Query 013618
Match_columns 439
No_of_seqs 133 out of 168
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:40:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013618.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013618hhsearch_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 7E-116 1E-120 840.1 25.8 264 156-419 1-264 (264)
2 KOG0632 Phytochelatin synthase 100.0 4E-103 9E-108 766.4 14.3 321 5-412 68-388 (388)
3 PF05023 Phytochelatin: Phytoc 100.0 2.7E-62 5.8E-67 461.0 12.5 147 7-153 66-212 (212)
4 PF14399 Transpep_BrtH: NlpC/p 96.5 0.037 8.1E-07 53.5 11.8 105 41-151 53-164 (317)
5 PF13529 Peptidase_C39_2: Pept 94.9 0.067 1.5E-06 44.2 5.8 76 35-118 62-144 (144)
6 cd02549 Peptidase_C39A A sub-f 93.4 0.43 9.2E-06 40.4 7.7 89 36-137 42-131 (141)
7 cd02259 Peptidase_C39_like Pep 93.3 0.43 9.4E-06 39.1 7.4 79 35-136 36-114 (122)
8 PF03412 Peptidase_C39: Peptid 92.7 0.12 2.6E-06 43.5 3.4 78 35-136 42-119 (131)
9 cd02420 Peptidase_C39D A sub-f 90.9 0.61 1.3E-05 39.0 5.7 76 36-135 42-117 (125)
10 cd02418 Peptidase_C39B A sub-f 90.6 1.6 3.5E-05 36.6 8.1 83 36-136 42-124 (136)
11 cd02423 Peptidase_C39G A sub-f 84.2 3.8 8.2E-05 34.1 6.5 78 36-134 43-120 (129)
12 cd02424 Peptidase_C39E A sub-f 84.1 3.8 8.2E-05 35.0 6.6 79 36-135 43-121 (129)
13 cd02419 Peptidase_C39C A sub-f 82.1 9.5 0.00021 31.8 8.1 76 36-135 42-117 (127)
14 TIGR03796 NHPM_micro_ABC1 NHPM 79.1 15 0.00034 40.2 10.6 83 28-134 29-117 (710)
15 cd02425 Peptidase_C39F A sub-f 73.8 15 0.00033 30.3 6.9 76 36-134 42-117 (126)
16 PF09778 Guanylate_cyc_2: Guan 71.2 17 0.00037 35.8 7.5 86 41-135 93-198 (212)
17 TIGR01193 bacteriocin_ABC ABC- 63.9 86 0.0019 34.6 11.9 84 35-134 36-119 (708)
18 cd02417 Peptidase_C39_likeA A 59.5 69 0.0015 26.4 8.1 78 36-136 37-114 (121)
19 cd04770 HTH_HMRTR Helix-Turn-H 57.6 17 0.00036 31.4 4.2 41 9-50 30-70 (123)
20 cd04781 HTH_MerR-like_sg6 Heli 56.5 7.9 0.00017 33.6 2.1 39 13-51 32-70 (120)
21 cd01106 HTH_TipAL-Mta Helix-Tu 55.5 15 0.00032 30.9 3.5 44 7-50 27-70 (103)
22 cd04768 HTH_BmrR-like Helix-Tu 54.0 8.8 0.00019 32.2 1.9 44 7-50 27-70 (96)
23 cd04785 HTH_CadR-PbrR-like Hel 53.0 22 0.00048 31.1 4.3 37 13-49 33-69 (126)
24 PRK15002 redox-sensitivie tran 52.3 19 0.0004 33.4 3.9 37 13-49 43-79 (154)
25 cd02421 Peptidase_C39_likeD A 51.9 84 0.0018 26.1 7.5 77 36-134 37-113 (124)
26 TIGR03375 type_I_sec_LssB type 49.9 59 0.0013 35.8 7.8 78 35-134 29-107 (694)
27 PRK10227 DNA-binding transcrip 48.8 26 0.00056 31.5 4.1 38 12-49 32-69 (135)
28 TIGR02044 CueR Cu(I)-responsiv 47.4 14 0.0003 32.4 2.1 37 13-49 33-69 (127)
29 cd04783 HTH_MerR1 Helix-Turn-H 45.0 15 0.00032 32.2 1.9 43 8-51 29-71 (126)
30 TIGR01950 SoxR redox-sensitive 44.4 15 0.00033 33.3 2.0 37 13-49 33-69 (142)
31 PRK13752 putative transcriptio 43.7 16 0.00035 33.2 2.1 42 8-50 36-77 (144)
32 KOG4621 Uncharacterized conser 42.7 47 0.001 31.2 4.9 72 60-137 80-152 (167)
33 cd01282 HTH_MerR-like_sg3 Heli 42.6 19 0.00041 31.1 2.2 42 8-50 28-69 (112)
34 cd04784 HTH_CadR-PbrR Helix-Tu 42.0 19 0.0004 31.5 2.1 41 8-49 29-69 (127)
35 cd01108 HTH_CueR Helix-Turn-He 41.8 35 0.00076 30.0 3.8 41 8-49 29-69 (127)
36 COG5559 Uncharacterized conser 41.7 13 0.00029 30.4 1.0 17 401-417 8-24 (65)
37 cd04763 HTH_MlrA-like Helix-Tu 40.7 22 0.00048 27.5 2.2 40 7-47 28-67 (68)
38 COG3323 Uncharacterized protei 39.9 20 0.00044 32.2 2.0 44 63-110 16-59 (109)
39 TIGR02047 CadR-PbrR Cd(II)/Pb( 39.4 22 0.00049 31.3 2.2 41 8-49 29-69 (127)
40 cd01109 HTH_YyaN Helix-Turn-He 37.4 53 0.0011 28.1 4.1 39 11-49 31-69 (113)
41 PF09312 SurA_N: SurA N-termin 36.8 16 0.00035 31.6 0.9 45 30-74 57-111 (118)
42 PF05381 Peptidase_C21: Tymovi 36.0 26 0.00056 31.2 2.1 49 6-58 16-64 (104)
43 COG5565 Bacteriophage terminas 35.8 20 0.00044 30.4 1.3 38 10-58 15-55 (79)
44 PF14214 Helitron_like_N: Heli 35.6 49 0.0011 30.3 3.9 44 156-206 102-145 (184)
45 cd01110 HTH_SoxR Helix-Turn-He 35.5 26 0.00056 31.5 2.0 42 7-49 28-69 (139)
46 cd04786 HTH_MerR-like_sg7 Heli 34.7 61 0.0013 29.0 4.2 41 9-50 30-70 (131)
47 cd04788 HTH_NolA-AlbR Helix-Tu 34.3 28 0.0006 29.2 1.9 38 13-50 33-70 (96)
48 PF05415 Peptidase_C36: Beet n 33.9 24 0.00051 31.2 1.4 39 34-72 16-59 (104)
49 PRK09514 zntR zinc-responsive 33.6 62 0.0013 29.1 4.1 37 13-49 34-70 (140)
50 TIGR03797 NHPM_micro_ABC2 NHPM 33.5 1.8E+02 0.0039 32.1 8.4 82 28-132 19-102 (686)
51 cd04789 HTH_Cfa Helix-Turn-Hel 33.4 22 0.00049 30.2 1.2 36 13-48 33-68 (102)
52 PF13411 MerR_1: MerR HTH fami 33.2 18 0.00038 27.6 0.5 42 6-48 26-67 (69)
53 cd04787 HTH_HMRTR_unk Helix-Tu 33.2 29 0.00064 30.7 2.0 43 8-50 28-70 (133)
54 PTZ00445 p36-lilke protein; Pr 32.1 1.5E+02 0.0032 29.7 6.7 99 41-142 32-159 (219)
55 cd01789 Alp11_N Ubiquitin-like 32.0 2.9E+02 0.0063 22.7 7.7 64 54-119 15-83 (84)
56 cd04776 HTH_GnyR Helix-Turn-He 31.9 32 0.00069 30.1 2.0 40 8-49 28-67 (118)
57 cd04782 HTH_BltR Helix-Turn-He 31.5 37 0.0008 28.5 2.2 43 7-49 27-69 (97)
58 cd04764 HTH_MlrA-like_sg1 Heli 30.7 27 0.00058 26.9 1.2 35 13-47 32-66 (67)
59 KOG4212 RNA-binding protein hn 30.6 60 0.0013 35.8 4.0 57 95-155 30-94 (608)
60 TIGR00987 himA integration hos 30.2 90 0.002 26.1 4.3 86 38-139 2-93 (96)
61 PF02775 TPP_enzyme_C: Thiamin 29.6 90 0.002 27.4 4.4 36 42-79 112-147 (153)
62 PRK13749 transcriptional regul 29.3 41 0.0009 30.1 2.3 40 13-52 36-75 (121)
63 cd04780 HTH_MerR-like_sg5 Heli 29.2 89 0.0019 26.4 4.1 51 13-72 33-84 (95)
64 TIGR02043 ZntR Zn(II)-responsi 29.2 39 0.00084 30.0 2.1 40 9-49 31-70 (131)
65 cd04790 HTH_Cfa-like_unk Helix 27.8 43 0.00094 31.2 2.2 44 8-51 29-72 (172)
66 TIGR00695 uxuA mannonate dehyd 26.9 2.4E+02 0.0052 30.3 7.7 60 14-76 3-94 (394)
67 cd01107 HTH_BmrR Helix-Turn-He 26.7 47 0.001 28.3 2.1 39 13-51 34-72 (108)
68 TIGR02051 MerR Hg(II)-responsi 26.0 46 0.001 29.1 2.0 39 12-50 31-69 (124)
69 TIGR01846 type_I_sec_HlyB type 25.4 2.8E+02 0.0061 30.7 8.2 77 35-135 29-105 (694)
