Query psy9715
Match_columns 92
No_of_seqs 105 out of 206
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 17:46:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9715.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9715hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4103|consensus 100.0 3.5E-42 7.5E-47 232.6 9.0 91 2-92 13-103 (103)
2 PF04718 ATP-synt_G: Mitochond 100.0 5.4E-38 1.2E-42 212.4 8.5 91 2-92 5-103 (103)
3 PF02899 Phage_int_SAM_1: Phag 53.2 28 0.00061 20.6 3.6 45 17-62 2-49 (84)
4 PF07295 DUF1451: Protein of u 49.1 53 0.0012 23.4 5.0 19 70-88 96-114 (146)
5 COG1306 Uncharacterized conser 44.0 11 0.00023 31.0 0.9 21 15-35 244-264 (400)
6 PF10958 DUF2759: Protein of u 40.0 41 0.00088 20.5 2.8 21 62-82 24-44 (52)
7 PF13333 rve_2: Integrase core 38.7 73 0.0016 18.2 3.7 45 18-62 2-47 (52)
8 cd08048 TAF11 TATA Binding Pro 37.1 87 0.0019 20.3 4.2 17 66-82 38-54 (85)
9 COG4973 XerC Site-specific rec 33.9 96 0.0021 24.9 4.7 47 13-62 7-58 (299)
10 PF14143 YrhC: YrhC-like prote 31.7 79 0.0017 20.2 3.3 25 59-83 7-31 (72)
11 PHA01757 hypothetical protein 31.6 69 0.0015 21.5 3.1 26 57-82 3-30 (98)
12 COG3124 Uncharacterized protei 29.6 1.4E+02 0.003 22.5 4.7 57 15-71 97-167 (193)
13 cd08305 Pyrin Pyrin: a protein 28.3 99 0.0022 19.3 3.3 36 9-44 6-41 (73)
14 PHA02094 hypothetical protein 27.9 26 0.00057 22.8 0.6 12 76-87 48-59 (81)
15 PF04454 Linocin_M18: Encapsul 25.7 77 0.0017 24.2 2.9 32 20-51 1-32 (255)
16 cd04761 HTH_MerR-SF Helix-Turn 24.7 1.1E+02 0.0023 16.4 2.7 16 16-31 14-29 (49)
17 cd04772 HTH_TioE_rpt1 First He 23.2 99 0.0021 20.0 2.7 24 8-31 6-29 (99)
18 PF12631 GTPase_Cys_C: Catalyt 22.8 1.9E+02 0.0042 17.6 4.4 19 67-85 40-59 (73)
19 PF02083 Urotensin_II: Urotens 22.2 35 0.00075 15.0 0.2 7 17-23 5-11 (12)
20 PF04719 TAFII28: hTAFII28-lik 21.8 2.1E+02 0.0046 18.8 4.1 57 10-83 7-63 (90)
21 PHA03348 tegument protein UL21 20.6 2.1E+02 0.0045 24.8 4.7 72 14-90 253-324 (526)
No 1
>KOG4103|consensus
Probab=100.00 E-value=3.5e-42 Score=232.64 Aligned_cols=91 Identities=51% Similarity=0.912 Sum_probs=88.9
Q ss_pred chhHHhHHHhccchHHHHHHHhhhccCCCChhhHHHHHHHHHHHHHHhhhCCCccccHHHHHHHHHHHHHHHHHHhhhhh
Q psy9715 2 SKLVSGVVAASKPILANFLHYGKVELIPPKPSEFGAIKDGIAHVVHQAKSGGWKNLTVKEAWLNSLIAAEITFWFYVGEV 81 (92)
Q Consensus 2 ~~l~~~~~~~~~P~~~~f~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~~~~k~lt~~ea~~~~l~~~Ev~gwF~VGEi 81 (92)
