Query 035269
Match_columns 69
No_of_seqs 90 out of 116
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 10:32:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035269.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035269hhsearch_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 5.6E-47 1.2E-51 238.1 8.4 68 1-68 1-68 (68)
2 COG2864 FdnI Cytochrome b subu 82.0 1 2.2E-05 33.6 1.9 50 11-69 123-174 (218)
3 KOG4580 Component of vacuolar 56.1 7.1 0.00015 26.9 1.4 25 2-26 84-108 (112)
4 COG5264 VTC1 Vacuolar transpor 44.9 12 0.00025 26.3 1.0 23 2-24 99-121 (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, 32.9 34 0.00075 17.4 1.4 10 5-14 6-15 (21)
7 COG3123 Uncharacterized protei 29.6 35 0.00075 23.0 1.4 14 17-30 65-78 (94)
8 PF04483 DUF565: Protein of un 29.1 48 0.001 19.8 1.8 54 2-63 3-57 (60)
9 PF09680 Tiny_TM_bacill: Prote 27.1 41 0.00088 17.7 1.1 9 10-18 9-17 (24)
10 COG3966 DltD Protein involved 25.6 51 0.0011 27.1 1.9 14 4-17 7-20 (415)
11 TIGR02615 spoVE stage V sporul 25.4 1.6E+02 0.0034 22.4 4.4 34 4-37 66-102 (354)
12 PF05440 MtrB: Tetrahydrometha 25.2 1.1E+02 0.0023 20.5 3.1 35 21-55 59-93 (97)
13 KOG4054 Uncharacterized conser 22.2 78 0.0017 23.5 2.2 14 43-56 40-53 (183)
14 TIGR03257 met_CoM_red_bet meth 21.1 54 0.0012 27.0 1.3 29 21-50 108-139 (433)
15 TIGR01732 tiny_TM_bacill conse 21.0 62 0.0013 17.2 1.1 10 8-17 9-18 (26)
16 PF01350 Flavi_NS4A: Flaviviru 20.7 2.7E+02 0.006 19.7 4.6 31 7-47 105-135 (144)
17 TIGR02794 tolA_full TolA prote 20.3 97 0.0021 24.0 2.5 15 41-55 5-19 (346)
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=5.6e-47 Score=238.05 Aligned_cols=68 Identities=59% Similarity=1.207 Sum_probs=67.4
Q ss_pred CCCchHHHHHHHHHHHhccceeEEecCCCceeeeeCccchHHHHHHHHHHHHHHHHHHHHHHhheecc
Q 035269 1 MKDWAPIVIGLLLFILLSPGLLFQLPGNHRHFEFGSFATNGKAVLVHTLIFFGIYTILILAVGIHIYM 68 (69)
Q Consensus 1 M~DWgpV~i~vvLFvlLsPGLLfQ~PG~~r~veFgn~~Tsg~si~vHalifF~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=82.00 E-value=1 Score=33.64 Aligned_cols=50 Identities=24% Similarity=0.379 Sum_probs=37.5
Q ss_pred HHHHHHhccceeE--EecCCCceeeeeCccchHHHHHHHHHHHHHHHHHHHHHHhheeccC
Q 035269 11 LLLFILLSPGLLF--QLPGNHRHFEFGSFATNGKAVLVHTLIFFGIYTILILAVGIHIYMG 69 (69)
Q Consensus 11 vvLFvlLsPGLLf--Q~PG~~r~veFgn~~Tsg~si~vHalifF~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 3446666778777 6664 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=56.11 E-value=7.1 Score=26.94 Aligned_cols=25 Identities=12% Similarity=0.404 Sum_probs=19.2
Q ss_pred CCchHHHHHHHHHHHhccceeEEec
Q 035269 2 KDWAPIVIGLLLFILLSPGLLFQLP 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 3599999999999998755554443
No 4
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=44.93 E-value=12 Score=26.30 Aligned_cols=23 Identities=13% Similarity=0.407 Sum_probs=17.4
Q ss_pred CCchHHHHHHHHHHHhccceeEE
Q 035269 2 KDWAPIVIGLLLFILLSPGLLFQ 24 (69)
Q Consensus 2 ~DWgpV~i~vvLFvlLsPGLLfQ 24 (69)
.-|||.+++++|++.+.=-..+.
