Query 009883
Match_columns 523
No_of_seqs 142 out of 189
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 18:28:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009883hhsearch_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 8E-123 2E-127 920.6 15.8 388 1-476 1-388 (388)
2 PF09328 Phytochelatin_C: Doma 100.0 8E-114 2E-118 841.8 24.5 264 220-483 1-264 (264)
3 PF05023 Phytochelatin: Phytoc 100.0 4.5E-82 9.7E-87 608.9 15.4 211 3-217 1-212 (212)
4 PF13529 Peptidase_C39_2: Pept 98.7 2.8E-08 6.1E-13 84.7 6.4 117 51-182 11-144 (144)
5 cd02549 Peptidase_C39A A sub-f 98.3 7E-06 1.5E-10 71.5 10.4 130 50-202 1-132 (141)
6 PF03412 Peptidase_C39: Peptid 97.9 9.2E-06 2E-10 70.4 4.4 116 47-200 4-119 (131)
7 cd02259 Peptidase_C39_like Pep 97.7 0.00052 1.1E-08 58.1 11.4 114 50-200 1-114 (122)
8 cd02418 Peptidase_C39B A sub-f 97.7 0.00048 1E-08 59.7 11.0 122 47-200 3-124 (136)
9 PF14399 Transpep_BrtH: NlpC/p 97.5 0.0022 4.7E-08 63.8 14.4 152 55-215 1-164 (317)
10 cd02424 Peptidase_C39E A sub-f 97.4 0.00096 2.1E-08 58.5 9.5 119 47-200 3-122 (129)
11 cd02423 Peptidase_C39G A sub-f 97.4 0.0025 5.3E-08 54.8 10.9 116 49-199 5-121 (129)
12 cd02420 Peptidase_C39D A sub-f 97.3 0.0026 5.5E-08 54.8 10.6 112 49-200 5-118 (125)
13 cd02425 Peptidase_C39F A sub-f 97.0 0.0077 1.7E-07 51.5 10.1 115 47-198 3-117 (126)
14 TIGR03796 NHPM_micro_ABC1 NHPM 96.9 0.0042 9.2E-08 69.1 9.4 114 47-198 4-117 (710)
15 cd02419 Peptidase_C39C A sub-f 96.7 0.027 5.8E-07 48.5 11.3 114 49-200 5-118 (127)
16 TIGR01193 bacteriocin_ABC ABC- 96.5 0.036 7.9E-07 61.9 13.3 119 50-198 1-119 (708)
17 PF11814 DUF3335: Peptidase_C3 96.1 0.092 2E-06 52.2 12.2 157 47-218 3-207 (207)
18 PF09778 Guanylate_cyc_2: Guan 95.9 0.049 1.1E-06 54.2 9.3 84 107-199 95-198 (212)
19 cd02417 Peptidase_C39_likeA A 91.5 3.1 6.6E-05 35.5 10.7 110 54-200 5-114 (121)
20 cd02421 Peptidase_C39_likeD A 90.1 4.9 0.00011 34.5 10.8 108 56-199 7-114 (124)
21 COG2274 SunT ABC-type bacterio 89.9 1 2.2E-05 51.9 8.1 116 46-199 3-118 (709)
22 TIGR03375 type_I_sec_LssB type 88.3 2.2 4.7E-05 47.9 9.2 103 58-198 2-107 (694)
23 TIGR01846 type_I_sec_HlyB type 85.9 4 8.6E-05 46.0 9.5 104 57-198 1-104 (694)
24 TIGR03797 NHPM_micro_ABC2 NHPM 78.7 15 0.00033 41.3 10.6 100 58-198 5-104 (686)
25 COG3271 Predicted double-glyci 76.7 3.4 7.4E-05 41.1 4.3 103 48-182 36-139 (201)
26 PF12385 Peptidase_C70: Papain 71.0 37 0.0008 33.2 9.6 130 43-199 22-160 (166)
27 KOG4621 Uncharacterized conser 59.9 53 0.0011 31.5 8.1 75 121-201 77-152 (167)
28 PF05381 Peptidase_C21: Tymovi 54.9 7.6 0.00016 35.3 1.7 55 62-120 8-62 (104)
29 PRK10227 DNA-binding transcrip 53.7 26 0.00056 32.3 5.1 42 72-113 28-69 (135)
30 TIGR02044 CueR Cu(I)-responsiv 52.6 14 0.00029 33.3 3.0 42 72-113 28-69 (127)
31 cd04770 HTH_HMRTR Helix-Turn-H 51.6 16 0.00034 32.4 3.2 38 77-114 33-70 (123)
32 cd04787 HTH_HMRTR_unk Helix-Tu 50.5 14 0.00031 33.5 2.8 43 72-114 28-70 (133)
33 cd04768 HTH_BmrR-like Helix-Tu 49.8 15 0.00033 31.6 2.7 42 72-113 28-69 (96)
34 TIGR02047 CadR-PbrR Cd(II)/Pb( 48.2 18 0.0004 32.7 3.1 37 77-113 33-69 (127)
35 cd04763 HTH_MlrA-like Helix-Tu 48.1 38 0.00082 26.9 4.6 44 68-111 24-67 (68)
36 cd04788 HTH_NolA-AlbR Helix-Tu 48.1 17 0.00036 31.4 2.7 43 72-114 28-70 (96)
37 cd04784 HTH_CadR-PbrR Helix-Tu 48.1 17 0.00037 32.5 2.9 37 77-113 33-69 (127)
38 cd04785 HTH_CadR-PbrR-like Hel 47.7 18 0.0004 32.5 3.0 42 72-113 28-69 (126)
39 cd01104 HTH_MlrA-CarA Helix-Tu 47.3 38 0.00082 26.5 4.4 52 59-111 15-67 (68)
40 PRK13752 putative transcriptio 46.1 18 0.00039 33.7 2.8 43 72-114 35-77 (144)
41 COG5559 Uncharacterized conser 43.5 12 0.00026 31.3 1.0 18 465-482 8-25 (65)
42 cd01282 HTH_MerR-like_sg3 Heli 43.1 24 0.00052 31.2 3.0 42 72-114 28-69 (112)
43 cd04781 HTH_MerR-like_sg6 Heli 42.7 24 0.00053 31.4 3.0 39 77-115 32-70 (120)
44 cd04783 HTH_MerR1 Helix-Turn-H 41.1 25 0.00055 31.5 2.9 38 77-114 33-70 (126)
45 PF13411 MerR_1: MerR HTH fami 40.4 32 0.00069 27.0 3.0 54 58-112 14-67 (69)
46 PRK13749 transcriptional regul 40.2 29 0.00063 31.9 3.1 39 77-115 36-74 (121)
47 cd01106 HTH_TipAL-Mta Helix-Tu 40.1 27 0.00059 30.2 2.8 43 72-114 28-70 (103)
48 PRK09514 zntR zinc-responsive 39.8 56 0.0012 30.2 5.0 42 72-113 29-70 (140)
49 cd01108 HTH_CueR Helix-Turn-He 39.2 29 0.00062 31.3 2.9 41 73-113 29-69 (127)
50 cd04786 HTH_MerR-like_sg7 Heli 38.3 29 0.00062 31.9 2.8 43 72-114 28-70 (131)
51 TIGR02043 ZntR Zn(II)-responsi 37.8 30 0.00066 31.5 2.9 42 72-113 29-70 (131)
52 PRK15002 redox-sensitivie tran 37.6 59 0.0013 30.9 4.8 41 72-113 39-79 (154)
53 cd04782 HTH_BltR Helix-Turn-He 37.6 34 0.00073 29.5 3.0 46 68-113 23-69 (97)
54 cd01109 HTH_YyaN Helix-Turn-He 37.3 37 0.0008 29.8 3.3 42 72-113 28-69 (113)
55 TIGR02051 MerR Hg(II)-responsi 37.0 30 0.00066 31.1 2.7 43 72-114 27-69 (124)
56 cd04776 HTH_GnyR Helix-Turn-He 36.9 31 0.00068 30.9 2.8 40 72-113 28-67 (118)
57 cd04764 HTH_MlrA-like_sg1 Heli 36.2 68 0.0015 25.3 4.3 51 60-111 16-66 (67)
58 PF04157 EAP30: EAP30/Vps36 fa 34.4 39 0.00084 33.3 3.2 113 38-159 36-167 (223)
59 cd04790 HTH_Cfa-like_unk Helix 34.0 38 0.00082 32.4 3.0 43 72-114 29-71 (172)
60 PF14538 Raptor_N: Raptor N-te 33.9 4.3E+02 0.0092 25.2 10.1 70 119-202 65-135 (154)
61 TIGR01950 SoxR redox-sensitive 33.6 39 0.00084 31.5 2.9 37 77-113 33-69 (142)
62 COG2841 Uncharacterized protei 32.3 42 0.0009 28.9 2.6 31 284-314 33-68 (72)
63 cd04773 HTH_TioE_rpt2 Second H 31.9 45 0.00098 29.4 2.9 43 72-114 28-70 (108)
64 PF08099 Toxin_27: Scorpion ca 31.7 14 0.0003 27.0 -0.2 20 484-506 5-24 (33)
65 cd04780 HTH_MerR-like_sg5 Heli 31.7 1E+02 0.0022 26.8 5.0 60 68-136 23-84 (95)
66 PF05543 Peptidase_C47: Stapho 30.9 2.2E+02 0.0048 28.2 7.6 115 46-174 15-133 (175)
67 cd04789 HTH_Cfa Helix-Turn-Hel 29.7 51 0.0011 28.8 2.8 40 72-112 29-68 (102)
68 TIGR02054 MerD mercuric resist 28.6 53 0.0011 30.0 2.9 43 72-114 31-73 (120)
69 COG3323 Uncharacterized protei 28.4 42 0.0009 30.9 2.1 53 117-174 7-59 (109)
70 PF14214 Helitron_like_N: Heli 28.1 75 0.0016 29.9 3.9 41 220-267 102-142 (184)
71 cd04775 HTH_Cfa-like Helix-Tur 27.4 59 0.0013 28.3 2.8 44 69-112 25-68 (102)
72 cd01111 HTH_MerD Helix-Turn-He 27.3 62 0.0013 28.7 3.0 46 68-113 23-69 (107)
73 cd01107 HTH_BmrR Helix-Turn-He 27.2 61 0.0013 28.4 2.9 38 78-115 35-72 (108)
74 cd01110 HTH_SoxR Helix-Turn-He 26.3 61 0.0013 30.0 2.9 41 72-113 29-69 (139)
75 cd01105 HTH_GlnR-like Helix-Tu 25.1 76 0.0016 26.9 3.0 43 72-114 29-71 (88)
76 COG0789 SoxR Predicted transcr 24.5 71 0.0015 27.8 2.8 43 72-114 28-70 (124)
77 PF09312 SurA_N: SurA N-termin 24.2 92 0.002 27.7 3.5 43 96-138 59-111 (118)
78 cd04765 HTH_MlrA-like_sg2 Heli 24.0 1.5E+02 0.0033 25.9 4.7 44 71-115 28-72 (99)
79 cd01805 RAD23_N Ubiquitin-like 23.4 3.3E+02 0.0071 21.7 6.3 55 124-183 19-75 (77)
80 PF14104 DUF4277: Domain of un 23.4 68 0.0015 29.6 2.6 51 50-108 39-89 (115)
81 PTZ00445 p36-lilke protein; Pr 22.7 2.1E+02 0.0045 29.3 6.0 97 106-205 33-158 (219)
82 cd04777 HTH_MerR-like_sg1 Heli 22.3 88 0.0019 27.2 3.0 36 78-113 32-67 (107)
83 cd04779 HTH_MerR-like_sg4 Heli 20.8 96 0.0021 28.8 3.0 43 72-115 28-70 (134)
No 1
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=7.5e-123 Score=920.63 Aligned_cols=388 Identities=62% Similarity=1.120 Sum_probs=368.4
Q ss_pred CcccccccccCCCCCccccCChhhHHHHHHHHhcCCccccccccccccccCCCccccHHHHHHHHHhccCCCCCCcCCCc
Q 009883 1 MAMAGLYRRMLPSPPAIDFASSEGKQLFLEAIQGGTMEGFYRLISYFQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPW 80 (523)
Q Consensus 1 ~~~~sfYrR~LP~P~~I~fsS~EGk~Lf~eAl~~g~~e~ff~La~qF~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpw 80 (523)
|+|++||||.||. ++|+|+|.+||++|.|||+.|+||+||.|++||+||++|||||+|||+||||||.|||+|.|||||
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 009883 81 RWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGT 160 (523)
Q Consensus 81 Rwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGg 160 (523)
|||||+|||||+|++.|++.||+|++|.|||+|||++|++++.++.++|+||..|+.|..++|+++|++|+|++|||||+
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 ccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhccccCCcCCceeeEEEEeCCCCCCCcceeeeccCCChHHHH
Q 009883 161 GHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVSRPHREPGLLYTLSCKHENWVGIA 240 (523)
Q Consensus 161 GHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~SgksRG~ilIs~~~~~p~~l~~l~~~~~~w~~~a 240 (523)
||||||||||+++|++||||||||||||||||++.||+||..||.+||++||||+|++++++|+ +|+++|++++|..++
