Query 011053
Match_columns 494
No_of_seqs 142 out of 192
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:35:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011053hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0632 Phytochelatin synthase 100.0 2E-120 4E-125 899.1 18.2 388 1-477 1-388 (388)
2 PF09328 Phytochelatin_C: Doma 100.0 4E-111 8E-116 819.1 24.7 264 220-484 1-264 (264)
3 PF05023 Phytochelatin: Phytoc 100.0 1.9E-81 4.1E-86 602.5 15.7 211 3-217 1-212 (212)
4 PF13529 Peptidase_C39_2: Pept 98.8 1E-08 2.2E-13 87.3 7.2 117 51-182 11-144 (144)
5 cd02549 Peptidase_C39A A sub-f 98.4 1.9E-06 4.2E-11 74.8 10.4 129 50-201 1-131 (141)
6 PF03412 Peptidase_C39: Peptid 98.3 2.9E-06 6.3E-11 73.4 7.5 117 47-201 4-120 (131)
7 cd02418 Peptidase_C39B A sub-f 97.9 0.00017 3.6E-09 62.4 12.2 122 47-200 3-124 (136)
8 cd02259 Peptidase_C39_like Pep 97.8 0.0002 4.4E-09 60.4 9.8 115 50-201 1-115 (122)
9 cd02424 Peptidase_C39E A sub-f 97.7 0.00015 3.3E-09 63.3 7.9 118 48-200 4-122 (129)
10 PF14399 Transpep_BrtH: NlpC/p 97.6 0.0017 3.6E-08 64.5 14.9 151 55-214 1-163 (317)
11 cd02420 Peptidase_C39D A sub-f 97.6 0.00097 2.1E-08 57.2 10.8 113 50-200 6-118 (125)
12 cd02423 Peptidase_C39G A sub-f 97.5 0.0011 2.4E-08 56.8 10.0 116 50-200 6-122 (129)
13 cd02425 Peptidase_C39F A sub-f 97.4 0.0026 5.5E-08 54.3 10.8 116 47-199 3-118 (126)
14 TIGR03796 NHPM_micro_ABC1 NHPM 97.4 0.0017 3.7E-08 72.0 12.3 114 47-198 4-117 (710)
15 cd02419 Peptidase_C39C A sub-f 97.1 0.012 2.6E-07 50.5 12.4 115 49-201 5-119 (127)
16 TIGR01193 bacteriocin_ABC ABC- 97.1 0.006 1.3E-07 67.8 12.8 120 50-199 1-120 (708)
17 PF11814 DUF3335: Peptidase_C3 96.9 0.019 4.1E-07 56.5 13.0 84 126-218 117-207 (207)
18 PF09778 Guanylate_cyc_2: Guan 95.5 0.038 8.3E-07 54.6 7.2 85 107-200 95-199 (212)
19 cd02417 Peptidase_C39_likeA A 94.0 1 2.2E-05 38.3 11.2 111 54-201 5-115 (121)
20 TIGR03375 type_I_sec_LssB type 93.2 0.51 1.1E-05 52.7 10.2 103 58-198 2-107 (694)
21 COG2274 SunT ABC-type bacterio 92.8 0.48 1E-05 54.2 9.4 117 46-200 3-119 (709)
22 cd02421 Peptidase_C39_likeD A 92.7 3.4 7.4E-05 35.3 12.4 109 56-200 7-115 (124)
23 TIGR01846 type_I_sec_HlyB type 91.1 1.4 3E-05 49.3 10.5 105 57-199 1-105 (694)
24 COG3271 Predicted double-glyci 87.0 0.85 1.8E-05 45.0 4.5 102 49-182 37-139 (201)
25 TIGR03797 NHPM_micro_ABC2 NHPM 85.9 4.3 9.4E-05 45.4 9.8 100 58-198 5-104 (686)
26 PF12385 Peptidase_C70: Papain 70.8 32 0.0007 33.3 9.1 138 43-200 22-161 (166)
27 KOG4621 Uncharacterized conser 56.4 43 0.00093 31.8 6.9 95 102-201 57-152 (167)
28 TIGR02044 CueR Cu(I)-responsiv 47.7 16 0.00034 32.8 2.6 42 72-113 28-69 (127)
29 cd04770 HTH_HMRTR Helix-Turn-H 47.0 18 0.00038 31.9 2.8 38 77-114 33-70 (123)
30 cd04768 HTH_BmrR-like Helix-Tu 44.8 17 0.00038 31.0 2.3 42 72-113 28-69 (96)
31 cd04787 HTH_HMRTR_unk Helix-Tu 44.4 18 0.00038 32.7 2.4 43 72-114 28-70 (133)
32 PF05381 Peptidase_C21: Tymovi 43.6 14 0.00031 33.2 1.7 55 62-120 8-62 (104)
33 PRK13752 putative transcriptio 43.1 19 0.00042 33.4 2.5 43 72-114 35-77 (144)
34 cd04784 HTH_CadR-PbrR Helix-Tu 43.1 20 0.00043 31.9 2.5 37 77-113 33-69 (127)
35 cd04785 HTH_CadR-PbrR-like Hel 43.0 21 0.00045 32.0 2.6 43 72-114 28-70 (126)
36 cd04763 HTH_MlrA-like Helix-Tu 42.7 41 0.00089 26.5 4.0 44 68-111 24-67 (68)
37 TIGR02047 CadR-PbrR Cd(II)/Pb( 42.6 22 0.00047 32.0 2.7 42 72-113 28-69 (127)
38 cd04788 HTH_NolA-AlbR Helix-Tu 42.1 20 0.00044 30.6 2.3 43 72-114 28-70 (96)
39 PRK10227 DNA-binding transcrip 41.8 22 0.00048 32.6 2.7 42 72-113 28-69 (135)
40 cd01104 HTH_MlrA-CarA Helix-Tu 40.8 47 0.001 25.7 4.1 34 78-111 34-67 (68)
41 cd04786 HTH_MerR-like_sg7 Heli 39.3 52 0.0011 30.0 4.7 43 72-114 28-70 (131)
42 COG5559 Uncharacterized conser 38.8 16 0.00034 30.3 1.0 17 466-482 8-24 (65)
43 cd01282 HTH_MerR-like_sg3 Heli 38.1 28 0.0006 30.6 2.6 42 72-114 28-69 (112)
44 PF14104 DUF4277: Domain of un 36.7 29 0.00063 31.7 2.5 51 50-108 39-89 (115)
45 cd04783 HTH_MerR1 Helix-Turn-H 36.6 28 0.00062 31.0 2.5 38 77-114 33-70 (126)
46 PF13411 MerR_1: MerR HTH fami 36.0 34 0.00073 26.7 2.5 54 58-112 14-67 (69)
47 cd01106 HTH_TipAL-Mta Helix-Tu 36.0 30 0.00064 29.7 2.4 43 72-114 28-70 (103)
48 cd04781 HTH_MerR-like_sg6 Heli 35.3 33 0.00072 30.4 2.7 39 77-115 32-70 (120)
49 PRK13749 transcriptional regul 35.1 34 0.00073 31.2 2.7 44 72-115 31-74 (121)
50 cd01108 HTH_CueR Helix-Turn-He 34.5 33 0.00071 30.8 2.5 42 72-113 28-69 (127)
51 PF05543 Peptidase_C47: Stapho 34.4 2E+02 0.0044 28.3 7.9 115 46-174 15-133 (175)
52 cd04782 HTH_BltR Helix-Turn-He 33.3 39 0.00085 28.9 2.7 42 72-113 28-69 (97)
53 TIGR02043 ZntR Zn(II)-responsi 32.8 36 0.00077 30.8 2.5 42 72-113 29-70 (131)
54 cd01109 HTH_YyaN Helix-Turn-He 32.2 42 0.00092 29.3 2.8 42 72-113 28-69 (113)
55 TIGR02051 MerR Hg(II)-responsi 32.1 36 0.00077 30.5 2.4 43 72-114 27-69 (124)
56 cd04764 HTH_MlrA-like_sg1 Heli 31.7 72 0.0016 25.0 3.8 35 77-111 32-66 (67)
57 PF14214 Helitron_like_N: Heli 31.2 76 0.0017 29.8 4.5 53 220-282 102-154 (184)
58 PRK15002 redox-sensitivie tran 30.6 78 0.0017 29.9 4.4 41 72-113 39-79 (154)
59 cd04790 HTH_Cfa-like_unk Helix 30.5 42 0.00092 31.9 2.7 43 72-114 29-71 (172)
60 PF04157 EAP30: EAP30/Vps36 fa 30.4 61 0.0013 31.7 3.9 114 37-159 35-167 (223)
61 PF14538 Raptor_N: Raptor N-te 30.2 4.8E+02 0.01 24.7 9.6 68 120-202 66-135 (154)
62 TIGR01950 SoxR redox-sensitive 28.5 47 0.001 30.8 2.5 37 77-113 33-69 (142)
63 PRK09514 zntR zinc-responsive 27.9 48 0.001 30.4 2.5 43 72-114 29-71 (140)
64 cd04765 HTH_MlrA-like_sg2 Heli 27.1 1.2E+02 0.0025 26.4 4.6 44 71-115 28-72 (99)
65 cd04780 HTH_MerR-like_sg5 Heli 27.0 1.2E+02 0.0025 26.2 4.5 56 72-136 28-84 (95)
66 cd04773 HTH_TioE_rpt2 Second H 26.7 55 0.0012 28.7 2.5 43 72-114 28-70 (108)
67 COG3323 Uncharacterized protei 24.7 51 0.0011 30.1 2.0 53 117-174 7-59 (109)
68 cd04789 HTH_Cfa Helix-Turn-Hel 24.4 63 0.0014 28.0 2.5 36 77-112 33-68 (102)
69 TIGR02054 MerD mercuric resist 24.2 62 0.0013 29.4 2.5 43 72-114 31-73 (120)
70 cd04776 HTH_GnyR Helix-Turn-He 23.3 64 0.0014 28.8 2.4 41 72-114 28-68 (118)
71 cd01107 HTH_BmrR Helix-Turn-He 22.7 74 0.0016 27.7 2.6 38 78-115 35-72 (108)
72 cd01111 HTH_MerD Helix-Turn-He 22.3 76 0.0016 27.9 2.6 46 69-114 24-70 (107)
73 cd04775 HTH_Cfa-like Helix-Tur 21.7 74 0.0016 27.5 2.4 44 69-112 25-68 (102)
74 cd01110 HTH_SoxR Helix-Turn-He 21.6 78 0.0017 29.1 2.6 41 72-113 29-69 (139)
75 COG3937 Uncharacterized conser 21.6 1.3E+02 0.0028 27.5 3.9 36 453-488 63-103 (108)
76 PF05372 Delta_lysin: Delta ly 21.0 54 0.0012 22.6 1.0 10 274-283 9-18 (25)
77 cd01105 HTH_GlnR-like Helix-Tu 20.7 90 0.002 26.3 2.6 43 72-114 29-71 (88)
78 cd01805 RAD23_N Ubiquitin-like 20.2 4.1E+02 0.0089 21.0 6.3 55 124-183 19-75 (77)
No 1
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.7e-120 Score=899.09 Aligned_cols=388 Identities=55% Similarity=0.989 Sum_probs=366.6
Q ss_pred CCccccccccCCCCCccccCChhhHHHHHHHHhcCCcccccccchhcccCCCCCcccHHHHHHHHHhcccCCCCCcCCCc
Q 011053 1 MAVAGVYRRVLPSPPAIEFASPQGKKLFIEALEGGTMEGFFKLISYYQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPW 80 (494)
Q Consensus 1 m~~~sfyrr~LP~p~~I~f~S~EGk~Lf~eAl~~g~~e~ff~La~~F~TQ~npayCGvASlamVLNAL~idP~r~wkgpw 80 (494)
|+|.+||||.||. ++|+|+|.+||++|.|||+.|+||+||.|++||+||++|||||+|||+||||||.|||+|.|||||
T Consensus 1 mt~ksfYrR~Lp~-~ci~FsS~lGK~iF~eALqkGtme~yF~Lasqf~TQ~EPAfCGL~tL~mvLNsL~vDPgr~WKgpW 79 (388)
T KOG0632|consen 1 MTMKSFYRRSLPP-PCIDFSSSLGKDIFNEALQKGTMEGYFSLASQFQTQSEPAFCGLATLSMVLNSLSVDPGRKWKGPW 79 (388)
T ss_pred CchhhhhccCCCc-hhhhhhhHhhHHHHHHHHHhcchhHHHHHHHHHhccCCcchhhhHHHHHHHHhhccCCcccccCCc
Confidence 8999999999985 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEeecccccccCC
Q 011053 81 RWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGT 160 (494)
Q Consensus 81 rwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~ 160 (494)
|||||+|||||+|++.|++.||+|.+|.|||+|+|++|+++|.+++++|+||..++.|..++|+++|.+|+|++|||||+
T Consensus 80 RwydesMLdCC~pLe~ikk~Gisl~~fsCLA~cnglk~~~~~~s~~t~d~FRk~vv~cstsen~~mi~sy~R~VlgQTGt 159 (388)
T KOG0632|consen 80 RWYDESMLDCCEPLEDIKKKGISLGKFSCLAHCNGLKVEAFRTSQSTIDDFRKDVVKCSTSENCHMISSYHRKVLGQTGT 159 (388)
