 16.8 232 47-282 111-352 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 4.1E-31 8.8E-36 248.4 6.4 231 67-300 2-314 (345)
5 KOG1267 Mitochondrial transcri 99.9 1.2E-21 2.5E-26 188.7 11.7 207 65-282 201-410 (413)
6 KOG1267 Mitochondrial transcri 99.8 2.7E-18 5.8E-23 165.4 12.8 212 62-282 91-341 (413)
7 smart00733 Mterf Mitochondrial 97.2 0.00024 5.1E-09 41.8 1.8 30 220-251 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.1 0.00038 8.3E-09 40.8 2.1 22 115-137 4-25 (31)
9 PF11955 PORR: Plant organelle 93.6 0.13 2.8E-06 48.4 5.4 235 35-281 47-330 (335)
10 cd04790 HTH_Cfa-like_unk Helix 72.3 7.3 0.00016 33.0 4.8 144 64-221 16-167 (172)
11 PF14490 HHH_4: Helix-hairpin- 70.4 10 0.00022 28.6 4.7 56 60-115 6-77 (94)
12 COG4669 EscJ Type III secretor 68.3 13 0.00028 33.1 5.5 97 60-164 31-130 (246)
13 PF11955 PORR: Plant organelle 65.8 16 0.00034 34.5 6.0 41 191-231 108-150 (335)
14 PF14490 HHH_4: Helix-hairpin- 65.4 16 0.00034 27.5 4.9 20 93-112 7-26 (94)
15 PF04695 Pex14_N: Peroxisomal 65.3 2.4 5.1E-05 34.5 0.3 25 94-118 23-47 (136)
16 COG1125 OpuBA ABC-type proline 64.2 8.6 0.00019 35.0 3.7 53 200-253 72-126 (309)
17 PF00627 UBA: UBA/TS-N domain; 63.6 11 0.00024 23.1 3.1 23 203-225 4-26 (37)
18 smart00165 UBA Ubiquitin assoc 61.8 13 0.00028 22.5 3.2 23 203-225 3-25 (37)
19 cd00194 UBA Ubiquitin Associat 57.3 17 0.00036 22.1 3.2 23 203-225 3-25 (38)
20 PF04695 Pex14_N: Peroxisomal 55.6 12 0.00026 30.4 2.9 30 200-229 22-51 (136)
21 COG3747 Phage terminase, small 45.2 19 0.00042 29.6 2.5 100 148-253 33-133 (160)
22 PF07499 RuvA_C: RuvA, C-termi 44.3 37 0.0008 22.0 3.4 26 201-226 3-28 (47)
23 PF02022 Integrase_Zn: Integra 43.1 42 0.00091 21.2 3.3 29 200-228 7-36 (40)
24 COG3747 Phage terminase, small 39.7 40 0.00086 27.8 3.5 111 32-151 24-138 (160)
25 PRK14136 recX recombination re 36.7 2.8E+02 0.006 25.9 8.9 110 89-225 191-302 (309)
26 PRK11613 folP dihydropteroate 35.1 61 0.0013 29.8 4.5 61 238-302 166-228 (282)
27 PF11212 DUF2999: Protein of u 32.2 47 0.001 23.9 2.4 20 96-115 3-22 (82)
28 PF08004 DUF1699: Protein of u 31.9 2E+02 0.0043 23.1 6.2 81 144-224 29-116 (131)
29 PF02126 PTE: Phosphotriestera 30.9 80 0.0017 29.4 4.6 124 93-227 168-304 (308)
30 KOG0400 40S ribosomal protein 30.0 41 0.00089 27.1 2.1 36 81-116 20-55 (151)
31 PF08069 Ribosomal_S13_N: Ribo 29.3 12 0.00026 26.0 -0.9 33 83-115 22-54 (60)
32 PF08671 SinI: Anti-repressor 27.3 85 0.0019 18.5 2.6 24 201-224 5-28 (30)
33 PF09288 UBA_3: Fungal ubiquit 27.0 84 0.0018 21.4 2.9 23 203-225 11-33 (55)
34 COG4003 Uncharacterized protei 27.0 85 0.0018 23.3 3.1 38 39-84 35-75 (98)
35 cd08313 Death_TNFR1 Death doma 26.7 1.3E+02 0.0027 22.1 4.1 45 94-143 11-55 (80)
36 COG1125 OpuBA ABC-type proline 25.4 2.5E+02 0.0053 25.9 6.4 95 121-233 65-161 (309)
37 PF12244 DUF3606: Protein of u 25.4 52 0.0011 22.4 1.7 25 131-155 20-44 (57)
38 cd08306 Death_FADD Fas-associa 24.9 86 0.0019 23.2 3.0 39 100-142 19-57 (86)
39 cd08315 Death_TRAILR_DR4_DR5 D 24.7 1.2E+02 0.0027 22.9 3.9 43 95-142 20-62 (96)
40 PRK09875 putative hydrolase; P 24.3 78 0.0017 29.2 3.2 27 201-227 262-288 (292)
41 PF10007 DUF2250: Uncharacteri 23.7 91 0.002 23.6 2.9 53 62-117 9-61 (92)
42 TIGR01448 recD_rel helicase, p 22.0 1.2E+02 0.0025 31.9 4.3 109 63-181 78-205 (720)
43 PF09278 MerR-DNA-bind: MerR, 21.9 1.1E+02 0.0023 20.8 2.8 18 205-222 7-24 (65)
44 KOG4168 Predicted RNA polymera 21.8 1.6E+02 0.0034 24.2 4.1 27 129-156 71-97 (149)
45 PF08212 Lipocalin_2: Lipocali 21.5 41 0.00088 27.2 0.7 17 62-78 121-137 (143)
46 cd04768 HTH_BmrR-like Helix-Tu 21.4 3.5E+02 0.0076 20.1 5.9 23 203-225 48-70 (96)
47 cd04790 HTH_Cfa-like_unk Helix 21.2 55 0.0012 27.6 1.5 51 93-151 117-167 (172)
48 cd08316 Death_FAS_TNFRSF6 Deat 21.0 2.1E+02 0.0046 21.7 4.5 74 94-172 20-93 (97)
49 cd04777 HTH_MerR-like_sg1 Heli 20.9 2.7E+02 0.0058 21.1 5.2 52 169-224 15-67 (107)
50 PF13411 MerR_1: MerR HTH fami 20.8 2.1E+02 0.0044 19.4 4.2 23 201-223 45-67 (69)
51 cd00739 DHPS DHPS subgroup of 20.6 2.1E+02 0.0046 25.7 5.2 61 237-302 152-215 (257)
52 PF10440 WIYLD: Ubiquitin-bind 20.4 1.6E+02 0.0034 20.8 3.4 35 199-233 9-43 (65)
53 cd04769 HTH_MerR2 Helix-Turn-H 20.2 2.5E+02 0.0054 21.7 5.0 54 169-225 15-69 (116)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2.7e-49 Score=384.74 Aligned_cols=263 Identities=25% Similarity=0.498 Sum_probs=238.9
Q ss_pred ccc-ccchhhhhhCCCCCCCCCChhhhHHHHHHHHhhcCCCh---hhhhhhCCCcccCCcc-CHHHHHHHHHhCCCCCCC
Q 035716 36 HLS-TKPKSLLQNHPLYPPTQANLSFQIKEKILCLEIMGVDS---GKALSLNPSLHSASLN-SIEGIISFLQSKGILQKD 110 (308)
Q Consensus 36 ~~~-~~~~~l~~~~P~~~~~~~d~~~~~~~~l~~L~~~G~~~---~~il~~~P~lL~~s~~-~l~~~v~~L~~lGls~~~ 110 (308)
.++ ..++.++.++|.++. +++..++.|+++||+++|++. ++++.++|.+|+++++ ++.++++||.++|++.++
T Consensus 135 G~s~~~i~~lI~~~P~lL~--~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~ 212 (487)
T PLN03196 135 GVTRSSLPELLRRYPQVLH--ASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRD 212 (487)
T ss_pred CCCHHHHHHHHHhCCceec--ccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHH
Confidence 344 567889999999998 789889999999999999975 7889999999999998 599999999999999999
Q ss_pred hhhhhhcCCceeeCCcccchhHHHHHhhhhcCCCcchHHHHHhhcCccccccchhchHHHHHHHHHcCCCCc--ch----
Q 035716 111 LPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDL--NA---- 184 (308)
Q Consensus 111 i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~--~~---- 184 (308)
+++++.++|++|+++++++++|+++||+ ++|++.++|++++.++|++|++++++++++++++|+++|+++. ..
T Consensus 213 i~~il~~~P~iL~~sve~~i~P~v~fL~-~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~ 291 (487)
T PLN03196 213 IGPMLTRFPEILGMRVGNNIKPKVDYLE-SLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQ 291 (487)
T ss_pred HHHHHHhCcHHhhcChhhhHHHHHHHHH-HcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 9999999999999999999999999996 8999999999999999999999998899999999999998742 12
Q ss_pred ---------------------------------hhhhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHHHhcCcceeee
Q 035716 185 ---------------------------------LAYQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLMVLRCPGLFTF 231 (308)
Q Consensus 185 ---------------------------------ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~ 231 (308)
++.++|.++..+ +++|.++++||+++||+.++|..|+.++|.+|++
T Consensus 292 ~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lS-e~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~ 370 (487)
T PLN03196 292 YPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLN-RNVALKHVEFLRGRGFSAQDVAKMVVRCPQILAL 370 (487)
T ss_pred CCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhccc-HHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeec
Confidence 344566666666 4578999999999999999999999999999999
Q ss_pred ccccchhHHHHHHHHHhCCChHHHhhcCccccccccCchHHHHHHHHHcCCCCCchhhcccCHHHHHHHhcc
Q 035716 232 SIENNFKPKFEYFNLEIKGKLEELKEFPQYFAFSLEKRIKPRHMQALRNGARLSLPVMLKTSDEEFNELIKP 303 (308)
Q Consensus 232 s~e~~l~~k~~fL~~~mg~~~~~l~~~P~~L~~sle~ri~pR~~~L~~~G~~~~l~~il~~sd~~F~~~~~~ 303 (308)
|.+ +|++|++||.++||++.++|++||++|+||+|+||+|||++|+++|+++++.++|++||++|+++|+.
