Query 011156
Match_columns 492
No_of_seqs 142 out of 192
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 08:44:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011156.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011156hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0632 Phytochelatin synthase 100.0 2E-119 5E-124 890.8 17.2 386 1-471 3-388 (388)
2 PF09328 Phytochelatin_C: Doma 100.0 8E-109 2E-113 802.5 24.3 259 218-478 1-264 (264)
3 PF05023 Phytochelatin: Phytoc 100.0 3.3E-82 7.2E-87 607.2 16.3 211 1-215 1-212 (212)
4 PF13529 Peptidase_C39_2: Pept 98.8 1.5E-08 3.3E-13 86.2 6.4 117 49-180 11-144 (144)
5 cd02549 Peptidase_C39A A sub-f 98.4 1.9E-06 4.2E-11 74.7 10.6 129 48-199 1-131 (141)
6 PF03412 Peptidase_C39: Peptid 98.1 4.9E-06 1.1E-10 71.9 6.3 117 45-199 4-120 (131)
7 cd02418 Peptidase_C39B A sub-f 97.9 0.00029 6.3E-09 60.8 13.1 122 45-198 3-124 (136)
8 cd02424 Peptidase_C39E A sub-f 97.8 0.00022 4.7E-09 62.3 11.3 119 45-198 3-122 (129)
9 cd02259 Peptidase_C39_like Pep 97.8 0.00032 7E-09 59.1 10.9 115 48-199 1-115 (122)
10 cd02420 Peptidase_C39D A sub-f 97.7 0.00045 9.8E-09 59.2 10.7 114 47-198 5-118 (125)
11 PF14399 Transpep_BrtH: NlpC/p 97.6 0.0016 3.4E-08 64.6 15.1 151 53-212 1-163 (317)
12 cd02423 Peptidase_C39G A sub-f 97.6 0.0012 2.6E-08 56.4 11.5 116 48-198 6-122 (129)
13 cd02425 Peptidase_C39F A sub-f 97.3 0.0041 8.9E-08 53.0 11.6 116 45-197 3-118 (126)
14 TIGR03796 NHPM_micro_ABC1 NHPM 97.3 0.0031 6.7E-08 69.9 13.8 114 45-196 4-117 (710)
15 cd02419 Peptidase_C39C A sub-f 97.1 0.012 2.5E-07 50.5 12.7 114 47-198 5-118 (127)
16 PF11814 DUF3335: Peptidase_C3 97.0 0.01 2.2E-07 58.4 12.4 161 43-216 2-207 (207)
17 TIGR01193 bacteriocin_ABC ABC- 96.9 0.021 4.6E-07 63.5 15.3 120 48-197 1-120 (708)
18 PF09778 Guanylate_cyc_2: Guan 96.4 0.024 5.3E-07 55.9 9.9 85 106-199 96-200 (212)
19 cd02417 Peptidase_C39_likeA A 94.3 1 2.2E-05 38.2 11.8 110 52-198 5-114 (121)
20 COG2274 SunT ABC-type bacterio 93.3 0.28 6E-06 56.0 8.5 117 44-198 3-119 (709)
21 cd02421 Peptidase_C39_likeD A 92.9 3.8 8.3E-05 34.9 13.0 109 54-198 7-115 (124)
22 TIGR03375 type_I_sec_LssB type 92.9 0.63 1.4E-05 51.9 10.3 103 56-196 2-107 (694)
23 TIGR01846 type_I_sec_HlyB type 90.7 1.7 3.7E-05 48.6 10.6 105 55-197 1-105 (694)
24 COG3271 Predicted double-glyci 87.0 0.87 1.9E-05 44.9 4.5 103 46-180 36-139 (201)
25 TIGR03797 NHPM_micro_ABC2 NHPM 85.2 6.2 0.00013 44.1 10.6 100 56-196 5-104 (686)
26 PF12385 Peptidase_C70: Papain 70.7 33 0.00073 33.2 9.2 138 41-198 22-161 (166)
27 KOG4621 Uncharacterized conser 65.4 23 0.00049 33.6 6.7 95 100-199 57-152 (167)
28 PF05543 Peptidase_C47: Stapho 49.6 72 0.0016 31.3 7.5 115 44-172 15-133 (175)
29 PF05381 Peptidase_C21: Tymovi 48.7 10 0.00022 34.2 1.5 55 60-118 8-62 (104)
30 TIGR02044 CueR Cu(I)-responsiv 48.3 16 0.00034 32.7 2.7 42 70-111 28-69 (127)
31 cd04770 HTH_HMRTR Helix-Turn-H 47.8 17 0.00038 31.9 2.9 43 70-112 28-70 (123)
32 cd04768 HTH_BmrR-like Helix-Tu 45.1 17 0.00038 31.0 2.4 42 70-111 28-69 (96)
33 PF14104 DUF4277: Domain of un 45.0 19 0.0004 32.9 2.6 49 51-106 41-89 (115)
34 cd04787 HTH_HMRTR_unk Helix-Tu 44.7 18 0.00039 32.7 2.5 43 70-112 28-70 (133)
35 cd04784 HTH_CadR-PbrR Helix-Tu 44.0 20 0.00043 32.0 2.6 37 75-111 33-69 (127)
36 cd04781 HTH_MerR-like_sg6 Heli 43.7 19 0.00042 31.8 2.5 43 70-113 28-70 (120)
37 cd04785 HTH_CadR-PbrR-like Hel 43.5 21 0.00045 32.0 2.7 43 70-112 28-70 (126)
38 cd04788 HTH_NolA-AlbR Helix-Tu 43.3 19 0.00042 30.7 2.4 43 70-112 28-70 (96)
39 PRK10227 DNA-binding transcrip 43.3 21 0.00045 32.7 2.7 42 70-111 28-69 (135)
40 TIGR02047 CadR-PbrR Cd(II)/Pb( 43.2 22 0.00047 32.0 2.8 42 70-111 28-69 (127)
41 cd04763 HTH_MlrA-like Helix-Tu 42.1 42 0.00092 26.4 4.0 44 66-109 24-67 (68)
42 cd01104 HTH_MlrA-CarA Helix-Tu 42.0 45 0.00098 25.8 4.1 52 57-109 15-67 (68)
43 PRK13752 putative transcriptio 42.0 21 0.00045 33.1 2.6 43 70-112 35-77 (144)
44 PRK15002 redox-sensitivie tran 40.1 43 0.00092 31.6 4.3 41 70-111 39-79 (154)
45 cd04786 HTH_MerR-like_sg7 Heli 39.0 55 0.0012 29.8 4.7 43 70-112 28-70 (131)
46 cd01282 HTH_MerR-like_sg3 Heli 38.4 28 0.00061 30.6 2.7 42 70-112 28-69 (112)
47 COG5559 Uncharacterized conser 38.3 16 0.00036 30.1 1.1 18 460-477 8-25 (65)
48 PRK13749 transcriptional regul 37.2 31 0.00066 31.5 2.8 44 70-113 31-74 (121)
49 PF13411 MerR_1: MerR HTH fami 36.5 33 0.00072 26.7 2.6 55 55-110 13-67 (69)
50 cd01106 HTH_TipAL-Mta Helix-Tu 36.0 31 0.00066 29.6 2.5 43 70-112 28-70 (103)
51 cd04783 HTH_MerR1 Helix-Turn-H 36.0 30 0.00065 30.8 2.5 39 74-112 32-70 (126)
52 PF04157 EAP30: EAP30/Vps36 fa 35.2 50 0.0011 32.3 4.1 115 35-156 35-166 (223)
53 cd04782 HTH_BltR Helix-Turn-He 34.6 37 0.0008 29.1 2.8 42 70-111 28-69 (97)
54 cd01108 HTH_CueR Helix-Turn-He 34.5 34 0.00073 30.7 2.6 42 70-111 28-69 (127)
55 TIGR02043 ZntR Zn(II)-responsi 33.3 36 0.00077 30.8 2.6 42 70-111 29-70 (131)
56 cd01109 HTH_YyaN Helix-Turn-He 32.9 42 0.00092 29.2 2.9 42 70-111 28-69 (113)
57 TIGR02051 MerR Hg(II)-responsi 31.0 39 0.00085 30.2 2.4 43 70-112 27-69 (124)
58 cd04790 HTH_Cfa-like_unk Helix 30.6 43 0.00093 31.8 2.8 43 70-112 29-71 (172)
59 PF14538 Raptor_N: Raptor N-te 30.3 4.8E+02 0.01 24.7 9.7 69 117-200 65-135 (154)
60 cd04764 HTH_MlrA-like_sg1 Heli 30.2 87 0.0019 24.5 4.0 36 74-109 31-66 (67)
61 PF14214 Helitron_like_N: Heli 30.2 73 0.0016 29.8 4.2 44 218-268 102-145 (184)
62 cd01110 HTH_SoxR Helix-Turn-He 30.0 42 0.00091 30.8 2.5 41 70-111 29-69 (139)
63 cd04780 HTH_MerR-like_sg5 Heli 28.9 1.1E+02 0.0023 26.4 4.6 56 70-134 28-84 (95)
64 PRK09514 zntR zinc-responsive 28.6 47 0.001 30.5 2.5 43 70-112 29-71 (140)
65 cd04773 HTH_TioE_rpt2 Second H 26.8 56 0.0012 28.6 2.6 43 70-112 28-70 (108)
66 TIGR01950 SoxR redox-sensitive 26.6 54 0.0012 30.3 2.6 38 74-111 32-69 (142)
67 cd04765 HTH_MlrA-like_sg2 Heli 25.9 1.2E+02 0.0026 26.3 4.4 44 69-113 28-72 (99)
68 TIGR02054 MerD mercuric resist 25.5 59 0.0013 29.5 2.6 43 70-112 31-73 (120)
69 COG3937 Uncharacterized conser 24.5 1.1E+02 0.0023 28.0 3.9 36 447-482 63-103 (108)
70 cd01111 HTH_MerD Helix-Turn-He 23.7 70 0.0015 28.1 2.7 46 67-112 24-70 (107)
71 cd04789 HTH_Cfa Helix-Turn-Hel 23.4 69 0.0015 27.7 2.5 40 70-110 29-68 (102)
72 cd04776 HTH_GnyR Helix-Turn-He 23.4 66 0.0014 28.7 2.4 41 70-112 28-68 (118)
73 cd01107 HTH_BmrR Helix-Turn-He 23.1 74 0.0016 27.7 2.7 38 76-113 35-72 (108)
74 COG3323 Uncharacterized protei 22.9 60 0.0013 29.6 2.1 53 115-172 7-59 (109)
75 cd01105 HTH_GlnR-like Helix-Tu 20.9 92 0.002 26.2 2.7 43 70-112 29-71 (88)
76 cd04775 HTH_Cfa-like Helix-Tur 20.4 87 0.0019 27.0 2.5 44 67-110 25-68 (102)
77 cd01805 RAD23_N Ubiquitin-like 20.3 4.1E+02 0.0089 21.0 6.3 55 122-181 19-75 (77)
No 1
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=2.3e-119 Score=890.77 Aligned_cols=386 Identities=54% Similarity=1.025 Sum_probs=363.5
Q ss_pred CCCcccccCCCCCccccCChhhHHHHHHHHhcCCcccchhchhcccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccc
Q 011156 1 MAGLYRRALPSPPAIEFASPEGKQLFTEALGEGTMEGFFKLISYYQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRW 80 (492)
Q Consensus 1 ~~sfyrR~LP~p~~I~fsS~EGk~lf~eAl~~g~~e~ff~L~~qF~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrw 80 (492)
|.+||||.||. ++|+|+|.+||++|.|||+.|+||+||.|++||+||++|||||+|||+||||||.|||+|.|||||||
T Consensus 3 ~ksfYrR~Lp~-~ci~FsS~lGK~iF~eALqkGtme~yF~Lasqf~TQ~EPAfCGL~tL~mvLNsL~vDPgr~WKgpWRw 81 (388)
T KOG0632|consen 3 MKSFYRRSLPP-PCIDFSSSLGKDIFNEALQKGTMEGYFSLASQFQTQSEPAFCGLATLSMVLNSLSVDPGRKWKGPWRW 81 (388)
T ss_pred hhhhhccCCCc-hhhhhhhHhhHHHHHHHHHhcchhHHHHHHHHHhccCCcchhhhHHHHHHHHhhccCCcccccCCchh
Confidence 57999999985 89999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCcc
Q 011156 81 FDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGH 160 (492)
Q Consensus 81 f~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GH 160 (492)
|||+|||||+|++.|++.||+|.+|.|||+|+|++|+++|.++.++|+||+.++.|.+++|+++|.+|+|++|||||+||
T Consensus 82 ydesMLdCC~pLe~ikk~Gisl~~fsCLA~cnglk~~~~~~s~~t~d~FRk~vv~cstsen~~mi~sy~R~VlgQTGtGH 161 (388)