T ss_pred hhhhhHHHhhcccHHHHHhcCcchheeehhhhcCCceeEEEecCcchHHHHHHHHHhcccccceeeehHhHHHHhcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhcccCCcCCCceeEEEEecCCCCCCcceeeeecCCChHHHH
Q 011053 161 GHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMDTIDNATGHRRGFMTVSRIPKAPSILYTVSCRHEGWNKVA 240 (494)
Q Consensus 161 GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~tiD~~sgrsRG~ilis~~~~~p~~l~~~~~~~~~w~~~~ 240 (494)
||||||||||+++|++||||||||||||||||++.||+||..||.+||++||||+|++++++|+ +||++|++++|..++
T Consensus 160 GHFSPiggy~e~~d~~LIlDVARFKYPphWV~Lkll~eam~siD~stg~pRG~~li~~~h~~~g-l~tl~lkk~sw~~i~ 238 (388)
T KOG0632|consen 160 GHFSPIGGYNEERDMALILDVARFKYPPHWVPLKLLWEAMDSIDQSTGQPRGFMLISRPHREPG-LYTLSLKKESWINIA 238 (388)
T ss_pred CccCcccccCcccCceEEeehhhccCCCcceeHHHHHHHhcchhhccCCCccceecccCCCCCc-eEEEEeccccHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred HHHHhhccccccCCCCCCHHHHHHHHHhcCchhHHHHHHhhheeeecccCCCCCCHHHHhhhhhHHHHHHHhccCchhHH
Q 011053 241 KYLTEDVPLRLKSDDVKSVENLLSVIFKSAPADLKEFIKWVAEVRRQEDGSMILSEEEKGRLVMKEEVLKQTRETELFKY 320 (494)
Q Consensus 241 ~~~~~~~p~l~~~~~~~~~~~v~~~~~~~~p~~~~~~i~w~~evr~~e~~~~~ls~e~~~~l~~k~~~l~q~~~t~l~~~ 320 (494)
|||.+|+|. |.++.|.++|.+++.|| |+|+|+.||.+++++.|| +|+.++
T Consensus 239 k~lk~~v~~------------i~~~dfas~~~s~NQf~--~~~i~~~~d~~q~~~~E~-----fk~c~r----------- 288 (388)
T KOG0632|consen 239 KYLKEDVPR------------IKNVDFASLPLSFNQFI--IAEIRETEDSNQNLSFEE-----FKQCIR----------- 288 (388)
T ss_pred HHHHHhhhh------------hhhhHHHhcchhHHHHH--HHHHHhhcCcccccCHHH-----HHHHHH-----------
Confidence 999999987 66677999999999999 999999999999999998 444333
Q ss_pred HHHhhhcccccccCCccCCCCCChHHHHHHhhhhhhhhhhccCCCCCCceeccccceeeeecCCCceEEEeeeEEeCCcc
Q 011053 321 VAKWSASKISLCKGVTSWGLKETLPELAADICCQGAELFMGKLSSSEGTCCRQTNVTLLKVDDEKAMTVVSGTVTTDGIE 400 (494)
Q Consensus 321 v~~~~~s~~~~~~~~~~~~~~~~l~~~a~~~ccqga~~l~g~~~~~~~~c~~~t~~~~~~~~~~~~~~~~s~~~~~~~~e 400 (494)
++ .+.++ -+++.+||+|+++++|. .+..+||++||++|.|.-++.-.|++
T Consensus 289 -----st----------~~y~~---f~~h~~~c~~~e~~s~~--~~~~~~c~~~~~ac~kg~~e~~~t~~---------- 338 (388)
T KOG0632|consen 289 -----ST----------VTYED---FAAHKNCCTGVEILSGA--FSAEFCCPETCVACIKGVLEEIQTVV---------- 338 (388)
T ss_pred -----hh----------hhHHh---hhhhhcccccceeecCC--cccccccHHHHHHhhhchhhhhhhee----------
Confidence 11 23333 56899999999999997 68899999999999998666655555
Q ss_pred ceeeeeecccccccccccCCCCCCccccCCCchhHHHHHHHhcCcCccCCCCchHHHHHHHhhhccCCCChhHHHHH
Q 011053 401 KEIETLVPSSITELSNLCDFDQSNCKGMHPSTADVLTVLLLALPQHTWSGIKEEELRMQFNHLASVDKLPSLLQQEV 477 (494)
Q Consensus 401 ~~~d~l~p~~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~e~~~l~s~~~lp~~l~~ev 477 (494)
.+|+.+||.|+|||||||+||+||||..|..|+.++.+.-+.|.++|.||
T Consensus 339 ---------------------------aev~~s~v~taLllAlp~q~~~~~k~dsl~~~~k~~~~~~S~~t~~~~~~ 388 (388)
T KOG0632|consen 339 ---------------------------AEVEGSDVFTALLLALPPQTWSGIKDDSLTHEMKQLISMCSSPTLLQTEV 388 (388)
T ss_pred ---------------------------eecccchHHHHHHHhcCcccccccccHHHHHHHHHHHhhcccHhhhhccC
Confidence 47899999999999999999999999999999999999999999999985
No 2
>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=3.9e-111 Score=819.05 Aligned_cols=264 Identities=58% Similarity=0.929 Sum_probs=261.8
Q ss_pred CCCCCcceeeeecCCChHHHHHHHHhhccccccCCCCCCHHHHHHHHHhcCchhHHHHHHhhheeeecccCCCCCCHHHH
Q 011053 220 PKAPSILYTVSCRHEGWNKVAKYLTEDVPLRLKSDDVKSVENLLSVIFKSAPADLKEFIKWVAEVRRQEDGSMILSEEEK 299 (494)
Q Consensus 220 ~~~p~~l~~~~~~~~~w~~~~~~~~~~~p~l~~~~~~~~~~~v~~~~~~~~p~~~~~~i~w~~evr~~e~~~~~ls~e~~ 299 (494)
+++|++|||+||+||+|.+|||||++|||.|||+++++||++|||+||+|||++|++||||||||||+|||+++||.|||
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHHHhccCchhHHHHHhhhcccccccCCccCCCCCChHHHHHHhhhhhhhhhhccCCCCCCceeccccceee
Q 011053 300 GRLVMKEEVLKQTRETELFKYVAKWSASKISLCKGVTSWGLKETLPELAADICCQGAELFMGKLSSSEGTCCRQTNVTLL 379 (494)
Q Consensus 300 ~~l~~k~~~l~q~~~t~l~~~v~~~~~s~~~~~~~~~~~~~~~~l~~~a~~~ccqga~~l~g~~~~~~~~c~~~t~~~~~ 379 (494)
+||++|++||||||+|+|||||++|+++.+|||+++++++++|+||+|||+||||||+||+|+++++++|||+|||+||+
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 eecCCCceEEEeeeEEeCCccceeeeeecccccccccccCCCCCCccccCCCchhHHHHHHHhcCcCccCCCCchHHHHH
Q 011053 380 KVDDEKAMTVVSGTVTTDGIEKEIETLVPSSITELSNLCDFDQSNCKGMHPSTADVLTVLLLALPQHTWSGIKEEELRMQ 459 (494)
Q Consensus 380 ~~~~~~~~~~~s~~~~~~~~e~~~d~l~p~~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~e 459 (494)
|+|||||+|||||+||+||+|||||||||+|+++++ +|+++.++|++|||+++||||||||||||+||+|||||+|++|
T Consensus 161 k~n~d~~~tvvsGtVv~~g~Eq~VD~LvP~s~~~~~-~c~~~~~~~~~~hPs~~DVLTvLLLALpp~TWs~Ikde~l~~E 239 (264)
T PF09328_consen 161 KANGDGPKTVVSGTVVSGGSEQGVDVLVPSSQTKTS-CCNSGSSNEIGMHPSSNDVLTVLLLALPPSTWSGIKDEKLLAE 239 (264)
T ss_pred eeCCCCceEEEeeeEEcCCCccceeEEeccccCCCC-ccCCCCCCccccCCCcccHHHHHHHhCCccccccCccHHHHHH
Confidence 999999999999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred HHhhhccCCCChhHHHHHHHHHHHH
Q 011053 460 FNHLASVDKLPSLLQQEVQHLRRQL 484 (494)
Q Consensus 460 ~~~l~s~~~lp~~l~~ev~~l~~q~ 484 (494)
|++||||||||++|||||+||||||
T Consensus 240 i~~LvSte~LP~lLQeEVlHLrrQL 264 (264)
T PF09328_consen 240 IQSLVSTENLPDLLQEEVLHLRRQL 264 (264)
T ss_pred HHHHhhhhhCcHHHHHHHHHHHhcC
Confidence 9999999999999999999999996
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=1.9e-81 Score=602.54 Aligned_cols=211 Identities=58% Similarity=1.082 Sum_probs=169.8
Q ss_pred ccccccccCCCCCccccCChhhHHHHHHHHhcCCcccccccchhcccCCCCCcccHHHHHHHHHhcccC-CCCCcCCCcc
Q 011053 3 VAGVYRRVLPSPPAIEFASPQGKKLFIEALEGGTMEGFFKLISYYQTQSEPAYCGLASLAVVLNALAID-PGRTWKGPWR 81 (494)
Q Consensus 3 ~~sfyrr~LP~p~~I~f~S~EGk~Lf~eAl~~g~~e~ff~La~~F~TQ~npayCGvASlamVLNAL~id-P~r~wkgpwr 81 (494)
+.+||+|+||+ ++|+|+|+||++||.+| ++|++||+|++||+||+|++||||||++||||||++| |++.||||||
T Consensus 1 ~~~~~~~~lp~-~~i~~~S~eG~~ll~~a---~~~~~~~~L~~~f~tQ~~~a~CGvASlamVLNAL~~d~P~~~~~~~~~ 76 (212)
T PF05023_consen 1 VQSFYRRPLPE-NLIAFSSPEGKRLLREA---GHMEDYFPLASQFVTQSNPAYCGVASLAMVLNALGIDAPGRVWKGPWR 76 (212)
T ss_dssp ----------T-TEEESSSHHHHHHHHT----SB-TTHHHHHHH----SSCCGHHHHHHHHHHHHHT------TTTTT--
T ss_pred CCccccCCCCh-hhccccCHHHHHHHHhc---CCchhHHHHHHHhccCCCCCcchHHHHHHHHHHhcccCCcccccCCcc
Confidence 47899999998 99999999999999999 8999999999999999999999999999999999999 9999999999
Q ss_pred ccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEeecccccccCCc
Q 011053 82 WFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTG 161 (494)
Q Consensus 82 wf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~G 161 (494)
||+|++++||.+++.++++||||+||+|||+|+|++|+++++++.++++||++|++++++++++|||||+|++|||+|+|
T Consensus 77 ~~tq~~l~~~~~~~~v~~~GiTL~e~~~la~~~g~~~~~~~~~~~s~~~FR~~l~~~~~~~~~~livnf~R~~lgq~G~G 156 (212)
T PF05023_consen 77 WFTQEMLDCCIPLESVKREGITLDEFACLAKCNGLRVEVYRADDSSLDEFRQHLKEALSDPNDFLIVNFDRKALGQTGGG 156 (212)
T ss_dssp ---TTTCCHHS-HHHHHHH---HHHHHHHHHTTT-EEEEEEGGGS-HHHHHHHHHHHCTSTTEEEEEEEEGGGGTSSSSE
T ss_pred eeehhhhhccccHHHHhhcCCCHHHHHHHHHhcCCceEEEeCCcCCHHHHHHHHHHHhCCCCCEEEEECcccccCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhcccCCcCCCceeEEEEe
Q 011053 162 HFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMDTIDNATGHRRGFMTVS 217 (494)
Q Consensus 162 HFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~tiD~~sgrsRG~ilis 217 (494)
|||||||||+++|+||||||||||||||||++++||+||+++|++||++||||+|+
T Consensus 157 HfSPigaY~~~tD~vLilDVar~kYpp~WV~~~~L~~AM~~~D~~s~~~RG~~~is 212 (212)
T PF05023_consen 157 HFSPIGAYDAETDRVLILDVARFKYPPYWVPLERLYEAMNTIDPDSGKSRGYLLIS 212 (212)
T ss_dssp EEEEEEEEETTTTEEEE--S-TTT---EEEEHHHHHHHHSSEETTTTEE-EEEEEE
T ss_pred cccccceecccCCeEEEEecccccCCCEEeEHHHHHHHHhccCCCCCCcceEEEeC
Confidence 99999999999999999999999999999999999999999999999999999986
No 4
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=98.82 E-value=1e-08 Score=87.34 Aligned_cols=117 Identities=22% Similarity=0.211 Sum_probs=66.6
Q ss_pred CCCCcccHHHHHHHHHhcccCCCCCc----------CCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEE
Q 011053 51 SEPAYCGLASLAVVLNALAIDPGRTW----------KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEA 120 (494)
Q Consensus 51 ~npayCGvASlamVLNAL~idP~r~w----------kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~ 120 (494)
+....||+||++|||+.+|+.+.+.- ..+..+|-.++ ......|+....+..+++..|.++.
