Query 035304
Match_columns 68
No_of_seqs 103 out of 115
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 10:48:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035304.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035304hhsearch_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 2.8E-47 6.1E-52 238.9 8.4 68 1-68 1-68 (68)
2 COG2864 FdnI Cytochrome b subu 70.5 3.6 7.9E-05 30.6 2.2 49 11-68 123-173 (218)
3 KOG4580 Component of vacuolar 56.9 6.8 0.00015 27.0 1.4 25 2-26 84-108 (112)
4 COG5264 VTC1 Vacuolar transpor 46.0 11 0.00024 26.4 1.0 22 3-24 100-121 (126)
5 PF07330 DUF1467: Protein of u 41.4 63 0.0014 20.7 4.0 47 11-57 16-70 (85)
6 PF13955 Fst_toxin: Toxin Fst, 36.9 28 0.0006 17.7 1.4 10 5-14 6-15 (21)
7 PF04483 DUF565: Protein of un 29.1 49 0.0011 19.7 1.9 54 2-63 3-57 (60)
8 COG3123 Uncharacterized protei 27.3 37 0.0008 22.8 1.2 14 17-30 65-78 (94)
9 PF09680 Tiny_TM_bacill: Prote 26.7 42 0.00092 17.5 1.1 9 10-18 9-17 (24)
10 PF05440 MtrB: Tetrahydrometha 25.7 1.1E+02 0.0023 20.4 3.2 35 21-55 59-93 (97)
11 COG3966 DltD Protein involved 25.4 53 0.0011 27.0 2.0 14 4-17 7-20 (415)
12 PF01350 Flavi_NS4A: Flaviviru 23.7 2.2E+02 0.0048 20.1 4.6 32 6-47 104-135 (144)
13 PF05398 PufQ: PufQ cytochrome 23.7 64 0.0014 20.6 1.8 14 50-65 23-36 (73)
14 KOG4054 Uncharacterized conser 23.5 71 0.0015 23.6 2.2 15 42-56 39-53 (183)
15 TIGR02615 spoVE stage V sporul 21.7 2E+02 0.0043 21.8 4.3 34 4-37 66-102 (354)
16 TIGR02794 tolA_full TolA prote 21.0 93 0.002 24.0 2.5 16 40-55 4-19 (346)
17 PF08523 MBF1: Multiprotein br 20.5 34 0.00073 21.2 0.0 9 2-10 1-10 (71)
18 TIGR01732 tiny_TM_bacill conse 20.4 66 0.0014 17.1 1.1 10 8-17 9-18 (26)
19 KOG2719 Metalloprotease [Gener 20.1 64 0.0014 26.4 1.5 41 4-44 186-226 (428)
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=2.8e-47 Score=238.85 Aligned_cols=68 Identities=46% Similarity=0.849 Sum_probs=67.4
Q ss_pred CCCchHHHHHHHHHHHhcCceeEEecCCCCeeeeecCcchHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 035304 1 MNDWAAPLIAAALFAFLSPGLVVQMPAKNRAVDFLNMKTSIAAIFVHTVLYGLFLILFLVILNVHLFI 68 (68)
Q Consensus 1 M~DWgpV~i~vvLFvlLsPGLLfq~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~~ai~vHiy~ 68 (68)
|+|||||+||++||++||||||||+|||+|++|||||||||+||+|||++||+++++|++|+|+|+|+
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 99999999999999999999999999999999999999999999999999999999999999999996
No 2
>COG2864 FdnI Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]
Probab=70.50 E-value=3.6 Score=30.63 Aligned_cols=49 Identities=16% Similarity=0.413 Sum_probs=36.5
Q ss_pred HHHHHHhcCceeE--EecCCCCeeeeecCcchHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 035304 11 AALFAFLSPGLVV--QMPAKNRAVDFLNMKTSIAAIFVHTVLYGLFLILFLVILNVHLFI 68 (68)
Q Consensus 11 vvLFvlLsPGLLf--q~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~~ai~vHiy~ 68 (68)
+..++++--|+.. |.|. .++++.+...|.++|+.--+.+.+++ .+|+|+
T Consensus 123 l~~~~l~iTGivmw~~y~~-----~~~~i~~~r~s~l~h~~~a~~l~~~~----~vHiy~ 173 (218)
T COG2864 123 LAIVLLLITGIVIWRPYFA-----PYFSIPLLRLSLLLHAFAAVILIFII----IVHIYM 173 (218)
T ss_pred HHHHHHHHHHHHHHhhhcc-----ccccHHHHHHHHHHHHHHHHHHHHHH----HHHHHH
Confidence 3446666677777 6654 46889999999999999888876654 478873
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=56.90 E-value=6.8 Score=26.95 Aligned_cols=25 Identities=12% Similarity=0.297 Sum_probs=19.2
Q ss_pred CCchHHHHHHHHHHHhcCceeEEec
Q 035304 2 NDWAAPLIAAALFAFLSPGLVVQMP 26 (68)
Q Consensus 2 ~DWgpV~i~vvLFvlLsPGLLfq~P 26 (68)
.-|||.+++++||+.++--..+.++
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=46.03 E-value=11 Score=26.35 Aligned_cols=22 Identities=14% Similarity=0.244 Sum_probs=17.0
Q ss_pred CchHHHHHHHHHHHhcCceeEE
Q 035304 3 DWAAPLIAAALFAFLSPGLVVQ 24 (68)
Q Consensus 3 DWgpV~i~vvLFvlLsPGLLfq 24 (68)
-|||.+++++|++.+.=-..+.
