Query 025415
Match_columns 253
No_of_seqs 44 out of 46
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 05:33:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025415.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025415hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0873 C-4 sterol methyl oxid 89.1 0.24 5.3E-06 46.6 2.1 57 189-245 10-67 (283)
2 PF09578 Spore_YabQ: Spore cor 64.5 7 0.00015 29.5 2.8 44 66-124 30-73 (80)
3 COG1058 CinA Predicted nucleot 52.6 5.4 0.00012 36.9 0.5 13 2-14 67-79 (255)
4 TIGR02893 spore_yabQ spore cor 45.6 20 0.00044 30.0 2.7 43 67-124 39-81 (130)
5 PF13807 GNVR: G-rich domain o 42.0 28 0.0006 26.0 2.8 19 112-130 60-78 (82)
6 PF11003 DUF2842: Protein of u 30.5 1.8E+02 0.0038 21.8 5.4 56 73-137 7-62 (62)
7 PF08551 DUF1751: Eukaryotic i 30.2 1.1E+02 0.0024 24.1 4.5 54 76-139 24-77 (99)
8 PF02249 MCR_alpha: Methyl-coe 28.8 22 0.00048 30.4 0.5 8 1-8 9-16 (127)
9 PF11931 DUF3449: Domain of un 26.4 22 0.00047 32.1 0.0 30 204-245 88-124 (196)
10 TIGR03462 CarR_dom_SF lycopene 26.4 63 0.0014 24.6 2.5 18 66-84 68-85 (89)
11 PF12841 YvrJ: YvrJ protein fa 25.5 44 0.00095 23.0 1.4 16 70-85 3-18 (38)
12 PRK03670 competence damage-ind 25.3 32 0.00069 31.4 0.8 15 1-15 66-80 (252)
13 PRK03673 hypothetical protein; 24.5 33 0.00072 33.4 0.9 14 1-14 66-79 (396)
14 PF07086 DUF1352: Protein of u 22.5 1.2E+02 0.0026 27.1 3.9 46 77-134 78-123 (186)
15 cd00885 cinA Competence-damage 21.8 44 0.00096 28.4 1.0 14 2-15 65-78 (170)
16 PF14475 Mso1_Sec1_bdg: Sec1-b 21.8 59 0.0013 23.0 1.4 12 236-247 23-34 (41)
17 PF03208 PRA1: PRA1 family pro 21.8 1.9E+02 0.0042 23.4 4.7 49 28-76 17-66 (153)
No 1
>KOG0873 consensus C-4 sterol methyl oxidase [Lipid transport and metabolism]
Probab=89.13 E-value=0.24 Score=46.62 Aligned_cols=57 Identities=18% Similarity=0.311 Sum_probs=43.4
Q ss_pred HHHHHHhhccCCCCccceeeehhhHHHHHHHHHHHHHHHHHhhhhhh-hHHHHHHHhh
Q 025415 189 WLKTEFSKAEGDNSASARRLYLGRALALANMAFWCFNLFGFLLPVYL-PKAFKKYYSA 245 (253)
Q Consensus 189 W~~~e~~k~~~~~~~~~~~~~fGR~LAvANl~yw~~NLFgFLiPvfL-PRAf~~Yy~~ 245 (253)
++.+-|.+-....+++.+..+.+-...+++++||++||..++|=+.. |+.|+||==.
T Consensus 10 flq~~W~~l~~~f~~d~~l~~~~~~~~~~~~~y~l~~lpf~~iD~t~~~~~~~rYKIQ 67 (283)
T KOG0873|consen 10 FLQPLWDYLYNTFSGDFLLLCVGGPFIVHELVYWLFCLPFIFIDVTNRPPFLRRYKIQ 67 (283)
T ss_pred HHHHHHHHHHhhCCCceEEEeechhHHHHHHHHHHhcchheEeecccCcchhhhhccC
Confidence 44444443333333677778888889999999999999999999998 9999998433
No 2
>PF09578 Spore_YabQ: Spore cortex protein YabQ (Spore_YabQ); InterPro: IPR019074 This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable.