T Consensus 11 ~~~~~Cg~as~~mvl~~~g~~~~~~~l~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~- 82 (144)
T PF13529_consen 11 ETSYGCGPASAAMVLNYYGKNISQEDLADEAGTNPDGDPNTGFVGNP-------YYDSGYGTSPDDLARYLEKYGYKAT- 82 (144)
T ss_dssp T-TT-HHHHHHHHHHHHTT----HHHHHHHS-EE-E--TTTSEEB-S-------STS-B----HHHHHHHHHHH-TTEE-
T ss_pred CCCCcCHHHHHHHHHHHcCCCCCHHHHHHHhhhccCCCCCcccccCc-------cccCCCccccHHHHHHHHHcCccee-
Confidence 78899999999999999987544320 00011110000 0123567888899999999987433
Q ss_pred EeCCCCCHHHHHHHHHHhhCCCCceEEEEeec--cc-----ccccCCccccccceeccCCCeeEEEecC
Q 011053 121 FRTNESSIDEFRRHVISSASSEDSHVITSYHR--GV-----FKQTGTGHFSPIGGYHAGKDMVLILDVA 182 (494)
Q Consensus 121 ~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R--~~-----LgQtG~GHFSPIGGYh~~tD~VLILDVA 182 (494)
.....+++++++.|. .++.||++..- .. .....+|||--|-||+..+ .|.|.|++
T Consensus 83 -~~~~~~~~~i~~~i~-----~G~Pvi~~~~~~~~~~~~~~~~~~~~~H~vvi~Gy~~~~-~~~v~DP~ 144 (144)
T PF13529_consen 83 -DTSDASFDDIKQEID-----AGRPVIVSVNSGWRPPNGDGYDGTYGGHYVVIIGYDEDG-YVYVNDPW 144 (144)
T ss_dssp -E-TTS-HHHHHHHHH-----TT--EEEEEETTSS--TTEEEEE-TTEEEEEEEEE-SSE--EEEE-TT
T ss_pred -eccCCcHHHHHHHHH-----CCCcEEEEEEcccccCCCCCcCCCcCCEEEEEEEEeCCC-EEEEeCCC
Confidence 334667777777664 57899999972 22 2566899999999999988 89999974
No 5
>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=98.43 E-value=1.9e-06 Score=74.85 Aligned_cols=129 Identities=19% Similarity=0.121 Sum_probs=86.7
Q ss_pred CCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccc-cchhhhhhcCCCHHHHHHH-HHhcCCeEEEEeCCCCC
Q 011053 50 QSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCC-EPLSKIKDEGITFGKVSCL-AFCNGANVEAFRTNESS 127 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c-~~le~V~~~GiTL~Ela~L-A~c~G~~V~~~ra~~~s 127 (494)
|+.+..||++|++|+|+-+|+..... .+...- .........|++..++... ++..|++++.+.. .
T Consensus 1 ~~~~~~C~~~slamvl~~~g~~~~~~----------~l~~~~~~~~~~~~~~g~~~~~l~~~~a~~~G~~~~~~~~---~ 67 (141)
T cd02549 1 PQLENGCGPTSLAMVLSYLGVKVTKP----------QLAAEGNTYDFAKDGYGTYPKPIVSAAARKYGLVVRPLTG---L 67 (141)
T ss_pred CCCCCccHHHHHHHHHHhcCCCCCHH----------HHHhhccccccCCCCCCcCHHHHHHHHHhhCCCcEEECCC---H
Confidence 46788999999999999999764321 110000 0000123468999999999 9999998765432 1
Q ss_pred HHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhc
Q 011053 128 IDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 128 ldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~ 201 (494)
.. +++.++ .+..+|+...- .....+.|||--|.||+ +.+.++|.|++. ..+..++.+++-++-.
T Consensus 68 ~~-----~~~~l~-~~~Pvi~~~~~-~~~~~~~gH~vVv~g~~-~~~~~~i~DP~~--~~~~~~~~~~f~~~w~ 131 (141)
T cd02549 68 LA-----LLRQLA-AGHPVIVSVNL-GVSITPSGHAMVVIGYD-RKGNVYVNDPGG--GRRLVVSFDEFEKAWK 131 (141)
T ss_pred HH-----HHHHHH-CCCeEEEEEec-CcccCCCCeEEEEEEEc-CCCCEEEECCCC--CcCEEEeHHHHHHHHH
Confidence 11 333333 56788887642 22334589999999999 456699999974 4678899888777665
No 6
>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=98.26 E-value=2.9e-06 Score=73.40 Aligned_cols=117 Identities=23% Similarity=0.228 Sum_probs=78.9
Q ss_pred cccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCC
Q 011053 47 YQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNES 126 (494)
Q Consensus 47 F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~ 126 (494)
+..|.++.-||+|+++|+++-+|++-+. +.+...+ .....|+++.++...++..|++++.++.+..
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~~g~~~s~----------~~l~~~~----~~~~~g~s~~~L~~~~~~~gl~~~~~~~~~~ 69 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKYYGIPVSE----------EELRRQL----GTSEEGTSLADLKRAARKYGLKAKAVKLNFE 69 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHHTT----H----------HHHHCCT----T-BTTB--CCCHHHHHHHTTEEEEEEE--GG
T ss_pred eEEeCCCCCHHHHHHHHHHHHhCCCchH----------HHHHHHh----cCCccCCCHHHHHHHHHhcccceeeeecchh
Confidence 4568999999999999999999875433 1222222 1346899999999999999999998875433
Q ss_pred CHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhc
Q 011053 127 SIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 127 sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~ 201 (494)
+| .+-...+|+.- +.|||--|-++ +.++++|.|+ +..+.|++.+++.+.-.
T Consensus 70 ---~l--------~~~~~P~I~~~--------~~~h~vVi~~~--~~~~~~i~dP---~~g~~~~~~~~f~~~w~ 120 (131)
T PF03412_consen 70 ---KL--------KRLPLPAIAHL--------KDGHFVVIYKI--DDGRVLIYDP---KKGKIKLSKEEFEEIWT 120 (131)
T ss_dssp ---GC--------TCGGSSEEEEE--------CCCEEEEEEEE--CCCEEEECCT---TTCEEEEEHHHHHHHEE
T ss_pred ---hh--------hhccccEEEEe--------cCcceEEEEeE--cCcEEEEEeC---CCCeEEEeHHHHHhhCC
Confidence 22 22223455544 77999999888 8889999998 56789999999877654
No 7
>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=97.95 E-value=0.00017 Score=62.41 Aligned_cols=122 Identities=16% Similarity=0.109 Sum_probs=85.1
Q ss_pred cccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCC
Q 011053 47 YQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNES 126 (494)
Q Consensus 47 F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~ 126 (494)
+.-|.++.-||+++++|+++=+|++.+.. .+...+ .....|+++..+...|+..|++++.++.+..
T Consensus 3 ~~~q~~~~~~gl~~l~~~~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~ 68 (136)
T cd02418 3 YVLQVDEMDCGAACLAMIAKYYGKNYSLA----------KLRELA----GTDREGTSLLGLVKAAEKLGFETRAVKADMD 68 (136)
T ss_pred eEEecCcccHHHHHHHHHHHHhCCCCCHH----------HHHHHc----CCCCCCcCHHHHHHHHHHCCCeeEEEEcccc
Confidence 44577888999999999999998764432 111111 1234789999999999999999988775432
Q ss_pred CHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 127 SIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 127 sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
. .. +. .-...+|+-.. ...+.|||--|.+++ .+.|+|.|+ ..++.+++.++|-+..
T Consensus 69 ~-~~----l~----~~~~P~I~~~~----~~~~~~~~~Vl~~~~--~~~~~i~dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 69 L-FE----LK----DIPLPFIAHVI----KEWKLNHYVVVYKIK--KKKILIADP---AVGITKISKEEFEKEW 124 (136)
T ss_pred h-hh----Hh----cCCCCEEEEEc----cCCCCCeEEEEEEEc--CCEEEEECC---CCCCEEeeHHHHHhhC
Confidence 1 01 11 12234555332 124789999999988 668999998 5679999999986644
No 8
>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=97.78 E-value=0.0002 Score=60.43 Aligned_cols=115 Identities=23% Similarity=0.306 Sum_probs=83.2
Q ss_pred CCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHH
Q 011053 50 QSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSID 129 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sld 129 (494)
|.+..-||+++++|+++-++++.... .+.. .......|.++.++..+|+..|++++.+.. +.+
T Consensus 1 ~~~~~~~gl~~l~~i~~~~g~~~~~~----------~l~~----~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~---~~~ 63 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYFGIPVRRD----------VLLN----AQQRRQQGLSLADLVSLANKLGLTAQGVKL---PLA 63 (122)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCHH----------HHHH----HHhhccCCCCHHHHHHHHHHcCCeeeEEEc---CHH
Confidence 45566899999999999998765431 1111 011235789999999999999999987664 333
Q ss_pred HHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhc
Q 011053 130 EFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 130 eFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~ 201 (494)
+++ .-+..+|+- .++|||--|.+++ .+.++|.|++ ...+.|++.++|.+...
T Consensus 64 ~l~--------~~~~P~i~~--------~~~~~~~Vl~~~~--~~~~~i~dp~--~~~~~~~~~~~l~~~w~ 115 (122)
T cd02259 64 ALS--------RLQLPALLL--------WKQGHFVILYGAD--KGQVLIADPL--EEGPVTLSESELEERWT 115 (122)
T ss_pred Hhc--------cCCCCEEEE--------cCCCcEEEEEEEc--CCEEEEECCc--ccCCEEeCHHHHHhhCC
Confidence 222 233355554 4789999999988 6689999987 57888999999877543
No 9
>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=97.69 E-value=0.00015 Score=63.34 Aligned_cols=118 Identities=16% Similarity=0.228 Sum_probs=80.3
Q ss_pred ccCCCCCcccHHHHHHHHHh-cccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCC
Q 011053 48 QTQSEPAYCGLASLAVVLNA-LAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNES 126 (494)
Q Consensus 48 ~TQ~npayCGvASlamVLNA-L~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~ 126 (494)
.-|.++.-||+|+++|+++- .|+.-... .+...+ .....|+++.++...|+..|+++++++.+
T Consensus 4 ~~q~~~~dcgla~l~~i~~~~~g~~~~~~----------~l~~~~----~~~~~g~s~~~l~~~a~~~Gl~~k~~~~~-- 67 (129)
T cd02424 4 IKQTDLNDCGIAVIQMLYNHYYKKKYDLN----------ELKIKA----NLKKNGLSIYDLENLAKKFGLETESYQGS-- 67 (129)
T ss_pred EEecCccchHHHHHHHHHHHhcCCCccHH----------HHHHHh----CCCCCCccHHHHHHHHHHcCCceeEEEcC--
Confidence 45778889999999999999 88653321 111111 12357999999999999999999998853
Q ss_pred CHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 127 SIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 127 sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
.++ +.+. . .--..|++ ..++.||--+.+.+ .+.|+|.|+ ..++.+++.+++-+.-
T Consensus 68 -~~~----l~~~-~-~p~P~i~~-------~~~~~hfvVl~~~~--~~~v~I~DP---~~g~~~~s~~~f~~~w 122 (129)
T cd02424 68 -FLE----FLEL-K-NKFIILLK-------SNGLNHFVIVKKIK--KNKFIVLDP---KKGKYKITYKEFEKIF 122 (129)
T ss_pred -HHH----Hhhc-c-CCEEEEEe-------cCCCCeEEEEEEEE--CCEEEEECC---CCCCEEeCHHHHHHHh
Confidence 332 2221 1 12345554 12445998888754 456999999 4688899988876654
No 10
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=97.61 E-value=0.0017 Score=64.50 Aligned_cols=151 Identities=17% Similarity=0.063 Sum_probs=101.9
Q ss_pred cccHHHHHHHHHhcccCC-CCC---cCCCccccccchhccccchhhhhhcCCCH-HHHHHHHHhcCCeEEEEeCCCCCHH
Q 011053 55 YCGLASLAVVLNALAIDP-GRT---WKGPWRWFDDTMLDCCEPLSKIKDEGITF-GKVSCLAFCNGANVEAFRTNESSID 129 (494)
Q Consensus 55 yCGvASlamVLNAL~idP-~r~---wkgpwrwf~e~mLd~c~~le~V~~~GiTL-~Ela~LA~c~G~~V~~~ra~~~sld 129 (494)
.|+-.+++++|+..|++- ... -.+.|.+.-..+-+ ..+. ..-.|-+. +-+..+++.+|++++... ..+.+
T Consensus 1 hC~~~~l~~ll~~~g~~~~e~l~fglg~g~gf~y~~~~~-~~~~--~~~~~r~~~~~~~~~~~~lG~~~~~~~--~~~~~ 75 (317)
T PF14399_consen 1 HCESNALRDLLAHYGLPLSEALIFGLGSGLGFSYLPFPD-SNPP--PLLGGRSPPDFEENLLERLGIKYEWRE--FSSPD 75 (317)
T ss_pred CchhHHHHHHHHhcCCCCCHHHHHHHcCCcceEEEeccc-cCCC--eeecCCCchHHHHHHHHHCCceEEEEe--cCCHH
Confidence 599999999999999762 111 01222111000000 0010 11223333 555678899999888555 35678
Q ss_pred HHHHHHHHhhCCCCceEEEEeecccc-------cccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhcc
Q 011053 130 EFRRHVISSASSEDSHVITSYHRGVF-------KQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMDT 202 (494)
Q Consensus 130 eFR~~l~~~~ss~~~~vIVNy~R~~L-------gQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~t 202 (494)
+..+.|++.+. .+..|+|..+..-| .....+|+.-|-|||++.+.|+|.|. ..+++..+|.+.|-+|+..