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 HHHHhhhchhhccCCCCCHHHHHHHHHhcCCcchhchheeeeEEEeccCCCCCCCHHHHhhhhhHHHHHHHHhccchhHH
Q 009883 241 KYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEKGRLALKEEVLRQVQETLLFKH 320 (523)
Q Consensus 241 ~~l~~~~p~l~~~~~~~~~~~v~~~~~~~lp~~~~~~ikw~~evr~~e~~~~~ls~ee~~rl~~k~~~l~qi~~t~l~~~ 320 (523)
|||.+++|. |.++.|.++|.++++|| ++|+|+.||.+++++.|| +|+.++
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 66778999999999999 899999999999999998 445333
Q ss_pred HHHhhhccccccccccccCCCCChHHHHHHhhchhhhhhhccCCCCCcceecccccceeeeCCCCCeEEEeeEEEeCCcc
Q 009883 321 VVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCLKANSDKPVTLVSGTVVNGSIE 400 (523)
Q Consensus 321 v~~~~~s~~~~~~~~~~~~~~~~l~~~~~~vccqga~~l~g~~~~~~~~c~~et~~~~~~~~~~~~~~~~~g~~~~~~~e 400 (523)
|..++++ .+++.+||+|+++++|. .+..|||++||++|.|.-++.-.|++
T Consensus 289 ---------------st~~y~~---f~~h~~~c~~~e~~s~~--~~~~~~c~~~~~ac~kg~~e~~~t~~---------- 338 (388)
T KOG0632|consen 289 ---------------STVTYED---FAAHKNCCTGVEILSGA--FSAEFCCPETCVACIKGVLEEIQTVV---------- 338 (388)
T ss_pred ---------------hhhhHHh---hhhhhcccccceeecCC--cccccccHHHHHHhhhchhhhhhhee----------
Confidence 1233444 67899999999999998 67899999999999998777766663
Q ss_pred ceeeEeecCCCCCCCccCCCCCCcceecCCcchHHHHHHHhCCCCccCCCCchHHHHHHhhhccCCCCchhHHHHH
Q 009883 401 QEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQILGLVTTENLPTLLQEEV 476 (523)
Q Consensus 401 q~vd~l~p~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~e~~~lvs~~~lp~~l~~ev 476 (523)
.+|.++||+|+|||||||+||+||+|..|..|+..+++.-+.|+++|.||
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 38999999999999999999999999999999999999999999999986
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=8.2e-114 Score=841.76 Aligned_cols=264 Identities=67% Similarity=1.078 Sum_probs=262.2
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhchhhccCCCCCHHHHHHHHHhcCCcchhchheeeeEEEeccCCCCCCCHHHH
Q 009883 220 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLFTSLPSNFGEFVKWVAEVRRREDGDHSLSQEEK 299 (523)
Q Consensus 220 ~~~p~~l~~l~~~~~~w~~~a~~l~~~~p~l~~~~~~~~~~~v~~~~~~~lp~~~~~~ikw~~evr~~e~~~~~ls~ee~ 299 (523)
+++|++|||+||+||+|.+|||||++|||.|||+++++||++||++||+|||+||++||||||||||+|||+++||.|||
T Consensus 1 ~r~P~lLYTlSCkhEsW~s~AKyL~eDvP~LLkse~v~~v~~vls~vf~SlPsn~~~FIKWVaEVRR~Edg~~~LS~EEk 80 (264)
T PF09328_consen 1 HRAPSLLYTLSCKHESWISMAKYLMEDVPRLLKSEDVKDVEEVLSVVFKSLPSNFGEFIKWVAEVRRQEDGGSSLSKEEK 80 (264)
T ss_pred CCCCceeEEeecCcCcHHHHHHHHHHHHHHHhhhcccCcHHHHHHHHHhcCchhHHHHhhhheeEEecccCCCCCCHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHHHHhccchhHHHHHhhhccccccccccccCCCCChHHHHHHhhchhhhhhhccCCCCCcceeccccccee
Q 009883 300 GRLALKEEVLRQVQETLLFKHVVTFLSSVNSCCRSMSVLVHKNELPDIAEKVCCQGARILAGKFDSSERFYCRETCVKCL 379 (523)
Q Consensus 300 ~rl~~k~~~l~qi~~t~l~~~v~~~~~s~~~~~~~~~~~~~~~~l~~~~~~vccqga~~l~g~~~~~~~~c~~et~~~~~ 379 (523)
+||++|++||||||+|+|||||++|+++.+|||+++++++++|+||+|||+||||||+||+|+++++++|||+|||+||+
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 eeCCCCCeEEEeeEEEeCCccceeeEeecCCCCCCCccCCCCCCcceecCCcchHHHHHHHhCCCCccCCCCchHHHHHH
Q 009883 380 KANSDKPVTLVSGTVVNGSIEQEVDVLVPSSQIGGCGCGCGPSNCIGIYPAGNDILTVLILALPKETWSGIRDEKLSRQI 459 (523)
Q Consensus 380 ~~~~~~~~~~~~g~~~~~~~eq~vd~l~p~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~e~ 459 (523)
|+|||||+|||||+||+||+|||||||||++++++++|+++.+++++|||+++||||||||||||+||+|||||+|++||
T Consensus 161 k~n~d~~~tvvsGtVv~~g~Eq~VD~LvP~s~~~~~~c~~~~~~~~~~hPs~~DVLTvLLLALpp~TWs~Ikde~l~~Ei 240 (264)
T PF09328_consen 161 KANGDGPKTVVSGTVVSGGSEQGVDVLVPSSQTKTSCCNSGSSNEIGMHPSSNDVLTVLLLALPPSTWSGIKDEKLLAEI 240 (264)
T ss_pred eeCCCCceEEEeeeEEcCCCccceeEEeccccCCCCccCCCCCCccccCCCcccHHHHHHHhCCccccccCccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCchhHHHHHHHHHHHH
Q 009883 460 LGLVTTENLPTLLQEEVLHLRRQL 483 (523)
Q Consensus 460 ~~lvs~~~lp~~l~~ev~hl~~ql 483 (523)
++||||||||++|||||+||||||
T Consensus 241 ~~LvSte~LP~lLQeEVlHLrrQL 264 (264)
T PF09328_consen 241 QSLVSTENLPDLLQEEVLHLRRQL 264 (264)
T ss_pred HHHhhhhhCcHHHHHHHHHHHhcC
Confidence 999999999999999999999997
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=4.5e-82 Score=608.85 Aligned_cols=211 Identities=55% Similarity=1.051 Sum_probs=170.0
Q ss_pred ccccccccCCCCCccccCChhhHHHHHHHHhcCCccccccccccccccCCCccccHHHHHHHHHhccCC-CCCCcCCCcc
Q 009883 3 MAGLYRRMLPSPPAIDFASSEGKQLFLEAIQGGTMEGFYRLISYFQTQSEPAYCGLASLSMVLNALAID-PGRKWKGPWR 81 (523)
Q Consensus 3 ~~sfYrR~LP~P~~I~fsS~EGk~Lf~eAl~~g~~e~ff~La~qF~TQ~npAyCGvASlamVLNAL~iD-P~r~wkgpwR 81 (523)
+.+||+|+||+ ++|+|+|+||++||.+| ++|++||+|++||+||+|++||||||++||||||++| |++.||||||
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 009883 82 WFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTG 161 (523)
Q Consensus 82 wf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgG 161 (523)
||+|++|+||++++.++++||||+||+|||+|+|++|+++++++.++++||++|++++++++++|||||+|++|||+|+|
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 cccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhccccCCcCCceeeEEEEe
Q 009883 162 HFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDDATGQRRGFVLVS 217 (523)
Q Consensus 162 HFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~SgksRG~ilIs 217 (523)
|||||||||+++|+|||||||||||||||||+++||+||+++|++|||+||||+|+
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 99999999999999999999999999999999999999999999999999999996
No 4
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=98.70 E-value=2.8e-08 Score=84.68 Aligned_cols=117 Identities=25% Similarity=0.220 Sum_probs=66.4
Q ss_pred CCCccccHHHHHHHHHhccCCCCCC----------cCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEE
Q 009883 51 SEPAYCGLASLSMVLNALAIDPGRK----------WKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEA 120 (523)
Q Consensus 51 ~npAyCGvASlamVLNAL~iDP~r~----------wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~ 120 (523)
.....||+||++|||+.+|+.+.+. +..+..+|-.++ ......|+....+..+++..|..+.
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 7889999999999999998754322 000111111000 0123457888899999999987443
Q ss_pred EeCCCCCHHHHHHHHHHhhcCCCceEEEEeec--cc-----ccccCCccccccceeecCCCeEEEEecC
Q 009883 121 FRTNQSTIDDFRKYIIRCSASEDCHVISSYHR--GA-----FKQTGTGHFSPIGGYHAGRDMALILDVA 182 (523)
Q Consensus 121 yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R--~~-----LgQtGgGHFSPIGGYh~~tD~VLILDVA 182 (523)
.....+++++++.|. .++.||++..- .. .....+|||--|-||+..+ .|.|.|++
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 334567777776664 57799999972 22 2567899999999999988 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=98.28 E-value=7e-06 Score=71.48 Aligned_cols=130 Identities=21% Similarity=0.153 Sum_probs=85.7
Q ss_pred cCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccc-cchHHHhhcCCCHHHHHHH-HHHcCCeEEEEeCCCCC
Q 009883 50 QSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCC-EPLEKVKEKGISFGKLVCL-AHCAGAKVEAFRTNQST 127 (523)
Q Consensus 50 Q~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc-~~le~Vk~~GiTL~Ela~L-A~c~G~~V~~yra~~~S 127 (523)
|+.+..||++|++|+|+-+|+..... .+...- .........|++..++... ++..|++++.+...
T Consensus 1 ~~~~~~C~~~slamvl~~~g~~~~~~----------~l~~~~~~~~~~~~~~g~~~~~l~~~~a~~~G~~~~~~~~~--- 67 (141)
T cd02549 1 PQLENGCGPTSLAMVLSYLGVKVTKP----------QLAAEGNTYDFAKDGYGTYPKPIVSAAARKYGLVVRPLTGL--- 67 (141)
T ss_pred CCCCCccHHHHHHHHHHhcCCCCCHH----------HHHhhccccccCCCCCCcCHHHHHHHHHhhCCCcEEECCCH---
Confidence 46788999999999999998763321 000000 0000122468999999999 99999987654432
Q ss_pred HHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhccc
Q 009883 128 IDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDR 202 (523)
Q Consensus 128 ldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~t 202 (523)
.. +++.++ .+.++|+...- .....++|||--|.||+ +.+.++|.|++. ..+..++.+++-++-..
T Consensus 68 ~~-----~~~~l~-~~~Pvi~~~~~-~~~~~~~gH~vVv~g~~-~~~~~~i~DP~~--~~~~~~~~~~f~~~w~~ 132 (141)
T cd02549 68 LA-----LLRQLA-AGHPVIVSVNL-GVSITPSGHAMVVIGYD-RKGNVYVNDPGG--GRRLVVSFDEFEKAWKR 132 (141)
T ss_pred HH-----HHHHHH-CCCeEEEEEec-CcccCCCCeEEEEEEEc-CCCCEEEECCCC--CcCEEEeHHHHHHHHHH
Confidence 11 333333 56788887653 12234589999999999 456699999964 45778998877666543
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=97.95 E-value=9.2e-06 Score=70.43 Aligned_cols=116 Identities=25% Similarity=0.242 Sum_probs=77.3
Q ss_pred ccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 47 FQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
+..|.++.-||+|+++|+++-+|+.-+.. .+...+ .....|+|+.++...|+..|++++.++.+..
