Query 029234
Match_columns 197
No_of_seqs 23 out of 25
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 09:39:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029234hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13374 TPR_10: Tetratricopep 81.9 0.82 1.8E-05 26.4 1.2 20 18-37 23-42 (42)
2 COG1595 RpoE DNA-directed RNA 35.3 23 0.00049 27.4 1.4 54 28-83 18-83 (182)
3 PF04971 Lysis_S: Lysis protei 34.9 26 0.00055 26.2 1.6 18 69-86 15-32 (68)
4 TIGR03165 F1F0_chp_2 F1/F0 ATP 33.4 25 0.00053 26.7 1.3 21 6-26 11-31 (83)
5 PHA00652 hypothetical protein 31.1 69 0.0015 26.4 3.6 37 40-76 76-118 (128)
6 KOG3801 Uncharacterized conser 25.8 89 0.0019 24.8 3.2 31 18-51 11-41 (94)
7 PRK12540 RNA polymerase sigma 24.3 50 0.0011 25.9 1.7 48 28-77 8-62 (182)
8 PF02184 HAT: HAT (Half-A-TPR) 23.8 52 0.0011 21.3 1.4 19 44-62 4-22 (32)
9 PF13232 Complex1_LYR_1: Compl 23.7 1.1E+02 0.0024 20.3 3.0 30 19-51 6-35 (61)
10 PRK05803 sporulation sigma fac 23.5 75 0.0016 25.8 2.6 51 29-79 53-110 (233)
11 PF08511 COQ9: COQ9; InterPro 23.2 1.1E+02 0.0025 22.6 3.3 30 23-52 45-74 (79)
12 PRK12514 RNA polymerase sigma 23.1 59 0.0013 24.7 1.8 46 30-76 24-76 (179)
13 PRK09191 two-component respons 23.0 56 0.0012 25.6 1.7 52 30-83 6-64 (261)
14 cd04450 DEP_RGS7-like DEP (Dis 20.7 60 0.0013 23.5 1.4 10 188-197 32-41 (88)
15 PRK12547 RNA polymerase sigma 20.6 65 0.0014 24.4 1.6 47 28-76 9-62 (164)
16 TIGR02846 spore_sigmaK RNA pol 20.3 52 0.0011 26.8 1.0 50 29-78 52-108 (227)
No 1
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=81.86 E-value=0.82 Score=26.44 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=8.1
Q ss_pred hHHHHHHHhhhhccCCCChh
Q 029234 18 RTYRLALRIKRRVISPKRPR 37 (197)
Q Consensus 18 RtYrlalr~qrrlisp~~p~ 37 (197)
.-|+-|+.+++++.+|+||.
T Consensus 23 ~~~~~al~~~~~~~G~~Hpd 42 (42)
T PF13374_consen 23 ELLEEALEIRERLLGPDHPD 42 (42)
T ss_dssp HHHHHHHHHH----------
T ss_pred HHHHHHHHHHHHHhcccccC
Confidence 45788999999999999994
No 2
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=35.28 E-value=23 Score=27.40 Aligned_cols=54 Identities=22% Similarity=0.444 Sum_probs=39.9
Q ss_pred hhccCCCChhHHHHHHHHhhHhh-------HHHHhhhhhhhhhhhhhhhhhhhHHHH-----hhhccC
Q 029234 28 RRVISPKRPRIRQFVHRRLRAVF-------DVALKFHKNIQERDIEVGRNVGNWILR-----WLDRMK 83 (197)
Q Consensus 28 rrlisp~~p~~r~F~~rRtr~vF-------dva~~vhkniq~rDievGrnlGN~iLr-----~Ldrmk 83 (197)
..++.+-||+++.|+.++++... |+-+++++++..- +-+.++..|+.+ |+|+.+
T Consensus 18 ~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~--~~~~~~~~wl~~Ia~n~~iD~~R 83 (182)
T COG1595 18 EELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF--RGRSSFKAWLYRIARNLAIDRLR 83 (182)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc--CCCCchHHHHHHHHHHHHHHHHH
Confidence 34556778999999999998766 5679999999876 445666666654 566665
No 3
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=34.85 E-value=26 Score=26.22 Aligned_cols=18 Identities=39% Similarity=0.898 Sum_probs=15.5
Q ss_pred hhhhhHHHHhhhccCCCc
Q 029234 69 RNVGNWILRWLDRMKPSA 86 (197)
Q Consensus 69 rnlGN~iLr~LdrmkPsA 86 (197)
-.+|+|+++|||.+.|+-
T Consensus 15 g~~~~wl~~lld~~sp~q 32 (68)
T PF04971_consen 15 GSAGYWLLQLLDQFSPSQ 32 (68)
T ss_pred hhHHHHHHHHHhccCccc
Confidence 467899999999999973
No 4
>TIGR03165 F1F0_chp_2 F1/F0 ATPase, Methanosarcina type, subunit 2. Members of this protein family are uncharacterized, highly hydrophobic proteins encoded in the middle of apparent F1/F0 ATPase operons. We note, however, that this protein is both broadly and sparsely distributed. It is found in about only about two percent of microbial genomes sequenced, with the first ten examples found coming from the Euryarchaeota, Chlorobia, Betaproteobacteria, Deltaproteobacteria, and Planctomycetes. In most of these species, surrounding operon appears to represent a second F1/F0 ATPase system, and the member proteins belong to subfamilies with the same phylogenetic distribution as the current protein family.
