Query 035243
Match_columns 69
No_of_seqs 105 out of 115
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 10:21:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035243.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035243hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11820 DUF3339: Protein of u 100.0 3.2E-47 6.8E-52 239.2 8.1 68 1-68 1-68 (68)
2 COG2864 FdnI Cytochrome b subu 83.7 0.82 1.8E-05 34.1 2.0 50 11-69 123-174 (218)
3 KOG4580 Component of vacuolar 56.7 7 0.00015 27.0 1.4 25 2-26 84-108 (112)
4 COG5264 VTC1 Vacuolar transpor 46.3 11 0.00024 26.4 1.1 21 3-23 100-120 (126)
5 PF07330 DUF1467: Protein of u 40.6 65 0.0014 20.7 3.9 47 11-57 16-70 (85)
6 PF13955 Fst_toxin: Toxin Fst, 35.0 26 0.00057 17.8 1.2 10 5-14 6-15 (21)
7 PF09680 Tiny_TM_bacill: Prote 30.4 33 0.00071 18.0 1.1 9 10-18 9-17 (24)
8 COG3123 Uncharacterized protei 28.6 37 0.00081 22.8 1.4 14 17-30 65-78 (94)
9 PF04483 DUF565: Protein of un 27.1 50 0.0011 19.7 1.7 54 2-63 3-57 (60)
10 COG3966 DltD Protein involved 25.8 47 0.001 27.3 1.8 14 4-17 7-20 (415)
11 PF05398 PufQ: PufQ cytochrome 25.7 55 0.0012 21.0 1.7 15 50-66 23-37 (73)
12 PF05440 MtrB: Tetrahydrometha 24.7 1.1E+02 0.0025 20.3 3.2 35 21-55 59-93 (97)
13 TIGR01732 tiny_TM_bacill conse 23.7 51 0.0011 17.6 1.1 10 8-17 9-18 (26)
14 KOG4054 Uncharacterized conser 22.8 74 0.0016 23.6 2.2 14 43-56 40-53 (183)
15 TIGR03257 met_CoM_red_bet meth 21.8 54 0.0012 27.1 1.4 29 21-50 108-139 (433)
16 PRK00753 psbL photosystem II r 21.8 1.1E+02 0.0025 17.6 2.4 19 47-65 16-34 (39)
17 TIGR02794 tolA_full TolA prote 20.7 94 0.002 24.1 2.5 15 41-55 5-19 (346)
18 PF08523 MBF1: Multiprotein br 20.2 34 0.00074 21.3 0.0 9 2-10 1-10 (71)
No 1
>PF11820 DUF3339: Protein of unknown function (DUF3339); InterPro: IPR021775 This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length.
Probab=100.00 E-value=3.2e-47 Score=239.20 Aligned_cols=68 Identities=68% Similarity=1.271 Sum_probs=67.4
Q ss_pred CCCcchHHHHHHHHHHhccceeEEecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 035243 1 MSDWGPVFVGVVLFILLSPGLLIQVPGRNRFFEFGNFQTSGASILVHSILYFALMCIFLLAIGVHMYL 68 (69)
Q Consensus 1 M~DWgPV~i~vvLFvlLsPGLLfQ~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~vai~vHiy~ 68 (69)
|+|||||+||++||++||||||||+|||+|++|||||||||+||+|||++||+++++|++|+++|+|+
T Consensus 1 M~DWgpv~i~vvLFvlLsPGLLfqlPG~~r~veFgn~~Tsg~si~vHa~iff~l~~i~~va~~vhiy~ 68 (68)
T PF11820_consen 1 MADWGPVLIAVVLFVLLSPGLLFQLPGRGRVVEFGNMKTSGKSILVHALIFFALFTIFLVAIGVHIYT 68 (68)
T ss_pred CCcchhHHHHHHHHHHhCCceEEEecCCCceEEEcCCcchHHHHHHHHHHHHHHHHHHHHHheeEeeC
Confidence 89999999999999999999999999999999999999999999999999999999999999999996
No 2
>COG2864 FdnI Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]
Probab=83.67 E-value=0.82 Score=34.11 Aligned_cols=50 Identities=24% Similarity=0.428 Sum_probs=37.6
Q ss_pred HHHHHHhccceeE--EecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHhhccccC
Q 035243 11 VVLFILLSPGLLI--QVPGRNRFFEFGNFQTSGASILVHSILYFALMCIFLLAIGVHMYLG 69 (69)