+.|+|+++.+++||+++||+|+|+||+||++||||++++++.++.+.++++++||+|++|+++|++|++|+++||+||||
T Consensus 13 ~~L~~~~~~~~~p~l~~~~~y~K~eL~PPt~Ad~pai~q~l~~~~~~~~t~~~Knltv~Eall~~~v~~Evi~wf~vGEi 92 (103)
T KOG4103|consen 13 ANLVNAALTYAKPRLAIFWKYAKVELAPPTPADIPAIKQDLAKLKKFAQTGCYKNLTVKEALLNGLVTLEVIFWFYVGEI 92 (103)
T ss_pred HHHHHHHHHhcCchHHHHHHHHhcccCCCChhhHHHHHHHHHHhHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCccccccC
Q psy9715 82 IGKRSLIGYEV 92 (92)
Q Consensus 82 IGRr~lvGY~V 92 (92)
||||+||||+|
T Consensus 93 IGrR~ivGY~v 103 (103)
T KOG4103|consen 93 IGRRHIVGYKV 103 (103)
T ss_pred hcccccccccC
Confidence 99999999997
No 2
>PF04718 ATP-synt_G: Mitochondrial ATP synthase g subunit; InterPro: IPR006808 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=100.00 E-value=5.4e-38 Score=212.39 Aligned_cols=91 Identities=49% Similarity=0.765 Sum_probs=87.4
Q ss_pred chhHHhHHHhccchHHHHHHHhhhccCCCChhhHHHHHHHHHHHHHHhhhCC--------CccccHHHHHHHHHHHHHHH
Q psy9715 2 SKLVSGVVAASKPILANFLHYGKVELIPPKPSEFGAIKDGIAHVVHQAKSGG--------WKNLTVKEAWLNSLIAAEIT 73 (92)
Q Consensus 2 ~~l~~~~~~~~~P~~~~f~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~~~--------~k~lt~~ea~~~~l~~~Ev~ 73 (92)
+.|++.++.++||+++.|++|+|.||+|||++|||++++++.+.++++++++ ++|+|++|++++|++|+|++
T Consensus 5 ~~l~~~~v~~~kv~le~~k~v~k~El~PPt~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~e~~~~~l~~~Ev~ 84 (103)
T PF04718_consen 5 TSLVNPAVYYSKVGLELFKQVYKKELAPPTPAEFQSVYQQLFKTVKSAKSGSSPKSKLKQWKNLTVKEAAKNGLVGAEVY 84 (103)
T ss_pred HHHHHHHHHHhHHHHHHHhHHHhhccCCcCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHhhcCCHHHHHHHHHHHHHHH
Confidence 4688999999999999999999999999999999999999999999888776 89999999999999999999
Q ss_pred HHHhhhhhcccCccccccC
Q psy9715 74 FWFYVGEVIGKRSLIGYEV 92 (92)
Q Consensus 74 gwF~VGEiIGRr~lvGY~V 92 (92)
|||||||||||||||||+|
T Consensus 85 ~wF~vGEiIGRr~ivGY~V 103 (103)
T PF04718_consen 85 GWFFVGEIIGRRSIVGYKV 103 (103)
T ss_pred HHHhhheeeccCceeCccC
Confidence 9999999999999999998
No 3
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=53.18 E-value=28 Score=20.60 Aligned_cols=45 Identities=16% Similarity=0.360 Sum_probs=18.7
Q ss_pred HHHHHHhhhccCCCChhhHHHHHHHHHHHHHHhhh---CCCccccHHHH
Q psy9715 17 ANFLHYGKVELIPPKPSEFGAIKDGIAHVVHQAKS---GGWKNLTVKEA 62 (92)
Q Consensus 17 ~~f~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~---~~~k~lt~~ea 62 (92)
+.|.+|...+ .-++++.+..-.+++..+++.... ..+.+++..+.