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=41.43 E-value=63 Score=20.70 Aligned_cols=47 Identities=17% Similarity=0.404 Sum_probs=28.9
Q ss_pred HHHHHHhcCceeEE------ecCCCC--eeeeecCcchHHHHHHHHHHHHHHHHH
Q 035304 11 AALFAFLSPGLVVQ------MPAKNR--AVDFLNMKTSIAAIFVHTVLYGLFLIL 57 (68)
Q Consensus 11 vvLFvlLsPGLLfq------~PG~~r--~veFgn~~Tsg~si~VHa~ifF~l~~i 57 (68)
.+||++|-=|+-=| .||.+. +.++.=.|--...-.+=+++|.+.+.+
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 677655 666655554444445555555544443
No 6
>PF13955 Fst_toxin: Toxin Fst, type I toxin-antitoxin system; PDB: 2KV5_A.
Probab=36.86 E-value=28 Score=17.71 Aligned_cols=10 Identities=20% Similarity=0.252 Sum_probs=8.3
Q ss_pred hHHHHHHHHH
Q 035304 5 AAPLIAAALF 14 (68)
Q Consensus 5 gpV~i~vvLF 14 (68)
||+++|++|=
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=29.12 E-value=49 Score=19.71 Aligned_cols=54 Identities=20% Similarity=0.298 Sum_probs=27.6
Q ss_pred CCchHHHHHHHHHHHhcCc-eeEEecCCCCeeeeecCcchHHHHHHHHHHHHHHHHHHHHHHh
Q 035304 2 NDWAAPLIAAALFAFLSPG-LVVQMPAKNRAVDFLNMKTSIAAIFVHTVLYGLFLILFLVILN 63 (68)
Q Consensus 2 ~DWgpV~i~vvLFvlLsPG-LLfq~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~~if~~ai~ 63 (68)
+||.|++.+.+++..=.=+ +...-|. +.+.+..--++..+=-..++.+|+=|.+
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 2222334444455555566666665543
No 8
>COG3123 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.31 E-value=37 Score=22.77 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=11.9
Q ss_pred hcCceeEEecCCCC
Q 035304 17 LSPGLVVQMPAKNR 30 (68)
Q Consensus 17 LsPGLLfq~PG~~r 30 (68)
-.||=-||+||+++
T Consensus 65 ~~~Ge~F~VpgnS~ 78 (94)
T COG3123 65 YTAGEVFNVPGNSE 78 (94)
T ss_pred ecCCceEEcCCCCe
Confidence 36899999999974
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=26.73 E-value=42 Score=17.54 Aligned_cols=9 Identities=33% Similarity=0.512 Sum_probs=6.2
Q ss_pred HHHHHHHhc
Q 035304 10 AAALFAFLS 18 (68)
Q Consensus 10 ~vvLFvlLs 18 (68)
-++||++|.
T Consensus 9 ivVLFILLi 17 (24)
T PF09680_consen 9 IVVLFILLI 17 (24)
T ss_pred HHHHHHHHH
Confidence 467888773
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=25.72 E-value=1.1e+02 Score=20.43 Aligned_cols=35 Identities=9% Similarity=0.120 Sum_probs=22.1
Q ss_pred eeEEecCCCCeeeeecCcchHHHHHHHHHHHHHHH
Q 035304 21 LVVQMPAKNRAVDFLNMKTSIAAIFVHTVLYGLFL 55 (68)
Q Consensus 21 LLfq~PG~~r~veFgn~~Tsg~si~VHa~ifF~l~ 55 (68)
.+-.-|||++.-+-.++-|+-.==++=.+++.+++
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 45578999988888887777544344344443333
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=25.40 E-value=53 Score=26.97 Aligned_cols=14 Identities=50% Similarity=0.686 Sum_probs=12.5
Q ss_pred chHHHHHHHHHHHh
Q 035304 4 WAAPLIAAALFAFL 17 (68)
Q Consensus 4 WgpV~i~vvLFvlL 17 (68)
-||++||.+||+++
T Consensus 7 fGPlliA~alf~~~ 20 (415)
T COG3966 7 FGPLLIAFALFILL 20 (415)
T ss_pred hhHHHHHHHHHHHH
Confidence 58999999999876
No 12
>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=23.69 E-value=2.2e+02 Score=20.06 Aligned_cols=32 Identities=31% Similarity=0.419 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhcCceeEEecCCCCeeeeecCcchHHHHHHH
Q 035304 6 APLIAAALFAFLSPGLVVQMPAKNRAVDFLNMKTSIAAIFVH 47 (68)
Q Consensus 6 pV~i~vvLFvlLsPGLLfq~PG~~r~veFgn~~Tsg~si~VH 47 (68)
-.++..++.++|.|= |||+| +.+-|..|.++=
T Consensus 104 ~~lv~filmvVLiPE-----pg~QR-----S~~DN~LA~~vi 135 (144)