T Consensus 76 ~~~~~l~~~l~-~g~pv~~~~D~~~lpy~~~~~~~~~~~H~i~v~G~d~~~~~~~v~D~--~~~~~~~~~~~~l~~A~~~ 152 (317)
T PF14399_consen 76 EAWEELKEALD-AGRPVIVWVDMYYLPYRPNYYKKHHADHYIVVYGYDEEEDVFYVSDP--PSYEPGRLPYEDLAKARFS 152 (317)
T ss_pred HHHHHHHHHHh-CCCceEEEeccccCCCCccccccccCCcEEEEEEEeCCCCEEEEEcC--CCCcceeecHHHHHHHHhc
Confidence 88888888877 66788888766655 23357999999999999999999998 4678899999999999987
Q ss_pred cCCcCCCceeEE
Q 011053 203 IDNATGHRRGFM 214 (494)
Q Consensus 203 iD~~sgrsRG~i 214 (494)
... ...+++.+
T Consensus 153 ~~~-~~~~~~~~ 163 (317)
T PF14399_consen 153 EGI-PFPPKNRW 163 (317)
T ss_pred cCC-CCCCCceE
Confidence 763 22344444
No 11
>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=97.55 E-value=0.00097 Score=57.25 Aligned_cols=113 Identities=21% Similarity=0.302 Sum_probs=79.7
Q ss_pred CCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHH
Q 011053 50 QSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSID 129 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sld 129 (494)
|.+...||+++++++++-.|+.-... .+.... .....|.+..++...|+..|++++.++. +.+
T Consensus 6 q~~~~~~gl~~l~~i~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~---~~~ 68 (125)
T cd02420 6 QMEATECGAASLAIILAYYGRYVPLS----------ELRIAC----GVSRDGSNASNLLKAAREYGLTAKGYKK---DLE 68 (125)
T ss_pred eCcccCHHHHHHHHHHHHcCCCCCHH----------HHHHHc----CCCCCCCCHHHHHHHHHHcCcccceEec---CHH
Confidence 55567999999999999998764331 111100 0124689999999999999999988774 333
Q ss_pred HHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 130 EFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 130 eFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
++.+ -.-.+|+-. +.|||--|.+++ .|.++|.|++. +|.|++.++|-+..
T Consensus 69 ~L~~--------~~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~~ 118 (125)
T cd02420 69 ALRE--------VSLPAIVFW--------NFNHFLVVEGFD--KRKVFLNDPAT---GRRTVSLEEFDQSF 118 (125)
T ss_pred HHhc--------CCCCEEEEe--------CCCEEEEEEEEe--CCEEEEECCCc---CceeecHHHHHhhC
Confidence 3322 123555532 469999999988 56899999964 79999999886654
No 12
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=97.47 E-value=0.0011 Score=56.75 Aligned_cols=116 Identities=26% Similarity=0.294 Sum_probs=79.4
Q ss_pred CCCCCcccHHHHHHHHHhcc-cCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCH
Q 011053 50 QSEPAYCGLASLAVVLNALA-IDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSI 128 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~-idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sl 128 (494)
|.+...||+++++|+++-++ +.-+.. .+...+ .....|.++.++..+++..|++++.++. +.
T Consensus 6 q~~~~~~~l~~l~~~~~~~g~~~~~~~----------~l~~~~----~~~~~~~s~~~l~~~a~~~Gl~~~~~~~---~~ 68 (129)
T cd02423 6 QSYDFSCGPAALATLLRYYGGINITEQ----------EVLKLM----LIRSEGFSMLDLKRYAEALGLKANGYRL---NL 68 (129)
T ss_pred cCCCCChHHHHHHHHHHhcCCCCCCHH----------HHHHHh----CcccCCcCHHHHHHHHHHCCCcceEEEc---CH
Confidence 66677999999999999998 664331 111111 1224689999999999999999988775 33
Q ss_pred HHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 129 DEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 129 deFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
+++. +. .-.+|+-. ...++|||--|.+++ .+.++|.|++. ++.+++.++|-+..
T Consensus 69 ~~L~----~~----~lP~i~~~-----~~~~~~~~vvl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~w 122 (129)
T cd02423 69 DKLN----AL----QIPVIVLV-----NNGGYGHFVVIKGID--GDRVLVGDPAL---GNISMSREEFERIW 122 (129)
T ss_pred HHHh----hC----CCCEEEEE-----ecCCCceEEEEEEEe--CCEEEEECCCC---CCcccCHHHHHHHh
Confidence 3332 21 12344433 123478999888888 67899999953 57899988876643
No 13
>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=97.35 E-value=0.0026 Score=54.33 Aligned_cols=116 Identities=18% Similarity=0.251 Sum_probs=80.7
Q ss_pred cccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCC
Q 011053 47 YQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNES 126 (494)
Q Consensus 47 F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~ 126 (494)
+..|.++.-||+++++|+++-++++-+.. .+.+.. .....|+++..+..+++..|++++.++.+..
T Consensus 3 ~~~q~~~~~~~l~~l~~~~~~~~~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~gl~~~~~~~~~~ 68 (126)
T cd02425 3 PILQNNQTECGLACYAMILNYFGYKVSLN----------ELREKY----ELGRDGLSLSYLKQLLEEYGFKCKVYKISFK 68 (126)
T ss_pred eEeecccccHHHHHHHHHHHHhCCCCCHH----------HHHHhc----cCCCCCcCHHHHHHHHHHCCCcceEEEEchH
Confidence 45688888999999999999998775442 111111 1234789999999999999999988875321
Q ss_pred CHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHh
Q 011053 127 SIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEA 199 (494)
Q Consensus 127 sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eA 199 (494)
+. +... .-.+|+-. .+|||--|.+++ .+.++|.|+.. ++.|++.++|-+.
T Consensus 69 --~~----l~~~----~lP~I~~~--------~~~~~~Vl~~~~--~~~~~i~dp~~---~~~~~~~~~l~~~ 118 (126)
T cd02425 69 --KN----LYPL----KLPVIIFW--------NNNHFVVLEKIK--KNKVTIVDPAI---GRIKISIDEFLEN 118 (126)
T ss_pred --HH----HhhC----CCCEEEEE--------cCCcEEEEEEEE--CCEEEEEcCCC---CCEEECHHHHHhh
Confidence 22 2221 12444422 248999999984 55799999954 5789999887553
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=97.35 E-value=0.0017 Score=71.99 Aligned_cols=114 Identities=24% Similarity=0.303 Sum_probs=85.7
Q ss_pred cccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCC
Q 011053 47 YQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNES 126 (494)
Q Consensus 47 F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~ 126 (494)
+.-|.+.+=||+|+++|++|-.|.+-+. +.+.+.+ .+.+.|+++.++..+|+..|++++.++.+
T Consensus 4 ~i~Q~~~~dCg~acl~mi~~~~g~~~~~----------~~lr~~~----~~~~~g~s~~~l~~~~~~~g~~~~~~~~~-- 67 (710)
T TIGR03796 4 TVLQMEAVECGAASLAMILAYYGRYVPL----------EELREEC----GVSRDGSKASNLLKAARSYGLEAKGFRKE-- 67 (710)
T ss_pred eEeecccccHHHHHHHHHHHHcCCCCCH----------HHHHHHc----CCCCCCCCHHHHHHHHHHCCCEeEEEecC--
Confidence 4568888999999999999999866433 1222222 24578999999999999999999999863
Q ss_pred CHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHH
Q 011053 127 SIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWE 198 (494)
Q Consensus 127 sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~e 198 (494)
++++ ..-.-+.|+.. +.+||--+-++ +.+.+.|.|++ +.+.|++.+++-+
T Consensus 68 -~~~l--------~~~~lP~i~~~--------~~~h~vvl~~~--~~~~~~i~dP~---~g~~~~~~~e~~~ 117 (710)
T TIGR03796 68 -LDAL--------AELPLPYIVFW--------NFNHFVVVEGF--RGGRVYLNDPA---LGPRTVSLEEFDE 117 (710)
T ss_pred -HHHh--------ccCCCCEEEEE--------cCCcEEEEEEE--eCCEEEEECCC---CCCEEccHHHHHh
Confidence 3222 12233667766 56899888776 56789999996 3789999999755
No 15
>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=97.10 E-value=0.012 Score=50.52 Aligned_cols=115 Identities=20% Similarity=0.241 Sum_probs=79.9
Q ss_pred cCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCH
Q 011053 49 TQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSI 128 (494)
Q Consensus 49 TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sl 128 (494)
.|.+..-||+++++|+++-.|++.... .+.... .....|.++..+..+|+..|++++.++. +.
T Consensus 5 ~q~~~~~~~l~~l~~~~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~---~~ 67 (127)
T cd02419 5 LQTEAAECGLACLAMIASYHGHHVDLA----------SLRQRF----PVSLKGATLADLIDIAQQLGLSTRALRL---DL 67 (127)
T ss_pred eeCccccHHHHHHHHHHHHcCCCCCHH----------HHHHHc----CCCCCCcCHHHHHHHHHHCCCceeEEEc---cH
Confidence 355666899999999999998775442 111100 1124689999999999999999988774 33
Q ss_pred HHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhc
Q 011053 129 DEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 129 deFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~ 201 (494)
+++++. .-.+|+-. ..|||--|.+. +.|.++|.|+.. ++.+++.++|-+...
T Consensus 68 ~~l~~~--------~lP~i~~~--------~~g~~~Vl~~~--~~~~~~i~dp~~---~~~~~~~~el~~~~~ 119 (127)
T cd02419 68 EELGQL--------KLPCILHW--------DMNHFVVLKKV--SRRRIVIHDPAL---GKRKLSLEEASRHFT 119 (127)
T ss_pred HHHhhC--------CCCEEEEE--------CCCEEEEEEEE--cCCEEEEECCcc---CCEEEcHHHHHhhCC
Confidence 444331 12344421 45899999886 567899999953 689999999865543
No 16
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=97.07 E-value=0.006 Score=67.85 Aligned_cols=120 Identities=17% Similarity=0.180 Sum_probs=84.8
Q ss_pred CCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHH
Q 011053 50 QSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSID 129 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sld 129 (494)
|.+..=||+|+++|+++-.|.+-+. +.+.+.+ .+.+.|+++.++..+|+..|++++.++.+ ++
T Consensus 1 Q~~~~dCg~~cl~~i~~~~g~~~~~----------~~lr~~~----~~~~~g~s~~~l~~~~~~~g~~~~~~~~~---~~ 63 (708)
T TIGR01193 1 QVDEKDCGIAALSMILKKYGTEYSL----------AKLRQLA----KTDLEGTTVLGLVKAAEYLNFEAKAIQAD---MS 63 (708)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCH----------HHHHHHh----CCCCCCCCHHHHHHHHHHCCCEEEEEecC---HH
Confidence 6778889999999999999876443 1222222 24578999999999999999999999963 22
Q ss_pred HHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHh
Q 011053 130 EFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEA 199 (494)
Q Consensus 130 eFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eA 199 (494)
++ .+ ..-.-+.|+...+. .+..||--+-+++ .+.|.|.|++. .+++.|++.+++.+.