T Consensus 371 S~~-~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r~v~ 441 (487)
T PLN03196 371 NLE-IMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQRMSG 441 (487)
T ss_pred cHH-HHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHHHhh
Confidence 995 99999999999999999999999999999999999999999999999999999999999999999983
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=3.7e-43 Score=330.16 Aligned_cols=257 Identities=37% Similarity=0.593 Sum_probs=198.8
Q ss_pred ccchhhhhhCCCCCCCCCChhhhHHHHHHHHhhcCCCh---hhhhhhCCCcccCCcc-CHHHHHHHHHhCCCCCCChhhh
Q 035716 39 TKPKSLLQNHPLYPPTQANLSFQIKEKILCLEIMGVDS---GKALSLNPSLHSASLN-SIEGIISFLQSKGILQKDLPRI 114 (308)
Q Consensus 39 ~~~~~l~~~~P~~~~~~~d~~~~~~~~l~~L~~~G~~~---~~il~~~P~lL~~s~~-~l~~~v~~L~~lGls~~~i~~l 114 (308)
.+|..+++++|.++. +|..+.+.|+++||.++|++. ++++.++|.++..+.+ ++.+.++||+++|++++++.++
T Consensus 12 ~~i~~~i~~~P~~l~--~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~ 89 (345)
T PF02536_consen 12 SQISKLIRRYPRLLL--CDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKV 89 (345)
T ss_dssp S-HHHHHH-H-HHHH--T-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHH
T ss_pred HHHHHHHHhCCceEE--ecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHH
Confidence 678889999998888 788889999999999999984 7899999999999965 6999999999999999999999
Q ss_pred hhcCCceeeCCcccchhHHHHHhhhhcC----------------------------------CCcchHHHHHhhcCcccc
Q 035716 115 FGMCPKVLTANIKTDLEPVFNFLSHDLE----------------------------------VPEHDFRKVINKCPRLLT 160 (308)
Q Consensus 115 i~~~P~lL~~~~e~~l~~~l~fL~~~~G----------------------------------~~~~~i~~li~~~P~lL~ 160 (308)
+.++|++|..+.+.++.++++||+ ++| ++++++.+++.++|+++.
T Consensus 90 l~r~p~~l~~~~~~~l~~~v~~L~-~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~ 168 (345)
T PF02536_consen 90 LKRYPRILSFSVEENLSPNVAFLR-SLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRVIAKNPRLLL 168 (345)
T ss_dssp HHH-SHHHHS---HHHHHHHHHHH-HTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHC
T ss_pred HHhcchhhccchHhhhhhhhhHHh-hcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhcccccccchhhc
Confidence 999999998877667888888885 455 455555557777776666
Q ss_pred ccchhchHHHHHHHHHcCCCCc--chhhhhchhhhhcchhh--------------------------------hHHHHHH
Q 035716 161 SSARDQLKPALFYLQRLGFKDL--NALAYQDSVLLVSKVEN--------------------------------TLIPKLK 206 (308)
Q Consensus 161 ~~~~~~l~~~v~~L~~lG~~~~--~~ii~~~P~ll~~~~~~--------------------------------~l~~~v~ 206 (308)
.+.+++++++++||+++|++.. .+++.++|.++..+.++ ++.++++
T Consensus 169 ~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~ 248 (345)
T PF02536_consen 169 SDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIE 248 (345)
T ss_dssp GSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHH
Confidence 6667888999999999998753 45666667666665543 6999999
Q ss_pred HHHHcCCCHHHHHHHHhcCcceeeeccccchhHHHHHHHHHhCCChHHHhhcCccccccccCchHHH---HHHHHHcC--
Q 035716 207 YLESIGFSKDEAVLMVLRCPGLFTFSIENNFKPKFEYFNLEIKGKLEELKEFPQYFAFSLEKRIKPR---HMQALRNG-- 281 (308)
Q Consensus 207 ~L~~lG~s~~~i~~~l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~~~~l~~~P~~L~~sle~ri~pR---~~~L~~~G-- 281 (308)
||+++||+++|+++|+.++|.||++|.| ++++|++||.++||++.++|+++|++|+||+|+||+|| +++|+++|
T Consensus 249 ~L~~lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~~ 327 (345)
T PF02536_consen 249 FLQSLGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGLI 327 (345)
T ss_dssp HHHTTT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTTG
T ss_pred HHHHhcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcCC
Confidence 9999999999999999999999999998 69999999999999999999999999999999999999 55678999
Q ss_pred CCCCchhhcccCHHHHHH
Q 035716 282 ARLSLPVMLKTSDEEFNE 299 (308)
Q Consensus 282 ~~~~l~~il~~sd~~F~~ 299 (308)
.++++.+++.+||++|++
T Consensus 328 ~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 328 INPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp GGGGS-HHHHHHHHHHT-
T ss_pred CCCCHHHHhhccHHHhcC
Confidence 678999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=5e-38 Score=305.88 Aligned_cols=232 Identities=18% Similarity=0.346 Sum_probs=127.9
Q ss_pred hCCCCCCCCCChhhhHHHHHHHHhhcCCCh---hhhhhhCCCcccCCcc-CHHHHHHHHHhCCCCCCChhhhhhcCCcee
Q 035716 47 NHPLYPPTQANLSFQIKEKILCLEIMGVDS---GKALSLNPSLHSASLN-SIEGIISFLQSKGILQKDLPRIFGMCPKVL 122 (308)
Q Consensus 47 ~~P~~~~~~~d~~~~~~~~l~~L~~~G~~~---~~il~~~P~lL~~s~~-~l~~~v~~L~~lGls~~~i~~li~~~P~lL 122 (308)
++|.++. +++.+.+.|+++||.++|++. ++++.++|.+|..+++ ++.|+++||+++|+++++|.+++.++|++|
T Consensus 111 ~~P~iL~--~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL 188 (487)
T PLN03196 111 EYPLVLG--CSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELL 188 (487)
T ss_pred cCcHHhh--cCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhh
Confidence 4555555 455555555555555555553 4555556655555554 355666666556665555666665566555
Q ss_pred eCCcccchhHHHHHhhhhcCCCcchHHHHHhhcCccccccchhchHHHHHHHHHcCCCCc--chhhhhchhhhhcchhhh
Q 035716 123 TANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDL--NALAYQDSVLLVSKVENT 200 (308)
Q Consensus 123 ~~~~e~~l~~~l~fL~~~~G~~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~--~~ii~~~P~ll~~~~~~~ 200 (308)
++++++++.++++||+ ++|++++++++++.++|++|+++++++++|+++||+++|+++. .+++.++|++++++++++
T Consensus 189 ~~~~e~~l~p~v~fL~-~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~ 267 (487)
T PLN03196 189 GFKLEGTMSTSVAYLV-SIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEET 267 (487)
T ss_pred cCCHHHHHHHHHHHHH-HcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHh
Confidence 5555555555666653 4566655666666666666655555555666666655555432 455555566655555555
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCcceeeeccccchhHHHHHHHHHhCCChHH----HhhcCccccccccCchHHHHHH
Q 035716 201 LIPKLKYLESIGFSKDEAVLMVLRCPGLFTFSIENNFKPKFEYFNLEIKGKLEE----LKEFPQYFAFSLEKRIKPRHMQ 276 (308)
Q Consensus 201 l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~~~~----l~~~P~~L~~sle~ri~pR~~~ 276 (308)
+++++++|.++|++.+++..++.++|.+++++.++++.++++|+.+++|++.++ +.++|.++++|.+ ++.+|++|
T Consensus 268 lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~-kl~~kvef 346 (487)
T PLN03196 268 VKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRN-VALKHVEF 346 (487)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHH-HHHHHHHH
Confidence 555555555555555555555555555555555444555555554444444433 2234444444432 44444445
Q ss_pred HHHcCC
Q 035716 277 ALRNGA 282 (308)
Q Consensus 277 L~~~G~ 282 (308)
|++.|+
T Consensus 347 L~~~Gl 352 (487)
T PLN03196 347 LRGRGF 352 (487)
T ss_pred HHHcCC
Confidence 444444
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=99.97 E-value=4.1e-31 Score=248.45 Aligned_cols=231 Identities=29% Similarity=0.561 Sum_probs=186.3
Q ss_pred HHHhhcCCCh---hhhhhhCCCcccCCcc-CHHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcC
Q 035716 67 LCLEIMGVDS---GKALSLNPSLHSASLN-SIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLE 142 (308)
Q Consensus 67 ~~L~~~G~~~---~~il~~~P~lL~~s~~-~l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G 142 (308)
++|+++|++. .++++++|.++.++++ ++.|+++||+++|++..++++++.+||.+|..++++++.|.++||+ ++|
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 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLK-SIG 80 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHT-TTS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHH-HHc
Confidence 5788899864 7889999999999998 5999999999999999999999999999999998889999999996 899
Q ss_pred CCcchHHHHHhhcCccccccchhchHHHHHHHHHcCCCCc------------------------------------chhh
Q 035716 143 VPEHDFRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDL------------------------------------NALA 186 (308)
Q Consensus 143 ~~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~------------------------------------~~ii 186 (308)
++++++.+++.++|++|..+.++++.+++.+|+++|+++. .+++
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 9999999999999999998877799999999999999741 1356
Q ss_pred hhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHHHhcCcceeeecccc-------------------------------
Q 035716 187 YQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLMVLRCPGLFTFSIEN------------------------------- 235 (308)
Q Consensus 187 ~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~s~e~------------------------------- 235 (308)