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~~g~~~s~~----------~l~~~~----~~~~~g~s~~~L~~~~~~~gl~~~~~~~~~~ 69 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKYYGIPVSEE----------ELRRQL----GTSEEGTSLADLKRAARKYGLKAKAVKLNFE 69 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHHTT----HH----------HHHCCT----T-BTTB--CCCHHHHHHHTTEEEEEEE--GG
T ss_pred eEEeCCCCCHHHHHHHHHHHHhCCCchHH----------HHHHHh----cCCccCCCHHHHHHHHHhcccceeeeecchh
Confidence 45689999999999999999998654331 122111 1346899999999999999999998874422
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
+| .+-...+|+.- +.|||--|-++ ..++++|.|+ +..+.|++.++|.+.-
T Consensus 70 ---~l--------~~~~~P~I~~~--------~~~h~vVi~~~--~~~~~~i~dP---~~g~~~~~~~~f~~~w 119 (131)
T PF03412_consen 70 ---KL--------KRLPLPAIAHL--------KDGHFVVIYKI--DDGRVLIYDP---KKGKIKLSKEEFEEIW 119 (131)
T ss_dssp ---GC--------TCGGSSEEEEE--------CCCEEEEEEEE--CCCEEEECCT---TTCEEEEEHHHHHHHE
T ss_pred ---hh--------hhccccEEEEe--------cCcceEEEEeE--cCcEEEEEeC---CCCeEEEeHHHHHhhC
Confidence 22 22233555544 78999999888 8889999998 5678999999887643
No 7
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=97.73 E-value=0.00052 Score=58.05 Aligned_cols=114 Identities=25% Similarity=0.340 Sum_probs=82.6
Q ss_pred cCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHH
Q 009883 50 QSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTID 129 (523)
Q Consensus 50 Q~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~Sld 129 (523)
|.+..-||+++++|+++-+++..... .+. ........|.++.++..+|+..|++++.+..+ .+
T Consensus 1 ~~~~~~~gl~~l~~i~~~~g~~~~~~----------~l~----~~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~~---~~ 63 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYFGIPVRRD----------VLL----NAQQRRQQGLSLADLVSLANKLGLTAQGVKLP---LA 63 (122)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCHH----------HHH----HHHhhccCCCCHHHHHHHHHHcCCeeeEEEcC---HH
Confidence 55666899999999999998764432 110 00122457899999999999999999877643 33
Q ss_pred HHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 130 DFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 130 eFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
.+ ..-+..+|+- .++|||--|.+++ .+.++|.|++ ...+.|++.+.|-+..
T Consensus 64 ~l--------~~~~~P~i~~--------~~~~~~~Vl~~~~--~~~~~i~dp~--~~~~~~~~~~~l~~~w 114 (122)
T cd02259 64 AL--------SRLQLPALLL--------WKQGHFVILYGAD--KGQVLIADPL--EEGPVTLSESELEERW 114 (122)
T ss_pred Hh--------ccCCCCEEEE--------cCCCcEEEEEEEc--CCEEEEECCc--ccCCEEeCHHHHHhhC
Confidence 22 2233455554 4789999999998 6689999986 5788899999887644
No 8
>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=97.70 E-value=0.00048 Score=59.67 Aligned_cols=122 Identities=15% Similarity=0.118 Sum_probs=84.4
Q ss_pred ccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 47 FQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
+.-|.++..||+++++|+++=+|++.... .+-.. ......|+++..+...|+..|++++.++.+..
T Consensus 3 ~~~q~~~~~~gl~~l~~~~~~~g~~~~~~----------~l~~~----~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~ 68 (136)
T cd02418 3 YVLQVDEMDCGAACLAMIAKYYGKNYSLA----------KLREL----AGTDREGTSLLGLVKAAEKLGFETRAVKADMD 68 (136)
T ss_pred eEEecCcccHHHHHHHHHHHHhCCCCCHH----------HHHHH----cCCCCCCcCHHHHHHHHHHCCCeeEEEEcccc
Confidence 45677888999999999999998764432 11110 01234789999999999999999988875422
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
. ..+ . .-...+|+-.. . ..+.|||--|.+++ .+.|+|.|+ ..++.+++.++|-+..
T Consensus 69 ~-~~l----~----~~~~P~I~~~~-~---~~~~~~~~Vl~~~~--~~~~~i~dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 69 L-FEL----K----DIPLPFIAHVI-K---EWKLNHYVVVYKIK--KKKILIADP---AVGITKISKEEFEKEW 124 (136)
T ss_pred h-hhH----h----cCCCCEEEEEc-c---CCCCCeEEEEEEEc--CCEEEEECC---CCCCEEeeHHHHHhhC
Confidence 1 011 1 12335555332 1 24789999999998 567999997 5679999999986643
No 9
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=97.53 E-value=0.0022 Score=63.81 Aligned_cols=152 Identities=16% Similarity=0.039 Sum_probs=102.4
Q ss_pred cccHHHHHHHHHhccCCC-CCC---cCCCccccccchhccccchHHHhhcCCCH-HHHHHHHHHcCCeEEEEeCCCCCHH
Q 009883 55 YCGLASLSMVLNALAIDP-GRK---WKGPWRWFDESMLDCCEPLEKVKEKGISF-GKLVCLAHCAGAKVEAFRTNQSTID 129 (523)
Q Consensus 55 yCGvASlamVLNAL~iDP-~r~---wkgpwRwf~E~mLdcc~~le~Vk~~GiTL-~Ela~LA~c~G~~V~~yra~~~Sld 129 (523)
+|+-.+++++|+..|++- ... -.++|.+.-..+ ....++ ..-.|-+. +-+..+++..|++++... ..+.+
T Consensus 1 hC~~~~l~~ll~~~g~~~~e~l~fglg~g~gf~y~~~-~~~~~~--~~~~~r~~~~~~~~~~~~lG~~~~~~~--~~~~~ 75 (317)
T PF14399_consen 1 HCESNALRDLLAHYGLPLSEALIFGLGSGLGFSYLPF-PDSNPP--PLLGGRSPPDFEENLLERLGIKYEWRE--FSSPD 75 (317)
T ss_pred CchhHHHHHHHHhcCCCCCHHHHHHHcCCcceEEEec-cccCCC--eeecCCCchHHHHHHHHHCCceEEEEe--cCCHH
Confidence 599999999999999762 111 011222110000 000010 11223333 455678899999888655 35678
Q ss_pred HHHHHHHHhhcCCCceEEEEeecccc-------cccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhccc
Q 009883 130 DFRKYIIRCSASEDCHVISSYHRGAF-------KQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAMDR 202 (523)
Q Consensus 130 eFR~~v~~~~ss~d~~vIVNY~R~~L-------gQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~t 202 (523)
+..+.|++.+. .+..|+|..+..-| .....+|+.-|-|||++.+.|+|.|. ..+++..+|.+.|-+|+..
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 88888888777 56788888776665 23367999999999999999999998 5778899999999999988
Q ss_pred cCCcCCceeeEEE
Q 009883 203 VDDATGQRRGFVL 215 (523)
Q Consensus 203 iD~~SgksRG~il 215 (523)
..+ ...+++.+.
T Consensus 153 ~~~-~~~~~~~~~ 164 (317)
T PF14399_consen 153 EGI-PFPPKNRWY 164 (317)
T ss_pred cCC-CCCCCceEE
Confidence 874 223344443
No 10
>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=97.45 E-value=0.00096 Score=58.53 Aligned_cols=119 Identities=17% Similarity=0.241 Sum_probs=80.0
Q ss_pred ccccCCCccccHHHHHHHHHh-ccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCC
Q 009883 47 FQTQSEPAYCGLASLSMVLNA-LAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQ 125 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNA-L~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~ 125 (523)
+.-|.+..-||+|+++|+++- .|+.-... .+-.. ......|+++.++...|+..|++++.++.+
T Consensus 3 ~~~q~~~~dcgla~l~~i~~~~~g~~~~~~----------~l~~~----~~~~~~g~s~~~l~~~a~~~Gl~~k~~~~~- 67 (129)
T cd02424 3 IIKQTDLNDCGIAVIQMLYNHYYKKKYDLN----------ELKIK----ANLKKNGLSIYDLENLAKKFGLETESYQGS- 67 (129)
T ss_pred eEEecCccchHHHHHHHHHHHhcCCCccHH----------HHHHH----hCCCCCCccHHHHHHHHHHcCCceeEEEcC-
Confidence 345778889999999999999 88653321 00000 112357999999999999999999999854
Q ss_pred CCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 126 STIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 126 ~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
.++ +.+. ...-..|++ ..++.||--+.+.+. +.|+|.|+ ..++.+++.+++-+.-
T Consensus 68 --~~~----l~~~--~~p~P~i~~-------~~~~~hfvVl~~~~~--~~v~I~DP---~~g~~~~s~~~f~~~w 122 (129)
T cd02424 68 --FLE----FLEL--KNKFIILLK-------SNGLNHFVIVKKIKK--NKFIVLDP---KKGKYKITYKEFEKIF 122 (129)
T ss_pred --HHH----Hhhc--cCCEEEEEe-------cCCCCeEEEEEEEEC--CEEEEECC---CCCCEEeCHHHHHHHh
Confidence 322 2211 112345554 134459988887654 55999998 4688899988775543
No 11
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=97.37 E-value=0.0025 Score=54.77 Aligned_cols=116 Identities=26% Similarity=0.303 Sum_probs=78.7
Q ss_pred ccCCCccccHHHHHHHHHhcc-CCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCC
Q 009883 49 TQSEPAYCGLASLSMVLNALA-IDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQST 127 (523)
Q Consensus 49 TQ~npAyCGvASlamVLNAL~-iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~S 127 (523)
-|.+...||+++++|+++-.+ +.-+.. .+.... .....|.++.++..+|+..|++++.++.+
T Consensus 5 ~q~~~~~~~l~~l~~~~~~~g~~~~~~~----------~l~~~~----~~~~~~~s~~~l~~~a~~~Gl~~~~~~~~--- 67 (129)
T cd02423 5 RQSYDFSCGPAALATLLRYYGGINITEQ----------EVLKLM----LIRSEGFSMLDLKRYAEALGLKANGYRLN--- 67 (129)
T ss_pred ecCCCCChHHHHHHHHHHhcCCCCCCHH----------HHHHHh----CcccCCcCHHHHHHHHHHCCCcceEEEcC---
Confidence 356667999999999999998 653331 010000 01246899999999999999999887753
Q ss_pred HHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHh
Q 009883 128 IDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 199 (523)
Q Consensus 128 ldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eA 199 (523)
.+++. . -.-.+|+-. ...++|||--|.+++ .+.++|.|++. ++.+++.++|-+.
T Consensus 68 ~~~L~----~----~~lP~i~~~-----~~~~~~~~vvl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~ 121 (129)
T cd02423 68 LDKLN----A----LQIPVIVLV-----NNGGYGHFVVIKGID--GDRVLVGDPAL---GNISMSREEFERI 121 (129)
T ss_pred HHHHh----h----CCCCEEEEE-----ecCCCceEEEEEEEe--CCEEEEECCCC---CCcccCHHHHHHH
Confidence 33332 1 122444433 123478998888888 67899999853 5789998887653
No 12
>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=97.33 E-value=0.0026 Score=54.79 Aligned_cols=112 Identities=21% Similarity=0.282 Sum_probs=79.4
Q ss_pred ccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHH--HhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 49 TQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEK--VKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 49 TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~--Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
-|.+...||+++++++++-.|+.-... -+. +. ....|.+..++...|+..|++++.++.+
T Consensus 5 ~q~~~~~~gl~~l~~i~~~~g~~~~~~-----------~l~-----~~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~-- 66 (125)
T cd02420 5 LQMEATECGAASLAIILAYYGRYVPLS-----------ELR-----IACGVSRDGSNASNLLKAAREYGLTAKGYKKD-- 66 (125)
T ss_pred eeCcccCHHHHHHHHHHHHcCCCCCHH-----------HHH-----HHcCCCCCCCCHHHHHHHHHHcCcccceEecC--
Confidence 355567899999999999998753331 010 11 1246899999999999999999887743
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
.+.+.+ -.-++|+-. +.|||--|.+++ .|.++|.|++. .|.+++.++|-+..
