Query psy15316
Match_columns 145
No_of_seqs 129 out of 182
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 17:54:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15316hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2381|consensus 100.0 5.2E-31 1.1E-35 222.8 3.3 140 3-145 28-286 (286)
2 TIGR03843 conserved hypothetic 97.6 3.5E-05 7.6E-10 65.7 3.0 47 8-75 30-76 (253)
3 KOG2381|consensus 93.4 0.02 4.4E-07 49.4 -0.2 45 67-112 66-110 (286)
4 PF07945 Toxin_16: Janus-atrac 53.3 5.8 0.00013 25.2 0.5 17 34-50 11-27 (36)
5 TIGR03843 conserved hypothetic 52.6 2.7 5.8E-05 36.4 -1.4 32 70-101 47-78 (253)
6 KOG2715|consensus 50.2 3.5 7.6E-05 34.8 -1.1 86 54-139 62-164 (210)
7 PF09000 Cytotoxic: Cytotoxic; 41.2 13 0.00029 27.5 0.9 25 3-27 56-80 (85)
8 COG5167 VID27 Protein involved 37.5 16 0.00036 35.5 1.1 19 1-19 430-448 (776)
9 TIGR02195 heptsyl_trn_II lipop 34.6 31 0.00067 28.2 2.2 39 8-47 272-311 (334)
10 PF15433 MRP-S31: Mitochondria 32.0 28 0.00061 30.8 1.6 32 6-37 158-193 (298)
11 KOG2913|consensus 30.3 31 0.00068 29.5 1.6 43 96-141 33-75 (260)
12 COG3363 Archaeal IMP cyclohydr 30.2 34 0.00073 28.8 1.7 16 6-21 129-144 (200)
13 PF15051 FAM198: FAM198 protei 26.0 49 0.0011 29.8 2.1 31 38-68 61-91 (326)
14 PF09006 Surfac_D-trimer: Lung 25.3 88 0.0019 20.9 2.7 21 108-128 4-24 (46)
15 TIGR00952 S15_bact ribosomal p 23.1 97 0.0021 22.5 2.8 28 103-130 17-44 (86)
16 PF07500 TFIIS_M: Transcriptio 22.4 67 0.0014 23.2 1.9 28 113-140 54-90 (115)
No 1
>KOG2381|consensus
Probab=99.96 E-value=5.2e-31 Score=222.75 Aligned_cols=140 Identities=46% Similarity=0.619 Sum_probs=117.2
Q ss_pred cCCCCcEEEEecCCCCCCCCCCCCchhhhhhhhccCCCCCCceecCCCcchhhhhhhhhhhhcCCceeeCccc-------
Q psy15316 3 YVPIHKKIGVFKPKDEEPYGRLNPKWTKWMHKLCCPCCFGRACLIPNQGYLSEAGASLVDQKLGLNIVPKTKG------- 75 (145)
Q Consensus 3 y~~~g~~vgvfKPkdEEPyg~lnPkw~kw~~r~~~~c~fgRsClipn~gYlsEaaAsllD~~l~~~iVP~T~~------- 75 (145)
++..|.++|||||+|||||+++||||++|.++..+ |+||+|+++|+||+||+||||||+. +++.||+|..