T KOG0632|consen 82 YDESMLDCCEPLEDIKKKGISLGKFSCLAHCNGLKVEAFRTSQSTIDDFRKDVVKCSTSENCHMISSYHRKVLGQTGTGH 161 (388)
T ss_pred hhhHHHhhcccHHHHHhcCcchheeehhhhcCCceeEEEecCcchHHHHHHHHHhcccccceeeehHhHHHHhcCCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhhcccCcCCCceeEEEEecCCCCCcceeeeeecCCChHHHHHH
Q 011156 161 FSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMDTIDKATGHPRGFMIISRFHKAPSVLYTVSCRHEGWSKVAKY 240 (492)
Q Consensus 161 FSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~sgrsRG~ills~~~~~~~~l~~~s~~~~~w~~~~~~ 240 (492)
||||||||+++|++||||||||||||||||++.||+||..||.+||++||||+|++++++|+ +|+++|++++|..+++|
T Consensus 162 FSPiggy~e~~d~~LIlDVARFKYPphWV~Lkll~eam~siD~stg~pRG~~li~~~h~~~g-l~tl~lkk~sw~~i~k~ 240 (388)
T KOG0632|consen 162 FSPIGGYNEERDMALILDVARFKYPPHWVPLKLLWEAMDSIDQSTGQPRGFMLISRPHREPG-LYTLSLKKESWINIAKY 240 (388)
T ss_pred cCcccccCcccCceEEeehhhccCCCcceeHHHHHHHhcchhhccCCCccceecccCCCCCc-eEEEEeccccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred HHhhcccccccCCCCCHHHHHHHHHhcCcchhHHHHhhheeeeeccccCCCCCHHHHHHhhhHHHHHHHhhccchhHHHH
Q 011156 241 LTEDVPHRLKMNDVKDVENLLSLVFKSAPVDLKEFIKWVAEVRRQDVAGVSSSEEEKARLIIKEEVLKQIKETEIFEHIN 320 (492)
Q Consensus 241 ~~~~~p~l~~~~~~~~~~~v~~~~~~~~p~~~~~~i~~~~evr~~e~~~~~ls~e~~~~l~~k~~~l~qi~~t~l~~~v~ 320 (492)
|.+|+|. |.++.|.++|.+++.|| ++|+|+.|+..++++.|| +|+.++
T Consensus 241 lk~~v~~------------i~~~dfas~~~s~NQf~--~~~i~~~~d~~q~~~~E~-----fk~c~r------------- 288 (388)
T KOG0632|consen 241 LKEDVPR------------IKNVDFASLPLSFNQFI--IAEIRETEDSNQNLSFEE-----FKQCIR------------- 288 (388)
T ss_pred HHHhhhh------------hhhhHHHhcchhHHHHH--HHHHHhhcCcccccCHHH-----HHHHHH-------------
Confidence 9999987 66677999999999999 999999999999999998 454443
Q ss_pred HhhccccccccCCCCchHHHHHHHhhhhhhHhhcccCCCCCccccccceeeEeeCCCCCeeEEeceEeeCCcccceeeec
Q 011156 321 RWLGSEISVCQGYKQTLPEIAANVCCQGAQLLAGQLSSLDETCCKETNVVLVQAGGVSPMTLVSGKITTNGVEQGIDMLV 400 (492)
Q Consensus 321 ~~~~~~~~~~~~~~~~l~~~~~~~ccqg~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~e~~~d~l~ 400 (492)
++ .++++ -+++..||+|+++++|. .+..+||++||++|.|.-++...|+
T Consensus 289 ---st-----~~y~~---f~~h~~~c~~~e~~s~~--~~~~~~c~~~~~ac~kg~~e~~~t~------------------ 337 (388)
T KOG0632|consen 289 ---ST-----VTYED---FAAHKNCCTGVEILSGA--FSAEFCCPETCVACIKGVLEEIQTV------------------ 337 (388)
T ss_pred ---hh-----hhHHh---hhhhhcccccceeecCC--cccccccHHHHHHhhhchhhhhhhe------------------
Confidence 11 12344 57899999999999997 5678999999999999855555554
Q ss_pred cCCCCCcccccccCCCCCccccCCCchhHHHHHHHhcCccccCCCCchHHHHHHHhhhccCCCChhHHHHH
Q 011156 401 PSSQTEPRNILCDFDRSNCKGMHPSTADVLTVILLALPQHTWSGIKEEKLLTQLNRCVSIENIPSLLQQEV 471 (492)
Q Consensus 401 p~~~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~e~~~l~s~~~lp~~l~~ev 471 (492)
..+|+.+||.|+|||||||+||+||||..|..|+.++.+.-+.|.++|.||
T Consensus 338 --------------------~aev~~s~v~taLllAlp~q~~~~~k~dsl~~~~k~~~~~~S~~t~~~~~~ 388 (388)
T KOG0632|consen 338 --------------------VAEVEGSDVFTALLLALPPQTWSGIKDDSLTHEMKQLISMCSSPTLLQTEV 388 (388)
T ss_pred --------------------eeecccchHHHHHHHhcCcccccccccHHHHHHHHHHHhhcccHhhhhccC
Confidence 347899999999999999999999999999999999999999999999985
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=7.8e-109 Score=802.46 Aligned_cols=259 Identities=61% Similarity=1.001 Sum_probs=255.9
Q ss_pred CCCCcceeeeeecCCChHHHHHHHHhhcccccccCCCCCHHHHHHHHHhcCcchhHHHHhhheeeeeccccCCCCCHHHH
Q 011156 218 HKAPSVLYTVSCRHEGWSKVAKYLTEDVPHRLKMNDVKDVENLLSLVFKSAPVDLKEFIKWVAEVRRQDVAGVSSSEEEK 297 (492)
Q Consensus 218 ~~~~~~l~~~s~~~~~w~~~~~~~~~~~p~l~~~~~~~~~~~v~~~~~~~~p~~~~~~i~~~~evr~~e~~~~~ls~e~~ 297 (492)
+++|++|||+||+||+|.+|||||++|||.|||+++++||++||++||+|||++|++||||||||||+|||+++||.|||
T Consensus 1 ~r~P~lLYTlSCkhEsW~s~AKyL~eDvP~LLkse~v~~v~~vls~vf~SlPsn~~~FIKWVaEVRR~Edg~~~LS~EEk 80 (264)
T PF09328_consen 1 HRAPSLLYTLSCKHESWISMAKYLMEDVPRLLKSEDVKDVEEVLSVVFKSLPSNFGEFIKWVAEVRRQEDGGSSLSKEEK 80 (264)
T ss_pred CCCCceeEEeecCcCcHHHHHHHHHHHHHHHhhhcccCcHHHHHHHHHhcCchhHHHHhhhheeEEecccCCCCCCHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhHHHHHHHhhccchhHHHHHhhcccccccc-----CCCCchHHHHHHHhhhhhhHhhcccCCCCCccccccceeeE
Q 011156 298 ARLIIKEEVLKQIKETEIFEHINRWLGSEISVCQ-----GYKQTLPEIAANVCCQGAQLLAGQLSSLDETCCKETNVVLV 372 (492)
Q Consensus 298 ~~l~~k~~~l~qi~~t~l~~~v~~~~~~~~~~~~-----~~~~~l~~~~~~~ccqg~~~l~~~~~~~~~~~~~~~~~~~~ 372 (492)
+||++|++||||||+|+|||||++|+++.+|||. +++|+||+|||+||||||+||+|+++++++|||+|||+||+
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 9999999999999999999999999999999994 89999999999999999999999999999999999999999
Q ss_pred eeCCCCCeeEEeceEeeCCcccceeeeccCCCCCcccccccCCCCCccccCCCchhHHHHHHHhcCccccCCCCchHHHH
Q 011156 373 QAGGVSPMTLVSGKITTNGVEQGIDMLVPSSQTEPRNILCDFDRSNCKGMHPSTADVLTVILLALPQHTWSGIKEEKLLT 452 (492)
Q Consensus 373 ~~~~~~~~~~~s~~~~~~~~e~~~d~l~p~~~~~~~~~~~~~~~~~~~~~~p~~~dvlt~lllal~~~tw~~i~~~~l~~ 452 (492)
|+|||||+|||||+||++|+|||||||||+++++++ +|+++.++|++|||+++||||||||||||+||+|||||+|++
T Consensus 161 k~n~d~~~tvvsGtVv~~g~Eq~VD~LvP~s~~~~~--~c~~~~~~~~~~hPs~~DVLTvLLLALpp~TWs~Ikde~l~~ 238 (264)
T PF09328_consen 161 KANGDGPKTVVSGTVVSGGSEQGVDVLVPSSQTKTS--CCNSGSSNEIGMHPSSNDVLTVLLLALPPSTWSGIKDEKLLA 238 (264)
T ss_pred eeCCCCceEEEeeeEEcCCCccceeEEeccccCCCC--ccCCCCCCccccCCCcccHHHHHHHhCCccccccCccHHHHH
Confidence 999999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred HHHhhhccCCCChhHHHHHHHHHHHH
Q 011156 453 QLNRCVSIENIPSLLQQEVLHLRRQL 478 (492)
Q Consensus 453 e~~~l~s~~~lp~~l~~ev~~lr~q~ 478 (492)
||++||||||||++||+||+||||||
T Consensus 239 Ei~~LvSte~LP~lLQeEVlHLrrQL 264 (264)
T PF09328_consen 239 EIQSLVSTENLPDLLQEEVLHLRRQL 264 (264)
T ss_pred HHHHHhhhhhCcHHHHHHHHHHHhcC
Confidence 99999999999999999999999996
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=3.3e-82 Score=607.18 Aligned_cols=211 Identities=58% Similarity=1.100 Sum_probs=169.9
Q ss_pred CCCcccccCCCCCccccCChhhHHHHHHHHhcCCcccchhchhcccccCCCCcccHHHHHHHHHhcccC-CCCCcCCCcc
Q 011156 1 MAGLYRRALPSPPAIEFASPEGKQLFTEALGEGTMEGFFKLISYYQTQSEPAYCGLATLAVILNALAID-PGRTWKGPWR 79 (492)
Q Consensus 1 ~~sfyrR~LP~p~~I~fsS~EGk~lf~eAl~~g~~e~ff~L~~qF~TQ~~payCGvASLaMVLNAL~id-P~r~wkgpwr 79 (492)
|++||+|+||+ ++|+|+|+||++||.+| ++|++||+|++||+||+|++||||||++||||||++| |++.||||||
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 57999999998 89999999999999998 8999999999999999999999999999999999999 9999999999
Q ss_pred ccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCc
Q 011156 80 WFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSG 159 (492)
Q Consensus 80 wf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~G 159 (492)
||+|++++||++++.++++||||+||+|||+|+|++|+++++++.++++||++|++++++++++|||||+|++|||+|+|
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 cccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhhcccCcCCCceeEEEEe
Q 011156 160 HFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMDTIDKATGHPRGFMIIS 215 (492)
Q Consensus 160 HFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~tiD~~sgrsRG~ills 215 (492)
|||||||||+++|+||||||||||||||||++++||+||+++|++|||+||||+|+
T Consensus 157 HfSPigaY~~~tD~vLilDVar~kYpp~WV~~~~L~~AM~~~D~~s~~~RG~~~is 212 (212)
T PF05023_consen 157 HFSPIGAYDAETDRVLILDVARFKYPPYWVPLERLYEAMNTIDPDSGKSRGYLLIS 212 (212)
T ss_dssp EEEEEEEEETTTTEEEE--S-TTT---EEEEHHHHHHHHSSEETTTTEE-EEEEEE
T ss_pred cccccceecccCCeEEEEecccccCCCEEeEHHHHHHHHhccCCCCCCcceEEEeC
Confidence 99999999999999999999999999999999999999999999999999999986
No 4
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=98.76 E-value=1.5e-08 Score=86.16 Aligned_cols=117 Identities=23% Similarity=0.224 Sum_probs=66.6
Q ss_pred CCCCcccHHHHHHHHHhcccCCCCCc----------CCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEE
Q 011156 49 SEPAYCGLATLAVILNALAIDPGRTW----------KGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEA 118 (492)
Q Consensus 49 ~~payCGvASLaMVLNAL~idP~r~w----------kgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~ 118 (492)
+....||+||++|||+.+|+++.+.- ..+..+|-.++ ......|+....+..+++..|.++.