T Consensus 67 -~~~L~~--------~~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~~ 118 (125)
T cd02420 67 -LEALRE--------VSLPAIVFW--------NFNHFLVVEGFD--KRKVFLNDPAT---GRRTVSLEEFDQSF 118 (125)
T ss_pred -HHHHhc--------CCCCEEEEe--------CCCEEEEEEEEe--CCEEEEECCCc---CceeecHHHHHhhC
Confidence 333321 223555532 569999999988 55799999964 79999998876543
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=96.99 E-value=0.0077 Score=51.51 Aligned_cols=115 Identities=19% Similarity=0.260 Sum_probs=79.8
Q ss_pred ccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 47 FQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
+..|.++.-||+++++|+++-++++-... .+... ......|+++..+..+|+..|++++.++.+..
T Consensus 3 ~~~q~~~~~~~l~~l~~~~~~~~~~~~~~----------~l~~~----~~~~~~~~~~~~l~~~a~~~gl~~~~~~~~~~ 68 (126)
T cd02425 3 PILQNNQTECGLACYAMILNYFGYKVSLN----------ELREK----YELGRDGLSLSYLKQLLEEYGFKCKVYKISFK 68 (126)
T ss_pred eEeecccccHHHHHHHHHHHHhCCCCCHH----------HHHHh----ccCCCCCcCHHHHHHHHHHCCCcceEEEEchH
Confidence 45688888999999999999998775442 11110 01234689999999999999999998875420
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHH
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 198 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~e 198 (523)
+. +... .-.+|+-. .+|||--|.+++ .+.++|.|+.. ++.|++.++|-+
T Consensus 69 --~~----l~~~----~lP~I~~~--------~~~~~~Vl~~~~--~~~~~i~dp~~---~~~~~~~~~l~~ 117 (126)
T cd02425 69 --KN----LYPL----KLPVIIFW--------NNNHFVVLEKIK--KNKVTIVDPAI---GRIKISIDEFLE 117 (126)
T ss_pred --HH----HhhC----CCCEEEEE--------cCCcEEEEEEEE--CCEEEEEcCCC---CCEEECHHHHHh
Confidence 22 2211 22444432 248999999984 55799999854 578999988754
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=96.85 E-value=0.0042 Score=69.07 Aligned_cols=114 Identities=25% Similarity=0.271 Sum_probs=85.2
Q ss_pred ccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 47 FQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
+.-|.+.+=||+|+++|++|-.|.+-+.. .+-+ ...+.+.|+++.++..+|+..|++++.++.+
T Consensus 4 ~i~Q~~~~dCg~acl~mi~~~~g~~~~~~----------~lr~----~~~~~~~g~s~~~l~~~~~~~g~~~~~~~~~-- 67 (710)
T TIGR03796 4 TVLQMEAVECGAASLAMILAYYGRYVPLE----------ELRE----ECGVSRDGSKASNLLKAARSYGLEAKGFRKE-- 67 (710)
T ss_pred eEeecccccHHHHHHHHHHHHcCCCCCHH----------HHHH----HcCCCCCCCCHHHHHHHHHHCCCEeEEEecC--
Confidence 56688889999999999999998663331 1111 1124568999999999999999999999864
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHH
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 198 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~e 198 (523)
++++ ..-.-+.|+.. +.+||--|-++ +.+.|.|.|++- .+.|++.+++-+
T Consensus 68 -~~~l--------~~~~lP~i~~~--------~~~h~vvl~~~--~~~~~~i~dP~~---g~~~~~~~e~~~ 117 (710)
T TIGR03796 68 -LDAL--------AELPLPYIVFW--------NFNHFVVVEGF--RGGRVYLNDPAL---GPRTVSLEEFDE 117 (710)
T ss_pred -HHHh--------ccCCCCEEEEE--------cCCcEEEEEEE--eCCEEEEECCCC---CCEEccHHHHHh
Confidence 2222 22334677766 57899888777 557899999964 788999998755
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=96.72 E-value=0.027 Score=48.51 Aligned_cols=114 Identities=23% Similarity=0.281 Sum_probs=78.6
Q ss_pred ccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCH
Q 009883 49 TQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTI 128 (523)
Q Consensus 49 TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~Sl 128 (523)
.|.+..-||+++++|+++-.|++.... .+... ......|.+...+..+|+..|++++.++.+ .
T Consensus 5 ~q~~~~~~~l~~l~~~~~~~g~~~~~~----------~l~~~----~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~ 67 (127)
T cd02419 5 LQTEAAECGLACLAMIASYHGHHVDLA----------SLRQR----FPVSLKGATLADLIDIAQQLGLSTRALRLD---L 67 (127)
T ss_pred eeCccccHHHHHHHHHHHHcCCCCCHH----------HHHHH----cCCCCCCcCHHHHHHHHHHCCCceeEEEcc---H
Confidence 355566899999999999998765442 01000 001246899999999999999999887743 3
Q ss_pred HHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 129 DDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 129 deFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
+++++. .-.+|+-. ..|||--|.+. +.|.++|.|+.. ++.+++.++|-+..
T Consensus 68 ~~l~~~--------~lP~i~~~--------~~g~~~Vl~~~--~~~~~~i~dp~~---~~~~~~~~el~~~~ 118 (127)
T cd02419 68 EELGQL--------KLPCILHW--------DMNHFVVLKKV--SRRRIVIHDPAL---GKRKLSLEEASRHF 118 (127)
T ss_pred HHHhhC--------CCCEEEEE--------CCCEEEEEEEE--cCCEEEEECCcc---CCEEEcHHHHHhhC
Confidence 343331 12444421 45899999887 567899999853 68999999885543
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=96.46 E-value=0.036 Score=61.86 Aligned_cols=119 Identities=18% Similarity=0.228 Sum_probs=83.7
Q ss_pred cCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHH
Q 009883 50 QSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTID 129 (523)
Q Consensus 50 Q~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~Sld 129 (523)
|.+..=||+|.++|+++-.|.+-+.. .+-+ ...+.+.|+++.++..+|+..|++++.++.+ ++
T Consensus 1 Q~~~~dCg~~cl~~i~~~~g~~~~~~----------~lr~----~~~~~~~g~s~~~l~~~~~~~g~~~~~~~~~---~~ 63 (708)
T TIGR01193 1 QVDEKDCGIAALSMILKKYGTEYSLA----------KLRQ----LAKTDLEGTTVLGLVKAAEYLNFEAKAIQAD---MS 63 (708)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCHH----------HHHH----HhCCCCCCCCHHHHHHHHHHCCCEEEEEecC---HH
Confidence 67788899999999999998764332 1111 1124568999999999999999999999964 22
Q ss_pred HHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHH
Q 009883 130 DFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 198 (523)
Q Consensus 130 eFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~e 198 (523)
++ . ...-.-+.|+...+ ..+..||--|-+++ .+.|.|.|++. .+.+.|++.+++.+
T Consensus 64 ~l----~--~~~~~~P~I~~~~~----~~~~~H~vVl~~~~--~~~~~i~dP~~-~~g~~~~~~~ef~~ 119 (708)
T TIGR01193 64 LF----E--DKNLPLPFIAHVIK----NGKLPHYYVVYGVT--KNHLIIADPDP-TVGITKISKEDFYE 119 (708)
T ss_pred Hh----c--cccCCCCEEEEEcc----CCCCCcEEEEEEEe--CCEEEEEcCCc-ccCCEEecHHHHHh
Confidence 11 0 11223467775332 12356998887776 67899999843 36789999999755
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=96.06 E-value=0.092 Score=52.16 Aligned_cols=157 Identities=21% Similarity=0.326 Sum_probs=89.7
Q ss_pred ccccCCCccccHHHHHHHHHhccCC--CCCC-----cCCCccccccchh---ccccchH---HHhhcCCCH---------
Q 009883 47 FQTQSEPAYCGLASLSMVLNALAID--PGRK-----WKGPWRWFDESML---DCCEPLE---KVKEKGISF--------- 104 (523)
Q Consensus 47 F~TQ~npAyCGvASlamVLNAL~iD--P~r~-----wkgpwRwf~E~mL---dcc~~le---~Vk~~GiTL--------- 104 (523)
|-.|..+..||+|++.|+|.+|+-. +++. |..-...| |- -.|.|.- .+.++|..-
T Consensus 3 yy~QTT~FTCGPa~lmMAm~~l~~~~~~~r~~EL~lWREATTif---mtsGhGGC~P~GLAlAA~rrG~~vev~~~~~~p 79 (207)
T PF11814_consen 3 YYRQTTEFTCGPACLMMAMAALDPEFELDRREELRLWREATTIF---MTSGHGGCGPFGLALAAARRGFKVEVWVSTDGP 79 (207)
T ss_pred ccccCCCCCcHHHHHHHHHHhcCCcCCCCHHHHHHHHHHhceec---ccCCCCCcChHHHHHHHHHcCCceEEEECCCCC
Confidence 4469999999999999999999733 2322 33222222 11 1344421 011122211
Q ss_pred -------------------HHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccc
Q 009883 105 -------------------GKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSP 165 (523)
Q Consensus 105 -------------------~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSP 165 (523)
++|..-|+..|+.++. .+.+++++++.+. .+..+||-.+-..+......|+--
T Consensus 80 lfld~vr~~~kk~v~~~v~~~f~~~a~~~gv~~~~---~~~~~~~l~~~l~-----~G~~~lvLIS~y~~~g~k~PHWV~ 151 (207)
T PF11814_consen 80 LFLDSVRSEEKKEVMELVHEDFREEAEQAGVPVHY---RPLSLADLRAALA-----AGAIVLVLISTYRMDGKKVPHWVV 151 (207)
T ss_pred ceeccCCCHHHHHHHHHHHHHHHHHHHHCCCceec---CCCCHHHHHHHHH-----CCCEEEEEEeecccCCCCCCeEEE
Confidence 1233333444544321 2355666555553 466788888888888888899999
Q ss_pred cceeecCCCeEEEEecCCC-CCCceeeehHH------HHHhccccCCcCCceeeEEEEeC
Q 009883 166 IGGYHAGRDMALILDVARF-KYPPHWVPLTL------LWEAMDRVDDATGQRRGFVLVSR 218 (523)
Q Consensus 166 IGGYh~~tD~VLILDVARf-KYPP~WVpl~~------L~eAM~tiD~~SgksRG~ilIs~ 218 (523)
+-|||+ |-|.|-|+.-- .-..-|++... =++.|...=+. +-|+-++|.+
T Consensus 152 v~g~d~--~~vyihDP~~d~~~~~~~~d~~~lPi~~~~f~~m~~~G~~--~lraaV~l~~ 207 (207)
T PF11814_consen 152 VTGVDD--DFVYIHDPDVDAERGESWVDCQHLPIPRADFDRMARFGKS--KLRAAVILRP 207 (207)
T ss_pred EEEecC--CEEEEeCCCCCcccCCCchhhccCCccHHHHHHHHhhccc--ccEEEEEeeC
Confidence 999876 67888887532 23444543222 24555554432 5677777754
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=95.87 E-value=0.049 Score=54.21 Aligned_cols=84 Identities=24% Similarity=0.211 Sum_probs=52.5
Q ss_pred HHHHHHHcCCeEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEeeccccc------------------cc--CCcccccc
Q 009883 107 LVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFK------------------QT--GTGHFSPI 166 (523)
Q Consensus 107 la~LA~c~G~~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~Lg------------------Qt--GgGHFSPI 166 (523)
+-.-|+.+|+.|+. ...+++++..++. +.+ .+||--+...|. +. =.|||--|
T Consensus 95 lF~~A~~~gi~V~~---rsvs~~ei~~hl~----~g~-~aIvLVd~~~L~C~~Ck~~~~~~~~~~~~~~~~~Y~GHYVVl 166 (212)
T PF09778_consen 95 LFQKAKAAGINVEK---RSVSIQEIIEHLS----SGG-PAIVLVDASLLHCDLCKSNCFDPIGSKCFGRSPDYQGHYVVL 166 (212)
T ss_pred HHHHHHHcCCceEE---eeccHHHHHHHHh----CCC-cEEEEEccccccChhhcccccccccccccCCCCCccEEEEEE
Confidence 33445556665542 1367777776664 233 555555554444 11 27999999
Q ss_pred ceeecCCCeEEEEecCCCCCCceeeehHHHHHh
Q 009883 167 GGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 199 (523)
Q Consensus 167 GGYh~~tD~VLILDVARfKYPP~WVpl~~L~eA 199 (523)
-|||++++.+++=|+|.-. ---=|+.+.|=+|
T Consensus 167 cGyd~~~~~~~yrdPa~~~-~~c~~s~~~ld~A 198 (212)
T PF09778_consen 167 CGYDAATKEFEYRDPASSD-RVCRVSPEALDEA 198 (212)
T ss_pred EeecCCCCeEEEeCCcccc-ceeecCHHHHHHH
Confidence 9999999999999998532 3334555555444
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=91.46 E-value=3.1 Score=35.48 Aligned_cols=110 Identities=14% Similarity=0.105 Sum_probs=74.1
Q ss_pred ccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHH
Q 009883 54 AYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRK 133 (523)
Q Consensus 54 AyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~ 133 (523)
.-||+++++|++.=.|+.-... .+.... .....|.+..++...|+..|++++.++.+ .+.+.