T Consensus 28 ~~~~~~~~~v~kP~deEp~~~~Npk~~~~~~~g~~--~~~~~~~v~~~g~~~E~aayLlD~~-~~~~Vp~t~~v~i~~~~ 104 (286)
T KOG2381|consen 28 QDTSGWIVGVFKPKDEEPYARNNPKGTKVLQRGQC--GCKRSCLVGNSGYRSEAAAYLLDHP-EFNDVPRTALVKITHFT 104 (286)
T ss_pred hccccceeeccCCCcccccccCCCccCchhhcccc--ccccceeccCccccchhhhhccCcc-ccCCCCceeeEEEeeec
Confidence 46778899999999999999999999999999866 9999999999999999999999999 9999999987
Q ss_pred ------eec-------ccc--------------------------ceeeeee----------------------------
Q psy15316 76 ------YLS-------EAG--------------------------ASLVDQK---------------------------- 88 (145)
Q Consensus 76 ------ylS-------E~g--------------------------AS~vD~k---------------------------- 88 (145)
+++ ..| =.+.|.+
T Consensus 105 f~~~~~~~~~~~~~~~k~gs~q~Fve~~~~~d~~~~~F~~~e~hkivvlD~ri~NtDRh~~N~lvk~~~~~~~~~~~~Dh 184 (286)
T KOG2381|consen 105 FNYNAAFLSKRQGKKSKIGSLQLFVEGYSAADYGLRRFEAEEVHKIVVLDIRIRNTDRHAGNWLVKKEPTLEQAAILGDH 184 (286)
T ss_pred ccccccceecccccccchhhHHHhhcCccccceeEEeccccccceeEEEEEEeeccCCCCCceeEEeccCcccccccccC
Confidence 221 100 0001110
Q ss_pred -------------------------------------ccccccc--------CccccCCCChHHHHHHHhhHhHHHHHHH
Q psy15316 89 -------------------------------------LGLNIVP--------KTKEDKGFDRHLFEKQMSVMRGQILNLN 123 (145)
Q Consensus 89 -------------------------------------l~ln~Vp--------ktKvdkgfD~~~F~kQmsvmrgqi~nl~ 123 (145)
.+.|.+- .++++++|++..|++||+||||||+|++
T Consensus 185 gl~fP~~~~d~~f~W~~~pqa~~pfs~~~~~yiL~~~~d~~~~r~l~~~~~~~~~~~~~f~k~~~~~~l~~~~~g~~~~r 264 (286)
T KOG2381|consen 185 GLCFPEKHPDEWFEWLYWPQAKIPFSEEIVDYILDPLTDCNLLRELPEDLLRLFKVDTGFLKKAFEKQLSVMRIGILNLR 264 (286)
T ss_pred ceeCcccCCccccchHHHHhhcccccHHHHhccCCcccCHHHHHHhHHHHHHHHhhchhhhHHHHHhCchHhhccceehH
Confidence 1222221 6889999999999999999999999999
Q ss_pred HHHhcCCCcchhhcCCceeeeC
Q psy15316 124 QALKDGKSPVQLVQMPAVIVER 145 (145)
Q Consensus 124 ~al~~~ksp~~lvqmp~~~ve~ 145 (145)
+|+++.+.|...|+++..++|+
T Consensus 265 e~~~~~~~~~~~~~~~~~~~~~ 286 (286)
T KOG2381|consen 265 EALKDSKLEQLCVEAKASVVEN 286 (286)
T ss_pred HHHhhCccHHHHHhhhhcccCC
Confidence 9999999999999999998874
No 2
>TIGR03843 conserved hypothetical protein. This model represents a protein family largely restricted to the Actinobacteria (high-GC Gram-positives), although it is also found in the Chloroflexi. Distant similarity to the phosphatidylinositol 3- and 4-kinase is suggested by the matching of some members to pfam00454.
Probab=97.64 E-value=3.5e-05 Score=65.67 Aligned_cols=47 Identities=34% Similarity=0.469 Sum_probs=39.2
Q ss_pred cEEEEecCCCCCCCCCCCCchhhhhhhhccCCCCCCceecCCCcchhhhhhhhhhhhcCCceeeCccc
Q psy15316 8 KKIGVFKPKDEEPYGRLNPKWTKWMHKLCCPCCFGRACLIPNQGYLSEAGASLVDQKLGLNIVPKTKG 75 (145)
Q Consensus 8 ~~vgvfKPkdEEPyg~lnPkw~kw~~r~~~~c~fgRsClipn~gYlsEaaAsllD~~l~~~iVP~T~~ 75 (145)
....|+||...| .|-|- |-+ .+.|.||+|||+||+.+|.++||+|-+
T Consensus 30 ~~~~VYKPv~gE-----rPLWD-----------Fpd-----GtLa~REvAAYlvs~~lGw~~VPpTvl 76 (253)
T TIGR03843 30 SARAVYKPVRGE-----RPLWD-----------FPD-----GTLAGREVAAYLVSEALGWGLVPPTVL 76 (253)
T ss_pred eEEEEECCcCCc-----ccccc-----------CCC-----CchHHHHHHHHHHHHHhCCCcCCCeee
Confidence 356999999999 78776 322 356899999999999999999999866
No 3
>KOG2381|consensus
Probab=93.43 E-value=0.02 Score=49.40 Aligned_cols=45 Identities=29% Similarity=0.227 Sum_probs=38.8
Q ss_pred CceeeCccceeccccceeeeeecccccccCccccCCCChHHHHHHH
Q psy15316 67 LNIVPKTKGYLSEAGASLVDQKLGLNIVPKTKEDKGFDRHLFEKQM 112 (145)
Q Consensus 67 ~~iVP~T~~ylSE~gAS~vD~kl~ln~VpktKvdkgfD~~~F~kQm 112 (145)
..+.-.+.+|+||++|++.|.. ++|.||.|..++.-+..||+.-.
