Query 012657
Match_columns 459
No_of_seqs 132 out of 168
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:57:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012657.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012657hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09328 Phytochelatin_C: Doma 100.0 2E-115 4E-120 840.2 25.7 264 156-419 1-264 (264)
2 KOG0632 Phytochelatin synthase 100.0 9E-103 2E-107 767.0 14.1 321 5-412 68-388 (388)
3 PF05023 Phytochelatin: Phytoc 100.0 7.3E-62 1.6E-66 459.6 12.4 147 7-153 66-212 (212)
4 PF14399 Transpep_BrtH: NlpC/p 96.4 0.045 9.8E-07 53.1 11.8 105 41-151 53-164 (317)
5 PF13529 Peptidase_C39_2: Pept 94.8 0.069 1.5E-06 44.3 5.7 76 35-118 62-144 (144)
6 cd02549 Peptidase_C39A A sub-f 93.4 0.38 8.3E-06 40.8 7.5 89 36-137 42-131 (141)
7 cd02259 Peptidase_C39_like Pep 93.2 0.47 1E-05 39.1 7.5 79 35-136 36-114 (122)
8 PF03412 Peptidase_C39: Peptid 92.3 0.15 3.2E-06 43.2 3.4 78 35-136 42-119 (131)
9 cd02420 Peptidase_C39D A sub-f 90.6 0.68 1.5E-05 38.8 5.7 76 36-135 42-117 (125)
10 cd02418 Peptidase_C39B A sub-f 90.3 1.8 4E-05 36.4 8.1 83 36-136 42-124 (136)
11 cd02424 Peptidase_C39E A sub-f 83.6 4 8.7E-05 35.0 6.5 79 36-135 43-121 (129)
12 cd02423 Peptidase_C39G A sub-f 83.4 4.2 9.2E-05 33.9 6.5 78 36-134 43-120 (129)
13 cd02419 Peptidase_C39C A sub-f 81.0 12 0.00025 31.4 8.3 76 36-135 42-117 (127)
14 TIGR03796 NHPM_micro_ABC1 NHPM 77.7 17 0.00038 39.9 10.5 76 35-134 42-117 (710)
15 cd02425 Peptidase_C39F A sub-f 73.6 16 0.00034 30.4 7.0 76 36-134 42-117 (126)
16 TIGR01193 bacteriocin_ABC ABC- 61.0 1E+02 0.0022 34.2 11.9 84 35-134 36-119 (708)
17 cd02417 Peptidase_C39_likeA A 57.6 77 0.0017 26.2 8.1 78 36-136 37-114 (121)
18 PF09778 Guanylate_cyc_2: Guan 54.0 55 0.0012 32.5 7.5 86 41-135 93-198 (212)
19 cd04770 HTH_HMRTR Helix-Turn-H 51.5 24 0.00053 30.5 4.3 41 9-50 30-70 (123)
20 cd04781 HTH_MerR-like_sg6 Heli 49.4 12 0.00026 32.7 2.0 39 13-51 32-70 (120)
21 cd02421 Peptidase_C39_likeD A 49.0 99 0.0022 25.8 7.5 77 36-134 37-113 (124)
22 TIGR03375 type_I_sec_LssB type 48.4 65 0.0014 35.6 7.9 78 35-134 29-107 (694)
23 cd01106 HTH_TipAL-Mta Helix-Tu 47.9 23 0.00049 30.0 3.5 44 7-50 27-70 (103)
24 KOG4621 Uncharacterized conser 46.6 37 0.0008 32.1 4.9 80 52-137 72-152 (167)
25 cd04785 HTH_CadR-PbrR-like Hel 46.5 33 0.00071 30.3 4.4 38 13-50 33-70 (126)
26 cd04768 HTH_BmrR-like Helix-Tu 46.3 14 0.0003 31.2 1.9 43 7-49 27-69 (96)
27 PRK15002 redox-sensitivie tran 46.0 27 0.00058 32.5 3.9 37 13-49 43-79 (154)
28 TIGR02044 CueR Cu(I)-responsiv 46.0 32 0.00068 30.3 4.2 37 13-49 33-69 (127)
29 PF05381 Peptidase_C21: Tymovi 45.8 17 0.00036 32.6 2.4 50 6-60 16-65 (104)
30 PRK10227 DNA-binding transcrip 42.2 38 0.00081 30.6 4.1 38 12-49 32-69 (135)
31 COG5559 Uncharacterized conser 41.6 13 0.00029 30.6 1.0 17 401-417 8-24 (65)
32 COG3323 Uncharacterized protei 39.9 20 0.00044 32.3 2.0 44 63-110 16-59 (109)
33 cd04783 HTH_MerR1 Helix-Turn-H 38.3 21 0.00046 31.3 1.9 42 8-50 29-70 (126)
34 TIGR01950 SoxR redox-sensitive 37.6 22 0.00048 32.4 2.0 37 13-49 33-69 (142)
35 PRK13752 putative transcriptio 37.1 24 0.00051 32.3 2.1 42 8-50 36-77 (144)
36 PF05415 Peptidase_C36: Beet n 36.2 21 0.00045 31.7 1.5 39 34-72 16-59 (104)
37 cd01282 HTH_MerR-like_sg3 Heli 36.1 27 0.00059 30.2 2.2 42 8-50 28-69 (112)
38 PF09312 SurA_N: SurA N-termin 35.9 17 0.00038 31.6 1.0 45 30-74 57-111 (118)
39 cd04763 HTH_MlrA-like Helix-Tu 35.3 30 0.00066 26.9 2.2 40 7-47 28-67 (68)
40 cd01108 HTH_CueR Helix-Turn-He 35.2 51 0.0011 29.1 3.8 41 8-49 29-69 (127)
41 cd04784 HTH_CadR-PbrR Helix-Tu 34.9 28 0.00061 30.5 2.1 41 8-49 29-69 (127)
42 PF14214 Helitron_like_N: Heli 33.8 55 0.0012 30.1 3.9 44 156-206 102-145 (184)
43 cd01789 Alp11_N Ubiquitin-like 33.3 2.8E+02 0.006 22.9 7.6 64 54-119 15-83 (84)
44 TIGR02047 CadR-PbrR Cd(II)/Pb( 32.6 33 0.00072 30.4 2.2 41 8-49 29-69 (127)
45 cd01109 HTH_YyaN Helix-Turn-He 30.9 78 0.0017 27.2 4.2 39 11-49 31-69 (113)
46 TIGR03797 NHPM_micro_ABC2 NHPM 30.8 2.1E+02 0.0045 31.7 8.4 82 28-132 19-102 (686)
47 COG5565 Bacteriophage terminas 30.3 28 0.00061 29.8 1.3 38 10-58 15-55 (79)
48 PF02775 TPP_enzyme_C: Thiamin 29.7 89 0.0019 27.6 4.4 36 42-79 112-147 (153)
49 cd01110 HTH_SoxR Helix-Turn-He 29.6 37 0.00081 30.7 2.1 42 7-49 28-69 (139)
50 COG1312 UxuA D-mannonate dehyd 29.1 3.5E+02 0.0076 29.2 9.2 153 14-186 3-201 (362)
51 cd04786 HTH_MerR-like_sg7 Heli 28.9 86 0.0019 28.2 4.2 41 9-50 30-70 (131)
52 cd04788 HTH_NolA-AlbR Helix-Tu 28.3 40 0.00088 28.4 1.9 38 13-50 33-70 (96)
53 PRK09514 zntR zinc-responsive 28.0 88 0.0019 28.3 4.1 37 13-49 34-70 (140)
54 PTZ00445 p36-lilke protein; Pr 27.7 1.9E+02 0.0042 29.0 6.7 98 41-141 32-158 (219)
55 PF13411 MerR_1: MerR HTH fami 27.6 25 0.00055 26.9 0.5 42 6-48 26-67 (69)
56 cd04789 HTH_Cfa Helix-Turn-Hel 27.4 33 0.00071 29.3 1.2 36 13-48 33-68 (102)
57 KOG4212 RNA-binding protein hn 27.0 71 0.0015 35.4 3.9 58 94-155 29-94 (608)
58 cd04787 HTH_HMRTR_unk Helix-Tu 27.0 43 0.00093 29.8 2.0 43 8-50 28-70 (133)
59 cd04776 HTH_GnyR Helix-Turn-He 26.4 46 0.00099 29.3 2.0 40 8-49 28-67 (118)
60 cd04782 HTH_BltR Helix-Turn-He 25.6 53 0.0012 27.7 2.2 43 7-49 27-69 (97)
61 cd04764 HTH_MlrA-like_sg1 Heli 25.2 38 0.00083 26.1 1.2 35 13-47 32-66 (67)
62 COG2841 Uncharacterized protei 24.8 72 0.0016 27.1 2.7 31 220-250 33-68 (72)
63 TIGR01846 type_I_sec_HlyB type 24.2 3E+02 0.0066 30.6 8.2 76 35-134 29-104 (694)
64 TIGR02043 ZntR Zn(II)-responsi 24.1 55 0.0012 29.2 2.1 40 9-49 31-70 (131)
65 PRK13749 transcriptional regul 23.8 60 0.0013 29.3 2.3 40 13-52 36-75 (121)
66 TIGR00987 himA integration hos 23.8 1.5E+02 0.0032 25.0 4.5 86 38-139 2-93 (96)
67 PRK05416 glmZ(sRNA)-inactivati 23.6 2.5E+02 0.0054 28.6 6.9 56 57-128 140-198 (288)
68 PF00120 Gln-synt_C: Glutamine 23.5 1.3E+02 0.0028 29.4 4.7 61 40-102 71-153 (259)
69 cd04780 HTH_MerR-like_sg5 Heli 23.3 1.3E+02 0.0029 25.5 4.1 51 13-72 33-84 (95)
70 cd04790 HTH_Cfa-like_unk Helix 23.2 59 0.0013 30.5 2.2 43 8-50 29-71 (172)
71 TIGR00695 uxuA mannonate dehyd 23.1 3.1E+02 0.0068 29.6 7.7 60 14-76 3-94 (394)
72 PF05372 Delta_lysin: Delta ly 21.9 57 0.0012 22.6 1.3 10 210-219 9-18 (25)
73 TIGR00653 GlnA glutamine synth 21.8 1.4E+02 0.0031 32.3 4.9 61 40-102 185-267 (460)
74 cd01107 HTH_BmrR Helix-Turn-He 21.0 71 0.0015 27.4 2.1 39 13-51 34-72 (108)
75 TIGR02051 MerR Hg(II)-responsi 20.9 67 0.0015 28.3 2.0 39 12-50 31-69 (124)
No 1
>PF09328 Phytochelatin_C: Domain of unknown function (DUF1984); InterPro: IPR015407 This entry represents the C-terminal region of plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process
Probab=100.00 E-value=1.9e-115 Score=840.19 Aligned_cols=264 Identities=67% Similarity=1.078 Sum_probs=262.2