.++|.++..+.++.|+++++||+++|++.+++.+++.++|.++.+|+++
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 6899887777788999999999999999999999999999999999975
Q ss_pred -chhHHHHHHHHHhCCChHH----HhhcCccccccccCchHHHHHHHHH-cCCC----CCchhhcccC-HHHHHHH
Q 035716 236 -NFKPKFEYFNLEIKGKLEE----LKEFPQYFAFSLEKRIKPRHMQALR-NGAR----LSLPVMLKTS-DEEFNEL 300 (308)
Q Consensus 236 -~l~~k~~fL~~~mg~~~~~----l~~~P~~L~~sle~ri~pR~~~L~~-~G~~----~~l~~il~~s-d~~F~~~ 300 (308)
++.++++||.+ +|++.++ +.++|++|++|.|+ ++|+++||.+ .|++ ...|.++.+| |++-..|
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 EKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPR 314 (345)
T ss_dssp HHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHH
T ss_pred HhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhH
Confidence 58899999996 9999877 46899999999985 9999999975 6764 3567889999 5678878
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.86 E-value=1.2e-21 Score=188.68 Aligned_cols=207 Identities=30% Similarity=0.477 Sum_probs=173.4
Q ss_pred HHHHHhhcCCCh---hhhhhhCCCcccCCccCHHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhc
Q 035716 65 KILCLEIMGVDS---GKALSLNPSLHSASLNSIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDL 141 (308)
Q Consensus 65 ~l~~L~~~G~~~---~~il~~~P~lL~~s~~~l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~ 141 (308)
.++++.++|+.. ...+..+|....... .+...+.++...|+.+.. +++.+.|.+++++.++++++++++|+ .+
T Consensus 201 ~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~-~~ 276 (413)
T KOG1267|consen 201 RLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLK-SL 276 (413)
T ss_pred cchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHH-Hc
Confidence 666777777664 344556666543322 566677777777776666 77778888888889999999999996 89
Q ss_pred CCCcchHHHHHhhcCccccccchhchHHHHHHHHHcCCCCcchhhhhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHH
Q 035716 142 EVPEHDFRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLM 221 (308)
Q Consensus 142 G~~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~~ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~ 221 (308)
|++.+++..++.++|++|+++.+ ++..++.++.+. .+ . +.++|+++.++ +..+.++++|+..+|++..|+..|
T Consensus 277 Gf~~~di~~~~~k~P~~l~~s~~-~~~~~~~~~~~~--~~-~--~~k~p~~l~~s-~~~l~~~ie~l~~~g~~~~q~~~~ 349 (413)
T KOG1267|consen 277 GFSREEIWKMVKKCPQILGYSVK-KNLKTTEYLLKN--PK-H--ILKFPQLLRSS-EDKLKPRIEFLLSLGFSDVQILEM 349 (413)
T ss_pred CCCHHHHHHHHHhCchheEeehh-hhhHHHHHHHhc--ch-h--hhhhhhhhhcc-chhhhhhHHHHHHcCCcHHHHHHH
Confidence 99999999999999999999955 555666666665 22 2 88999999665 678999999999999999999999
Q ss_pred HhcCcceeeeccccchhHHHHHHHHHhCCChHHHhhcCccccccccCchHHHHHHHHHcCC
Q 035716 222 VLRCPGLFTFSIENNFKPKFEYFNLEIKGKLEELKEFPQYFAFSLEKRIKPRHMQALRNGA 282 (308)
Q Consensus 222 l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~~~~l~~~P~~L~~sle~ri~pR~~~L~~~G~ 282 (308)
+.++|+++.+|+++.++++.+|+.+.|+++.++++.+|++++|++|+|+.||+...+++|.
T Consensus 350 ~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~ 410 (413)
T KOG1267|consen 350 VKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGV 410 (413)
T ss_pred HhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhc
Confidence 9999999999998788999999999999999999999999999999999999999888764
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.77 E-value=2.7e-18 Score=165.43 Aligned_cols=212 Identities=25% Similarity=0.402 Sum_probs=151.1
Q ss_pred HHHHHHHHhhcCCCh---hhhhhhCCCcccCCccC-HHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHh
Q 035716 62 IKEKILCLEIMGVDS---GKALSLNPSLHSASLNS-IEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFL 137 (308)
Q Consensus 62 ~~~~l~~L~~~G~~~---~~il~~~P~lL~~s~~~-l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL 137 (308)
....+++|++.|++. ..++..+|.++..+.++ +.++..+|.+.|++..++.+++...|.+|..+.+.++.+.++|+
T Consensus 91 p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l 170 (413)
T KOG1267|consen 91 PSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFL 170 (413)
T ss_pred cHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHh
Confidence 356788999999985 67888899999888875 88888899999999999999999988888877666788888888
Q ss_pred hhhcC--CCcchHHHHHhhcC---------------------------------ccccccchhchHHHHHHHHHcCCCCc
Q 035716 138 SHDLE--VPEHDFRKVINKCP---------------------------------RLLTSSARDQLKPALFYLQRLGFKDL 182 (308)
Q Consensus 138 ~~~~G--~~~~~i~~li~~~P---------------------------------~lL~~~~~~~l~~~v~~L~~lG~~~~ 182 (308)
+ +++ .....+.++....| +...... .+...+.++..+|+++.
T Consensus 171 ~-~~~~~~~~s~~~~~~~~~~~~~~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~ 247 (413)
T KOG1267|consen 171 K-SIPPELLSSVVERLLTPVPSFLLNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPK 247 (413)
T ss_pred h-ccchhhhhhHHHHhccccccccccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCc
Confidence 5 553 44444444444443 3332221 34444455555555554
Q ss_pred chhhhhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHHHhcCcceeeeccccchhHHHHHHHHHhCCChHHHhhcCccc
Q 035716 183 NALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLMVLRCPGLFTFSIENNFKPKFEYFNLEIKGKLEELKEFPQYF 262 (308)
Q Consensus 183 ~~ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~~~~l~~~P~~L 262 (308)
.+++.+.|.++.++.++++++++++|+++||+.+||..|+.++|++|++|.+ ++..+++|+.+. .+++.++|+++
T Consensus 248 ~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~-~~~~~~~~~~~~----~~~~~k~p~~l 322 (413)
T KOG1267|consen 248 TREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVK-KNLKTTEYLLKN----PKHILKFPQLL 322 (413)
T ss_pred hhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehh-hhhHHHHHHHhc----chhhhhhhhhh
Confidence 5566678888888889999999999999999999999999999999999996 555555555543 22244555555
Q ss_pred cccccCchHHHHHHHHHcCC
Q 035716 263 AFSLEKRIKPRHMQALRNGA 282 (308)
Q Consensus 263 ~~sle~ri~pR~~~L~~~G~ 282 (308)
.++. ..+.+|++++...|.
T Consensus 323 ~~s~-~~l~~~ie~l~~~g~ 341 (413)
T KOG1267|consen 323 RSSE-DKLKPRIEFLLSLGF 341 (413)
T ss_pred hccc-hhhhhhHHHHHHcCC
Confidence 3332 345555555555443
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=97.17 E-value=0.00024 Score=41.78 Aligned_cols=30 Identities=23% Similarity=0.515 Sum_probs=20.6
Q ss_pred HHHhcCcceeeeccccchhHHHHHHHHHhCCC
Q 035716 220 LMVLRCPGLFTFSIENNFKPKFEYFNLEIKGK 251 (308)
Q Consensus 220 ~~l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~ 251 (308)
+++.++|.+|+++. ++|+++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~-~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSE-KKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccH-HHhhHHHHHHH-HcCCC
Confidence 35667777777774 47777777777 57653
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.08 E-value=0.00038 Score=40.84 Aligned_cols=22 Identities=27% Similarity=0.567 Sum_probs=8.8
Q ss_pred hhcCCceeeCCcccchhHHHHHh
Q 035716 115 FGMCPKVLTANIKTDLEPVFNFL 137 (308)
Q Consensus 115 i~~~P~lL~~~~e~~l~~~l~fL 137 (308)
+.++|.+|+++ ++++.++++||
T Consensus 4 ~~~~P~il~~~-~~~l~~~~~~l 25 (31)
T smart00733 4 LKKFPQILGYS-EKKLKPKVEFL 25 (31)
T ss_pred hhhCcCccccc-HHHhhHHHHHH
Confidence 33444444444 22344444444
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=93.60 E-value=0.13 Score=48.39 Aligned_cols=235 Identities=15% Similarity=0.147 Sum_probs=129.6
Q ss_pred cccc-ccchhhhhhCCCCCCCCC---------ChhhhHHHHHHHHhh-cCCChhhhhhhCCCcccCCccC--HHHHHHHH
Q 035716 35 IHLS-TKPKSLLQNHPLYPPTQA---------NLSFQIKEKILCLEI-MGVDSGKALSLNPSLHSASLNS--IEGIISFL 101 (308)
Q Consensus 35 ~~~~-~~~~~l~~~~P~~~~~~~---------d~~~~~~~~l~~L~~-~G~~~~~il~~~P~lL~~s~~~--l~~~v~~L 101 (308)
.++. .++...+++||.+..... ..+.++...++-=.. ..-....++.+--.+|-++.++ .-.+++.+
T Consensus 47 L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l 126 (335)
T PF11955_consen 47 LGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIAHL 126 (335)
T ss_pred cCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHHHH
Confidence 3443 667889999998776421 112222221111111 1111234555555567777763 45677777
Q ss_pred H-hCCCCCCChhhhhhcCCceeeCCc---ccchhHHHHHhhhhcCCCcchHHHHH-------------hhcCccc--ccc
Q 035716 102 Q-SKGILQKDLPRIFGMCPKVLTANI---KTDLEPVFNFLSHDLEVPEHDFRKVI-------------NKCPRLL--TSS 162 (308)
Q Consensus 102 ~-~lGls~~~i~~li~~~P~lL~~~~---e~~l~~~l~fL~~~~G~~~~~i~~li-------------~~~P~lL--~~~ 162 (308)
+ ++|++.+=...++.+||..+..-- ......-+.+= .++.++.-+-.... -.+|--+ ++.