T Consensus 66 ~~~~v~~~g~~~E~aayLlD~~-~~~~Vp~t~~v~i~~~~f~~~~~ 110 (286)
T KOG2381|consen 66 RSCLVGNSGYRSEAAAYLLDHP-EFNDVPRTALVKITHFTFNYNAA 110 (286)
T ss_pred cceeccCccccchhhhhccCcc-ccCCCCceeeEEEeeeccccccc
Confidence 4444457899999999999999 99999999999999999988544
No 4
>PF07945 Toxin_16: Janus-atracotoxin; InterPro: IPR012499 This family includes three peptides secreted by the spider Hadronyche versuta (Blue mountains funnel-web spider) (P82226 from SWISSPROT, P82227 from SWISSPROT, P82228 from SWISSPROT). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle acetylcholine receptors, or acetylcholine receptor subtypes present in other invertebrate neurons []. Janus atracotoxin-Hv1c (J-ACTX-Hv1c, P82228 from SWISSPROT) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity []. ; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1DL0_A.
Probab=53.32 E-value=5.8 Score=25.18 Aligned_cols=17 Identities=47% Similarity=1.359 Sum_probs=8.4
Q ss_pred hhccCCCCCCceecCCC
Q psy15316 34 KLCCPCCFGRACLIPNQ 50 (145)
Q Consensus 34 r~~~~c~fgRsClipn~ 50 (145)
..++|||.|.||--|+.
T Consensus 11 aaccpccpgtsc~~pe~ 27 (36)
T PF07945_consen 11 AACCPCCPGTSCQGPEP 27 (36)
T ss_dssp -SS----TTEEEEE--T
T ss_pred ccccCCCCCccccccCC
Confidence 46899999999997653
No 5
>TIGR03843 conserved hypothetical protein. This model represents a protein family largely restricted to the Actinobacteria (high-GC Gram-positives), although it is also found in the Chloroflexi. Distant similarity to the phosphatidylinositol 3- and 4-kinase is suggested by the matching of some members to pfam00454.
Probab=52.65 E-value=2.7 Score=36.37 Aligned_cols=32 Identities=31% Similarity=0.331 Sum_probs=26.7
Q ss_pred eeCccceeccccceeeeeecccccccCccccC
Q psy15316 70 VPKTKGYLSEAGASLVDQKLGLNIVPKTKEDK 101 (145)
Q Consensus 70 VP~T~~ylSE~gAS~vD~kl~ln~VpktKvdk 101 (145)
.|.-.++..|.+|.++|+.++.++||.|-+-+
T Consensus 47 FpdGtLa~REvAAYlvs~~lGw~~VPpTvlrD 78 (253)
T TIGR03843 47 FPDGTLAGREVAAYLVSEALGWGLVPPTVLRD 78 (253)
T ss_pred CCCCchHHHHHHHHHHHHHhCCCcCCCeeeec
Confidence 35445688999999999999999999997754
No 6
>KOG2715|consensus
Probab=50.22 E-value=3.5 Score=34.75 Aligned_cols=86 Identities=19% Similarity=0.181 Sum_probs=43.0
Q ss_pred hhhhhhhhhhhcCCceeeCc-----cc---eecccc----ceeeeeecccccc-----cCccccCCCChHHHHHHHhhHh
Q psy15316 54 SEAGASLVDQKLGLNIVPKT-----KG---YLSEAG----ASLVDQKLGLNIV-----PKTKEDKGFDRHLFEKQMSVMR 116 (145)
Q Consensus 54 sEaaAsllD~~l~~~iVP~T-----~~---ylSE~g----AS~vD~kl~ln~V-----pktKvdkgfD~~~F~kQmsvmr 116 (145)
-|.||||+||+-....+--| ++ -|||+| |-||.--.-..++ -+--..+--++.|-|+++.--.