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhhhhhccCCCCCHHHHHHHHHhcCCcchhhHhhhheeeeecccCCCCCCHHHH
Q 012657 156 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEK 235 (459)
Q Consensus 156 ~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~slP~~~~~~ikwv~evrr~e~~~~~ls~eek 235 (459)
+++|++|||+||+||+|.+|||||++|||.||++++++||++||++||+|||+||++||||||||||+|||+++||.|||
T Consensus 1 ~r~P~lLYTlSCkhEsW~s~AKyL~eDvP~LLkse~v~~v~~vls~vf~SlPsn~~~FIKWVaEVRR~Edg~~~LS~EEk 80 (264)
T PF09328_consen 1 HRAPSLLYTLSCKHESWISMAKYLMEDVPRLLKSEDVKDVEEVLSVVFKSLPSNFGEFIKWVAEVRRQEDGGSSLSKEEK 80 (264)
T ss_pred CCCCceeEEeecCcCcHHHHHHHHHHHHHHHhhhcccCcHHHHHHHHHhcCchhHHHHhhhheeEEecccCCCCCCHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhhHHHHHHHHHhccchhHHHHHhhhcccccccccccccCCCChhHHHHHhhhhhhHHhhCcCCCCCcceeccccccee
Q 012657 236 GRLALKEEVLRQVQETLLFKHVVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCL 315 (459)
Q Consensus 236 ~rl~~k~~vl~qi~~t~lf~~V~~~~~s~~~~c~~~~~~~~~~~l~~iaa~vcCqga~~l~g~~~~~~~~cc~etc~kc~ 315 (459)
+||++|++||||||+|+|||||++||++.+|||+++++++++|+||+|||+||||||+||+|+++++++|||+|||+||+
T Consensus 81 ~RL~lKe~VL~Qvr~T~LFk~V~~~L~s~~s~c~~~~~~~~~dsL~~iaa~vCCQGA~iL~G~~~s~~~~Cc~etcvkc~ 160 (264)
T PF09328_consen 81 ERLALKEEVLQQVRETELFKHVTKWLSSSNSCCCNCSNSGDEDSLPDIAASVCCQGAAILSGNLGSSDGFCCKETCVKCV 160 (264)
T ss_pred HHHHHHHHHHHHHHhchHHHHHHHHHhccccccccccccCccccHHHHHHHHhhhhHHHHcCCCCCCCCceEccccccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCeeEEeeeEEeCCccceeeEeecCCCCCCCccCCCCCCcccccCCcchHHHHHHHhCCCCccCCCCchHHHHHH
Q 012657 316 KANSDKPVTLVSGTVVNGSIEQEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQI 395 (459)
Q Consensus 316 ~~~~~~~~t~vsg~v~~~~~eq~vd~lvp~~~~~~~~~~~~~~~~~~~~p~~~dvltvlllal~~~tw~~i~de~l~~e~ 395 (459)
|+|||||+|||||+||+||+|||||||||+||+++++|+++.+++++|||+++||||||||||||+||+|||||+|++||
T Consensus 161 k~n~d~~~tvvsGtVv~~g~Eq~VD~LvP~s~~~~~~c~~~~~~~~~~hPs~~DVLTvLLLALpp~TWs~Ikde~l~~Ei 240 (264)
T PF09328_consen 161 KANGDGPKTVVSGTVVSGGSEQGVDVLVPSSQTKTSCCNSGSSNEIGMHPSSNDVLTVLLLALPPSTWSGIKDEKLLAEI 240 (264)
T ss_pred eeCCCCceEEEeeeEEcCCCccceeEEeccccCCCCccCCCCCCccccCCCcccHHHHHHHhCCccccccCccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCchhHHHHHHHHHHHH
Q 012657 396 LGLVTTENLPTLLQEEVLHLRRQL 419 (459)
Q Consensus 396 ~~lvs~~~lp~~lq~evlhlr~ql 419 (459)
++||||||||++|||||+||||||
T Consensus 241 ~~LvSte~LP~lLQeEVlHLrrQL 264 (264)
T PF09328_consen 241 QSLVSTENLPDLLQEEVLHLRRQL 264 (264)
T ss_pred HHHhhhhhCcHHHHHHHHHHHhcC
Confidence 999999999999999999999997
No 2
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=8.6e-103 Score=766.97 Aligned_cols=321 Identities=59% Similarity=1.059 Sum_probs=301.5
Q ss_pred CCCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEE
Q 012657 5 NKARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVIS 84 (459)
Q Consensus 5 ~~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIV 84 (459)
..||.|.||||||||||+|||||+|||.|+++||||+||+|||+|||++|+++|++++++|+||..|+.|.+++|+|||.
T Consensus 68 ~vDPgr~WKgpWRwydesMLdCC~pLe~ikk~Gisl~~fsCLA~cnglk~~~~~~s~~t~d~FRk~vv~cstsen~~mi~ 147 (388)
T KOG0632|consen 68 SVDPGRKWKGPWRWYDESMLDCCEPLEDIKKKGISLGKFSCLAHCNGLKVEAFRTSQSTIDDFRKDVVKCSTSENCHMIS 147 (388)
T ss_pred ccCCcccccCCchhhhhHHHhhcccHHHHHhcCcchheeehhhhcCCceeEEEecCcchHHHHHHHHHhcccccceeeeh
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecccccccCCCccccccccccCCCCeEEEEecCCCCCCceeeehhHHHHhccccCCCCCceeeEEEEeCCCCCCCccee
Q 012657 85 SYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVSRPHREPGLLYT 164 (459)
Q Consensus 85 nY~Rk~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRGfllIsk~~~~ps~l~~ 164 (459)
+|+|++|||||+||||||||||+++|++|||||||||||||||||++||+||..||.+||++||||+|+++|++|+ ||+
T Consensus 148 sy~R~VlgQTGtGHFSPiggy~e~~d~~LIlDVARFKYPphWV~Lkll~eam~siD~stg~pRG~~li~~~h~~~g-l~t 226 (388)
T KOG0632|consen 148 SYHRKVLGQTGTGHFSPIGGYNEERDMALILDVARFKYPPHWVPLKLLWEAMDSIDQSTGQPRGFMLISRPHREPG-LYT 226 (388)
T ss_pred HhHHHHhcCCCCCccCcccccCcccCceEEeehhhccCCCcceeHHHHHHHhcchhhccCCCccceecccCCCCCc-eEE
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred eeccCCChHHHHHHHHhhhhhhhccCCCCCHHHHHHHHHhcCCcchhhHhhhheeeeecccCCCCCCHHHHhHhhHHHHH
Q 012657 165 LSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEKGRLALKEEV 244 (459)
Q Consensus 165 ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~slP~~~~~~ikwv~evrr~e~~~~~ls~eek~rl~~k~~v 244 (459)
++|++++|..+||||.+|+|. |.++.|.++|.+|++|| ++|+|+.||.+++++.|| +|+.+
T Consensus 227 l~lkk~sw~~i~k~lk~~v~~------------i~~~dfas~~~s~NQf~--~~~i~~~~d~~q~~~~E~-----fk~c~ 287 (388)
T KOG0632|consen 227 LSLKKESWINIAKYLKEDVPR------------IKNVDFASLPLSFNQFI--IAEIRETEDSNQNLSFEE-----FKQCI 287 (388)
T ss_pred EEeccccHHHHHHHHHHhhhh------------hhhhHHHhcchhHHHHH--HHHHHhhcCcccccCHHH-----HHHHH
Confidence 999999999999999999988 66677999999999999 899999999999999988 44433
Q ss_pred HHHHhccchhHHHHHhhhcccccccccccccCCCChhHHHHHhhhhhhHHhhCcCCCCCcceecccccceeecCCCCCee
Q 012657 245 LRQVQETLLFKHVVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCLKANSDKPVT 324 (459)
Q Consensus 245 l~qi~~t~lf~~V~~~~~s~~~~c~~~~~~~~~~~l~~iaa~vcCqga~~l~g~~~~~~~~cc~etc~kc~~~~~~~~~t 324 (459)
+ |..++++ .+|+.+||+|+++++|. .+..|||++||++|.|.-++...|
T Consensus 288 r--------------------------st~~y~~---f~~h~~~c~~~e~~s~~--~~~~~~c~~~~~ac~kg~~e~~~t 336 (388)
T KOG0632|consen 288 R--------------------------STVTYED---FAAHKNCCTGVEILSGA--FSAEFCCPETCVACIKGVLEEIQT 336 (388)
T ss_pred H--------------------------hhhhHHh---hhhhhcccccceeecCC--cccccccHHHHHHhhhchhhhhhh
Confidence 3 1133455 67899999999999997 688999999999999987777666
Q ss_pred EEeeeEEeCCccceeeEeecCCCCCCCccCCCCCCcccccCCcchHHHHHHHhCCCCccCCCCchHHHHHHhhhccCCCC
Q 012657 325 LVSGTVVNGSIEQEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQILGLVTTENL 404 (459)
Q Consensus 325 ~vsg~v~~~~~eq~vd~lvp~~~~~~~~~~~~~~~~~~~~p~~~dvltvlllal~~~tw~~i~de~l~~e~~~lvs~~~l 404 (459)
++ .+|.++||+|+|||||||+||+||+|..|..|+..+++.-+.
T Consensus 337 ~~------------------------------------aev~~s~v~taLllAlp~q~~~~~k~dsl~~~~k~~~~~~S~ 380 (388)
T KOG0632|consen 337 VV------------------------------------AEVEGSDVFTALLLALPPQTWSGIKDDSLTHEMKQLISMCSS 380 (388)
T ss_pred ee------------------------------------eecccchHHHHHHHhcCcccccccccHHHHHHHHHHHhhccc
Confidence 63 389999999999999999999999999999999999999999
Q ss_pred chhHHHHH
Q 012657 405 PTLLQEEV 412 (459)
Q Consensus 405 p~~lq~ev 412 (459)
|+++|.||
T Consensus 381 ~t~~~~~~ 388 (388)
T KOG0632|consen 381 PTLLQTEV 388 (388)
T ss_pred HhhhhccC
Confidence 99999985
No 3
>PF05023 Phytochelatin: Phytochelatin synthase; InterPro: IPR007719 This entry represents plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process; PDB: 2BTW_A 2BU3_B.