T Consensus 127 ~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd-~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~G~~ 205 (335)
T PF11955_consen 127 RRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWD-PELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPKGFR 205 (335)
T ss_pred HHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecC-CccCcCccchhhhhccccccccccCCceeeeecCCCCcc
Confidence 7 599999999999999999876532 00111111111 23344333322221 0122111 234
Q ss_pred chhchHHHHHHHHHcCCCC----------c-----chhhhhchhhhhcchhhh-HHHHHHHH-HHcCCCHHHHHHHHhcC
Q 035716 163 ARDQLKPALFYLQRLGFKD----------L-----NALAYQDSVLLVSKVENT-LIPKLKYL-ESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 163 ~~~~l~~~v~~L~~lG~~~----------~-----~~ii~~~P~ll~~~~~~~-l~~~v~~L-~~lG~s~~~i~~~l~~~ 225 (308)
+.++.+..++-++++-+.. . .+.+.---.+|...+++. ...++..| +++|++ +.+..++.+|
T Consensus 206 l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~rH 284 (335)
T PF11955_consen 206 LKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLLRH 284 (335)
T ss_pred ccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHHhC
Confidence 4567777777787764421 0 123333344554444433 35567777 489999 5788999999
Q ss_pred cceeeeccccchhHHHHHHHHHhCCChHHHhhcCccccccccCchHHHHHHHHHcC
Q 035716 226 PGLFTFSIENNFKPKFEYFNLEIKGKLEELKEFPQYFAFSLEKRIKPRHMQALRNG 281 (308)
Q Consensus 226 P~iL~~s~e~~l~~k~~fL~~~mg~~~~~l~~~P~~L~~sle~ri~pR~~~L~~~G 281 (308)
|.|+..|. +-+.-.-||++....+ +-|.++|.+ .++-|+.-|...|
T Consensus 285 PgIFYvS~--kg~~~TVfLrEAY~~~-~Liek~Pl~-------~~r~k~~~Lm~~~ 330 (335)
T PF11955_consen 285 PGIFYVSL--KGKRHTVFLREAYDGG-ELIEKHPLV-------VIREKFLELMQEG 330 (335)
T ss_pred CCeEEEec--cCCceEEEEeeccCCC-CCCCCCchH-------HHHHHHHHHHhhc
Confidence 99999997 4555556666544433 234555553 4555666666555
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=72.32 E-value=7.3 Score=32.99 Aligned_cols=144 Identities=12% Similarity=0.159 Sum_probs=71.7
Q ss_pred HHHHHHhhcCCC-hhhhhhhCC-CcccCCcc---CHHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhh
Q 035716 64 EKILCLEIMGVD-SGKALSLNP-SLHSASLN---SIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLS 138 (308)
Q Consensus 64 ~~l~~L~~~G~~-~~~il~~~P-~lL~~s~~---~l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~ 138 (308)
..|.|....|+= +.. +.+ .--.++.+ .+ ..+..|+++|++-++|..++..... +....+...++.+.
T Consensus 16 ~tLRyYe~~GLl~p~~---r~~~gyR~Y~~~dl~rL-~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~ 87 (172)
T cd04790 16 STLLYYERIGLLSPSA---RSESNYRLYGERDLERL-EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELN 87 (172)
T ss_pred HHHHHHHHCCCCCCCc---cCCCCCccCCHHHHHHH-HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHH
Confidence 567788888863 321 112 12234444 34 5777889999999999998875442 11122333444432
Q ss_pred hhcC---CCcchHHHHHhhcCccccccchhchHHHHHHHHHcCCCCcchhhhhchhhhhcchhhhHHHHHHHHHHcCCCH
Q 035716 139 HDLE---VPEHDFRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSK 215 (308)
Q Consensus 139 ~~~G---~~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~~ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~ 215 (308)
+++. -....+..++...+..-... .-+....++.++..|+++.. + .+.-..|-.. .=..-.+||+++|+++
T Consensus 88 ~ei~~L~~~~~~l~~ll~~~~~~~~~~-~V~~~~w~~l~~~~g~~~~~-m-~~wh~~fe~~---~p~~h~~~l~~~g~~~ 161 (172)
T cd04790 88 REIQRLRQQQRAIATLLKQPTLLKEQR-LVTKEKWVAILKAAGMDEAD-M-RRWHIEFEKM---EPEAHQEFLQSLGIPE 161 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccc-cCCHHHHHHHHHHcCCChHH-H-HHHHHHHHHh---CcHHHHHHHHHcCCCH
Confidence 2111 11223333433222221111 11134555666677876431 1 1111111111 1123478999999999
Q ss_pred HHHHHH
Q 035716 216 DEAVLM 221 (308)
Q Consensus 216 ~~i~~~ 221 (308)
+|+..+
T Consensus 162 ~~~~~i 167 (172)
T cd04790 162 DEIERI 167 (172)
T ss_pred HHHHHH
Confidence 998644
No 11
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=70.37 E-value=10 Score=28.60 Aligned_cols=56 Identities=20% Similarity=0.145 Sum_probs=26.7
Q ss_pred hhHHHHHHHHhhcCCCh--------------hhhhhhCCCcccCCccC-HHHHHHHHH-hCCCCCCChhhhh
Q 035716 60 FQIKEKILCLEIMGVDS--------------GKALSLNPSLHSASLNS-IEGIISFLQ-SKGILQKDLPRIF 115 (308)
Q Consensus 60 ~~~~~~l~~L~~~G~~~--------------~~il~~~P~lL~~s~~~-l~~~v~~L~-~lGls~~~i~~li 115 (308)
..++..+.||..+|++. -.+|+.+|..|..+... =...++-+. ++|++.++-.++.
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~Ri~ 77 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPRRIR 77 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHHHHH
Confidence 44667788999999884 14566677766654542 133333333 3676666655443
No 12
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=68.25 E-value=13 Score=33.10 Aligned_cols=97 Identities=12% Similarity=0.257 Sum_probs=63.2
Q ss_pred hhHHHHHHHHhhcCCChhhhhhhCCCc-ccCCccCHHHHHHHHHhCCCCCCChhhhhhcCCc--eeeCCcccchhHHHHH
Q 035716 60 FQIKEKILCLEIMGVDSGKALSLNPSL-HSASLNSIEGIISFLQSKGILQKDLPRIFGMCPK--VLTANIKTDLEPVFNF 136 (308)
Q Consensus 60 ~~~~~~l~~L~~~G~~~~~il~~~P~l-L~~s~~~l~~~v~~L~~lGls~~~i~~li~~~P~--lL~~~~e~~l~~~l~f 136 (308)
.+.-+++..|.+.|++..|.-.+.-.. +....+.+...+++|+..|++++....+-.-+|. +.+...+ =+.++.|
T Consensus 31 ~eANemlAlL~~~gI~A~K~~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~e--EkaR~~~ 108 (246)
T COG4669 31 KEANEMLALLMSHGINAEKKADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTE--EKARLNY 108 (246)
T ss_pred hHHHHHHHHHHHcCCcceeeccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHH--HHHHHHH
Confidence 455678888888888875543333322 3333345888888888888888877777777775 4444333 2555556
Q ss_pred hhhhcCCCcchHHHHHhhcCccccccch
Q 035716 137 LSHDLEVPEHDFRKVINKCPRLLTSSAR 164 (308)
Q Consensus 137 L~~~~G~~~~~i~~li~~~P~lL~~~~~ 164 (308)
.. ++++.+.+.+-..++..++.
T Consensus 109 ~~------eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 109 AK------EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HH------HHHHHHHHHhcCceEEEEEE
Confidence 53 35777888888888776643
No 13
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=65.81 E-value=16 Score=34.46 Aligned_cols=41 Identities=24% Similarity=0.419 Sum_probs=26.7
Q ss_pred hhhhcchhhhH-HHHHHHHH-HcCCCHHHHHHHHhcCcceeee
Q 035716 191 VLLVSKVENTL-IPKLKYLE-SIGFSKDEAVLMVLRCPGLFTF 231 (308)
Q Consensus 191 ~ll~~~~~~~l-~~~v~~L~-~lG~s~~~i~~~l~~~P~iL~~ 231 (308)
.+|..+.+..| -.++..++ ++|++.+-...++.++|..+.+
T Consensus 108 KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 108 KLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 34444433332 34566674 7888888888888888887765
No 14
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=65.35 E-value=16 Score=27.51 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=11.3
Q ss_pred CHHHHHHHHHhCCCCCCChh
Q 035716 93 SIEGIISFLQSKGILQKDLP 112 (308)
Q Consensus 93 ~l~~~v~~L~~lGls~~~i~ 112 (308)
.+...+.||..+|++.....
