Query psy11606
Match_columns 111
No_of_seqs 35 out of 37
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 22:57:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0577|consensus 100.0 5.5E-42 1.2E-46 305.3 12.5 111 1-111 745-855 (948)
2 PF07544 Med9: RNA polymerase 67.4 13 0.00029 25.1 4.3 31 70-100 52-82 (83)
3 PRK09706 transcriptional repre 39.5 95 0.0021 21.8 5.0 36 25-68 95-130 (135)
4 PF03763 Remorin_C: Remorin, C 36.2 1.2E+02 0.0026 21.8 5.2 41 69-109 7-47 (111)
5 PF11084 DUF2621: Protein of u 33.5 31 0.00068 26.6 1.9 18 27-44 113-130 (141)
6 PF15233 SYCE1: Synaptonemal c 33.4 89 0.0019 23.9 4.3 40 57-96 9-49 (134)
7 COG1638 DctP TRAP-type C4-dica 25.2 4E+02 0.0087 22.1 8.2 61 25-86 246-307 (332)
8 PF08289 Flu_M1_C: Influenza M 23.2 81 0.0018 22.9 2.4 16 89-104 76-91 (95)
9 PF03693 RHH_2: Uncharacterise 22.1 1.7E+02 0.0037 19.7 3.7 31 59-90 28-58 (80)
10 cd01421 IMPCH Inosine monophos 20.0 1.9E+02 0.0041 22.8 4.1 38 25-62 138-185 (187)
No 1
>KOG0577|consensus
Probab=100.00 E-value=5.5e-42 Score=305.31 Aligned_cols=111 Identities=62% Similarity=0.916 Sum_probs=109.8
Q ss_pred ChhhHHHHHHHHHhhhhHHHHHHHHhhcCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhhHHHHHH
Q psy11606 1 MLIRKQFRETCKIQTRQYKALKAQMLATASKEDQKTVIKKLKQDQRRKLALLGDQYEQSIAEMLQKQSIRLDESQEVECH 80 (111)
Q Consensus 1 ~qIkKQf~dt~kiQtrQyKal~~q~l~~~Pk~~~k~vlk~lKeEq~RKlA~L~eQYe~sI~em~~~q~~rLde~Qe~E~~ 80 (111)
+||||||++||||||+|||++++|+|+++||++||+++|+||+|++||+|||||||++||++|+++|+++|||||++||+
T Consensus 745 lqIrkqfq~tck~qtrqyk~~~~~~le~tpk~e~K~l~k~lk~eq~rklaiLaeqye~si~~m~~~q~lklde~qe~E~q 824 (948)
T KOG0577|consen 745 LQIRKQFQQTCKTQTRQYKAYRAQLLETTPKDEQKELLKRLKEEQTRKLAILAEQYEQSINEMLQSQALKLDEAQEAECQ 824 (948)
T ss_pred hhHHHHHHhhhhHHHHHHHHHHHhhhhcCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhhccceechHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy11606 81 HLKERLHYELEILMAYQSKNKMQAEAQRNRE 111 (111)
Q Consensus 81 ~L~~~Lq~ElelL~aYQsK~k~q~eaq~~rE 111 (111)
+|+.+|++|||+|+|||||+||++++||+||
T Consensus 825 ~l~~ql~qEle~l~ayq~k~k~~~e~q~~re 855 (948)
T KOG0577|consen 825 VLREQLEQELELLNAYQSKIKMQAEEQHERE 855 (948)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999986
No 2
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 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 Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=67.35 E-value=13 Score=25.09 Aligned_cols=31 Identities=29% Similarity=0.414 Sum_probs=27.2
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy11606 70 RLDESQEVECHHLKERLHYELEILMAYQSKN 100 (111)
Q Consensus 70 rLde~Qe~E~~~L~~~Lq~ElelL~aYQsK~ 100 (111)
+=-+.|+.|.+.|+.++..--++|..|.++.