T Consensus 64 ~l--~~----~~~~~P~I~~~~~~----~~~~H~vVl~~~~--~~~~~i~dP~~-~~g~~~~~~~ef~~~ 120 (708)
T TIGR01193 64 LF--ED----KNLPLPFIAHVIKN----GKLPHYYVVYGVT--KNHLIIADPDP-TVGITKISKEDFYEE 120 (708)
T ss_pred Hh--cc----ccCCCCEEEEEccC----CCCCcEEEEEEEe--CCEEEEEcCCc-ccCCEEecHHHHHhh
Confidence 11 01 11234667653321 2346998887766 67899999953 368899999997653
No 17
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=96.88 E-value=0.019 Score=56.54 Aligned_cols=84 Identities=15% Similarity=0.200 Sum_probs=54.2
Q ss_pred CCHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCC-CCCceeeehHH------HHH
Q 011053 126 SSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARF-KYPPHWVPLTL------LWE 198 (494)
Q Consensus 126 ~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARf-KYpP~WVpl~~------L~e 198 (494)
.+++++++.+. .+..+||-.+-..+.+....|+--+-|||. |-|.|-|+.-. .-..-|++... =++
T Consensus 117 ~~~~~l~~~l~-----~G~~~lvLIS~y~~~g~k~PHWV~v~g~d~--~~vyihDP~~d~~~~~~~~d~~~lPi~~~~f~ 189 (207)
T PF11814_consen 117 LSLADLRAALA-----AGAIVLVLISTYRMDGKKVPHWVVVTGVDD--DFVYIHDPDVDAERGESWVDCQHLPIPRADFD 189 (207)
T ss_pred CCHHHHHHHHH-----CCCEEEEEEeecccCCCCCCeEEEEEEecC--CEEEEeCCCCCcccCCCchhhccCCccHHHHH
Confidence 45555555543 466888888888888888999999999865 77889998543 23444543222 244
Q ss_pred hhcccCCcCCCceeEEEEec
Q 011053 199 AMDTIDNATGHRRGFMTVSR 218 (494)
Q Consensus 199 AM~tiD~~sgrsRG~ilis~ 218 (494)
.|...=+ .+-|+-++|.+
T Consensus 190 ~m~~~G~--~~lraaV~l~~ 207 (207)
T PF11814_consen 190 RMARFGK--SKLRAAVILRP 207 (207)
T ss_pred HHHhhcc--cccEEEEEeeC
Confidence 5554432 35777777754
No 18
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=95.55 E-value=0.038 Score=54.62 Aligned_cols=85 Identities=26% Similarity=0.199 Sum_probs=53.3
Q ss_pred HHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEeeccccc------------------cc--CCcccccc
Q 011053 107 VSCLAFCNGANVEAFRTNESSIDEFRRHVISSASSEDSHVITSYHRGVFK------------------QT--GTGHFSPI 166 (494)
Q Consensus 107 la~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~Lg------------------Qt--G~GHFSPI 166 (494)
+-.-|+.+|+.|+.- ..+++++..+|.+ .+ .+||=-+...|. +. =.|||--|
T Consensus 95 lF~~A~~~gi~V~~r---svs~~ei~~hl~~----g~-~aIvLVd~~~L~C~~Ck~~~~~~~~~~~~~~~~~Y~GHYVVl 166 (212)
T PF09778_consen 95 LFQKAKAAGINVEKR---SVSIQEIIEHLSS----GG-PAIVLVDASLLHCDLCKSNCFDPIGSKCFGRSPDYQGHYVVL 166 (212)
T ss_pred HHHHHHHcCCceEEe---eccHHHHHHHHhC----CC-cEEEEEccccccChhhcccccccccccccCCCCCccEEEEEE
Confidence 344555667655432 3577777777642 22 444444444443 21 27999999
Q ss_pred ceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 167 GGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 167 GGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
-|||++++.+++=|+|.- -----|+.+.|=+|=
T Consensus 167 cGyd~~~~~~~yrdPa~~-~~~c~~s~~~ld~AR 199 (212)
T PF09778_consen 167 CGYDAATKEFEYRDPASS-DRVCRVSPEALDEAR 199 (212)
T ss_pred EeecCCCCeEEEeCCccc-cceeecCHHHHHHHH
Confidence 999999999999999853 233446666555543
No 19
>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=93.99 E-value=1 Score=38.27 Aligned_cols=111 Identities=14% Similarity=0.087 Sum_probs=75.2
Q ss_pred CcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHH
Q 011053 54 AYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRR 133 (494)
Q Consensus 54 ayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~ 133 (494)
.-||+++++|++.-.|+.-... .+.... .....|.+..++...++..|++++.++.+ .+++.+
T Consensus 5 ~~~~l~~l~~i~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~ 67 (121)
T cd02417 5 PDSGLLALVLLARYHGIAADPE----------QLRHEF----GLAGEPFNSTELLLAAKSLGLKAKAVRQP---VERLAR 67 (121)
T ss_pred cccHHHHHHHHHHHcCCCCCHH----------HHHHHh----cCCCCCCCHHHHHHHHHHcCCeeEEEecC---HHHhcc
Confidence 3599999999999998764431 111111 01246799999999999999999887743 322221
Q ss_pred HHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhhc
Q 011053 134 HVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 134 ~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM~ 201 (494)
-.-++|+-. .+|||--|.+.+ .+.++|.|++. ..|..++.++|.+...
T Consensus 68 --------~~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~--~~~~~~~~~el~~~~~ 115 (121)
T cd02417 68 --------LPLPALAWD--------DDGGHFILAKLD--GQKYLIQDPIS--QRPEVLSREEFEARWS 115 (121)
T ss_pred --------CCCCEEEEc--------cCCCEEEEEEEc--CCCEEEECCCc--CCCeecCHHHHHhhcC
Confidence 122444432 357988888876 67899999964 3688899998877653
No 20
>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=93.21 E-value=0.51 Score=52.69 Aligned_cols=103 Identities=17% Similarity=0.118 Sum_probs=71.2
Q ss_pred HHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHH
Q 011053 58 LASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVIS 137 (494)
Q Consensus 58 vASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~~ 137 (494)
+|+++|++|..|.+-+. +.+.+.+ .+.+.|+|+.++..+++..|++++.++. +++++
T Consensus 2 laclami~~~~g~~~~l----------~~lr~~~----~~~~~g~sl~~l~~~~~~~g~~~~~~~~---~~~~l------ 58 (694)
T TIGR03375 2 LDCLLLLARHYGRPVSR----------EALVAGL----PLEDGRLTPELLPRAARRAGLSARLVKR---SLDDI------ 58 (694)
T ss_pred HHHHHHHHHHcCCCCCH----------HHHHhhC----CCCCCCCCHHHHHHHHHHCCCEEEEecC---CHhhc------
Confidence 68999999999865433 1222222 2357899999999999999999999884 23322
Q ss_pred hhCCCCceEEEEeecccccccCCccccccceeccCCCe-eEEEecCCCCCC--ceeeehHHHHH
Q 011053 138 SASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDM-VLILDVARFKYP--PHWVPLTLLWE 198 (494)
Q Consensus 138 ~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~-VLILDVARfKYp--P~WVpl~~L~e 198 (494)
.....+.|+.+. ++||--+-+ -..+. |.|+|++ ++ +.|++.+++-+
T Consensus 59 --~~~~~P~i~~~~--------~~h~vvl~~--~~~~~~~~i~DP~---~g~~~~~~~~~e~~~ 107 (694)
T TIGR03375 59 --SPLLLPAILLLK--------DGRACVLLG--IDEDGKARVLLPE---TGDGEQELSLDALEA 107 (694)
T ss_pred --CcCCCCEEEEEc--------CCcEEEEEE--EcCCCcEEEEccC---CCCCceEecHHHHHh
Confidence 223446666653 369844444 45565 9999985 44 78999988754
No 21
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=92.82 E-value=0.48 Score=54.17 Aligned_cols=117 Identities=17% Similarity=0.200 Sum_probs=83.7
Q ss_pred hcccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCC
Q 011053 46 YYQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNE 125 (494)
Q Consensus 46 ~F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~ 125 (494)
.+..|.+..=||+|+++|+.|..|.+-+.. .+.+.+ .....|.++.++...|+..|++++.++.+
T Consensus 3 ~~~~q~~~~dcgla~l~mia~~~g~~~~~~----------~lr~~~----~~~~~g~sl~~l~~~a~~lGl~~~~~~~~- 67 (709)
T COG2274 3 PIVLQQSANDCGLACLAMIANYHGKKISLN----------ELRELV----GLSRNGLSLLELKQAAEKLGLSARAVKLS- 67 (709)
T ss_pred cccccCCccchHHHHHHHHHHHhCCCCCHH----------HHHHHc----CCCCCCCChHHHHHHHHHcCCccccccCC-
Confidence 456799999999999999999988664431 222222 12356999999999999999999988864
Q ss_pred CCHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 126 SSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 126 ~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
.+++.+ ..-..|++... +||--+-+++.+ .+.|.|+ .-.+++.+.+++-+.-
T Consensus 68 --~~~l~~--------~~lP~ii~~~~--------~h~vVl~~~~~~--~~~v~dp---~~g~~~l~~~e~~~~~ 119 (709)
T COG2274 68 --LEELKQ--------LPLPAIIHWNG--------NHFVVLYKIDKN--KVVVLDP---AKGIRRLSLEEFEKLW 119 (709)
T ss_pred --HHHhcc--------cCCCEEEEEcC--------CcEEEEEEecCC--eEEEEeC---CCCcEEcCHHHHHHhh
Confidence 333222 22255666543 498888776666 9999998 5688999888865543
No 22
>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=92.65 E-value=3.4 Score=35.31 Aligned_cols=109 Identities=16% Similarity=0.081 Sum_probs=73.3
Q ss_pred ccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHH
Q 011053 56 CGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHV 135 (494)
Q Consensus 56 CGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l 135 (494)
||+++++|++.-+|+.-... .+-.. ......|.+..++...|+..|++++..+. +.+.+.+
T Consensus 7 ~~l~~l~~i~~~~g~~~~~~----------~l~~~----~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~---~~~~l~~-- 67 (124)
T cd02421 7 PLLDCLVLLARQFGKPASRD----------SLVAG----LPLDDGRLSPALFPRAAARAGLSARVVRR---PLDAIPT-- 67 (124)
T ss_pred hHHHHHHHHHHHhCCCCCHH----------HHHhc----CCCCCCCcCHHHHHHHHHHCCCcceeeeC---CHHHCCc--
Confidence 99999999999998764431 11000 01124679999999999999998887764 2222211
Q ss_pred HHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 136 ISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 136 ~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
-.-..|+- ..+|||--|.+.+. +.++|.|+.. ..+|.+++.++|-+..
T Consensus 68 ------~~lP~i~~--------~~~g~~~Vl~~~~~--~~~~i~dp~~-~~~~~~~~~~el~~~~ 115 (124)
T cd02421 68 ------LLLPAILL--------LKNGRACVLLGVDD--GHARILDPES-GGGEVEISLEELEEEY 115 (124)
T ss_pred ------ccCCEEEE--------EcCCCEEEEEEecC--CeEEEEccCC-CCCcEEEcHHHHHhhC
Confidence 11234442 23589988888765 7799999862 3678899998876644
No 23
>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=91.12 E-value=1.4 Score=49.35 Aligned_cols=105 Identities=14% Similarity=0.110 Sum_probs=72.5
Q ss_pred cHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHH
Q 011053 57 GLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVI 136 (494)
Q Consensus 57 GvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~ 136 (494)
|+|+++|++|-.|.+-+. +.+.+.+. +.+.|+++.++...++..|++++.++.+ .+++
T Consensus 1 g~acl~~i~~~~g~~~~~----------~~lr~~~~----~~~~g~~~~~l~~~~~~~G~~~~~~~~~---~~~l----- 58 (694)
T TIGR01846 1 GLEALSLLAQVHNIAVTP----------SQLRHMLG----HAGASLDDLEILLAAKQLGLKAKAVKVS---IGRL----- 58 (694)
T ss_pred CHHHHHHHHHHcCCCCCH----------HHHHHhcC----CCCCCCCHHHHHHHHHHCCCEEEEEeCC---HHHc-----
Confidence 789999999999866443 12333331 3468999999999999999999999863 3322
Q ss_pred HhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHh
Q 011053 137 SSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEA 199 (494)
Q Consensus 137 ~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eA 199 (494)
..-.-+.|+.. .+||--|-+ -+.+.|.|.|++. ..+.|++.+++.+.