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~ 26 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAM 26 (94)
T ss_dssp --HHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHH
Confidence 46777888888888754333
No 15
>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=65.32 E-value=2.4 Score=34.55 Aligned_cols=25 Identities=32% Similarity=0.656 Sum_probs=12.0
Q ss_pred HHHHHHHHHhCCCCCCChhhhhhcC
Q 035716 94 IEGIISFLQSKGILQKDLPRIFGMC 118 (308)
Q Consensus 94 l~~~v~~L~~lGls~~~i~~li~~~ 118 (308)
+..+++||++.|++.+||..++.+.
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a 47 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRA 47 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhc
Confidence 3345555555555555555555443
No 16
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=64.23 E-value=8.6 Score=35.02 Aligned_cols=53 Identities=19% Similarity=0.240 Sum_probs=38.0
Q ss_pred hHHHHHHHH-HHcC-CCHHHHHHHHhcCcceeeeccccchhHHHHHHHHHhCCChH
Q 035716 200 TLIPKLKYL-ESIG-FSKDEAVLMVLRCPGLFTFSIENNFKPKFEYFNLEIKGKLE 253 (308)
Q Consensus 200 ~l~~~v~~L-~~lG-~s~~~i~~~l~~~P~iL~~s~e~~l~~k~~fL~~~mg~~~~ 253 (308)
.++.++-|. +..| |+.-.+.+=+.-.|.++.++.+ +++.|.+=|.+-+|+++.
T Consensus 72 ~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~-~i~~r~~ELl~lvgL~p~ 126 (309)
T COG1125 72 ELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKE-RIKKRADELLDLVGLDPS 126 (309)
T ss_pred HHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHH-HHHHHHHHHHHHhCCCHH
Confidence 477777776 5666 5555666666777888888875 788888777777777764
No 17
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=63.65 E-value=11 Score=23.05 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 035716 203 PKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 203 ~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
..++-|.++||+.++..+.+..+
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 56788888999999988887766
No 18
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=61.79 E-value=13 Score=22.51 Aligned_cols=23 Identities=30% Similarity=0.492 Sum_probs=18.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 035716 203 PKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 203 ~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
.+++-|.++||+++++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46778889999999988887766
No 19
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=57.31 E-value=17 Score=22.08 Aligned_cols=23 Identities=35% Similarity=0.450 Sum_probs=18.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 035716 203 PKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 203 ~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
.+++-|.++||+++++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46778889999999888777665
No 20
>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=55.56 E-value=12 Score=30.37 Aligned_cols=30 Identities=27% Similarity=0.278 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHhcCccee
Q 035716 200 TLIPKLKYLESIGFSKDEAVLMVLRCPGLF 229 (308)
Q Consensus 200 ~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL 229 (308)
.+.+|++||++=|++.+||..++.+.+.--
T Consensus 22 p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 22 PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp -HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 377899999999999999999998876544
No 21
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=45.19 E-value=19 Score=29.61 Aligned_cols=100 Identities=16% Similarity=0.157 Sum_probs=43.0
Q ss_pred HHHHHhhcCccccccchhchHHHHHHHHHcCCCCcchhhhhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHH-HhcCc
Q 035716 148 FRKVINKCPRLLTSSARDQLKPALFYLQRLGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLM-VLRCP 226 (308)
Q Consensus 148 i~~li~~~P~lL~~~~~~~l~~~v~~L~~lG~~~~~~ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~-l~~~P 226 (308)
+.+..-++|..|.---.+.++.++-+|.+++.-....+-.-.-.+..++ ....-++-+++.|+....-... +.++|
T Consensus 33 ~~r~~pkaPdwLd~~A~~~Wrrvvp~L~e~~ll~~~D~~~Le~YC~~ys---iY~~av~~lkk~G~ii~~~~~g~~krNP 109 (160)
T COG3747 33 FGRLAPKAPDWLDPTAKKEWRRVVPFLEELKLLKPADLTLLELYCVAYS---IYRNAVAHLKKHGFIITNQFSGRVKRNP 109 (160)
T ss_pred ccccCCCCccccCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHH---HHHHHHHHHHHcceeeeccccceecCCh
Confidence 3344445666665444455666666666655433222111111112221 2344455555555543311111 44555
Q ss_pred ceeeeccccchhHHHHHHHHHhCCChH
Q 035716 227 GLFTFSIENNFKPKFEYFNLEIKGKLE 253 (308)
Q Consensus 227 ~iL~~s~e~~l~~k~~fL~~~mg~~~~ 253 (308)
.+=.+|- ....+--|-.++|+++.
T Consensus 110 av~~~sd---A~~~l~klaSeLGltP~ 133 (160)
T COG3747 110 AVQAASD---AIRNLLKLASELGLTPS 133 (160)
T ss_pred HHHHHHH---HHHHHHHHHHHhCCChH
Confidence 5544432 23333334445565543
No 22
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=44.30 E-value=37 Score=21.98 Aligned_cols=26 Identities=38% Similarity=0.363 Sum_probs=19.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCc
Q 035716 201 LIPKLKYLESIGFSKDEAVLMVLRCP 226 (308)
Q Consensus 201 l~~~v~~L~~lG~s~~~i~~~l~~~P 226 (308)
+..-++-|..+||++.++.+++.+-.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 45567788899999999988887653
No 23
>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=43.09 E-value=42 Score=21.20 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=21.7
Q ss_pred hHHHHHHHHH-HcCCCHHHHHHHHhcCcce
Q 035716 200 TLIPKLKYLE-SIGFSKDEAVLMVLRCPGL 228 (308)
Q Consensus 200 ~l~~~v~~L~-~lG~s~~~i~~~l~~~P~i 228 (308)
.+..+...|. ++|++..+...||..||..
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 4667788885 8999999999999999863
No 24
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=39.66 E-value=40 Score=27.81 Aligned_cols=111 Identities=14% Similarity=0.147 Sum_probs=72.7
Q ss_pred cccccccccchhhhhhCCCCCCCCCChhhhHHHHHHHHhhcCC-Chh--hhhhhCCCcccCCccCHHHHHHHHHhCCCCC
Q 035716 32 QLNIHLSTKPKSLLQNHPLYPPTQANLSFQIKEKILCLEIMGV-DSG--KALSLNPSLHSASLNSIEGIISFLQSKGILQ 108 (308)
Q Consensus 32 ~~~~~~~~~~~~l~~~~P~~~~~~~d~~~~~~~~l~~L~~~G~-~~~--~il~~~P~lL~~s~~~l~~~v~~L~~lGls~ 108 (308)
-.++.=+.++..+.-+.|..+. .-...+++.++-+|...+. +++ .+++.+ +..-+.....++-++..|+.-
T Consensus 24 ~~K~~~~~~~~r~~pkaPdwLd--~~A~~~Wrrvvp~L~e~~ll~~~D~~~Le~Y----C~~ysiY~~av~~lkk~G~ii 97 (160)
T COG3747 24 GRKVFEDAKFGRLAPKAPDWLD--PTAKKEWRRVVPFLEELKLLKPADLTLLELY----CVAYSIYRNAVAHLKKHGFII 97 (160)
T ss_pred cccCCCCccccccCCCCccccC--HHHHHHHHHHHHHHHHhccCCHHHHHHHHHH----HHHHHHHHHHHHHHHHcceee
Confidence 3445556777778888888888 4455778899999999885 443 234433 112245667788888888775
Q ss_pred CCh-hhhhhcCCceeeCCcccchhHHHHHhhhhcCCCcchHHHH
Q 035716 109 KDL-PRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKV 151 (308)
Q Consensus 109 ~~i-~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~~~~~i~~l 151 (308)
..- ...+.++|.+-.++ +....+--|-+++|+++..=.++
T Consensus 98 ~~~~~g~~krNPav~~~s---dA~~~l~klaSeLGltP~arakL 138 (160)
T COG3747 98 TNQFSGRVKRNPAVQAAS---DAIRNLLKLASELGLTPSARAKL 138 (160)
T ss_pred eccccceecCChHHHHHH---HHHHHHHHHHHHhCCChHHHHhh
Confidence 433 34488899877665 35555555657899988655443
No 25
>PRK14136 recX recombination regulator RecX; Provisional
Probab=36.75 E-value=2.8e+02 Score=25.87 Aligned_cols=110 Identities=13% Similarity=0.147 Sum_probs=62.8
Q ss_pred CCccCHHHHHHHHHhCC-CCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcCCCcchHHHHHhhcCccccccchhch
Q 035716 89 ASLNSIEGIISFLQSKG-ILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPRLLTSSARDQL 167 (308)
Q Consensus 89 ~s~~~l~~~v~~L~~lG-ls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~~~~~i~~li~~~P~lL~~~~~~~l 167 (308)
++.+.++.+|+.|.+.| +++...+..+.+. .. .. .. -...-.-|+ .-||+.+.|..++... . ++.+
T Consensus 191 ~~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~--~k-kG-p~rIrqELr-QKGId~eLIEqALeei------e-EDE~ 257 (309)
T PRK14136 191 DESDSVEPLLDALEREGWLSDARFAESLVHR-RA--SR-VG-SARIVSELK-RHAVGDALVESVGAQL------R-ETEF 257 (309)
T ss_pred CCHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-Hh--hc-hh-HHHHHHHHH-HcCCCHHHHHHHHHhc------c-HhHH
Confidence 34456889999999988 5566666665532 11 11 11 122234453 6899998888877633 1 1122
Q ss_pred HHHHHHHHH-cCCCCcchhhhhchhhhhcchhhhHHHHHHHHHHcCCCHHHHHHHHhcC
Q 035716 168 KPALFYLQR-LGFKDLNALAYQDSVLLVSKVENTLIPKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 168 ~~~v~~L~~-lG~~~~~~ii~~~P~ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
......+++ ++- .+. . .....+.+.||..-||+.+.|..++..+
T Consensus 258 E~A~~L~eKK~~~---------~~~----d-~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 258 ERAQAVWRKKFGA---------LPQ----T-PAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHHHHHHHhcc---------cCc----C-HHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 222233322 221 111 1 1223455899999999999999888654
No 26
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=35.12 E-value=61 Score=29.76 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=32.5
Q ss_pred hHHHHHHHHHhCCChHHHhhcCccccccccCchHHHHHHHHHcCC--CCCchhhcccCHHHHHHHhc
Q 035716 238 KPKFEYFNLEIKGKLEELKEFPQYFAFSLEKRIKPRHMQALRNGA--RLSLPVMLKTSDEEFNELIK 302 (308)
Q Consensus 238 ~~k~~fL~~~mg~~~~~l~~~P~~L~~sle~ri~pR~~~L~~~G~--~~~l~~il~~sd~~F~~~~~ 302 (308)
+.+++.+.+ .|++.+.|.--|. +++. +.....++.|+.... ...++.++..|.|.|...+.