70 COG2841 Uncharacterized protei 24.9 72 0.0016 26.9 2.7 31 220-250 33-68 (72)
71 PRK05416 glmZ(sRNA)-inactivati 24.2 2.4E+02 0.0053 28.5 6.9 56 57-128 140-198 (288)
72 cd01104 HTH_MlrA-CarA Helix-Tu 23.2 44 0.00094 25.4 1.1 34 14-47 34-67 (68)
73 cd04773 HTH_TioE_rpt2 Second H 23.1 61 0.0013 27.8 2.1 43 7-49 27-69 (108)
74 PF14430 Imm1: Immunity protei 22.1 1.9E+02 0.0041 25.4 5.0 55 80-140 58-113 (127)
75 PF04614 Pex19: Pex19 protein 22.0 97 0.0021 30.7 3.5 72 191-268 120-212 (248)
76 PF00120 Gln-synt_C: Glutamine 22.0 1.4E+02 0.0031 29.0 4.6 61 40-102 71-153 (259)
77 COG1312 UxuA D-mannonate dehyd 21.4 5.5E+02 0.012 27.6 8.9 153 14-186 3-201 (362)
78 TIGR02054 MerD mercuric resist 20.8 71 0.0015 28.5 2.1 44 7-50 30-73 (120)
79 TIGR00653 GlnA glutamine synth 20.2 1.6E+02 0.0035 31.7 4.9 61 40-102 185-267 (460)
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=6.9e-116 Score=840.06 Aligned_cols=264 Identities=67% Similarity=1.078 Sum_probs=262.2
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhhhhhccCCCCCHHHHHHHHHhcCCcchhhHHhhheeeeecccCCCCCCHHHH
Q 013618 156 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEK 235 (439)
Q Consensus 156 ~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~slP~~~~~~ikwv~evr~~e~~~~~ls~eek 235 (439)
+++|++|||+||+||+|.+|||||++|||.||++++++||++||++||+|||+||++||||||||||+|||+++||.|||
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 013618 236 GRLALKEEVLRQVQETLLFKHVVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCL 315 (439)
Q Consensus 236 ~rl~~k~~vl~qi~~t~lf~~v~~~~~s~~~~~~~~~~~~~~~~l~~iaa~vccqga~~l~g~~~~~~~~c~~et~~kc~ 315 (439)
+||++|++||||||+|+|||||++|+++.+|||+++++++++|+||+|||+||||||+||+|+++++++|||+|||+||+
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 013618 316 KANSDKPVTLVSGTVVNGSIEQEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQI 395 (439)
Q Consensus 316 ~~~~~~~~t~vsg~v~~~~~eq~vd~lvp~~~~~~~~~~~~~~~~~~~~p~~~dvltvlllal~~~tw~~i~~e~l~~e~ 395 (439)
|+|||||+|||||+||+||+|||||||||+||+++++|+++.+++++|||+++||||||||||||+||+|||||+|++||
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 013618 396 LGLVTTENLPTLLQEEVLHLRRQL 419 (439)
Q Consensus 396 ~~lvs~~~lp~~lq~evlhlr~ql 419 (439)
++||||||||++|||||+||||||
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=3.9e-103 Score=766.38 Aligned_cols=321 Identities=59% Similarity=1.059 Sum_probs=301.4
Q ss_pred CCCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEE
Q 013618 5 NKARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVIS 84 (439)
Q Consensus 5 ~~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIV 84 (439)
..||.|.||||||||||+|||||+|||.|+++||||+||+|||+|||++|+++|.+++++|+||+.|..|.+++|++||.
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 013618 85 SYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVSRPHREPGLLYT 164 (439)
Q Consensus 85 nY~R~~LgQtG~GHFSPIGGYh~~sD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRG~lllsk~~~~ps~l~~ 164 (439)
+|+|++|||||+||||||||||+++|++|||||||||||||||||++||+||..||.+||++||||+|++++++|+ |||
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 013618 165 LSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEKGRLALKEEV 244 (439)
Q Consensus 165 ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~slP~~~~~~ikwv~evr~~e~~~~~ls~eek~rl~~k~~v 244 (439)
++|++++|..++|||.+|+|. |.++.|.++|.+|++|| ++|+|+.|+.+++++.|| +|+.+
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 56677999999999999 899999999999999988 34433
Q ss_pred HHHHhccchhHHHHHhhhcccccccccccccCCCChhHHHHHhhhhhhHHhhCcCCCCCcceecccccceeecCCCCCee
Q 013618 245 LRQVQETLLFKHVVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCLKANSDKPVT 324 (439)
Q Consensus 245 l~qi~~t~lf~~v~~~~~s~~~~~~~~~~~~~~~~l~~iaa~vccqga~~l~g~~~~~~~~c~~et~~kc~~~~~~~~~t 324 (439)
+ |..++++ .+|+.+||+|+++++|. .+..|||++||++|.|.-++...|
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 013618 325 LVSGTVVNGSIEQEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQILGLVTTENL 404 (439)
Q Consensus 325 ~vsg~v~~~~~eq~vd~lvp~~~~~~~~~~~~~~~~~~~~p~~~dvltvlllal~~~tw~~i~~e~l~~e~~~lvs~~~l 404 (439)
++ .+|.++||+|+|||||||+||+||+|..|..|+..+++.-+.
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 013618 405 PTLLQEEV 412 (439)
Q Consensus 405 p~~lq~ev 412 (439)
|+++|.||
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=2.7e-62 Score=461.03 Aligned_cols=147 Identities=49% Similarity=0.984 Sum_probs=123.8
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEe
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSY 86 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY 86 (439)
+|+++||||||||+|+||+||.|++.|+++||||+||+|||+|||+.|+++++++.|+++||++|++++++++++|||||
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 013618 87 HRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVS 153 (439)
Q Consensus 87 ~R~~LgQtG~GHFSPIGGYh~~sD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRG~llls 153 (439)
+|++|||+|+||||||||||+++|+|||||||||||||||||+++||+||+++|++||++|||++|+
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=96.47 E-value=0.037 Score=53.50 Aligned_cols=105 Identities=18% Similarity=0.059 Sum_probs=80.4
Q ss_pred HHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEeccccc-------ccCCCccccccccccCCCCeEE
Q 013618 41 GKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAF-------KQTGTGHFSPIGGYHAGRDMAL 113 (439)
Q Consensus 41 ~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~L-------gQtG~GHFSPIGGYh~~sD~VL 113 (439)
.-+..+++..|++++.... .+.++..+.|++.+. .+..++|.-+...| ...+.+|+--|=|||++.+.++
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 5667889999999986554 367888888888775 44577776654444 3446899999999999999999
Q ss_pred EEecCCCCCCceeeehhHHHHhccccCCCCCceeeEEE
Q 013618 114 ILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVL 151 (439)
Q Consensus 114 ILDVARfKYPP~WVpl~~L~eAM~tiD~~TgrsRG~ll 151 (439)
|.|. ..+++..+|.+.|-+|+..... ...+++.+.