T Consensus 59 ---~~~~lP~i~~~---------~~~~vvl~~--~~~~~~~i~Dp~~--g~~~~i~~~e~~~~ 105 (694)
T TIGR01846 59 ---NKLPLPALIDG---------EGGWFVLGK--LTANGVTIYDPPG--DAPEVLSREVLEAL 105 (694)
T ss_pred ---cCCCCCEEEEE---------CCcEEEEEE--EcCCEEEEEcCCC--CCceeeCHHHHHhh
Confidence 12233566644 146444434 4578899999863 25889999998653
No 24
>COG3271 Predicted double-glycine peptidase [General function prediction only]
Probab=87.04 E-value=0.85 Score=45.02 Aligned_cols=102 Identities=22% Similarity=0.285 Sum_probs=68.7
Q ss_pred cCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhh-hhhcCCCHHHHHHHHHhcCCeEEEEeCCCCC
Q 011053 49 TQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSK-IKDEGITFGKVSCLAFCNGANVEAFRTNESS 127 (494)
Q Consensus 49 TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~-V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~s 127 (494)
.|.--..||-||++.+||=+...+-.. ++. ..+. +.+.|.++..++..++..|.+.+.|.....+
T Consensus 37 rq~~d~ScGaaalatll~n~~gk~~~e----------~~~----~~~m~~~~~~~s~~g~~~~~~~~g~~a~~~~~~~~~ 102 (201)
T COG3271 37 RQTTDFSCGAAALATLLNNDYGKLADE----------SLV----LIEMNLEEFGESFSGMARAIKSLGNRAQGYENEFES 102 (201)
T ss_pred HhhhccCchHHHHHHHHHhhccccCCH----------HHH----HHHhhHHHhhhcHHHHHHHhhCCCCcccccccchhh
Confidence 366678899999999999987554331 111 1122 5689999999999999999888777653333
Q ss_pred HHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecC
Q 011053 128 IDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVA 182 (494)
Q Consensus 128 ldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVA 182 (494)
++ +.- ..+|| .+.-.+.-||+-+=+ .+.|-|++.|++
T Consensus 103 l~---q~~--------~p~iV-----~~~~~~~~hf~v~~~--v~~~~v~l~Dp~ 139 (201)
T COG3271 103 LA---QLK--------IPVIV-----TLKYPANNHFDVVIG--VDGDNVTLADPA 139 (201)
T ss_pred hh---hcc--------CCeeE-----EeecCCCceeEEEEe--ccCCeeEEcChh
Confidence 22 211 13333 334455679996655 567889999986
No 25
>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=85.87 E-value=4.3 Score=45.38 Aligned_cols=100 Identities=13% Similarity=0.059 Sum_probs=68.9
Q ss_pred HHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHH
Q 011053 58 LASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVIS 137 (494)
Q Consensus 58 vASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~~ 137 (494)
+|+++|+++-.|.+-+.. ++.+. ..| ++..+...|+..|++++.++.+ ++++.+
T Consensus 5 ~~~l~~i~~~~~~~~~~~----------~lr~~--------~~g-~~~~l~~~~~~~g~~~~~~~~~---~~~l~~---- 58 (686)
T TIGR03797 5 LVACAAVGRAMGIEIRPP----------ARSEN--------LSR-SPEPLEAIARASRLRIRRVRLE---GGWWRQ---- 58 (686)
T ss_pred HHHHHHHHHHhCCCCChH----------HHHHH--------cCC-CHHHHHHHHHHCCCceEEEecC---HHHHhh----
Confidence 689999999998764441 22221 168 8999999999999999999863 332221
Q ss_pred hhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHH
Q 011053 138 SASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWE 198 (494)
Q Consensus 138 ~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~e 198 (494)
-.-+.|+..+ +.|||--+-++ +.+.+.|+|++. -++.|++.+++-+
T Consensus 59 ----~~lP~i~~~~-------~~~h~vvl~~~--~~~~~~i~dP~~--g~~~~~~~~e~~~ 104 (686)
T TIGR03797 59 ----DSGPLLAYTA-------EDGRPVALLPV--SRGGYEIFDPAT--GTRRRVDAAMAAT 104 (686)
T ss_pred ----CCCCEEEEEc-------CCCCEEEEEEE--cCCEEEEECCCC--CCCcccCHHHHHh
Confidence 1224555543 24798777664 678999999974 3345999988743
No 26
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=70.84 E-value=32 Score=33.32 Aligned_cols=138 Identities=14% Similarity=0.100 Sum_probs=82.1
Q ss_pred cchhcccCCCC-CcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEEE
Q 011053 43 LISYYQTQSEP-AYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEAF 121 (494)
Q Consensus 43 La~~F~TQ~np-ayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~~ 121 (494)
++-.|..|++. .-|=-|+++||+--..-.|...+ .++.++=+-+..-.+.|..- ..+.+..|++--..
T Consensus 22 ~~v~~v~Qq~~~mgCWaA~~~Mv~~w~~~~prlg~--------~eLyra~~Glp~~lq~g~d~---~~~~~~~gl~~v~~ 90 (166)
T PF12385_consen 22 FAVPYVPQQNTRMGCWAACACMVGGWRDQGPRLGP--------PELYRADEGLPSQLQDGLDP---EDFIRNEGLKEVPE 90 (166)
T ss_pred eEeeeeccCCCcccHHHHHHHHHHHHhcCCCCCCc--------HHHHHHhcCCchhhcccccH---HHHHHhcCccccCC
Confidence 34677788874 69999999999988865554432 11212111111112233333 34444444322111
Q ss_pred eC-CCCCHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHHHhh
Q 011053 122 RT-NESSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLWEAM 200 (494)
Q Consensus 122 ra-~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~eAM 200 (494)
-+ ..-+.+.|++.|++. ..|.+--.+. +..=.||.+-|-|.+.+.|.+.+.|+.+ -|--=++++.+-.+.
T Consensus 91 P~~~~~t~e~~~~LL~~y-----GPLwv~~~~P--~~~~~~H~~ViTGI~~dg~~i~~~DP~~--gP~~~m~l~~fn~~~ 161 (166)
T PF12385_consen 91 PANASYTAEGLANLLREY-----GPLWVAWEAP--GDSWVAHASVITGIDGDGDSIHVHDPEQ--GPNLRMSLDMFNQAL 161 (166)
T ss_pred CcccccCHHHHHHHHHHc-----CCeEEEecCC--CCcceeeEEEEEeecCCCCeEEecCccc--CCCceecHHHHhhhh
Confidence 12 235889999999753 3555553332 2222479999999999999999999976 344447777665543
No 27
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.40 E-value=43 Score=31.78 Aligned_cols=95 Identities=20% Similarity=0.199 Sum_probs=58.2
Q ss_pred CCHHHHHHHH-HhcCCeEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCCeeEEEe
Q 011053 102 ITFGKVSCLA-FCNGANVEAFRTNESSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILD 180 (494)
Q Consensus 102 iTL~Ela~LA-~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILD 180 (494)
++..++.+++ +-|-+.+..+..+...-+-..+-++.++-+++.+- -|.|.. .=.|||--|-|||+.+|-+-|=|
T Consensus 57 VSi~dIqahLaqGnhiAIaLVdq~~Lhcdlceeplk~ccfspnghh--cfcrtp---~YqGHfiVi~GYd~a~~c~~~nd 131 (167)
T KOG4621|consen 57 VSIHDIQAHLAQGNHIAIALVDQDKLHCDLCEEPLKSCCFSPNGHH--CFCRTP---CYQGHFIVICGYDAARDCFEIND 131 (167)
T ss_pred eeHHHHHHHHhcCCeEEEEEecCCceehHHHHhHHHHhccCCCCcc--ccccCC---cccccEEEEeccccccCeEEEcC
Confidence 3445665533 44334333333344555666666776655444332 245533 23699999999999999999999
Q ss_pred cCCCCCCceeeehHHHHHhhc
Q 011053 181 VARFKYPPHWVPLTLLWEAMD 201 (494)
Q Consensus 181 VARfKYpP~WVpl~~L~eAM~ 201 (494)
+|.-+-.---++.+-+=+|-.
T Consensus 132 PA~adpg~c~~Sik~fEeARk 152 (167)
T KOG4621|consen 132 PASADPGHCRISIKCFEEARK 152 (167)
T ss_pred cccCCCcceeehhhHHHHHHh
Confidence 996543333467766666654
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=47.69 E-value=16 Score=32.76 Aligned_cols=42 Identities=19% Similarity=0.273 Sum_probs=30.8
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.||+|+++-+..-.-+...+..|++++|+..+...
T Consensus 28 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T TIGR02044 28 PPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNL 69 (127)
T ss_pred CCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 433334679999987776544445568899999999998864
No 29
>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=46.96 E-value=18 Score=31.92 Aligned_cols=38 Identities=11% Similarity=0.218 Sum_probs=29.1
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
.+.||||+++-+..-.-+...+..|++++|+..+....
T Consensus 33 ~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 33 ENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 56799999866654444445688999999999988754
No 30
>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=44.75 E-value=17 Score=31.02 Aligned_cols=42 Identities=12% Similarity=0.245 Sum_probs=30.5
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.||+|++.-+..-.-+...+..|++++++..+...
T Consensus 28 p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (96)
T cd04768 28 PAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT 69 (96)
T ss_pred CCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 444445679999986665443344567899999999988865
No 31
>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=44.44 E-value=18 Score=32.74 Aligned_cols=43 Identities=12% Similarity=0.179 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-++.-.-+...++.|+|++|+..++...
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 4444336799999877664444455688999999999988753
No 32
>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=43.61 E-value=14 Score=33.23 Aligned_cols=55 Identities=20% Similarity=0.367 Sum_probs=37.6
Q ss_pred HHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcCCeEEE
Q 011053 62 AVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNGANVEA 120 (494)
Q Consensus 62 amVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G~~V~~ 120 (494)
+.+=+|.++.+.+-|..==.-+.+++|+- ++|...|++-|-|+.|+.....++..
T Consensus 8 ~A~s~at~~~~~~LW~~L~~~lPDSlL~n----~ei~~~GLSTDhltaLa~~~~~~~~~ 62 (104)
T PF05381_consen 8 VAISQATSISPETLWATLCEILPDSLLDN----PEIRTLGLSTDHLTALAYRYHFQCTF 62 (104)
T ss_pred HhhhhhhCCCHHHHHHHHHHhCchhhcCc----hhhhhcCCcHHHHHHHHHHHheEEEE
Confidence 34456777777777643223334455542 46889999999999999888777754
No 33
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=43.11 E-value=19 Score=33.35 Aligned_cols=43 Identities=9% Similarity=0.101 Sum_probs=32.4
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.||+|+++.+....-+...+..|++++|+..++...
T Consensus 35 p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~~ 77 (144)
T PRK13752 35 EPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLE 77 (144)
T ss_pred CCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 3344356799999987775555566789999999999988654
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=43.10 E-value=20 Score=31.94 Aligned_cols=37 Identities=11% Similarity=0.252 Sum_probs=29.0
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
.+.||+|+++.+..-.-+...+..|++++|+..+...
T Consensus 33 ~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 33 ANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4669999987776554445568899999999998864
No 35
>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=43.02 E-value=21 Score=32.00 Aligned_cols=43 Identities=12% Similarity=0.248 Sum_probs=31.1
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-++.-.-+...+..|++++|+..+....
T Consensus 28 ~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 28 EPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred CCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence 4333357799999877765444455688999999999988643
No 36
>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=42.68 E-value=41 Score=26.52 Aligned_cols=44 Identities=23% Similarity=0.323 Sum_probs=28.3
Q ss_pred cccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHH
Q 011053 68 LAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLA 111 (494)
Q Consensus 68 L~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA 111 (494)
.|..+...=.+-+|+|+++-++.-..+...++.|+|++++..++
T Consensus 24 ~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 24 FGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred cCCCCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 35543333346678998765553333445567999999998765
No 37
>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=42.57 E-value=22 Score=32.03 Aligned_cols=42 Identities=7% Similarity=0.116 Sum_probs=30.8
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..++..
T Consensus 28 ~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 28 PPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 333335679999987776554445568899999999998864
No 38
>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=42.14 E-value=20 Score=30.62 Aligned_cols=43 Identities=12% Similarity=0.212 Sum_probs=31.7
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-+....-+...++.|++++|+..+....
T Consensus 28 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 28 PSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred CCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 4333356799999877765554555688999999999988653
No 39
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=41.79 E-value=22 Score=32.57 Aligned_cols=42 Identities=14% Similarity=0.182 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.||+|++..+..-.-+...+..|++++|+..+...