Probab=100.00 E-value=7.3e-62 Score=459.58 Aligned_cols=147 Identities=49% Similarity=0.984 Sum_probs=123.9
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEe
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSY 86 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY 86 (459)
+|+++||||||||+|+||+||.|++.|+++||||+||+|||+|||+.|+++++++.|+++||++|++++++++++|||||
T Consensus 66 ~P~~~~~~~~~~~tq~~l~~~~~~~~v~~~GiTL~e~~~la~~~g~~~~~~~~~~~s~~~FR~~l~~~~~~~~~~livnf 145 (212)
T PF05023_consen 66 APGRVWKGPWRWFTQEMLDCCIPLESVKREGITLDEFACLAKCNGLRVEVYRADDSSLDEFRQHLKEALSDPNDFLIVNF 145 (212)
T ss_dssp ----TTTTT-----TTTCCHHS-HHHHHHH---HHHHHHHHHTTT-EEEEEEGGGS-HHHHHHHHHHHCTSTTEEEEEEE
T ss_pred CCcccccCCcceeehhhhhccccHHHHhhcCCCHHHHHHHHHhcCCceEEEeCCcCCHHHHHHHHHHHhCCCCCEEEEEC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCCccccccccccCCCCeEEEEecCCCCCCceeeehhHHHHhccccCCCCCceeeEEEEe
Q 012657 87 HRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVS 153 (459)
Q Consensus 87 ~Rk~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRGfllIs 153 (459)
+|++|||+|+||||||||||+++|+|||||||||||||||||+++||+||+++|++||++|||++|+
T Consensus 146 ~R~~lgq~G~GHfSPigaY~~~tD~vLilDVar~kYpp~WV~~~~L~~AM~~~D~~s~~~RG~~~is 212 (212)
T PF05023_consen 146 DRKALGQTGGGHFSPIGAYDAETDRVLILDVARFKYPPYWVPLERLYEAMNTIDPDSGKSRGYLLIS 212 (212)
T ss_dssp EGGGGTSSSSEEEEEEEEEETTTTEEEE--S-TTT---EEEEHHHHHHHHSSEETTTTEE-EEEEEE
T ss_pred cccccCCCCCCcccccceecccCCeEEEEecccccCCCEEeEHHHHHHHHhccCCCCCCcceEEEeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999996
No 4
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=96.38 E-value=0.045 Score=53.09 Aligned_cols=105 Identities=18% Similarity=0.059 Sum_probs=80.2
Q ss_pred HHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEeccccc-------ccCCCccccccccccCCCCeEE
Q 012657 41 GKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAF-------KQTGTGHFSPIGGYHAGRDMAL 113 (459)
Q Consensus 41 ~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~L-------gQtG~GHFSPIGGYh~~tD~VL 113 (459)
.-+..+++.+|++++.... .+.++..+.|++.+. .+..++|.-+...| ...+.+|+--|=|||++.+.++
T Consensus 53 ~~~~~~~~~lG~~~~~~~~--~~~~~~~~~l~~~l~-~g~pv~~~~D~~~lpy~~~~~~~~~~~H~i~v~G~d~~~~~~~ 129 (317)
T PF14399_consen 53 DFEENLLERLGIKYEWREF--SSPDEAWEELKEALD-AGRPVIVWVDMYYLPYRPNYYKKHHADHYIVVYGYDEEEDVFY 129 (317)
T ss_pred HHHHHHHHHCCceEEEEec--CCHHHHHHHHHHHHh-CCCceEEEeccccCCCCccccccccCCcEEEEEEEeCCCCEEE
Confidence 5567889999999986654 367888888887775 44567776655444 3446899999999999999999
Q ss_pred EEecCCCCCCceeeehhHHHHhccccCCCCCceeeEEE
Q 012657 114 ILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVL 151 (459)
Q Consensus 114 ILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRGfll 151 (459)
|.|. ..+++..+|.+.|-+|+..... ...+++.+.
T Consensus 130 v~D~--~~~~~~~~~~~~l~~A~~~~~~-~~~~~~~~~ 164 (317)
T PF14399_consen 130 VSDP--PSYEPGRLPYEDLAKARFSEGI-PFPPKNRWY 164 (317)
T ss_pred EEcC--CCCcceeecHHHHHHHHhccCC-CCCCCceEE
Confidence 9998 5778899999999999988874 234455443
No 5
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=94.84 E-value=0.069 Score=44.28 Aligned_cols=76 Identities=25% Similarity=0.257 Sum_probs=47.9
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEec--ccc-----cccCCCccccccccccC
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYH--RGA-----FKQTGTGHFSPIGGYHA 107 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~--Rk~-----LgQtG~GHFSPIGGYh~ 107 (459)
..|+....+..+++..|..+. .....+++++++.|. .+..+|++.+ ... ....+.|||--|=||+.
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~~~i~-----~G~Pvi~~~~~~~~~~~~~~~~~~~~~H~vvi~Gy~~ 134 (144)
T PF13529_consen 62 GYGTSPDDLARYLEKYGYKAT--DTSDASFDDIKQEID-----AGRPVIVSVNSGWRPPNGDGYDGTYGGHYVVIIGYDE 134 (144)
T ss_dssp B----HHHHHHHHHHH-TTEE--E-TTS-HHHHHHHHH-----TT--EEEEEETTSS--TTEEEEE-TTEEEEEEEEE-S
T ss_pred CCccccHHHHHHHHHcCccee--eccCCcHHHHHHHHH-----CCCcEEEEEEcccccCCCCCcCCCcCCEEEEEEEEeC
Confidence 457788899999999998443 344567877777776 3668888886 233 26678999999999999
Q ss_pred CCCeEEEEecC
Q 012657 108 GRDMALILDVA 118 (459)
Q Consensus 108 ~tD~VLILDVA 118 (459)
.. .|.|.|.+
T Consensus 135 ~~-~~~v~DP~ 144 (144)
T PF13529_consen 135 DG-YVYVNDPW 144 (144)
T ss_dssp SE--EEEE-TT
T ss_pred CC-EEEEeCCC
Confidence 77 89999964
No 6
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=93.42 E-value=0.38 Score=40.80 Aligned_cols=89 Identities=18% Similarity=0.122 Sum_probs=61.3
Q ss_pred cCCcHHHHHHH-HHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 36 KGISFGKLVCL-AHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 36 ~GITL~ef~cL-A~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
.|.+..++... |+..|++++..... .. +++.+. .+..+|+..+- ..-..+.|||--|.||+ +.+.++|
T Consensus 42 ~g~~~~~l~~~~a~~~G~~~~~~~~~---~~-~~~~l~-----~~~Pvi~~~~~-~~~~~~~gH~vVv~g~~-~~~~~~i 110 (141)
T cd02549 42 YGTYPKPIVSAAARKYGLVVRPLTGL---LA-LLRQLA-----AGHPVIVSVNL-GVSITPSGHAMVVIGYD-RKGNVYV 110 (141)
T ss_pred CCcCHHHHHHHHHhhCCCcEEECCCH---HH-HHHHHH-----CCCeEEEEEec-CcccCCCCeEEEEEEEc-CCCCEEE
Confidence 58899999999 99999988764432 11 223322 45577776542 12234589999999999 4566999
Q ss_pred EecCCCCCCceeeehhHHHHhcc
Q 012657 115 LDVARFKYPPHWVPLTLLWEAMD 137 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM~ 137 (459)
.|.+. -.+..++.+.+-++..
T Consensus 111 ~DP~~--~~~~~~~~~~f~~~w~ 131 (141)
T cd02549 111 NDPGG--GRRLVVSFDEFEKAWK 131 (141)
T ss_pred ECCCC--CcCEEEeHHHHHHHHH
Confidence 99864 4577888877665553
No 7
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=93.15 E-value=0.47 Score=39.06 Aligned_cols=79 Identities=22% Similarity=0.269 Sum_probs=59.3
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
..|.++.++..+|+..|++++.+.. +++.+++ -+..+|+- .++|||--|.+++ .+.++|
T Consensus 36 ~~~~~~~~l~~~a~~~gl~~~~~~~---~~~~l~~--------~~~P~i~~--------~~~~~~~Vl~~~~--~~~~~i 94 (122)
T cd02259 36 QQGLSLADLVSLANKLGLTAQGVKL---PLAALSR--------LQLPALLL--------WKQGHFVILYGAD--KGQVLI 94 (122)
T ss_pred cCCCCHHHHHHHHHHcCCeeeEEEc---CHHHhcc--------CCCCEEEE--------cCCCcEEEEEEEc--CCEEEE
Confidence 3689999999999999999998764 3433222 22234433 4789999999998 668999
Q ss_pred EecCCCCCCceeeehhHHHHhc
Q 012657 115 LDVARFKYPPHWVPLTLLWEAM 136 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM 136 (459)
.|.+ ...+.|++.+.|-+..
T Consensus 95 ~dp~--~~~~~~~~~~~l~~~w 114 (122)
T cd02259 95 ADPL--EEGPVTLSESELEERW 114 (122)
T ss_pred ECCc--ccCCEEeCHHHHHhhC
Confidence 9986 5678899998876644
No 8
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=92.27 E-value=0.15 Score=43.15 Aligned_cols=78 Identities=24% Similarity=0.192 Sum_probs=55.8
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
..|+|+.++..+|+.+|++++.++.+. ++| .+-...+|+.- +.|||--|-++ ..+.++|
T Consensus 42 ~~g~s~~~L~~~~~~~gl~~~~~~~~~---~~l--------~~~~~P~I~~~--------~~~h~vVi~~~--~~~~~~i 100 (131)
T PF03412_consen 42 EEGTSLADLKRAARKYGLKAKAVKLNF---EKL--------KRLPLPAIAHL--------KDGHFVVIYKI--DDGRVLI 100 (131)
T ss_dssp TTB--CCCHHHHHHHTTEEEEEEE--G---GGC--------TCGGSSEEEEE--------CCCEEEEEEEE--CCCEEEE
T ss_pred ccCCCHHHHHHHHHhcccceeeeecch---hhh--------hhccccEEEEe--------cCcceEEEEeE--cCcEEEE
Confidence 579999999999999999999887543 233 11122333332 88999999888 7789999
Q ss_pred EecCCCCCCceeeehhHHHHhc
Q 012657 115 LDVARFKYPPHWVPLTLLWEAM 136 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM 136 (459)
.|. +..+.|++.+.+.+.-
T Consensus 101 ~dP---~~g~~~~~~~~f~~~w 119 (131)
T PF03412_consen 101 YDP---KKGKIKLSKEEFEEIW 119 (131)
T ss_dssp CCT---TTCEEEEEHHHHHHHE
T ss_pred EeC---CCCeEEEeHHHHHhhC
Confidence 998 5678999988876543
No 9
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=90.57 E-value=0.68 Score=38.83 Aligned_cols=76 Identities=17% Similarity=0.280 Sum_probs=56.2
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|.+...+...|+..|++++.++. +++.+.+. .-.+|+-. +.|||--|.+++ .|.++|.
T Consensus 42 ~~~~~~~l~~~a~~~Gl~~~~~~~---~~~~L~~~--------~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~ 100 (125)
T cd02420 42 DGSNASNLLKAAREYGLTAKGYKK---DLEALREV--------SLPAIVFW--------NFNHFLVVEGFD--KRKVFLN 100 (125)
T ss_pred CCCCHHHHHHHHHHcCcccceEec---CHHHHhcC--------CCCEEEEe--------CCCEEEEEEEEe--CCEEEEE
Confidence 589999999999999999988774 34443321 12344422 579999999988 5579999
Q ss_pred ecCCCCCCceeeehhHHHHh
Q 012657 116 DVARFKYPPHWVPLTLLWEA 135 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (459)
|.+. .|.+++.++|-+.
T Consensus 101 dp~~---~~~~~s~~el~~~ 117 (125)
T cd02420 101 DPAT---GRRTVSLEEFDQS 117 (125)
T ss_pred CCCc---CceeecHHHHHhh
Confidence 9864 7899999887543
No 10
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=90.29 E-value=1.8 Score=36.45 Aligned_cols=83 Identities=14% Similarity=0.053 Sum_probs=58.4
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|+++..+...|+..|++++.++.+... ..+ .+ -...+|+-.. . ..+.|||--|.+++ .+.++|.
T Consensus 42 ~~~~~~~l~~~a~~~Gl~~~~~~~~~~~-~~l----~~----~~~P~I~~~~-~---~~~~~~~~Vl~~~~--~~~~~i~ 106 (136)
T cd02418 42 EGTSLLGLVKAAEKLGFETRAVKADMDL-FEL----KD----IPLPFIAHVI-K---EWKLNHYVVVYKIK--KKKILIA 106 (136)
T ss_pred CCcCHHHHHHHHHHCCCeeEEEEcccch-hhH----hc----CCCCEEEEEc-c---CCCCCeEEEEEEEc--CCEEEEE
Confidence 6899999999999999999988764321 012 11 1223444221 1 24789999999998 5579999
Q ss_pred ecCCCCCCceeeehhHHHHhc
Q 012657 116 DVARFKYPPHWVPLTLLWEAM 136 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~eAM 136 (459)
|. ..++.+++.++|-+..