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 9999 4778899999999999998874 223344443
No 5
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=94.89 E-value=0.067 Score=44.22 Aligned_cols=76 Identities=25% Similarity=0.257 Sum_probs=48.0
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEec--ccc-----cccCCCccccccccccC
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYH--RGA-----FKQTGTGHFSPIGGYHA 107 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~--R~~-----LgQtG~GHFSPIGGYh~ 107 (439)
..|+....+..+++..|..+. .....+++++++.|. .+..+|++.. ... ....+.|||=-|=||+.
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 334567777777776 3668888886 233 36678999999999999
Q ss_pred CCCeEEEEecC
Q 013618 108 GRDMALILDVA 118 (439)
Q Consensus 108 ~sD~VLILDVA 118 (439)
.. .|.|.|.+
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 89999974
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=93.36 E-value=0.43 Score=40.39 Aligned_cols=89 Identities=18% Similarity=0.122 Sum_probs=61.5
Q ss_pred cCCcHHHHHHH-HHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 013618 36 KGISFGKLVCL-AHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (439)
Q Consensus 36 ~GITL~e~~cL-A~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLI 114 (439)
.|++..++... |+..|++++..... .. .++.+. .+..+|+...- .....+.|||=-|.||+ +.+.++|
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 223332 45677776542 12234589999999999 4566999
Q ss_pred EecCCCCCCceeeehhHHHHhcc
Q 013618 115 LDVARFKYPPHWVPLTLLWEAMD 137 (439)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM~ 137 (439)
.|.+. -.+..++.+.+-++..
T Consensus 111 ~DP~~--~~~~~~~~~~f~~~w~ 131 (141)
T cd02549 111 NDPGG--GRRLVVSFDEFEKAWK 131 (141)
T ss_pred ECCCC--CcCEEEeHHHHHHHHH
Confidence 99974 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=93.28 E-value=0.43 Score=39.12 Aligned_cols=79 Identities=22% Similarity=0.269 Sum_probs=59.4
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLI 114 (439)
..|.++.++..+|+..|++++.+.. +++.+++ -+..+|+- .++|||--|.+++ .+.++|
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 22234443 4789999999998 668999
Q ss_pred EecCCCCCCceeeehhHHHHhc
Q 013618 115 LDVARFKYPPHWVPLTLLWEAM 136 (439)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM 136 (439)
.|.+ ...+.|++.+.|-+..
T Consensus 95 ~dp~--~~~~~~~~~~~l~~~w 114 (122)
T cd02259 95 ADPL--EEGPVTLSESELEERW 114 (122)
T ss_pred ECCc--ccCCEEeCHHHHHhhC
Confidence 9987 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=92.66 E-value=0.12 Score=43.54 Aligned_cols=78 Identities=24% Similarity=0.192 Sum_probs=56.0
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLI 114 (439)
..|+|+.++..+|+.+|++++.++.+. ++| .+-...+|+.- +.|||--|-++ ..+.++|
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 11222333332 88999999888 7789999
Q ss_pred EecCCCCCCceeeehhHHHHhc
Q 013618 115 LDVARFKYPPHWVPLTLLWEAM 136 (439)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eAM 136 (439)
.|. +..+.|++.+++.+.-
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 999 5578999988876643
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=90.86 E-value=0.61 Score=38.96 Aligned_cols=76 Identities=17% Similarity=0.280 Sum_probs=56.5
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|.+...+...|+..|++++.++. +++.+.+. .-.+|+-. +.|||--|.+++ .|.++|.
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 013618 116 DVARFKYPPHWVPLTLLWEA 135 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (439)
|.+. .|.|++.++|-+.
T Consensus 101 dp~~---~~~~~s~~el~~~ 117 (125)
T cd02420 101 DPAT---GRRTVSLEEFDQS 117 (125)
T ss_pred CCCc---CceeecHHHHHhh
Confidence 9964 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=90.63 E-value=1.6 Score=36.61 Aligned_cols=83 Identities=14% Similarity=0.053 Sum_probs=58.6
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|+++..+...|+..|++++.+..+... ..+ .+ -...+|+-.. . ..+.|||--|.+++ .+.++|.
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 1223444321 1 24789999999998 5579999
Q ss_pred ecCCCCCCceeeehhHHHHhc
Q 013618 116 DVARFKYPPHWVPLTLLWEAM 136 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~eAM 136 (439)
|. ..++.+++.++|-+..
T Consensus 107 dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 107 DP---AVGITKISKEEFEKEW 124 (136)
T ss_pred CC---CCCCEEeeHHHHHhhC
Confidence 98 5679999998875533
No 11
>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=84.22 E-value=3.8 Score=34.11 Aligned_cols=78 Identities=27% Similarity=0.299 Sum_probs=55.3
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|.++.++..+|+..|++++.++.+ .+.+.+ . .-.+|+-. ...++|||--|.+++ .+.++|.
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 11333322 123578998888888 6679999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 013618 116 DVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (439)
|.+. ++.+++.+.|-+
T Consensus 105 dp~~---~~~~~s~~el~~ 120 (129)
T cd02423 105 DPAL---GNISMSREEFER 120 (129)
T ss_pred CCCC---CCcccCHHHHHH
Confidence 9953 678888877654
No 12
>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=84.12 E-value=3.8 Score=34.97 Aligned_cols=79 Identities=18% Similarity=0.254 Sum_probs=54.1
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
+|.++.++...|+..|+++++++.+ .+++ .+. ...-..|+. ..++.||=-+.+.+. +.|+|.
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 013618 116 DVARFKYPPHWVPLTLLWEA 135 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (439)
|. .+++.+++.+++-+.
T Consensus 105 DP---~~g~~~~s~~~f~~~ 121 (129)
T cd02424 105 DP---KKGKYKITYKEFEKI 121 (129)
T ss_pred CC---CCCCEEeCHHHHHHH
Confidence 99 467888888776544
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=82.12 E-value=9.5 Score=31.80 Aligned_cols=76 Identities=20% Similarity=0.243 Sum_probs=55.3
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|.++..+..+|+..|++++.++.+ .+.+++. .-.+|+- ...|||--|.+. ..|.++|.
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 5899999999999999999888753 4444332 1123332 156999888886 56789999
Q ss_pred ecCCCCCCceeeehhHHHHh
Q 013618 116 DVARFKYPPHWVPLTLLWEA 135 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~eA 135 (439)
|+.. ++.+++.++|-+.