T Consensus 5 ~~~~l~~l~~i~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~- 66 (121)
T cd02417 5 PDSGLLALVLLARYHGIAADPE----------QLRHEF----GLAGEPFNSTELLLAAKSLGLKAKAVRQP---VERLA- 66 (121)
T ss_pred cccHHHHHHHHHHHcCCCCCHH----------HHHHHh----cCCCCCCCHHHHHHHHHHcCCeeEEEecC---HHHhc-
Confidence 3599999999999998664332 000000 01246899999999999999999888753 22221
Q ss_pred HHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHhc
Q 009883 134 YIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEAM 200 (523)
Q Consensus 134 ~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eAM 200 (523)
.-.-++|+-. .+|||--|.+.+ .+.++|.|++. -.|..++.++|-+..
T Consensus 67 -------~~~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~--~~~~~~~~~el~~~~ 114 (121)
T cd02417 67 -------RLPLPALAWD--------DDGGHFILAKLD--GQKYLIQDPIS--QRPEVLSREEFEARW 114 (121)
T ss_pred -------cCCCCEEEEc--------cCCCEEEEEEEc--CCCEEEECCCc--CCCeecCHHHHHhhc
Confidence 1122444432 357888888877 56899999865 368889998887654
No 20
>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=90.09 E-value=4.9 Score=34.47 Aligned_cols=108 Identities=19% Similarity=0.076 Sum_probs=72.4
Q ss_pred ccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHH
Q 009883 56 CGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYI 135 (523)
Q Consensus 56 CGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v 135 (523)
||+++++|++.-.++.-... -+..- ......|.+..++...|+..|++++..+.+ .+.+
T Consensus 7 ~~l~~l~~i~~~~g~~~~~~-----------~l~~~---~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l---- 65 (124)
T cd02421 7 PLLDCLVLLARQFGKPASRD-----------SLVAG---LPLDDGRLSPALFPRAAARAGLSARVVRRP---LDAI---- 65 (124)
T ss_pred hHHHHHHHHHHHhCCCCCHH-----------HHHhc---CCCCCCCcCHHHHHHHHHHCCCcceeeeCC---HHHC----
Confidence 99999999999998764332 00000 011246799999999999999988877643 2222
Q ss_pred HHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHh
Q 009883 136 IRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 199 (523)
Q Consensus 136 ~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eA 199 (523)
..-.-+.|+- ..+|||--|.+.+. +.++|.|+.. ..+|.+++.++|-+.
T Consensus 66 ----~~~~lP~i~~--------~~~g~~~Vl~~~~~--~~~~i~dp~~-~~~~~~~~~~el~~~ 114 (124)
T cd02421 66 ----PTLLLPAILL--------LKNGRACVLLGVDD--GHARILDPES-GGGEVEISLEELEEE 114 (124)
T ss_pred ----CcccCCEEEE--------EcCCCEEEEEEecC--CeEEEEccCC-CCCcEEEcHHHHHhh
Confidence 1112234442 23689988888775 7799999862 467889998887653
No 21
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=89.91 E-value=1 Score=51.88 Aligned_cols=116 Identities=17% Similarity=0.213 Sum_probs=82.6
Q ss_pred cccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCC
Q 009883 46 YFQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQ 125 (523)
Q Consensus 46 qF~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~ 125 (523)
.+..|.+..=||+|.++|+.|..|.+-+.. .+.+. ....+.|.++.++..+|+..|++++.++.+
T Consensus 3 ~~~~q~~~~dcgla~l~mia~~~g~~~~~~----------~lr~~----~~~~~~g~sl~~l~~~a~~lGl~~~~~~~~- 67 (709)
T COG2274 3 PIVLQQSANDCGLACLAMIANYHGKKISLN----------ELREL----VGLSRNGLSLLELKQAAEKLGLSARAVKLS- 67 (709)
T ss_pred cccccCCccchHHHHHHHHHHHhCCCCCHH----------HHHHH----cCCCCCCCChHHHHHHHHHcCCccccccCC-
Confidence 456799999999999999999988664332 11110 112356999999999999999999888865
Q ss_pred CCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHHh
Q 009883 126 STIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWEA 199 (523)
Q Consensus 126 ~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~eA 199 (523)
.+++.+ ..-+.|++... +||--+-+++.+ .+.|.|. .-.++..+.+++-+.
T Consensus 68 --~~~l~~--------~~lP~ii~~~~--------~h~vVl~~~~~~--~~~v~dp---~~g~~~l~~~e~~~~ 118 (709)
T COG2274 68 --LEELKQ--------LPLPAIIHWNG--------NHFVVLYKIDKN--KVVVLDP---AKGIRRLSLEEFEKL 118 (709)
T ss_pred --HHHhcc--------cCCCEEEEEcC--------CcEEEEEEecCC--eEEEEeC---CCCcEEcCHHHHHHh
Confidence 333322 22255666543 498888777776 9999998 558888887776443
No 22
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=88.35 E-value=2.2 Score=47.92 Aligned_cols=103 Identities=17% Similarity=0.114 Sum_probs=69.7
Q ss_pred HHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHHH
Q 009883 58 LASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIR 137 (523)
Q Consensus 58 vASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~ 137 (523)
+|.++|++|..|..-+.. .+-+.+ .+.+.|+|+.++..+|+..|++++.++.+ +++
T Consensus 2 laclami~~~~g~~~~l~----------~lr~~~----~~~~~g~sl~~l~~~~~~~g~~~~~~~~~---~~~------- 57 (694)
T TIGR03375 2 LDCLLLLARHYGRPVSRE----------ALVAGL----PLEDGRLTPELLPRAARRAGLSARLVKRS---LDD------- 57 (694)
T ss_pred HHHHHHHHHHcCCCCCHH----------HHHhhC----CCCCCCCCHHHHHHHHHHCCCEEEEecCC---Hhh-------
Confidence 689999999998653321 111111 24578999999999999999999998853 332
Q ss_pred hhcCCCceEEEEeecccccccCCccccccceeecCCCe-EEEEecCCCCCC--ceeeehHHHHH
Q 009883 138 CSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDM-ALILDVARFKYP--PHWVPLTLLWE 198 (523)
Q Consensus 138 ~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~-VLILDVARfKYP--P~WVpl~~L~e 198 (523)
+.....+.|+.++ ++||--+-+ -..+. |.|.|++ +. +.|++.+++-+
T Consensus 58 -l~~~~~P~i~~~~--------~~h~vvl~~--~~~~~~~~i~DP~---~g~~~~~~~~~e~~~ 107 (694)
T TIGR03375 58 -ISPLLLPAILLLK--------DGRACVLLG--IDEDGKARVLLPE---TGDGEQELSLDALEA 107 (694)
T ss_pred -cCcCCCCEEEEEc--------CCcEEEEEE--EcCCCcEEEEccC---CCCCceEecHHHHHh
Confidence 2233446666653 379844444 44565 9999985 34 77999888644
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=85.88 E-value=4 Score=45.95 Aligned_cols=104 Identities=15% Similarity=0.147 Sum_probs=70.7
Q ss_pred cHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHH
Q 009883 57 GLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYII 136 (523)
Q Consensus 57 GvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~ 136 (523)
|+|.++|++|-.|.+-+.. .+-+.+ .+.+.|+++.++...|+..|++++.++.+ .+++
T Consensus 1 g~acl~~i~~~~g~~~~~~----------~lr~~~----~~~~~g~~~~~l~~~~~~~G~~~~~~~~~---~~~l----- 58 (694)
T TIGR01846 1 GLEALSLLAQVHNIAVTPS----------QLRHML----GHAGASLDDLEILLAAKQLGLKAKAVKVS---IGRL----- 58 (694)
T ss_pred CHHHHHHHHHHcCCCCCHH----------HHHHhc----CCCCCCCCHHHHHHHHHHCCCEEEEEeCC---HHHc-----
Confidence 7899999999998664331 111111 13468999999999999999999999864 3322
Q ss_pred HhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHH
Q 009883 137 RCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 198 (523)
Q Consensus 137 ~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~e 198 (523)
..-.-+.|+.. .+||--|-+ -+.+.|.|.|++. . .+.|++.+++.+
T Consensus 59 ---~~~~lP~i~~~---------~~~~vvl~~--~~~~~~~i~Dp~~-g-~~~~i~~~e~~~ 104 (694)
T TIGR01846 59 ---NKLPLPALIDG---------EGGWFVLGK--LTANGVTIYDPPG-D-APEVLSREVLEA 104 (694)
T ss_pred ---cCCCCCEEEEE---------CCcEEEEEE--EcCCEEEEEcCCC-C-CceeeCHHHHHh
Confidence 22233666644 146444434 4567899999864 2 578999999764
No 24
>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=78.70 E-value=15 Score=41.33 Aligned_cols=100 Identities=15% Similarity=0.081 Sum_probs=67.8
Q ss_pred HHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHHH
Q 009883 58 LASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIR 137 (523)
Q Consensus 58 vASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~ 137 (523)
+|+++|+++-.|.+-+.. .+-+ . ..| ++..+...|+..|++++.++.+ ++++.+
T Consensus 5 ~~~l~~i~~~~~~~~~~~----------~lr~------~--~~g-~~~~l~~~~~~~g~~~~~~~~~---~~~l~~---- 58 (686)
T TIGR03797 5 LVACAAVGRAMGIEIRPP----------ARSE------N--LSR-SPEPLEAIARASRLRIRRVRLE---GGWWRQ---- 58 (686)
T ss_pred HHHHHHHHHHhCCCCChH----------HHHH------H--cCC-CHHHHHHHHHHCCCceEEEecC---HHHHhh----
Confidence 689999999998664432 1111 1 168 9999999999999999999864 332221
Q ss_pred hhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHHH
Q 009883 138 CSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLWE 198 (523)
Q Consensus 138 ~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~e 198 (523)
-.-+.|+..+ +.|||--|-++ +.+.+.|+|+|. =++.|++.+++-+
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 2235555543 24798777665 678899999964 2244899988733
No 25
>COG3271 Predicted double-glycine peptidase [General function prediction only]
Probab=76.71 E-value=3.4 Score=41.15 Aligned_cols=103 Identities=22% Similarity=0.310 Sum_probs=68.3
Q ss_pred cccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHH-HhhcCCCHHHHHHHHHHcCCeEEEEeCCCC
Q 009883 48 QTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEK-VKEKGISFGKLVCLAHCAGAKVEAFRTNQS 126 (523)
Q Consensus 48 ~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~-Vk~~GiTL~Ela~LA~c~G~~V~~yra~~~ 126 (523)
..|.-...||-||++.+||=+...+-.. ++ ...+. +.+.|.++..++..++..|.+.+.|.....