T Consensus 107 dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 107 DP---AVGITKISKEEFEKEW 124 (136)
T ss_pred CC---CCCCEEeeHHHHHhhC
Confidence 97 5689999998875533
No 11
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=83.57 E-value=4 Score=34.95 Aligned_cols=79 Identities=18% Similarity=0.254 Sum_probs=54.1
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
+|.++.++...|+..|+++++++.+ .+++ .+. ...-..|+. ..++.||=-+.+.+. +.|+|.
T Consensus 43 ~g~s~~~l~~~a~~~Gl~~k~~~~~---~~~l----~~~--~~p~P~i~~-------~~~~~hfvVl~~~~~--~~v~I~ 104 (129)
T cd02424 43 NGLSIYDLENLAKKFGLETESYQGS---FLEF----LEL--KNKFIILLK-------SNGLNHFVIVKKIKK--NKFIVL 104 (129)
T ss_pred CCccHHHHHHHHHHcCCceeEEEcC---HHHH----hhc--cCCEEEEEe-------cCCCCeEEEEEEEEC--CEEEEE
Confidence 5999999999999999999999863 3332 211 112234443 123459888887644 559999
Q ss_pred ecCCCCCCceeeehhHHHHh
Q 012657 116 DVARFKYPPHWVPLTLLWEA 135 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (459)
|. .+++.+++.+++-+.
T Consensus 105 DP---~~g~~~~s~~~f~~~ 121 (129)
T cd02424 105 DP---KKGKYKITYKEFEKI 121 (129)
T ss_pred CC---CCCCEEeCHHHHHHH
Confidence 98 468888888776544
No 12
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=83.42 E-value=4.2 Score=33.93 Aligned_cols=78 Identities=27% Similarity=0.299 Sum_probs=55.1
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|.++.++..+|+..|++++.++.+ .+.+.+ . .-.+|+-. ...++|||--|.+++ .+.++|.
T Consensus 43 ~~~s~~~l~~~a~~~Gl~~~~~~~~---~~~L~~----~----~lP~i~~~-----~~~~~~~~vvl~~~~--~~~~~i~ 104 (129)
T cd02423 43 EGFSMLDLKRYAEALGLKANGYRLN---LDKLNA----L----QIPVIVLV-----NNGGYGHFVVIKGID--GDRVLVG 104 (129)
T ss_pred CCcCHHHHHHHHHHCCCcceEEEcC---HHHHhh----C----CCCEEEEE-----ecCCCceEEEEEEEe--CCEEEEE
Confidence 5899999999999999999988753 333332 1 11233322 123578998888888 6679999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 012657 116 DVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (459)
|.+. ++.+++.+.|-+
T Consensus 105 dp~~---~~~~~s~~el~~ 120 (129)
T cd02423 105 DPAL---GNISMSREEFER 120 (129)
T ss_pred CCCC---CCcccCHHHHHH
Confidence 9853 678888877654
No 13
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=81.01 E-value=12 Score=31.37 Aligned_cols=76 Identities=20% Similarity=0.243 Sum_probs=55.1
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|.++..+..+|+..|++++.++.+ .+.+++. .-.+|+- ...|||--|.+. ..|.++|.
T Consensus 42 ~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~~--------~lP~i~~--------~~~g~~~Vl~~~--~~~~~~i~ 100 (127)
T cd02419 42 KGATLADLIDIAQQLGLSTRALRLD---LEELGQL--------KLPCILH--------WDMNHFVVLKKV--SRRRIVIH 100 (127)
T ss_pred CCcCHHHHHHHHHHCCCceeEEEcc---HHHHhhC--------CCCEEEE--------ECCCEEEEEEEE--cCCEEEEE
Confidence 5899999999999999999887753 4444332 1123332 156999888886 56789999
Q ss_pred ecCCCCCCceeeehhHHHHh
Q 012657 116 DVARFKYPPHWVPLTLLWEA 135 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (459)
|+.. ++.+++.+.|-+.
T Consensus 101 dp~~---~~~~~~~~el~~~ 117 (127)
T cd02419 101 DPAL---GKRKLSLEEASRH 117 (127)
T ss_pred CCcc---CCEEEcHHHHHhh
Confidence 9853 6889999887543
No 14
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=77.73 E-value=17 Score=39.93 Aligned_cols=76 Identities=24% Similarity=0.300 Sum_probs=57.9
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
++|+|+..+..+|+..|++++.++.+ ++++ ..-.-..|+.. +.+||=-+-++ ..+.+.|
T Consensus 42 ~~g~s~~~l~~~~~~~g~~~~~~~~~---~~~l--------~~~~lP~i~~~--------~~~h~vvl~~~--~~~~~~i 100 (710)
T TIGR03796 42 RDGSKASNLLKAARSYGLEAKGFRKE---LDAL--------AELPLPYIVFW--------NFNHFVVVEGF--RGGRVYL 100 (710)
T ss_pred CCCCCHHHHHHHHHHCCCEeEEEecC---HHHh--------ccCCCCEEEEE--------cCCcEEEEEEE--eCCEEEE
Confidence 47999999999999999999999964 3332 12223455554 67999888776 5578999
Q ss_pred EecCCCCCCceeeehhHHHH
Q 012657 115 LDVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~e 134 (459)
+|++- .+.|++.+++-+
T Consensus 101 ~dP~~---g~~~~~~~e~~~ 117 (710)
T TIGR03796 101 NDPAL---GPRTVSLEEFDE 117 (710)
T ss_pred ECCCC---CCEEccHHHHHh
Confidence 99964 688999988644
No 15
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=73.63 E-value=16 Score=30.41 Aligned_cols=76 Identities=18% Similarity=0.241 Sum_probs=53.1
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|+++..+..+|+..|++++.++.+.. +.+.+ . . -..|+-. .+|||--|.+++ .+.++|+
T Consensus 42 ~~~~~~~l~~~a~~~gl~~~~~~~~~~--~~l~~----~---~-lP~I~~~--------~~~~~~Vl~~~~--~~~~~i~ 101 (126)
T cd02425 42 DGLSLSYLKQLLEEYGFKCKVYKISFK--KNLYP----L---K-LPVIIFW--------NNNHFVVLEKIK--KNKVTIV 101 (126)
T ss_pred CCcCHHHHHHHHHHCCCcceEEEEchH--HHHhh----C---C-CCEEEEE--------cCCcEEEEEEEE--CCEEEEE
Confidence 689999999999999999998875421 22222 1 1 1233321 248998888984 5579999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 012657 116 DVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (459)
|.+. .+.|++.+.|=+
T Consensus 102 dp~~---~~~~~~~~~l~~ 117 (126)
T cd02425 102 DPAI---GRIKISIDEFLE 117 (126)
T ss_pred cCCC---CCEEECHHHHHh
Confidence 9854 567999888644
No 16
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=61.01 E-value=1e+02 Score=34.20 Aligned_cols=84 Identities=14% Similarity=0.119 Sum_probs=57.7
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
+.|+|+..+..+|+..|++++.++.+ ++++. + ..-.-..|+...+. .+..||=-+=+++ .+.|.|
T Consensus 36 ~~g~s~~~l~~~~~~~g~~~~~~~~~---~~~l~--~----~~~~~P~I~~~~~~----~~~~H~vVl~~~~--~~~~~i 100 (708)
T TIGR01193 36 LEGTTVLGLVKAAEYLNFEAKAIQAD---MSLFE--D----KNLPLPFIAHVIKN----GKLPHYYVVYGVT--KNHLII 100 (708)
T ss_pred CCCCCHHHHHHHHHHCCCEEEEEecC---HHHhc--c----ccCCCCEEEEEccC----CCCCcEEEEEEEe--CCEEEE
Confidence 58999999999999999999999974 32210 1 11123455542221 2456987777766 678999
Q ss_pred EecCCCCCCceeeehhHHHH
Q 012657 115 LDVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~e 134 (459)
+|++. .+.+.|++.+++.+
T Consensus 101 ~dP~~-~~g~~~~~~~ef~~ 119 (708)
T TIGR01193 101 ADPDP-TVGITKISKEDFYE 119 (708)
T ss_pred EcCCc-ccCCEEecHHHHHh
Confidence 99843 25788999999754
No 17
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=57.59 E-value=77 Score=26.23 Aligned_cols=78 Identities=14% Similarity=0.130 Sum_probs=54.6
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|.++..+...|+..|++++.++.+ ++.+.+. .-..|+- ..+|||--|.+.+ .+.++|.
T Consensus 37 ~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~~--------~lP~I~~--------~~~g~~~Vl~~~~--~~~~~i~ 95 (121)
T cd02417 37 EPFNSTELLLAAKSLGLKAKAVRQP---VERLARL--------PLPALAW--------DDDGGHFILAKLD--GQKYLIQ 95 (121)
T ss_pred CCCCHHHHHHHHHHcCCeeEEEecC---HHHhccC--------CCCEEEE--------ccCCCEEEEEEEc--CCCEEEE
Confidence 5799999999999999999888753 3332221 1123332 1357888888877 5679999
Q ss_pred ecCCCCCCceeeehhHHHHhc
Q 012657 116 DVARFKYPPHWVPLTLLWEAM 136 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~eAM 136 (459)
|++. -.|..++.+.|-+..
T Consensus 96 dp~~--~~~~~~~~~el~~~~ 114 (121)
T cd02417 96 DPIS--QRPEVLSREEFEARW 114 (121)
T ss_pred CCCc--CCCeecCHHHHHhhc
Confidence 9854 367888988876654
No 18
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=53.96 E-value=55 Score=32.48 Aligned_cols=86 Identities=22% Similarity=0.211 Sum_probs=57.3
Q ss_pred HHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccc------------------cC-C-Ccccc
Q 012657 41 GKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFK------------------QT-G-TGHFS 100 (459)
Q Consensus 41 ~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~Lg------------------Qt-G-~GHFS 100 (459)
.++-..|+.+|+.|+.- ..|+++...++.. .+ .+||--+...|. +. + .|||=
T Consensus 93 ~~lF~~A~~~gi~V~~r---svs~~ei~~hl~~----g~-~aIvLVd~~~L~C~~Ck~~~~~~~~~~~~~~~~~Y~GHYV 164 (212)
T PF09778_consen 93 NRLFQKAKAAGINVEKR---SVSIQEIIEHLSS----GG-PAIVLVDASLLHCDLCKSNCFDPIGSKCFGRSPDYQGHYV 164 (212)
T ss_pred HHHHHHHHHcCCceEEe---eccHHHHHHHHhC----CC-cEEEEEccccccChhhcccccccccccccCCCCCccEEEE
Confidence 46677789999988642 3789998888774 22 444444443333 22 2 79999
Q ss_pred ccccccCCCCeEEEEecCCCCCCceeeehhHHHHh
Q 012657 101 PIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 135 (459)
Q Consensus 101 PIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eA 135 (459)
-|=|||++++.+++=|+|--. --.=|+.+.|=+|
T Consensus 165 VlcGyd~~~~~~~yrdPa~~~-~~c~~s~~~ld~A 198 (212)
T PF09778_consen 165 VLCGYDAATKEFEYRDPASSD-RVCRVSPEALDEA 198 (212)
T ss_pred EEEeecCCCCeEEEeCCcccc-ceeecCHHHHHHH
Confidence 999999999999999987533 2223554444433
No 19
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=51.52 E-value=24 Score=30.53 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=33.2
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
.|- .|.+|+|+++-+..=.-+-..++-|++++|+..+....