T Consensus 101 dp~~---~~~~~~~~el~~~ 117 (127)
T cd02419 101 DPAL---GKRKLSLEEASRH 117 (127)
T ss_pred CCcc---CCEEEcHHHHHhh
Confidence 9953 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=79.13 E-value=15 Score=40.19 Aligned_cols=83 Identities=25% Similarity=0.351 Sum_probs=61.7
Q ss_pred CChHHHH------HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccc
Q 013618 28 EPLEKVK------EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSP 101 (439)
Q Consensus 28 ~ple~Vk------~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSP 101 (439)
.+++.++ +.|+|+..+..+|+..|++++.++.+ ++++ ..-.-..|+.. +.+||=-
T Consensus 29 ~~~~~lr~~~~~~~~g~s~~~l~~~~~~~g~~~~~~~~~---~~~l--------~~~~lP~i~~~--------~~~h~vv 89 (710)
T TIGR03796 29 VPLEELREECGVSRDGSKASNLLKAARSYGLEAKGFRKE---LDAL--------AELPLPYIVFW--------NFNHFVV 89 (710)
T ss_pred CCHHHHHHHcCCCCCCCCHHHHHHHHHHCCCEeEEEecC---HHHh--------ccCCCCEEEEE--------cCCcEEE
Confidence 4555544 47999999999999999999999874 3332 12233555555 6799988
Q ss_pred cccccCCCCeEEEEecCCCCCCceeeehhHHHH
Q 013618 102 IGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 102 IGGYh~~sD~VLILDVARfKYPP~WVpl~~L~e 134 (439)
+-++ ..+.+.|+|++- .+.|++.+++-+
T Consensus 90 l~~~--~~~~~~i~dP~~---g~~~~~~~e~~~ 117 (710)
T TIGR03796 90 VEGF--RGGRVYLNDPAL---GPRTVSLEEFDE 117 (710)
T ss_pred EEEE--eCCEEEEECCCC---CCEEccHHHHHh
Confidence 8776 557899999974 688999988654
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=73.79 E-value=15 Score=30.35 Aligned_cols=76 Identities=18% Similarity=0.241 Sum_probs=53.2
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|+++..+..+|+..|++++.++.+.. +.+.+ . . -..|+-. .+|||=-|.+++ .+.++|+
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 589999999999999999998875420 22222 1 1 1333321 248998888984 5579999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 013618 116 DVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (439)
|... ++.|++.+.|=+
T Consensus 102 dp~~---~~~~~~~~~l~~ 117 (126)
T cd02425 102 DPAI---GRIKISIDEFLE 117 (126)
T ss_pred cCCC---CCEEECHHHHHh
Confidence 9954 567999888643
No 16
>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=71.20 E-value=17 Score=35.76 Aligned_cols=86 Identities=22% Similarity=0.211 Sum_probs=57.3
Q ss_pred HHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccc------------------cC-C-Ccccc
Q 013618 41 GKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFK------------------QT-G-TGHFS 100 (439)
Q Consensus 41 ~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~Lg------------------Qt-G-~GHFS 100 (439)
.++-..|+.+|+.|+.- ..|+++...++.. .+ .+||--+...|. +. + .|||=
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 46677888999988642 3789988888774 22 444444443333 22 2 79999
Q ss_pred ccccccCCCCeEEEEecCCCCCCceeeehhHHHHh
Q 013618 101 PIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 135 (439)
Q Consensus 101 PIGGYh~~sD~VLILDVARfKYPP~WVpl~~L~eA 135 (439)
-|=|||++++.+++=|+|--. --.=|+.+.|=+|
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 999999999999999998532 2223444444333
No 17
>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=63.89 E-value=86 Score=34.62 Aligned_cols=84 Identities=14% Similarity=0.119 Sum_probs=58.0
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLI 114 (439)
+.|+|+..+..+|+..|++++.++.+ ++++. + ..-.-..|+...+. .+..||=-+=+++ .+.|.|
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 47999999999999999999999974 32210 1 11123455543221 2456987777766 678999
Q ss_pred EecCCCCCCceeeehhHHHH
Q 013618 115 LDVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 115 LDVARfKYPP~WVpl~~L~e 134 (439)
+|++. .+.+.|++.+++.+
T Consensus 101 ~dP~~-~~g~~~~~~~ef~~ 119 (708)
T TIGR01193 101 ADPDP-TVGITKISKEDFYE 119 (708)
T ss_pred EcCCc-ccCCEEecHHHHHh
Confidence 99943 25788999999755
No 18
>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=59.49 E-value=69 Score=26.40 Aligned_cols=78 Identities=14% Similarity=0.130 Sum_probs=54.8
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|.+...+...|+..|++++.++.+ ++.+.+. .-..|+- ..+|||--|.+.+ .+.++|.
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 5799999999999999999988753 3332221 1123332 1357888888877 5679999
Q ss_pred ecCCCCCCceeeehhHHHHhc
Q 013618 116 DVARFKYPPHWVPLTLLWEAM 136 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~eAM 136 (439)
|++. -.|..++.+.|-+..
T Consensus 96 dp~~--~~~~~~~~~el~~~~ 114 (121)
T cd02417 96 DPIS--QRPEVLSREEFEARW 114 (121)
T ss_pred CCCc--CCCeecCHHHHHhhc
Confidence 9965 367888988876654
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=57.59 E-value=17 Score=31.38 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=33.3
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|- .+.+|+|+++-+..=.-+-..++.|++++|+..+....
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 67899999988876666667789999999999998764
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=56.49 E-value=7.9 Score=33.62 Aligned_cols=39 Identities=18% Similarity=0.266 Sum_probs=33.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcC
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG 51 (439)
.|.+|.|+++-+..-.-+...+..|+|++++..+....+
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 479999999888877777888899999999999887643
No 21
>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=55.48 E-value=15 Score=30.93 Aligned_cols=44 Identities=18% Similarity=0.214 Sum_probs=33.3
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|.+...|.+|+|+++-++.=.-+-..+..|+|++++..+....
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 22
>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=53.95 E-value=8.8 Score=32.21 Aligned_cols=44 Identities=14% Similarity=0.216 Sum_probs=34.6
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|.+.-.+.+|+|+++-+..=.-+-..++.|++++++..+....
T Consensus 27 ~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 27 KPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred CCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 45555577899999988876555667788999999999988753
No 23
>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=53.05 E-value=22 Score=31.14 Aligned_cols=37 Identities=11% Similarity=0.287 Sum_probs=31.6
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|.+|+|+++-+..-.-+-..+..|++++|+..+...
T Consensus 33 ~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 33 AGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 7889999998887666666788999999999998875
No 24
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=52.34 E-value=19 Score=33.38 Aligned_cols=37 Identities=11% Similarity=0.134 Sum_probs=31.2
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|..|+|+++.+..=.-+-..++-|+||+|+..+...
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 6778999998887666666778999999999999875
No 25
>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=51.94 E-value=84 Score=26.08 Aligned_cols=77 Identities=21% Similarity=0.060 Sum_probs=52.6
Q ss_pred cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEE
Q 013618 36 KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALIL 115 (439)
Q Consensus 36 ~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLIL 115 (439)
.|.+..++...|+..|++++..+.+ .+.+.+ -.-..|+- ..+|||--|.+.+. +.++|.
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 4788999999999999999877643 332211 11123331 24689888888775 679999
Q ss_pred ecCCCCCCceeeehhHHHH
Q 013618 116 DVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 116 DVARfKYPP~WVpl~~L~e 134 (439)
|+.- ...|.+++.+.|=+
T Consensus 96 dp~~-~~~~~~~~~~el~~ 113 (124)
T cd02421 96 DPES-GGGEVEISLEELEE 113 (124)
T ss_pred ccCC-CCCcEEEcHHHHHh
Confidence 9862 36788899887654
No 26
>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=49.95 E-value=59 Score=35.76 Aligned_cols=78 Identities=18% Similarity=0.066 Sum_probs=51.2
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCe-EE
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDM-AL 113 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~-VL 113 (439)
+.|+|+.++..+|+..|++++.++.+ ++++. ......|+.++ ++||=-+-+ -..+. |.
T Consensus 29 ~~g~sl~~l~~~~~~~g~~~~~~~~~---~~~l~--------~~~~P~i~~~~--------~~h~vvl~~--~~~~~~~~ 87 (694)
T TIGR03375 29 DGRLTPELLPRAARRAGLSARLVKRS---LDDIS--------PLLLPAILLLK--------DGRACVLLG--IDEDGKAR 87 (694)
T ss_pred CCCCCHHHHHHHHHHCCCEEEEecCC---HhhcC--------cCCCCEEEEEc--------CCcEEEEEE--EcCCCcEE
Confidence 48999999999999999999999853 33321 22334555442 368733333 34455 99
Q ss_pred EEecCCCCCCceeeehhHHHH
Q 013618 114 ILDVARFKYPPHWVPLTLLWE 134 (439)
Q Consensus 114 ILDVARfKYPP~WVpl~~L~e 134 (439)
|+|.+.- =.+.|++.+++-+
T Consensus 88 i~DP~~g-~~~~~~~~~e~~~ 107 (694)
T TIGR03375 88 VLLPETG-DGEQELSLDALEA 107 (694)
T ss_pred EEccCCC-CCceEecHHHHHh
Confidence 9998531 0166888877643
No 27
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=48.83 E-value=26 Score=31.53 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=32.4
Q ss_pred ccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 12 SGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 12 WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
=.+.+|.|+++-+..-.-+-..+..|++++|+..+...
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 46889999998888777777788899999999998875
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=47.37 E-value=14 Score=32.44 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=31.0
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.+.+|+|+++-+..-.-+-..++.|+|++|+..+...
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 5679999998887666666788999999999998874
No 29
>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=45.04 E-value=15 Score=32.17 Aligned_cols=43 Identities=12% Similarity=0.201 Sum_probs=34.8
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcC
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG 51 (439)
|.|. .|..|+|+++-+..-.-+-..++-|+|++|+..+.....
