Query 040541
Match_columns 69
No_of_seqs 101 out of 115
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 09:25:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040541hhsearch_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 4.6E-47 9.9E-52 238.4 8.7 68 1-68 1-68 (68)
2 COG2864 FdnI Cytochrome b subu 81.3 1 2.2E-05 33.6 1.7 50 11-69 123-174 (218)
3 KOG4580 Component of vacuolar 57.0 6.8 0.00015 27.0 1.4 25 2-26 84-108 (112)
4 COG5264 VTC1 Vacuolar transpor 46.4 11 0.00024 26.4 1.1 22 3-24 100-121 (126)
5 PF07330 DUF1467: Protein of u 42.8 63 0.0014 20.8 4.1 47 11-57 16-70 (85)
6 PF13955 Fst_toxin: Toxin Fst, 36.2 27 0.00059 17.8 1.3 10 5-14 6-15 (21)
7 PF04483 DUF565: Protein of un 27.7 51 0.0011 19.7 1.8 54 2-63 3-57 (60)
8 PF09680 Tiny_TM_bacill: Prote 27.5 40 0.00086 17.7 1.1 9 10-18 9-17 (24)
9 COG3123 Uncharacterized protei 26.0 45 0.00096 22.4 1.4 14 17-30 65-78 (94)
10 PF05440 MtrB: Tetrahydrometha 25.8 1.1E+02 0.0024 20.4 3.2 36 21-56 59-94 (97)
11 COG3966 DltD Protein involved 24.4 54 0.0012 27.0 1.9 14 4-17 7-20 (415)
12 TIGR02615 spoVE stage V sporul 24.1 1.6E+02 0.0034 22.4 4.2 34 4-37 66-102 (354)
13 KOG4054 Uncharacterized conser 22.9 74 0.0016 23.6 2.2 14 43-56 40-53 (183)
14 TIGR01732 tiny_TM_bacill conse 21.0 62 0.0013 17.2 1.1 10 8-17 9-18 (26)
15 TIGR03257 met_CoM_red_bet meth 20.8 60 0.0013 26.8 1.5 29 21-50 108-139 (433)
16 TIGR02794 tolA_full TolA prote 20.7 94 0.002 24.1 2.5 15 41-55 5-19 (346)
17 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=4.6e-47 Score=238.44 Aligned_cols=68 Identities=65% Similarity=1.249 Sum_probs=67.4
Q ss_pred CCCchhHHHHHHHHHHhccceeEEecCCCceeeeecccchHHHHHHHHHHHHHHHHHHHHHhheeeec
Q 040541 1 MSDWGPVFVAVILFVLLSPGLLFQVPGRHRCVEFGNFQTSGAAIMVHSLLYFALVCVFFLAVKVHLYL 68 (69)
Q Consensus 1 M~DWgPV~i~vvLFvlLsPGLLfQ~PG~~r~veFgn~~Tsg~si~vHa~ifF~l~~if~~ai~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=81.26 E-value=1 Score=33.64 Aligned_cols=50 Identities=16% Similarity=0.423 Sum_probs=37.5
Q ss_pred HHHHHHhccceeE--EecCCCceeeeecccchHHHHHHHHHHHHHHHHHHHHHhheeeecC
Q 040541 11 VILFVLLSPGLLF--QVPGRHRCVEFGNFQTSGAAIMVHSLLYFALVCVFFLAVKVHLYLG 69 (69)
Q Consensus 11 vvLFvlLsPGLLf--Q~PG~~r~veFgn~~Tsg~si~vHa~ifF~l~~if~~ai~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-----PYFSIPLLRLSLLLHAFAAVILIFIII----VHIYMA 174 (218)
T ss_pred HHHHHHHHHHHHHHhhhcc-----ccccHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH
Confidence 3446666778777 6654 458899999999999998888766554 788864
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=57.04 E-value=6.8 Score=27.03 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=19.1
Q ss_pred CCchhHHHHHHHHHHhccceeEEec
Q 040541 2 SDWGPVFVAVILFVLLSPGLLFQVP 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 3599999999999998755544443
No 4
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=46.40 E-value=11 Score=26.43 Aligned_cols=22 Identities=32% Similarity=0.612 Sum_probs=17.0
Q ss_pred CchhHHHHHHHHHHhccceeEE
Q 040541 3 DWGPVFVAVILFVLLSPGLLFQ 24 (69)
Q Consensus 3 DWgPV~i~vvLFvlLsPGLLfQ 24 (69)
-|||.+++++|++.+.=-..+.