T Consensus 30 ~r~-~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 30 QRS-ENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCC-CCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 444 67899999988876566667789999999999998764
No 20
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=49.41 E-value=12 Score=32.68 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=33.1
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcC
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnG 51 (459)
.|.+|.|+++-+..-.-+...+..|+|++++..+....+
T Consensus 32 ~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~~ 70 (120)
T cd04781 32 RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDG 70 (120)
T ss_pred CCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccC
Confidence 479999999888877777788899999999999887643
No 21
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=49.03 E-value=99 Score=25.76 Aligned_cols=77 Identities=21% Similarity=0.060 Sum_probs=52.2
Q ss_pred cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 012657 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (459)
Q Consensus 36 ~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLIL 115 (459)
.|.+..++...|+..|++++..+.+ .+.+.+ -.-..|+- ..+|||--|.+.+. +.++|.
T Consensus 37 ~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~--------~~lP~i~~--------~~~g~~~Vl~~~~~--~~~~i~ 95 (124)
T cd02421 37 GRLSPALFPRAAARAGLSARVVRRP---LDAIPT--------LLLPAILL--------LKNGRACVLLGVDD--GHARIL 95 (124)
T ss_pred CCcCHHHHHHHHHHCCCcceeeeCC---HHHCCc--------ccCCEEEE--------EcCCCEEEEEEecC--CeEEEE
Confidence 4688889999999999988876643 322211 11123321 24689888888775 679999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 012657 116 DVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (459)
|+.- ...|.+++.+.|=+
T Consensus 96 dp~~-~~~~~~~~~~el~~ 113 (124)
T cd02421 96 DPES-GGGEVEISLEELEE 113 (124)
T ss_pred ccCC-CCCcEEEcHHHHHh
Confidence 9852 36788899887654
No 22
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=48.37 E-value=65 Score=35.59 Aligned_cols=78 Identities=18% Similarity=0.066 Sum_probs=51.0
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCe-EE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDM-AL 113 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~-VL 113 (459)
+.|+|+.++..+|+..|++++.++.+ ++++. ......|+.++ ++||=-+-+. ..+. |.
T Consensus 29 ~~g~sl~~l~~~~~~~g~~~~~~~~~---~~~l~--------~~~~P~i~~~~--------~~h~vvl~~~--~~~~~~~ 87 (694)
T TIGR03375 29 DGRLTPELLPRAARRAGLSARLVKRS---LDDIS--------PLLLPAILLLK--------DGRACVLLGI--DEDGKAR 87 (694)
T ss_pred CCCCCHHHHHHHHHHCCCEEEEecCC---HhhcC--------cCCCCEEEEEc--------CCcEEEEEEE--cCCCcEE
Confidence 48999999999999999999999853 33321 22334555442 3787333333 4455 99
Q ss_pred EEecCCCCCCceeeehhHHHH
Q 012657 114 ILDVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 114 ILDVARfKYPP~WVpl~~L~e 134 (459)
|+|.|.- =.+.|++.+++-+
T Consensus 88 i~DP~~g-~~~~~~~~~e~~~ 107 (694)
T TIGR03375 88 VLLPETG-DGEQELSLDALEA 107 (694)
T ss_pred EEccCCC-CCceEecHHHHHh
Confidence 9998531 0166888877543
No 23
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=47.92 E-value=23 Score=29.97 Aligned_cols=44 Identities=18% Similarity=0.214 Sum_probs=33.0
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
.|.+...|.+|+|+++-++.=.-+-..+..|+|++++..+....
T Consensus 27 ~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 27 KPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDP 70 (103)
T ss_pred CCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 35456678899999976664444556778999999999988653
No 24
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.61 E-value=37 Score=32.08 Aligned_cols=80 Identities=26% Similarity=0.333 Sum_probs=47.4
Q ss_pred CeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEEecCCCCCCcee-eehh
Q 012657 52 AKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHW-VPLT 130 (459)
Q Consensus 52 a~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYPP~W-Vpl~ 130 (459)
+.+..+..+..+-+-..+-++.++-+++.|- -|-|..- =.|||=-|-|||+++|-+.+=|.|--+ |-|- ++++
T Consensus 72 iAIaLVdq~~Lhcdlceeplk~ccfspnghh--cfcrtp~---YqGHfiVi~GYd~a~~c~~~ndPA~ad-pg~c~~Sik 145 (167)
T KOG4621|consen 72 IAIALVDQDKLHCDLCEEPLKSCCFSPNGHH--CFCRTPC---YQGHFIVICGYDAARDCFEINDPASAD-PGHCRISIK 145 (167)
T ss_pred EEEEEecCCceehHHHHhHHHHhccCCCCcc--ccccCCc---ccccEEEEeccccccCeEEEcCcccCC-Ccceeehhh
Confidence 3333333344444555555555544443321 2333321 269999999999999999999998644 5454 6666
Q ss_pred HHHHhcc
Q 012657 131 LLWEAMD 137 (459)
Q Consensus 131 ~L~eAM~ 137 (459)
-+=+|-.
T Consensus 146 ~fEeARk 152 (167)
T KOG4621|consen 146 CFEEARK 152 (167)
T ss_pred HHHHHHh
Confidence 6555543
No 25
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=46.54 E-value=33 Score=30.26 Aligned_cols=38 Identities=11% Similarity=0.289 Sum_probs=31.8
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
.|..|+|+++-+..-.-+-..+..|++++|+..+....
T Consensus 33 ~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 33 AGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence 78899999988876666667788999999999987653
No 26
>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=46.34 E-value=14 Score=31.22 Aligned_cols=43 Identities=14% Similarity=0.221 Sum_probs=34.0
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|.+.-.+.+|+|+++-+..=.-+-..++.|++++++..+...
T Consensus 27 ~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (96)
T cd04768 27 KPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT 69 (96)
T ss_pred CCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3555557789999998887655566678899999999998875
No 27
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=46.02 E-value=27 Score=32.52 Aligned_cols=37 Identities=11% Similarity=0.134 Sum_probs=31.0
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|..|+|+++.+..=.-+-..++-|+||+|+..+...
T Consensus 43 ~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~ 79 (154)
T PRK15002 43 SGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV 79 (154)
T ss_pred CCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6778999998887656666778999999999999875
No 28
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=45.96 E-value=32 Score=30.33 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=30.8
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.+.+|+|+++-+..-.-+-..++-|+|++|+..+...
T Consensus 33 ~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T TIGR02044 33 EGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNL 69 (127)
T ss_pred CCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5779999998887655666778999999999998864
No 29
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=45.82 E-value=17 Score=32.58 Aligned_cols=50 Identities=18% Similarity=0.174 Sum_probs=33.7
Q ss_pred CCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcCCeEEEEecC
Q 012657 6 KARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTN 60 (459)
Q Consensus 6 ~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnGa~Vq~~r~~ 60 (459)
..+.++|+.==--+-.++| .-++|.+.|++=+-|..||.-..+++.. |.+
T Consensus 16 ~~~~~LW~~L~~~lPDSlL----~n~ei~~~GLSTDhltaLa~~~~~~~~~-hs~ 65 (104)
T PF05381_consen 16 ISPETLWATLCEILPDSLL----DNPEIRTLGLSTDHLTALAYRYHFQCTF-HSD 65 (104)
T ss_pred CCHHHHHHHHHHhCchhhc----CchhhhhcCCcHHHHHHHHHHHheEEEE-EcC
Confidence 3455566542222222344 4567999999999999999999999854 443
No 30
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=42.23 E-value=38 Score=30.65 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=32.2
Q ss_pred ccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 12 SGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 12 WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
=.+.+|.|+++-+..-.-+-..+.-|++++|+..+...
T Consensus 32 ~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 32 SENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred CCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 46889999998888776777778899999999998765
No 31
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=41.55 E-value=13 Score=30.60 Aligned_cols=17 Identities=35% Similarity=0.456 Sum_probs=14.4
Q ss_pred CCCCchhHHHHHHHHHH
Q 012657 401 TENLPTLLQEEVLHLRR 417 (459)
Q Consensus 401 ~~~lp~~lq~evlhlr~ 417 (459)
.++|||.|+.||+|--.
T Consensus 8 fqkLPDdLKrEvldY~E 24 (65)
T COG5559 8 FQKLPDDLKREVLDYIE 24 (65)
T ss_pred HHHCcHHHHHHHHHHHH
Confidence 36899999999999654
No 32
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.90 E-value=20 Score=32.34 Aligned_cols=44 Identities=23% Similarity=0.462 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCC
Q 012657 63 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRD 110 (459)
Q Consensus 63 SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD 110 (459)
-++.+|+.|-+ .+..-|-||+-=...-+|.|||-|+.|=|+--+
T Consensus 16 ~~e~vr~aL~~----aGag~iG~Y~~C~~~~~g~G~frP~egAnP~iG 59 (109)
T COG3323 16 YVEQVRDALFE----AGAGHIGNYDHCTFSSEGTGQFRPLEGANPFIG 59 (109)
T ss_pred HHHHHHHHHHh----cCCcceeccceEEEEeeeeEEEeecCCCCCccc
Confidence 45666665554 555667799999999999999999998887654
No 33
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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=38.34 E-value=21 Score=31.31 Aligned_cols=42 Identities=12% Similarity=0.205 Sum_probs=34.3
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
|.|. .|..|+|+++-+..-.-+-..++-|+|++|+..+....
T Consensus 29 ~~r~-~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 29 PPRP-EGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4454 67799999988887666777899999999999988754
No 34
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=37.55 E-value=22 Score=32.41 Aligned_cols=37 Identities=11% Similarity=0.160 Sum_probs=31.5
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|..|+|+++-+..-.-+-..++.|+|++++..+..+
T Consensus 33 ~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 33 SGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred CCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5679999998887766677788999999999999875
No 35
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=37.05 E-value=24 Score=32.33 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=34.7
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
|+|. .|.+|+|+++-+..-.-+-..++-|++|+|+..+...+
T Consensus 36 ~~r~-~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~~ 77 (144)
T PRK13752 36 PDKP-YGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLE 77 (144)
T ss_pred CccC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 3444 57799999999987777788889999999999998754
No 36
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=36.16 E-value=21 Score=31.69 Aligned_cols=39 Identities=26% Similarity=0.353 Sum_probs=29.9
Q ss_pred HHcCCcHHHHHHHHHHcCCeEEEEec-----CCCCHHHHHHHHH
Q 012657 34 KEKGISFGKLVCLAHCAGAKVEAFRT-----NQSTIDDFRKYII 72 (459)
Q Consensus 34 k~~GITL~ef~cLA~CnGa~Vq~~r~-----~~~SldeFR~~V~ 72 (459)
.--|.||+.+..+-+.+-+..+.|++ .++|.++-|-+..
T Consensus 16 ~~L~~T~e~l~~~M~An~~~i~~y~~W~r~~~~STW~DC~mFA~ 59 (104)
T PF05415_consen 16 ECLGVTLEKLDNLMQANVSTIKKYHTWLRKKRPSTWDDCRMFAD 59 (104)
T ss_pred HHhcchHHHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHH
Confidence 44699999999998888777777775 4678888665544
No 37
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=36.11 E-value=27 Score=30.20 Aligned_cols=42 Identities=14% Similarity=0.362 Sum_probs=33.0
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
|.|. .+..|+|+++-+..-.-+-..++.|++++|+..+....
