Query psy5791
Match_columns 81
No_of_seqs 40 out of 42
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 18:04:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5791hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4512|consensus 99.4 5.2E-14 1.1E-18 117.5 2.7 54 26-80 349-402 (625)
2 KOG4512|consensus 98.9 1.2E-10 2.6E-15 97.6 -0.1 33 2-34 4-36 (625)
3 PF10156 Med17: Subunit 17 of 93.0 0.029 6.2E-07 45.2 0.0 34 3-37 32-65 (467)
4 PF08141 SspH: Small acid-solu 31.3 31 0.00068 21.4 1.3 17 15-31 15-31 (58)
5 PF15507 DUF4649: Domain of un 29.1 42 0.00092 21.9 1.7 19 12-30 37-56 (72)
6 PF08153 NGP1NT: NGP1NT (NUC09 29.0 40 0.00086 24.1 1.7 49 28-76 73-124 (130)
7 PRK01625 sspH acid-soluble spo 28.3 42 0.00091 21.1 1.5 18 14-31 14-31 (59)
8 PF01021 TYA: TYA transposon p 27.0 42 0.00091 23.2 1.5 26 39-64 50-78 (98)
9 PRK03174 sspH acid-soluble spo 26.8 46 0.00099 20.9 1.5 17 15-31 15-31 (59)
10 KOG1859|consensus 26.7 59 0.0013 30.3 2.7 45 17-67 313-359 (1096)
11 TIGR02861 SASP_H small acid-so 24.3 55 0.0012 20.3 1.5 17 15-31 15-31 (58)
12 KOG0846|consensus 24.0 71 0.0015 25.7 2.4 72 4-77 149-238 (274)
13 PF14851 FAM176: FAM176 family 23.5 11 0.00024 27.4 -2.0 25 12-36 129-153 (153)
14 COG1117 PstB ABC-type phosphat 23.2 73 0.0016 25.3 2.3 35 16-51 67-101 (253)
15 PF07550 DUF1533: Protein of u 22.2 47 0.001 20.0 0.9 13 13-25 6-18 (65)
16 PF06799 DUF1230: Protein of u 21.6 40 0.00088 24.4 0.6 20 19-39 106-125 (144)
No 1
>KOG4512|consensus
Probab=99.43 E-value=5.2e-14 Score=117.48 Aligned_cols=54 Identities=24% Similarity=0.236 Sum_probs=48.4
Q ss_pred eecCcchhhhhhcCCCCCCCCCCCCCCCCCccccccCCCccChHHHHHhhhhccC
Q psy5791 26 YQLSDNTFMVHHKNTHHPFPHPSSGPIGPSKRRCIAGPTGADRYELLELTKSEIL 80 (81)
Q Consensus 26 y~~p~~lrE~H~qn~s~~~PhPasaP~G~kK~R~lAGP~a~dr~ei~~m~kte~L 80 (81)
|..-+-+||||++++|+++|||+|||||+||++ ++||+|+|+++|++|+.++|+
T Consensus 349 h~lHll~refh~~ss~~m~phpaSapfg~K~~~-l~gpma~d~n~l~~~~~s~g~ 402 (625)
T KOG4512|consen 349 HMLHLLRREFHDFSSSIMKPHPASAPFGAKSCK-LEGPMAEDQNRLKKTLFSFGK 402 (625)
T ss_pred HHHHHHHHHHHhhccccCCCCCccccccchhhh-ccCcchhhHHHHHHHHHHHHH
Confidence 344456899999999999999999999977777 999999999999999999875
No 2
>KOG4512|consensus
Probab=98.95 E-value=1.2e-10 Score=97.62 Aligned_cols=33 Identities=30% Similarity=0.534 Sum_probs=31.3
Q ss_pred ceeeeeecchhceeeeeecCceeeeecCcchhh
Q psy5791 2 SVNISVEAPVENIIQEISYDGQEIYQLSDNTFM 34 (81)
Q Consensus 2 ~v~isiE~~~e~~vqEi~~dG~E~y~~p~~lrE 34 (81)
|||||||+.||+||.||++||+|+|+||+++-|
T Consensus 4 av~isiesace~qv~evg~DGtE~y~Pp~~~Se 36 (625)
T KOG4512|consen 4 AVRISIESACEKQVHEVGEDGTEVYEPPEPESE 36 (625)
T ss_pred ceeeehhhHHHHHHHHHccCCceeecCCCccch
Confidence 699999999999999999999999999998765
No 3
>PF10156 Med17: Subunit 17 of Mediator complex; InterPro: IPR019313 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 entry represents subunit Med17 of the Mediator complex. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of Saccharomyces cerevisiae (Baker's yeast) lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_B.