T Consensus 52 ~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 52 RSVEEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3447899999999999999999999998864
No 3
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=39.54 E-value=95 Score=21.79 Aligned_cols=36 Identities=8% Similarity=0.339 Sum_probs=23.7
Q ss_pred HhhcCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy11606 25 MLATASKEDQKTVIKKLKQDQRRKLALLGDQYEQSIAEMLQKQS 68 (111)
Q Consensus 25 ~l~~~Pk~~~k~vlk~lKeEq~RKlA~L~eQYe~sI~em~~~q~ 68 (111)
++...|.+++..+|+-++ .+.+-|+..++||+....
T Consensus 95 ~~~~L~~~~~~~~l~~l~--------~~~~~~~~~~~~~~~~~~ 130 (135)
T PRK09706 95 LFDALPESEQDAQLSEMR--------ARVENFNKLFEELLKARK 130 (135)
T ss_pred HHHHCCHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHh
Confidence 344455555555555443 456789999999998764
No 4
>PF03763 Remorin_C: Remorin, C-terminal region ; InterPro: IPR005516 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=36.20 E-value=1.2e+02 Score=21.78 Aligned_cols=41 Identities=24% Similarity=0.301 Sum_probs=33.4
Q ss_pred hcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy11606 69 IRLDESQEVECHHLKERLHYELEILMAYQSKNKMQAEAQRN 109 (111)
Q Consensus 69 ~rLde~Qe~E~~~L~~~Lq~ElelL~aYQsK~k~q~eaq~~ 109 (111)
-+.+.|.++|.-....+.+.+..-..++-+..++.+++.-.
T Consensus 7 a~a~aWe~ae~aK~~~r~~ree~~I~aWEn~qkaKaea~m~ 47 (111)
T PF03763_consen 7 AKADAWEEAEKAKINNRYEREEAKIQAWENLQKAKAEAEMR 47 (111)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 45678888888888888888888888888888888887643
No 5
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=33.53 E-value=31 Score=26.59 Aligned_cols=18 Identities=39% Similarity=0.484 Sum_probs=15.7
Q ss_pred hcCChHHHHHHHHHhHHH
Q psy11606 27 ATASKEDQKTVIKKLKQD 44 (111)
Q Consensus 27 ~~~Pk~~~k~vlk~lKeE 44 (111)
-.|||.|||-.+++|++.
T Consensus 113 ~ATPKRDhkfL~k~L~~~ 130 (141)
T PF11084_consen 113 LATPKRDHKFLRKKLKEK 130 (141)
T ss_pred hcCCchhHHHHHHHHHHc
Confidence 469999999999999864
No 6
>PF15233 SYCE1: Synaptonemal complex central element protein 1
Probab=33.43 E-value=89 Score=23.94 Aligned_cols=40 Identities=25% Similarity=0.201 Sum_probs=27.3
Q ss_pred HHHHHHHHHHh-hhcchhhHHHHHHHHHHHHHHHHHHHHHH
Q psy11606 57 EQSIAEMLQKQ-SIRLDESQEVECHHLKERLHYELEILMAY 96 (111)
Q Consensus 57 e~sI~em~~~q-~~rLde~Qe~E~~~L~~~Lq~ElelL~aY 96 (111)
|--|+.+..-| +=+-.+....|.+++.+-|++|+|-|++=
T Consensus 9 E~LInrInelQQaKKk~~EELgEa~~l~eaL~~ELDsL~~E 49 (134)
T PF15233_consen 9 EDLINRINELQQAKKKSSEELGEAQALWEALQRELDSLNGE 49 (134)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 34444444433 34555666789999999999999888653
No 7
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=25.15 E-value=4e+02 Score=22.14 Aligned_cols=61 Identities=16% Similarity=0.294 Sum_probs=45.2