T Consensus 29 ~~r~-~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 29 PPRP-EGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDD 71 (126)
T ss_pred CCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 4454 677999999888876667778999999999999887543
No 30
>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=44.44 E-value=15 Score=33.35 Aligned_cols=37 Identities=11% Similarity=0.160 Sum_probs=31.7
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|..|+|+++-+..-.-+-..++.|+||+++..+..+
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 5679999998887766677788999999999999876
No 31
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=43.73 E-value=16 Score=33.20 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=34.9
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
|+|. .|.+|+|+++-+..-.-+-..++.|++|+|+..+...+
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 57799999999988777788899999999999998754
No 32
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.66 E-value=47 Score=31.21 Aligned_cols=72 Identities=29% Similarity=0.367 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEEEecCCCCCCcee-eehhHHHHhcc
Q 013618 60 NQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHW-VPLTLLWEAMD 137 (439)
Q Consensus 60 d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLILDVARfKYPP~W-Vpl~~L~eAM~ 137 (439)
+..+-+-..+-++.++-+++.|- -|-|..- =.|||=-|-|||+++|-+.+=|.|--+ |-|- +.++-+=+|-.
T Consensus 80 ~~Lhcdlceeplk~ccfspnghh--cfcrtp~---YqGHfiVi~GYd~a~~c~~~ndPA~ad-pg~c~~Sik~fEeARk 152 (167)
T KOG4621|consen 80 DKLHCDLCEEPLKSCCFSPNGHH--CFCRTPC---YQGHFIVICGYDAARDCFEINDPASAD-PGHCRISIKCFEEARK 152 (167)
T ss_pred CceehHHHHhHHHHhccCCCCcc--ccccCCc---ccccEEEEeccccccCeEEEcCcccCC-CcceeehhhHHHHHHh
Confidence 33444444455555544443321 2333221 269999999999999999999998644 4444 55665555543
No 33
>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=42.61 E-value=19 Score=31.05 Aligned_cols=42 Identities=14% Similarity=0.362 Sum_probs=33.2
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
|.|. .+..|+|+++-+..-.-+-..++.|++++|+..+....
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 68899999977766556666788999999999998763
No 34
>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=42.03 E-value=19 Score=31.49 Aligned_cols=41 Identities=15% Similarity=0.251 Sum_probs=33.5
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
|+|. .+.+|+|+++-+..-.-+-..++-|+|+.|+..+...
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 35
>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=41.82 E-value=35 Score=29.98 Aligned_cols=41 Identities=10% Similarity=0.206 Sum_probs=32.2
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
|+|. .+.+|+|+++-+..=.-+-..++.|+||+|+..+...
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 36
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=41.67 E-value=13 Score=30.40 Aligned_cols=17 Identities=35% Similarity=0.456 Sum_probs=14.3
Q ss_pred CCCCchhHHHHHHHHHH
Q 013618 401 TENLPTLLQEEVLHLRR 417 (439)
Q Consensus 401 ~~~lp~~lq~evlhlr~ 417 (439)
.++|||.|+.||+|--.
T Consensus 8 fqkLPDdLKrEvldY~E 24 (65)
T COG5559 8 FQKLPDDLKREVLDYIE 24 (65)
T ss_pred HHHCcHHHHHHHHHHHH
Confidence 36899999999999654
No 37
>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=40.74 E-value=22 Score=27.49 Aligned_cols=40 Identities=15% Similarity=0.241 Sum_probs=29.6
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHH
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 47 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA 47 (439)
.|.|. .|..|+|+++-+..=.-+-..++.|+|++++..+.
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 38
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.91 E-value=20 Score=32.16 Aligned_cols=44 Identities=23% Similarity=0.462 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCC
Q 013618 63 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRD 110 (439)
Q Consensus 63 SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD 110 (439)
-++.+|+.+-+ .+..-|-||+-=...-+|.|||-|+.|=||--+
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 39
>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=39.36 E-value=22 Score=31.30 Aligned_cols=41 Identities=7% Similarity=0.136 Sum_probs=33.1
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
|.|. .+.+|+|+++-+..-.-+-..++-|+|++|+..+...
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 5789999998887666666778999999999998864
No 40
>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=37.42 E-value=53 Score=28.09 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=31.0
Q ss_pred cccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 11 LSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 11 ~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.-.+.+|+|+++-+..=.-+-..++.|+||+|+..+...
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 346789999997776555556678899999999998875
No 41
>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=36.84 E-value=16 Score=31.58 Aligned_cols=45 Identities=22% Similarity=0.384 Sum_probs=26.8
Q ss_pred hHHHHHcCCcHH------HHHHHHHhcCCeEEEEec----CCCCHHHHHHHHHHH
Q 013618 30 LEKVKEKGISFG------KLVCLAHCAGAKVEAFRT----NQSTIDDFRKYIIRC 74 (439)
Q Consensus 30 le~Vk~~GITL~------e~~cLA~CnG~~Vq~~r~----d~~SldeFR~~V~~~ 74 (439)
+...++.||+.+ .+..+|+.||++.+.++. .-.|+++||+.++.-
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 455678888874 566888888887765553 446899999998863
No 42
>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=36.01 E-value=26 Score=31.23 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=33.4
Q ss_pred CCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcCCeEEEEe
Q 013618 6 KARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFR 58 (439)
Q Consensus 6 ~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG~~Vq~~r 58 (439)
..+.++|+.==--+-.++| .-++|.+.|++=+-|..||.-..+++..+.
T Consensus 16 ~~~~~LW~~L~~~lPDSlL----~n~ei~~~GLSTDhltaLa~~~~~~~~~hs 64 (104)
T PF05381_consen 16 ISPETLWATLCEILPDSLL----DNPEIRTLGLSTDHLTALAYRYHFQCTFHS 64 (104)
T ss_pred CCHHHHHHHHHHhCchhhc----CchhhhhcCCcHHHHHHHHHHHheEEEEEc
Confidence 3455666642222223344 456799999999999999999999985433
No 43
>COG5565 Bacteriophage terminase large (ATPase) subunit and inactivated derivatives [General function prediction only]
Probab=35.81 E-value=20 Score=30.39 Aligned_cols=38 Identities=29% Similarity=0.508 Sum_probs=27.9
Q ss_pred CcccC---cccccccccccccCChHHHHHcCCcHHHHHHHHHhcCCeEEEEe
Q 013618 10 TLSGR---PWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFR 58 (439)
Q Consensus 10 r~WKG---pWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG~~Vq~~r 58 (439)
+.|.+ -|-|||| .|.+.|-.+|||..+ +-.|+.+.+|-
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 44
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=35.59 E-value=49 Score=30.33 Aligned_cols=44 Identities=23% Similarity=0.532 Sum_probs=32.4
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhhhhhccCCCCCHHHHHHHHHhcC
Q 013618 156 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSL 206 (439)
Q Consensus 156 ~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~ll~~~~~~~~~~vl~~v~~sl 206 (439)
-..|+.+.|++| +..|.++.+.+.+ ..++..|-+.++..+|..-
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 357999999999 8999999999763 3455556666666665543
No 45
>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=35.53 E-value=26 Score=31.55 Aligned_cols=42 Identities=12% Similarity=0.095 Sum_probs=33.7
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|.|. .|..|.|+++-+..-.-+...++.|+|++|+..+...
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 6779999998888766667788999999999998764
No 46
>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=34.73 E-value=61 Score=29.02 Aligned_cols=41 Identities=12% Similarity=0.170 Sum_probs=32.7
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|. .+.+|.|+++-+..=.-+-..++.|+||+|+..+..+.
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 68899999988875555556788999999999998753
No 47
>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=34.32 E-value=28 Score=29.21 Aligned_cols=38 Identities=11% Similarity=0.135 Sum_probs=32.6
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|.+|.|+++-+..-.-+-..++.|++++|+..+....
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 67899999988887777777889999999999998653
No 48
>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=33.92 E-value=24 Score=31.16 Aligned_cols=39 Identities=26% Similarity=0.353 Sum_probs=29.6
Q ss_pred HHcCCcHHHHHHHHHhcCCeEEEEec-----CCCCHHHHHHHHH
Q 013618 34 KEKGISFGKLVCLAHCAGAKVEAFRT-----NQSTIDDFRKYII 72 (439)
Q Consensus 34 k~~GITL~e~~cLA~CnG~~Vq~~r~-----d~~SldeFR~~V~ 72 (439)
.--|.||+.+..+-..+-...+.|++ ..+|.++-|-...