T Consensus 36 Irq~~d~ScGaaalatll~n~~gk~~~e----------~~----~~~~m~~~~~~~s~~g~~~~~~~~g~~a~~~~~~~~ 101 (201)
T COG3271 36 IRQTTDFSCGAAALATLLNNDYGKLADE----------SL----VLIEMNLEEFGESFSGMARAIKSLGNRAQGYENEFE 101 (201)
T ss_pred HHhhhccCchHHHHHHHHHhhccccCCH----------HH----HHHHhhHHHhhhcHHHHHHHhhCCCCcccccccchh
Confidence 4477778999999999999886543331 11 11122 678999999999999999988887775433
Q ss_pred CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecC
Q 009883 127 TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVA 182 (523)
Q Consensus 127 SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVA 182 (523)
++++ . +..+|| .+.-.+.-||+-+=+ -+.|-|++.|.+
T Consensus 102 ~l~q---~--------~~p~iV-----~~~~~~~~hf~v~~~--v~~~~v~l~Dp~ 139 (201)
T COG3271 102 SLAQ---L--------KIPVIV-----TLKYPANNHFDVVIG--VDGDNVTLADPA 139 (201)
T ss_pred hhhh---c--------cCCeeE-----EeecCCCceeEEEEe--ccCCeeEEcChh
Confidence 3222 1 113344 334456679885533 345789999976
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=71.00 E-value=37 Score=33.22 Aligned_cols=130 Identities=15% Similarity=0.103 Sum_probs=80.9
Q ss_pred ccccccccCCC-ccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhh-cCCCH-----HHHHHHHHHcC
Q 009883 43 LISYFQTQSEP-AYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKE-KGISF-----GKLVCLAHCAG 115 (523)
Q Consensus 43 La~qF~TQ~np-AyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~-~GiTL-----~Ela~LA~c~G 115 (523)
++-.|..|++. .-|=-|+++||+--..--|...+ .+..+. .|..- .+...+.+..|
T Consensus 22 ~~v~~v~Qq~~~mgCWaA~~~Mv~~w~~~~prlg~-----------------~eLyra~~Glp~~lq~g~d~~~~~~~~g 84 (166)
T PF12385_consen 22 FAVPYVPQQNTRMGCWAACACMVGGWRDQGPRLGP-----------------PELYRADEGLPSQLQDGLDPEDFIRNEG 84 (166)
T ss_pred eEeeeeccCCCcccHHHHHHHHHHHHhcCCCCCCc-----------------HHHHHHhcCCchhhcccccHHHHHHhcC
Confidence 44778888885 69999999999988765454432 111222 33332 23344555555
Q ss_pred CeEEEEeC-CCCCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCcee-eeh
Q 009883 116 AKVEAFRT-NQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHW-VPL 193 (523)
Q Consensus 116 ~~V~~yra-~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~W-Vpl 193 (523)
++--..-+ ..-+.+.|++.+++. -.|.+--.+- +..=.||.+-|-|.+.+.|.+-+.|+.+ +|-- +++
T Consensus 85 l~~v~~P~~~~~t~e~~~~LL~~y-----GPLwv~~~~P--~~~~~~H~~ViTGI~~dg~~i~~~DP~~---gP~~~m~l 154 (166)
T PF12385_consen 85 LKEVPEPANASYTAEGLANLLREY-----GPLWVAWEAP--GDSWVAHASVITGIDGDGDSIHVHDPEQ---GPNLRMSL 154 (166)
T ss_pred ccccCCCcccccCHHHHHHHHHHc-----CCeEEEecCC--CCcceeeEEEEEeecCCCCeEEecCccc---CCCceecH
Confidence 43211222 235889999999753 2555553222 2222379999999999999999999876 4444 666
Q ss_pred HHHHHh
Q 009883 194 TLLWEA 199 (523)
Q Consensus 194 ~~L~eA 199 (523)
+.|-.+
T Consensus 155 ~~fn~~ 160 (166)
T PF12385_consen 155 DMFNQA 160 (166)
T ss_pred HHHhhh
Confidence 665544
No 27
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.91 E-value=53 Score=31.48 Aligned_cols=75 Identities=28% Similarity=0.352 Sum_probs=46.4
Q ss_pred EeCCCCCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCcee-eehHHHHHh
Q 009883 121 FRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHW-VPLTLLWEA 199 (523)
Q Consensus 121 yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~W-Vpl~~L~eA 199 (523)
+..+...-+-..+-++.++-+++.+. -|.|..- =.|||--|-|||+.+|-+-|=|+|.-+ |-+- +++.-+=+|
T Consensus 77 Vdq~~Lhcdlceeplk~ccfspnghh--cfcrtp~---YqGHfiVi~GYd~a~~c~~~ndPA~ad-pg~c~~Sik~fEeA 150 (167)
T KOG4621|consen 77 VDQDKLHCDLCEEPLKSCCFSPNGHH--CFCRTPC---YQGHFIVICGYDAARDCFEINDPASAD-PGHCRISIKCFEEA 150 (167)
T ss_pred ecCCceehHHHHhHHHHhccCCCCcc--ccccCCc---ccccEEEEeccccccCeEEEcCcccCC-CcceeehhhHHHHH
Confidence 33333444555555555554443322 2344321 259999999999999999999999644 4444 666666555
Q ss_pred cc
Q 009883 200 MD 201 (523)
Q Consensus 200 M~ 201 (523)
-.
T Consensus 151 Rk 152 (167)
T KOG4621|consen 151 RK 152 (167)
T ss_pred Hh
Confidence 43
No 28
>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=54.95 E-value=7.6 Score=35.27 Aligned_cols=55 Identities=22% Similarity=0.292 Sum_probs=37.3
Q ss_pred HHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcCCeEEE
Q 009883 62 SMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAGAKVEA 120 (523)
Q Consensus 62 amVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G~~V~~ 120 (523)
+.+=+|.++.+.+-|..==.-+..++|+ -..|...|++-|-|+.||.....++..
T Consensus 8 ~A~s~at~~~~~~LW~~L~~~lPDSlL~----n~ei~~~GLSTDhltaLa~~~~~~~~~ 62 (104)
T PF05381_consen 8 VAISQATSISPETLWATLCEILPDSLLD----NPEIRTLGLSTDHLTALAYRYHFQCTF 62 (104)
T ss_pred HhhhhhhCCCHHHHHHHHHHhCchhhcC----chhhhhcCCcHHHHHHHHHHHheEEEE
Confidence 3445677777777764322233344443 256899999999999999988777754
No 29
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=53.73 E-value=26 Score=32.33 Aligned_cols=42 Identities=14% Similarity=0.232 Sum_probs=32.1
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.||+|++..+..-.-+...+..|++++|+..++..
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 433345779999998877665556678899999999988864
No 30
>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=52.57 E-value=14 Score=33.35 Aligned_cols=42 Identities=19% Similarity=0.316 Sum_probs=31.6
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.+|+|+++.+..-.-+...+..|++++|+..++..
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 433334679999987776555556678999999999998864
No 31
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=51.55 E-value=16 Score=32.40 Aligned_cols=38 Identities=16% Similarity=0.254 Sum_probs=30.0
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
.+.+|+|+++-+..-.-+...++.|++++|+..++...
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 56799999877765545556789999999999988754
No 32
>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=50.49 E-value=14 Score=33.52 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=32.3
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.+|+|+++-+..-.-+...++.|+||+|+..++...
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 5444336799999877765555566789999999999988753
No 33
>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=49.84 E-value=15 Score=31.63 Aligned_cols=42 Identities=17% Similarity=0.265 Sum_probs=31.4
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.||+|++.-+..-.-+...++.|++++++..+...
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 444445679999987776544445678899999999988864
No 34
>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=48.16 E-value=18 Score=32.70 Aligned_cols=37 Identities=8% Similarity=0.180 Sum_probs=29.9
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.+.+|+|+++-+..-.-+...+..|+|++|+..++..
T Consensus 33 ~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 33 DNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5679999998776555556678999999999998864
No 35
>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=48.13 E-value=38 Score=26.90 Aligned_cols=44 Identities=16% Similarity=0.295 Sum_probs=29.2
Q ss_pred ccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHH
Q 009883 68 LAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 111 (523)
Q Consensus 68 L~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA 111 (523)
.|..+...=.+..|+|+++-++.-.-+...++.|+|++++..++
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 35543333346689998866654444455677999999998765
No 36
>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=48.12 E-value=17 Score=31.35 Aligned_cols=43 Identities=14% Similarity=0.261 Sum_probs=32.4
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.+|+|+++-+....-+...++.|++++|+..+....
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 4333356799999877766555566789999999999988643
No 37
>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=48.10 E-value=17 Score=32.54 Aligned_cols=37 Identities=16% Similarity=0.303 Sum_probs=29.7
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.+.+|+|++..+..-.-+...++.|+|++|+..++..
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 4669999997776555556678999999999998864
No 38
>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=47.75 E-value=18 Score=32.54 Aligned_cols=42 Identities=12% Similarity=0.279 Sum_probs=31.6
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..+...
T Consensus 28 ~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 28 EPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred CCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 333335779999987776555555678999999999998864
No 39
>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=47.29 E-value=38 Score=26.46 Aligned_cols=52 Identities=17% Similarity=0.298 Sum_probs=29.7
Q ss_pred HHHHHHHHhccCC-CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHH
Q 009883 59 ASLSMVLNALAID-PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 111 (523)
Q Consensus 59 ASlamVLNAL~iD-P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA 111 (523)
.++.---+..+.. |.+.- +..|+|+++-+..-..+...++.|+|++|+..++
T Consensus 15 ~tlr~w~~~~g~~~~~r~~-~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 15 DTLRAWERRYGLPAPQRTD-GGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHhCCCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3444333433443 33332 3468887654443333445677999999998764
No 40
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=46.12 E-value=18 Score=33.75 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=33.0
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.||+|++..+....-+...+..|++++|+..++...
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 3343346699999988876666667789999999999988643
No 41
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=43.45 E-value=12 Score=31.25 Aligned_cols=18 Identities=33% Similarity=0.383 Sum_probs=14.7
Q ss_pred CCCCchhHHHHHHHHHHH
Q 009883 465 TENLPTLLQEEVLHLRRQ 482 (523)
Q Consensus 465 ~~~lp~~l~~ev~hl~~q 482 (523)
.++|||.|+.||+|--.=
T Consensus 8 fqkLPDdLKrEvldY~Ef 25 (65)
T COG5559 8 FQKLPDDLKREVLDYIEF 25 (65)
T ss_pred HHHCcHHHHHHHHHHHHH
Confidence 368999999999996543
No 42
>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=43.13 E-value=24 Score=31.20 Aligned_cols=42 Identities=19% Similarity=0.463 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+. .+.+|+|++.-+..-.-+...++.|++++|+..+....
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 5444 56799999876655444456788999999999988764
No 43
>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=42.75 E-value=24 Score=31.42 Aligned_cols=39 Identities=21% Similarity=0.362 Sum_probs=31.1
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcC
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 115 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G 115 (523)
.+.+|+|++.-++.-.-+...+..|+|++|+..+....+
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 468999999777665555667889999999999886543
No 44
>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=41.13 E-value=25 Score=31.49 Aligned_cols=38 Identities=16% Similarity=0.345 Sum_probs=30.8
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
.+.+|+|++..+..-.-+...+..|++++|+..+....
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 56799999988776555566789999999999988654
No 45
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.37 E-value=32 Score=26.97 Aligned_cols=54 Identities=15% Similarity=0.312 Sum_probs=35.0
Q ss_pred HHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHH
Q 009883 58 LASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 112 (523)
Q Consensus 58 vASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~ 112 (523)
..++..-.+.--+.|.+.- +.+|.|++.-++.-..+....+.|+|++++..+++
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 4455555555556677743 44689987666544445566779999999988764
No 46
>PRK13749 transcriptional regulator MerD; Provisional
Probab=40.20 E-value=29 Score=31.87 Aligned_cols=39 Identities=23% Similarity=0.323 Sum_probs=30.2
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcC
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 115 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G 115 (523)
.+.+|+|++.-+..-.-+...+..|++++|+..++...+
T Consensus 36 ~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~ 74 (121)
T PRK13749 36 TGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALD 74 (121)
T ss_pred CCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 478999998777644444556789999999999987653
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=40.06 E-value=27 Score=30.18 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=30.7
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+...+.+|+|+++-++.-.-+...+..|+|++++..+....