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 78899999999999999987533210 00011110000 0123567888899999999987443
Q ss_pred EecCCCCHHHHHHHHHHHhcCCCceEEEEeec--cc-----ccccCCccccccceeecCCCeEEEEecC
Q 011156 119 FRTNESSIDDFRRHVISCASSEDCHVISSYHR--GV-----FKQTGSGHFSPIGGYHARKDLVLILDVA 180 (492)
Q Consensus 119 ~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR--~~-----LgQtG~GHFSPIGGY~~~tD~VLILDVA 180 (492)
.....+++++++.|. .++.||++..- .. .....+|||--|-||+..+ .|.|.|++
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 334567777777664 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=98.43 E-value=1.9e-06 Score=74.73 Aligned_cols=129 Identities=19% Similarity=0.127 Sum_probs=86.7
Q ss_pred cCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccc-CChhhHhhcCCCHHHHHHH-HHHcCCeEEEEecCCCC
Q 011156 48 QSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCC-KPLSKIKAEGITFGKVACL-AYCNGAKVEAFRTNESS 125 (492)
Q Consensus 48 Q~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c-~~le~V~~~GiTLdEla~L-A~c~G~~V~~~ra~~~s 125 (492)
|+.+..||++|++|+|+-+|++.... .+...- ...-.....|++..++... ++..|++++.+...
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 46788999999999999999763221 111000 0000112468999999999 99999987654421
Q ss_pred HHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhh
Q 011156 126 IDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMD 199 (492)
Q Consensus 126 ldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~ 199 (492)
.. +++.. +.+..+|+...- .....+.|||--|.||+ +.+.++|.|++. ..+..++.+++-++..
T Consensus 68 ~~-----~~~~l-~~~~Pvi~~~~~-~~~~~~~gH~vVv~g~~-~~~~~~i~DP~~--~~~~~~~~~~f~~~w~ 131 (141)
T cd02549 68 LA-----LLRQL-AAGHPVIVSVNL-GVSITPSGHAMVVIGYD-RKGNVYVNDPGG--GRRLVVSFDEFEKAWK 131 (141)
T ss_pred HH-----HHHHH-HCCCeEEEEEec-CcccCCCCeEEEEEEEc-CCCCEEEECCCC--CcCEEEeHHHHHHHHH
Confidence 11 33333 356788887653 22234589999999999 456699999974 4678899888877665
No 6
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=98.13 E-value=4.9e-06 Score=71.89 Aligned_cols=117 Identities=24% Similarity=0.252 Sum_probs=78.9
Q ss_pred ccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCC
Q 011156 45 YQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNES 124 (492)
Q Consensus 45 F~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~ 124 (492)
+.-|.++.-||+|+++|+++-++++-.. +.+...+ .....|+++.++...++..|++++.++.+
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~~g~~~s~----------~~l~~~~----~~~~~g~s~~~L~~~~~~~gl~~~~~~~~-- 67 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKYYGIPVSE----------EELRRQL----GTSEEGTSLADLKRAARKYGLKAKAVKLN-- 67 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHHTT----H----------HHHHCCT----T-BTTB--CCCHHHHHHHTTEEEEEEE----
T ss_pred eEEeCCCCCHHHHHHHHHHHHhCCCchH----------HHHHHHh----cCCccCCCHHHHHHHHHhcccceeeeecc--
Confidence 4569999999999999999999976222 2233222 12468999999999999999999988754
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhh
Q 011156 125 SIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMD 199 (492)
Q Consensus 125 sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~ 199 (492)
.++| .+-...+|+.- +.|||--|-++ +.++++|.|+ +..+.|++.+++.+.-.
T Consensus 68 -~~~l--------~~~~~P~I~~~--------~~~h~vVi~~~--~~~~~~i~dP---~~g~~~~~~~~f~~~w~ 120 (131)
T PF03412_consen 68 -FEKL--------KRLPLPAIAHL--------KDGHFVVIYKI--DDGRVLIYDP---KKGKIKLSKEEFEEIWT 120 (131)
T ss_dssp -GGGC--------TCGGSSEEEEE--------CCCEEEEEEEE--CCCEEEECCT---TTCEEEEEHHHHHHHEE
T ss_pred -hhhh--------hhccccEEEEe--------cCcceEEEEeE--cCcEEEEEeC---CCCeEEEeHHHHHhhCC
Confidence 2233 12223555544 77999999887 8889999998 56789999999877554
No 7
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=97.91 E-value=0.00029 Score=60.82 Aligned_cols=122 Identities=16% Similarity=0.111 Sum_probs=84.7
Q ss_pred ccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCC
Q 011156 45 YQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNES 124 (492)
Q Consensus 45 F~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~ 124 (492)
+.-|.++..||+++++|+++=+|++... +.+...+ .....|+++..+...|+..|++++.++.+..
T Consensus 3 ~~~q~~~~~~gl~~l~~~~~~~g~~~~~----------~~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~ 68 (136)
T cd02418 3 YVLQVDEMDCGAACLAMIAKYYGKNYSL----------AKLRELA----GTDREGTSLLGLVKAAEKLGFETRAVKADMD 68 (136)
T ss_pred eEEecCcccHHHHHHHHHHHHhCCCCCH----------HHHHHHc----CCCCCCcCHHHHHHHHHHCCCeeEEEEcccc
Confidence 4557788899999999999999976322 1111111 1124789999999999999999988875422
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 125 SIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 125 sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
. .++ . .-...+|+-.. ...+.|||--|.+++ .+.|+|.|+ ..++.+++.++|-+..
T Consensus 69 ~-~~l----~----~~~~P~I~~~~----~~~~~~~~~Vl~~~~--~~~~~i~dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 69 L-FEL----K----DIPLPFIAHVI----KEWKLNHYVVVYKIK--KKKILIADP---AVGITKISKEEFEKEW 124 (136)
T ss_pred h-hhH----h----cCCCCEEEEEc----cCCCCCeEEEEEEEc--CCEEEEECC---CCCCEEeeHHHHHhhC
Confidence 1 012 1 12235555332 124789999999988 668999998 5679999999986644
No 8
>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=97.85 E-value=0.00022 Score=62.33 Aligned_cols=119 Identities=16% Similarity=0.251 Sum_probs=80.7
Q ss_pred ccccCCCCcccHHHHHHHHHh-cccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCC
Q 011156 45 YQTQSEPAYCGLATLAVILNA-LAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNE 123 (492)
Q Consensus 45 F~TQ~~payCGvASLaMVLNA-L~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~ 123 (492)
+.-|.++.-||+|+++|+++- .|++-.. +.+...+ .....|+++.++...|+..|+++++++.+
T Consensus 3 ~~~q~~~~dcgla~l~~i~~~~~g~~~~~----------~~l~~~~----~~~~~g~s~~~l~~~a~~~Gl~~k~~~~~- 67 (129)
T cd02424 3 IIKQTDLNDCGIAVIQMLYNHYYKKKYDL----------NELKIKA----NLKKNGLSIYDLENLAKKFGLETESYQGS- 67 (129)
T ss_pred eEEecCccchHHHHHHHHHHHhcCCCccH----------HHHHHHh----CCCCCCccHHHHHHHHHHcCCceeEEEcC-
Confidence 345778889999999999999 8865221 1111111 12357999999999999999999999854
Q ss_pred CCHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 124 SSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 124 ~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
.+++ .+. ...-..|++ ..++.||--+.+.+ .+.|+|.|+ ..++.+++.+++-+.-
T Consensus 68 --~~~l----~~~--~~p~P~i~~-------~~~~~hfvVl~~~~--~~~v~I~DP---~~g~~~~s~~~f~~~w 122 (129)
T cd02424 68 --FLEF----LEL--KNKFIILLK-------SNGLNHFVIVKKIK--KNKFIVLDP---KKGKYKITYKEFEKIF 122 (129)
T ss_pred --HHHH----hhc--cCCEEEEEe-------cCCCCeEEEEEEEE--CCEEEEECC---CCCCEEeCHHHHHHHh
Confidence 3332 221 112345554 13445998888754 456999999 4688899988876654
No 9
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=97.78 E-value=0.00032 Score=59.13 Aligned_cols=115 Identities=23% Similarity=0.317 Sum_probs=83.0
Q ss_pred cCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHH
Q 011156 48 QSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSID 127 (492)
Q Consensus 48 Q~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sld 127 (492)
|.+..-||+++++|+++-++++... +.+.. .......|.++.++..+|+..|++++.+..+ .+
T Consensus 1 ~~~~~~~gl~~l~~i~~~~g~~~~~----------~~l~~----~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~~---~~ 63 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYFGIPVRR----------DVLLN----AQQRRQQGLSLADLVSLANKLGLTAQGVKLP---LA 63 (122)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCH----------HHHHH----HHhhccCCCCHHHHHHHHHHcCCeeeEEEcC---HH
Confidence 4566689999999999999977322 11111 0112357899999999999999999877643 33
Q ss_pred HHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhh
Q 011156 128 DFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMD 199 (492)
Q Consensus 128 eFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~ 199 (492)
+++ .-+..+|+- .++|||--|.+++ .+.++|.|++ ...+.|++.++|.+...
T Consensus 64 ~l~--------~~~~P~i~~--------~~~~~~~Vl~~~~--~~~~~i~dp~--~~~~~~~~~~~l~~~w~ 115 (122)
T cd02259 64 ALS--------RLQLPALLL--------WKQGHFVILYGAD--KGQVLIADPL--EEGPVTLSESELEERWT 115 (122)
T ss_pred Hhc--------cCCCCEEEE--------cCCCcEEEEEEEc--CCEEEEECCc--ccCCEEeCHHHHHhhCC
Confidence 322 223355554 4789999999988 6689999986 57888999999877543
No 10
>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=97.69 E-value=0.00045 Score=59.23 Aligned_cols=114 Identities=21% Similarity=0.297 Sum_probs=80.0
Q ss_pred ccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCH
Q 011156 47 TQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSI 126 (492)
Q Consensus 47 TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sl 126 (492)
-|.+...||+++++++++-.|++-.. +.+.... .....|.+...+...|+..|++++.++.+ .
T Consensus 5 ~q~~~~~~gl~~l~~i~~~~g~~~~~----------~~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~ 67 (125)
T cd02420 5 LQMEATECGAASLAIILAYYGRYVPL----------SELRIAC----GVSRDGSNASNLLKAAREYGLTAKGYKKD---L 67 (125)
T ss_pred eeCcccCHHHHHHHHHHHHcCCCCCH----------HHHHHHc----CCCCCCCCHHHHHHHHHHcCcccceEecC---H
Confidence 35566799999999999999976222 1111100 01246899999999999999999887743 4
Q ss_pred HHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 127 DDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 127 deFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
+++.+ -.-++|+-. +.|||--|.+++ .|.++|.|++. +|.|++.++|-+..