T Consensus 62 DetGAYlIDRDP~~FgpvLNylRhgklvl~~l~eeGvL~EAefyn~~~li~likd~i~dRd~~~tq~~~k~vyrvLqcqe 141 (210)
T KOG2715|consen 62 DETGAYLIDRDPFYFGPVLNYLRHGKLVLNKLSEEGVLEEAEFYNDPSLIQLIKDRIQDRDAMVTQEADKFVYRVLQCQE 141 (210)
T ss_pred cccCceEeccCcchHHHHHHHHhcchhhhhhhhhhccchhhhccCChHHHHHHHHHHHHHhhhccccchhHHHHHHHHHH
Confidence 48999999998443211111 11 167765 5554332100000 1111222334455565443333
Q ss_pred HHHHHHHHHHhcCCCcchhhcCC
Q psy15316 117 GQILNLNQALKDGKSPVQLVQMP 139 (145)
Q Consensus 117 gqi~nl~~al~~~ksp~~lvqmp 139 (145)
-...-++.+|.||---.|||.|-
T Consensus 142 eeltqmvStmsDgw~~~qlv~i~ 164 (210)
T KOG2715|consen 142 EELTQMVSTMSDGWKIEQLVSIS 164 (210)
T ss_pred HHHHHHHhhccccHhHHHHhhcc
Confidence 33445566788888888887663
No 7
>PF09000 Cytotoxic: Cytotoxic; InterPro: IPR009105 Colicins are plasmid-encoded protein antibiotics, or bacteriocins, produced by strains of Escherichia coli that kill closely related bacteria. Colicins are classified according to the cell-surface receptor they bind to, colicin E3 binding to the BtuB receptor involved in vitamin B12 uptake. The lethal action of colicin E3 arises from its ability to inactivate the ribosome by site-specific RNase cleavage of the 16S ribosomal RNA, which is carried out by the catalytic, or ribonuclease domain. Colicin E3 is comprised of three domains, each domain being involved in a different stage of infection: receptor binding, translocation and cytotoxicity. Colicin E3 is a Y-shaped molecule with the receptor-binding middle domain forming the stalk, the N-terminal translocation domain forming the two globular heads (IPR003058 from INTERPRO), and the C-terminal catalytic domain forming the two globular arms. To neutralise the toxic effects of colicin E3, the host cell produces an immunity protein, which binds to the C-terminal end of the ribonuclease domain and effectively suppresses its activity. This entry represents the ribonuclease domain (also called catalytic or cytotoxic domain) found in various colicins. This domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix [, ]. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0043022 ribosome binding, 0009405 pathogenesis; PDB: 2B5U_C 1JCH_A 1E44_B 2XFZ_Y.