Q Consensus 11 vvLFvlLsPGLLf--Q~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~vai~vHiy~g 69 (69)
+..++++--|+.. |.|. .++++.+...|.++|+.--+.+.+++ .+|+|++
T Consensus 123 l~~~~l~iTGivmw~~y~~-----~~~~i~~~r~s~l~h~~~a~~l~~~~----~vHiy~a 174 (218)
T COG2864 123 LAIVLLLITGIVIWRPYFA-----PYFSIPLLRLSLLLHAFAAVILIFII----IVHIYMA 174 (218)
T ss_pred HHHHHHHHHHHHHHhhhcc-----ccccHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence 3446666777777 6654 45889999999999999888876654 4788864
No 3
>KOG4580 consensus Component of vacuolar transporter chaperone (Vtc) involved in vacuole fusion [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=56.73 E-value=7 Score=26.97 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=18.9
Q ss_pred CCcchHHHHHHHHHHhccceeEEec
Q 035243 2 SDWGPVFVGVVLFILLSPGLLIQVP 26 (69)
Q Consensus 2 ~DWgPV~i~vvLFvlLsPGLLfQ~P 26 (69)
.-|||.+++++||+.++--..+.++
T Consensus 84 d~~GP~~v~~vl~valivN~~~~f~ 108 (112)
T KOG4580|consen 84 DRLGPTLVCVVLLVALIVNFILAFK 108 (112)
T ss_pred CcccchHHHHHHHHHHHHHHHHhhh
Confidence 3599999999999988755444443
No 4
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=46.34 E-value=11 Score=26.36 Aligned_cols=21 Identities=33% Similarity=0.618 Sum_probs=16.5
Q ss_pred CcchHHHHHHHHHHhccceeE
Q 035243 3 DWGPVFVGVVLFILLSPGLLI 23 (69)
Q Consensus 3 DWgPV~i~vvLFvlLsPGLLf 23 (69)
-|||.+++++|++-+.=-..+
T Consensus 100 ~~GP~lv~vvL~valivNf~~ 120 (126)
T COG5264 100 RLGPTLVCVVLLVALIVNFFL 120 (126)
T ss_pred ccCCchhHHHHHHHHHHHHhh
Confidence 599999999999987644333
No 5
>PF07330 DUF1467: Protein of unknown function (DUF1467); InterPro: IPR009935 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=40.59 E-value=65 Score=20.69 Aligned_cols=47 Identities=21% Similarity=0.337 Sum_probs=28.7
Q ss_pred HHHHHHhccceeEE------ecCCCc--eeEeecccchHHHHHHHHHHHHHHHHH
Q 035243 11 VVLFILLSPGLLIQ------VPGRNR--FFEFGNFQTSGASILVHSILYFALMCI 57 (69)
Q Consensus 11 vvLFvlLsPGLLfQ------~PG~~r--~veFgn~~Tsg~si~VHa~ifF~l~~i 57 (69)
.+||++|-=|+==| .||... +..+.=.|--...-++=+++|.+.+.+
T Consensus 16 ~~lF~vLP~gvrtq~E~g~vv~Gt~~sAP~~~~l~rk~~~TTiiaavi~~~~~~~ 70 (85)
T PF07330_consen 16 IVLFAVLPFGVRTQDEAGEVVPGTDPSAPANPRLKRKALITTIIAAVIFAIIYLI 70 (85)
T ss_pred HHHHHHccCCccccCcCCCcCCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899998888666 677765 666655544444444555555444433
No 6
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=35.03 E-value=26 Score=17.83 Aligned_cols=10 Identities=60% Similarity=0.996 Sum_probs=8.2
Q ss_pred chHHHHHHHH
Q 035243 5 GPVFVGVVLF 14 (69)
Q Consensus 5 gPV~i~vvLF 14 (69)
||+++|++|=
T Consensus 6 aPi~VGvvl~ 15 (21)
T PF13955_consen 6 APIVVGVVLT 15 (21)
T ss_dssp HHHHHHHHHH
T ss_pred hhHHHHHHHH
Confidence 7999999874
No 7
>PF09680 Tiny_TM_bacill: Protein of unknown function (Tiny_TM_bacill); InterPro: IPR010070 This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=30.41 E-value=33 Score=18.02 Aligned_cols=9 Identities=78% Similarity=0.870 Sum_probs=6.3
Q ss_pred HHHHHHHhc
Q 035243 10 GVVLFILLS 18 (69)
Q Consensus 10 ~vvLFvlLs 18 (69)
-++||+||.