T Consensus 68 ~~L~~--------~~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~~ 118 (125)
T cd02420 68 EALRE--------VSLPAIVFW--------NFNHFLVVEGFD--KRKVFLNDPAT---GRRTVSLEEFDQSF 118 (125)
T ss_pred HHHhc--------CCCCEEEEe--------CCCEEEEEEEEe--CCEEEEECCCc---CceeecHHHHHhhC
Confidence 44332 122555532 569999999988 56899999964 79999999886554
No 11
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=97.64 E-value=0.0016 Score=64.56 Aligned_cols=151 Identities=18% Similarity=0.093 Sum_probs=102.2
Q ss_pred cccHHHHHHHHHhcccCC-CCC---cCCCccccccchhcccCChhhHhhcCCCH-HHHHHHHHHcCCeEEEEecCCCCHH
Q 011156 53 YCGLATLAVILNALAIDP-GRT---WKGPWRWFDDTMLDCCKPLSKIKAEGITF-GKVACLAYCNGAKVEAFRTNESSID 127 (492)
Q Consensus 53 yCGvASLaMVLNAL~idP-~r~---wkgpwrwf~E~mLd~c~~le~V~~~GiTL-dEla~LA~c~G~~V~~~ra~~~sld 127 (492)
.|+-.+++|+|+..|++- ... -.+.|...-..+-+ ..+. ..-.|-+. +-+..+++.+|++++... ..+.+
T Consensus 1 hC~~~~l~~ll~~~g~~~~e~l~fglg~g~gf~y~~~~~-~~~~--~~~~~r~~~~~~~~~~~~lG~~~~~~~--~~~~~ 75 (317)
T PF14399_consen 1 HCESNALRDLLAHYGLPLSEALIFGLGSGLGFSYLPFPD-SNPP--PLLGGRSPPDFEENLLERLGIKYEWRE--FSSPD 75 (317)
T ss_pred CchhHHHHHHHHhcCCCCCHHHHHHHcCCcceEEEeccc-cCCC--eeecCCCchHHHHHHHHHCCceEEEEe--cCCHH
Confidence 599999999999999761 111 01122111000000 0010 11233333 556678899999888655 35678
Q ss_pred HHHHHHHHHhcCCCceEEEEeecccc-------cccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHhhc
Q 011156 128 DFRRHVISCASSEDCHVISSYHRGVF-------KQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAMDT 200 (492)
Q Consensus 128 eFR~~l~~~~ss~~~~vIVNysR~~L-------gQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~t 200 (492)
+..+.|++.+ +.+..|+|..+..-| .....+|+.-|-|||++.+.|+|.|. ..+++..+|.+.|-+|+..
T Consensus 76 ~~~~~l~~~l-~~g~pv~~~~D~~~lpy~~~~~~~~~~~H~i~v~G~d~~~~~~~v~D~--~~~~~~~~~~~~l~~A~~~ 152 (317)
T PF14399_consen 76 EAWEELKEAL-DAGRPVIVWVDMYYLPYRPNYYKKHHADHYIVVYGYDEEEDVFYVSDP--PSYEPGRLPYEDLAKARFS 152 (317)
T ss_pred HHHHHHHHHH-hCCCceEEEeccccCCCCccccccccCCcEEEEEEEeCCCCEEEEEcC--CCCcceeecHHHHHHHHhc
Confidence 8888888887 567789988876666 22357999999999999999999998 4678899999999999987
Q ss_pred ccCcCCCceeEE
Q 011156 201 IDKATGHPRGFM 212 (492)
Q Consensus 201 iD~~sgrsRG~i 212 (492)
..+ ...+++.+
T Consensus 153 ~~~-~~~~~~~~ 163 (317)
T PF14399_consen 153 EGI-PFPPKNRW 163 (317)
T ss_pred cCC-CCCCCceE
Confidence 764 22344444
No 12
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=97.56 E-value=0.0012 Score=56.45 Aligned_cols=116 Identities=28% Similarity=0.313 Sum_probs=79.5
Q ss_pred cCCCCcccHHHHHHHHHhcc-cCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCH
Q 011156 48 QSEPAYCGLATLAVILNALA-IDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSI 126 (492)
Q Consensus 48 Q~~payCGvASLaMVLNAL~-idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sl 126 (492)
|.+...||+++++|+++-++ +.-.. +.+...+ .....|.++.++..+++..|++++.++.+ .
T Consensus 6 q~~~~~~~l~~l~~~~~~~g~~~~~~----------~~l~~~~----~~~~~~~s~~~l~~~a~~~Gl~~~~~~~~---~ 68 (129)
T cd02423 6 QSYDFSCGPAALATLLRYYGGINITE----------QEVLKLM----LIRSEGFSMLDLKRYAEALGLKANGYRLN---L 68 (129)
T ss_pred cCCCCChHHHHHHHHHHhcCCCCCCH----------HHHHHHh----CcccCCcCHHHHHHHHHHCCCcceEEEcC---H
Confidence 66677999999999999999 76222 1111111 01246899999999999999999888753 3
Q ss_pred HHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 127 DDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 127 deFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
+++. +. .-.+|+-. + ..++|||--|.+++ .+.++|.|++. ++.+++.++|-+..
T Consensus 69 ~~L~----~~----~lP~i~~~-~----~~~~~~~vvl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~w 122 (129)
T cd02423 69 DKLN----AL----QIPVIVLV-N----NGGYGHFVVIKGID--GDRVLVGDPAL---GNISMSREEFERIW 122 (129)
T ss_pred HHHh----hC----CCCEEEEE-e----cCCCceEEEEEEEe--CCEEEEECCCC---CCcccCHHHHHHHh
Confidence 3332 21 12444433 1 23478999888888 67899999853 57899988876543
No 13
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=97.31 E-value=0.0041 Score=52.97 Aligned_cols=116 Identities=20% Similarity=0.259 Sum_probs=80.5
Q ss_pred ccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCC
Q 011156 45 YQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNES 124 (492)
Q Consensus 45 F~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~ 124 (492)
+..|.++.-||+++++|+++-++++-... .+.... .....|+++..+..+++..|++++.++.+..
T Consensus 3 ~~~q~~~~~~~l~~l~~~~~~~~~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~gl~~~~~~~~~~ 68 (126)
T cd02425 3 PILQNNQTECGLACYAMILNYFGYKVSLN----------ELREKY----ELGRDGLSLSYLKQLLEEYGFKCKVYKISFK 68 (126)
T ss_pred eEeecccccHHHHHHHHHHHHhCCCCCHH----------HHHHhc----cCCCCCcCHHHHHHHHHHCCCcceEEEEchH
Confidence 45688888999999999999999873331 111111 1234789999999999999999998875421
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHH
Q 011156 125 SIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEA 197 (492)
Q Consensus 125 sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eA 197 (492)
+.+. .. .-.+|+-. .+|||--|.+++ .+.++|.|+.. ++.|++.++|-+.
T Consensus 69 --~~l~----~~----~lP~I~~~--------~~~~~~Vl~~~~--~~~~~i~dp~~---~~~~~~~~~l~~~ 118 (126)
T cd02425 69 --KNLY----PL----KLPVIIFW--------NNNHFVVLEKIK--KNKVTIVDPAI---GRIKISIDEFLEN 118 (126)
T ss_pred --HHHh----hC----CCCEEEEE--------cCCcEEEEEEEE--CCEEEEEcCCC---CCEEECHHHHHhh
Confidence 2222 21 12444422 248999999984 55799999854 5789999887553
No 14
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=97.31 E-value=0.0031 Score=69.90 Aligned_cols=114 Identities=25% Similarity=0.310 Sum_probs=85.5
Q ss_pred ccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCC
Q 011156 45 YQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNES 124 (492)
Q Consensus 45 F~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~ 124 (492)
+.-|.+.+=||+|+++|++|-.|.+-+. +.+.+.+ .+.+.|+++.++..+|+..|++++.++.+
T Consensus 4 ~i~Q~~~~dCg~acl~mi~~~~g~~~~~----------~~lr~~~----~~~~~g~s~~~l~~~~~~~g~~~~~~~~~-- 67 (710)
T TIGR03796 4 TVLQMEAVECGAASLAMILAYYGRYVPL----------EELREEC----GVSRDGSKASNLLKAARSYGLEAKGFRKE-- 67 (710)
T ss_pred eEeecccccHHHHHHHHHHHHcCCCCCH----------HHHHHHc----CCCCCCCCHHHHHHHHHHCCCEeEEEecC--
Confidence 5668889999999999999999976222 1222211 24468999999999999999999999964
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHH
Q 011156 125 SIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWE 196 (492)
Q Consensus 125 sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~e 196 (492)
++++ . .-.-+.|+.. +.+||--+-++ +.+.|.|.|++. .+.|++.+++-+
T Consensus 68 -~~~l----~----~~~lP~i~~~--------~~~h~vvl~~~--~~~~~~i~dP~~---g~~~~~~~e~~~ 117 (710)
T TIGR03796 68 -LDAL----A----ELPLPYIVFW--------NFNHFVVVEGF--RGGRVYLNDPAL---GPRTVSLEEFDE 117 (710)
T ss_pred -HHHh----c----cCCCCEEEEE--------cCCcEEEEEEE--eCCEEEEECCCC---CCEEccHHHHHh
Confidence 3322 1 2233667766 56899888776 567899999963 789999999755
No 15
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=97.14 E-value=0.012 Score=50.51 Aligned_cols=114 Identities=20% Similarity=0.252 Sum_probs=79.5
Q ss_pred ccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCH
Q 011156 47 TQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSI 126 (492)
Q Consensus 47 TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sl 126 (492)
.|.+..-||+++++|+++-.|++.... .+.... .....|.++..+..+|+..|++++.++.+ .
T Consensus 5 ~q~~~~~~~l~~l~~~~~~~g~~~~~~----------~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~ 67 (127)
T cd02419 5 LQTEAAECGLACLAMIASYHGHHVDLA----------SLRQRF----PVSLKGATLADLIDIAQQLGLSTRALRLD---L 67 (127)
T ss_pred eeCccccHHHHHHHHHHHHcCCCCCHH----------HHHHHc----CCCCCCcCHHHHHHHHHHCCCceeEEEcc---H
Confidence 455667899999999999999773321 111111 01246899999999999999999887743 4
Q ss_pred HHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 127 DDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 127 deFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
+++++. .-.+|+-. ..|||--|.+. +.|.++|.|+.. ++.+++.++|-+..
