Query 042029
Match_columns 316
No_of_seqs 114 out of 142
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 13:15:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042029.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042029hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09328 Phytochelatin_C: Doma 100.0 4E-104 9E-109 730.3 19.8 237 65-302 1-264 (264)
2 KOG0632 Phytochelatin synthase 100.0 1.4E-64 2.9E-69 478.7 11.5 233 1-295 155-388 (388)
3 PF05023 Phytochelatin: Phytoc 100.0 2.4E-32 5.3E-37 246.6 4.5 62 1-62 151-212 (212)
4 PF14399 Transpep_BrtH: NlpC/p 86.5 1.4 3E-05 40.4 5.3 53 4-59 111-163 (317)
5 cd02549 Peptidase_C39A A sub-f 64.4 7.4 0.00016 31.1 3.0 41 4-47 92-132 (141)
6 PF14214 Helitron_like_N: Heli 58.1 16 0.00034 31.8 4.2 24 66-90 103-126 (184)
7 cd02259 Peptidase_C39_like Pep 46.4 21 0.00046 27.5 2.9 39 3-45 76-114 (122)
8 cd02418 Peptidase_C39B A sub-f 45.4 23 0.0005 28.0 3.0 38 3-45 87-124 (136)
9 cd02420 Peptidase_C39D A sub-f 44.6 19 0.00041 28.4 2.4 38 3-45 81-118 (125)
10 COG5559 Uncharacterized conser 38.5 16 0.00035 28.8 1.0 17 284-300 8-24 (65)
11 PF03412 Peptidase_C39: Peptid 36.6 30 0.00064 27.5 2.3 37 4-45 83-119 (131)
12 KOG4621 Uncharacterized conser 31.8 23 0.0005 32.0 1.1 40 5-45 111-151 (167)
13 KOG2382 Predicted alpha/beta h 28.7 48 0.001 32.9 2.8 102 14-126 145-253 (315)
14 KOG4212 RNA-binding protein hn 24.9 1E+02 0.0022 32.9 4.3 59 3-64 29-94 (608)
15 PF14376 Haem_bd: Haem-binding 23.9 94 0.002 26.7 3.4 47 99-155 90-137 (137)
16 PF10047 DUF2281: Protein of u 23.1 39 0.00085 25.8 0.8 14 285-298 10-23 (66)
17 PF14223 UBN2: gag-polypeptide 23.0 1.5E+02 0.0032 23.7 4.2 61 79-143 41-101 (119)
18 cd02423 Peptidase_C39G A sub-f 22.6 70 0.0015 25.0 2.2 36 4-44 86-121 (129)
19 COG3937 Uncharacterized conser 22.3 1.3E+02 0.0027 26.1 3.8 36 271-306 63-103 (108)
20 PRK11546 zraP zinc resistance 21.6 1.3E+02 0.0028 26.9 3.9 33 274-306 73-109 (143)
21 PF05397 Med15_fungi: Mediator 21.6 1.1E+02 0.0024 26.0 3.3 29 137-165 27-56 (115)
No 1
>PF09328 Phytochelatin_C: Domain of unknown function (DUF1984); InterPro: IPR015407 This entry represents the C-terminal region of plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process
Probab=100.00 E-value=4.2e-104 Score=730.29 Aligned_cols=237 Identities=49% Similarity=0.706 Sum_probs=232.7
Q ss_pred CCCceeEEEeeeCCcChHHHHHHHHhcCccccccCCCCCHHHHHHHHHhcCCcchhhhheeeeEEeeccccCCCCCHHH-
Q 042029 65 HKAFVSSLMHSSGHEDLKKVAKYLIEDVPPRMKLKDIKGVENILSVLFKSAPVDLKDFIKCVAEFWRQEDAGVFSSKIE- 143 (316)
Q Consensus 65 ~~~p~~l~~~s~~~~~W~~~ak~l~~~vp~ll~~~~~~~v~~vls~v~~slP~~~~~fikwv~Evrr~e~~~~~ls~ee- 143 (316)
+++|++|||+||+||+|.+|||||+||||.||++++++||++||++||+|||+||++||||||||||+|||+++||+||
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 5799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -----HHHHHHHHhcchhHHHHHHHhhcccccccccccCCCCcc-------------ceeeccccccccccccccccccc