T Consensus 28 p~r~-~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (112)
T cd01282 28 PERS-ANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCL 69 (112)
T ss_pred CCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 4444 68899999977766556666788999999999998764
No 38
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=35.86 E-value=17 Score=31.56 Aligned_cols=45 Identities=22% Similarity=0.384 Sum_probs=27.1
Q ss_pred hHHHHHcCCcHH------HHHHHHHHcCCeEEEEec----CCCCHHHHHHHHHHH
Q 012657 30 LEKVKEKGISFG------KLVCLAHCAGAKVEAFRT----NQSTIDDFRKYIIRC 74 (459)
Q Consensus 30 le~Vk~~GITL~------ef~cLA~CnGa~Vq~~r~----~~~SldeFR~~V~~~ 74 (459)
+...++.||+.+ .+..+|+.||++++.++. ...|+++||+.++.-
T Consensus 57 ~q~ak~~gI~vsd~evd~~i~~ia~~n~ls~~ql~~~L~~~G~s~~~~r~~ir~~ 111 (118)
T PF09312_consen 57 LQEAKRLGIKVSDEEVDEAIANIAKQNNLSVEQLRQQLEQQGISYEEYREQIRKQ 111 (118)
T ss_dssp HHHHHHCT----HHHHHHHHHHHHHHTT--HHHHHHHCHHCT--HHHHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 456678888875 566888888887766553 457899999998863
No 39
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=35.33 E-value=30 Score=26.87 Aligned_cols=40 Identities=15% Similarity=0.241 Sum_probs=29.5
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHH
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 47 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA 47 (459)
.|.|. .|..|+|+++-++.=.-+-..++.|+|++++..+.
T Consensus 28 ~~~r~-~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 28 KPQRS-DGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCCcC-CCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 35443 57789999977765555666777999999988764
No 40
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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=35.22 E-value=51 Score=29.08 Aligned_cols=41 Identities=10% Similarity=0.206 Sum_probs=32.0
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
|+|. .+.+|+|+++-+..=.-+-..++.|+||+|+..+...
T Consensus 29 ~~r~-~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 29 PSRS-DNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCcC-CCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3444 5789999998777555566678899999999998864
No 41
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=34.92 E-value=28 Score=30.52 Aligned_cols=41 Identities=15% Similarity=0.251 Sum_probs=33.2
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
|+|. .+.+|+|+++-+..-.-+-..++-|+|+.|+..+...
T Consensus 29 ~~r~-~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 29 PARS-ANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3454 5779999998887666667778999999999998875
No 42
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=33.79 E-value=55 Score=30.15 Aligned_cols=44 Identities=23% Similarity=0.532 Sum_probs=32.2
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhhhhhccCCCCCHHHHHHHHHhcC
Q 012657 156 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSL 206 (459)
Q Consensus 156 ~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~sl 206 (459)
-..|+.+.|++| +..|.++.+.|.+ ..++..|-+.++..+|..-
T Consensus 102 ~G~P~~FiT~s~-~~~w~ei~~~l~~------~~~~~~d~P~~~ar~F~~k 145 (184)
T PF14214_consen 102 FGKPTLFITFSC-NPQWPEIQQALAK------PGQNWSDNPDIVARFFHIK 145 (184)
T ss_pred cCCCcEEEEEcC-ccccHHHHHHHHh------ccCCcccCcHHHHHHHHHH
Confidence 347899999999 8999999999773 3455556666666665543
No 43
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=33.31 E-value=2.8e+02 Score=22.95 Aligned_cols=64 Identities=13% Similarity=0.152 Sum_probs=42.0
Q ss_pred EEEEecCCCCHHHHHHHHHHHhcCCCcEEEEE-ecccccccC---CCccccccccccCCCC-eEEEEecCC
Q 012657 54 VEAFRTNQSTIDDFRKYIIRCSASEDCHVISS-YHRGAFKQT---GTGHFSPIGGYHAGRD-MALILDVAR 119 (459)
Q Consensus 54 Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVn-Y~Rk~LgQt---G~GHFSPIGGYh~~tD-~VLILDVAR 119 (459)
.+.......|+.++++.+......+-..+-+. |+.+ ++. =+....++|.|..+.+ .++|.|..+
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~--~~~~~~l~~d~~~L~~y~~~dg~~IhVvD~~p 83 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD--DKLVSKLDDDDALLGSYPVDDGCRIHVIDVSG 83 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC--CCeEeecCCCccEeeeccCCCCCEEEEEeCCC
Confidence 44444567899999999988765444444444 5544 222 2456669999999886 577777654
No 44
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=32.58 E-value=33 Score=30.37 Aligned_cols=41 Identities=7% Similarity=0.136 Sum_probs=32.9
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
|.|. .+.+|+|+++-+..-.-+-..++-|+|++|+..+...
T Consensus 29 ~~r~-~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 29 PART-DNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CCcC-CCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3444 5789999998887666666778899999999998764
No 45
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=30.93 E-value=78 Score=27.19 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=30.8
Q ss_pred cccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 11 LSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 11 ~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.-.+..|+|+++-+..=.-+-..++-|+||+|+..+...
T Consensus 31 r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 31 RDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 346789999997776545556678899999999998875
No 46
>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Probab=30.77 E-value=2.1e+02 Score=31.67 Aligned_cols=82 Identities=15% Similarity=0.035 Sum_probs=54.0
Q ss_pred CChHHHHH--cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccc
Q 012657 28 EPLEKVKE--KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGY 105 (459)
Q Consensus 28 ~ple~Vk~--~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGY 105 (459)
.+++.+++ +| ++..+...|+..|++++.++.+ ++++.+. .-..|+..+ +.|||=-+-++
T Consensus 19 ~~~~~lr~~~~g-~~~~l~~~~~~~g~~~~~~~~~---~~~l~~~--------~lP~i~~~~-------~~~h~vvl~~~ 79 (686)
T TIGR03797 19 IRPPARSENLSR-SPEPLEAIARASRLRIRRVRLE---GGWWRQD--------SGPLLAYTA-------EDGRPVALLPV 79 (686)
T ss_pred CChHHHHHHcCC-CHHHHHHHHHHCCCceEEEecC---HHHHhhC--------CCCEEEEEc-------CCCCEEEEEEE
Confidence 34455544 48 9999999999999999999874 3333221 113343322 35787666554
Q ss_pred cCCCCeEEEEecCCCCCCceeeehhHH
Q 012657 106 HAGRDMALILDVARFKYPPHWVPLTLL 132 (459)
Q Consensus 106 h~~tD~VLILDVARfKYPP~WVpl~~L 132 (459)
+.+.+.|+|+|. =++.|++.+++
T Consensus 80 --~~~~~~i~dP~~--g~~~~~~~~e~ 102 (686)
T TIGR03797 80 --SRGGYEIFDPAT--GTRRRVDAAMA 102 (686)
T ss_pred --cCCEEEEECCCC--CCCcccCHHHH
Confidence 567899999864 22448888886
No 47
>COG5565 Bacteriophage terminase large (ATPase) subunit and inactivated derivatives [General function prediction only]
Probab=30.33 E-value=28 Score=29.76 Aligned_cols=38 Identities=29% Similarity=0.508 Sum_probs=27.6
Q ss_pred CcccC---cccccccccccccCChHHHHHcCCcHHHHHHHHHHcCCeEEEEe
Q 012657 10 TLSGR---PWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFR 58 (459)
Q Consensus 10 r~WKG---pWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnGa~Vq~~r 58 (459)
+.|.+ -|-|||| .|.+.|-.+|||..+ +-.|+.+.+|-
T Consensus 15 ~kwq~~~v~y~wfde------qpp~dvy~eGiTrtn-----rt~g~~~vtft 55 (79)
T COG5565 15 EKWQARTVDYVWFDE------QPPEDVYFEGITRTN-----RTSGITIVTFT 55 (79)
T ss_pred HHhhcCccCCCcccc------CChHHhhhccceeec-----cccceEEEEec
Confidence 44554 3889999 799999999999765 34566665554
No 48
>PF02775 TPP_enzyme_C: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; InterPro: IPR011766 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the C-terminal TPP binding domain of TPP enzymes.; GO: 0003824 catalytic activity, 0030976 thiamine pyrophosphate binding; PDB: 2WVA_V 1ZPD_F 2WVG_B 2WVH_B 3OE1_D 2NXW_A 2Q5L_B 2Q5Q_B 2Q5J_A 2Q5O_A ....
Probab=29.71 E-value=89 Score=27.56 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=28.7
Q ss_pred HHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCC
Q 012657 42 KLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASED 79 (459)
Q Consensus 42 ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d 79 (459)
+|..+|+..|+... +.+..+.++|++.++++...+.
T Consensus 112 d~~~~a~a~G~~~~--~v~~~~~~el~~al~~a~~~~g 147 (153)
T PF02775_consen 112 DFAALAEAFGIKGA--RVTTPDPEELEEALREALESGG 147 (153)
T ss_dssp GHHHHHHHTTSEEE--EESCHSHHHHHHHHHHHHHSSS
T ss_pred CHHHHHHHcCCcEE--EEccCCHHHHHHHHHHHHhCCC
Confidence 68889999999854 5556678999999999885444
No 49
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=29.59 E-value=37 Score=30.69 Aligned_cols=42 Identities=12% Similarity=0.095 Sum_probs=33.5
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|.|. .|..|.|+++-+..-.-+...++.|+|++|+..+...
T Consensus 28 ~p~r~-~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 28 ASWRN-AGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred CCCcC-CCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 35444 6779999998887766667788899999999998764
No 50
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=29.13 E-value=3.5e+02 Score=29.15 Aligned_cols=153 Identities=19% Similarity=0.272 Sum_probs=78.1
Q ss_pred CcccccccccccccCChHHHHHcCCcH-------------------HHHHHHHHHcCCeEEEEecCC-------------
Q 012657 14 RPWRWFDESMLDCCEPLEKVKEKGISF-------------------GKLVCLAHCAGAKVEAFRTNQ------------- 61 (459)
Q Consensus 14 GpWRWf~EsmLdCC~ple~Vk~~GITL-------------------~ef~cLA~CnGa~Vq~~r~~~------------- 61 (459)
--||||-. +-=++++.|++.|++= .++....+.+|+.-.+.-..+
T Consensus 3 ~~~rw~g~---~D~v~l~~irQ~Gv~gIV~aLh~iP~g~~W~~~~I~~~k~~ie~~Gl~~~vvESvPvhedIK~g~~~rd 79 (362)
T COG1312 3 QTWRWYGP---NDPVTLEDIRQAGVKGVVTALHHIPAGEVWPVEEILKRKEEIESAGLTWSVVESVPVHEDIKLGTPTRD 79 (362)
T ss_pred eeEEEecC---CCCccHHHHHHhCccceeccCCCCCCCCcCcHHHHHHHHHHHHHcCceEEeecCCCHHHHHHhcCCcHH
Confidence 35999988 2236788899877752 344455778999776654322
Q ss_pred CCHHHHHHHHHHHhcCCCcE-----E-EEEeccccccc-CCCccccccccccCCCCeEEEEecCCCC-CCce------ee
Q 012657 62 STIDDFRKYIIRCSASEDCH-----V-ISSYHRGAFKQ-TGTGHFSPIGGYHAGRDMALILDVARFK-YPPH------WV 127 (459)
Q Consensus 62 ~SldeFR~~V~~~~ss~d~~-----l-IVnY~Rk~LgQ-tG~GHFSPIGGYh~~tD~VLILDVARfK-YPP~------WV 127 (459)
--++...+.|+...+..=+. | |+...|.-|.- .++|- .+|-+|-+.|. |++| =+
T Consensus 80 ~~Ieny~~tirnLa~~GI~vvCYNfMpv~dWtRTdl~~~l~~gs------------~alrfd~~~~~a~~~~a~~~~~~~ 147 (362)
T COG1312 80 RYIENYKQTIRNLARAGIKVVCYNFMPVFDWTRTDLEYPLPDGS------------EALRFDKADFAAFDLHAEYQEEIA 147 (362)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEeccccccCccccceeeecCCCC------------eeEeeeHhhhhccccccccHHHHH
Confidence 24566666666544333122 2 33335666632 23443 45666655555 4444 24
Q ss_pred ehhHHHHhccccCCCCCceeeEEEEeCCCCCCCcceeeeccCCChHHHHHHHHhhhhhh
Q 012657 128 PLTLLWEAMDRVDDATGQRRGFVLVSRPHREPGLLYTLSCKHENWVGIAKYLVDEVPKI 186 (459)
Q Consensus 128 pl~~L~eAM~tiD~~TgrsRGfllIsk~~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~l 186 (459)
.++..+++|.. +| |-..||-+=+-+. ---.|.---....|.+++-||.+-+|.-
T Consensus 148 ~~~~~~~~m~g-lP--G~~~~~tl~~~~~--~~~~y~~Id~~~L~~nL~yFL~~ViPVA 201 (362)
T COG1312 148 RAEERFAEMSG-LP--GWEEGYTLDQFRE--LLELYGGIDEEKLWENLAYFLKEVIPVA 201 (362)
T ss_pred HHHHhhhcccC-CC--CCcccccHHHHHH--HHHHhcCCCHHHHHHHHHHHHHhhcchH
Confidence 44455555540 00 1111110000000 0001111113468999999998877753
No 51
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=28.89 E-value=86 Score=28.22 Aligned_cols=41 Identities=12% Similarity=0.170 Sum_probs=32.5
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
.|. .+.+|.|+++-+..=.-+-..++.|+||+|+..+..+.