T Consensus 28 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 28 PPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred CcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 434445779999997776555445567899999999988864
No 40
>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=40.77 E-value=47 Score=25.75 Aligned_cols=34 Identities=18% Similarity=0.421 Sum_probs=21.5
Q ss_pred CCccccccchhccccchhhhhhcCCCHHHHHHHH
Q 011053 78 GPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLA 111 (494)
Q Consensus 78 gpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA 111 (494)
+..|+|+++-+..-..+...++.|+|++|+..++
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 3457787644432223344567999999998764
No 41
>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=39.33 E-value=52 Score=30.00 Aligned_cols=43 Identities=12% Similarity=0.129 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.||+|+++.++.-.-+...+..|++++|+..+..+.
T Consensus 28 p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~ 70 (131)
T cd04786 28 SVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPAD 70 (131)
T ss_pred CCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4444457799999877654444445688999999999988653
No 42
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=38.80 E-value=16 Score=30.25 Aligned_cols=17 Identities=35% Similarity=0.454 Sum_probs=14.3
Q ss_pred cCCCChhHHHHHHHHHH
Q 011053 466 VDKLPSLLQQEVQHLRR 482 (494)
Q Consensus 466 ~~~lp~~l~~ev~~l~~ 482 (494)
.++||+.|++||+|--+
T Consensus 8 fqkLPDdLKrEvldY~E 24 (65)
T COG5559 8 FQKLPDDLKREVLDYIE 24 (65)
T ss_pred HHHCcHHHHHHHHHHHH
Confidence 46899999999998654
No 43
>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=38.10 E-value=28 Score=30.64 Aligned_cols=42 Identities=19% Similarity=0.456 Sum_probs=30.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+. .+.+|+|++.-+..-.-+...+..|++++|+..+....
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 4443 56799999866654433445678999999999988764
No 44
>PF14104 DUF4277: Domain of unknown function (DUF4277)
Probab=36.70 E-value=29 Score=31.69 Aligned_cols=51 Identities=24% Similarity=0.320 Sum_probs=35.6
Q ss_pred CCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHH
Q 011053 50 QSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVS 108 (494)
Q Consensus 50 Q~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela 108 (494)
|. .-.+|.+-.+||||.||....+- +--.+||.+ .+.|..-+.|++.+.|-
T Consensus 39 ~~-~vs~G~~vkamilN~Lg~~~~pL-yl~~~ff~~------~~~E~L~g~gi~~~~lN 89 (115)
T PF14104_consen 39 QE-KVSHGQVVKAMILNGLGFVSRPL-YLFEEFFED------KPVERLLGEGISPEDLN 89 (115)
T ss_pred Cc-cccHHHHHHHHHHHhcCCCCcch-hhhHHHHcc------CCHHHHhcCCCCHHHcc
Confidence 44 48899999999999999654332 233467743 34566777888887663
No 45
>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=36.65 E-value=28 Score=31.00 Aligned_cols=38 Identities=13% Similarity=0.308 Sum_probs=30.1
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
.+.+|+|+++-+..-.-+...+..|++++|+..+....
T Consensus 33 ~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 33 EGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 56799999877765544556789999999999988654
No 46
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.01 E-value=34 Score=26.66 Aligned_cols=54 Identities=11% Similarity=0.274 Sum_probs=33.9
Q ss_pred HHHHHHHHHhcccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHH
Q 011053 58 LASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAF 112 (494)
Q Consensus 58 vASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~ 112 (494)
+.++..-.+.--+.|.+.- +.+|.|+++-++.-..+....+.|+|++++..+++
T Consensus 14 ~~tlr~y~~~gll~~~~~~-~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 14 PSTLRYYEREGLLPPPRDE-NGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHHHHHHTTSSTTBEST-TSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred HHHHHHHHHhcCccccccc-CceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 4455555555556676643 44688887555544344556679999999988764
No 47
>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=35.98 E-value=30 Score=29.75 Aligned_cols=43 Identities=16% Similarity=0.284 Sum_probs=29.8
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+...+.+|+|+++-++.-..+...+..|++++++..+....
T Consensus 28 ~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 28 PSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDP 70 (103)
T ss_pred CCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 4455566799998755543333344678999999999888653
No 48
>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=35.25 E-value=33 Score=30.36 Aligned_cols=39 Identities=18% Similarity=0.369 Sum_probs=30.4
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcC
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNG 115 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G 115 (494)
.+.+|+|+++-++.-.-+...+..|+|++|+..+....+
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 468999998777655445567889999999999886543
No 49
>PRK13749 transcriptional regulator MerD; Provisional
Probab=35.10 E-value=34 Score=31.24 Aligned_cols=44 Identities=20% Similarity=0.218 Sum_probs=31.1
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhcC
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNG 115 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G 115 (494)
|...=.+.+|+|++.-+..-.-+...+..|++++|+..++...+
T Consensus 31 p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~ 74 (121)
T PRK13749 31 PVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALD 74 (121)
T ss_pred CCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 43333478999998766543333445789999999999987653
No 50
>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=34.50 E-value=33 Score=30.76 Aligned_cols=42 Identities=12% Similarity=0.239 Sum_probs=30.2
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.+|+|+++-++.-.-+...+..|++++|+..+...
T Consensus 28 ~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 28 PPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 343335679999987766444445567899999999998864
No 51
>PF05543 Peptidase_C47: Staphopain peptidase C47; InterPro: IPR008750 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 belong to the peptidase family C47 (staphopain family, clan CA). The type example are the staphopains, which are one of four major families of proteinases secreted by the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme [, , ].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1X9Y_D 1Y4H_B 1PXV_B 1CV8_A.
Probab=34.39 E-value=2e+02 Score=28.25 Aligned_cols=115 Identities=17% Similarity=0.198 Sum_probs=64.6
Q ss_pred hcccCCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccc---cchhhhhhcCCCHHHHHHHHHhcCCeEEEEe
Q 011053 46 YYQTQSEPAYCGLASLAVVLNALAIDPGRTWKGPWRWFDDTMLDCC---EPLSKIKDEGITFGKVSCLAFCNGANVEAFR 122 (494)
Q Consensus 46 ~F~TQ~npayCGvASlamVLNAL~idP~r~wkgpwrwf~e~mLd~c---~~le~V~~~GiTL~Ela~LA~c~G~~V~~~r 122 (494)
-.+||-+...|.=-+++.+||++.- .. ...-+.|+..- .+.+..+..|++.+|+-..++..|..++. -
T Consensus 15 I~EtQg~~pWCa~Ya~aailN~~~~---~~-----~~~A~~iMr~~yPn~s~~~l~~~~~~~~~~i~y~ks~g~~~~~-~ 85 (175)
T PF05543_consen 15 IRETQGYNPWCAGYAMAAILNATTN---TK-----IYNAKDIMRYLYPNVSEEQLKFTSLTPNQMIKYAKSQGRNPQY-N 85 (175)
T ss_dssp -----SSSS-HHHHHHHHHHHHHCT----S--------HHHHHHHHSTTS-CCCHHH--B-HHHHHHHHHHTTEEEEE-E
T ss_pred EeeccCcCcHHHHHHHHHHHHhhhC---cC-----cCCHHHHHHHHCCCCCHHHHhhcCCCHHHHHHHHHHcCcchhH-h
Confidence 4578999999999999999999941 11 12224444322 12245667899999999999999987754 3
Q ss_pred CCCCCHHHHHHHHHHhhCCCCceEEEEeeccccc-ccCCccccccceeccCCC
Q 011053 123 TNESSIDEFRRHVISSASSEDSHVITSYHRGVFK-QTGTGHFSPIGGYHAGKD 174 (494)
Q Consensus 123 a~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~Lg-QtG~GHFSPIGGYh~~tD 174 (494)
.+-.+.++..+.++ +++.+++.-++-.-. ..-.||=--+.||-.-.+
T Consensus 86 n~~~s~~eV~~~~~-----~nk~i~i~~~~v~~~~~~~~gHAlavvGya~~~~ 133 (175)
T PF05543_consen 86 NRMPSFDEVKKLID-----NNKGIAILADRVEQTNGPHAGHALAVVGYAKPNN 133 (175)
T ss_dssp CS---HHHHHHHHH-----TT-EEEEEEEETTSCTTB--EEEEEEEEEEEETT
T ss_pred cCCCCHHHHHHHHH-----cCCCeEEEecccccCCCCccceeEEEEeeeecCC
Confidence 34557777777775 344566655533222 223789888889966443
No 52
>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=33.29 E-value=39 Score=28.94 Aligned_cols=42 Identities=12% Similarity=0.207 Sum_probs=29.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..+...
T Consensus 28 p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 28 PEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 433334669999986665433334568899999999988865
No 53
>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=32.78 E-value=36 Score=30.80 Aligned_cols=42 Identities=19% Similarity=0.224 Sum_probs=30.2
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+.-.+.+|+|+++-+..-.-+-..+..|++++|+..+...
T Consensus 29 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 29 PAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI 70 (131)
T ss_pred CCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 433335669999987665444444567899999999998874
No 54
>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=32.23 E-value=42 Score=29.28 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=29.4
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|...-.+.+|+|++.-++.-.-+...+..|++++|+..+...
T Consensus 28 ~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 28 PVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred CCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 433345668999876665433334567899999999998865
No 55
>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=32.09 E-value=36 Score=30.47 Aligned_cols=43 Identities=9% Similarity=0.161 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-++.-.-+...+..|++++|+..++...
T Consensus 27 ~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 27 EPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLV 69 (124)
T ss_pred CCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcc
Confidence 3444456799999877764444455689999999999988643
No 56
>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=31.68 E-value=72 Score=24.97 Aligned_cols=35 Identities=9% Similarity=0.367 Sum_probs=25.0
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHH
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLA 111 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA 111 (494)
.+.+|+|+.+-++.-.-+...++.|++++|+..+.
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 46689998766654444445677999999998764
No 57
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=31.18 E-value=76 Score=29.75 Aligned_cols=53 Identities=19% Similarity=0.433 Sum_probs=36.8
Q ss_pred CCCCCcceeeeecCCChHHHHHHHHhhccccccCCCCCCHHHHHHHHHhcCchhHHHHHHhhh
Q 011053 220 PKAPSILYTVSCRHEGWNKVAKYLTEDVPLRLKSDDVKSVENLLSVIFKSAPADLKEFIKWVA 282 (494)
Q Consensus 220 ~~~p~~l~~~~~~~~~w~~~~~~~~~~~p~l~~~~~~~~~~~v~~~~~~~~p~~~~~~i~w~~ 282 (494)
...|+.+.|++| +..|.++.+.+.+ ..++..|-+.++..+|..- +..|++-|.
T Consensus 102 ~G~P~~FiT~s~-~~~w~ei~~~l~~------~~~~~~d~P~~~ar~F~~k---~~~f~~~~~ 154 (184)
T PF14214_consen 102 FGKPTLFITFSC-NPQWPEIQQALAK------PGQNWSDNPDIVARFFHIK---FQAFFKDVL 154 (184)
T ss_pred cCCCcEEEEEcC-ccccHHHHHHHHh------ccCCcccCcHHHHHHHHHH---HHHHHHHHh
Confidence 457999999999 8999999999773 3355556666666666543 444454443
No 58
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=30.55 E-value=78 Score=29.88 Aligned_cols=41 Identities=15% Similarity=0.152 Sum_probs=30.5
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+. .+.+|+|+++.+..-.-+...+..|++++|+..++..
T Consensus 39 ~~r~-~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~ 79 (154)
T PRK15002 39 SIRN-SGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV 79 (154)
T ss_pred CccC-CCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4343 5668999987776544445568899999999998865
No 59
>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=30.50 E-value=42 Score=31.87 Aligned_cols=43 Identities=14% Similarity=0.324 Sum_probs=31.2
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.||+|+++-+..-.-+-..+..|++++|+..++...
T Consensus 29 p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 29 PSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred CCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 5444457799999876654444445688999999999988654
No 60
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=30.43 E-value=61 Score=31.74 Aligned_cols=114 Identities=14% Similarity=0.244 Sum_probs=66.1
Q ss_pred cccccccchhcccC------CCCCcccHHHHHHHHHhcccCCCCCcC-------CCcccccc---chhccccchhhhhhc
Q 011053 37 MEGFFKLISYYQTQ------SEPAYCGLASLAVVLNALAIDPGRTWK-------GPWRWFDD---TMLDCCEPLSKIKDE 100 (494)
Q Consensus 37 ~e~ff~La~~F~TQ------~npayCGvASlamVLNAL~idP~r~wk-------gpwrwf~e---~mLd~c~~le~V~~~ 100 (494)
+..|-.+++.|... .+|.|= +....++.+||+||...-+ |.-.||.| .+.+.|. ....+.