Q 042029 144 -----KEEVLKLVEETELFKHLNRWLASEISSCKSLISFGFNEN-------------TVFHMKLSLLDQTCRKETNLTLA 205 (316)
Q Consensus 144 -----k~~vlqqv~~T~Lfk~V~~~~~s~~s~c~~~~~~~~~d~-------------~il~g~~~~~~~~cc~et~vkc~ 205 (316)
|++||||||+|+|||||++||++.+|||+++++++++|+ +||+|+++++++|||+|||+||+
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 899999999999999999999999999999999999999 89999999999999999999999
Q ss_pred ccCCCCCeeEeeceEeeCCcccceeeeeccCcccc--------CCccccCCCchhHHHHHHHhcCcchhcCCCchhHHHH
Q 042029 206 KADGAKPMTLVSGKIRTNGIDQGIDMLLVPSSLTS--------QSRNLLHPSTAGILTLLVLALRQRTWAGIKQENLLAQ 277 (316)
Q Consensus 206 k~~~~~~~tvvsg~vv~~g~eqgvD~L~vP~s~~~--------~~~~~~hPs~~DvlTvLLLaLp~~TWs~Ikde~L~~E 277 (316)
|+|||||+|||||+||++|+||||||| ||+|+++ +++++|||+++||||||||||||+||+|||||+|++|
T Consensus 161 k~n~d~~~tvvsGtVv~~g~Eq~VD~L-vP~s~~~~~~c~~~~~~~~~~hPs~~DVLTvLLLALpp~TWs~Ikde~l~~E 239 (264)
T PF09328_consen 161 KANGDGPKTVVSGTVVSGGSEQGVDVL-VPSSQTKTSCCNSGSSNEIGMHPSSNDVLTVLLLALPPSTWSGIKDEKLLAE 239 (264)
T ss_pred eeCCCCceEEEeeeEEcCCCccceeEE-eccccCCCCccCCCCCCccccCCCcccHHHHHHHhCCccccccCccHHHHHH
Confidence 999999999999999999999999999 9999998 3566999999999999999999999999999999999
Q ss_pred HHhhhccCCCChhHHHHHHHHHHHH
Q 042029 278 FNHLTSIDNLPTPLQLEVLHLRRQL 302 (316)
Q Consensus 278 ~~~LvSt~~LP~~Lq~EVlhLrrQl 302 (316)
|++||||||||++||+||+||||||
T Consensus 240 i~~LvSte~LP~lLQeEVlHLrrQL 264 (264)
T PF09328_consen 240 IQSLVSTENLPDLLQEEVLHLRRQL 264 (264)
T ss_pred HHHHhhhhhCcHHHHHHHHHHHhcC
Confidence 9999999999999999999999996
No 2
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.4e-64 Score=478.74 Aligned_cols=233 Identities=43% Similarity=0.677 Sum_probs=208.7
Q ss_pred CCCCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhhccccCcCCCceeEEEEecCCCCceeEEEeeeCCcC
Q 042029 1 MQNGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDTIDESTGQHRGFMVISRSHKAFVSSLMHSSGHED 80 (316)
Q Consensus 1 gQtG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~~D~~tg~~RG~~~is~~~~~p~~l~~~s~~~~~ 80 (316)
||||+||||||||||+++|++||||||||||||||||++.||+||..||.+||++||||+|+++|++|. |||++|++++
T Consensus 155 gQTGtGHFSPiggy~e~~d~~LIlDVARFKYPphWV~Lkll~eam~siD~stg~pRG~~li~~~h~~~g-l~tl~lkk~s 233 (388)
T KOG0632|consen 155 GQTGTGHFSPIGGYNEERDMALILDVARFKYPPHWVPLKLLWEAMDSIDQSTGQPRGFMLISRPHREPG-LYTLSLKKES 233 (388)
T ss_pred cCCCCCccCcccccCcccCceEEeehhhccCCCcceeHHHHHHHhcchhhccCCCccceecccCCCCCc-eEEEEecccc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999 9999999999
Q ss_pred hHHHHHHHHhcCccccccCCCCCHHHHHHHHHhcCCcchhhhheeeeEEeeccccCCCCCHHH-HHHHHHHHhcchhHHH
Q 042029 81 LKKVAKYLIEDVPPRMKLKDIKGVENILSVLFKSAPVDLKDFIKCVAEFWRQEDAGVFSSKIE-KEEVLKLVEETELFKH 159 (316)
Q Consensus 81 W~~~ak~l~~~vp~ll~~~~~~~v~~vls~v~~slP~~~~~fikwv~Evrr~e~~~~~ls~ee-k~~vlqqv~~T~Lfk~ 159 (316)
|.++||||.+++|. |..+.|+++|.+|++|| ++|+|+.||.+++++.|| |+.+ |.|.-|..