Probab=92.96 E-value=0.029 Score=45.24 Aligned_cols=34 Identities=21% Similarity=0.017 Sum_probs=0.0
Q ss_pred eeeeeecchhceeeeeecCceeeeecCcchhhhhh
Q psy5791 3 VNISVEAPVENIIQEISYDGQEIYQLSDNTFMVHH 37 (81)
Q Consensus 3 v~isiE~~~e~~vqEi~~dG~E~y~~p~~lrE~H~ 37 (81)
.+++||++++.++||+++ |.+.|+.+++|++-=.
T Consensus 32 ~~~~l~~~i~ri~~Erg~-~~f~~lte~sL~~ei~ 65 (467)
T PF10156_consen 32 DPLSLEELIERINQERGP-GSFRDLTEESLQEEIA 65 (467)
T ss_dssp -----------------------------------
T ss_pred CCCcHHHHHHHHHhCcCC-CCcccCCHHHHHHHHH
Confidence 368999999999999999 9999999999987543
No 4
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=31.25 E-value=31 Score=21.39 Aligned_cols=17 Identities=18% Similarity=0.491 Sum_probs=14.0
Q ss_pred eeeeecCceeeeecCcc
Q psy5791 15 IQEISYDGQEIYQLSDN 31 (81)
Q Consensus 15 vqEi~~dG~E~y~~p~~ 31 (81)
.-+|.|+|+.+|+.-.+
T Consensus 15 ~i~V~y~G~pV~Ie~vd 31 (58)
T PF08141_consen 15 MIEVTYNGVPVWIEHVD 31 (58)
T ss_pred eEEEEECCEEEEEEEEc
Confidence 34799999999998664
No 5
>PF15507 DUF4649: Domain of unknown function (DUF4649)
Probab=29.11 E-value=42 Score=21.95 Aligned_cols=19 Identities=26% Similarity=0.541 Sum_probs=15.8
Q ss_pred hceeeeeecCceee-eecCc
Q psy5791 12 ENIIQEISYDGQEI-YQLSD 30 (81)
Q Consensus 12 e~~vqEi~~dG~E~-y~~p~ 30 (81)
.-.|.+|.+||+++ |++..
T Consensus 37 ~~~V~svt~~G~~ldy~G~~ 56 (72)
T PF15507_consen 37 YYPVTSVTYNGQDLDYQGTY 56 (72)
T ss_pred ceEEEEEEECCEEeccccch
Confidence 34799999999999 88764
No 6
>PF08153 NGP1NT: NGP1NT (NUC091) domain; InterPro: IPR012971 This N-terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1 [].
Probab=29.03 E-value=40 Score=24.12 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=34.2
Q ss_pred cCcchhhhh--hcC-CCCCCCCCCCCCCCCCccccccCCCccChHHHHHhhh
Q psy5791 28 LSDNTFMVH--HKN-THHPFPHPSSGPIGPSKRRCIAGPTGADRYELLELTK 76 (81)
Q Consensus 28 ~p~~lrE~H--~qn-~s~~~PhPasaP~G~kK~R~lAGP~a~dr~ei~~m~k 76 (81)
.|.||.+=. ++. .+..---|=.-+||+|+.|.-.--.+.|..+|++...
T Consensus 73 LPmsLL~d~~~k~~~~~il~te~F~~tFGpKaqRKRpkL~~~~~eeLa~~a~ 124 (130)
T PF08153_consen 73 LPMSLLQDSGTKQKRVHILETEPFEDTFGPKAQRKRPKLSVSSLEELAKKAE 124 (130)
T ss_pred CCHHHhcccccccCCcceeecCCHHHHhCCcccccCccccccCHHHHHHHHH
Confidence 477777655 222 3343333666699999998778888999999987644
No 7
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=28.27 E-value=42 Score=21.05 Aligned_cols=18 Identities=17% Similarity=0.372 Sum_probs=14.5
Q ss_pred eeeeeecCceeeeecCcc
Q psy5791 14 IIQEISYDGQEIYQLSDN 31 (81)
Q Consensus 14 ~vqEi~~dG~E~y~~p~~ 31 (81)
..-+|.|+|+..|+.-.+
T Consensus 14 ~~i~V~Y~G~pV~Iq~vd 31 (59)
T PRK01625 14 SRIDVTYEGVPVWIESCD 31 (59)
T ss_pred cceEEEECCEEEEEEEEc
Confidence 345899999999998654
No 8
>PF01021 TYA: TYA transposon protein; InterPro: IPR015820 Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. This signature defines TYA, found at the N terminus of the gag and gag-pol polyproteins of approximately 440 amino acids and 1755 amino acids in length respectively. Yeast retrotransposon Ty1 produces its proteins as precursors that are subsequently cleaved by an aspartic protease encoded by the element. Cleavage of the gag and gag-Pol polyprotein precursors is a critical step in proliferation of retroviruses and retroelements. These cleavage events are essential for transposition as they release the active reverse transcriptase and integrase and they modify the structure of the virus-like particles in a way that is analogous to the morphological changes that occur during retrovirus core maturation [, , ].; GO: 0003723 RNA binding, 0005737 cytoplasm