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 44699999999999888777777775 4578887665544
No 49
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=33.59 E-value=62 Score=29.12 Aligned_cols=37 Identities=16% Similarity=0.254 Sum_probs=30.6
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.+.+|+|+++-+..=.-+-..++.|+++.|+..+...
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 7789999997776555556678899999999999875
No 50
>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=33.50 E-value=1.8e+02 Score=32.07 Aligned_cols=82 Identities=15% Similarity=0.035 Sum_probs=54.4
Q ss_pred CChHHHHH--cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccc
Q 013618 28 EPLEKVKE--KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGY 105 (439)
Q Consensus 28 ~ple~Vk~--~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGY 105 (439)
.+++.+++ .| ++..+...|+..|++++.++.+ ++++.+. .-..|+..+ +.|||=-+-++
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 34555554 48 9999999999999999999874 3333221 123444332 35787666554
Q ss_pred cCCCCeEEEEecCCCCCCceeeehhHH
Q 013618 106 HAGRDMALILDVARFKYPPHWVPLTLL 132 (439)
Q Consensus 106 h~~sD~VLILDVARfKYPP~WVpl~~L 132 (439)
+.+.+.|+|+|. =++.|++.+++
T Consensus 80 --~~~~~~i~dP~~--g~~~~~~~~e~ 102 (686)
T TIGR03797 80 --SRGGYEIFDPAT--GTRRRVDAAMA 102 (686)
T ss_pred --cCCEEEEECCCC--CCCcccCHHHH
Confidence 567899999975 22448888886
No 51
>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=33.36 E-value=22 Score=30.15 Aligned_cols=36 Identities=14% Similarity=0.288 Sum_probs=29.6
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHH
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 48 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~ 48 (439)
.+..|+|+|+-+..-.-+-..++.|++++|+..+..
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 488999999888766666678889999999887653
No 52
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.24 E-value=18 Score=27.65 Aligned_cols=42 Identities=12% Similarity=0.305 Sum_probs=29.9
Q ss_pred CCCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHH
Q 013618 6 KARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 48 (439)
Q Consensus 6 ~~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~ 48 (439)
+.|.+. .+.+|.|+++=+..-.-+...++.|+|++++..+.+
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 53
>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=33.18 E-value=29 Score=30.68 Aligned_cols=43 Identities=14% Similarity=0.133 Sum_probs=33.4
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
|.|.=.+.+|.|+++-+..=.-+-..++.|+||+|+..+....
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 4443337899999988876666667889999999999998753
No 54
>PTZ00445 p36-lilke protein; Provisional
Probab=32.14 E-value=1.5e+02 Score=29.68 Aligned_cols=99 Identities=18% Similarity=0.144 Sum_probs=60.8
Q ss_pred HHHHHHHHhcCCeEEEEecCC-------------C---------CHHHHHHHHHHHhcCCCcEEEEEecccccccCCCcc
Q 013618 41 GKLVCLAHCAGAKVEAFRTNQ-------------S---------TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGH 98 (439)
Q Consensus 41 ~e~~cLA~CnG~~Vq~~r~d~-------------~---------SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GH 98 (439)
+.|+.+.+..|+++.+..-|. . --++|+..+.++....=...||-|+.+.. -.+.+|
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 468888999999987765321 1 24579998888766666789999999987 223344
Q ss_pred cccccc-------ccCCCCeEEEEecCCCCCCceeeehhHHHHhccccCCC
Q 013618 99 FSPIGG-------YHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDA 142 (439)
Q Consensus 99 FSPIGG-------Yh~~sD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~ 142 (439)
=.=|.| -....=.+.|--| .-.||++|=. +..|.+|..+=|+
T Consensus 111 ~~~Isg~~li~~~lk~s~~~~~i~~~-~~yyp~~w~~-p~~y~~~gl~KPd 159 (219)
T PTZ00445 111 PRYISGDRMVEAALKKSKCDFKIKKV-YAYYPKFWQE-PSDYRPLGLDAPM 159 (219)
T ss_pred cceechHHHHHHHHHhcCccceeeee-eeeCCcccCC-hhhhhhhcccCCC
Confidence 333321 1111223333333 2379999944 3447777665553
No 55
>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=31.97 E-value=2.9e+02 Score=22.72 Aligned_cols=64 Identities=13% Similarity=0.152 Sum_probs=42.4
Q ss_pred EEEEecCCCCHHHHHHHHHHHhcCCCcEEEEE-ecccccccC---CCccccccccccCCCC-eEEEEecCC
Q 013618 54 VEAFRTNQSTIDDFRKYIIRCSASEDCHVISS-YHRGAFKQT---GTGHFSPIGGYHAGRD-MALILDVAR 119 (439)
Q Consensus 54 Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVn-Y~R~~LgQt---G~GHFSPIGGYh~~sD-~VLILDVAR 119 (439)
.+.......|+.++++.+...+..+-..+-+. |+.+ ++. =+....++|.|..+.+ .++|.|..+
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 44445567899999999988765544444444 5544 222 2456669999999886 577777654
No 56
>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=31.95 E-value=32 Score=30.08 Aligned_cols=40 Identities=13% Similarity=0.031 Sum_probs=31.5
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
|.|. +.+|.|+++-+..=.-+-..+..|+|++++..+...
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 589999998877555556688899999999998875
No 57
>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=31.47 E-value=37 Score=28.53 Aligned_cols=43 Identities=14% Similarity=0.227 Sum_probs=32.3
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|.+.=.|.+|+|+++-+..=.-+-..++.|++++|+..+...
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 3444334779999997776554556678899999999998875
No 58
>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=30.68 E-value=27 Score=26.88 Aligned_cols=35 Identities=14% Similarity=0.346 Sum_probs=28.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHH
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 47 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA 47 (439)
.|..|.|+++-+..-.-+-..++.|+|++|+..+.
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 67899999987776666677888999999987654
No 59
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=30.61 E-value=60 Score=35.77 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=44.3
Q ss_pred CCccccccccccCCCCeEEEEecCCCCCCceeeehhHHHHhcc--------ccCCCCCceeeEEEEeCC
Q 013618 95 GTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMD--------RVDDATGQRRGFVLVSRP 155 (439)
Q Consensus 95 G~GHFSPIGGYh~~sD~VLILDVARfKYPP~WVpl~~L~eAM~--------tiD~~TgrsRG~lllsk~ 155 (439)
|.|-|||-|.--+...+|.|-.. -|---|++|++|++... -.|. +||+||.-++.=.
T Consensus 30 G~~~gs~~gn~~~r~R~vfItNI---pyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk 94 (608)
T KOG4212|consen 30 GNGAGSQGGNVAARDRSVFITNI---PYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFK 94 (608)
T ss_pred cccccCCCCCcccccceEEEecC---cchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEee
Confidence 89999998877666666988755 45557999999998653 2455 8999999999843
No 60
>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=30.25 E-value=90 Score=26.15 Aligned_cols=86 Identities=13% Similarity=0.138 Sum_probs=57.4
Q ss_pred CcHHHHHH-HHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCcccccc-----ccccCCCCe
Q 013618 38 ISFGKLVC-LAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPI-----GGYHAGRDM 111 (439)
Q Consensus 38 ITL~e~~c-LA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPI-----GGYh~~sD~ 111 (439)
||..||.. +|...|+.-.. -..-+++|-..|.+++...+..-+ .|-|.|++. .|.|+.+..
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 67777764 45555542211 123578888888888876654332 456777654 579999977
Q ss_pred EEEEecCCCCCCceeeehhHHHHhcccc
Q 013618 112 ALILDVARFKYPPHWVPLTLLWEAMDRV 139 (439)
Q Consensus 112 VLILDVARfKYPP~WVpl~~L~eAM~ti 139 (439)
.... +.++-+.+.|...|-+.++..
T Consensus 69 ~~~i---~~~~~v~Fkpsk~lk~~vn~~ 93 (96)
T TIGR00987 69 EIPI---TARRVVTFRPGQKLKSRVENA 93 (96)
T ss_pred EEEE---eCCccEEEeeCHHHHHHHhcc
Confidence 6654 246679999999998888763
No 61
>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=29.55 E-value=90 Score=27.42 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCC
Q 013618 42 KLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASED 79 (439)
Q Consensus 42 e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d 79 (439)
.+..+|+..|+... +.+..+.++|++.++++...+.