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 444331 12444421 45899999886 567899999953 68999999986544
No 16
>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=97.03 E-value=0.01 Score=58.42 Aligned_cols=161 Identities=21% Similarity=0.292 Sum_probs=88.9
Q ss_pred hcccccCCCCcccHHHHHHHHHhcccC--CCCC-----cCCCccccccchhcccCChh---hHhhcCCCH----------
Q 011156 43 SYYQTQSEPAYCGLATLAVILNALAID--PGRT-----WKGPWRWFDDTMLDCCKPLS---KIKAEGITF---------- 102 (492)
Q Consensus 43 ~qF~TQ~~payCGvASLaMVLNAL~id--P~r~-----wkgpwrwf~E~mLd~c~~le---~V~~~GiTL---------- 102 (492)
++|. |..+..||+|++-|+|.+|+-. +++. |..-+..|=-+=--.|.|.- .+.++|..-
T Consensus 2 Pyy~-QTT~FTCGPa~lmMAm~~l~~~~~~~r~~EL~lWREATTifmtsGhGGC~P~GLAlAA~rrG~~vev~~~~~~pl 80 (207)
T PF11814_consen 2 PYYR-QTTEFTCGPACLMMAMAALDPEFELDRREELRLWREATTIFMTSGHGGCGPFGLALAAARRGFKVEVWVSTDGPL 80 (207)
T ss_pred Cccc-cCCCCCcHHHHHHHHHHhcCCcCCCCHHHHHHHHHHhceecccCCCCCcChHHHHHHHHHcCCceEEEECCCCCc
Confidence 3454 9999999999999999999843 2332 33222222000001343311 011111111
Q ss_pred ------------------HHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCcccccc
Q 011156 103 ------------------GKVACLAYCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPI 164 (492)
Q Consensus 103 ------------------dEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPI 164 (492)
++|..-|+..|+.++. .+.+++++++.+. .+..+||=.+-..+.+....|+--+
T Consensus 81 fld~vr~~~kk~v~~~v~~~f~~~a~~~gv~~~~---~~~~~~~l~~~l~-----~G~~~lvLIS~y~~~g~k~PHWV~v 152 (207)
T PF11814_consen 81 FLDSVRSEEKKEVMELVHEDFREEAEQAGVPVHY---RPLSLADLRAALA-----AGAIVLVLISTYRMDGKKVPHWVVV 152 (207)
T ss_pred eeccCCCHHHHHHHHHHHHHHHHHHHHCCCceec---CCCCHHHHHHHHH-----CCCEEEEEEeecccCCCCCCeEEEE
Confidence 1223333334443321 2345555555553 4668888888888888889999999
Q ss_pred ceeecCCCeEEEEecCCC-CCCCeeeehHH------HHHHhhcccCcCCCceeEEEEec
Q 011156 165 GGYHARKDLVLILDVARF-KYPPHWVPLAL------LWEAMDTIDKATGHPRGFMIISR 216 (492)
Q Consensus 165 GGY~~~tD~VLILDVARf-KYPP~WVpl~~------L~eAM~tiD~~sgrsRG~ills~ 216 (492)
-|||. |-|.|-|+.-. .-..-|++... =++.|...=+ .+-|+-++|.+
T Consensus 153 ~g~d~--~~vyihDP~~d~~~~~~~~d~~~lPi~~~~f~~m~~~G~--~~lraaV~l~~ 207 (207)
T PF11814_consen 153 TGVDD--DFVYIHDPDVDAERGESWVDCQHLPIPRADFDRMARFGK--SKLRAAVILRP 207 (207)
T ss_pred EEecC--CEEEEeCCCCCcccCCCchhhccCCccHHHHHHHHhhcc--cccEEEEEeeC
Confidence 99865 77889998543 23444543222 2444554432 35777777764
No 17
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=96.90 E-value=0.021 Score=63.46 Aligned_cols=120 Identities=18% Similarity=0.187 Sum_probs=84.4
Q ss_pred cCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHH
Q 011156 48 QSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSID 127 (492)
Q Consensus 48 Q~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sld 127 (492)
|.+..=||+|+++|+++-.|.+-+. +.+.+.+ .+.+.|+++.++..+|+..|++++.++.+ ++
T Consensus 1 Q~~~~dCg~~cl~~i~~~~g~~~~~----------~~lr~~~----~~~~~g~s~~~l~~~~~~~g~~~~~~~~~---~~ 63 (708)
T TIGR01193 1 QVDEKDCGIAALSMILKKYGTEYSL----------AKLRQLA----KTDLEGTTVLGLVKAAEYLNFEAKAIQAD---MS 63 (708)
T ss_pred CCCccchHHHHHHHHHHHcCCCCCH----------HHHHHHh----CCCCCCCCHHHHHHHHHHCCCEEEEEecC---HH
Confidence 6778889999999999999976222 1222222 24468999999999999999999999964 32
Q ss_pred HHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHH
Q 011156 128 DFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEA 197 (492)
Q Consensus 128 eFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eA 197 (492)
++. +. .-.-+.|+...+ ..+..||--+-+++ .+.|.|+|++. .+++.|++.+++.+.
T Consensus 64 ~l~--~~----~~~~P~I~~~~~----~~~~~H~vVl~~~~--~~~~~i~dP~~-~~g~~~~~~~ef~~~ 120 (708)
T TIGR01193 64 LFE--DK----NLPLPFIAHVIK----NGKLPHYYVVYGVT--KNHLIIADPDP-TVGITKISKEDFYEE 120 (708)
T ss_pred Hhc--cc----cCCCCEEEEEcc----CCCCCcEEEEEEEe--CCEEEEEcCCc-ccCCEEecHHHHHhh
Confidence 210 11 123366775332 12346998887766 67899999943 367899999997653
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=96.36 E-value=0.024 Score=55.93 Aligned_cols=85 Identities=24% Similarity=0.188 Sum_probs=52.8
Q ss_pred HHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeeccccc------------------cc--CCccccccc
Q 011156 106 ACLAYCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFK------------------QT--GSGHFSPIG 165 (492)
Q Consensus 106 a~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~Lg------------------Qt--G~GHFSPIG 165 (492)
-..|+.+|+.|+.- ..+++++..+|.+ .+ .+||=-+...|. +. =.|||--|-
T Consensus 96 F~~A~~~gi~V~~r---svs~~ei~~hl~~----g~-~aIvLVd~~~L~C~~Ck~~~~~~~~~~~~~~~~~Y~GHYVVlc 167 (212)
T PF09778_consen 96 FQKAKAAGINVEKR---SVSIQEIIEHLSS----GG-PAIVLVDASLLHCDLCKSNCFDPIGSKCFGRSPDYQGHYVVLC 167 (212)
T ss_pred HHHHHHcCCceEEe---eccHHHHHHHHhC----CC-cEEEEEccccccChhhcccccccccccccCCCCCccEEEEEEE
Confidence 34455556555431 2567777666642 22 555444444443 21 279999999
Q ss_pred eeecCCCeEEEEecCCCCCCCeeeehHHHHHHhh
Q 011156 166 GYHARKDLVLILDVARFKYPPHWVPLALLWEAMD 199 (492)
Q Consensus 166 GY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM~ 199 (492)
|||++++.+++=|+|.-. ----|+.+.|=+|=.
T Consensus 168 Gyd~~~~~~~yrdPa~~~-~~c~~s~~~ld~AR~ 200 (212)
T PF09778_consen 168 GYDAATKEFEYRDPASSD-RVCRVSPEALDEARK 200 (212)
T ss_pred eecCCCCeEEEeCCcccc-ceeecCHHHHHHHHh
Confidence 999999999999998532 334466666555543
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=94.28 E-value=1 Score=38.18 Aligned_cols=110 Identities=15% Similarity=0.115 Sum_probs=74.8
Q ss_pred CcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHH
Q 011156 52 AYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRR 131 (492)
Q Consensus 52 ayCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~ 131 (492)
.-||+++++|++.-.|+.-.. +.+.... .....|.+..++...++..|++++.++.+ .+++.+
T Consensus 5 ~~~~l~~l~~i~~~~g~~~~~----------~~l~~~~----~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~ 67 (121)
T cd02417 5 PDSGLLALVLLARYHGIAADP----------EQLRHEF----GLAGEPFNSTELLLAAKSLGLKAKAVRQP---VERLAR 67 (121)
T ss_pred cccHHHHHHHHHHHcCCCCCH----------HHHHHHh----cCCCCCCCHHHHHHHHHHcCCeeEEEecC---HHHhcc
Confidence 359999999999999976222 1111111 01246899999999999999999888743 333221
Q ss_pred HHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 132 HVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 132 ~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
. .-++|+-. .+|||--|.+.+ .+.++|.|++. ..|..++.++|.+..
T Consensus 68 ~--------~lP~I~~~--------~~g~~~Vl~~~~--~~~~~i~dp~~--~~~~~~~~~el~~~~ 114 (121)
T cd02417 68 L--------PLPALAWD--------DDGGHFILAKLD--GQKYLIQDPIS--QRPEVLSREEFEARW 114 (121)
T ss_pred C--------CCCEEEEc--------cCCCEEEEEEEc--CCCEEEECCCc--CCCeecCHHHHHhhc
Confidence 1 12444432 357988888866 67899999964 368889999887765
No 20
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=93.33 E-value=0.28 Score=55.97 Aligned_cols=117 Identities=17% Similarity=0.201 Sum_probs=83.7
Q ss_pred cccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCC
Q 011156 44 YYQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNE 123 (492)
Q Consensus 44 qF~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~ 123 (492)
.+..|.+..=||+|+++|+.|..|.+-+. +.+.+.+ .....|.++.++..+|+..|++++.++.+
T Consensus 3 ~~~~q~~~~dcgla~l~mia~~~g~~~~~----------~~lr~~~----~~~~~g~sl~~l~~~a~~lGl~~~~~~~~- 67 (709)
T COG2274 3 PIVLQQSANDCGLACLAMIANYHGKKISL----------NELRELV----GLSRNGLSLLELKQAAEKLGLSARAVKLS- 67 (709)
T ss_pred cccccCCccchHHHHHHHHHHHhCCCCCH----------HHHHHHc----CCCCCCCChHHHHHHHHHcCCccccccCC-
Confidence 45679999999999999999998876222 2222222 12356999999999999999999988865
Q ss_pred CCHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 124 SSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 124 ~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
.+++.+. .-+.|++... +||--+-+++.+ .+.|.|+ .-.+++.+.+++-+.-
T Consensus 68 --~~~l~~~--------~lP~ii~~~~--------~h~vVl~~~~~~--~~~v~dp---~~g~~~l~~~e~~~~~ 119 (709)
T COG2274 68 --LEELKQL--------PLPAIIHWNG--------NHFVVLYKIDKN--KVVVLDP---AKGIRRLSLEEFEKLW 119 (709)
T ss_pred --HHHhccc--------CCCEEEEEcC--------CcEEEEEEecCC--eEEEEeC---CCCcEEcCHHHHHHhh
Confidence 3333221 1255666544 498887776665 9999998 5688998888865543
No 21
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=92.89 E-value=3.8 Score=34.95 Aligned_cols=109 Identities=16% Similarity=0.042 Sum_probs=73.2
Q ss_pred ccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHH
Q 011156 54 CGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHV 133 (492)
Q Consensus 54 CGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l 133 (492)
||+++++|++.-+++.-... -+..- ......|.+..++...|+..|++++..+.+ .+.+.+
T Consensus 7 ~~l~~l~~i~~~~g~~~~~~-----------~l~~~---~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~---~~~l~~-- 67 (124)
T cd02421 7 PLLDCLVLLARQFGKPASRD-----------SLVAG---LPLDDGRLSPALFPRAAARAGLSARVVRRP---LDAIPT-- 67 (124)
T ss_pred hHHHHHHHHHHHhCCCCCHH-----------HHHhc---CCCCCCCcCHHHHHHHHHHCCCcceeeeCC---HHHCCc--
Confidence 99999999999999772221 11100 011246799999999999999998877643 332211
Q ss_pred HHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 134 ISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 134 ~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
-.-..|+- ..+|||--|.+.+. +.++|.|+.. ..+|.+++.++|-+..
T Consensus 68 ------~~lP~i~~--------~~~g~~~Vl~~~~~--~~~~i~dp~~-~~~~~~~~~~el~~~~ 115 (124)
T cd02421 68 ------LLLPAILL--------LKNGRACVLLGVDD--GHARILDPES-GGGEVEISLEELEEEY 115 (124)
T ss_pred ------ccCCEEEE--------EcCCCEEEEEEecC--CeEEEEccCC-CCCcEEEcHHHHHhhC
Confidence 11234442 23689988888764 7799999862 3678899998876644
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=92.88 E-value=0.63 Score=51.88 Aligned_cols=103 Identities=16% Similarity=0.103 Sum_probs=70.8
Q ss_pred HHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHH
Q 011156 56 LATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVIS 135 (492)
Q Consensus 56 vASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~ 135 (492)
+|+++|++|..|.+-.. +.+.+.+ .+.+.|+|+.++..+++..|++++.++.+ ++++
T Consensus 2 laclami~~~~g~~~~l----------~~lr~~~----~~~~~g~sl~~l~~~~~~~g~~~~~~~~~---~~~l------ 58 (694)
T TIGR03375 2 LDCLLLLARHYGRPVSR----------EALVAGL----PLEDGRLTPELLPRAARRAGLSARLVKRS---LDDI------ 58 (694)
T ss_pred HHHHHHHHHHcCCCCCH----------HHHHhhC----CCCCCCCCHHHHHHHHHHCCCEEEEecCC---Hhhc------
Confidence 68999999999965221 1222222 23478999999999999999999998853 3322
Q ss_pred HhcCCCceEEEEeecccccccCCccccccceeecCCCe-EEEEecCCCCCC--CeeeehHHHHH
Q 011156 136 CASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDL-VLILDVARFKYP--PHWVPLALLWE 196 (492)
Q Consensus 136 ~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~-VLILDVARfKYP--P~WVpl~~L~e 196 (492)
.....+.|+.+. ++||--+-+ -..+. |.|+|++ ++ +.|++.+++-+
T Consensus 59 --~~~~~P~i~~~~--------~~h~vvl~~--~~~~~~~~i~DP~---~g~~~~~~~~~e~~~ 107 (694)
T TIGR03375 59 --SPLLLPAILLLK--------DGRACVLLG--IDEDGKARVLLPE---TGDGEQELSLDALEA 107 (694)
T ss_pred --CcCCCCEEEEEc--------CCcEEEEEE--EcCCCcEEEEccC---CCCCceEecHHHHHh
Confidence 223346666653 379844444 45565 9999985 44 78999988754
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=90.72 E-value=1.7 Score=48.64 Aligned_cols=105 Identities=15% Similarity=0.122 Sum_probs=72.3
Q ss_pred cHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHH
Q 011156 55 GLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVI 134 (492)
Q Consensus 55 GvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~ 134 (492)
|+|+++|++|-.|.+-+. +.+.+.+. +.+.|+++.++...++..|++++.++.+ .+++.