T Consensus 2 ~~f~~~l~~~-~~ls~~T~~~Y~~~l~~f~~~~~~~~~~~~~~i~~~~v 49 (84)
T PF02899_consen 2 ERFLRYLEQE-RGLSPNTIRSYRRDLRRFIRWLEEHGIIDWEDITEEDV 49 (84)
T ss_dssp HHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHHHHHTTS-CGGG--HHHH
T ss_pred HHHHHHHHHc-cCCcHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhHHH
Confidence 4566665421 122334444444444444444443 34555655554
No 4
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=49.08 E-value=53 Score=23.41 Aligned_cols=19 Identities=32% Similarity=0.427 Sum_probs=14.5
Q ss_pred HHHHHHHhhhhhcccCccc
Q psy9715 70 AEITFWFYVGEVIGKRSLI 88 (92)
Q Consensus 70 ~Ev~gwF~VGEiIGRr~lv 88 (92)
++--|-|..||++|.+.++
T Consensus 96 ~~h~g~Y~sGE~~g~G~l~ 114 (146)
T PF07295_consen 96 LEHHGVYHSGEVVGPGTLV 114 (146)
T ss_pred HHhcCCeecCcEecCceEe
Confidence 3445578899999998765
No 5
>COG1306 Uncharacterized conserved protein [Function unknown]
Probab=44.04 E-value=11 Score=31.03 Aligned_cols=21 Identities=38% Similarity=0.695 Sum_probs=17.6
Q ss_pred hHHHHHHHhhhccCCCChhhH
Q psy9715 15 ILANFLHYGKVELIPPKPSEF 35 (92)
Q Consensus 15 ~~~~f~~Y~k~eL~PPs~ae~ 35 (92)
.|+.|++||||+|--|-.+||
T Consensus 244 Al~sfL~yArE~l~vpIS~DI 264 (400)
T COG1306 244 ALQSFLHYAREELEVPISADI 264 (400)
T ss_pred HHHHHHHHHHHhcccceEEEe
Confidence 588999999999988866554
No 6
>PF10958 DUF2759: Protein of unknown function (DUF2759); InterPro: IPR024490 This family of proteins with unknown function appear to be restricted to Bacillales.
Probab=40.03 E-value=41 Score=20.49 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhc
Q psy9715 62 AWLNSLIAAEITFWFYVGEVI 82 (92)
Q Consensus 62 a~~~~l~~~Ev~gwF~VGEiI 82 (92)
+...++..+-+.|||+|--+|
T Consensus 24 ~i~F~~~t~~VFGwFtimTii 44 (52)
T PF10958_consen 24 GIGFALVTVAVFGWFTIMTII 44 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 567789999999999997776
No 7
>PF13333 rve_2: Integrase core domain
Probab=38.73 E-value=73 Score=18.17 Aligned_cols=45 Identities=18% Similarity=0.154 Sum_probs=32.3
Q ss_pred HHHHHhhhccCCCC-hhhHHHHHHHHHHHHHHhhhCCCccccHHHH
Q psy9715 18 NFLHYGKVELIPPK-PSEFGAIKDGIAHVVHQAKSGGWKNLTVKEA 62 (92)
Q Consensus 18 ~f~~Y~k~eL~PPs-~ae~~~i~~~~~~~~~~~~~~~~k~lt~~ea 62 (92)
.|+.-.|.|+.... ..++.++.+.+.+-++.-.+.+.+.+|..|-
T Consensus 2 sff~~lK~E~~~~~~~~t~eel~~~I~~YI~~yN~~Rl~~lsP~ey 47 (52)
T PF13333_consen 2 SFFGTLKTEMLYRQKFKTREELKQAIDEYIDYYNNERLKGLSPVEY 47 (52)
T ss_pred cchHhhcchhcCCcccchHHHHHHHHHHHHHHhccCCCCCcCHHHH
Confidence 47777888887775 5667777777777677666667777777654
No 8
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=37.10 E-value=87 Score=20.32 Aligned_cols=17 Identities=29% Similarity=0.421 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHhhhhhc
Q psy9715 66 SLIAAEITFWFYVGEVI 82 (92)
Q Consensus 66 ~l~~~Ev~gwF~VGEiI 82 (92)
.+.++--++.-||||||
T Consensus 38 v~i~v~glaKvFVGeiv 54 (85)
T cd08048 38 VVIAVAGIAKVFVGEIV 54 (85)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45666677888999987
No 9
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=33.87 E-value=96 Score=24.85 Aligned_cols=47 Identities=21% Similarity=0.444 Sum_probs=32.3
Q ss_pred cchHHHHHHHhhhc--cCCCChhhHHHHHHHHHHHHHHhh---hCCCccccHHHH
Q psy9715 13 KPILANFLHYGKVE--LIPPKPSEFGAIKDGIAHVVHQAK---SGGWKNLTVKEA 62 (92)
Q Consensus 13 ~P~~~~f~~Y~k~e--L~PPs~ae~~~i~~~~~~~~~~~~---~~~~k~lt~~ea 62 (92)
.|.+..||.|++.| |.|=|+.... +++..+++... .++|.+++..+.