Probab=64.50 E-value=7 Score=29.55 Aligned_cols=44 Identities=23% Similarity=0.581 Sum_probs=34.0
Q ss_pred CCCCchhHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccCCCccchhhhhhHHHHHHHHH
Q 025415 66 GMISAEDFAFVIFSLIYMFFLFKIAFPPPPQSKESSVFDPNTTILRVYVLVGAIIGLLL 124 (253)
Q Consensus 66 GlVpl~DlaF~~f~siYl~~Ls~~AFP~~~~~~~~~Vf~g~~klfq~Yv~~G~~VGLfl 124 (253)
-.+.++|++|-++++++++.+-- ..|.--+|.|+++|..+|..+
T Consensus 30 ~~~~i~DllfWl~~~~~~F~~l~---------------~~N~G~iR~Y~~lg~~~G~~l 73 (80)
T PF09578_consen 30 WLTGIEDLLFWLLAALIVFYFLY---------------WTNYGEIRFYIFLGILLGMIL 73 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---------------HccceeeeHHHHHHHHHHHHH
Confidence 34678999999999998884421 122468999999999999876
No 3
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=52.63 E-value=5.4 Score=36.95 Aligned_cols=13 Identities=38% Similarity=0.871 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCCC
Q 025415 2 SGGVGATSKDISL 14 (253)
Q Consensus 2 sggvgpt~~~i~l 14 (253)
|||.|||-.|||-
T Consensus 67 tGGLGPT~DDiT~ 79 (255)
T COG1058 67 TGGLGPTHDDLTA 79 (255)
T ss_pred CCCcCCCccHhHH
Confidence 8999999999974
No 4
>TIGR02893 spore_yabQ spore cortex biosynthesis protein YabQ. YabQ, a protein predicted to span the membrane several times, is found in exactly those genomes whose species perform sporulation in the style of Bacillus subtilis, Clostridium tetani, and others of the Firmicutes. Mutation of this sigma(E)-dependent gene blocks development of the spore cortex. The length of the C-terminal region, including some hydrophobic regions, is rather variable between members.
Probab=45.57 E-value=20 Score=29.98 Aligned_cols=43 Identities=26% Similarity=0.518 Sum_probs=32.8
Q ss_pred CCCchhHHHHHHHHHHHHHHHhhcCCCCCCCCCCcccCCCccchhhhhhHHHHHHHHH
Q 025415 67 MISAEDFAFVIFSLIYMFFLFKIAFPPPPQSKESSVFDPNTTILRVYVLVGAIIGLLL 124 (253)
Q Consensus 67 lVpl~DlaF~~f~siYl~~Ls~~AFP~~~~~~~~~Vf~g~~klfq~Yv~~G~~VGLfl 124 (253)
++.+||++|=++++++++.+-- ..|.--+|.|+.+|..+|..+
T Consensus 39 ~~~ieDilFWi~~~~~vF~~L~---------------~~N~G~lR~Y~~lg~~~G~~l 81 (130)
T TIGR02893 39 LVFIEDILFWIVQALIVFYFLL---------------YVNEGEIRFYVFLALLCGLAI 81 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---------------HhccchhhHHHHHHHHHHHHH
Confidence 4667999999999988874321 112357899999999999876
No 5
>PF13807 GNVR: G-rich domain on putative tyrosine kinase
Probab=41.96 E-value=28 Score=25.97 Aligned_cols=19 Identities=26% Similarity=0.600 Sum_probs=16.3
Q ss_pred hhhhHHHHHHHHHHHHHHh
Q 025415 112 VYVLVGAIIGLLLPIAYIL 130 (253)
Q Consensus 112 ~Yv~~G~~VGLflPlaYIL 130 (253)
+.+.+|+++|+++++++++
T Consensus 60 lil~l~~~~Gl~lgi~~~~ 78 (82)
T PF13807_consen 60 LILALGLFLGLILGIGLAF 78 (82)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3467999999999999986
No 6
>PF11003 DUF2842: Protein of unknown function (DUF2842); InterPro: IPR021265 This bacterial family of proteins have no known function.