T Consensus 1 g~acl~~i~~~~g~~~~~----------~~lr~~~~----~~~~g~~~~~l~~~~~~~G~~~~~~~~~---~~~l~---- 59 (694)
T TIGR01846 1 GLEALSLLAQVHNIAVTP----------SQLRHMLG----HAGASLDDLEILLAAKQLGLKAKAVKVS---IGRLN---- 59 (694)
T ss_pred CHHHHHHHHHHcCCCCCH----------HHHHHhcC----CCCCCCCHHHHHHHHHHCCCEEEEEeCC---HHHcc----
Confidence 789999999999965222 22333331 3468999999999999999999999864 33322
Q ss_pred HHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHH
Q 011156 135 SCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEA 197 (492)
Q Consensus 135 ~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eA 197 (492)
.-.-+.|+.. .+||--|-+ -+.+.|.|.|++. ..+.|++.+++.+.
T Consensus 60 ----~~~lP~i~~~---------~~~~vvl~~--~~~~~~~i~Dp~~--g~~~~i~~~e~~~~ 105 (694)
T TIGR01846 60 ----KLPLPALIDG---------EGGWFVLGK--LTANGVTIYDPPG--DAPEVLSREVLEAL 105 (694)
T ss_pred ----CCCCCEEEEE---------CCcEEEEEE--EcCCEEEEEcCCC--CCceeeCHHHHHhh
Confidence 2233566644 146444434 5578899999864 25889999998653
No 24
>COG3271 Predicted double-glycine peptidase [General function prediction only]
Probab=87.01 E-value=0.87 Score=44.90 Aligned_cols=103 Identities=22% Similarity=0.290 Sum_probs=69.8
Q ss_pred cccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhh-HhhcCCCHHHHHHHHHHcCCeEEEEecCCC
Q 011156 46 QTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSK-IKAEGITFGKVACLAYCNGAKVEAFRTNES 124 (492)
Q Consensus 46 ~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~-V~~~GiTLdEla~LA~c~G~~V~~~ra~~~ 124 (492)
..|.....||-||++.+||=+...+-. |++. ..+. +.+.|.++..++..++..|.+.+.|.....
T Consensus 36 Irq~~d~ScGaaalatll~n~~gk~~~----------e~~~----~~~m~~~~~~~s~~g~~~~~~~~g~~a~~~~~~~~ 101 (201)
T COG3271 36 IRQTTDFSCGAAALATLLNNDYGKLAD----------ESLV----LIEMNLEEFGESFSGMARAIKSLGNRAQGYENEFE 101 (201)
T ss_pred HHhhhccCchHHHHHHHHHhhccccCC----------HHHH----HHHhhHHHhhhcHHHHHHHhhCCCCcccccccchh
Confidence 346667889999999999998865333 2111 1122 568999999999999999988877765433
Q ss_pred CHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecC
Q 011156 125 SIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVA 180 (492)
Q Consensus 125 sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVA 180 (492)
+++ +.- ..+|| .+.-.+.-||+-+=+ .+.|-|++.|++
T Consensus 102 ~l~---q~~--------~p~iV-----~~~~~~~~hf~v~~~--v~~~~v~l~Dp~ 139 (201)
T COG3271 102 SLA---QLK--------IPVIV-----TLKYPANNHFDVVIG--VDGDNVTLADPA 139 (201)
T ss_pred hhh---hcc--------CCeeE-----EeecCCCceeEEEEe--ccCCeeEEcChh
Confidence 322 211 13333 334456679986655 577889999986
No 25
>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Probab=85.21 E-value=6.2 Score=44.14 Aligned_cols=100 Identities=13% Similarity=0.068 Sum_probs=68.7
Q ss_pred HHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHH
Q 011156 56 LATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVIS 135 (492)
Q Consensus 56 vASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~ 135 (492)
+|+++|+++-.|.+-+. +++.+. ..| ++..+...|+..|++++.++.+ ++++.+
T Consensus 5 ~~~l~~i~~~~~~~~~~----------~~lr~~--------~~g-~~~~l~~~~~~~g~~~~~~~~~---~~~l~~---- 58 (686)
T TIGR03797 5 LVACAAVGRAMGIEIRP----------PARSEN--------LSR-SPEPLEAIARASRLRIRRVRLE---GGWWRQ---- 58 (686)
T ss_pred HHHHHHHHHHhCCCCCh----------HHHHHH--------cCC-CHHHHHHHHHHCCCceEEEecC---HHHHhh----
Confidence 68999999999976222 112111 158 8999999999999999999864 333221
Q ss_pred HhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHH
Q 011156 136 CASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWE 196 (492)
Q Consensus 136 ~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~e 196 (492)
-.-+.|+..+ +.|||--+-++ +.+.+.|+|++. -++.|++.+++-+
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 1225555543 24798777664 678999999974 3345999988743
No 26
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=70.72 E-value=33 Score=33.22 Aligned_cols=138 Identities=13% Similarity=0.089 Sum_probs=82.4
Q ss_pred chhcccccCCC-CcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEEE
Q 011156 41 LISYYQTQSEP-AYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEAF 119 (492)
Q Consensus 41 L~~qF~TQ~~p-ayCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~~ 119 (492)
+...|..|++. .-|=-|+++||+--..-.|+..+ .++.++-+-+..-.+.|..- ..+.+..|++--..
T Consensus 22 ~~v~~v~Qq~~~mgCWaA~~~Mv~~w~~~~prlg~--------~eLyra~~Glp~~lq~g~d~---~~~~~~~gl~~v~~ 90 (166)
T PF12385_consen 22 FAVPYVPQQNTRMGCWAACACMVGGWRDQGPRLGP--------PELYRADEGLPSQLQDGLDP---EDFIRNEGLKEVPE 90 (166)
T ss_pred eEeeeeccCCCcccHHHHHHHHHHHHhcCCCCCCc--------HHHHHHhcCCchhhcccccH---HHHHHhcCccccCC
Confidence 44778888885 69999999999988775554432 11122111111111233333 34444444422111
Q ss_pred ec-CCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHHHHHh
Q 011156 120 RT-NESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALLWEAM 198 (492)
Q Consensus 120 ra-~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L~eAM 198 (492)
-+ ..-+.+.|+..|++. ..|.+--.+. +..=.||.+-|.|.+.+.|.+.+.|+.+ -|--=++++.|-.+.
T Consensus 91 P~~~~~t~e~~~~LL~~y-----GPLwv~~~~P--~~~~~~H~~ViTGI~~dg~~i~~~DP~~--gP~~~m~l~~fn~~~ 161 (166)
T PF12385_consen 91 PANASYTAEGLANLLREY-----GPLWVAWEAP--GDSWVAHASVITGIDGDGDSIHVHDPEQ--GPNLRMSLDMFNQAL 161 (166)
T ss_pred CcccccCHHHHHHHHHHc-----CCeEEEecCC--CCcceeeEEEEEeecCCCCeEEecCccc--CCCceecHHHHhhhh
Confidence 22 235789999999753 3566653332 2222479999999999999999999976 344447777665543
No 27
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.37 E-value=23 Score=33.56 Aligned_cols=95 Identities=21% Similarity=0.220 Sum_probs=59.7
Q ss_pred CCHHHHHHHH-HHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCCeEEEEe
Q 011156 100 ITFGKVACLA-YCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILD 178 (492)
Q Consensus 100 iTLdEla~LA-~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILD 178 (492)
++..++.+++ .-|-+.+..+..+...-+-..+-++.++-+++.+- -|.|..- =.|||--|-|||+.+|-+-|=|
T Consensus 57 VSi~dIqahLaqGnhiAIaLVdq~~Lhcdlceeplk~ccfspnghh--cfcrtp~---YqGHfiVi~GYd~a~~c~~~nd 131 (167)
T KOG4621|consen 57 VSIHDIQAHLAQGNHIAIALVDQDKLHCDLCEEPLKSCCFSPNGHH--CFCRTPC---YQGHFIVICGYDAARDCFEIND 131 (167)
T ss_pred eeHHHHHHHHhcCCeEEEEEecCCceehHHHHhHHHHhccCCCCcc--ccccCCc---ccccEEEEeccccccCeEEEcC
Confidence 4455666533 44444444444444566666777777665554332 2445322 2699999999999999999999
Q ss_pred cCCCCCCCeeeehHHHHHHhh
Q 011156 179 VARFKYPPHWVPLALLWEAMD 199 (492)
Q Consensus 179 VARfKYPP~WVpl~~L~eAM~ 199 (492)
+|.-+-.---++.+-+=+|-.
T Consensus 132 PA~adpg~c~~Sik~fEeARk 152 (167)
T KOG4621|consen 132 PASADPGHCRISIKCFEEARK 152 (167)
T ss_pred cccCCCcceeehhhHHHHHHh
Confidence 996553434477777666654
No 28
>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=49.61 E-value=72 Score=31.25 Aligned_cols=115 Identities=17% Similarity=0.183 Sum_probs=66.1
Q ss_pred cccccCCCCcccHHHHHHHHHhcccCCCCCcCCCccccccchhccc---CChhhHhhcCCCHHHHHHHHHHcCCeEEEEe
Q 011156 44 YYQTQSEPAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCC---KPLSKIKAEGITFGKVACLAYCNGAKVEAFR 120 (492)
Q Consensus 44 qF~TQ~~payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c---~~le~V~~~GiTLdEla~LA~c~G~~V~~~r 120 (492)
-.+||-+...|.=-+++.+||++.-. -...-+.|+..- .+.+..+..|++.+|+-..++..|..++. -
T Consensus 15 I~EtQg~~pWCa~Ya~aailN~~~~~--------~~~~A~~iMr~~yPn~s~~~l~~~~~~~~~~i~y~ks~g~~~~~-~ 85 (175)
T PF05543_consen 15 IRETQGYNPWCAGYAMAAILNATTNT--------KIYNAKDIMRYLYPNVSEEQLKFTSLTPNQMIKYAKSQGRNPQY-N 85 (175)
T ss_dssp -----SSSS-HHHHHHHHHHHHHCT---------S---HHHHHHHHSTTS-CCCHHH--B-HHHHHHHHHHTTEEEEE-E
T ss_pred EeeccCcCcHHHHHHHHHHHHhhhCc--------CcCCHHHHHHHHCCCCCHHHHhhcCCCHHHHHHHHHHcCcchhH-h
Confidence 35789999999999999999999521 112334555432 12345677899999999999999987754 3
Q ss_pred cCCCCHHHHHHHHHHHhcCCCceEEEEeeccccc-ccCCccccccceeecCCC
Q 011156 121 TNESSIDDFRRHVISCASSEDCHVISSYHRGVFK-QTGSGHFSPIGGYHARKD 172 (492)
Q Consensus 121 a~~~sldeFR~~l~~~~ss~~~~vIVNysR~~Lg-QtG~GHFSPIGGY~~~tD 172 (492)
.+-.++++..+.++ +++.+++.-++-.-. ..-.||==-|.||-.-.+
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 34467777777765 445666655543322 223789888889966443
No 29
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=48.66 E-value=10 Score=34.22 Aligned_cols=55 Identities=24% Similarity=0.384 Sum_probs=38.7
Q ss_pred HHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcCCeEEE
Q 011156 60 AVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNGAKVEA 118 (492)
Q Consensus 60 aMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G~~V~~ 118 (492)
+.+=+|.++.+.+-|..-=..+.+++|+ -++|...|++-|-|+.|+.....++..