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 5555678999999999985444
No 62
>PRK13749 transcriptional regulator MerD; Provisional
Probab=29.33 E-value=41 Score=30.14 Aligned_cols=40 Identities=23% Similarity=0.262 Sum_probs=31.6
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcCC
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGA 52 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG~ 52 (439)
.|.+|+|+|.-+..=.-+-..+.-|++++|+..|......
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 5899999997776544555566899999999999987543
No 63
>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=29.21 E-value=89 Score=26.43 Aligned_cols=51 Identities=4% Similarity=0.110 Sum_probs=37.1
Q ss_pred cCcccccccccccccCChHHHHH-cCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHH
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKE-KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYII 72 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~-~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~ 72 (439)
++..|+|++.-+..-.-+-..++ -|++++++..+... .++.++.+=++.+.
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 45568999988887766666776 69999999998876 33456665555554
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=29.19 E-value=39 Score=29.96 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=32.0
Q ss_pred CCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 9 KTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 9 ~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|. .+..|+|+++-+..-.-+-..++.|++++|+..+...
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 6779999998777655566678899999999999875
No 65
>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=27.83 E-value=43 Score=31.17 Aligned_cols=44 Identities=20% Similarity=0.318 Sum_probs=33.3
Q ss_pred CCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcC
Q 013618 8 RKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (439)
Q Consensus 8 ~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG 51 (439)
|.+.=.+.||+|+++-+..-.-+-..+.-|++++++..+.....
T Consensus 29 p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 29 PSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPG 72 (172)
T ss_pred CCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 43333688999999877655566667889999999999887543
No 66
>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=26.91 E-value=2.4e+02 Score=30.28 Aligned_cols=60 Identities=18% Similarity=0.391 Sum_probs=40.2
Q ss_pred CcccccccccccccCChHHHHHcCCc-------------------HHHHHHHHHhcCCeEEEEecC-------------C
Q 013618 14 RPWRWFDESMLDCCEPLEKVKEKGIS-------------------FGKLVCLAHCAGAKVEAFRTN-------------Q 61 (439)
Q Consensus 14 GpWRWf~EsmLdCC~ple~Vk~~GIT-------------------L~e~~cLA~CnG~~Vq~~r~d-------------~ 61 (439)
--||||.+ +--.+|+.+++.|+| +.+.....+.+|++..+.-.- +
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 445788899988876 345556777899988775321 1
Q ss_pred CCHHHHHHHHHHHhc
Q 013618 62 STIDDFRKYIIRCSA 76 (439)
Q Consensus 62 ~SldeFR~~V~~~~s 76 (439)
.-++.+.+.|+...+
T Consensus 80 ~~Ienyk~~irNla~ 94 (394)
T TIGR00695 80 RWIENYKQTLRNLAQ 94 (394)
T ss_pred HHHHHHHHHHHHHHH
Confidence 246666666665543
No 67
>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=26.75 E-value=47 Score=28.34 Aligned_cols=39 Identities=8% Similarity=0.319 Sum_probs=31.4
Q ss_pred cCcccccccccccccCChHHHHHcCCcHHHHHHHHHhcC
Q 013618 13 GRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 51 (439)
Q Consensus 13 KGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~CnG 51 (439)
.+.+|+|++.-+..-.-+-..++.|++++++..+.....
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 368999999777655566667889999999999988754
No 68
>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=25.97 E-value=46 Score=29.15 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=32.0
Q ss_pred ccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 12 SGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 12 WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
=.|.+|+|+++-+..-.-+-..+..|+|++|+..+....
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 357899999988876666667889999999999988753
No 69
>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=25.38 E-value=2.8e+02 Score=30.68 Aligned_cols=77 Identities=14% Similarity=0.108 Sum_probs=52.7
Q ss_pred HcCCcHHHHHHHHHhcCCeEEEEecCCCCHHHHHHHHHHHhcCCCcEEEEEecccccccCCCccccccccccCCCCeEEE
Q 013618 35 EKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALI 114 (439)
Q Consensus 35 ~~GITL~e~~cLA~CnG~~Vq~~r~d~~SldeFR~~V~~~~ss~d~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLI 114 (439)
+.|+++.++...|+..|++++.++.+ ++++. .-....|+.. .+||=-|-+ -+++.|.|
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 1223455533 145433433 34678999
Q ss_pred EecCCCCCCceeeehhHHHHh
Q 013618 115 LDVARFKYPPHWVPLTLLWEA 135 (439)
Q Consensus 115 LDVARfKYPP~WVpl~~L~eA 135 (439)
.|++.- .+.|++.+++.+.
T Consensus 87 ~Dp~~g--~~~~i~~~e~~~~ 105 (694)
T TIGR01846 87 YDPPGD--APEVLSREVLEAL 105 (694)
T ss_pred EcCCCC--CceeeCHHHHHhh
Confidence 999642 5789999887643
No 70
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.92 E-value=72 Score=26.92 Aligned_cols=31 Identities=32% Similarity=0.488 Sum_probs=24.4
Q ss_pred eeecccCCCCCCHHH-----HhHhhhHHHHHHHHhc
Q 013618 220 VRRREDGDHSLSQEE-----KGRLALKEEVLRQVQE 250 (439)
Q Consensus 220 vr~~e~~~~~ls~ee-----k~rl~~k~~vl~qi~~ 250 (439)
+.+.|.|.+++|.+| |+||.+|.++.+-++.
T Consensus 33 I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~L~~ 68 (72)
T COG2841 33 IKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASILQK 68 (72)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 446777888888875 8999999998877654
No 71
>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional
Probab=24.18 E-value=2.4e+02 Score=28.54 Aligned_cols=56 Identities=27% Similarity=0.480 Sum_probs=37.1
Q ss_pred EecCCCCHHHHHHHHHHHhcCCCc---EEEEEecccccccCCCccccccccccCCCCeEEEEecCCCCCCceeee
Q 013618 57 FRTNQSTIDDFRKYIIRCSASEDC---HVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVP 128 (439)
Q Consensus 57 ~r~d~~SldeFR~~V~~~~ss~d~---~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLILDVARfKYPP~WVp 128 (439)
..++..+.++.++.|.+....... ..|.||.=|. |. |.-| | +|+|| ||==-|||+|
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 355667899999998876543222 4555553321 32 5533 4 89999 8998999998
No 72
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), 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- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=23.24 E-value=44 Score=25.40 Aligned_cols=34 Identities=15% Similarity=0.307 Sum_probs=24.1
Q ss_pred CcccccccccccccCChHHHHHcCCcHHHHHHHH
Q 013618 14 RPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 47 (439)
Q Consensus 14 GpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA 47 (439)
+..|+|+++=+..=.-+-..++.|||++|+..++
T Consensus 34 ~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 34 GGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3558898855554445556777999999988764
No 73
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=23.09 E-value=61 Score=27.81 Aligned_cols=43 Identities=9% Similarity=0.163 Sum_probs=34.4
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHh
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 49 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~C 49 (439)
.|.+.-.+..|.|+++-+..=.-+-..++.|++++++..+...
T Consensus 27 ~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 27 SPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 3556666889999997776555666778899999999999876
No 74
>PF14430 Imm1: Immunity protein Imm1
Probab=22.12 E-value=1.9e+02 Score=25.40 Aligned_cols=55 Identities=18% Similarity=0.181 Sum_probs=36.8
Q ss_pred cEEEEEecccccccCCCccccccccccCCCCeEEEEecCCCCCCcee-eehhHHHHhccccC
Q 013618 80 CHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHW-VPLTLLWEAMDRVD 140 (439)
Q Consensus 80 ~~lIVnY~R~~LgQtG~GHFSPIGGYh~~sD~VLILDVARfKYPP~W-Vpl~~L~eAM~tiD 140 (439)
.+..++|.. .+.|+|+-.++.- ..+....+++..--||+.| ||++..++|+...=
T Consensus 58 ~~g~l~~~~-----~d~~~~~~~~~~~-~~~~~~~~~~~~~e~Pa~~~vpl~~~~~A~~eF~ 113 (127)
T PF14430_consen 58 DYGVLHYFG-----DDDGFWSSGDPNP-PGDVEYDLNNGGTEFPADSEVPLETARQALREFL 113 (127)
T ss_pred CEEEEEEEe-----CCCCeEecCCCCC-CCceeEEecCCCcccCCCceecHHHHHHHHHHHH
Confidence 345555555 3346665554444 4456666666666799999 99999999997643
No 75
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=22.01 E-value=97 Score=30.72 Aligned_cols=72 Identities=17% Similarity=0.336 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHhcCCcc----------hhhHHhhheeeeecccCCCCCCHHHHhHhhhHHHHHHHHhc----------
Q 013618 191 DFKDFEEVLTVLFTSLPSN----------FGEFVKWVAEVRRREDGDHSLSQEEKGRLALKEEVLRQVQE---------- 250 (439)
Q Consensus 191 ~~~~~~~vl~~v~~slP~~----------~~~~ikwv~evr~~e~~~~~ls~eek~rl~~k~~vl~qi~~---------- 250 (439)
.-.++..++..++.+|.+. ...|=+|+.+.+ .+||.|+++||.--.+++++|..