T Consensus 234 w~~i~k~lk~~v~~------------i~~~dfas~~~s~NQf~--~~~i~~~~d~~q~~~~E~fk~c~----rst~~y~~ 295 (388)
T KOG0632|consen 234 WINIAKYLKEDVPR------------IKNVDFASLPLSFNQFI--IAEIRETEDSNQNLSFEEFKQCI----RSTVTYED 295 (388)
T ss_pred HHHHHHHHHHhhhh------------hhhhHHHhcchhHHHHH--HHHHHhhcCcccccCHHHHHHHH----HhhhhHHh
Confidence 99999999999998 66778999999999999 999999999999999997 4444 44444433
Q ss_pred HHHHhhcccccccccccCCCCccceeecccccccccccccccccccccCCCCCeeEeeceEeeCCcccceeeeeccCccc
Q 042029 160 LNRWLASEISSCKSLISFGFNENTVFHMKLSLLDQTCRKETNLTLAKADGAKPMTLVSGKIRTNGIDQGIDMLLVPSSLT 239 (316)
Q Consensus 160 V~~~~~s~~s~c~~~~~~~~~d~~il~g~~~~~~~~cc~et~vkc~k~~~~~~~tvvsg~vv~~g~eqgvD~L~vP~s~~ 239 (316)
++.. .-||.. .++++|. .+++|||++||++|.|.-++.-.|+
T Consensus 296 ---f~~h-~~~c~~--------~e~~s~~--~~~~~~c~~~~~ac~kg~~e~~~t~------------------------ 337 (388)
T KOG0632|consen 296 ---FAAH-KNCCTG--------VEILSGA--FSAEFCCPETCVACIKGVLEEIQTV------------------------ 337 (388)
T ss_pred ---hhhh-hccccc--------ceeecCC--cccccccHHHHHHhhhchhhhhhhe------------------------
Confidence 4443 345533 3788887 6789999999999999866655555
Q ss_pred cCCccccCCCchhHHHHHHHhcCcchhcCCCchhHHHHHHhhhccCCCChhHHHHH
Q 042029 240 SQSRNLLHPSTAGILTLLVLALRQRTWAGIKQENLLAQFNHLTSIDNLPTPLQLEV 295 (316)
Q Consensus 240 ~~~~~~~hPs~~DvlTvLLLaLp~~TWs~Ikde~L~~E~~~LvSt~~LP~~Lq~EV 295 (316)
..+|..+||.|+|||||||+||+||||..|..|+.++.+.-+.|+++|.||
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 258899999999999999999999999999999999999999999999985
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=99.97 E-value=2.4e-32 Score=246.64 Aligned_cols=62 Identities=63% Similarity=1.144 Sum_probs=54.2
Q ss_pred CCCCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhhccccCcCCCceeEEEEe
Q 042029 1 MQNGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDTIDESTGQHRGFMVIS 62 (316)
Q Consensus 1 gQtG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~~D~~tg~~RG~~~is 62 (316)
||+|+||||||||||+++|+||||||||||||||||++++||+||+++|++||++|||++|+
T Consensus 151 gq~G~GHfSPigaY~~~tD~vLilDVar~kYpp~WV~~~~L~~AM~~~D~~s~~~RG~~~is 212 (212)
T PF05023_consen 151 GQTGGGHFSPIGAYDAETDRVLILDVARFKYPPYWVPLERLYEAMNTIDPDSGKSRGYLLIS 212 (212)
T ss_dssp TSSSSEEEEEEEEEETTTTEEEE--S-TTT---EEEEHHHHHHHHSSEETTTTEE-EEEEEE
T ss_pred CCCCCCcccccceecccCCeEEEEecccccCCCEEeEHHHHHHHHhccCCCCCCcceEEEeC
Confidence 79999999999999999999999999999999999999999999999999999999999986
No 4
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=86.47 E-value=1.4 Score=40.38 Aligned_cols=53 Identities=21% Similarity=0.212 Sum_probs=43.9
Q ss_pred CCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhhccccCcCCCceeEE
Q 042029 4 GNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDTIDESTGQHRGFM 59 (316)
Q Consensus 4 G~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~~D~~tg~~RG~~ 59 (316)
+.+|+--|=|||.+.+.++|.|. ..+++..+|.+.|-+|+..... ...+++.+
T Consensus 111 ~~~H~i~v~G~d~~~~~~~v~D~--~~~~~~~~~~~~l~~A~~~~~~-~~~~~~~~ 163 (317)
T PF14399_consen 111 HADHYIVVYGYDEEEDVFYVSDP--PSYEPGRLPYEDLAKARFSEGI-PFPPKNRW 163 (317)
T ss_pred cCCcEEEEEEEeCCCCEEEEEcC--CCCcceeecHHHHHHHHhccCC-CCCCCceE
Confidence 57999999999999999999999 4677899999999999988774 22344444
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=64.39 E-value=7.4 Score=31.06 Aligned_cols=41 Identities=17% Similarity=0.140 Sum_probs=32.2
Q ss_pred CCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhhcc
Q 042029 4 GNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDT 47 (316)
Q Consensus 4 G~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~ 47 (316)
+.|||--|.||+ +.+.++|.|.+. -.+..++.+++-++...