T Consensus 35 a~~~~~~l~~fa~k~~~~i~~~~~~r--~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~--~~~~~~ 110 (223)
T PF04157_consen 35 AKDFVELLENFARKHKSEIKSDPEFR--SQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCL--ATRSKN 110 (223)
T ss_dssp HHHHHHHHHHHHHHHCCCCCCSHHHH--HHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHH--HHCCTT
T ss_pred HHHHHHHHHHHHHHhhccccCCchHH--HHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHH--HHHhcC
Confidence 35555666666542 222221 2778889999999754323 33456655 4556664 233467
Q ss_pred C--CCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEee-cccccccC
Q 011053 101 G--ITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVISSASSEDSHVITSYH-RGVFKQTG 159 (494)
Q Consensus 101 G--iTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~-R~~LgQtG 159 (494)
| |+|.|+.|+.....-.+ +..|-++|++.++....-...+-++.|. ...+-|+.
T Consensus 111 GGii~L~dl~~~~nr~R~g~-----~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~ 167 (223)
T PF04157_consen 111 GGIISLSDLYCRYNRARGGS-----ELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSV 167 (223)
T ss_dssp TSEEEHHHHHHHHHHCTTTS-----ST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECS
T ss_pred CCEEEHHHHHHHHHHhcccC-----CCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeC
Confidence 7 99999999996642111 2579999999999764333347777776 44444443
No 61
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=30.16 E-value=4.8e+02 Score=24.70 Aligned_cols=68 Identities=12% Similarity=0.185 Sum_probs=45.5
Q ss_pred EEeCCCCCHHHHHHHHHHhh-CCCCceEEEEeecccccc-cCCccccccceeccCCCeeEEEecCCCCCCceeeehHHHH
Q 011053 120 AFRTNESSIDEFRRHVISSA-SSEDSHVITSYHRGVFKQ-TGTGHFSPIGGYHAGKDMVLILDVARFKYPPHWVPLTLLW 197 (494)
Q Consensus 120 ~~ra~~~sldeFR~~l~~~~-ss~~~~vIVNy~R~~LgQ-tG~GHFSPIGGYh~~tD~VLILDVARfKYpP~WVpl~~L~ 197 (494)
....-+.+++++++.+...- +..+.+++.+|..-...+ +. .+.+-+.|-++-+| ..+++.+|+
T Consensus 66 ~~~~~dpt~e~~~~~~~~~R~~a~~~RvLFHYnGhGvP~Pt~-------------~GeIw~f~~~~tqy--ip~si~dL~ 130 (154)
T PF14538_consen 66 YKQSLDPTVEDLKRLCQSLRRNAKDERVLFHYNGHGVPRPTE-------------NGEIWVFNKNYTQY--IPLSIYDLQ 130 (154)
T ss_pred EEEecCCCHHHHHHHHHHHHhhCCCceEEEEECCCCCCCCCC-------------CCeEEEEcCCCCcc--eEEEHHHHH
Confidence 33444679999999777653 334579999998543332 22 33677888654433 458999999
Q ss_pred Hhhcc
Q 011053 198 EAMDT 202 (494)
Q Consensus 198 eAM~t 202 (494)
++|.+
T Consensus 131 ~~lg~ 135 (154)
T PF14538_consen 131 SWLGS 135 (154)
T ss_pred HhcCC
Confidence 99873
No 62
>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=28.46 E-value=47 Score=30.78 Aligned_cols=37 Identities=14% Similarity=0.208 Sum_probs=28.7
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
.+.+|+|+++.+..-.-+...+..|++++++..++.+
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 4568999987776544445568899999999998875
No 63
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=27.88 E-value=48 Score=30.45 Aligned_cols=43 Identities=19% Similarity=0.276 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..++...
T Consensus 29 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 71 (140)
T PRK09514 29 PEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIR 71 (140)
T ss_pred CcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 4333356799999866654433445678999999999988653
No 64
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=27.06 E-value=1.2e+02 Score=26.43 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=28.7
Q ss_pred CCCCCcCCCccccccchhccccchhh-hhhcCCCHHHHHHHHHhcC
Q 011053 71 DPGRTWKGPWRWFDDTMLDCCEPLSK-IKDEGITFGKVSCLAFCNG 115 (494)
Q Consensus 71 dP~r~wkgpwrwf~e~mLd~c~~le~-V~~~GiTL~Ela~LA~c~G 115 (494)
.|.+. .|.+|+|+++-+..-..+.. .+..|++++++..+....+
T Consensus 28 ~p~r~-~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 28 KPVKR-AGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred CCcCC-CCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence 34443 46689998755543322333 3678999999999886554
No 65
>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=26.96 E-value=1.2e+02 Score=26.22 Aligned_cols=56 Identities=7% Similarity=0.124 Sum_probs=35.6
Q ss_pred CCCCcCCCccccccchhccccchhhhhh-cCCCHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHH
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKD-EGITFGKVSCLAFCNGANVEAFRTNESSIDEFRRHVI 136 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~-~GiTL~Ela~LA~c~G~~V~~~ra~~~sldeFR~~l~ 136 (494)
|.+.-++.+|+|++.-++...-+...++ .|++++++..+.... .+.++.+=++.+.
T Consensus 28 p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~~---------~~~~~~~~~~~~~ 84 (95)
T cd04780 28 EGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAI---------ADASLPSTLLALA 84 (95)
T ss_pred CCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc---------CcccHHHHHHHHH
Confidence 4333345578898877765544444565 799999999988762 2445555555444
No 66
>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=26.71 E-value=55 Score=28.65 Aligned_cols=43 Identities=12% Similarity=0.196 Sum_probs=30.8
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+...+.+|.|++.-+..-.-+...++.|++++++..++...
T Consensus 28 p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 28 PDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred CCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 5555556789998766654333455678999999999988753
No 67
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.68 E-value=51 Score=30.05 Aligned_cols=53 Identities=23% Similarity=0.469 Sum_probs=37.8
Q ss_pred eEEEEeCCCCCHHHHHHHHHHhhCCCCceEEEEeecccccccCCccccccceeccCCC
Q 011053 117 NVEAFRTNESSIDEFRRHVISSASSEDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKD 174 (494)
Q Consensus 117 ~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD 174 (494)
++.+|-+ ..-++.+|+.|- ..+..-|-||+-=...-+|.|||-|+.|=++--+
T Consensus 7 K~~vyVP-~~~~e~vr~aL~----~aGag~iG~Y~~C~~~~~g~G~frP~egAnP~iG 59 (109)
T COG3323 7 KIEVYVP-EEYVEQVRDALF----EAGAGHIGNYDHCTFSSEGTGQFRPLEGANPFIG 59 (109)
T ss_pred EEEEEeC-HHHHHHHHHHHH----hcCCcceeccceEEEEeeeeEEEeecCCCCCccc
Confidence 3444544 335666776665 4455667799999999999999999988776544
No 68
>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=24.37 E-value=63 Score=27.97 Aligned_cols=36 Identities=11% Similarity=0.224 Sum_probs=27.1
Q ss_pred CCCccccccchhccccchhhhhhcCCCHHHHHHHHH
Q 011053 77 KGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAF 112 (494)
Q Consensus 77 kgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~ 112 (494)
.+.+|+|+++-++.-.-+...+..|++++|+..++.
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 477999998777654444556789999999887663
No 69
>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=24.22 E-value=62 Score=29.36 Aligned_cols=43 Identities=23% Similarity=0.292 Sum_probs=30.7
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|++.-++.-.-+...+..|++++++..+....
T Consensus 31 p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~~ 73 (120)
T TIGR02054 31 PVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRAL 73 (120)
T ss_pred CCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 4444457799999866654433345678999999999988654
No 70
>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=23.27 E-value=64 Score=28.76 Aligned_cols=41 Identities=17% Similarity=0.139 Sum_probs=29.8
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+. +.+|+|++.-++.-.-+...+..|++++++..+....
T Consensus 28 p~r~--~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~ 68 (118)
T cd04776 28 PERR--GQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLY 68 (118)
T ss_pred CcCC--CCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 5443 4799999877654433445688999999999988653
No 71
>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=22.75 E-value=74 Score=27.70 Aligned_cols=38 Identities=11% Similarity=0.318 Sum_probs=28.4
Q ss_pred CCccccccchhccccchhhhhhcCCCHHHHHHHHHhcC
Q 011053 78 GPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCNG 115 (494)
Q Consensus 78 gpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~G 115 (494)
+.+|+|++.-++.-..+...+..|++++++..+.....
T Consensus 35 ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 35 TGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADN 72 (108)
T ss_pred CCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 56999998666544444456789999999999887654
No 72
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=22.26 E-value=76 Score=27.93 Aligned_cols=46 Identities=20% Similarity=0.241 Sum_probs=31.6
Q ss_pred ccC-CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 69 AID-PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 69 ~id-P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.- |.+.-.+.+|+|+++-+..-.-+...+..|+++.++..+....
T Consensus 24 GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (107)
T cd01111 24 GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRAL 70 (107)
T ss_pred CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 443 4344456799999876654333345678999999999988653
No 73
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 dissimil
Probab=21.67 E-value=74 Score=27.49 Aligned_cols=44 Identities=11% Similarity=0.250 Sum_probs=29.7
Q ss_pred ccCCCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHH
Q 011053 69 AIDPGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAF 112 (494)
Q Consensus 69 ~idP~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~ 112 (494)
|+-|...-.+.+|+|+++-++.-.-+-..+..|++++|+..+..
T Consensus 25 Gll~~~r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~ 68 (102)
T cd04775 25 GLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA 68 (102)
T ss_pred CCCCCCCCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 44443333467899998666544334446789999999988764
No 74
>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=21.61 E-value=78 Score=29.06 Aligned_cols=41 Identities=12% Similarity=0.157 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHh
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFC 113 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c 113 (494)
|.+. .+.+|+|+++-++.-.-+...+..|+|++|+..++..
T Consensus 29 p~r~-~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 29 SWRN-AGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred CCcC-CCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4443 5668999987776554455568899999999998764
No 75
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=21.57 E-value=1.3e+02 Score=27.51 Aligned_cols=36 Identities=25% Similarity=0.281 Sum_probs=30.0
Q ss_pred chHHHHHHHhhhccCCCC-----hhHHHHHHHHHHHHHHHh
Q 011053 453 EEELRMQFNHLASVDKLP-----SLLQQEVQHLRRQLHFLM 488 (494)
Q Consensus 453 ~~~l~~e~~~l~s~~~lp-----~~l~~ev~~l~~q~~~l~ 488 (494)
++|+..-|+.+.+-.++| +.|.++|..||||+.-|+
T Consensus 63 e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Le 103 (108)
T COG3937 63 EEKIPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLE 103 (108)
T ss_pred HHhhhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHH
Confidence 567888888888888877 488999999999998775
No 76
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=20.95 E-value=54 Score=22.62 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=8.4
Q ss_pred HHHHHHhhhe
Q 011053 274 LKEFIKWVAE 283 (494)
Q Consensus 274 ~~~~i~w~~e 283 (494)
+++|+||++|
T Consensus 9 IgdfvKlI~~ 18 (25)
T PF05372_consen 9 IGDFVKLIIE 18 (25)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4799999985
No 77
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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 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 dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.67 E-value=90 Score=26.29 Aligned_cols=43 Identities=19% Similarity=0.078 Sum_probs=28.5
Q ss_pred CCCCcCCCccccccchhccccchhhhhhcCCCHHHHHHHHHhc
Q 011053 72 PGRTWKGPWRWFDDTMLDCCEPLSKIKDEGITFGKVSCLAFCN 114 (494)
Q Consensus 72 P~r~wkgpwrwf~e~mLd~c~~le~V~~~GiTL~Ela~LA~c~ 114 (494)
|.+.-.+.+|+|+++-+..-.-+...++.|++++++..++...
T Consensus 29 p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~ 71 (88)
T cd01105 29 SIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRR 71 (88)
T ss_pred CCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence 4443334688888755543333344678999999999988754
No 78
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=20.24 E-value=4.1e+02 Score=21.02 Aligned_cols=55 Identities=9% Similarity=0.276 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHhhCC--CCceEEEEeecccccccCCccccccceeccCCCeeEEEecCC
Q 011053 124 NESSIDEFRRHVISSASS--EDSHVITSYHRGVFKQTGTGHFSPIGGYHAGKDMVLILDVAR 183 (494)
Q Consensus 124 ~~~sldeFR~~l~~~~ss--~~~~vIVNy~R~~LgQtG~GHFSPIGGYh~~tD~VLILDVAR 183 (494)
...++.+|++.+.+...- +-....+-|..+.|... .++..|+-..+..+++-+..
T Consensus 19 ~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~-----~~L~~~~i~~~~~i~~~~~~ 75 (77)
T cd01805 19 PDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDD-----TTLEEYKIDEKDFVVVMVSK 75 (77)
T ss_pred CCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCC-----CCHHHcCCCCCCEEEEEEec
Confidence 357999999999876542 22334445777777532 38899999888888776643
Done!