T Consensus 30 ~r~-~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~ 70 (131)
T cd04786 30 ERS-ANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPAD 70 (131)
T ss_pred CcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 443 68899999988875555556788999999999998754
No 52
>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=28.26 E-value=40 Score=28.39 Aligned_cols=38 Identities=11% Similarity=0.135 Sum_probs=32.3
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
.|.+|.|+++-+..-.-+-..++.|++++|+..+....
T Consensus 33 ~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 33 EGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred CCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 67899999988887777777889999999999988653
No 53
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=28.00 E-value=88 Score=28.30 Aligned_cols=37 Identities=16% Similarity=0.254 Sum_probs=30.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.+.+|+|+++-+..=.-+-..++.|+++.|+..+...
T Consensus 34 ~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 34 EGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred CCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 7789999997776555555678899999999999875
No 54
>PTZ00445 p36-lilke protein; Provisional
Probab=27.66 E-value=1.9e+02 Score=29.04 Aligned_cols=98 Identities=18% Similarity=0.145 Sum_probs=59.7
Q ss_pred HHHHHHHHHcCCeEEEEecC-------------CC---------CHHHHHHHHHHHhcCCCcEEEEEecccccccCCCcc
Q 012657 41 GKLVCLAHCAGAKVEAFRTN-------------QS---------TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGH 98 (459)
Q Consensus 41 ~ef~cLA~CnGa~Vq~~r~~-------------~~---------SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GH 98 (459)
+.|+.+.+-.|+++-+..-| +. --++|+..+.++....=...||-|+.+.+ -.+.+|
T Consensus 32 ~~~v~~L~~~GIk~Va~D~DnTlI~~HsgG~~~~~~~~~~~~~~~tpefk~~~~~l~~~~I~v~VVTfSd~~~-~~~~~~ 110 (219)
T PTZ00445 32 DKFVDLLNECGIKVIASDFDLTMITKHSGGYIDPDNDDIRVLTSVTPDFKILGKRLKNSNIKISVVTFSDKEL-IPSENR 110 (219)
T ss_pred HHHHHHHHHcCCeEEEecchhhhhhhhcccccCCCcchhhhhccCCHHHHHHHHHHHHCCCeEEEEEccchhh-ccccCC
Confidence 46888899999998776522 11 24569998888766666789999999987 223344
Q ss_pred cccccc-------ccCCCCeEEEEecCCCCCCceeeehhHHHHhccccCC
Q 012657 99 FSPIGG-------YHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDD 141 (459)
Q Consensus 99 FSPIGG-------Yh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~ 141 (459)
=.=|.| -...+=.+.|--| .-.||++|=.- ..|.+|..+=|
T Consensus 111 ~~~Isg~~li~~~lk~s~~~~~i~~~-~~yyp~~w~~p-~~y~~~gl~KP 158 (219)
T PTZ00445 111 PRYISGDRMVEAALKKSKCDFKIKKV-YAYYPKFWQEP-SDYRPLGLDAP 158 (219)
T ss_pred cceechHHHHHHHHHhcCccceeeee-eeeCCcccCCh-hhhhhhcccCC
Confidence 323321 1111223333333 22899999543 34777765544
No 55
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.60 E-value=25 Score=26.93 Aligned_cols=42 Identities=12% Similarity=0.305 Sum_probs=29.7
Q ss_pred CCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHH
Q 012657 6 KARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 48 (459)
Q Consensus 6 ~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~ 48 (459)
+.|.+. .+.+|.|+++=++--.-+...++.|+|+.++..+.+
T Consensus 26 l~~~~~-~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 26 LPPPRD-ENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp STTBES-TTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred cccccc-cCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 445553 445699999777666667778889999999987764
No 56
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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 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=27.38 E-value=33 Score=29.32 Aligned_cols=36 Identities=14% Similarity=0.288 Sum_probs=29.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 48 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~ 48 (459)
.+..|+|+|+-+..-.-+-..++.|++++|+..+..
T Consensus 33 ~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 33 ANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred CCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 488999999888766666678889999999877653
No 57
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=27.03 E-value=71 Score=35.42 Aligned_cols=58 Identities=26% Similarity=0.349 Sum_probs=44.7
Q ss_pred CCCccccccccccCCCCeEEEEecCCCCCCceeeehhHHHHhcc--------ccCCCCCceeeEEEEeCC
Q 012657 94 TGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMD--------RVDDATGQRRGFVLVSRP 155 (459)
Q Consensus 94 tG~GHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~--------tiD~~TgrsRGfllIsk~ 155 (459)
.|.|-|||-|.--+...+|.|-.. -|---|++|++|++... -.|. +||+||.-++.=.
T Consensus 29 ~G~~~gs~~gn~~~r~R~vfItNI---pyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk 94 (608)
T KOG4212|consen 29 AGNGAGSQGGNVAARDRSVFITNI---PYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFK 94 (608)
T ss_pred ccccccCCCCCcccccceEEEecC---cchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEee
Confidence 389999998877666666888775 34557999999998753 2465 8999999999843
No 58
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=27.02 E-value=43 Score=29.77 Aligned_cols=43 Identities=14% Similarity=0.133 Sum_probs=33.2
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
|.|.=.+.+|.|+++-+..=.-+-..++-|+||+|+..+....
T Consensus 28 p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (133)
T cd04787 28 PTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHA 70 (133)
T ss_pred CCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhh
Confidence 4443337899999988776556667789999999999998753
No 59
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.36 E-value=46 Score=29.27 Aligned_cols=40 Identities=13% Similarity=0.031 Sum_probs=31.3
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
|.|. +.+|.|+++-++.=.-+-..+..|+|++++..+...
T Consensus 28 p~r~--~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 28 PERR--GQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CcCC--CCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4443 589999998877555555688899999999988875
No 60
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.58 E-value=53 Score=27.72 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=32.2
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|.+.=.|.+|.|+++-+..=.-+-..++.|++++++..+...
T Consensus 27 ~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 27 KPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3444334779999997776554556678899999999998765
No 61
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=25.16 E-value=38 Score=26.14 Aligned_cols=35 Identities=14% Similarity=0.346 Sum_probs=28.2
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 47 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA 47 (459)
.|..|.|+++-+..-.-+-..++.|+|++|+..+.
T Consensus 32 ~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 32 ENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 67899999977776666677788999999987653
No 62
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.84 E-value=72 Score=27.09 Aligned_cols=31 Identities=32% Similarity=0.488 Sum_probs=24.4
Q ss_pred eeecccCCCCCCHHH-----HhHhhHHHHHHHHHhc
Q 012657 220 VRRREDGDHSLSQEE-----KGRLALKEEVLRQVQE 250 (459)
Q Consensus 220 vrr~e~~~~~ls~ee-----k~rl~~k~~vl~qi~~ 250 (459)
+.+.|.|.+++|.+| |+||.+|.++.+-++.
T Consensus 33 I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~L~~ 68 (72)
T COG2841 33 IKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASILQK 68 (72)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 446778888888875 8999999998877654
No 63
>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
Probab=24.19 E-value=3e+02 Score=30.56 Aligned_cols=76 Identities=14% Similarity=0.114 Sum_probs=52.1
Q ss_pred HcCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 012657 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (459)
Q Consensus 35 ~~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLI 114 (459)
+.|+++.++...|+..|++++.++.+ ++++. .-....|+.. .+||=-|-+ -+++.|.|
T Consensus 29 ~~g~~~~~l~~~~~~~G~~~~~~~~~---~~~l~--------~~~lP~i~~~---------~~~~vvl~~--~~~~~~~i 86 (694)
T TIGR01846 29 GASLDDLEILLAAKQLGLKAKAVKVS---IGRLN--------KLPLPALIDG---------EGGWFVLGK--LTANGVTI 86 (694)
T ss_pred CCCCCHHHHHHHHHHCCCEEEEEeCC---HHHcc--------CCCCCEEEEE---------CCcEEEEEE--EcCCEEEE
Confidence 47999999999999999999999864 33332 1223445533 145433433 34678999
Q ss_pred EecCCCCCCceeeehhHHHH
Q 012657 115 LDVARFKYPPHWVPLTLLWE 134 (459)
Q Consensus 115 LDVARfKYPP~WVpl~~L~e 134 (459)
.|++.- .+.|++.+++.+
T Consensus 87 ~Dp~~g--~~~~i~~~e~~~ 104 (694)
T TIGR01846 87 YDPPGD--APEVLSREVLEA 104 (694)
T ss_pred EcCCCC--CceeeCHHHHHh
Confidence 998542 578999988754
No 64
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=24.06 E-value=55 Score=29.17 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=31.8
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHH
Q 012657 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (459)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~C 49 (459)
.|. .+..|+|+++-+..-.-+-..++.|++++|+..+...
T Consensus 31 ~r~-~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 31 GRT-DSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI 70 (131)
T ss_pred CcC-CCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 344 6779999998777555556678899999999999875
No 65
>PRK13749 transcriptional regulator MerD; Provisional
Probab=23.80 E-value=60 Score=29.27 Aligned_cols=40 Identities=23% Similarity=0.262 Sum_probs=31.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcCC
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGA 52 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnGa 52 (459)
.|.+|.|+|.-+..=.-+-..+.-|++++|+..|......
T Consensus 36 ~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~~ 75 (121)
T PRK13749 36 TGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDA 75 (121)
T ss_pred CCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhcC
Confidence 5899999997776444455556899999999999887543
No 66
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=23.80 E-value=1.5e+02 Score=24.97 Aligned_cols=86 Identities=13% Similarity=0.139 Sum_probs=57.4
Q ss_pred CcHHHHHH-HHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCcccccc-----ccccCCCCe
Q 012657 38 ISFGKLVC-LAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPI-----GGYHAGRDM 111 (459)
Q Consensus 38 ITL~ef~c-LA~CnGa~Vq~~r~~~~SldeFR~~V~~~~ss~d~~lIVnY~Rk~LgQtG~GHFSPI-----GGYh~~tD~ 111 (459)
||..||.. +|...|++-.. -..-+++|-..|.+++...+..-+ .|-|.|++. .|.|+.+..