T Consensus 92 ~~gH~vVv~g~~-~~~~~~i~DP~~--~~~~~~~~~~f~~~w~~ 132 (141)
T cd02549 92 PSGHAMVVIGYD-RKGNVYVNDPGG--GRRLVVSFDEFEKAWKR 132 (141)
T ss_pred CCCeEEEEEEEc-CCCCEEEECCCC--CcCEEEeHHHHHHHHHH
Confidence 489999999999 556699999975 45778888777666643
No 6
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=58.06 E-value=16 Score=31.81 Aligned_cols=24 Identities=8% Similarity=0.034 Sum_probs=21.6
Q ss_pred CCceeEEEeeeCCcChHHHHHHHHh
Q 042029 66 KAFVSSLMHSSGHEDLKKVAKYLIE 90 (316)
Q Consensus 66 ~~p~~l~~~s~~~~~W~~~ak~l~~ 90 (316)
..|+++.|+|| +..|..+...|.+
T Consensus 103 G~P~~FiT~s~-~~~w~ei~~~l~~ 126 (184)
T PF14214_consen 103 GKPTLFITFSC-NPQWPEIQQALAK 126 (184)
T ss_pred CCCcEEEEEcC-ccccHHHHHHHHh
Confidence 48999999999 8999999999873
No 7
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=46.38 E-value=21 Score=27.48 Aligned_cols=39 Identities=26% Similarity=0.234 Sum_probs=32.2
Q ss_pred CCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhh
Q 042029 3 NGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAM 45 (316)
Q Consensus 3 tG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM 45 (316)
.+.|||-=|.+++ .+.++|.|.+ ...+.|++.++|-+..
T Consensus 76 ~~~~~~~Vl~~~~--~~~~~i~dp~--~~~~~~~~~~~l~~~w 114 (122)
T cd02259 76 WKQGHFVILYGAD--KGQVLIADPL--EEGPVTLSESELEERW 114 (122)
T ss_pred cCCCcEEEEEEEc--CCEEEEECCc--ccCCEEeCHHHHHhhC
Confidence 3679999999998 6689999997 5678899998887654
No 8
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=45.41 E-value=23 Score=28.03 Aligned_cols=38 Identities=13% Similarity=0.025 Sum_probs=31.3
Q ss_pred CCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhh
Q 042029 3 NGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAM 45 (316)
Q Consensus 3 tG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM 45 (316)
.+.|||-=|.+++ .+.++|.|. ...+.+++.+++-+..
T Consensus 87 ~~~~~~~Vl~~~~--~~~~~i~dp---~~~~~~~~~~ef~~~w 124 (136)
T cd02418 87 WKLNHYVVVYKIK--KKKILIADP---AVGITKISKEEFEKEW 124 (136)
T ss_pred CCCCeEEEEEEEc--CCEEEEECC---CCCCEEeeHHHHHhhC
Confidence 5689999999998 567999998 5678899998886643
No 9
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=44.63 E-value=19 Score=28.36 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=30.8
Q ss_pred CCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhh
Q 042029 3 NGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAM 45 (316)
Q Consensus 3 tG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM 45 (316)
.+.|||-=|.+++ .|.++|.|.+. .|.|++.++|-+..