Probab=30.50 E-value=1.8e+02 Score=21.77 Aligned_cols=56 Identities=11% Similarity=0.005 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCcccCCCccchhhhhhHHHHHHHHHHHHHHhhhhcccc
Q 025415 73 FAFVIFSLIYMFFLFKIAFPPPPQSKESSVFDPNTTILRVYVLVGAIIGLLLPIAYILEGIFEGD 137 (253)
Q Consensus 73 laF~~f~siYl~~Ls~~AFP~~~~~~~~~Vf~g~~klfq~Yv~~G~~VGLflPlaYILgGf~~GD 137 (253)
++..++..+|...-..++-....+. +.+.|+=.-+.+-++=.+|+--++.+.-++|
T Consensus 7 v~ll~~l~vY~~~a~~l~~~~~~~~---------~~~~~l~~Yvv~G~~WvlP~~~li~Wm~~~D 62 (62)
T PF11003_consen 7 VLLLVGLPVYAVLAVTLADWLLARW---------PWWVQLIYYVVLGLLWVLPAKPLIRWMERPD 62 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCc---------hHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 5677888999987777665432111 4677654444444566799999999999988
No 7
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=30.19 E-value=1.1e+02 Score=24.12 Aligned_cols=54 Identities=24% Similarity=0.373 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHhhcCCCCCCCCCCcccCCCccchhhhhhHHHHHHHHHHHHHHhhhhcccchh
Q 025415 76 VIFSLIYMFFLFKIAFPPPPQSKESSVFDPNTTILRVYVLVGAIIGLLLPIAYILEGIFEGDKE 139 (253)
Q Consensus 76 ~~f~siYl~~Ls~~AFP~~~~~~~~~Vf~g~~klfq~Yv~~G~~VGLflPlaYILgGf~~GD~~ 139 (253)
.++....++..+|..=|.-+. .++++.+.+++++.++...+.|++.....+|.+
T Consensus 24 ~l~~~~~l~~~g~~lE~~WGs----------~E~lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~ 77 (99)
T PF08551_consen 24 LLFSLLTLFYGGRYLEPIWGS----------REFLKFILVVNVITNLLTFLLYLLLYAITGNES 77 (99)
T ss_pred HHHHHHHHHHhhHHHHHhcCh----------HHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCc
Confidence 445666677788887776532 589999999999999999999999999998877
No 8
>PF02249 MCR_alpha: Methyl-coenzyme M reductase alpha subunit, C-terminal domain; InterPro: IPR009047 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the C-terminal domain of the alpha subunit, which is comprised of an all-alpha multi-helical bundle. ; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity, 0015948 methanogenesis; PDB: 3SQG_A 1HBU_D 3M2V_D 3POT_A 3M2U_A 1HBN_A 1HBO_A 3M30_A 3M2R_A 3M1V_A ....
Probab=28.83 E-value=22 Score=30.43 Aligned_cols=8 Identities=88% Similarity=1.244 Sum_probs=4.4
Q ss_pred CCCCCCCC
Q 025415 1 MSGGVGAT 8 (253)
Q Consensus 1 msggvgpt 8 (253)
||||||=|
T Consensus 9 msGGVGFT 16 (127)
T PF02249_consen 9 MSGGVGFT 16 (127)
T ss_dssp TS-TT--H
T ss_pred ccCCcccc
Confidence 89999965
No 9
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=26.45 E-value=22 Score=32.08 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=0.0
Q ss_pred cceeeehhhHHHH-------HHHHHHHHHHHHHhhhhhhhHHHHHHHhh
Q 025415 204 SARRLYLGRALAL-------ANMAFWCFNLFGFLLPVYLPKAFKKYYSA 245 (253)
Q Consensus 204 ~~~~~~fGR~LAv-------ANl~yw~~NLFgFLiPvfLPRAf~~Yy~~ 245 (253)
-..|+|==..|.+ .|..||+ ||||+|+|++
T Consensus 88 IPyWLYKLhGL~~ey~CEICGN~~Y~G------------rkaFekHF~E 124 (196)
T PF11931_consen 88 IPYWLYKLHGLGVEYKCEICGNQSYKG------------RKAFEKHFQE 124 (196)
T ss_dssp -------------------------------------------------
T ss_pred ccHHHHHHhCCCCeeeeEeCCCcceec------------HHHHHHhcCh
Confidence 3677776666654 6999999 9999999998
No 10
>TIGR03462 CarR_dom_SF lycopene cyclase domain. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly.
Probab=26.36 E-value=63 Score=24.59 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=12.4
Q ss_pred CCCCchhHHHHHHHHHHHH
Q 025415 66 GMISAEDFAFVIFSLIYMF 84 (253)
Q Consensus 66 GlVpl~DlaF~~f~siYl~ 84 (253)
|-+|+||.+| .....++.
T Consensus 68 ~~lPiEE~~F-f~~~~~~~ 85 (89)
T TIGR03462 68 GDLPIEEFLF-FLLTPLLT 85 (89)
T ss_pred cCCCHHHHHH-HHHHHHHH
Confidence 4689999999 44444443
No 11
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=25.52 E-value=44 Score=23.03 Aligned_cols=16 Identities=25% Similarity=0.492 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHH
Q 025415 70 AEDFAFVIFSLIYMFF 85 (253)
Q Consensus 70 l~DlaF~~f~siYl~~ 85 (253)
+.|..||++.++|++.