T Consensus 166 ~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l~~lg~Pilvg~SRKsfig~~~ 228 (282)
T PRK11613 166 IEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEFHHFNLPLLVGMSRKSMIGQLL 228 (282)
T ss_pred HHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHHHhCCCCEEEEecccHHHHhhc
Confidence 444444443 6777777666675 3443 344444444433111 23356667777777776554
No 27
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=32.16 E-value=47 Score=23.88 Aligned_cols=20 Identities=20% Similarity=0.522 Sum_probs=9.1
Q ss_pred HHHHHHHhCCCCCCChhhhh
Q 035716 96 GIISFLQSKGILQKDLPRIF 115 (308)
Q Consensus 96 ~~v~~L~~lGls~~~i~~li 115 (308)
|.++.|++..+++++|..++
T Consensus 3 PIia~LKehnvsd~qi~elF 22 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELF 22 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHH
Confidence 34444444444444444443
No 28
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=31.93 E-value=2e+02 Score=23.15 Aligned_cols=81 Identities=20% Similarity=0.338 Sum_probs=49.3
Q ss_pred CcchHHHHHhhcCccccccchhchHHHH-----HHHHHcCCCCcchhhhhch-hh-hhcchhhhHHHHHHHHHHcCCCHH
Q 035716 144 PEHDFRKVINKCPRLLTSSARDQLKPAL-----FYLQRLGFKDLNALAYQDS-VL-LVSKVENTLIPKLKYLESIGFSKD 216 (308)
Q Consensus 144 ~~~~i~~li~~~P~lL~~~~~~~l~~~v-----~~L~~lG~~~~~~ii~~~P-~l-l~~~~~~~l~~~v~~L~~lG~s~~ 216 (308)
+..++-.++.+||.+=...++....+++ .||...|+.=...=++-|- .+ =.+.++..+-.+++-|..-|.+.+
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 6678889999999876655555454444 3444456542111111111 01 012334568889999999999999
Q ss_pred HHHHHHhc
Q 035716 217 EAVLMVLR 224 (308)
Q Consensus 217 ~i~~~l~~ 224 (308)
++..-+.+
T Consensus 109 ei~~ki~~ 116 (131)
T PF08004_consen 109 EIAEKISR 116 (131)
T ss_pred HHHHHHHH
Confidence 99866654
No 29
>PF02126 PTE: Phosphotriesterase family; InterPro: IPR001559 Synonym(s): Paraoxonase, A-esterase, Aryltriphosphatase, Phosphotriesterase, Paraoxon hydrolase Bacteria such as Brevundimonas diminuta (Pseudomonas diminuta) harbour a plasmid that carries the gene for Aryldialkylphosphatase (3.1.8.1 from EC) (PTE) (also known as parathion hydrolase). This enzyme has attracted interest because of its potential use in the detoxification of chemical waste and warfare agents and its ability to degrade agricultural pesticides such as parathion. It acts specifically on synthetic organophosphate triesters and phosphorofluoridates. It does not seem to have a natural occuring substrate and may thus have optimally evolved for utilizing paraoxon. Aryldialkylphosphatase belongs to a family [, ] of enzymes that possess a binuclear zinc metal centre at their active site. The two zinc ions are coordinated by six different residues, six of which being histidines. This family so far includes, in addition to the parathion hydrolase, the following proteins: Escherichia coli protein Php, the substrate of which is not yet known. Mycobacterium tuberculosis phosphotriesterase homology protein Rv0230C. Mammalian phosphotriesterase related protein (PTER) (RPR-1). ; GO: 0008270 zinc ion binding, 0016788 hydrolase activity, acting on ester bonds, 0009056 catabolic process; PDB: 3MSR_A 3OVG_D 3K2G_C 1BF6_B 3OQE_A 3C86_A 3SO7_A 2D2G_A 2R1P_A 2D2H_A ....
Probab=30.94 E-value=80 Score=29.38 Aligned_cols=124 Identities=14% Similarity=0.086 Sum_probs=56.3
Q ss_pred CHHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcCC--CcchHHH-H--HhhcCccccccchhch
Q 035716 93 SIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEV--PEHDFRK-V--INKCPRLLTSSARDQL 167 (308)
Q Consensus 93 ~l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~--~~~~i~~-l--i~~~P~lL~~~~~~~l 167 (308)
...+.+++|.+.|++.+.+ +-.|- +...++.-..+++. .|+ .=+.++. . ...+|.+=..+ ++.-
T Consensus 168 ~~~e~~~il~e~Gv~~~rv---vigH~-----D~~~D~~y~~~la~--~G~~l~~D~~g~~~~g~~~~~~~~~~~-d~~r 236 (308)
T PF02126_consen 168 MGLEQLDILEEEGVDPSRV---VIGHM-----DRNPDLDYHRELAD--RGVYLEFDTIGREFSGKDKNPRVGYPP-DEER 236 (308)
T ss_dssp CHHHHHHHHHHTT--GGGE---EETSG-----GGST-HHHHHHHHH--TT-EEEETTTT-B-TTTTTCHSCTTS--HHHH
T ss_pred CHHHHHHHHHHcCCChhHe---EEeCC-----CCCCCHHHHHHHHh--cCCEEEecCCcccccCcccCccCCCCC-HHHH
Confidence 3567888899998876554 22221 11122333333332 232 1222211 0 01122222223 3334
Q ss_pred HHHHHHHHHcCCCCc----chhhhhchh----hhhcchhhhHHHHHHHHHHcCCCHHHHHHHHhcCcc
Q 035716 168 KPALFYLQRLGFKDL----NALAYQDSV----LLVSKVENTLIPKLKYLESIGFSKDEAVLMVLRCPG 227 (308)
Q Consensus 168 ~~~v~~L~~lG~~~~----~~ii~~~P~----ll~~~~~~~l~~~v~~L~~lG~s~~~i~~~l~~~P~ 227 (308)
...+..|.+-|+.+. ..+-.+... .-.+...--+..-+-.|++.|+++++|.+|+..+|.
T Consensus 237 i~~l~~L~~~Gy~~qIlLS~D~~~k~~~~~~gg~g~~~~~i~~~fiP~L~~~Gv~~~~i~~ilv~NP~ 304 (308)
T PF02126_consen 237 IELLKELIEEGYADQILLSHDIGRKSRLYRYGGGGYGYIYILTRFIPRLKERGVSEEDIDKILVENPA 304 (308)
T ss_dssp HHHHHHHHHTTTGGGEEE-HHHESEEGSSSCCHHHHTTTHHHHTHHHHHHHTTS-HHHHHHHHTHHHH
T ss_pred HHHHHHHHHcCCcCcEEEeccccccccccccCCCCccHHHHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 456666777788652 112111111 111111111233345667889999999999999985
No 30
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=30.04 E-value=41 Score=27.11 Aligned_cols=36 Identities=17% Similarity=0.229 Sum_probs=21.6
Q ss_pred hhCCCcccCCccCHHHHHHHHHhCCCCCCChhhhhh
Q 035716 81 SLNPSLHSASLNSIEGIISFLQSKGILQKDLPRIFG 116 (308)
Q Consensus 81 ~~~P~lL~~s~~~l~~~v~~L~~lGls~~~i~~li~ 116 (308)
+..|.-+..+.|.+++-+--|..-|+++.||+-++.