T PF01350_consen 104 VLLVFFILMVVLIPE-----PGKQR-----SQQDNQLAYFVI 135 (144)
T ss_pred HHHHHHHHHHhcccC-----CCCcC-----CcccchHHHHHH
Confidence 346667788888885 99998 455677666543
No 13
>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=23.68 E-value=64 Score=20.61 Aligned_cols=14 Identities=29% Similarity=0.493 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHhhc
Q 035304 50 LYGLFLILFLVILNVH 65 (68)
Q Consensus 50 ifF~l~~if~~ai~vH 65 (68)
+||++ ||+.|+..+
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 14
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.51 E-value=71 Score=23.65 Aligned_cols=15 Identities=40% Similarity=0.747 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHH
Q 035304 42 AAIFVHTVLYGLFLI 56 (68)
Q Consensus 42 ~si~VHa~ifF~l~~ 56 (68)
.-|+||++||+...+
T Consensus 39 ~lifvh~lI~v~mla 53 (183)
T KOG4054|consen 39 KLIFVHALIWVLMLA 53 (183)
T ss_pred HHHHHHHHHHHHHHH
Confidence 348899999987754
No 15
>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=21.66 E-value=2e+02 Score=21.77 Aligned_cols=34 Identities=21% Similarity=0.396 Sum_probs=21.6
Q ss_pred chHHHHHHHH---HHHhcCceeEEecCCCCeeeeecC
Q 035304 4 WAAPLIAAAL---FAFLSPGLVVQMPAKNRAVDFLNM 37 (68)
Q Consensus 4 WgpV~i~vvL---FvlLsPGLLfq~PG~~r~veFgn~ 37 (68)
|++.+..+.+ ...+.||.--+..|..|++++|.+
T Consensus 66 ~~~~~~~~~~~lLll~~~~~~g~~~~Ga~rWi~lg~~ 102 (354)
T TIGR02615 66 WAKMLMVICFVLLLLVLIPGVGMERNGARRWIGVGAF 102 (354)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcccCCcccceeCCCc
Confidence 4554443332 333447655688999999999865
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=21.00 E-value=93 Score=24.02 Aligned_cols=16 Identities=25% Similarity=0.690 Sum_probs=12.3
Q ss_pred hHHHHHHHHHHHHHHH
Q 035304 40 SIAAIFVHTVLYGLFL 55 (68)
Q Consensus 40 sg~si~VHa~ifF~l~ 55 (68)
-..|+++|.+++.+|+
T Consensus 4 ~~lSv~lHvlLi~lL~ 19 (346)
T TIGR02794 4 FLLSLLLHILLLGLLI 19 (346)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3579999998886663
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=20.45 E-value=34 Score=21.24 Aligned_cols=9 Identities=33% Similarity=0.892 Sum_probs=0.0
Q ss_pred CCchHH-HHH
Q 035304 2 NDWAAP-LIA 10 (68)
Q Consensus 2 ~DWgpV-~i~ 10 (68)
+||-|| +|.
T Consensus 1 qDWd~vtvi~ 10 (71)
T PF08523_consen 1 QDWDPVTVIG 10 (71)
T ss_dssp ----------
T ss_pred CCCcccceec
Confidence 588888 553
No 18
>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=20.38 E-value=66 Score=17.08 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=6.7
Q ss_pred HHHHHHHHHh
Q 035304 8 LIAAALFAFL 17 (68)
Q Consensus 8 ~i~vvLFvlL 17 (68)
..-++||++|
T Consensus 9 ~livVLFILL 18 (26)
T TIGR01732 9 ALIVVLFILL 18 (26)
T ss_pred HHHHHHHHHH
Confidence 3446788876
No 19
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=20.14 E-value=64 Score=26.35 Aligned_cols=41 Identities=17% Similarity=0.362 Sum_probs=33.3
Q ss_pred chHHHHHHHHHHHhcCceeEEecCCCCeeeeecCcchHHHH
Q 035304 4 WAAPLIAAALFAFLSPGLVVQMPAKNRAVDFLNMKTSIAAI 44 (68)
Q Consensus 4 WgpV~i~vvLFvlLsPGLLfq~PG~~r~veFgn~~Tsg~si 44 (68)
|.-.+|...+=+.+-||..--.=||.++.|.||+||+-...
T Consensus 186 w~f~~v~~l~l~ti~p~~i~P~f~K~~PLe~g~l~~~Ie~l 226 (428)
T KOG2719|consen 186 WLFYFVLSLLLLTIYPGFIAPLFGKFTPLEEGDLKEKIERL 226 (428)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCCCCCCCCchHHHHHHH
Confidence 55556666677778899999899999999999999987543
Done!