T Consensus 3 I~n~GFPi~va~yLL~ 18 (38)
T PF12841_consen 3 ISNVGFPIAVAIYLLV 18 (38)
T ss_pred hhhcCcHHHHHHHHHH
Confidence 4688999999999974
No 12
>PRK03670 competence damage-inducible protein A; Provisional
Probab=25.32 E-value=32 Score=31.40 Aligned_cols=15 Identities=40% Similarity=0.871 Sum_probs=12.7
Q ss_pred CCCCCCCCCCCCCCC
Q 025415 1 MSGGVGATSKDISLP 15 (253)
Q Consensus 1 msggvgpt~~~i~lp 15 (253)
.+||.|||-.|++--
T Consensus 66 ttGGlGpt~dD~T~e 80 (252)
T PRK03670 66 ISGGLGPTHDDVTML 80 (252)
T ss_pred ECCCccCCCCCchHH
Confidence 489999999999754
No 13
>PRK03673 hypothetical protein; Provisional
Probab=24.54 E-value=33 Score=33.41 Aligned_cols=14 Identities=50% Similarity=0.907 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCCC
Q 025415 1 MSGGVGATSKDISL 14 (253)
Q Consensus 1 msggvgpt~~~i~l 14 (253)
.|||+|||..|++-
T Consensus 66 ~tGGlGpt~dD~t~ 79 (396)
T PRK03673 66 VNGGLGPTSDDLSA 79 (396)
T ss_pred EcCCCCCCCcccHH
Confidence 38999999999874
No 14
>PF07086 DUF1352: Protein of unknown function (DUF1352); InterPro: IPR009787 This family consists of several hypothetical eukaryotic proteins of around 190 residues in length. The function of this family is unknown.
Probab=22.52 E-value=1.2e+02 Score=27.08 Aligned_cols=46 Identities=22% Similarity=0.335 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCcccCCCccchhhhhhHHHHHHHHHHHHHHhhhhc
Q 025415 77 IFSLIYMFFLFKIAFPPPPQSKESSVFDPNTTILRVYVLVGAIIGLLLPIAYILEGIF 134 (253)
Q Consensus 77 ~f~siYl~~Ls~~AFP~~~~~~~~~Vf~g~~klfq~Yv~~G~~VGLflPlaYILgGf~ 134 (253)
...++-..+++..++|..+ .+.++.|.+-..+.|+ +|+.|=..+.+
T Consensus 78 ~~lS~ip~~~G~~s~~rN~-----------i~~l~~y~~~~~~~gl-~pl~~g~~~~~ 123 (186)
T PF07086_consen 78 WCLSLIPSLLGLLSLRRNN-----------ISLLRLYMIGSSLFGL-LPLIYGAMYYF 123 (186)
T ss_pred HHHHHHHHHHHHHhcccch-----------HHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 3445666678888888642 2689999875555566 88888665544
No 15
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=21.84 E-value=44 Score=28.42 Aligned_cols=14 Identities=36% Similarity=0.774 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCCCC
Q 025415 2 SGGVGATSKDISLP 15 (253)
Q Consensus 2 sggvgpt~~~i~lp 15 (253)
+||+|||..|++-.
T Consensus 65 tGG~G~t~~D~t~e 78 (170)
T cd00885 65 TGGLGPTHDDLTRE 78 (170)
T ss_pred CCCCCCCCCChHHH
Confidence 79999999888754
No 16
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=21.80 E-value=59 Score=23.02 Aligned_cols=12 Identities=33% Similarity=0.946 Sum_probs=9.8
Q ss_pred hHHHHHHHhhcC
Q 025415 236 PKAFKKYYSANG 247 (253)
Q Consensus 236 PRAf~~Yy~~~~ 247 (253)
=|+|++||.+++
T Consensus 23 ~r~l~~yY~~k~ 34 (41)
T PF14475_consen 23 HRVLRKYYTEKG 34 (41)
T ss_pred HHHHHHHHHHcC
Confidence 489999998864
No 17
>PF03208 PRA1: PRA1 family protein; InterPro: IPR004895 This family includes yeast hypothetical proteins and the uncharacterised rat prenylated rab acceptor protein PRA1.
Probab=21.76 E-value=1.9e+02 Score=23.38 Aligned_cols=49 Identities=14% Similarity=0.124 Sum_probs=29.2
Q ss_pred CCccCCCCCcCC-CCccccccchhhhhHHHHHHHHHhhcCCCCchhHHHH
Q 025415 28 PTSFQSTKSTAT-PSKASSNFLSFRQLNALAVVTVFAASGMISAEDFAFV 76 (253)
Q Consensus 28 ~~~~~~~~~~~~-~~~~~~~~~s~~qL~~la~iiVfsaSGlVpl~DlaF~ 76 (253)
.++++.|+|... .++...|+..+..-.++-+++++....+..|..++..
T Consensus 17 ~~~fs~P~~~~~~~~Ri~~Nl~~F~~NY~~i~~~~~~~~ll~~P~~l~~~ 66 (153)
T PF03208_consen 17 TSRFSVPSSFSEAKSRIKRNLSYFQTNYLLIFLLLFLIFLLTNPFFLLVL 66 (153)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666644332 5555667777777777777777666666655555433
Done!