T Consensus 20 r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400|consen 20 RSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred cCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeee
Confidence 345555666666666666666666666666654443
No 31
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=29.33 E-value=12 Score=25.95 Aligned_cols=33 Identities=27% Similarity=0.353 Sum_probs=15.5
Q ss_pred CCCcccCCccCHHHHHHHHHhCCCCCCChhhhh
Q 035716 83 NPSLHSASLNSIEGIISFLQSKGILQKDLPRIF 115 (308)
Q Consensus 83 ~P~lL~~s~~~l~~~v~~L~~lGls~~~i~~li 115 (308)
.|.-+..+.++++..+--|..-|+++.+|+-++
T Consensus 22 ~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iL 54 (60)
T PF08069_consen 22 PPSWLKYSPEEVEELIVKLAKKGLTPSQIGVIL 54 (60)
T ss_dssp --TT--S-HHHHHHHHHHHCCTTHCHHHHHHHH
T ss_pred CCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhh
Confidence 345555555555555555555555555555444
No 32
>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=27.35 E-value=85 Score=18.53 Aligned_cols=24 Identities=21% Similarity=0.191 Sum_probs=14.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhc
Q 035716 201 LIPKLKYLESIGFSKDEAVLMVLR 224 (308)
Q Consensus 201 l~~~v~~L~~lG~s~~~i~~~l~~ 224 (308)
|..-+.--+++|++.+|++..+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 444444445789999998876643
No 33
>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=26.96 E-value=84 Score=21.39 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=14.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 035716 203 PKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 203 ~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
.-++-|.+|||+.+.+...+++.
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrrl 33 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRRL 33 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHS
T ss_pred HHHHHHHHcCCcHHHHHHHHHHh
Confidence 34667778888888887777653
No 34
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.96 E-value=85 Score=23.32 Aligned_cols=38 Identities=24% Similarity=0.238 Sum_probs=26.2
Q ss_pred ccchhhhhhCCCCCCCCCChhhhHHHHHHHHhhcC-CCh--hhhhhhCC
Q 035716 39 TKPKSLLQNHPLYPPTQANLSFQIKEKILCLEIMG-VDS--GKALSLNP 84 (308)
Q Consensus 39 ~~~~~l~~~~P~~~~~~~d~~~~~~~~l~~L~~~G-~~~--~~il~~~P 84 (308)
|.|.+.+.+ +|..++..+.|+||+.-| +++ ++.++..+
T Consensus 35 PtV~D~L~r--------CdT~EEAlEii~yleKrGEi~~E~A~~L~~~~ 75 (98)
T COG4003 35 PTVIDFLRR--------CDTEEEALEIINYLEKRGEITPEMAKALRVTL 75 (98)
T ss_pred chHHHHHHH--------hCcHHHHHHHHHHHHHhCCCCHHHHHHHHhhH
Confidence 555555544 567778888999999887 565 66666654
No 35
>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=26.74 E-value=1.3e+02 Score=22.12 Aligned_cols=45 Identities=7% Similarity=0.029 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcCC
Q 035716 94 IEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEV 143 (308)
Q Consensus 94 l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~ 143 (308)
+...-+|.+.+|+++.+|-.+=..+| +..+.....+.-+++..|-
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~-----~~~Eq~yqmL~~W~~~~g~ 55 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR-----RCRDAQYQMLKVWKERGPR 55 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC-----ChHHHHHHHHHHHHHhcCC
Confidence 44555677778888888877777766 2223455555555544453
No 36
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=25.45 E-value=2.5e+02 Score=25.89 Aligned_cols=95 Identities=13% Similarity=0.187 Sum_probs=62.8
Q ss_pred eeeCCcccchhHHHHHhhhhcCC-CcchHHHHHhhcCccccccchhchHHHHHHHHH-cCCCCcchhhhhchhhhhcchh
Q 035716 121 VLTANIKTDLEPVFNFLSHDLEV-PEHDFRKVINKCPRLLTSSARDQLKPALFYLQR-LGFKDLNALAYQDSVLLVSKVE 198 (308)
Q Consensus 121 lL~~~~e~~l~~~l~fL~~~~G~-~~~~i~~li~~~P~lL~~~~~~~l~~~v~~L~~-lG~~~~~~ii~~~P~ll~~~~~ 198 (308)
+-..+.. .++.++.|--+..|+ +--.+..=|...|.++..+ +++++.+++-|.. +|+++ .....++|.-|.-.-
T Consensus 65 i~~~d~~-~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~-k~~i~~r~~ELl~lvgL~p-~~~~~RyP~eLSGGQ- 140 (309)
T COG1125 65 ISDLDPV-ELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWD-KERIKKRADELLDLVGLDP-SEYADRYPHELSGGQ- 140 (309)
T ss_pred cccCCHH-HHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCC-HHHHHHHHHHHHHHhCCCH-HHHhhcCchhcCcch-
Confidence 4444443 577788887777775 4455777788889999888 6788888888776 78753 345667887775431
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhcCcceeeecc
Q 035716 199 NTLIPKLKYLESIGFSKDEAVLMVLRCPGLFTFSI 233 (308)
Q Consensus 199 ~~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~s~ 233 (308)
++++- |.+.+...|.++-.+.
T Consensus 141 ---QQRVG-----------v~RALAadP~ilLMDE 161 (309)
T COG1125 141 ---QQRVG-----------VARALAADPPILLMDE 161 (309)
T ss_pred ---hhHHH-----------HHHHHhcCCCeEeecC
Confidence 23332 3445567777776543
No 37
>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=25.36 E-value=52 Score=22.41 Aligned_cols=25 Identities=12% Similarity=0.286 Sum_probs=19.8
Q ss_pred hHHHHHhhhhcCCCcchHHHHHhhc
Q 035716 131 EPVFNFLSHDLEVPEHDFRKVINKC 155 (308)
Q Consensus 131 ~~~l~fL~~~~G~~~~~i~~li~~~ 155 (308)
.--+.||.+.+|++++++..+|...
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 3447888889999999999888753
No 38
>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=24.94 E-value=86 Score=23.15 Aligned_cols=39 Identities=10% Similarity=0.210 Sum_probs=19.8
Q ss_pred HHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcC
Q 035716 100 FLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLE 142 (308)
Q Consensus 100 ~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G 142 (308)
+-+.+|++..+|..+-..+|. ++.+.....+..+++..|
T Consensus 19 laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g 57 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHC
Confidence 334566666666666666662 222234444544443334
No 39
>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=24.72 E-value=1.2e+02 Score=22.87 Aligned_cols=43 Identities=5% Similarity=0.044 Sum_probs=28.9
Q ss_pred HHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcC
Q 035716 95 EGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLE 142 (308)
Q Consensus 95 ~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G 142 (308)
+..-.+.+.+|++..+|..+-..+|. + .+.....+..+++..|
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~----~-~eq~~qmL~~W~~~~G 62 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERV----T-REQLYQMLLTWVNKTG 62 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCC----C-HHHHHHHHHHHHHhhC
Confidence 34455667788888888888888874 2 2356666666665555
No 40
>PRK09875 putative hydrolase; Provisional
Probab=24.26 E-value=78 Score=29.19 Aligned_cols=27 Identities=26% Similarity=0.405 Sum_probs=23.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhcCcc
Q 035716 201 LIPKLKYLESIGFSKDEAVLMVLRCPG 227 (308)
Q Consensus 201 l~~~v~~L~~lG~s~~~i~~~l~~~P~ 227 (308)
+..-+-.|++.|+++++|.+|+..+|.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 555566788889999999999999995
No 41
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=23.66 E-value=91 Score=23.57 Aligned_cols=53 Identities=15% Similarity=0.189 Sum_probs=39.6
Q ss_pred HHHHHHHHhhcCCChhhhhhhCCCcccCCccCHHHHHHHHHhCCCCCCChhhhhhc
Q 035716 62 IKEKILCLEIMGVDSGKALSLNPSLHSASLNSIEGIISFLQSKGILQKDLPRIFGM 117 (308)
Q Consensus 62 ~~~~l~~L~~~G~~~~~il~~~P~lL~~s~~~l~~~v~~L~~lGls~~~i~~li~~ 117 (308)
....+.+|...|.+-++.+.+. +..+.+.+...++-|.+.|+=...=++++.+
T Consensus 9 ~~~IL~hl~~~~~Dy~k~ia~~---l~~~~~~v~~~l~~Le~~GLler~~g~~iK~ 61 (92)
T PF10007_consen 9 DLKILQHLKKAGPDYAKSIARR---LKIPLEEVREALEKLEEMGLLERVEGKTIKR 61 (92)
T ss_pred HHHHHHHHHHHCCCcHHHHHHH---HCCCHHHHHHHHHHHHHCCCeEEecCcccch
Confidence 3467889999999987777664 4677788999999999999754444555544
No 42
>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=22.01 E-value=1.2e+02 Score=31.86 Aligned_cols=109 Identities=17% Similarity=0.148 Sum_probs=0.0
Q ss_pred HHHHHHHhh---cCCCh---hhhhhhCCCcccCCccCHHHHHHHHHhC-CCCCCChhhhhhcCCceeeCCcccchhHHHH
Q 035716 63 KEKILCLEI---MGVDS---GKALSLNPSLHSASLNSIEGIISFLQSK-GILQKDLPRIFGMCPKVLTANIKTDLEPVFN 135 (308)
Q Consensus 63 ~~~l~~L~~---~G~~~---~~il~~~P~lL~~s~~~l~~~v~~L~~l-Gls~~~i~~li~~~P~lL~~~~e~~l~~~l~ 135 (308)
+..+.||.+ -|+.+ .+++.++. ....+.+....+-|.++ |++++.+..+...+ .-.......+.
T Consensus 78 ~~i~~yL~s~~~~GIG~~~A~~iv~~fg---~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~------~~~~~~~~~~~ 148 (720)
T TIGR01448 78 EGIVAYLSSRSIKGVGKKLAQRIVKTFG---EAAFDVLDDDPEKLLEVPGISKANLEKFVSQW------SQQGDERRLLA 148 (720)
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHHhC---HhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH------HHhHHHHHHHH
Q ss_pred HhhhhcCCCcchHHH-----------HHhhcCccccccchhchHHHHHHHHH-cCCCC
Q 035716 136 FLSHDLEVPEHDFRK-----------VINKCPRLLTSSARDQLKPALFYLQR-LGFKD 181 (308)
Q Consensus 136 fL~~~~G~~~~~i~~-----------li~~~P~lL~~~~~~~l~~~v~~L~~-lG~~~ 181 (308)
|| ..+|++.+...+ +|..+|+.|..++..-=-..+|.+.. +|+..