Probab=33.37 E-value=25 Score=26.70 Aligned_cols=21 Identities=38% Similarity=0.444 Sum_probs=17.8
Q ss_pred ehhhhHhhhhhhhHHHHHHHh
Q 029234 6 ITLGTAYFLGLKRTYRLALRI 26 (197)
Q Consensus 6 itl~TAYfLGlkRtYrlalr~ 26 (197)
+.+|+.||-||.-|-|+.++.
T Consensus 11 ~~lG~~~F~gLw~tvr~~~~~ 31 (83)
T TIGR03165 11 FLLGAFFFGGLWWTVRKGLAS 31 (83)
T ss_pred HHHHHHHHHHHHHHHHHhccC
Confidence 468899999999999888763
No 5
>PHA00652 hypothetical protein
Probab=31.07 E-value=69 Score=26.39 Aligned_cols=37 Identities=27% Similarity=0.301 Sum_probs=27.6
Q ss_pred HHHHHHhhHhh---HHH---HhhhhhhhhhhhhhhhhhhhHHH
Q 029234 40 QFVHRRLRAVF---DVA---LKFHKNIQERDIEVGRNVGNWIL 76 (197)
Q Consensus 40 ~F~~rRtr~vF---dva---~~vhkniq~rDievGrnlGN~iL 76 (197)
+++...+|-.+ |.. ++=++...+.=-|+|+-||-||=
T Consensus 76 d~LR~~vRLa~~l~~~~~i~~~rYe~~~~~l~EIGrmLGGWIk 118 (128)
T PHA00652 76 AMLRFWLRFLAGIQKPHAMTPHQVETAQVLIAEVGRILGSWIA 118 (128)
T ss_pred HHHHHHHHHHhhhhhhhccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777788888 552 35566777888899999999763
No 6
>KOG3801 consensus Uncharacterized conserved protein BCN92 [RNA processing and modification]
Probab=25.83 E-value=89 Score=24.79 Aligned_cols=31 Identities=32% Similarity=0.604 Sum_probs=24.0
Q ss_pred hHHHHHHHhhhhccCCCChhHHHHHHHHhhHhhH
Q 029234 18 RTYRLALRIKRRVISPKRPRIRQFVHRRLRAVFD 51 (197)
Q Consensus 18 RtYrlalr~qrrlisp~~p~~r~F~~rRtr~vFd 51 (197)
+-||..||.=+.+ |.| -.|.|..||||+-|-
T Consensus 11 sLyr~~lr~s~qf--p~Y-NyReY~~RrtRD~Fr 41 (94)
T KOG3801|consen 11 SLYRNLLRESKQF--PQY-NYREYFQRRTRDTFR 41 (94)
T ss_pred HHHHHHHHHHhhC--Ccc-cHHHHHHHHHHHHHH
Confidence 4588888887765 333 579999999999984
No 7
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=24.30 E-value=50 Score=25.93 Aligned_cols=48 Identities=23% Similarity=0.359 Sum_probs=33.6
Q ss_pred hhccCCCChhHHHHHHHHhhHh-------hHHHHhhhhhhhhhhhhhhhhhhhHHHH
Q 029234 28 RRVISPKRPRIRQFVHRRLRAV-------FDVALKFHKNIQERDIEVGRNVGNWILR 77 (197)
Q Consensus 28 rrlisp~~p~~r~F~~rRtr~v-------Fdva~~vhkniq~rDievGrnlGN~iLr 77 (197)
|.++.+-+|.+..|+++++..- =||-+++.+++.+ ++...++..|+.+
T Consensus 8 ~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~--~~~~~~~~~WL~~ 62 (182)
T PRK12540 8 RDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDS--FQPGSNLPAWLFT 62 (182)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHh--cCCCchHHHHHHH
Confidence 3455677899999999988743 3577888888764 4444577777643
No 8
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=23.76 E-value=52 Score=21.29 Aligned_cols=19 Identities=16% Similarity=0.478 Sum_probs=15.5
Q ss_pred HHhhHhhHHHHhhhhhhhh
Q 029234 44 RRLRAVFDVALKFHKNIQE 62 (197)
Q Consensus 44 rRtr~vFdva~~vhkniq~ 62 (197)
.|.|+||.-.|.||.++..