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 4445566799999866654444455678999999999888653
No 48
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=39.84 E-value=56 Score=30.18 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=31.0
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.+|+|++.-+..-.-+...+..|++++|+..++..
T Consensus 29 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 29 PEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred CcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 433335669999987776544455678899999999998865
No 49
>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=39.19 E-value=29 Score=31.33 Aligned_cols=41 Identities=10% Similarity=0.216 Sum_probs=30.7
Q ss_pred CCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 73 GRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 73 ~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.+.-.+.+|+|++.-++.-.-+...+..|++++|+..++..
T Consensus 29 ~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 29 PSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 33335679999987776554555678999999999998864
No 50
>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=38.32 E-value=29 Score=31.90 Aligned_cols=43 Identities=12% Similarity=0.141 Sum_probs=32.0
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.||+|+++.+..-.-+...+..|++|+|+..+..+.
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 4443356799999877765544556789999999999988653
No 51
>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=37.78 E-value=30 Score=31.45 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=31.1
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+.-.+.+|+|+++-+..-.-+-..+..|++++|+..++..
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 433335669999987776554455578899999999998874
No 52
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=37.64 E-value=59 Score=30.91 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=31.5
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+. .+.+|+|+++.+..-.-+...+..|++|+|+..++..
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 5668999998876555556678999999999998865
No 53
>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=37.60 E-value=34 Score=29.53 Aligned_cols=46 Identities=15% Similarity=0.224 Sum_probs=31.9
Q ss_pred ccCC-CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 68 LAID-PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 68 L~iD-P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.|+- |.+.-.+.+|+|++.-+..-.-+...++.|++++|+..+...
T Consensus 23 ~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 23 IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3443 433334669999986665444445578899999999988765
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=37.34 E-value=37 Score=29.84 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=30.3
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|...-.+.+|+|++.-++.-.-+...+..|++++|+..+...
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 433335668999986665444445568899999999998865
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=36.96 E-value=30 Score=31.10 Aligned_cols=43 Identities=16% Similarity=0.242 Sum_probs=31.9
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|...-.+.+|+|++..+..-.-+...+..|++++|+..++...
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 3333456799999877765555566789999999999988643
No 56
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.86 E-value=31 Score=30.92 Aligned_cols=40 Identities=20% Similarity=0.229 Sum_probs=30.5
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+. +.+|+|++.-++.-.-+...+..|+|++++..+...
T Consensus 28 p~r~--~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 28 PERR--GQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CcCC--CCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5444 479999987776544445678999999999998865
No 57
>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=36.21 E-value=68 Score=25.28 Aligned_cols=51 Identities=14% Similarity=0.257 Sum_probs=31.7
Q ss_pred HHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHH
Q 009883 60 SLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLA 111 (523)
Q Consensus 60 SlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA 111 (523)
++..--...++.+.+ -.+.+|+|+.+-+..-.-+...++.|+|++|+..+.
T Consensus 16 tlR~~~~~g~l~~~~-~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 16 TLRYYEKEFNLYIPR-TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHhcCCCCCC-CCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 333333333444333 346689998766654444555678999999998764
No 58
>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=34.36 E-value=39 Score=33.28 Aligned_cols=113 Identities=18% Similarity=0.270 Sum_probs=65.6
Q ss_pred ccccccccccccc------CCCccccHHHHHHHHHhccCCCCCCcC-------CCcccccc---chhccccchHHHhhcC
Q 009883 38 EGFYRLISYFQTQ------SEPAYCGLASLSMVLNALAIDPGRKWK-------GPWRWFDE---SMLDCCEPLEKVKEKG 101 (523)
Q Consensus 38 e~ff~La~qF~TQ------~npAyCGvASlamVLNAL~iDP~r~wk-------gpwRwf~E---~mLdcc~~le~Vk~~G 101 (523)
..|-.+++.|... .+|.|= +...-++.+||+||...-+ |.-.||.| .+.+.|. ....+.|
T Consensus 36 ~~~~~~l~~fa~k~~~~i~~~~~~r--~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~--~~~~~~G 111 (223)
T PF04157_consen 36 KDFVELLENFARKHKSEIKSDPEFR--SQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCL--ATRSKNG 111 (223)
T ss_dssp HHHHHHHHHHHHHHCCCCCCSHHHH--HHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHH--HHCCTTT
T ss_pred HHHHHHHHHHHHHhhccccCCchHH--HHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHH--HHHhcCC
Confidence 4555566666542 222211 2778889999999754333 44456655 4445554 3345678
Q ss_pred --CCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEee-cccccccC
Q 009883 102 --ISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYH-RGAFKQTG 159 (523)
Q Consensus 102 --iTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~-R~~LgQtG 159 (523)
|+|.|+.|+.....-.+ +-.|-++|++.+.....-...+-++.|. ...+-|+.
T Consensus 112 Gii~L~dl~~~~nr~R~g~-----~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~ 167 (223)
T PF04157_consen 112 GIISLSDLYCRYNRARGGS-----ELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSV 167 (223)
T ss_dssp SEEEHHHHHHHHHHCTTTS-----ST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECS
T ss_pred CEEEHHHHHHHHHHhcccC-----CCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeC
Confidence 99999999996542111 2579999999999764433347788887 44444443
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=34.04 E-value=38 Score=32.38 Aligned_cols=43 Identities=19% Similarity=0.349 Sum_probs=31.9
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.||+|++.-+..-.-+-..+..|++++|+..++...
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 4443457799999876655455556788999999999888654
No 60
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=33.86 E-value=4.3e+02 Score=25.23 Aligned_cols=70 Identities=11% Similarity=0.167 Sum_probs=46.1
Q ss_pred EEEeCCCCCHHHHHHHHHHhh-cCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCceeeehHHHH
Q 009883 119 EAFRTNQSTIDDFRKYIIRCS-ASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVARFKYPPHWVPLTLLW 197 (523)
Q Consensus 119 ~~yra~~~SldeFR~~v~~~~-ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVARfKYPP~WVpl~~L~ 197 (523)
.....-+.+++++|+.+...- +..+.+++.+|..-.+-+ | -+.+.+-+.|-++-+| ..+++.+|+
T Consensus 65 ~~~~~~dpt~e~~~~~~~~~R~~a~~~RvLFHYnGhGvP~-------P-----t~~GeIw~f~~~~tqy--ip~si~dL~ 130 (154)
T PF14538_consen 65 RYKQSLDPTVEDLKRLCQSLRRNAKDERVLFHYNGHGVPR-------P-----TENGEIWVFNKNYTQY--IPLSIYDLQ 130 (154)
T ss_pred cEEEecCCCHHHHHHHHHHHHhhCCCceEEEEECCCCCCC-------C-----CCCCeEEEEcCCCCcc--eEEEHHHHH
Confidence 333445789999999877653 334579999998543322 1 1234677888655444 458999999
Q ss_pred Hhccc
Q 009883 198 EAMDR 202 (523)
Q Consensus 198 eAM~t 202 (523)
++|.+
T Consensus 131 ~~lg~ 135 (154)
T PF14538_consen 131 SWLGS 135 (154)
T ss_pred HhcCC
Confidence 99864
No 61
>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=33.61 E-value=39 Score=31.52 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=29.5
Q ss_pred CCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 77 KGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 77 kgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.+.+|+|+++.+..-.-+...++.|+|++++..++.+
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 4568999987776555556678999999999998875
No 62
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.26 E-value=42 Score=28.85 Aligned_cols=31 Identities=32% Similarity=0.488 Sum_probs=25.0
Q ss_pred EEeccCCCCCCCHHH-----HhhhhhHHHHHHHHhc
Q 009883 284 VRRREDGDHSLSQEE-----KGRLALKEEVLRQVQE 314 (523)
Q Consensus 284 vr~~e~~~~~ls~ee-----~~rl~~k~~~l~qi~~ 314 (523)
+.+.|.|.+++|.+| |+||.+|.++.+-++.
T Consensus 33 I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~L~~ 68 (72)
T COG2841 33 IKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASILQK 68 (72)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 346778888999887 8999999998877754
No 63
>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=31.94 E-value=45 Score=29.35 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=31.8
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+...+.+|.|++.-+..-.-+...++.|++++++..++...
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 5555556799999866654444456788999999999988753
No 64
>PF08099 Toxin_27: Scorpion calcine family; InterPro: IPR012632 Toxins of the scorpion calcine family bind directly to ryanodine receptors (RyRs), intracellular channel targets of the endoplasmic reticulum, and induce long lasting channel openings in a mode of smaller conductance. They have the ability to translocate into cells by crossing the plasma membrane [, , ]. Toxins of scorpion calcine family are highly basic 33-amino acid peptides that present three disulphide bridges (C1-C4, C2-C5, and C3-C6) and fold along a knottin or inhibitor cystine knot motif (http://knottin.cbs.cnrs.fr) [, , ]. Their three dimensional structure consists of a compact disulphide-bonded core from which emerge loops and the N terminus. The main element of regular secondary structure is a double-stranded antiparallel beta-sheet. A third peripheral extended strand is almost perpendicular to the double-stranded antiparallel beta-sheet [, ]. Scorpion calcine mimic the activating segment of the dihydropyridine receptor II-III loop, which interacts with a region of the ryanodine receptor [, , ]. This family includes: Imperatoxin-A (IpTx A) from Pandinus imperator (Emperor scorpion). Opicalcin-1 and -2 from Opistophthalmus carinatus (African yellow leg scorpion). Maurocalcin (MCa) from Scorpio maurus palmatus (Chactoid scorpion). ; GO: 0019855 calcium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1IE6_A.
Probab=31.74 E-value=14 Score=27.05 Aligned_cols=20 Identities=55% Similarity=0.943 Sum_probs=12.3
Q ss_pred HHHhhcccccccccccccccccc
Q 009883 484 HILRRCQENKVVPSCRSKWCLPR 506 (523)
Q Consensus 484 ~~~~~c~~~~~~~~~~~~~~~~~ 506 (523)
-.|+||+||+ ||-||=|--|
T Consensus 5 phlkrcken~---dccskkckrr 24 (33)
T PF08099_consen 5 PHLKRCKENK---DCCSKKCKRR 24 (33)
T ss_dssp -TTSB-SSGG---GBSSS-B--S
T ss_pred HHHHHHHhcc---chHHHHhhhc
Confidence 4589999876 8989988655
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=31.65 E-value=1e+02 Score=26.81 Aligned_cols=60 Identities=7% Similarity=0.135 Sum_probs=38.2
Q ss_pred ccCC-CCCCcCCCccccccchhccccchHHHhh-cCCCHHHHHHHHHHcCCeEEEEeCCCCCHHHHHHHHH
Q 009883 68 LAID-PGRKWKGPWRWFDESMLDCCEPLEKVKE-KGISFGKLVCLAHCAGAKVEAFRTNQSTIDDFRKYII 136 (523)
Q Consensus 68 L~iD-P~r~wkgpwRwf~E~mLdcc~~le~Vk~-~GiTL~Ela~LA~c~G~~V~~yra~~~SldeFR~~v~ 136 (523)
.|+- |.+.-++.+|+|++.-+....-+...++ .|++++++..+.... .+.++.+=++.+.
T Consensus 23 ~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~~---------~~~~~~~~~~~~~ 84 (95)
T cd04780 23 EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAI---------ADASLPSTLLALA 84 (95)
T ss_pred CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc---------CcccHHHHHHHHH
Confidence 3443 4333345578999877765555555665 799999999988762 2455555555444
No 66
>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=30.92 E-value=2.2e+02 Score=28.22 Aligned_cols=115 Identities=17% Similarity=0.224 Sum_probs=65.0
Q ss_pred cccccCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccc---cchHHHhhcCCCHHHHHHHHHHcCCeEEEEe
Q 009883 46 YFQTQSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCC---EPLEKVKEKGISFGKLVCLAHCAGAKVEAFR 122 (523)
Q Consensus 46 qF~TQ~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc---~~le~Vk~~GiTL~Ela~LA~c~G~~V~~yr 122 (523)
-.+||-+...|.=-+++.+||++.- .. ...-++|+..- .+.+..+..|++-+|.-.+++..|..++. -
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 12224454322 12245677889999999999999987754 3
Q ss_pred CCCCCHHHHHHHHHHhhcCCCceEEEEeeccccc-ccCCccccccceeecCCC
Q 009883 123 TNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFK-QTGTGHFSPIGGYHAGRD 174 (523)
Q Consensus 123 a~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~Lg-QtGgGHFSPIGGYh~~tD 174 (523)
.+-.++++..+.+. .++.+++.-++-.-. ..-.||---|.||-.-.+
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 44467888777765 445566655533222 223789888889966443
No 67
>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=29.67 E-value=51 Score=28.76 Aligned_cols=40 Identities=15% Similarity=0.276 Sum_probs=29.5
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 112 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~ 112 (523)
|.+. .+.+|+|+++-++.-.-+...++.|++++|+..++.
