Query psy13710
Match_columns 615
No_of_seqs 264 out of 496
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 18:31:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13710hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07810 TMC: TMC domain; Int 94.9 0.012 2.7E-07 53.6 1.5 28 525-557 46-73 (111)
2 PF02714 DUF221: Domain of unk 90.0 1.8 4E-05 45.8 9.9 45 430-474 103-147 (325)
3 PF04547 Anoctamin: Calcium-ac 66.3 35 0.00075 38.1 9.9 25 211-235 1-29 (452)
4 KOG2513|consensus 56.7 1.7E+02 0.0037 34.4 13.1 76 389-464 263-347 (647)
5 PF11214 Med2: Mediator comple 50.9 7.1 0.00015 35.4 0.9 34 559-592 52-86 (105)
6 KOG1134|consensus 50.5 70 0.0015 38.4 9.3 61 430-490 409-478 (728)
7 COG2443 Sss1 Preprotein transl 35.0 1.9E+02 0.0041 24.3 6.8 51 368-418 6-58 (65)
8 COG5594 Uncharacterized integr 19.8 3.1E+02 0.0068 33.4 7.6 78 391-468 408-503 (827)
9 PF10886 DUF2685: Protein of u 19.8 18 0.00039 29.1 -1.7 22 16-37 20-41 (54)
10 COG4499 Predicted membrane pro 17.9 7.4E+02 0.016 27.8 9.3 32 287-320 125-156 (434)
No 1
>PF07810 TMC: TMC domain; InterPro: IPR012496 These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 (Q7TN63 from SWISSPROT) and EVIN2 (Q8IU68 from SWISSPROT) - this region is termed the TMC domain []. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis []. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters []. ; GO: 0016021 integral to membrane
Probab=94.87 E-value=0.012 Score=53.62 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=26.1
Q ss_pred hhhhcccccchhHHHHHHHhHHHhhhheeeeec
Q psy13710 525 KLGNLEQLHPRKHLRMLLARNEYSESIGCQIIK 557 (615)
Q Consensus 525 ~ig~~E~yhPr~~l~~~l~r~~~~~~~~~~~~~ 557 (615)
..|..|+..|+|+|.+ +|+|+++|+|..
T Consensus 46 ~~g~~eF~i~~nvL~l-----iY~Qtl~WiG~f 73 (111)
T PF07810_consen 46 FPGKPEFDIPKNVLDL-----IYNQTLVWIGMF 73 (111)
T ss_pred CCCCCCccHhhhHHHH-----HHcchhhhhhHH
Confidence 5689999999999999 999999999974
No 2
>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length.; GO: 0016020 membrane
Probab=90.03 E-value=1.8 Score=45.76 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=37.0
Q ss_pred hhhhhhhHHHHHHHHhhhhHHHHhhhhccccChhhHHHHHHHHHH
Q psy13710 430 VWHKNEAVVVIWIIGVTFPRLLEKLGNLEQLHPRKHLRMLLASFH 474 (615)
Q Consensus 430 l~~~~~~sIViSliN~i~P~lF~~i~~~E~y~Pr~~Lrv~L~R~l 474 (615)
++..++|+++++++|.++|.++..++++|++.-+++....+++..
T Consensus 103 ~i~~~lp~l~l~~~~~llp~ii~~ls~~e~~~s~S~~~~sv~~k~ 147 (325)
T PF02714_consen 103 LIQGILPSLLLSIFNALLPIIIRFLSKFEGHKSRSEVERSVLRKL 147 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHH
Confidence 566788999999999999999999999999876666665555443
No 3
>PF04547 Anoctamin: Calcium-activated chloride channel; InterPro: IPR007632 This family contains the anoctamin/TMEM16 proteins which are thought to be calcium-dependent chloride channel [].