T Consensus 81 ~~~g~~~Vl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~~ 118 (125)
T cd02420 81 WNFNHFLVVEGFD--KRKVFLNDPAT---GRRTVSLEEFDQSF 118 (125)
T ss_pred eCCCEEEEEEEEe--CCEEEEECCCc---CceeecHHHHHhhC
Confidence 3579999999988 56799999964 68999998886543
No 10
>COG5559 Uncharacterized conserved small protein [Function unknown]
Probab=38.47 E-value=16 Score=28.84 Aligned_cols=17 Identities=35% Similarity=0.516 Sum_probs=14.5
Q ss_pred cCCCChhHHHHHHHHHH
Q 042029 284 IDNLPTPLQLEVLHLRR 300 (316)
Q Consensus 284 t~~LP~~Lq~EVlhLrr 300 (316)
.++||+.|+.||+|--+
T Consensus 8 fqkLPDdLKrEvldY~E 24 (65)
T COG5559 8 FQKLPDDLKREVLDYIE 24 (65)
T ss_pred HHHCcHHHHHHHHHHHH
Confidence 46899999999999654
No 11
>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=36.64 E-value=30 Score=27.50 Aligned_cols=37 Identities=24% Similarity=0.161 Sum_probs=31.3
Q ss_pred CCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhh
Q 042029 4 GNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAM 45 (316)
Q Consensus 4 G~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM 45 (316)
+.|||--|-++ +.++++|.|. +..+.|++.+++.+.-
T Consensus 83 ~~~h~vVi~~~--~~~~~~i~dP---~~g~~~~~~~~f~~~w 119 (131)
T PF03412_consen 83 KDGHFVVIYKI--DDGRVLIYDP---KKGKIKLSKEEFEEIW 119 (131)
T ss_dssp CCCEEEEEEEE--CCCEEEECCT---TTCEEEEEHHHHHHHE
T ss_pred cCcceEEEEeE--cCcEEEEEeC---CCCeEEEeHHHHHhhC
Confidence 67999999988 8899999999 4567899998887653
No 12
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.77 E-value=23 Score=32.00 Aligned_cols=40 Identities=38% Similarity=0.517 Sum_probs=30.8
Q ss_pred CccccccccccCCCCeEEEEecCCCCCCcee-cchHHHHHhh
Q 042029 5 NGHYSPIGGYHAGRDMVLILDVARFKYPPHW-MPLTLLWEAM 45 (316)
Q Consensus 5 ~GHFSPIggYh~~~D~vLILDVARfKYpp~W-V~~~~L~~AM 45 (316)
.|||=-|-|||+.+|-+.|=|+|.-+ |-+- ++...+=+|-
T Consensus 111 qGHfiVi~GYd~a~~c~~~ndPA~ad-pg~c~~Sik~fEeAR 151 (167)
T KOG4621|consen 111 QGHFIVICGYDAARDCFEINDPASAD-PGHCRISIKCFEEAR 151 (167)
T ss_pred cccEEEEeccccccCeEEEcCcccCC-CcceeehhhHHHHHH
Confidence 59999999999999999999998754 4443 5555555543
No 13
>KOG2382 consensus Predicted alpha/beta hydrolase [General function prediction only]
Probab=28.71 E-value=48 Score=32.93 Aligned_cols=102 Identities=15% Similarity=0.057 Sum_probs=66.7
Q ss_pred ccCCCCeEEEEecCCCCCCceecchHHHHHhhccccCcCCCceeEEEEecCCCCceeEEEeeeCCcChHHHHHHHHhcC-
Q 042029 14 YHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDTIDESTGQHRGFMVISRSHKAFVSSLMHSSGHEDLKKVAKYLIEDV- 92 (316)
Q Consensus 14 Yh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~~D~~tg~~RG~~~is~~~~~p~~l~~~s~~~~~W~~~ak~l~~~v- 92 (316)
|...--++++.|.+.+.||.---...++++||..+|.+-|..+|.--+- +.+ |.-..=..+..|+..++
T Consensus 145 ~p~~~~rliv~D~sP~~~~~~~~e~~e~i~~m~~~d~~~~~~~~rke~~-----~~l-----~~~~~d~~~~~fi~~nl~ 214 (315)
T KOG2382|consen 145 KPDLIERLIVEDISPGGVGRSYGEYRELIKAMIQLDLSIGVSRGRKEAL-----KSL-----IEVGFDNLVRQFILTNLK 214 (315)
T ss_pred cCcccceeEEEecCCccCCcccchHHHHHHHHHhccccccccccHHHHH-----HHH-----HHHhcchHHHHHHHHhcC
Confidence 3444568899999999888888889999999999999876633322221 111 11122223445555444
Q ss_pred -----ccccccCCCCCHHHHHHHH-HhcCCcchhhhheee
Q 042029 93 -----PPRMKLKDIKGVENILSVL-FKSAPVDLKDFIKCV 126 (316)
Q Consensus 93 -----p~ll~~~~~~~v~~vls~v-~~slP~~~~~fikwv 126 (316)
+.+.+.-|+.+|.+.+... +.+.+.++.+ -.|.