T Consensus 9 ivVLFILLi 17 (24)
T PF09680_consen 9 IVVLFILLI 17 (24)
T ss_pred HHHHHHHHH
Confidence 467888873
No 8
>COG3123 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.60 E-value=37 Score=22.83 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=12.1
Q ss_pred hccceeEEecCCCc
Q 035243 17 LSPGLLIQVPGRNR 30 (69)
Q Consensus 17 LsPGLLfQ~PG~~r 30 (69)
-.||=-||+||+++
T Consensus 65 ~~~Ge~F~VpgnS~ 78 (94)
T COG3123 65 YTAGEVFNVPGNSE 78 (94)
T ss_pred ecCCceEEcCCCCe
Confidence 46999999999984
No 9
>PF04483 DUF565: Protein of unknown function (DUF565); InterPro: IPR007572 This family represents Ycf20, it is found in cyanobacteria and is also encoded in plant and algal chloroplasts; its function is unknown. As the family is exclusively found in phototrophic organisms it may therefore play a role in photosynthesis.
Probab=27.07 E-value=50 Score=19.73 Aligned_cols=54 Identities=19% Similarity=0.247 Sum_probs=26.9
Q ss_pred CCcchHHHHHHHHHHhccc-eeEEecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHh
Q 035243 2 SDWGPVFVGVVLFILLSPG-LLIQVPGRNRFFEFGNFQTSGASILVHSILYFALMCIFLLAIG 63 (69)
Q Consensus 2 ~DWgPV~i~vvLFvlLsPG-LLfQ~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~vai~ 63 (69)
+||.|++.+.+++..=.=+ +...-|. +.+.+-.--++..+=-..++.+|+=|.+
T Consensus 3 g~wD~i~a~~iv~~~E~i~~l~Y~~~~--------~~~~~~~~~~lN~~KiGl~YgLfleAFK 57 (60)
T PF04483_consen 3 GDWDVIAAAIIVLFIEVISRLRYSKPK--------KKRKSLLVELLNNFKIGLLYGLFLEAFK 57 (60)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhcccc--------ccccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 6999998887765431111 1122222 2222333344444444566666665543
No 10
>COG3966 DltD Protein involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=25.82 E-value=47 Score=27.32 Aligned_cols=14 Identities=50% Similarity=1.151 Sum_probs=12.5
Q ss_pred cchHHHHHHHHHHh
Q 035243 4 WGPVFVGVVLFILL 17 (69)
Q Consensus 4 WgPV~i~vvLFvlL 17 (69)
-||++||.+||+++
T Consensus 7 fGPlliA~alf~~~ 20 (415)
T COG3966 7 FGPLLIAFALFILL 20 (415)
T ss_pred hhHHHHHHHHHHHH
Confidence 58999999999876
No 11
>PF05398 PufQ: PufQ cytochrome subunit; InterPro: IPR008800 This family consists of bacterial PufQ proteins. PufQ is required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes [].; GO: 0015979 photosynthesis, 0030494 bacteriochlorophyll biosynthetic process
Probab=25.70 E-value=55 Score=20.97 Aligned_cols=15 Identities=53% Similarity=0.868 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHhhcc
Q 035243 50 LYFALMCIFLLAIGVHM 66 (69)
Q Consensus 50 ifF~l~~if~vai~vHi 66 (69)
+||++ ||+.|+..+.