T Consensus 99 D~~GP~lv~vvL~valivNf~~~ 121 (126)
T COG5264 99 DRLGPTLVCVVLLVALIVNFFLA 121 (126)
T ss_pred cccCCchhHHHHHHHHHHHHhhc
Confidence 35999999999999886444333
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=40.62 E-value=65 Score=20.69 Aligned_cols=47 Identities=26% Similarity=0.332 Sum_probs=29.5
Q ss_pred HHHHHHhccceeEE------ecCCCc--eeeeeCccchHHHHHHHHHHHHHHHHH
Q 035269 11 LLLFILLSPGLLFQ------LPGNHR--HFEFGSFATNGKAVLVHTLIFFGIYTI 57 (69)
Q Consensus 11 vvLFvlLsPGLLfQ------~PG~~r--~veFgn~~Tsg~si~vHalifF~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 666655554444455555555554443
No 6
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=32.89 E-value=34 Score=17.40 Aligned_cols=10 Identities=60% Similarity=1.082 Sum_probs=8.2
Q ss_pred hHHHHHHHHH
Q 035269 5 APIVIGLLLF 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
>COG3123 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.63 E-value=35 Score=22.97 Aligned_cols=14 Identities=36% Similarity=0.835 Sum_probs=12.1
Q ss_pred hccceeEEecCCCc
Q 035269 17 LSPGLLFQLPGNHR 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 8
>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=29.12 E-value=48 Score=19.80 Aligned_cols=54 Identities=15% Similarity=0.258 Sum_probs=27.0
Q ss_pred CCchHHHHHHHHHHHhccc-eeEEecCCCceeeeeCccchHHHHHHHHHHHHHHHHHHHHHHh
Q 035269 2 KDWAPIVIGLLLFILLSPG-LLFQLPGNHRHFEFGSFATNGKAVLVHTLIFFGIYTILILAVG 63 (69)
Q Consensus 2 ~DWgpV~i~vvLFvlLsPG-LLfQ~PG~~r~veFgn~~Tsg~si~vHalifF~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 6999998887765432111 1222222 2222333344444444566666665543
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=27.10 E-value=41 Score=17.67 Aligned_cols=9 Identities=56% Similarity=0.752 Sum_probs=6.2
Q ss_pred HHHHHHHhc
Q 035269 10 GLLLFILLS 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=25.58 E-value=51 Score=27.12 Aligned_cols=14 Identities=50% Similarity=1.061 Sum_probs=12.5
Q ss_pred chHHHHHHHHHHHh
Q 035269 4 WAPIVIGLLLFILL 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
>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=25.45 E-value=1.6e+02 Score=22.39 Aligned_cols=34 Identities=26% Similarity=0.679 Sum_probs=21.5
Q ss_pred chHHHHHHHH---HHHhccceeEEecCCCceeeeeCc
Q 035269 4 WAPIVIGLLL---FILLSPGLLFQLPGNHRHFEFGSF 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 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=25.24 E-value=1.1e+02 Score=20.46 Aligned_cols=35 Identities=20% Similarity=0.262 Sum_probs=21.6
Q ss_pred eeEEecCCCceeeeeCccchHHHHHHHHHHHHHHH
Q 035269 21 LLFQLPGNHRHFEFGSFATNGKAVLVHTLIFFGIY 55 (69)
Q Consensus 21 LLfQ~PG~~r~veFgn~~Tsg~si~vHalifF~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 45568999988887777776443344344443333
No 13
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.16 E-value=78 Score=23.49 Aligned_cols=14 Identities=29% Similarity=0.579 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHH
Q 035269 43 AVLVHTLIFFGIYT 56 (69)
Q Consensus 43 si~vHalifF~l~~ 56 (69)
-|+||++||+...+
T Consensus 40 lifvh~lI~v~mla 53 (183)
T KOG4054|consen 40 LIFVHALIWVLMLA 53 (183)
T ss_pred HHHHHHHHHHHHHH
Confidence 47899999987654
No 14
>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=21.10 E-value=54 Score=27.04 Aligned_cols=29 Identities=31% Similarity=0.450 Sum_probs=24.7
Q ss_pred eeEEecCCCce---eeeeCccchHHHHHHHHHH
Q 035269 21 LLFQLPGNHRH---FEFGSFATNGKAVLVHTLI 50 (69)
Q Consensus 21 LLfQ~PG~~r~---veFgn~~Tsg~si~vHali 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 15
>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=20.95 E-value=62 Score=17.23 Aligned_cols=10 Identities=50% Similarity=0.833 Sum_probs=6.7
Q ss_pred HHHHHHHHHh
Q 035269 8 VIGLLLFILL 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 16
>PF01350 Flavi_NS4A: Flavivirus non-structural protein NS4A; InterPro: IPR000404 Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions []. NS4A has only been found in cells infected by Kunjin virus [].; GO: 0016032 viral reproduction, 0016070 RNA metabolic process, 0044423 virion part
Probab=20.68 E-value=2.7e+02 Score=19.66 Aligned_cols=31 Identities=32% Similarity=0.563 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhccceeEEecCCCceeeeeCccchHHHHHHH
Q 035269 7 IVIGLLLFILLSPGLLFQLPGNHRHFEFGSFATNGKAVLVH 47 (69)
Q Consensus 7 V~i~vvLFvlLsPGLLfQ~PG~~r~veFgn~~Tsg~si~vH 47 (69)
.++..++.++|.|= |||+| +.+-|..|.++=
T Consensus 105 ~lv~filmvVLiPE-----pg~QR-----S~~DN~LA~~vi 135 (144)
T PF01350_consen 105 LLVFFILMVVLIPE-----PGKQR-----SQQDNQLAYFVI 135 (144)
T ss_pred HHHHHHHHHhcccC-----CCCcC-----CcccchHHHHHH
Confidence 46667788888885 99998 456677666543
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=20.26 E-value=97 Score=23.98 Aligned_cols=15 Identities=20% Similarity=0.199 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHH
Q 035269 41 GKAVLVHTLIFFGIY 55 (69)
Q Consensus 41 g~si~vHalifF~l~ 55 (69)
..|+++|.+++.+|+
T Consensus 5 ~lSv~lHvlLi~lL~ 19 (346)
T TIGR02794 5 LLSLLLHILLLGLLI 19 (346)
T ss_pred HHHHHHHHHHHHHHH
Confidence 579999998886663
Done!