T Consensus 215 ~~~~~~s~~w~~nl~~i~~~~~~~~~~s~~~~l~~-~~~~ 253 (315)
T KOG2382|consen 215 KSPSDGSFLWRVNLDSIASLLDEYEILSYWADLED-GPYT 253 (315)
T ss_pred cCCCCCceEEEeCHHHHHHHHHHHHhhcccccccc-cccc
Confidence 4666677888888888776 6677777755 4443
No 14
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=24.89 E-value=1e+02 Score=32.85 Aligned_cols=59 Identities=27% Similarity=0.361 Sum_probs=45.5
Q ss_pred CCCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHhhcc-------ccCcCCCceeEEEEecC
Q 042029 3 NGNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEAMDT-------IDESTGQHRGFMVISRS 64 (316)
Q Consensus 3 tG~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~AM~~-------~D~~tg~~RG~~~is~~ 64 (316)
.|.|-|||-|.--+...+|+|-.. -|---|.++++|++-..- +=..+||+||-.++.-.
T Consensus 29 ~G~~~gs~~gn~~~r~R~vfItNI---pyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk 94 (608)
T KOG4212|consen 29 AGNGAGSQGGNVAARDRSVFITNI---PYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFK 94 (608)
T ss_pred ccccccCCCCCcccccceEEEecC---cchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEee
Confidence 588999998887776666999877 345579999999986532 33457999999998844
No 15
>PF14376 Haem_bd: Haem-binding domain
Probab=23.90 E-value=94 Score=26.72 Aligned_cols=47 Identities=19% Similarity=0.198 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHh-cCCcchhhhheeeeEEeeccccCCCCCHHHHHHHHHHHhcch
Q 042029 99 KDIKGVENILSVLFK-SAPVDLKDFIKCVAEFWRQEDAGVFSSKIEKEEVLKLVEETE 155 (316)
Q Consensus 99 ~~~~~v~~vls~v~~-slP~~~~~fikwv~Evrr~e~~~~~ls~eek~~vlqqv~~T~ 155 (316)
.+....+++..+|-. ++|...=..++|- .+||.+||+.+++=+++++
T Consensus 90 ~~~~~l~~i~~~I~~g~MP~~~Y~~~H~~----------a~Ls~~ek~~Ll~Wi~~~R 137 (137)
T PF14376_consen 90 KQEAKLAKIEEVIEDGEMPPPSYTLLHWE----------AKLSEEEKQALLNWIKEQR 137 (137)
T ss_pred cCHHHHHHHHHHHHcCCCChHHHhhhCCC----------CCCCHHHHHHHHHHHHHcC
Confidence 344456677777776 8999888888883 6999999999998877653
No 16
>PF10047 DUF2281: Protein of unknown function (DUF2281); InterPro: IPR018739 This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Probab=23.05 E-value=39 Score=25.78 Aligned_cols=14 Identities=50% Similarity=0.740 Sum_probs=12.0
Q ss_pred CCCChhHHHHHHHH
Q 042029 285 DNLPTPLQLEVLHL 298 (316)
Q Consensus 285 ~~LP~~Lq~EVlhL 298 (316)
++||+.+|.||++.