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 3445677787777764433344455554 356899999999999999888777754
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=48.27 E-value=16 Score=32.74 Aligned_cols=42 Identities=19% Similarity=0.292 Sum_probs=31.0
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..++..
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 444445679999987776544445568899999999998864
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=47.80 E-value=17 Score=31.92 Aligned_cols=43 Identities=14% Similarity=0.266 Sum_probs=31.0
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|...-.+.+|+|+++-+..-.-+...+..|++++|+..+....
T Consensus 28 p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 28 PPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 3333356799999866654444445688999999999988754
No 32
>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=45.14 E-value=17 Score=31.00 Aligned_cols=42 Identities=12% Similarity=0.232 Sum_probs=30.7
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.||+|++.-+..-.-+...+..|++++++..+...
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 545445779999986665443344567899999999998865
No 33
>PF14104 DUF4277: Domain of unknown function (DUF4277)
Probab=45.03 E-value=19 Score=32.88 Aligned_cols=49 Identities=27% Similarity=0.339 Sum_probs=35.0
Q ss_pred CCcccHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHH
Q 011156 51 PAYCGLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVA 106 (492)
Q Consensus 51 payCGvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla 106 (492)
.-.+|.+-.+||||.||..+.. -+--.+||.. ++.|..-+.|++.+.|-
T Consensus 41 ~vs~G~~vkamilN~Lg~~~~p-Lyl~~~ff~~------~~~E~L~g~gi~~~~lN 89 (115)
T PF14104_consen 41 KVSHGQVVKAMILNGLGFVSRP-LYLFEEFFED------KPVERLLGEGISPEDLN 89 (115)
T ss_pred cccHHHHHHHHHHHhcCCCCcc-hhhhHHHHcc------CCHHHHhcCCCCHHHcc
Confidence 4889999999999999965322 2233457743 46677778888887664
No 34
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=44.66 E-value=18 Score=32.69 Aligned_cols=43 Identities=12% Similarity=0.192 Sum_probs=31.5
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|+++-++.-.-+...++.|+|++|+..++...
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 5444446799999877654444455688999999999988753
No 35
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.96 E-value=20 Score=31.98 Aligned_cols=37 Identities=11% Similarity=0.268 Sum_probs=29.1
Q ss_pred CCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 75 KGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 75 kgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
.+.+|+|+++.+..-.-+...+..|++++|+..+...
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 4679999987776554445568899999999998864
No 36
>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=43.71 E-value=19 Score=31.84 Aligned_cols=43 Identities=19% Similarity=0.315 Sum_probs=31.9
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcC
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNG 113 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G 113 (492)
|.+. .+.+|+|++.-++.-.-+...+..|+|++|+..+....+
T Consensus 28 p~~~-~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~~ 70 (120)
T cd04781 28 SIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDG 70 (120)
T ss_pred CCcC-CCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccC
Confidence 4333 468999998777655444567889999999999886543
No 37
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.51 E-value=21 Score=31.96 Aligned_cols=43 Identities=9% Similarity=0.225 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|+++-+..-.-+-..+..|++++|+..+....
T Consensus 28 ~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 28 EPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred CCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence 4444467799999877764444455678999999999988643
No 38
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.33 E-value=19 Score=30.71 Aligned_cols=43 Identities=12% Similarity=0.225 Sum_probs=31.9
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|+++-+....-+...++.|++++|+..+....
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 5444457799999877765544555688999999999988653
No 39
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=43.32 E-value=21 Score=32.70 Aligned_cols=42 Identities=14% Similarity=0.189 Sum_probs=31.6
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.||+|++..+..-.-+...+..|++++|+..+...
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 444445779999997776554445567899999999998864
No 40
>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=43.18 E-value=22 Score=32.01 Aligned_cols=42 Identities=7% Similarity=0.125 Sum_probs=31.0
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.+|+|+++-++.-.-+...+..|++++|+..++..
T Consensus 28 ~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 28 PPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 333335779999987776554445567899999999998864
No 41
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=42.07 E-value=42 Score=26.42 Aligned_cols=44 Identities=20% Similarity=0.286 Sum_probs=28.3
Q ss_pred cccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHH
Q 011156 66 LAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLA 109 (492)
Q Consensus 66 L~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA 109 (492)
.|..+...-.+.+|+|+++-++.-.-+...++.|+|++++..++
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 35553333356678998755543333445567999999998765
No 42
>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=42.05 E-value=45 Score=25.84 Aligned_cols=52 Identities=21% Similarity=0.369 Sum_probs=28.0
Q ss_pred HHHHHHHHhcccCC-CCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHH
Q 011156 57 ATLAVILNALAIDP-GRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLA 109 (492)
Q Consensus 57 ASLaMVLNAL~idP-~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA 109 (492)
.++.---+..+..+ .+. .+..|+|+++-+..-.-+...++.|+|++|+..++
T Consensus 15 ~tlr~w~~~~g~~~~~r~-~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 15 DTLRAWERRYGLPAPQRT-DGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHhCCCCCCCcC-CCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 34443333334443 332 23457776543332222344567999999998764
No 43
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=41.99 E-value=21 Score=33.10 Aligned_cols=43 Identities=12% Similarity=0.138 Sum_probs=32.5
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.||+|+++.+....-+...+..|++++|+..++...
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 3444456799999987765555556789999999999988654
No 44
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=40.08 E-value=43 Score=31.60 Aligned_cols=41 Identities=15% Similarity=0.156 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+. .+.+|+|+++.+..-.-+...+..|++++|+..++..
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 4333 5678999987776444445567899999999998865
No 45
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=39.00 E-value=55 Score=29.85 Aligned_cols=43 Identities=9% Similarity=0.105 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.||+|+++.++.-.-+...+..|++++|+..+..+.
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 4444457799999876654433445688999999999988753
No 46
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.37 E-value=28 Score=30.56 Aligned_cols=42 Identities=21% Similarity=0.498 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+. .+.+|+|++.-+..-.-+-..+..|++++|+..+....
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 5443 56799999866654433445678999999999988764
No 47
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=38.34 E-value=16 Score=30.11 Aligned_cols=18 Identities=28% Similarity=0.449 Sum_probs=14.9
Q ss_pred cCCCChhHHHHHHHHHHH
Q 011156 460 IENIPSLLQQEVLHLRRQ 477 (492)
Q Consensus 460 ~~~lp~~l~~ev~~lr~q 477 (492)
.++||+.|++||+|--+=
T Consensus 8 fqkLPDdLKrEvldY~Ef 25 (65)
T COG5559 8 FQKLPDDLKREVLDYIEF 25 (65)
T ss_pred HHHCcHHHHHHHHHHHHH
Confidence 468999999999997543
No 48
>PRK13749 transcriptional regulator MerD; Provisional
Probab=37.20 E-value=31 Score=31.48 Aligned_cols=44 Identities=23% Similarity=0.219 Sum_probs=31.5
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcC
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNG 113 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G 113 (492)
|...-.+.+|+|++.-+.--.-+...+..|++++|+..++...+
T Consensus 31 p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~ 74 (121)
T PRK13749 31 PVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALD 74 (121)
T ss_pred CCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhc
Confidence 44344588999998766543333445789999999999987653
No 49
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.52 E-value=33 Score=26.69 Aligned_cols=55 Identities=13% Similarity=0.293 Sum_probs=34.6
Q ss_pred cHHHHHHHHHhcccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHH
Q 011156 55 GLATLAVILNALAIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAY 110 (492)
Q Consensus 55 GvASLaMVLNAL~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~ 110 (492)
.+.++..-.+.--+.|.+.. +.+|.|+++-++.-.-+....+.|+|++++..+++
T Consensus 13 s~~tlr~y~~~gll~~~~~~-~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 13 SPSTLRYYEREGLLPPPRDE-NGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp THHHHHHHHHTTSSTTBEST-TSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred CHHHHHHHHHhcCccccccc-CceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 34555555555556677743 44688887555444334556679999999988764
No 50
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=35.99 E-value=31 Score=29.65 Aligned_cols=43 Identities=16% Similarity=0.267 Sum_probs=29.9
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+...+.+|+|+++-++.-.-+...+..|++++++..+....
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 5455567799998755543333344678999999999888653
No 51
>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=35.96 E-value=30 Score=30.81 Aligned_cols=39 Identities=15% Similarity=0.275 Sum_probs=30.5
Q ss_pred cCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 74 WKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 74 wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
-.+.+|+|+++-+..-.-+...+..|++++|+..+....
T Consensus 32 ~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 32 PEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 356799999877765544556789999999999988654
No 52
>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=35.25 E-value=50 Score=32.32 Aligned_cols=115 Identities=13% Similarity=0.204 Sum_probs=66.5
Q ss_pred cccchhchhcccccCCCCc-ccH---HHHHHHHHhcccCCCCCcC-------CCcccccc---chhcccCChhhHhhcC-
Q 011156 35 MEGFFKLISYYQTQSEPAY-CGL---ATLAVILNALAIDPGRTWK-------GPWRWFDD---TMLDCCKPLSKIKAEG- 99 (492)
Q Consensus 35 ~e~ff~L~~qF~TQ~~pay-CGv---ASLaMVLNAL~idP~r~wk-------gpwrwf~E---~mLd~c~~le~V~~~G- 99 (492)
+..|-.+++.|...-...- ..+ +...-++.+||+||...-+ |.-.||.| .+.+.|. ....+.|
T Consensus 35 a~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~--~~~~~~GG 112 (223)
T PF04157_consen 35 AKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCL--ATRSKNGG 112 (223)
T ss_dssp HHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHH--HHCCTTTS
T ss_pred HHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHH--HHHhcCCC
Confidence 3555556666654322211 112 2678889999999754333 44456665 5557774 3345677
Q ss_pred -CCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEee-ccccccc
Q 011156 100 -ITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVISCASSEDCHVISSYH-RGVFKQT 156 (492)
Q Consensus 100 -iTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNys-R~~LgQt 156 (492)
|+|.|+.|+.....-.+ +-.|-++|++.++....-...+-++.|. ...+=|+
T Consensus 113 ii~L~dl~~~~nr~R~g~-----~lISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s 166 (223)
T PF04157_consen 113 IISLSDLYCRYNRARGGS-----ELISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQS 166 (223)
T ss_dssp EEEHHHHHHHHHHCTTTS-----ST--HHHHHHHHHHHCCCTSSEEEEEETTTEEEEEC
T ss_pred EEEHHHHHHHHHHhcccC-----CCcCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEe
Confidence 99999999996642111 2578999999999764333347777776 3333333
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=34.55 E-value=37 Score=29.06 Aligned_cols=42 Identities=12% Similarity=0.178 Sum_probs=29.5
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.+|+|+++-+..-.-+-..+..|++++|+..+...
T Consensus 28 p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 28 PEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 444334679999986655333334568899999999998865
No 54
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=34.48 E-value=34 Score=30.66 Aligned_cols=42 Identities=10% Similarity=0.215 Sum_probs=30.3
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.+|+|+++-++.-.-+...+..|++++|+..+...
T Consensus 28 ~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 28 PPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 344345779999987665444444567899999999998864
No 55
>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=33.26 E-value=36 Score=30.78 Aligned_cols=42 Identities=19% Similarity=0.224 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+.-.+.+|+|+++-+..-.-+-..+..|++++|+..+...
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 544335669999987665443344567899999999998875
No 56
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.88 E-value=42 Score=29.25 Aligned_cols=42 Identities=14% Similarity=0.173 Sum_probs=29.5
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|...-.+.+|+|++.-++.-.-+...+..|++++|+..+...
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 444445678999876665333334567899999999998865
No 57
>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=30.99 E-value=39 Score=30.18 Aligned_cols=43 Identities=9% Similarity=0.168 Sum_probs=31.3
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|...-.+.+|+|+++-+..-.-+...+..|++++|+..++...