T Consensus 149 ~L-~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~ 205 (720)
T TIGR01448 149 GL-QGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIAL 205 (720)
T ss_pred HH-HHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCC
No 43
>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=21.89 E-value=1.1e+02 Score=20.81 Aligned_cols=18 Identities=28% Similarity=0.558 Sum_probs=13.0
Q ss_pred HHHHHHcCCCHHHHHHHH
Q 035716 205 LKYLESIGFSKDEAVLMV 222 (308)
Q Consensus 205 v~~L~~lG~s~~~i~~~l 222 (308)
+..++.+|||-+||..++
T Consensus 7 I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 445568999999999998
No 44
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=21.81 E-value=1.6e+02 Score=24.23 Aligned_cols=27 Identities=15% Similarity=0.340 Sum_probs=14.9
Q ss_pred chhHHHHHhhhhcCCCcchHHHHHhhcC
Q 035716 129 DLEPVFNFLSHDLEVPEHDFRKVINKCP 156 (308)
Q Consensus 129 ~l~~~l~fL~~~~G~~~~~i~~li~~~P 156 (308)
.+...+.-+. ++|++..++..++..-|
T Consensus 71 ~i~el~~k~~-~fkLtKAE~LqiiN~rP 97 (149)
T KOG4168|consen 71 SIIELITKLK-SFKLTKAEILQIINLRP 97 (149)
T ss_pred HHHHHHHHhc-cccchHHHHHHHhccCc
Confidence 3444444453 55666666666666655
No 45
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=21.51 E-value=41 Score=27.19 Aligned_cols=17 Identities=24% Similarity=0.137 Sum_probs=6.7
Q ss_pred HHHHHHHHhhcCCChhh
Q 035716 62 IKEKILCLEIMGVDSGK 78 (308)
Q Consensus 62 ~~~~l~~L~~~G~~~~~ 78 (308)
+...++.+...|++..+
T Consensus 121 ~~~~~~~~~~~G~d~~~ 137 (143)
T PF08212_consen 121 YAEILDRAKQQGYDVSK 137 (143)
T ss_dssp HHHHHHHHHHTT--GGG
T ss_pred HHHHHHHHHHcCCCHHH
Confidence 33444444444544443
No 46
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.38 E-value=3.5e+02 Score=20.09 Aligned_cols=23 Identities=22% Similarity=0.274 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 035716 203 PKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 203 ~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
..+.+|+++|++-++|..++...
T Consensus 48 ~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 48 QFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Confidence 45677889999999999988754
No 47
>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=21.19 E-value=55 Score=27.59 Aligned_cols=51 Identities=22% Similarity=0.405 Sum_probs=35.5
Q ss_pred CHHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcCCCcchHHHH
Q 035716 93 SIEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKV 151 (308)
Q Consensus 93 ~l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~~~~~i~~l 151 (308)
+....++.++..|++++++.+.=.. |-. .+-..-.+||. .+|++++++..+
T Consensus 117 ~~~~w~~l~~~~g~~~~~m~~wh~~----fe~---~~p~~h~~~l~-~~g~~~~~~~~i 167 (172)
T cd04790 117 TKEKWVAILKAAGMDEADMRRWHIE----FEK---MEPEAHQEFLQ-SLGIPEDEIERI 167 (172)
T ss_pred CHHHHHHHHHHcCCChHHHHHHHHH----HHH---hCcHHHHHHHH-HcCCCHHHHHHH
Confidence 3577888889999998886433322 111 13466789995 899999988754
No 48
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=20.99 E-value=2.1e+02 Score=21.72 Aligned_cols=74 Identities=9% Similarity=0.184 Sum_probs=0.0
Q ss_pred HHHHHHHHHhCCCCCCChhhhhhcCCceeeCCcccchhHHHHHhhhhcCCCcchHHHHHhhcCccccccchhchHHHHH
Q 035716 94 IEGIISFLQSKGILQKDLPRIFGMCPKVLTANIKTDLEPVFNFLSHDLEVPEHDFRKVINKCPRLLTSSARDQLKPALF 172 (308)
Q Consensus 94 l~~~v~~L~~lGls~~~i~~li~~~P~lL~~~~e~~l~~~l~fL~~~~G~~~~~i~~li~~~P~lL~~~~~~~l~~~v~ 172 (308)
++..-+|-+.+|++..+|..+-..+| .+..+.....+.-+++..| .......++..-..+=...+.++++..+.
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~----~d~~Eq~~qmL~~W~~~~G-~~a~~~~Li~aLr~~~l~~~Ad~I~~~l~ 93 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNP----QDTAEQKVQLLRAWYQSHG-KTGAYRTLIKTLRKAKLCTKADKIQDIIE 93 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCC----CChHHHHHHHHHHHHHHhC-CCchHHHHHHHHHHccchhHHHHHHHHHH
No 49
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.92 E-value=2.7e+02 Score=21.09 Aligned_cols=52 Identities=13% Similarity=0.001 Sum_probs=31.0
Q ss_pred HHHHHHHHcCCCCcchhhhhchhhhhcch-hhhHHHHHHHHHHcCCCHHHHHHHHhc
Q 035716 169 PALFYLQRLGFKDLNALAYQDSVLLVSKV-ENTLIPKLKYLESIGFSKDEAVLMVLR 224 (308)
Q Consensus 169 ~~v~~L~~lG~~~~~~ii~~~P~ll~~~~-~~~l~~~v~~L~~lG~s~~~i~~~l~~ 224 (308)
.++.|..+.|+-.... ...=.. ++- +-..-..+..++++||+-++|..++..
T Consensus 15 ~tlRyYe~~GLl~p~~--~~g~r~--Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 15 DTVRHYIDLGLLIPEK--KGGQYF--FDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHCCCcCCcc--CCCccc--cCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5678888888743221 011111 221 112344566777999999999998853
No 50
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.84 E-value=2.1e+02 Score=19.43 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=17.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHh
Q 035716 201 LIPKLKYLESIGFSKDEAVLMVL 223 (308)
Q Consensus 201 l~~~v~~L~~lG~s~~~i~~~l~ 223 (308)
.-..+..|.+.|++.++|.+++.
T Consensus 45 ~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 45 RLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHHHHHHHTTTHHHHHHHHH-
T ss_pred HHHHHHHHHHCcCCHHHHHHHHc
Confidence 34557777789999999998875
No 51
>cd00739 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS.
Probab=20.62 E-value=2.1e+02 Score=25.75 Aligned_cols=61 Identities=16% Similarity=0.173 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHhCCChHHHhhcCcc-ccccccC--chHHHHHHHHHcCCCCCchhhcccCHHHHHHHhc
Q 035716 237 FKPKFEYFNLEIKGKLEELKEFPQY-FAFSLEK--RIKPRHMQALRNGARLSLPVMLKTSDEEFNELIK 302 (308)
Q Consensus 237 l~~k~~fL~~~mg~~~~~l~~~P~~-L~~sle~--ri~pR~~~L~~~G~~~~l~~il~~sd~~F~~~~~ 302 (308)
++.+++.+. ..|++.+.|.--|.+ +.-+.+. .+.-+++.+++. .++.++..|.+.|...+.
T Consensus 152 ~~~~i~~~~-~~Gi~~~~Ii~DPg~gf~ks~~~~~~~l~~i~~l~~~----~~pil~G~SrkSfig~~~ 215 (257)
T cd00739 152 LEARLEAAE-SAGVARNRIILDPGIGFGKTPEHNLELLRRLDELKQL----GLPVLVGASRKSFIGALL 215 (257)
T ss_pred HHHHHHHHH-HcCCCHHHEEEecCCCcccCHHHHHHHHHHHHHHHhC----CCcEEEEecccHHHHHhc
Confidence 344444444 378877777777754 2222110 011133444444 356677778888877665
No 52
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=20.42 E-value=1.6e+02 Score=20.79 Aligned_cols=35 Identities=17% Similarity=0.238 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHcCCCHHHHHHHHhcCcceeeecc
Q 035716 199 NTLIPKLKYLESIGFSKDEAVLMVLRCPGLFTFSI 233 (308)
Q Consensus 199 ~~l~~~v~~L~~lG~s~~~i~~~l~~~P~iL~~s~ 233 (308)
.++...++.++.+||+..+|...+.+-=.+...+.
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~nW 43 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGNW 43 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCc
Confidence 45777888888999999888776665544444444
No 53
>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=20.18 E-value=2.5e+02 Score=21.68 Aligned_cols=54 Identities=13% Similarity=0.108 Sum_probs=32.7
Q ss_pred HHHHHHHHcCCCCcchhhhhchhhhhcchh-hhHHHHHHHHHHcCCCHHHHHHHHhcC
Q 035716 169 PALFYLQRLGFKDLNALAYQDSVLLVSKVE-NTLIPKLKYLESIGFSKDEAVLMVLRC 225 (308)
Q Consensus 169 ~~v~~L~~lG~~~~~~ii~~~P~ll~~~~~-~~l~~~v~~L~~lG~s~~~i~~~l~~~ 225 (308)
.++.|..+.|+-...+ +.+.-=.++.. -..-..+.+|+++||+-++|..++..+
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 5677888888743211 12221123321 123345777889999999999888654
Done!