T Consensus 10 ~~LP~~~~~Evldf 23 (66)
T PF10047_consen 10 QQLPEELQQEVLDF 23 (66)
T ss_pred HHCCHHHHHHHHHH
Confidence 46899999999875
No 17
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=22.95 E-value=1.5e+02 Score=23.69 Aligned_cols=61 Identities=16% Similarity=0.136 Sum_probs=38.4
Q ss_pred cChHHHHHHHHhcCccccccCCCCCHHHHHHHHHhcCCcchhhhheeeeEEeeccccCCCCCHHH
Q 042029 79 EDLKKVAKYLIEDVPPRMKLKDIKGVENILSVLFKSAPVDLKDFIKCVAEFWRQEDAGVFSSKIE 143 (316)
Q Consensus 79 ~~W~~~ak~l~~~vp~ll~~~~~~~v~~vls~v~~slP~~~~~fikwv~Evrr~e~~~~~ls~ee 143 (316)
++=......+..-+-.|-.....-+-.+++..++.+||+.|..|+.-+.+.... ..+|-++
T Consensus 41 ~sv~~y~~~~~~i~~~L~~~g~~i~d~~~v~~iL~~Lp~~y~~~~~~i~~~~~~----~~~t~~e 101 (119)
T PF14223_consen 41 ESVDEYISRLKEIVDELRAIGKPISDEDLVSKILRSLPPSYDTFVTAIRNSKDL----PKMTLEE 101 (119)
T ss_pred ccHHHHHHHHHHhhhhhhhcCCcccchhHHHHHHhcCCchhHHHHHHHHhcCCC----CcCCHHH
Confidence 333333333444444445555666778899999999999999998865432222 3466775
No 18
>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=22.59 E-value=70 Score=25.04 Aligned_cols=36 Identities=31% Similarity=0.274 Sum_probs=28.6
Q ss_pred CCccccccccccCCCCeEEEEecCCCCCCceecchHHHHHh
Q 042029 4 GNGHYSPIGGYHAGRDMVLILDVARFKYPPHWMPLTLLWEA 44 (316)
Q Consensus 4 G~GHFSPIggYh~~~D~vLILDVARfKYpp~WV~~~~L~~A 44 (316)
+.|||-=|.+++ .+.++|.|++. .+.+++.++|-+.
T Consensus 86 ~~~~~vvl~~~~--~~~~~i~dp~~---~~~~~s~~el~~~ 121 (129)
T cd02423 86 GYGHFVVIKGID--GDRVLVGDPAL---GNISMSREEFERI 121 (129)
T ss_pred CCceEEEEEEEe--CCEEEEECCCC---CCcccCHHHHHHH
Confidence 478999999888 67799999953 5788988887653
No 19
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=22.29 E-value=1.3e+02 Score=26.09 Aligned_cols=36 Identities=22% Similarity=0.173 Sum_probs=30.3
Q ss_pred chhHHHHHHhhhccCCCCh-----hHHHHHHHHHHHHHHHh
Q 042029 271 QENLLAQFNHLTSIDNLPT-----PLQLEVLHLRRQLHFLM 306 (316)
Q Consensus 271 de~L~~E~~~LvSt~~LP~-----~Lq~EVlhLrrQl~~l~ 306 (316)
++|....|+.+.+-.+++. .|.++|-.||||+.-|.
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 5678888888888888774 89999999999998765
No 20
>PRK11546 zraP zinc resistance protein; Provisional
Probab=21.64 E-value=1.3e+02 Score=26.89 Aligned_cols=33 Identities=21% Similarity=0.236 Sum_probs=26.1
Q ss_pred HHHHHHhhhccCCCChh----HHHHHHHHHHHHHHHh
Q 042029 274 LLAQFNHLTSIDNLPTP----LQLEVLHLRRQLHFLM 306 (316)
Q Consensus 274 L~~E~~~LvSt~~LP~~----Lq~EVlhLrrQl~~l~ 306 (316)
-++|++.|.+.++-.+. |+.||-.||.||.-..
T Consensus 73 Kr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r 109 (143)
T PRK11546 73 KRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELR 109 (143)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 36788899888877665 8899999999887543
No 21
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=21.64 E-value=1.1e+02 Score=25.95 Aligned_cols=29 Identities=14% Similarity=0.236 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHHHHhc-chhHHHHHHHhh
Q 042029 137 VFSSKIEKEEVLKLVEE-TELFKHLNRWLA 165 (316)
Q Consensus 137 ~~ls~eek~~vlqqv~~-T~Lfk~V~~~~~ 165 (316)
..+|.|+|..|.+|+++ +.+|..|..++.
T Consensus 27 ~~ls~eeK~~i~~~l~~~~~m~~~vd~li~ 56 (115)
T PF05397_consen 27 NSLSPEEKAAIRQQLQEIQDMLARVDSLIP 56 (115)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999999986 678999888776
Done!