Probab=27.03 E-value=42 Score=23.23 Aligned_cols=26 Identities=42% Similarity=0.898 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCC---CCCccccccCCC
Q psy5791 39 NTHHPFPHPSSGPI---GPSKRRCIAGPT 64 (81)
Q Consensus 39 n~s~~~PhPasaP~---G~kK~R~lAGP~ 64 (81)
|-||++|+|++.|. |+--..+++.|+
T Consensus 50 N~hhasPq~A~vp~pqng~y~Q~~MMt~~ 78 (98)
T PF01021_consen 50 NHHHASPQPASVPPPQNGPYSQQCMMTPN 78 (98)
T ss_pred CCCcCCCCcccCCCCCCCccccccccccc
Confidence 45788999999875 444444455554
No 9
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=26.81 E-value=46 Score=20.87 Aligned_cols=17 Identities=24% Similarity=0.585 Sum_probs=14.0
Q ss_pred eeeeecCceeeeecCcc
Q psy5791 15 IQEISYDGQEIYQLSDN 31 (81)
Q Consensus 15 vqEi~~dG~E~y~~p~~ 31 (81)
.-+|.|+|...|+.-.+
T Consensus 15 ~i~VtY~G~pV~Ie~vd 31 (59)
T PRK03174 15 MANVTYNGVPIYIQHVD 31 (59)
T ss_pred ceEEEECCEEEEEEEEc
Confidence 45789999999998654
No 10
>KOG1859|consensus
Probab=26.70 E-value=59 Score=30.33 Aligned_cols=45 Identities=16% Similarity=0.186 Sum_probs=36.6
Q ss_pred eeecCceeeeecCcchhhhhhcC--CCCCCCCCCCCCCCCCccccccCCCccC
Q psy5791 17 EISYDGQEIYQLSDNTFMVHHKN--THHPFPHPSSGPIGPSKRRCIAGPTGAD 67 (81)
Q Consensus 17 Ei~~dG~E~y~~p~~lrE~H~qn--~s~~~PhPasaP~G~kK~R~lAGP~a~d 67 (81)
+.-|||. -+++|||-+-. -++++++|++=+|+..-+- .+||+.-+
T Consensus 313 ~f~LDgk-----~l~~~efwk~~s~~~hr~~~p~s~~~~S~a~~-~~~~dgS~ 359 (1096)
T KOG1859|consen 313 KFKLDGK-----ALGGREFWKRQSGVSHRSSRPASYGFYSPARS-ENTSDGSQ 359 (1096)
T ss_pred ceEecce-----eccchhhhhhhhheecCCCCCCCCCCCCchhc-cCCCccch
Confidence 4568887 67889987666 8899999999999998877 88887654
No 11
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=24.33 E-value=55 Score=20.32 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=13.9
Q ss_pred eeeeecCceeeeecCcc
Q psy5791 15 IQEISYDGQEIYQLSDN 31 (81)
Q Consensus 15 vqEi~~dG~E~y~~p~~ 31 (81)
.-+|.|+|+..|+.-.+
T Consensus 15 ~i~V~Y~G~pV~Ie~vd 31 (58)
T TIGR02861 15 MINVTYKGVPVYIEHVD 31 (58)
T ss_pred ceEEEECCEEEEEEEEc
Confidence 35799999999998654
No 12
>KOG0846|consensus
Probab=24.04 E-value=71 Score=25.65 Aligned_cols=72 Identities=18% Similarity=0.196 Sum_probs=44.7
Q ss_pred eeeeec--chhceeeeeecCc---eeeeecCcchhhh------hhcCCCCCCCCCCC-----CCC--CCCccccccCCCc
Q psy5791 4 NISVEA--PVENIIQEISYDG---QEIYQLSDNTFMV------HHKNTHHPFPHPSS-----GPI--GPSKRRCIAGPTG 65 (81)
Q Consensus 4 ~isiE~--~~e~~vqEi~~dG---~E~y~~p~~lrE~------H~qn~s~~~PhPas-----aP~--G~kK~R~lAGP~a 65 (81)
.|+||. .-+.-|+-|-=.| +-.|-.|++||.+ +.. ..+.|.-+- ..+ -++++=.|+.|.+
T Consensus 149 ~i~iEvs~aS~~AiaaIEkaGG~vtt~yy~p~~Lra~lnP~~wf~~--g~~vP~~~rPp~~~idyYtd~k~rGyl~~~~~ 226 (274)
T KOG0846|consen 149 KINIEVSRASVQAIAAIEKAGGSVTTAYYDPLSLRAHLNPKKWFEP--GSPVPKRARPPQKDIDYYTDPKNRGYLAAPEA 226 (274)
T ss_pred eEEEEehhhhHHHHHHHHhcCCeEEEEEEcchhhhhhcCchhhccc--CCcCccccCCChhhhhhhhchhhcccccCccc
Confidence 344443 3455566666677 6789999999854 433 334443222 233 3444445899999
Q ss_pred cChHHHHHhhhh
Q psy5791 66 ADRYELLELTKS 77 (81)
Q Consensus 66 ~dr~ei~~m~kt 77 (81)
.-+..+.+.|+.