T Consensus 2 mtk~eli~~ia~~~~~s~~~---v~~vv~~~~~~i~~~L~~g~~V~l----------~gfG~F~~~~r~~r~~~np~t~e 68 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKRE---AKELVELFFEEIRRALENGEQVKL----------SGFGNFDLRDKNQRPGRNPKTGE 68 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHH---HHHHHHHHHHHHHHHHHcCCeEEe----------cCCEEEEEEEEcCccCcCCCCCC
Confidence 67778764 45555542211 123578888888888876654332 456777654 579999977
Q ss_pred EEEEecCCCCCCceeeehhHHHHhcccc
Q 012657 112 ALILDVARFKYPPHWVPLTLLWEAMDRV 139 (459)
Q Consensus 112 VLILDVARfKYPP~WVpl~~L~eAM~ti 139 (459)
..... .++-+.+.|...|-+.++..
T Consensus 69 ~~~i~---~~~~v~Fkpsk~lk~~vn~~ 93 (96)
T TIGR00987 69 EIPIT---ARRVVTFRPGQKLKSRVENA 93 (96)
T ss_pred EEEEe---CCccEEEeeCHHHHHHHhcc
Confidence 66544 45679999999998888763
No 67
>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional
Probab=23.58 E-value=2.5e+02 Score=28.58 Aligned_cols=56 Identities=27% Similarity=0.480 Sum_probs=37.2
Q ss_pred EecCCCCHHHHHHHHHHHhcCCCc---EEEEEecccccccCCCccccccccccCCCCeEEEEecCCCCCCceeee
Q 012657 57 FRTNQSTIDDFRKYIIRCSASEDC---HVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVP 128 (459)
Q Consensus 57 ~r~~~~SldeFR~~V~~~~ss~d~---~lIVnY~Rk~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYPP~WVp 128 (459)
..++..+.++.++.|.+.....+. ..|.||.=|. |. |.-| | +|+|| ||==-|||+|
T Consensus 140 IDTs~ls~~el~e~I~~~l~~~~~~~~i~~~SFg~k~------g~--p~da-----d--~vfDv-R~lpNP~~~~ 198 (288)
T PRK05416 140 IDTSELSVHQLRERIRERFGGRERGLTVTVESFGFKY------GI--PLDA-----D--LVFDV-RFLPNPHYDP 198 (288)
T ss_pred EECCCCCHHHHHHHHHHHHhcCCCceEEEEEeecccC------CC--CCCC-----C--EEEEe-CcCCCCCCCh
Confidence 356677899999998876543222 4555653321 32 5533 4 89999 7888999998
No 68
>PF00120 Gln-synt_C: Glutamine synthetase, catalytic domain; InterPro: IPR008146 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006807 nitrogen compound metabolic process; PDB: 2J9I_E 3ZXV_D 1HTQ_D 1HTO_F 2BVC_F 2WGS_G 3ZXR_B 2WHI_D 3NG0_A 1LGR_C ....
Probab=23.46 E-value=1.3e+02 Score=29.45 Aligned_cols=61 Identities=20% Similarity=0.319 Sum_probs=40.5
Q ss_pred HHHHHHHHHHcCCeEEEEecCC------------------CCHHHHHHHHHHHhcCCCcEEEEEeccccc-ccCCCc---
Q 012657 40 FGKLVCLAHCAGAKVEAFRTNQ------------------STIDDFRKYIIRCSASEDCHVISSYHRGAF-KQTGTG--- 97 (459)
Q Consensus 40 L~ef~cLA~CnGa~Vq~~r~~~------------------~SldeFR~~V~~~~ss~d~~lIVnY~Rk~L-gQtG~G--- 97 (459)
++++...+...|+.|+.+|... ..+-.||..|++....- -+.++|.=|.+ ++.|.|
T Consensus 71 ~~~i~~~l~~~Gi~ve~~h~E~gpgQ~Ei~~~~~~~l~aaD~~~~~k~~ik~vA~~~--Gl~atFmpKP~~~~~GsG~H~ 148 (259)
T PF00120_consen 71 LEEIVDALEQAGIPVEQIHHEVGPGQYEINLGPCDPLEAADNLVLFKEIIKEVARKH--GLTATFMPKPFSGDNGSGMHL 148 (259)
T ss_dssp HHHHHHHHHHCT--EEEEEEESSTTEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHT--TEEEE-SSSSSTTSS--BEEE
T ss_pred HHHHHHHHHHhhccccccccccchHhhccccccCcHHHHHHHHHHHHHHHHHHHHHc--CCceeeeccccCCcCccchhh
Confidence 3577777888999999988531 14557999999876544 58999999996 777866
Q ss_pred ccccc
Q 012657 98 HFSPI 102 (459)
Q Consensus 98 HFSPI 102 (459)
|+|-.
T Consensus 149 h~Sl~ 153 (259)
T PF00120_consen 149 HISLW 153 (259)
T ss_dssp EEEEC
T ss_pred hhhhh
Confidence 55543
No 69
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.26 E-value=1.3e+02 Score=25.54 Aligned_cols=51 Identities=4% Similarity=0.110 Sum_probs=36.7
Q ss_pred cCcccccccccccccCChHHHHH-cCCcHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHH
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKE-KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYII 72 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~-~GITL~ef~cLA~CnGa~Vq~~r~~~~SldeFR~~V~ 72 (459)
++..|+|+++-+..-.-+-..++ -|++++++..+... .++.++.+=++.+.
T Consensus 33 ~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~---------~~~~~~~~~~~~~~ 84 (95)
T cd04780 33 APNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA---------IADASLPSTLLALA 84 (95)
T ss_pred CCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh---------cCcccHHHHHHHHH
Confidence 45568999988887666666776 69999999988875 33455665555554
No 70
>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=23.18 E-value=59 Score=30.45 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=32.7
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
|.+.=.+.+|+|+++-+..-.-+-..+.-|++++++..+....
T Consensus 29 p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 29 PSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred CCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 4333368899999987765556666788999999999888754
No 71
>TIGR00695 uxuA mannonate dehydratase. This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6.
Probab=23.14 E-value=3.1e+02 Score=29.63 Aligned_cols=60 Identities=18% Similarity=0.391 Sum_probs=39.8
Q ss_pred CcccccccccccccCChHHHHHcCCc-------------------HHHHHHHHHHcCCeEEEEecC-------------C
Q 012657 14 RPWRWFDESMLDCCEPLEKVKEKGIS-------------------FGKLVCLAHCAGAKVEAFRTN-------------Q 61 (459)
Q Consensus 14 GpWRWf~EsmLdCC~ple~Vk~~GIT-------------------L~ef~cLA~CnGa~Vq~~r~~-------------~ 61 (459)
--||||.+ +--.+|+.+++.|+| +.+.....+.+|++..+.-.- +
T Consensus 3 ~t~rw~gp---~d~v~l~~irQ~G~~giV~al~~~p~gevW~~~~i~~~k~~ie~~GL~~~vvEs~pv~e~Ik~g~~~rd 79 (394)
T TIGR00695 3 QTWRWYGP---NDPVSLEDVRQAGATGIVTALHHIPNGEVWEKEEIRKRKEYIESAGLHWSVVESVPVHEAIKTGTGNYG 79 (394)
T ss_pred ceeeeeCC---CCcchHHHHhhcCCcceeecCCCCCCCCCCCHHHHHHHHHHHHHcCCeEEEEeCCCccHHHHcCCCcHH
Confidence 35999988 445688899988876 244556677899988775421 1
Q ss_pred CCHHHHHHHHHHHhc
Q 012657 62 STIDDFRKYIIRCSA 76 (459)
Q Consensus 62 ~SldeFR~~V~~~~s 76 (459)
.-++.+.+.|+...+
T Consensus 80 ~~Ienyk~~irNla~ 94 (394)
T TIGR00695 80 RWIENYKQTLRNLAQ 94 (394)
T ss_pred HHHHHHHHHHHHHHH
Confidence 245666666665543
No 72
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=21.92 E-value=57 Score=22.59 Aligned_cols=10 Identities=50% Similarity=0.969 Sum_probs=8.1
Q ss_pred hhhHhhhhee
Q 012657 210 FGEFVKWVAE 219 (459)
Q Consensus 210 ~~~~ikwv~e 219 (459)
+++|+||++|
T Consensus 9 IgdfvKlI~~ 18 (25)
T PF05372_consen 9 IGDFVKLIIE 18 (25)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4789999885
No 73
>TIGR00653 GlnA glutamine synthetase, type I. Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon Sulfolobus acidocaldarius differs from that in E. coli in that it is not regulated by adenylylation.
Probab=21.78 E-value=1.4e+02 Score=32.26 Aligned_cols=61 Identities=15% Similarity=0.224 Sum_probs=45.6
Q ss_pred HHHHHHHHHHcCCeEEEEecCC------------------CCHHHHHHHHHHHhcCCCcEEEEEeccccc-ccCCCc---
Q 012657 40 FGKLVCLAHCAGAKVEAFRTNQ------------------STIDDFRKYIIRCSASEDCHVISSYHRGAF-KQTGTG--- 97 (459)
Q Consensus 40 L~ef~cLA~CnGa~Vq~~r~~~------------------~SldeFR~~V~~~~ss~d~~lIVnY~Rk~L-gQtG~G--- 97 (459)
++++...+...|+.++.+|... ..+-.||+.|++..+.- .++++|-=|.+ |+.|.|
T Consensus 185 ~~~i~~~l~~~Gi~v~~~~~E~gpGQ~Ei~l~~~~~l~aAD~~~~~k~~ik~vA~~~--G~~ATFmpKP~~~~~GSG~H~ 262 (460)
T TIGR00653 185 RREMVLYLEQLGFDVEVHHHEVATGQHEIDFKFDTLLKTADDIQTYKYVVKNVARKH--GKTATFMPKPLFGDNGSGMHC 262 (460)
T ss_pred HHHHHHHHHHcCCCceeeecCcCCCceeEecCCCCHHHHHHHHHHHHHHHHHHHHHh--CCEEEEecccCCCCCcCceeE
Confidence 3577788889999999988531 13346899999876543 68999998887 778877
Q ss_pred ccccc
Q 012657 98 HFSPI 102 (459)
Q Consensus 98 HFSPI 102 (459)
|+|-.
T Consensus 263 H~Sl~ 267 (460)
T TIGR00653 263 HQSLW 267 (460)
T ss_pred EECcc
Confidence 77765
No 74
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=20.97 E-value=71 Score=27.43 Aligned_cols=39 Identities=8% Similarity=0.319 Sum_probs=31.2
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHHcC
Q 012657 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (459)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~CnG 51 (459)
.+.+|+|++.-+..=.-+-..++.|++++++..+.....
T Consensus 34 ~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 34 DTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADN 72 (108)
T ss_pred CCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 368999999777655556667789999999999987754
No 75
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=20.88 E-value=67 Score=28.30 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=31.8
Q ss_pred ccCcccccccccccccCChHHHHHcCCcHHHHHHHHHHc
Q 012657 12 SGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (459)
Q Consensus 12 WKGpWRWf~EsmLdCC~ple~Vk~~GITL~ef~cLA~Cn 50 (459)
=.|.+|+|+++-+..-.-+-..+..|+|++|+..+....
T Consensus 31 ~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 31 PEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLV 69 (124)
T ss_pred CCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcc
Confidence 357899999988876566667889999999999988653
Done!