Probab=66.33 E-value=35 Score=38.13 Aligned_cols=25 Identities=44% Similarity=0.816 Sum_probs=18.7
Q ss_pred hcccccccchhhhHHHH----HHHHHHHH
Q psy13710 211 IESHFGSAVASYFTFLR----WLFFVNFI 235 (615)
Q Consensus 211 IEG~FGSgVaSYF~FLR----wLf~LNlv 235 (615)
|..+||..|+=||.||. ||....++
T Consensus 1 Ir~YFGekia~YFafl~~yt~~L~~~ai~ 29 (452)
T PF04547_consen 1 IRSYFGEKIAFYFAFLGFYTRWLIPPAIF 29 (452)
T ss_pred ChHHhchHHHHHHHHHHHHHHHHHHHHHH
Confidence 56799999999999976 44444443
No 4
>KOG2513|consensus
Probab=56.70 E-value=1.7e+02 Score=34.40 Aligned_cols=76 Identities=21% Similarity=0.231 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHHHHHHH-HHH--HhHHHHHhhhhc--cCCCCCCcchhhhhhhHHHHHHHHhhhhHHHHh----hhhccc
Q psy13710 389 SWKIICIRIIVNILVVF-LLG--ISAYTIIEVVSR--SQDPNRPQTVWHKNEAVVVIWIIGVTFPRLLEK----LGNLEQ 459 (615)
Q Consensus 389 ~~kl~~~Ril~nllvl~-lL~--~s~y~I~~~~~~--s~~~~~~~~l~~~~~~sIViSliN~i~P~lF~~----i~~~E~ 459 (615)
.|+.+..|.++++-+.+ +++ +++.++++.... .++..+...=+..|.|+|+.+++..++-.++.. ++++||
T Consensus 263 ~w~~~~~~~~vsvPv~l~c~~i~l~f~l~~f~ie~~~~s~~~~~~~sils~lP~iv~~~li~~~t~~Y~k~Ae~Lt~~EN 342 (647)
T KOG2513|consen 263 EWKRILRRYLVSVPVILLCLCILLSFMLYCFQIEVWVLSDYGGPLISILSYLPTIVYAVLIPVLTRIYKKLAEFLTKLEN 342 (647)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 67878888777775433 222 233333333221 122222222356789999999888877766665 468899
Q ss_pred cChhh
Q psy13710 460 LHPRK 464 (615)
Q Consensus 460 y~Pr~ 464 (615)
|.-+.
T Consensus 343 ~r~~s 347 (647)
T KOG2513|consen 343 HRLES 347 (647)
T ss_pred hhhHH
Confidence 86443
No 5
>PF11214 Med2: Mediator complex subunit 2; InterPro: IPR021017 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 of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression [, ].
Probab=50.89 E-value=7.1 Score=35.41 Aligned_cols=34 Identities=21% Similarity=0.478 Sum_probs=23.5
Q ss_pred CchhhHHHHHhhhccccccc-hhhheeeeeccchh
Q psy13710 559 DDVTQFQRIIDSLDSSVDLT-RYACQIYLIKKQEE 592 (615)
Q Consensus 559 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 592 (615)
+.++.|..|+|.++++..-+ .|.-++.-++++.|
T Consensus 52 eki~~Fh~ILDd~~~~l~~sk~~v~~m~e~~q~~e 86 (105)
T PF11214_consen 52 EKIHKFHSILDDTESKLNDSKWYVDTMVELKQKQE 86 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999887554 45556666655533
No 6
>KOG1134|consensus
Probab=50.49 E-value=70 Score=38.42 Aligned_cols=61 Identities=25% Similarity=0.236 Sum_probs=44.3
Q ss_pred hhhhhhhHHHHHHHHhhhhHHHHhhhhccccChhhHH---------HHHHHHHHHHHHhhhhhhhhhhhc
Q psy13710 430 VWHKNEAVVVIWIIGVTFPRLLEKLGNLEQLHPRKHL---------RMLLASFHLLFLLGISAYTIIEVV 490 (615)
Q Consensus 430 l~~~~~~sIViSliN~i~P~lF~~i~~~E~y~Pr~~L---------rv~L~R~l~L~Llslsly~~i~~v 490 (615)
++.+++|+++..+...++|.++..++.+|++..+-+. .+++.+++++..++.|.+.+...+
T Consensus 409 vI~gfLP~l~l~~~~~~lP~~l~~ls~~eG~~s~S~~e~~a~~k~~~F~~~nvFl~~~l~~sa~~~~~~~ 478 (728)
T KOG1134|consen 409 VITGFLPTLALVIFLALLPPFLRYLSKLEGLISRSEEERSALNKYYIFLLVNVFLVVTLSGSALRQLLSI 478 (728)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHhHHHHHHhhhHHHhhhhHHHHHHHHHH
Confidence 5678899999999999999999999999999644443 233455566665555555544444
No 7
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=35.00 E-value=1.9e+02 Score=24.26 Aligned_cols=51 Identities=20% Similarity=0.238 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHHH--hccccchHHHHHHHHHHHHHHHHHHHHhHHHHHhhh
Q psy13710 368 SIILGFKEALVEEAE--KQRDHLSWKIICIRIIVNILVVFLLGISAYTIIEVV 418 (615)
Q Consensus 368 sI~~elKe~L~Ee~~--~~~~~~~~kl~~~Ril~nllvl~lL~~s~y~I~~~~ 418 (615)
....++++.+.|.++ +.-.+-+|.=|+.=.-++.+.+.++|+.+|+|+...