T Consensus 227 ~~~e~~~~Aq~~ 238 (274)
T KOG0846|consen 227 KTSERAASAQKY 238 (274)
T ss_pred cccchhHHHhhc
Confidence 998888888764
No 13
>PF14851 FAM176: FAM176 family
Probab=23.55 E-value=11 Score=27.38 Aligned_cols=25 Identities=32% Similarity=0.171 Sum_probs=18.5
Q ss_pred hceeeeeecCceeeeecCcchhhhh
Q psy5791 12 ENIIQEISYDGQEIYQLSDNTFMVH 36 (81)
Q Consensus 12 e~~vqEi~~dG~E~y~~p~~lrE~H 36 (81)
|..||||..|||.---++-+|-.+|
T Consensus 129 e~iirEIW~n~~~d~~~~~~~~~~~ 153 (153)
T PF14851_consen 129 ERIIREIWMNGQPDILGTRTLGRVY 153 (153)
T ss_pred HHHHHHHHHhcCCCCCCCCCCCCCC
Confidence 6789999999997666666655544
No 14
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=23.18 E-value=73 Score=25.32 Aligned_cols=35 Identities=23% Similarity=0.431 Sum_probs=24.4
Q ss_pred eeeecCceeeeecCcchhhhhhcCCCCCCCCCCCCC
Q psy5791 16 QEISYDGQEIYQLSDNTFMVHHKNTHHPFPHPSSGP 51 (81)
Q Consensus 16 qEi~~dG~E~y~~p~~lrE~H~qn~s~~~PhPasaP 51 (81)
=||.|||+.+|-+..+.-++-+. -+++|.+|..=|
T Consensus 67 G~v~~~g~ni~~~~~d~~~lRr~-vGMVFQkPnPFp 101 (253)
T COG1117 67 GEVLLDGKNIYDPKVDVVELRRR-VGMVFQKPNPFP 101 (253)
T ss_pred EEEEECCeeccCCCCCHHHHHHH-heeeccCCCCCC
Confidence 38999999999997777666444 455666655433
No 15
>PF07550 DUF1533: Protein of unknown function (DUF1533); InterPro: IPR011432 This domain is found duplicated in proteins of unknown function. The proteins typically also contain leucine-rich repeats.
Probab=22.18 E-value=47 Score=20.01 Aligned_cols=13 Identities=23% Similarity=0.537 Sum_probs=11.5
Q ss_pred ceeeeeecCceee
Q psy5791 13 NIIQEISYDGQEI 25 (81)
Q Consensus 13 ~~vqEi~~dG~E~ 25 (81)
+.|.+|.+||++.
T Consensus 6 ~~I~~V~VNg~~y 18 (65)
T PF07550_consen 6 KAITSVTVNGKEY 18 (65)
T ss_pred hhCCEEEECCEEe
Confidence 5789999999987
No 16
>PF06799 DUF1230: Protein of unknown function (DUF1230); InterPro: IPR009631 This family represents Ycf36, which is found in plants, encoded in the genomes of algal chloroplasts and in cyanobacteria. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=21.61 E-value=40 Score=24.45 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=16.0
Q ss_pred ecCceeeeecCcchhhhhhcC
Q psy5791 19 SYDGQEIYQLSDNTFMVHHKN 39 (81)
Q Consensus 19 ~~dG~E~y~~p~~lrE~H~qn 39 (81)
-|||| +|+.|+..+...+-.
T Consensus 106 WYDGQ-~W~Kp~e~l~rDrLi 125 (144)
T PF06799_consen 106 WYDGQ-VWVKPPEVLARDRLI 125 (144)
T ss_pred ccCCc-cccCCHHHHHHHHHH
Confidence 38998 799999988876655
Done!