T Consensus 29 ~~r~-~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 29 GTRN-ANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred CCcC-CCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 4443 467999999777655555567889999999887663
No 68
>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=28.60 E-value=53 Score=30.02 Aligned_cols=43 Identities=26% Similarity=0.383 Sum_probs=31.5
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.+|+|++.-++.-.-+...+..|++++++..++...
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 4434457799999877764444455688999999999988653
No 69
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.37 E-value=42 Score=30.88 Aligned_cols=53 Identities=23% Similarity=0.478 Sum_probs=37.7
Q ss_pred eEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEeecccccccCCccccccceeecCCC
Q 009883 117 KVEAFRTNQSTIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRD 174 (523)
Q Consensus 117 ~V~~yra~~~SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD 174 (523)
++++|-+ ..-++.+|+.|- ..+..-|-||+-=...-+|.|||-|+.|=++--+
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 3444443 244566666554 4555667799999999999999999998777654
No 70
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=28.09 E-value=75 Score=29.94 Aligned_cols=41 Identities=24% Similarity=0.605 Sum_probs=28.8
Q ss_pred CCCCCcceeeeccCCChHHHHHHHHhhhchhhccCCCCCHHHHHHHHH
Q 009883 220 HREPGLLYTLSCKHENWVGIAKYLVDEVPKIVKSKDFKDFEEVLTVLF 267 (523)
Q Consensus 220 ~~~p~~l~~l~~~~~~w~~~a~~l~~~~p~l~~~~~~~~~~~v~~~~~ 267 (523)
-..|+.+.|++| +..|.++.+.|.+ ..++..|-+.++..+|
T Consensus 102 ~G~P~~FiT~s~-~~~w~ei~~~l~~------~~~~~~d~P~~~ar~F 142 (184)
T PF14214_consen 102 FGKPTLFITFSC-NPQWPEIQQALAK------PGQNWSDNPDIVARFF 142 (184)
T ss_pred cCCCcEEEEEcC-ccccHHHHHHHHh------ccCCcccCcHHHHHHH
Confidence 357999999999 8999999999773 2344444444444444
No 71
>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=27.36 E-value=59 Score=28.29 Aligned_cols=44 Identities=14% Similarity=0.272 Sum_probs=30.7
Q ss_pred cCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHH
Q 009883 69 AIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAH 112 (523)
Q Consensus 69 ~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~ 112 (523)
|+-|...-.+.+|+|+++-++.-.-+...++.|++++|+..+..
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 44443333467899998777654444556889999999998764
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=27.33 E-value=62 Score=28.69 Aligned_cols=46 Identities=22% Similarity=0.319 Sum_probs=32.5
Q ss_pred ccCC-CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 68 LAID-PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 68 L~iD-P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
.|.- |.+.-.+.+|+|++.-+..-.-+...+..|+++.++..+...
T Consensus 23 ~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (107)
T cd01111 23 RGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA 69 (107)
T ss_pred CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3444 433445679999987776444445567899999999998865
No 73
>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=27.21 E-value=61 Score=28.43 Aligned_cols=38 Identities=8% Similarity=0.318 Sum_probs=29.3
Q ss_pred CCccccccchhccccchHHHhhcCCCHHHHHHHHHHcC
Q 009883 78 GPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 115 (523)
Q Consensus 78 gpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G 115 (523)
+.+|+|++.-++.-..+...+..|++++++..+.....
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 56999998766654445566889999999999887643
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=26.33 E-value=61 Score=29.95 Aligned_cols=41 Identities=15% Similarity=0.204 Sum_probs=31.4
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
|.+. .+.+|+|++.-+..-.-+...+..|+|++|+..++..
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 4444 5669999987776655556678999999999998764
No 75
>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=25.12 E-value=76 Score=26.95 Aligned_cols=43 Identities=14% Similarity=0.085 Sum_probs=29.6
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.+|+|+++-+..-.-+...++.|++++++..++...
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 4444334789998755544334455678999999999988753
No 76
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=24.52 E-value=71 Score=27.76 Aligned_cols=43 Identities=21% Similarity=0.427 Sum_probs=30.0
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHc
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCA 114 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~ 114 (523)
|.+.-.+.+|.|++..+.--.-+...++.|++++++..+....
T Consensus 28 p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~~ 70 (124)
T COG0789 28 PERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDLL 70 (124)
T ss_pred CcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 5544446799999866653333344567899999999988654
No 77
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=24.23 E-value=92 Score=27.67 Aligned_cols=43 Identities=21% Similarity=0.357 Sum_probs=19.8
Q ss_pred HHhhcCCCHH------HHHHHHHHcCCeEEEEeC----CCCCHHHHHHHHHHh
Q 009883 96 KVKEKGISFG------KLVCLAHCAGAKVEAFRT----NQSTIDDFRKYIIRC 138 (523)
Q Consensus 96 ~Vk~~GiTL~------Ela~LA~c~G~~V~~yra----~~~SldeFR~~v~~~ 138 (523)
.+++.||+.+ .+..+|+.+|++.+.++. ...++++||+.++.-
T Consensus 59 ~ak~~gI~vsd~evd~~i~~ia~~n~ls~~ql~~~L~~~G~s~~~~r~~ir~~ 111 (118)
T PF09312_consen 59 EAKRLGIKVSDEEVDEAIANIAKQNNLSVEQLRQQLEQQGISYEEYREQIRKQ 111 (118)
T ss_dssp HHHHCT----HHHHHHHHHHHHHHTT--HHHHHHHCHHCT--HHHHHHHHHHH
T ss_pred HHHHcCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3455555543 234555555554443331 236888999888753
No 78
>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=23.96 E-value=1.5e+02 Score=25.91 Aligned_cols=44 Identities=16% Similarity=0.256 Sum_probs=29.4
Q ss_pred CCCCCcCCCccccccchhccccchHH-HhhcCCCHHHHHHHHHHcC
Q 009883 71 DPGRKWKGPWRWFDESMLDCCEPLEK-VKEKGISFGKLVCLAHCAG 115 (523)
Q Consensus 71 DP~r~wkgpwRwf~E~mLdcc~~le~-Vk~~GiTL~Ela~LA~c~G 115 (523)
.|.+. .|..|+|++.-+..-..+.. .+..|+|++++..+....+
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 34444 46689998755543333333 4678999999998886544
No 79
>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=23.41 E-value=3.3e+02 Score=21.75 Aligned_cols=55 Identities=11% Similarity=0.178 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHhhcC--CCceEEEEeecccccccCCccccccceeecCCCeEEEEecCC
Q 009883 124 NQSTIDDFRKYIIRCSAS--EDCHVISSYHRGAFKQTGTGHFSPIGGYHAGRDMALILDVAR 183 (523)
Q Consensus 124 ~~~SldeFR~~v~~~~ss--~d~~vIVNY~R~~LgQtGgGHFSPIGGYh~~tD~VLILDVAR 183 (523)
...|+.+|++.|.....- +-....+-|..+.|.. + .+|+.|+-..+..+++-+..
T Consensus 19 ~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d---~--~~L~~~~i~~~~~i~~~~~~ 75 (77)
T cd01805 19 PDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKD---D--TTLEEYKIDEKDFVVVMVSK 75 (77)
T ss_pred CCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccC---C--CCHHHcCCCCCCEEEEEEec
Confidence 457999999999876542 3234444588887752 2 38999999888888776643
No 80
>PF14104 DUF4277: Domain of unknown function (DUF4277)
Probab=23.39 E-value=68 Score=29.55 Aligned_cols=51 Identities=25% Similarity=0.304 Sum_probs=34.7
Q ss_pred cCCCccccHHHHHHHHHhccCCCCCCcCCCccccccchhccccchHHHhhcCCCHHHHH
Q 009883 50 QSEPAYCGLASLSMVLNALAIDPGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLV 108 (523)
Q Consensus 50 Q~npAyCGvASlamVLNAL~iDP~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela 108 (523)
|. .-.+|.+-.+||||.||..+.+- +--.+||.. .+.|..-..|++-+.|.
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 223467743 45566777777776653
No 81
>PTZ00445 p36-lilke protein; Provisional
Probab=22.65 E-value=2.1e+02 Score=29.29 Aligned_cols=97 Identities=19% Similarity=0.154 Sum_probs=56.6
Q ss_pred HHHHHHHHcCCeEEEEeC-------------CCC---------CHHHHHHHHHHhhcCCCceEEEEeecccccccCCccc
Q 009883 106 KLVCLAHCAGAKVEAFRT-------------NQS---------TIDDFRKYIIRCSASEDCHVISSYHRGAFKQTGTGHF 163 (523)
Q Consensus 106 Ela~LA~c~G~~V~~yra-------------~~~---------SldeFR~~v~~~~ss~d~~vIVNY~R~~LgQtGgGHF 163 (523)
.|..+++..|+++-+..= ++. --++|+..+.++...+=..+||-|+.+.. -.+.+|=
T Consensus 33 ~~v~~L~~~GIk~Va~D~DnTlI~~HsgG~~~~~~~~~~~~~~~tpefk~~~~~l~~~~I~v~VVTfSd~~~-~~~~~~~ 111 (219)
T PTZ00445 33 KFVDLLNECGIKVIASDFDLTMITKHSGGYIDPDNDDIRVLTSVTPDFKILGKRLKNSNIKISVVTFSDKEL-IPSENRP 111 (219)
T ss_pred HHHHHHHHcCCeEEEecchhhhhhhhcccccCCCcchhhhhccCCHHHHHHHHHHHHCCCeEEEEEccchhh-ccccCCc
Confidence 466777888887766541 111 24579998887766565789999999877 1122332
Q ss_pred cccce-------eecCCCeEEEEecCCCCCCceeeehHHHHHhccccCC
Q 009883 164 SPIGG-------YHAGRDMALILDVARFKYPPHWVPLTLLWEAMDRVDD 205 (523)
Q Consensus 164 SPIGG-------Yh~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~ 205 (523)
.-|.| -...+=.+.|--| .-.||+||=. +..|.+|..+=|
T Consensus 112 ~~Isg~~li~~~lk~s~~~~~i~~~-~~yyp~~w~~-p~~y~~~gl~KP 158 (219)
T PTZ00445 112 RYISGDRMVEAALKKSKCDFKIKKV-YAYYPKFWQE-PSDYRPLGLDAP 158 (219)
T ss_pred ceechHHHHHHHHHhcCccceeeee-eeeCCcccCC-hhhhhhhcccCC
Confidence 22321 1222334444444 2289999954 334776665444
No 82
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.31 E-value=88 Score=27.20 Aligned_cols=36 Identities=25% Similarity=0.251 Sum_probs=27.1
Q ss_pred CCccccccchhccccchHHHhhcCCCHHHHHHHHHH
Q 009883 78 GPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHC 113 (523)
Q Consensus 78 gpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c 113 (523)
+..|.|++.-++.-.-+...++.|++++|+..+...
T Consensus 32 ~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 32 GGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred CCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 456678776665444556678999999999998865
No 83
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.78 E-value=96 Score=28.80 Aligned_cols=43 Identities=23% Similarity=0.428 Sum_probs=31.7
Q ss_pred CCCCcCCCccccccchhccccchHHHhhcCCCHHHHHHHHHHcC
Q 009883 72 PGRKWKGPWRWFDESMLDCCEPLEKVKEKGISFGKLVCLAHCAG 115 (523)
Q Consensus 72 P~r~wkgpwRwf~E~mLdcc~~le~Vk~~GiTL~Ela~LA~c~G 115 (523)
|.+. .+.+|+|+++-+..-.-+...++.|+|++|+..+....+
T Consensus 28 p~r~-~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 28 PERS-DSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CccC-CCCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhc
Confidence 5443 346999998777655555567899999999999886654
Done!