Probab=41.15 E-value=13 Score=27.51 Aligned_cols=25 Identities=32% Similarity=0.510 Sum_probs=17.0
Q ss_pred cCCCCcEEEEecCCCCCCCCCCCCc
Q psy15316 3 YVPIHKKIGVFKPKDEEPYGRLNPK 27 (145)
Q Consensus 3 y~~~g~~vgvfKPkdEEPyg~lnPk 27 (145)
|+.+|+++|.|-|..-|-...-+|+
T Consensus 56 y~~~GkHLGe~Dp~TGe~~k~~~p~ 80 (85)
T PF09000_consen 56 YNKRGKHLGEFDPKTGEQIKPADPG 80 (85)
T ss_dssp EETT-BEEEEE-TTTS-EEE---TT
T ss_pred EcCCCcCcccccCCcccCcCCCCCC
Confidence 8999999999999998888777775
No 8
>COG5167 VID27 Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]
Probab=37.50 E-value=16 Score=35.54 Aligned_cols=19 Identities=53% Similarity=0.698 Sum_probs=17.9
Q ss_pred CCcCCCCcEEEEecCCCCC
Q psy15316 1 MSYVPIHKKIGVFKPKDEE 19 (145)
Q Consensus 1 ~~y~~~g~~vgvfKPkdEE 19 (145)
+||-..|+.|||||-.||-
T Consensus 430 rsyVtR~n~IGVFk~~de~ 448 (776)
T COG5167 430 RSYVTRGNSIGVFKNTDEG 448 (776)
T ss_pred ceeEeeCCeeeeEeccCCc
Confidence 6899999999999999997
No 9
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II. This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=34.56 E-value=31 Score=28.20 Aligned_cols=39 Identities=21% Similarity=0.436 Sum_probs=22.9
Q ss_pred cEEEEecCCCCCCCCCCCCchhh-hhhhhccCCCCCCceec
Q psy15316 8 KKIGVFKPKDEEPYGRLNPKWTK-WMHKLCCPCCFGRACLI 47 (145)
Q Consensus 8 ~~vgvfKPkdEEPyg~lnPkw~k-w~~r~~~~c~fgRsCli 47 (145)
.+||+|-|++.+=++|.+.+..- +....|.|| +++.|..
T Consensus 272 P~i~lfG~t~p~~~~P~~~~~~vl~~~~~c~pC-~~~~c~~ 311 (334)
T TIGR02195 272 PLVALYGSTSPDFTPPLSEKAEVIRLNLECSPC-FKRDCPY 311 (334)
T ss_pred CEEEEECCCChhhcCCCCCCceEEecCCCccCC-CCCCCCC
Confidence 47999999998755665543111 111234555 5667764
No 10
>PF15433 MRP-S31: Mitochondrial 28S ribosomal protein S31
Probab=32.04 E-value=28 Score=30.82 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=24.1
Q ss_pred CCcEEEEecCCCCCCC----CCCCCchhhhhhhhcc
Q psy15316 6 IHKKIGVFKPKDEEPY----GRLNPKWTKWMHKLCC 37 (145)
Q Consensus 6 ~g~~vgvfKPkdEEPy----g~lnPkw~kw~~r~~~ 37 (145)
.|+++|||+++..+.. ....+.|..|..+-+.
T Consensus 158 ~g~~LnIF~~~~~~e~~~~~~~~~~~W~~~~~~el~ 193 (298)
T PF15433_consen 158 SGKRLNIFKPAAVPEESPETEDSLSLWDKEFAKELS 193 (298)
T ss_pred CCCccccccCCcccccccCCCCCccHHHHHHHHHHH
Confidence 4899999999974443 5666788888888543
No 11
>KOG2913|consensus
Probab=30.34 E-value=31 Score=29.45 Aligned_cols=43 Identities=19% Similarity=0.178 Sum_probs=38.1
Q ss_pred CccccCCCChHHHHHHHhhHhHHHHHHHHHHhcCCCcchhhcCCce
Q psy15316 96 KTKEDKGFDRHLFEKQMSVMRGQILNLNQALKDGKSPVQLVQMPAV 141 (145)
Q Consensus 96 ktKvdkgfD~~~F~kQmsvmrgqi~nl~~al~~~ksp~~lvqmp~~ 141 (145)
+.|-..|+|..|.--| ++|-|.|+..++-+.-.|.|.+++...