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 3444457799999877654444455688999999999988643
No 58
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=30.62 E-value=43 Score=31.80 Aligned_cols=43 Identities=12% Similarity=0.314 Sum_probs=31.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.||+|++.-+..-.-+-..+..|++++|+..++...
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 5444467899999876654444445678999999999988754
No 59
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=30.32 E-value=4.8e+02 Score=24.70 Aligned_cols=69 Identities=13% Similarity=0.168 Sum_probs=46.3
Q ss_pred EEEecCCCCHHHHHHHHHHHhc-CCCceEEEEeecccccc-cCCccccccceeecCCCeEEEEecCCCCCCCeeeehHHH
Q 011156 117 EAFRTNESSIDDFRRHVISCAS-SEDCHVISSYHRGVFKQ-TGSGHFSPIGGYHARKDLVLILDVARFKYPPHWVPLALL 194 (492)
Q Consensus 117 ~~~ra~~~sldeFR~~l~~~~s-s~~~~vIVNysR~~LgQ-tG~GHFSPIGGY~~~tD~VLILDVARfKYPP~WVpl~~L 194 (492)
.....-+.+++++++.+...-+ ..+.+|+.+|..-...+ +. .+.+-+.|-.+-+| ..+++.+|
T Consensus 65 ~~~~~~dpt~e~~~~~~~~~R~~a~~~RvLFHYnGhGvP~Pt~-------------~GeIw~f~~~~tqy--ip~si~dL 129 (154)
T PF14538_consen 65 RYKQSLDPTVEDLKRLCQSLRRNAKDERVLFHYNGHGVPRPTE-------------NGEIWVFNKNYTQY--IPLSIYDL 129 (154)
T ss_pred cEEEecCCCHHHHHHHHHHHHhhCCCceEEEEECCCCCCCCCC-------------CCeEEEEcCCCCcc--eEEEHHHH
Confidence 3334447899999998776532 34579999998543332 22 33677888654433 45899999
Q ss_pred HHHhhc
Q 011156 195 WEAMDT 200 (492)
Q Consensus 195 ~eAM~t 200 (492)
+++|.+
T Consensus 130 ~~~lg~ 135 (154)
T PF14538_consen 130 QSWLGS 135 (154)
T ss_pred HHhcCC
Confidence 999873
No 60
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=30.24 E-value=87 Score=24.50 Aligned_cols=36 Identities=11% Similarity=0.314 Sum_probs=25.4
Q ss_pred cCCCccccccchhcccCChhhHhhcCCCHHHHHHHH
Q 011156 74 WKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLA 109 (492)
Q Consensus 74 wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA 109 (492)
-.+.+|+|+.+-++.-.-+...++.|+|++|+..+.
T Consensus 31 ~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 31 TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 356789998766554434445677999999998764
No 61
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=30.17 E-value=73 Score=29.83 Aligned_cols=44 Identities=18% Similarity=0.455 Sum_probs=32.1
Q ss_pred CCCCcceeeeeecCCChHHHHHHHHhhcccccccCCCCCHHHHHHHHHhcC
Q 011156 218 HKAPSVLYTVSCRHEGWSKVAKYLTEDVPHRLKMNDVKDVENLLSLVFKSA 268 (492)
Q Consensus 218 ~~~~~~l~~~s~~~~~w~~~~~~~~~~~p~l~~~~~~~~~~~v~~~~~~~~ 268 (492)
...|+.+.|++| +..|.++.+.+.+ ..++..|-+.++..+|..-
T Consensus 102 ~G~P~~FiT~s~-~~~w~ei~~~l~~------~~~~~~d~P~~~ar~F~~k 145 (184)
T PF14214_consen 102 FGKPTLFITFSC-NPQWPEIQQALAK------PGQNWSDNPDIVARFFHIK 145 (184)
T ss_pred cCCCcEEEEEcC-ccccHHHHHHHHh------ccCCcccCcHHHHHHHHHH
Confidence 457999999999 8999999999773 3345555566666665543
No 62
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=29.97 E-value=42 Score=30.78 Aligned_cols=41 Identities=15% Similarity=0.162 Sum_probs=30.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
|.+. .+.+|+|+++-++.-.-+...+..|+|++|+..++..
T Consensus 29 p~r~-~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 29 SWRN-AGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred CCcC-CCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4443 5669999987776544445568899999999998764
No 63
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.88 E-value=1.1e+02 Score=26.44 Aligned_cols=56 Identities=7% Similarity=0.140 Sum_probs=36.2
Q ss_pred CCCCcCCCccccccchhcccCChhhHhh-cCCCHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKA-EGITFGKVACLAYCNGAKVEAFRTNESSIDDFRRHVI 134 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~-~GiTLdEla~LA~c~G~~V~~~ra~~~sldeFR~~l~ 134 (492)
|.+.-++.+|+|++.-++...-+...++ .|++++++..+.... .+.++.+=++.+.
T Consensus 28 p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~~---------~~~~~~~~~~~~~ 84 (95)
T cd04780 28 EGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAI---------ADASLPSTLLALA 84 (95)
T ss_pred CCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc---------CcccHHHHHHHHH
Confidence 4444445578898877765544445565 799999999988762 2455555555544
No 64
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=28.60 E-value=47 Score=30.47 Aligned_cols=43 Identities=19% Similarity=0.289 Sum_probs=30.6
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|+++-+..-.-+...+..|++++|+..++...
T Consensus 29 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 71 (140)
T PRK09514 29 PEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIR 71 (140)
T ss_pred CcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 5443356799999866654433445678999999999988653
No 65
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=26.82 E-value=56 Score=28.57 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=30.9
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+...+.+|.|++.-+..-.-+...++.|++++++..++...
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 5555556789998766554333445678999999999988753
No 66
>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=26.56 E-value=54 Score=30.33 Aligned_cols=38 Identities=13% Similarity=0.167 Sum_probs=29.0
Q ss_pred cCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHH
Q 011156 74 WKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYC 111 (492)
Q Consensus 74 wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c 111 (492)
-.+.+|+|+++.+..-.-+...+..|++++|+..++.+
T Consensus 32 ~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 32 NSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred CCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 34668999987776544445568899999999998875
No 67
>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=25.88 E-value=1.2e+02 Score=26.32 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=28.6
Q ss_pred CCCCCcCCCccccccchhcccCChhh-HhhcCCCHHHHHHHHHHcC
Q 011156 69 DPGRTWKGPWRWFDDTMLDCCKPLSK-IKAEGITFGKVACLAYCNG 113 (492)
Q Consensus 69 dP~r~wkgpwrwf~E~mLd~c~~le~-V~~~GiTLdEla~LA~c~G 113 (492)
.|.+. .|.+|+|+++-+..-.-+.. .+..|+|++++..+....+
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 35443 56689998755543222233 3678999999999886554
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=25.48 E-value=59 Score=29.51 Aligned_cols=43 Identities=26% Similarity=0.310 Sum_probs=31.0
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|++.-++.-.-+...+..|++++|+..+....
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 5544557799999866654333345578999999999988654
No 69
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=24.53 E-value=1.1e+02 Score=28.03 Aligned_cols=36 Identities=28% Similarity=0.278 Sum_probs=30.3
Q ss_pred chHHHHHHHhhhccCCCC-----hhHHHHHHHHHHHHHHHh
Q 011156 447 EEKLLTQLNRCVSIENIP-----SLLQQEVLHLRRQLHFLM 482 (492)
Q Consensus 447 ~~~l~~e~~~l~s~~~lp-----~~l~~ev~~lr~q~~~l~ 482 (492)
++|+..-|+.+.+-.++| +.|.++|..||||+.-|+
T Consensus 63 e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Le 103 (108)
T COG3937 63 EEKIPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLE 103 (108)
T ss_pred HHhhhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHH
Confidence 567888888888888877 489999999999998775
No 70
>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=23.74 E-value=70 Score=28.12 Aligned_cols=46 Identities=22% Similarity=0.257 Sum_probs=31.7
Q ss_pred ccC-CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 67 AID-PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 67 ~id-P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.- |.+.-.+.+|+|+++-+..-.-+...+..|+++.++..+....
T Consensus 24 GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (107)
T cd01111 24 GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRAL 70 (107)
T ss_pred CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 443 4444557799999866653333345678999999999988653
No 71
>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=23.39 E-value=69 Score=27.70 Aligned_cols=40 Identities=15% Similarity=0.232 Sum_probs=28.8
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHH
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAY 110 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~ 110 (492)
|.+ -.+.+|+|+++-++.-.-+...+..|++++|+..++.
T Consensus 29 ~~r-~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 29 GTR-NANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred CCc-CCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 433 3477999998777644444456789999999987663
No 72
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.36 E-value=66 Score=28.67 Aligned_cols=41 Identities=20% Similarity=0.164 Sum_probs=29.8
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+. +.+|+|++.-++.-.-+...+..|+|++++..+....
T Consensus 28 p~r~--~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~ 68 (118)
T cd04776 28 PERR--GQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLY 68 (118)
T ss_pred CcCC--CCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 5443 4799999876654433445788999999999988653
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=23.14 E-value=74 Score=27.71 Aligned_cols=38 Identities=8% Similarity=0.284 Sum_probs=28.3
Q ss_pred CCccccccchhcccCChhhHhhcCCCHHHHHHHHHHcC
Q 011156 76 GPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCNG 113 (492)
Q Consensus 76 gpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~G 113 (492)
+.+|+|++.-++.-.-+...+..|++++++..+.....
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 57999998666543334456789999999999887654
No 74
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.89 E-value=60 Score=29.62 Aligned_cols=53 Identities=23% Similarity=0.491 Sum_probs=37.2
Q ss_pred eEEEEecCCCCHHHHHHHHHHHhcCCCceEEEEeecccccccCCccccccceeecCCC
Q 011156 115 KVEAFRTNESSIDDFRRHVISCASSEDCHVISSYHRGVFKQTGSGHFSPIGGYHARKD 172 (492)
Q Consensus 115 ~V~~~ra~~~sldeFR~~l~~~~ss~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD 172 (492)
++++|-+ ..-++.+|+.|- ..+..-|-||+-=...-+|.|||-|+.|=++--+
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 244566666654 4555667799999999999999999988776544
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=20.86 E-value=92 Score=26.23 Aligned_cols=43 Identities=16% Similarity=0.064 Sum_probs=28.4
Q ss_pred CCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHHHc
Q 011156 70 PGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAYCN 112 (492)
Q Consensus 70 P~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~c~ 112 (492)
|.+.-.+.+|+|+++-+..-.-+...++.|+++.++..++...
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 4444334688887655443333345678999999999988753
No 76
>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=20.40 E-value=87 Score=27.05 Aligned_cols=44 Identities=14% Similarity=0.263 Sum_probs=29.7
Q ss_pred ccCCCCCcCCCccccccchhcccCChhhHhhcCCCHHHHHHHHH
Q 011156 67 AIDPGRTWKGPWRWFDDTMLDCCKPLSKIKAEGITFGKVACLAY 110 (492)
Q Consensus 67 ~idP~r~wkgpwrwf~E~mLd~c~~le~V~~~GiTLdEla~LA~ 110 (492)
|+-|...-.+.+|+|+++-++.-.-+-..++.|++++|+..+..
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 44343333567899988666543333446789999999998764
No 77
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=20.34 E-value=4.1e+02 Score=21.00 Aligned_cols=55 Identities=7% Similarity=0.219 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHhcC--CCceEEEEeecccccccCCccccccceeecCCCeEEEEecCC
Q 011156 122 NESSIDDFRRHVISCASS--EDCHVISSYHRGVFKQTGSGHFSPIGGYHARKDLVLILDVAR 181 (492)
Q Consensus 122 ~~~sldeFR~~l~~~~ss--~~~~vIVNysR~~LgQtG~GHFSPIGGY~~~tD~VLILDVAR 181 (492)
...++.+|++.|.....- +-....+-|..+.|.. + .++..|+-..+..+++-+..
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 357899999999876542 3234444577877752 2 38899999888888776643
Done!