T Consensus 7 ~~~l~~yl~~L~~Er~lS~hTl~~Y~---rqL~~l~~~~~~~~~~~w~~ld~~~v 58 (299)
T COG4973 7 AADLDAYLRYLRVERQLSPHTLANYR---RQLEALIALLAQMGLGSWQQLDPADV 58 (299)
T ss_pred HHHHHHHHHHHHHhhccCHHHHHHHH---HHHHHHHHHHHHcCccchhhcCHHHH
Confidence 46789999999876 7776766443 56666555544 357888876554
No 10
>PF14143 YrhC: YrhC-like protein
Probab=31.68 E-value=79 Score=20.24 Aligned_cols=25 Identities=16% Similarity=0.414 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhcc
Q psy9715 59 VKEAWLNSLIAAEITFWFYVGEVIG 83 (92)
Q Consensus 59 ~~ea~~~~l~~~Ev~gwF~VGEiIG 83 (92)
..|..+++.+-+=+-.|+++|=+|.
T Consensus 7 i~DyKrf~~vLLAvs~FlYiG~viP 31 (72)
T PF14143_consen 7 IEDYKRFAFVLLAVSTFLYIGTVIP 31 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 4788999999999999999999986
No 11
>PHA01757 hypothetical protein
Probab=31.59 E-value=69 Score=21.54 Aligned_cols=26 Identities=27% Similarity=0.493 Sum_probs=18.5
Q ss_pred ccHHHHHHHHHHHHH--HHHHHhhhhhc
Q psy9715 57 LTVKEAWLNSLIAAE--ITFWFYVGEVI 82 (92)
Q Consensus 57 lt~~ea~~~~l~~~E--v~gwF~VGEiI 82 (92)
++.-|..++|.+++- +.+-|.||||.
T Consensus 3 i~l~e~al~gf~a~~g~l~~~fii~e~~ 30 (98)
T PHA01757 3 ITLLEGALYGFFAVTGALSASFIIGEIV 30 (98)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666777766653 67889999985
No 12
>COG3124 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.58 E-value=1.4e+02 Score=22.53 Aligned_cols=57 Identities=16% Similarity=0.254 Sum_probs=34.2
Q ss_pred hHHHHHHHhhh---ccCCCChhhHHHHHHHHHH-----------HHHHhhhCCCccccHHHHHHHHHHHHH
Q psy9715 15 ILANFLHYGKV---ELIPPKPSEFGAIKDGIAH-----------VVHQAKSGGWKNLTVKEAWLNSLIAAE 71 (92)
Q Consensus 15 ~~~~f~~Y~k~---eL~PPs~ae~~~i~~~~~~-----------~~~~~~~~~~k~lt~~ea~~~~l~~~E 71 (92)
.|..|..|+.+ +-.||+|..|..+-..++. +++.+-+|-....+.-+++.++-+++|
T Consensus 97 pL~qFv~~a~~q~~~~~~~~P~Rf~~ln~~lwse~WL~~Yre~~~ir~vL~gMa~R~prl~~L~~Sw~~l~ 167 (193)
T COG3124 97 PLQQFVCYAQEQVLTILPDLPERFVRLNNYLWSEQWLVRYREMAFIRNVLNGMASRRPRLDALRDSWYDLD 167 (193)
T ss_pred cHHHHHHHHHHhHhccCCCCcHHHHHHhHHHHHHHHHHHHHhHHHHHHHHHHHHhcCCcchhhhchHHHHH
Confidence 47788888876 5678888877665544321 222222444455566667777666654
No 13
>cd08305 Pyrin Pyrin: a protein-protein interaction domain. The Pyrin domain (or PYD), also called DAPIN or PAAD, is a subfamily of the Death Domain (DD) superfamily and it functions in several signaling pathways. The Pyrin domain is found at the N-terminus of a variety of proteins and serves as a linker that recruits other domains into signaling complexes. Pyrin-containing proteins include NALPs, ASC (Apoptosis-associated speck-like protein containing a CARD), and the interferon-inducible p200 (IFI-200) family of proteins which includes the human IFI-16, myeloid cell nuclear differentiation antigen (MNDA) and absent in melanoma (AIM) 2. NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case
Probab=28.28 E-value=99 Score=19.26 Aligned_cols=36 Identities=14% Similarity=0.074 Sum_probs=27.2
Q ss_pred HHhccchHHHHHHHhhhccCCCChhhHHHHHHHHHH
Q psy9715 9 VAASKPILANFLHYGKVELIPPKPSEFGAIKDGIAH 44 (92)
Q Consensus 9 ~~~~~P~~~~f~~Y~k~eL~PPs~ae~~~i~~~~~~ 44 (92)
=.-+...+.+|..+++.++.+|+..+.+....++..
