Query 035259
Match_columns 69
No_of_seqs 91 out of 115
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 10:28:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035259.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035259hhsearch_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 5.9E-47 1.3E-51 237.9 8.2 68 1-68 1-68 (68)
2 COG2864 FdnI Cytochrome b subu 82.1 1.2 2.6E-05 33.3 2.3 50 11-69 123-174 (218)
3 KOG4580 Component of vacuolar 55.8 7.2 0.00016 26.9 1.3 25 2-26 84-108 (112)
4 COG5264 VTC1 Vacuolar transpor 44.5 12 0.00026 26.2 1.0 22 3-24 100-121 (126)
5 PF07330 DUF1467: Protein of u 41.9 59 0.0013 20.9 3.9 47 11-57 16-70 (85)
6 PF13955 Fst_toxin: Toxin Fst, 34.2 32 0.00069 17.5 1.4 10 5-14 6-15 (21)
7 PF04483 DUF565: Protein of un 27.9 51 0.0011 19.7 1.8 54 2-63 3-57 (60)
8 COG3123 Uncharacterized protei 27.0 41 0.00089 22.6 1.4 14 17-30 65-78 (94)
9 PF09680 Tiny_TM_bacill: Prote 26.7 42 0.0009 17.6 1.1 9 10-18 9-17 (24)
10 COG3966 DltD Protein involved 25.2 52 0.0011 27.1 1.9 14 4-17 7-20 (415)
11 PF05440 MtrB: Tetrahydrometha 24.5 1.2E+02 0.0025 20.3 3.2 34 21-54 59-92 (97)
12 KOG4054 Uncharacterized conser 23.8 69 0.0015 23.8 2.2 14 43-56 40-53 (183)
13 TIGR02615 spoVE stage V sporul 23.1 1.8E+02 0.0038 22.1 4.3 34 4-37 66-102 (354)
14 PF05398 PufQ: PufQ cytochrome 21.2 77 0.0017 20.3 1.7 14 50-65 23-36 (73)
15 TIGR02794 tolA_full TolA prote 20.6 95 0.0021 24.0 2.5 15 41-55 5-19 (346)
16 TIGR01732 tiny_TM_bacill conse 20.4 65 0.0014 17.1 1.1 10 8-17 9-18 (26)
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=5.9e-47 Score=237.88 Aligned_cols=68 Identities=85% Similarity=1.358 Sum_probs=67.4
Q ss_pred CCCchHHHHHHHHHHHhccceeEeecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 035259 1 MADWGPVVIAVVLFVLLSPGLLFQLPGRNRVVEFGNMHTSGLSILVHTIIFFGLVTIFLIAIGVHIHT 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=82.14 E-value=1.2 Score=33.27 Aligned_cols=50 Identities=24% Similarity=0.337 Sum_probs=37.4
Q ss_pred HHHHHHhccceeE--eecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHhhccccC
Q 035259 11 VVLFVLLSPGLLF--QLPGRNRVVEFGNMHTSGLSILVHTIIFFGLVTIFLIAIGVHIHTG 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-----PYFSIPLLRLSLLLHAFAAVILIFII----IVHIYMA 174 (218)
T ss_pred HHHHHHHHHHHHHHhhhcc-----ccccHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence 3446666677777 6664 45889999999999999888776554 4798864
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=55.78 E-value=7.2 Score=26.90 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=19.3
Q ss_pred CCchHHHHHHHHHHHhccceeEeec
Q 035259 2 ADWGPVVIAVVLFVLLSPGLLFQLP 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 3599999999999998765554444
No 4
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=44.47 E-value=12 Score=26.25 Aligned_cols=22 Identities=32% Similarity=0.609 Sum_probs=17.1
Q ss_pred CchHHHHHHHHHHHhccceeEe
Q 035259 3 DWGPVVIAVVLFVLLSPGLLFQ 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 5999999999999886444433
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=41.89 E-value=59 Score=20.87 Aligned_cols=47 Identities=23% Similarity=0.372 Sum_probs=29.7
Q ss_pred HHHHHHhccceeEe------ecCCCc--eeEeecccchHHHHHHHHHHHHHHHHH
Q 035259 11 VVLFVLLSPGLLFQ------LPGRNR--VVEFGNMHTSGLSILVHTIIFFGLVTI 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 666655554444555555555554443
No 6
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=34.17 E-value=32 Score=17.53 Aligned_cols=10 Identities=50% Similarity=0.893 Sum_probs=8.3