T Consensus 4 dRAR~IyeR~v~~hp~~k~ 22 (32)
T PF02184_consen 4 DRARSIYERFVLVHPEVKN 22 (32)
T ss_pred HHHHHHHHHHHHhCCCchH
Confidence 5899999999999976653
No 9
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=23.65 E-value=1.1e+02 Score=20.29 Aligned_cols=30 Identities=27% Similarity=0.394 Sum_probs=24.8
Q ss_pred HHHHHHHhhhhccCCCChhHHHHHHHHhhHhhH
Q 029234 19 TYRLALRIKRRVISPKRPRIRQFVHRRLRAVFD 51 (197)
Q Consensus 19 tYrlalr~qrrlisp~~p~~r~F~~rRtr~vFd 51 (197)
-||-.||.-+.+-+++.. .++.++.|.-|.
T Consensus 6 LYR~lLR~~~~~~~~~~r---~~~~~~ir~~Fr 35 (61)
T PF13232_consen 6 LYRQLLREASKFPDYNFR---SYFRRRIRDRFR 35 (61)
T ss_pred HHHHHHHHhhhcCCcchH---HHHHHHHHHHHH
Confidence 488899999988876654 888889999887
No 10
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.50 E-value=75 Score=25.83 Aligned_cols=51 Identities=14% Similarity=0.126 Sum_probs=37.1
Q ss_pred hccCCCChhHHHHHHHHhhHh-------hHHHHhhhhhhhhhhhhhhhhhhhHHHHhh
Q 029234 29 RVISPKRPRIRQFVHRRLRAV-------FDVALKFHKNIQERDIEVGRNVGNWILRWL 79 (197)
Q Consensus 29 rlisp~~p~~r~F~~rRtr~v-------Fdva~~vhkniq~rDievGrnlGN~iLr~L 79 (197)
.++..-+|.+..+..+....- =|+-+++.++++.=|-+-|.++..|+.+|.
T Consensus 53 ~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~ 110 (233)
T PRK05803 53 ILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCI 110 (233)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHH
Confidence 455566677777777766432 257889999999888877778888887764
No 11
>PF08511 COQ9: COQ9; InterPro: IPR013718 COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q []. It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role. ; PDB: 3NI7_B.
Probab=23.22 E-value=1.1e+02 Score=22.62 Aligned_cols=30 Identities=20% Similarity=0.207 Sum_probs=19.6
Q ss_pred HHHhhhhccCCCChhHHHHHHHHhhHhhHH
Q 029234 23 ALRIKRRVISPKRPRIRQFVHRRLRAVFDV 52 (197)
Q Consensus 23 alr~qrrlisp~~p~~r~F~~rRtr~vFdv 52 (197)
.+=..=.--||++-....||.||...|.++
T Consensus 45 t~l~~l~d~S~~~~~T~~Fl~rri~~v~~~ 74 (79)
T PF08511_consen 45 TELYMLQDKSPDFEDTWAFLDRRIDDVMQF 74 (79)
T ss_dssp HHHHHHT--SGGGHHHHHHHHHHHHHH---
T ss_pred HHHHHhhCCCCCHHHHHHHHHHHHHhhhcc
Confidence 333333445899999999999999887653
No 12
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.08 E-value=59 Score=24.70 Aligned_cols=46 Identities=15% Similarity=0.287 Sum_probs=27.9
Q ss_pred ccCCCChhHHHHHHHHhhHhh-------HHHHhhhhhhhhhhhhhhhhhhhHHH
Q 029234 30 VISPKRPRIRQFVHRRLRAVF-------DVALKFHKNIQERDIEVGRNVGNWIL 76 (197)
Q Consensus 30 lisp~~p~~r~F~~rRtr~vF-------dva~~vhkniq~rDievGrnlGN~iL 76 (197)
++..-++.+..|+.+++...- |+.|++++++..-+.+ ..++..|+.