T Consensus 6 e~L~~~efk~FK~~L~~~~~~~~~~~~~~a~~~la~ 41 (73)
T cd08305 6 ENITDEELKRFKSLLANDLFLETKAQLEYTRIQIAD 41 (73)
T ss_pred HHcCHHHHHHHHHHHHhcCCCCCcccccccHHHHHH
Confidence 345677899999999999888887777665555543
No 14
>PHA02094 hypothetical protein
Probab=27.85 E-value=26 Score=22.77 Aligned_cols=12 Identities=33% Similarity=0.376 Sum_probs=9.7
Q ss_pred HhhhhhcccCcc
Q psy9715 76 FYVGEVIGKRSL 87 (92)
Q Consensus 76 F~VGEiIGRr~l 87 (92)
=+||||||-.|-
T Consensus 48 ksig~m~g~~hp 59 (81)
T PHA02094 48 KSVGAMIGELHP 59 (81)
T ss_pred HHHHHHhcccCc
Confidence 479999998763
No 15
>PF04454 Linocin_M18: Encapsulating protein for peroxidase; InterPro: IPR007544 Many Gram-positive bacteria produce antimicrobial peptides, generally termed bacteriocins. These peptides are usually cationic, less than 50 amino acid residues long, contain an amphiphilic or hydrophobic region, and often kill their target cells by permeabilizing the cell membrane. Antimicrobial peptides with these characteristics are also produced by plants and a wide variety of animals, including humans, and are thus widely distributed in nature. The Linocin_M18 region is found mostly in eubacteria, though homologous sequences have been identified in archaea [, ].; GO: 0008233 peptidase activity, 0042742 defense response to bacterium; PDB: 3DKT_E 2E0Z_C.
Probab=25.68 E-value=77 Score=24.25 Aligned_cols=32 Identities=19% Similarity=0.288 Sum_probs=21.2
Q ss_pred HHHhhhccCCCChhhHHHHHHHHHHHHHHhhh
Q psy9715 20 LHYGKVELIPPKPSEFGAIKDGIAHVVHQAKS 51 (92)
Q Consensus 20 ~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~ 51 (92)
|+|+|.+++|=|.++|..+-+...+.++..-+
T Consensus 1 Md~L~R~~aPls~~~W~~id~~a~~~~~~~L~ 32 (255)
T PF04454_consen 1 MDFLKRELAPLSAEAWEEIDEEARETAKRHLS 32 (255)
T ss_dssp --SS-GGGSS--HHHHHHHHHHHHHHHHHH-G
T ss_pred CCccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 57899999999999999988777766655444
No 16
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons 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 homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.73 E-value=1.1e+02 Score=16.37 Aligned_cols=16 Identities=19% Similarity=0.486 Sum_probs=13.0
Q ss_pred HHHHHHHhhhccCCCC
Q psy9715 16 LANFLHYGKVELIPPK 31 (92)
Q Consensus 16 ~~~f~~Y~k~eL~PPs 31 (92)
-.++.+|.++++.||.
T Consensus 14 ~~tlr~~~~~g~l~~~ 29 (49)
T cd04761 14 PSTLRYYERIGLLSPA 29 (49)
T ss_pred HHHHHHHHHCCCCCCC
Confidence 3578899999998874
No 17
>cd04772 HTH_TioE_rpt1 First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=23.20 E-value=99 Score=19.97 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=17.4
Q ss_pred HHHhccchHHHHHHHhhhccCCCC
Q psy9715 8 VVAASKPILANFLHYGKVELIPPK 31 (92)
Q Consensus 8 ~~~~~~P~~~~f~~Y~k~eL~PPs 31 (92)
++....=.-.|..+|-+++|.||.
T Consensus 6 ~A~~~gvs~~tlR~Ye~~Gll~~~ 29 (99)
T cd04772 6 LARAIGLSPQTVRNYESLGLIPPA 29 (99)
T ss_pred HHHHHCcCHHHHHHHHHcCCCCCC
Confidence 334444455788999999999984
No 18
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=22.81 E-value=1.9e+02 Score=17.60 Aligned_cols=19 Identities=26% Similarity=0.464 Sum_probs=12.8
Q ss_pred HHHHHH-HHHHhhhhhcccC
Q psy9715 67 LIAAEI-TFWFYVGEVIGKR 85 (92)
Q Consensus 67 l~~~Ev-~gwF~VGEiIGRr 85 (92)
+++.++ .+|-.+|||+|..