Q ss_pred hHHHHHHHHH
Q 035259 5 GPVVIAVVLF 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 7999998874
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=27.92 E-value=51 Score=19.66 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=27.8
Q ss_pred CCchHHHHHHHHHHHhccce-eEeecCCCceeEeecccchHHHHHHHHHHHHHHHHHHHHHHh
Q 035259 2 ADWGPVVIAVVLFVLLSPGL-LFQLPGRNRVVEFGNMHTSGLSILVHTIIFFGLVTIFLIAIG 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 222222 2222334444555555566666665543
No 8
>COG3123 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.03 E-value=41 Score=22.60 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=12.0
Q ss_pred hccceeEeecCCCc
Q 035259 17 LSPGLLFQLPGRNR 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 46999999999983
No 9
>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=26.69 E-value=42 Score=17.61 Aligned_cols=9 Identities=67% Similarity=0.973 Sum_probs=6.2
Q ss_pred HHHHHHHhc
Q 035259 10 AVVLFVLLS 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 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=25.23 E-value=52 Score=27.06 Aligned_cols=14 Identities=57% Similarity=1.191 Sum_probs=12.5
Q ss_pred chHHHHHHHHHHHh
Q 035259 4 WGPVVIAVVLFVLL 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 58999999999875
No 11
>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=24.48 E-value=1.2e+02 Score=20.31 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=21.3
Q ss_pred eeEeecCCCceeEeecccchHHHHHHHHHHHHHH
Q 035259 21 LLFQLPGRNRVVEFGNMHTSGLSILVHTIIFFGL 54 (69)
Q Consensus 21 LLfQ~PG~~r~veFgn~~Tsg~si~vHa~ifF~l 54 (69)
.+=..|||++.-+-..+-|+-.==++=.+++.++
T Consensus 59 ~l~S~PgREg~~~~AG~~tn~fyGf~igL~i~~l 92 (97)
T PF05440_consen 59 PLNSFPGREGTYYIAGIFTNMFYGFIIGLVIAGL 92 (97)
T ss_pred ccccCCCCccceeehhhhhhHHHHHHHHHHHHHH
Confidence 4557899998888777777644333334444333
No 12
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.80 E-value=69 Score=23.75 Aligned_cols=14 Identities=29% Similarity=0.600 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHH
Q 035259 43 SILVHTIIFFGLVT 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 13
>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=23.13 E-value=1.8e+02 Score=22.10 Aligned_cols=34 Identities=21% Similarity=0.623 Sum_probs=21.5
Q ss_pred chHHHHHHHH---HHHhccceeEeecCCCceeEeecc
Q 035259 4 WGPVVIAVVL---FVLLSPGLLFQLPGRNRVVEFGNM 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 4554443332 233446655688999999999865
No 14
>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=21.15 E-value=77 Score=20.31 Aligned_cols=14 Identities=43% Similarity=0.876 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHhhc
Q 035259 50 IFFGLVTIFLIAIGVH 65 (69)
Q Consensus 50 ifF~l~~if~~ai~vH 65 (69)
+||++ ||+.|+..+
T Consensus 23 vYFal--IflaAlP~a 36 (73)
T PF05398_consen 23 VYFAL--IFLAALPFA 36 (73)
T ss_pred HHHHH--HHHHHHHHH
Confidence 78888 777776654
No 15
>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=20.57 E-value=95 Score=24.04 Aligned_cols=15 Identities=33% Similarity=0.465 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHH
Q 035259 41 GLSILVHTIIFFGLV 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 16
>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=20.39 E-value=65 Score=17.15 Aligned_cols=10 Identities=60% Similarity=1.032 Sum_probs=6.6
Q ss_pred HHHHHHHHHh
Q 035259 8 VIAVVLFVLL 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
Done!