T Consensus 23 vYFal--IflaAlP~a~ 37 (73)
T PF05398_consen 23 VYFAL--IFLAALPFAT 37 (73)
T ss_pred HHHHH--HHHHHHHHHH
Confidence 78888 7777776553
No 12
>PF05440 MtrB: Tetrahydromethanopterin S-methyltransferase subunit B; InterPro: IPR008690 The N5-methyltetrahydromethanopterin: coenzyme M (2.1.1.86 from EC) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [].; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=24.68 E-value=1.1e+02 Score=20.34 Aligned_cols=35 Identities=17% Similarity=0.199 Sum_probs=21.6
Q ss_pred eeEEecCCCceeEeecccchHHHHHHHHHHHHHHH
Q 035243 21 LLIQVPGRNRFFEFGNFQTSGASILVHSILYFALM 55 (69)
Q Consensus 21 LLfQ~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~ 55 (69)
.+=..|||.+.-+-..+-|+-.==++=.+++.+++
T Consensus 59 ~l~S~PgREg~~~~AG~~tn~fyGf~igL~i~~lv 93 (97)
T PF05440_consen 59 PLNSFPGREGTYYIAGIFTNMFYGFIIGLVIAGLV 93 (97)
T ss_pred ccccCCCCccceeehhhhhhHHHHHHHHHHHHHHH
Confidence 45578999988887777776543333344443333
No 13
>TIGR01732 tiny_TM_bacill conserved hypothetical tiny transmembrane protein. This model represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=23.69 E-value=51 Score=17.57 Aligned_cols=10 Identities=70% Similarity=0.826 Sum_probs=6.8
Q ss_pred HHHHHHHHHh
Q 035243 8 FVGVVLFILL 17 (69)
Q Consensus 8 ~i~vvLFvlL 17 (69)
..-++||++|
T Consensus 9 ~livVLFILL 18 (26)
T TIGR01732 9 ALIVVLFILL 18 (26)
T ss_pred HHHHHHHHHH
Confidence 3456788876
No 14
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.81 E-value=74 Score=23.60 Aligned_cols=14 Identities=21% Similarity=0.693 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHH
Q 035243 43 SILVHSILYFALMC 56 (69)
Q Consensus 43 si~VHa~ifF~l~~ 56 (69)
-|+||++||+...+
T Consensus 40 lifvh~lI~v~mla 53 (183)
T KOG4054|consen 40 LIFVHALIWVLMLA 53 (183)
T ss_pred HHHHHHHHHHHHHH
Confidence 48899999987654
No 15
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=21.80 E-value=54 Score=27.08 Aligned_cols=29 Identities=34% Similarity=0.524 Sum_probs=24.8
Q ss_pred eeEEecCCCce---eEeecccchHHHHHHHHHH
Q 035243 21 LLIQVPGRNRF---FEFGNFQTSGASILVHSIL 50 (69)
Q Consensus 21 LLfQ~PG~~r~---veFgn~~Tsg~si~VHa~i 50 (69)
+|.|+|-+ |. -|+..--|+..+-++|++|
T Consensus 108 llvqvPs~-Ri~~aa~y~v~~~~~~~A~~~aii 139 (433)
T TIGR03257 108 LLIQVPSS-RLIAAAEYSVATLVTAAAVTQTII 139 (433)
T ss_pred EEEeCChH-hhhhhcchhHHHHHHHHHHHHHHH
Confidence 78999954 65 7888889999999999987
No 16
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=21.79 E-value=1.1e+02 Score=17.63 Aligned_cols=19 Identities=32% Similarity=0.628 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q 035243 47 HSILYFALMCIFLLAIGVH 65 (69)
Q Consensus 47 Ha~ifF~l~~if~vai~vH 65 (69)
.|-+|.+++.||++|+-.-
T Consensus 16 RTSLy~GlLlifvl~vLFs 34 (39)
T PRK00753 16 RTSLYLGLLLVFVLGILFS 34 (39)
T ss_pred hhhHHHHHHHHHHHHHHHH
Confidence 3458999999998887543
No 17
>TIGR02794 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB.
Probab=20.72 E-value=94 Score=24.06 Aligned_cols=15 Identities=33% Similarity=0.363 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHH
Q 035243 41 GASILVHSILYFALM 55 (69)
Q Consensus 41 g~si~VHa~ifF~l~ 55 (69)
..|+++|.+++.+|+
T Consensus 5 ~lSv~lHvlLi~lL~ 19 (346)
T TIGR02794 5 LLSLLLHILLLGLLI 19 (346)
T ss_pred HHHHHHHHHHHHHHH
Confidence 579999998886663
No 18
>PF08523 MBF1: Multiprotein bridging factor 1; InterPro: IPR013729 This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex []. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC []. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (IPR001387 from INTERPRO) is found to its C terminus. ; PDB: 1X57_A.
Probab=20.21 E-value=34 Score=21.26 Aligned_cols=9 Identities=56% Similarity=1.479 Sum_probs=0.0
Q ss_pred CCcchH-HHH
Q 035243 2 SDWGPV-FVG 10 (69)
Q Consensus 2 ~DWgPV-~i~ 10 (69)
+||-|| +|.
T Consensus 1 qDWd~vtvi~ 10 (71)
T PF08523_consen 1 QDWDPVTVIG 10 (71)
T ss_dssp ----------
T ss_pred CCCcccceec
Confidence 588888 553
Done!