T Consensus 40 l~a~~L~~A~~~L~~ItG~~ 59 (73)
T PF12631_consen 40 LVAEDLREALESLGEITGEV 59 (73)
T ss_dssp HHHHHHHHHHHHHHHHCTSS
T ss_pred HHHHHHHHHHHHHHHHhCCC
Confidence 444443 3678899999974
No 19
>PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=22.15 E-value=35 Score=15.03 Aligned_cols=7 Identities=29% Similarity=0.520 Sum_probs=4.8
Q ss_pred HHHHHHh
Q psy9715 17 ANFLHYG 23 (92)
Q Consensus 17 ~~f~~Y~ 23 (92)
.-||+|.
T Consensus 5 ~CFWKYC 11 (12)
T PF02083_consen 5 ECFWKYC 11 (12)
T ss_pred chhhhhc
Confidence 3489984
No 20
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=21.80 E-value=2.1e+02 Score=18.82 Aligned_cols=57 Identities=19% Similarity=0.304 Sum_probs=27.8
Q ss_pred HhccchHHHHHHHhhhccCCCChhhHHHHHHHHHHHHHHhhhCCCccccHHHHHHHHHHHHHHHHHHhhhhhcc
Q psy9715 10 AASKPILANFLHYGKVELIPPKPSEFGAIKDGIAHVVHQAKSGGWKNLTVKEAWLNSLIAAEITFWFYVGEVIG 83 (92)
Q Consensus 10 ~~~~P~~~~f~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~~~~k~lt~~ea~~~~l~~~Ev~gwF~VGEiIG 83 (92)
+.+.-++..|-.|-+..|.- ..+.++++..-+ +-++.+ +.++++--++=.||||||=
T Consensus 7 ~f~~eQ~~Rye~fRRs~~~k----------~~ikkli~~~~~----~qsv~~---~v~i~v~g~aKvFVGEiVE 63 (90)
T PF04719_consen 7 NFDEEQLDRYEAFRRSSFNK----------AAIKKLINQVLG----NQSVSQ---NVVIAVAGIAKVFVGEIVE 63 (90)
T ss_dssp ---HHHHHHHHHHHH----H----------HHHHHHHHHHHS-----S---H---HHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHccCCH----------HHHHHHHHHHcC----CCCCCh---hHHHHHHHHHHHHHHHHHH
Confidence 34555666777776666521 234445544432 123332 3456677778889999983
No 21
>PHA03348 tegument protein UL21; Provisional
Probab=20.64 E-value=2.1e+02 Score=24.81 Aligned_cols=72 Identities=22% Similarity=0.276 Sum_probs=40.9
Q ss_pred chHHHHHHHhhhccCCCChhhHHHHHHHHHHHHHHhhhCCCccccHHHHHHHHHHHHHHHHHHhhhhhcccCccccc
Q psy9715 14 PILANFLHYGKVELIPPKPSEFGAIKDGIAHVVHQAKSGGWKNLTVKEAWLNSLIAAEITFWFYVGEVIGKRSLIGY 90 (92)
Q Consensus 14 P~~~~f~~Y~k~eL~PPs~ae~~~i~~~~~~~~~~~~~~~~k~lt~~ea~~~~l~~~Ev~gwF~VGEiIGRr~lvGY 90 (92)
||.-.+|.....-..|+|+.++-.+.......+. +...|-.++.++--.-+.++.++...| |+ .|+|-++|.
T Consensus 253 prv~~iW~~~~~~~~~~sl~~Lw~vf~~~D~vl~--~~~~w~GL~~e~~~ar~~l~~~a~alf--G~-~g~~~F~G~ 324 (526)
T PHA03348 253 PRVCNIWAPRSPPSSPASLQELWELFCGADEVLL--KADAWAGLDEELNEARSTIVEAVWALF--GR-EGARPFFGA 324 (526)
T ss_pred cCccccccCCCCCCCCcCHHHHHHHHHHHHHHHh--ccCCccccCHHHHHHHHHHHHHHHHHh--CC-CCCccccCc
Confidence 5555567766544444445444444444443332 236788888765555566666666655 55 566666665
Done!