T Consensus 24 l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~-~~~~~~wl~ 76 (179)
T PRK12514 24 LYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVS-GLSPMTWLI 76 (179)
T ss_pred HHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcc-cccHHHHHH
Confidence 333455666666666665433 5889999988865533 244555553
No 13
>PRK09191 two-component response regulator; Provisional
Probab=22.98 E-value=56 Score=25.58 Aligned_cols=52 Identities=13% Similarity=0.116 Sum_probs=36.3
Q ss_pred ccCCCChhHHHHHHHHhhH-------hhHHHHhhhhhhhhhhhhhhhhhhhHHHHhhhccC
Q 029234 30 VISPKRPRIRQFVHRRLRA-------VFDVALKFHKNIQERDIEVGRNVGNWILRWLDRMK 83 (197)
Q Consensus 30 lisp~~p~~r~F~~rRtr~-------vFdva~~vhkniq~rDievGrnlGN~iLr~Ldrmk 83 (197)
++..-+|.++.|++++++. +=||.+++++++..-+- ..++-.|+.|++++..
T Consensus 6 l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~--~~~~~~wl~~~~~~~~ 64 (261)
T PRK09191 6 RIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPE--ASSPRVGLYRLFHRLW 64 (261)
T ss_pred HHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCC--CcchhhHHHHHHHHHh
Confidence 4445677888888888763 33677888888766542 3567789999987753
No 14
>cd04450 DEP_RGS7-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction.
Probab=20.74 E-value=60 Score=23.54 Aligned_cols=10 Identities=50% Similarity=1.009 Sum_probs=8.8
Q ss_pred HHHHHHHhhC
Q 029234 188 KDIMQWLLQK 197 (197)
Q Consensus 188 KDI~Qwm~Q~ 197 (197)
+|+.|||+++
T Consensus 32 ~~~v~WL~~~ 41 (88)
T cd04450 32 KAIVQWLMDC 41 (88)
T ss_pred HHHHHHHHHC
Confidence 8999999875
No 15
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.63 E-value=65 Score=24.37 Aligned_cols=47 Identities=19% Similarity=0.355 Sum_probs=32.8
Q ss_pred hhccCCCChhHHHHHHHHhhH-------hhHHHHhhhhhhhhhhhhhhhhhhhHHH
Q 029234 28 RRVISPKRPRIRQFVHRRLRA-------VFDVALKFHKNIQERDIEVGRNVGNWIL 76 (197)
Q Consensus 28 rrlisp~~p~~r~F~~rRtr~-------vFdva~~vhkniq~rDievGrnlGN~iL 76 (197)
..++.+.||.++.|++++++. +=||-|++.+++..-| .+.++..|+.
T Consensus 9 ~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~--~~~~~~~wl~ 62 (164)
T PRK12547 9 KQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFE--MGTNLKAWLF 62 (164)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcC--CcccHHHHHH
Confidence 345567788888888888875 3367789998877644 3456776664
No 16
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=20.27 E-value=52 Score=26.75 Aligned_cols=50 Identities=14% Similarity=0.113 Sum_probs=33.6
Q ss_pred hccCCCChhHHHHHHHHhhHhh-------HHHHhhhhhhhhhhhhhhhhhhhHHHHh
Q 029234 29 RVISPKRPRIRQFVHRRLRAVF-------DVALKFHKNIQERDIEVGRNVGNWILRW 78 (197)
Q Consensus 29 rlisp~~p~~r~F~~rRtr~vF-------dva~~vhkniq~rDievGrnlGN~iLr~ 78 (197)
.++.-.+|.+..|+++.++.-. ||-+++.+++..-|-+-|.++..|+.++
T Consensus 52 ~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i 108 (227)
T TIGR02846 52 VLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARC 108 (227)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHH
Confidence 3455566777777777665422 5779999999887766666676666544
Done!