T Consensus 33 r~Ks~~glS~lfl~~W---ligdi~nl~g~~l~~~~~~~~~~~~yy 75 (260)
T KOG2913|consen 33 RRKSTEGLSPLFLLTW---LIGDIFNLVGFFLQPLGSTLKVQAVYY 75 (260)
T ss_pred hccccCCCCHHHHHHH---HHccHHHHHHHHhcccchhHHHHHHHH
Confidence 7889999999999766 589999999999999999999888764
No 12
>COG3363 Archaeal IMP cyclohydrolase [Nucleotide transport and metabolism]
Probab=30.21 E-value=34 Score=28.83 Aligned_cols=16 Identities=44% Similarity=0.544 Sum_probs=12.8
Q ss_pred CCcEEEEecCCCCCCC
Q psy15316 6 IHKKIGVFKPKDEEPY 21 (145)
Q Consensus 6 ~g~~vgvfKPkdEEPy 21 (145)
++-.|-+.||||||||
T Consensus 129 d~v~vr~v~~kd~e~~ 144 (200)
T COG3363 129 DEVYVRVVKPKDGEGY 144 (200)
T ss_pred cceEEEEeccCCCCce
Confidence 4445778999999996
No 13
>PF15051 FAM198: FAM198 protein
Probab=25.96 E-value=49 Score=29.83 Aligned_cols=31 Identities=39% Similarity=0.366 Sum_probs=27.7
Q ss_pred CCCCCCceecCCCcchhhhhhhhhhhhcCCc
Q psy15316 38 PCCFGRACLIPNQGYLSEAGASLVDQKLGLN 68 (145)
Q Consensus 38 ~c~fgRsClipn~gYlsEaaAsllD~~l~~~ 68 (145)
.|.-|.+.+|-..+=++|+-|.=|||-||+|
T Consensus 61 ~C~~~~CGLiKrp~D~~EVfAFHLDRVLGLN 91 (326)
T PF15051_consen 61 RCGPGLCGLIKRPLDMSEVFAFHLDRVLGLN 91 (326)
T ss_pred ccCCCceeeECCCCcHHHHHHHHHHHHhccc
Confidence 5777777788889999999999999999998
No 14
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=25.35 E-value=88 Score=20.91 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=17.8
Q ss_pred HHHHHhhHhHHHHHHHHHHhc
Q psy15316 108 FEKQMSVMRGQILNLNQALKD 128 (145)
Q Consensus 108 F~kQmsvmrgqi~nl~~al~~ 128 (145)
-..|+.-+.||+-||-.++..
T Consensus 4 LrqQv~aL~~qv~~Lq~~fs~ 24 (46)
T PF09006_consen 4 LRQQVEALQGQVQRLQAAFSQ 24 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 457999999999999988753
No 15
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=23.09 E-value=97 Score=22.53 Aligned_cols=28 Identities=29% Similarity=0.297 Sum_probs=23.0
Q ss_pred CChHHHHHHHhhHhHHHHHHHHHHhcCC
Q psy15316 103 FDRHLFEKQMSVMRGQILNLNQALKDGK 130 (145)
Q Consensus 103 fD~~~F~kQmsvmrgqi~nl~~al~~~k 130 (145)
.|-.-=+-|+++|.-.|.||++-|+..+
T Consensus 17 ~DtGS~eVQiA~LT~rI~~L~~Hl~~h~ 44 (86)
T TIGR00952 17 KDTGSPEVQIALLTERINQLTEHLKANK 44 (86)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence 4455557899999999999999998654
No 16
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=22.38 E-value=67 Score=23.21 Aligned_cols=28 Identities=32% Similarity=0.485 Sum_probs=20.7
Q ss_pred hhHhHHHHHHH---------HHHhcCCCcchhhcCCc
Q psy15316 113 SVMRGQILNLN---------QALKDGKSPVQLVQMPA 140 (145)
Q Consensus 113 svmrgqi~nl~---------~al~~~ksp~~lvqmp~ 140 (145)
.-+|-=++||. .-|...-||.+||.|.+
T Consensus 54 ~k~Rsl~~NLkd~~N~~L~~~il~g~i~p~~lv~ms~ 90 (115)
T PF07500_consen 54 QKFRSLMFNLKDPKNPDLRRRILSGEISPEELVTMSP 90 (115)
T ss_dssp HHHHHHHHHHCSSTTCCHHHHHHHSSSTTCHHHHCTT
T ss_pred HHHHHHHHHhccCCcHHHHHHHHcCCCCHHHHhcCCH
Confidence 34566677877 34556689999999987
Done!