T Consensus 100 ~~GP~lv~vvL~valivNf~~~ 121 (126)
T COG5264 100 RLGPTLVCVVLLVALIVNFFLA 121 (126)
T ss_pred ccCCchhHHHHHHHHHHHHhhc
Confidence 5999999999999876444333
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=42.76 E-value=63 Score=20.76 Aligned_cols=47 Identities=17% Similarity=0.309 Sum_probs=29.3
Q ss_pred HHHHHHhccceeEE------ecCCCc--eeeeecccchHHHHHHHHHHHHHHHHH
Q 040541 11 VILFVLLSPGLLFQ------VPGRHR--CVEFGNFQTSGAAIMVHSLLYFALVCV 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 666655554444445555555544443
No 6
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=36.16 E-value=27 Score=17.79 Aligned_cols=10 Identities=40% Similarity=0.783 Sum_probs=8.3
Q ss_pred hhHHHHHHHH
Q 040541 5 GPVFVAVILF 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
>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=27.71 E-value=51 Score=19.70 Aligned_cols=54 Identities=19% Similarity=0.258 Sum_probs=27.4
Q ss_pred CCchhHHHHHHHHHHhccce-eEEecCCCceeeeecccchHHHHHHHHHHHHHHHHHHHHHhh
Q 040541 2 SDWGPVFVAVILFVLLSPGL-LFQVPGRHRCVEFGNFQTSGAAIMVHSLLYFALVCVFFLAVK 63 (69)
Q Consensus 2 ~DWgPV~i~vvLFvlLsPGL-LfQ~PG~~r~veFgn~~Tsg~si~vHa~ifF~l~~if~~ai~ 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 69999988877654321111 122222 2222333444455445566666665543
No 8
>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=27.47 E-value=40 Score=17.70 Aligned_cols=9 Identities=56% Similarity=0.962 Sum_probs=6.2
Q ss_pred HHHHHHHhc
Q 040541 10 AVILFVLLS 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 467888773
No 9
>COG3123 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.04 E-value=45 Score=22.45 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=12.0
Q ss_pred hccceeEEecCCCc
Q 040541 17 LSPGLLFQVPGRHR 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 46899999999983
No 10
>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=25.81 E-value=1.1e+02 Score=20.43 Aligned_cols=36 Identities=22% Similarity=0.170 Sum_probs=22.6
Q ss_pred eeEEecCCCceeeeecccchHHHHHHHHHHHHHHHH
Q 040541 21 LLFQVPGRHRCVEFGNFQTSGAAIMVHSLLYFALVC 56 (69)
Q Consensus 21 LLfQ~PG~~r~veFgn~~Tsg~si~vHa~ifF~l~~ 56 (69)
.+-..|||++.-+-..+-|+-.==++=.+++.++++
T Consensus 59 ~l~S~PgREg~~~~AG~~tn~fyGf~igL~i~~lva 94 (97)
T PF05440_consen 59 PLNSFPGREGTYYIAGIFTNMFYGFIIGLVIAGLVA 94 (97)
T ss_pred ccccCCCCccceeehhhhhhHHHHHHHHHHHHHHHH
Confidence 456789999888888777775444444444444433
No 11
>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=24.38 E-value=54 Score=26.97 Aligned_cols=14 Identities=50% Similarity=1.153 Sum_probs=12.5
Q ss_pred chhHHHHHHHHHHh
Q 040541 4 WGPVFVAVILFVLL 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 12
>TIGR02615 spoVE stage V sporulation protein E. This model represents an exception within the members of the FtsW model TIGR02614. This exception occurs only in endospore-forming genera such as Bacillus, Geobacillus, and Oceanobacillus. Like FtsW, members are found in a peptidoglycan operon context, but in these genera they part of a larger set of paralogs (not just the pair FtsW and RodA) and are required specifically for sporulation, not for viability.
Probab=24.09 E-value=1.6e+02 Score=22.39 Aligned_cols=34 Identities=24% Similarity=0.679 Sum_probs=21.6
Q ss_pred chhHHHHHHH---HHHhccceeEEecCCCceeeeecc
Q 040541 4 WGPVFVAVIL---FVLLSPGLLFQVPGRHRCVEFGNF 37 (69)
Q Consensus 4 WgPV~i~vvL---FvlLsPGLLfQ~PG~~r~veFgn~ 37 (69)
|++.+..+.+ ...+.||.--+..|.+|++++|.+
T Consensus 66 ~~~~~~~~~~~lLll~~~~~~g~~~~Ga~rWi~lg~~ 102 (354)
T TIGR02615 66 WAKMLMVICFVLLLLVLIPGVGMERNGARRWIGVGAF 102 (354)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcccCCcccceeCCCc
Confidence 4454443332 333447655688999999999865
No 13
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.88 E-value=74 Score=23.61 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHH
Q 040541 43 AIMVHSLLYFALVC 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 48899999987754
No 14
>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=20.99 E-value=62 Score=17.23 Aligned_cols=10 Identities=50% Similarity=0.909 Sum_probs=6.7
Q ss_pred HHHHHHHHHh
Q 040541 8 FVAVILFVLL 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 3446788876
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=20.79 E-value=60 Score=26.81 Aligned_cols=29 Identities=31% Similarity=0.476 Sum_probs=24.8
Q ss_pred eeEEecCCCce---eeeecccchHHHHHHHHHH
Q 040541 21 LLFQVPGRHRC---VEFGNFQTSGAAIMVHSLL 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
>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=20.67 E-value=94 Score=24.05 Aligned_cols=15 Identities=27% Similarity=0.352 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHH
Q 040541 41 GAAIMVHSLLYFALV 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 17
>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=20.22 E-value=34 Score=21.26 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=0.0
Q ss_pred CCchhH-HHH
Q 040541 2 SDWGPV-FVA 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!