T Consensus 6 ~~~e~~~~~lke~~rvl~~arKP~~eEy~~~aKi~~~Gi~liG~IGfiI~li~ 58 (65)
T COG2443 6 DKPEELREFLKEYRRVLKVARKPDWEEYSKIAKITGLGILLIGIIGFIIYLIM 58 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566666666553 222244666666655566666777778888887543
No 8
>COG5594 Uncharacterized integral membrane protein [Function unknown]
Probab=19.81 E-value=3.1e+02 Score=33.36 Aligned_cols=78 Identities=17% Similarity=0.211 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHhhhhccCCCC------------CCc----chhhhhhhHHHHHHHHhhhhHHHHhh
Q psy13710 391 KIICIRIIVNILVVFLLGISAYTIIEVVSRSQDPN------------RPQ----TVWHKNEAVVVIWIIGVTFPRLLEKL 454 (615)
Q Consensus 391 kl~~~Ril~nllvl~lL~~s~y~I~~~~~~s~~~~------------~~~----~l~~~~~~sIViSliN~i~P~lF~~i 454 (615)
-.+..|..+|++...++.++..-+-++...++-.. .+. +.+...+|+++.++++.++|.++..+
T Consensus 408 ~r~~k~~~~ni~~il~II~w~~pVa~v~~i~Nl~~l~~~~p~l~~il~~~~~l~~iltglLptv~~~~l~~ivP~fir~L 487 (827)
T COG5594 408 ERLFKRISANILFILLIILWAFPVAFVGTISNLNTLSSLWPFLKFILKDPPFLAGILTGLLPTVALSLLMSIVPYFIRWL 487 (827)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhHhhhhHHHHHHHhccHHHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Confidence 34667788888765555444433333333332110 011 23456789999999999999999999
Q ss_pred hhccccC--hhhHHHH
Q psy13710 455 GNLEQLH--PRKHLRM 468 (615)
Q Consensus 455 ~~~E~y~--Pr~~Lrv 468 (615)
+.++.-. -..|.++
T Consensus 488 s~~qG~~S~se~E~~~ 503 (827)
T COG5594 488 SYMQGLVSYSEEEIYV 503 (827)
T ss_pred HHhcCccchHHHHHHH
Confidence 9999875 3344443
No 9
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=19.76 E-value=18 Score=29.11 Aligned_cols=22 Identities=27% Similarity=0.418 Sum_probs=17.8
Q ss_pred CCCCCccceEEEEeeccCCCCC
Q psy13710 16 TGGPDHVGQIYIYLIKMTILLP 37 (615)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~ 37 (615)
-+||-|.++++.|.+.+..+..
T Consensus 20 ~~G~VH~g~C~~y~~e~~~SEs 41 (54)
T PF10886_consen 20 ESGPVHPGVCAQYLEELPVSES 41 (54)
T ss_pred CCCccCcHHHHHHHHhcccccC
Confidence 3689999999999998875543
No 10
>COG4499 Predicted membrane protein [Function unknown]
Probab=17.91 E-value=7.4e+02 Score=27.81 Aligned_cols=32 Identities=13% Similarity=0.047 Sum_probs=19.4
Q ss_pred ceeeecccCCCCccCCCchHHHHHHHHHHHHHHH
Q psy13710 287 PIFYGYYNNQDNSRYKTPLAFFIVTLLLYIYSFV 320 (615)
Q Consensus 287 ~LFYGyYsn~~~~~YnlPLAYllt~i~~~~~sli 320 (615)
.+-||--+ ...+|.+.=+=|+.-.=++++|.+
T Consensus 125 ~vH~Glk~--~lpPye~tee~f~~~ykA~~~~~f 156 (434)
T COG4499 125 FVHRGLKN--SLPPYEMTEERFLKEYKALAIYAF 156 (434)
T ss_pred EEecchhc--cCCCCCCCHHHHHHHHHHHHHHHH
Confidence 33455433 234788877777777666666544
Done!