Q ss_pred HhhcCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhhHHHH-HHHHHHHH
Q psy11606 25 MLATASKEDQKTVIKKLKQDQRRKLALLGDQYEQSIAEMLQKQSIRLDESQEVE-CHHLKERL 86 (111)
Q Consensus 25 ~l~~~Pk~~~k~vlk~lKeEq~RKlA~L~eQYe~sI~em~~~q~~rLde~Qe~E-~~~L~~~L 86 (111)
..+..|.++|+.|.+-+++-..+--. +++-++..+.+-+.+..+.+.+....+ .++..+.+
T Consensus 246 ~w~~L~~e~q~il~~aa~e~~~~~~~-~~~~~e~~~~e~lk~~Gv~v~~~~~~~~~~~~~~~~ 307 (332)
T COG1638 246 FWDSLPEEDQTILLEAAKEAAEEQRK-LVEELEDELLEKLKEAGVEVVEPDAAEAFREAAKPV 307 (332)
T ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCEEecCCchHHHHHHHHHH
Confidence 45778999998888888776655544 888899999999988888887765555 44444443
No 8
>PF08289 Flu_M1_C: Influenza Matrix protein (M1) C-terminal domain; InterPro: IPR013188 Matrix protein (M1) of Influenza virus is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of RNA-nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously. M1 is comprised of two domains connected by a linker sequence. The C-terminal domain contains alpha-helical structure and appears to be involved in growth and virulence of the virus [, ].; GO: 0003723 RNA binding, 0005198 structural molecule activity
Probab=23.19 E-value=81 Score=22.86 Aligned_cols=16 Identities=44% Similarity=0.391 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHH
Q psy11606 89 ELEILMAYQSKNKMQA 104 (111)
Q Consensus 89 ElelL~aYQsK~k~q~ 104 (111)
=||.|++||+..-.++
T Consensus 76 lle~Lq~yQk~MG~~m 91 (95)
T PF08289_consen 76 LLENLQAYQKRMGAQM 91 (95)
T ss_pred HHHHHHHHHHHHhHHH
Confidence 3799999999876554
No 9
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=22.07 E-value=1.7e+02 Score=19.72 Aligned_cols=31 Identities=32% Similarity=0.465 Sum_probs=21.2
Q ss_pred HHHHHHHHhhhcchhhHHHHHHHHHHHHHHHH
Q psy11606 59 SIAEMLQKQSIRLDESQEVECHHLKERLHYEL 90 (111)
Q Consensus 59 sI~em~~~q~~rLde~Qe~E~~~L~~~Lq~El 90 (111)
|.+|.+..- +||.+.++...++|+..|...+
T Consensus 28 s~SEvvR~a-LRlle~~e~~~~~Lr~~l~~g~ 58 (80)
T PF03693_consen 28 SASEVVREA-LRLLEEREAKLEALREALQEGL 58 (80)
T ss_dssp SHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 344444433 7888888888888888877654
No 10
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=20.00 E-value=1.9e+02 Score=22.85 Aligned_cols=38 Identities=29% Similarity=0.545 Sum_probs=29.8
Q ss_pred HhhcCChHHHHHHHHHhHH------HHHHHHHHHH----HHHHHHHHH
Q psy11606 25 MLATASKEDQKTVIKKLKQ------DQRRKLALLG----DQYEQSIAE 62 (111)
Q Consensus 25 ~l~~~Pk~~~k~vlk~lKe------Eq~RKlA~L~----eQYe~sI~e 62 (111)
+.-.+..+|...|+..|+. +-+++||.-| ..|+..|+.
T Consensus 138 V~vv~dp~dY~~v~~~l~~~g~~~~~~R~~lA~kAF~~ta~YD~~I~~ 185 (187)
T cd01421 138 VTVLVDPADYQKVLEELKSNGSISEETRRRLALKAFAHTAEYDAAISN 185 (187)
T ss_pred eEEEcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5556778999999999975 6788898754 678888875
Done!