T Consensus 120 ~~~~~~~~l~~mm~qL~SKevLYePmKel~~kyP~wL~~n~------~~l~~ed~~rY~~Q~~~v~~I~~~fE~~~~~d~ 193 (248)
T PF04614_consen 120 GDEDFDKMLQGMMQQLLSKEVLYEPMKELRDKYPEWLEENK------SKLSAEDYERYEKQYELVKEICAIFEKPPYDDE 193 (248)
T ss_dssp -----HHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHC------CCS-HHHHHHHHHHHHHHHHHHHHHHH--TT--
T ss_pred CchhHHHHHHHHHHHhccHhhhhhhHHHHHHHhHHHHHhCc------CcCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence 3345555555555555432 235779988555 59999999999877777777642
Q ss_pred -cchhHHHHHhhhcccccc
Q 013618 251 -TLLFKHVVTFLSSVNSCC 268 (439)
Q Consensus 251 -t~lf~~v~~~~~s~~~~~ 268 (439)
..-|..|.+++..-+.|-
T Consensus 194 ~~~~~~~i~~lmqemQ~~G 212 (248)
T PF04614_consen 194 DPERREKIMELMQEMQELG 212 (248)
T ss_dssp HHHHHHHHHHHHHHHHHT-
T ss_pred cHHHHHHHHHHHHHHHHcC
Confidence 235677777777666654
No 76
>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=21.98 E-value=1.4e+02 Score=29.02 Aligned_cols=61 Identities=20% Similarity=0.319 Sum_probs=40.6
Q ss_pred HHHHHHHHHhcCCeEEEEecCC------------------CCHHHHHHHHHHHhcCCCcEEEEEeccccc-ccCCCc---
Q 013618 40 FGKLVCLAHCAGAKVEAFRTNQ------------------STIDDFRKYIIRCSASEDCHVISSYHRGAF-KQTGTG--- 97 (439)
Q Consensus 40 L~e~~cLA~CnG~~Vq~~r~d~------------------~SldeFR~~V~~~~ss~d~~lIVnY~R~~L-gQtG~G--- 97 (439)
++++...+...|+.|+.+|... ..+-.||..|++....- -+.++|.=|.+ ++.|.|
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 3577778888999999988632 14557999999876544 58999999986 777866
Q ss_pred ccccc
Q 013618 98 HFSPI 102 (439)
Q Consensus 98 HFSPI 102 (439)
|+|-.
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 77
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=21.42 E-value=5.5e+02 Score=27.56 Aligned_cols=153 Identities=19% Similarity=0.298 Sum_probs=78.3
Q ss_pred CcccccccccccccCChHHHHHcCCc-------------------HHHHHHHHHhcCCeEEEEecCC-------------
Q 013618 14 RPWRWFDESMLDCCEPLEKVKEKGIS-------------------FGKLVCLAHCAGAKVEAFRTNQ------------- 61 (439)
Q Consensus 14 GpWRWf~EsmLdCC~ple~Vk~~GIT-------------------L~e~~cLA~CnG~~Vq~~r~d~------------- 61 (439)
--||||-.+ -=++++.|++.|++ +.++....+.+|+.-.+.-..+
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 QTWRWYGPN---DPVTLEDIRQAGVKGVVTALHHIPAGEVWPVEEILKRKEEIESAGLTWSVVESVPVHEDIKLGTPTRD 79 (362)
T ss_pred eeEEEecCC---CCccHHHHHHhCccceeccCCCCCCCCcCcHHHHHHHHHHHHHcCceEEeecCCCHHHHHHhcCCcHH
Confidence 359999882 23678889887775 2345566778999776654322
Q ss_pred CCHHHHHHHHHHHhcCCCcE-----E-EEEecccccccC-CCccccccccccCCCCeEEEEecCCCC-CCce------ee
Q 013618 62 STIDDFRKYIIRCSASEDCH-----V-ISSYHRGAFKQT-GTGHFSPIGGYHAGRDMALILDVARFK-YPPH------WV 127 (439)
Q Consensus 62 ~SldeFR~~V~~~~ss~d~~-----l-IVnY~R~~LgQt-G~GHFSPIGGYh~~sD~VLILDVARfK-YPP~------WV 127 (439)
--++.+.+.|+...+..=+. | |+...|.-|.-. ++|- .+|-+|-+.|. |++| =+
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 24566666666554333222 2 333456666332 3332 45555555554 4444 24
Q ss_pred ehhHHHHhccccCCCCCceeeEEEEeCCCCCCCcceeeeccCCChHHHHHHHHhhhhhh
Q 013618 128 PLTLLWEAMDRVDDATGQRRGFVLVSRPHREPGLLYTLSCKHENWVGIAKYLVDEVPKI 186 (439)
Q Consensus 128 pl~~L~eAM~tiD~~TgrsRG~lllsk~~~~ps~l~~ls~~~~~w~~~ak~l~~d~p~l 186 (439)
..+..+++|..+ | |-..||-+=+-+. ---.|.---....|.+++-||.+-+|.-
T Consensus 148 ~~~~~~~~m~gl-P--G~~~~~tl~~~~~--~~~~y~~Id~~~L~~nL~yFL~~ViPVA 201 (362)
T COG1312 148 RAEERFAEMSGL-P--GWEEGYTLDQFRE--LLELYGGIDEEKLWENLAYFLKEVIPVA 201 (362)
T ss_pred HHHHhhhcccCC-C--CCcccccHHHHHH--HHHHhcCCCHHHHHHHHHHHHHhhcchH
Confidence 455555555400 0 0001110000000 0001111113468999998888877753
No 78
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=20.78 E-value=71 Score=28.51 Aligned_cols=44 Identities=20% Similarity=0.266 Sum_probs=33.9
Q ss_pred CCCCcccCcccccccccccccCChHHHHHcCCcHHHHHHHHHhc
Q 013618 7 ARKTLSGRPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 50 (439)
Q Consensus 7 ~~~r~WKGpWRWf~EsmLdCC~ple~Vk~~GITL~e~~cLA~Cn 50 (439)
.|.+.=.+..|+|+++-+..=.-+-..+.-|++++++..+....
T Consensus 30 ~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~~ 73 (120)
T TIGR02054 30 HPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRAL 73 (120)
T ss_pred CCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 34444568899999987776555666778999999999988753
No 79
>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=20.17 E-value=1.6e+02 Score=31.71 Aligned_cols=61 Identities=15% Similarity=0.224 Sum_probs=45.6
Q ss_pred HHHHHHHHHhcCCeEEEEecCC------------------CCHHHHHHHHHHHhcCCCcEEEEEeccccc-ccCCCc---
Q 013618 40 FGKLVCLAHCAGAKVEAFRTNQ------------------STIDDFRKYIIRCSASEDCHVISSYHRGAF-KQTGTG--- 97 (439)
Q Consensus 40 L~e~~cLA~CnG~~Vq~~r~d~------------------~SldeFR~~V~~~~ss~d~~lIVnY~R~~L-gQtG~G--- 97 (439)
++++...+...|+.++.+|... -.+=-||..|++..+.- .++++|-=|.+ |+.|.|
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 3577888889999999988631 13346899999876443 68999998886 778877
Q ss_pred ccccc
Q 013618 98 HFSPI 102 (439)
Q Consensus 98 HFSPI 102 (439)
|+|-.
T Consensus 263 H~Sl~ 267 (460)
T TIGR00653 263 HQSLW 267 (460)
T ss_pred EECcc
Confidence 77765
Done!