Query 032451
Match_columns 140
No_of_seqs 160 out of 1042
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 14:15:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032451.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032451hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944 Peroxisomal membrane p 100.0 2.4E-28 5.2E-33 184.6 13.4 124 16-140 46-175 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 98.0 1.8E-06 4E-11 53.6 0.9 30 110-140 1-30 (68)
3 TIGR02163 napH_ ferredoxin-typ 61.9 51 0.0011 25.3 7.2 80 50-130 4-102 (255)
4 PF10929 DUF2811: Protein of u 55.8 22 0.00049 21.2 3.3 29 36-64 12-40 (57)
5 PF00140 Sigma70_r1_2: Sigma-7 48.9 9 0.0002 20.5 0.8 18 7-24 2-19 (37)
6 TIGR02230 ATPase_gene1 F0F1-AT 45.2 69 0.0015 21.3 4.7 34 50-83 39-74 (100)
7 COG1284 Uncharacterized conser 43.7 1.6E+02 0.0035 23.2 8.3 57 19-75 111-186 (289)
8 KOG0769 Predicted mitochondria 41.4 80 0.0017 25.1 5.2 69 35-103 47-125 (308)
9 PRK09609 hypothetical protein; 36.5 1.8E+02 0.004 23.4 6.7 54 27-82 58-111 (312)
10 smart00337 BCL BCL (B-Cell lym 33.7 1.1E+02 0.0025 19.8 4.5 28 35-63 35-62 (100)
11 PF09105 SelB-wing_1: Elongati 31.3 44 0.00096 19.3 1.8 22 36-57 5-27 (61)
12 PF10960 DUF2762: Protein of u 28.2 87 0.0019 19.5 2.9 25 87-111 4-28 (71)
13 PF03698 UPF0180: Uncharacteri 26.1 59 0.0013 20.7 1.9 16 115-130 64-79 (80)
14 PF06027 DUF914: Eukaryotic pr 25.4 1.7E+02 0.0037 23.6 4.9 45 25-70 173-217 (334)
15 PF04835 Pox_A9: A9 protein co 23.3 1.7E+02 0.0037 17.2 4.9 41 68-108 6-46 (54)
16 PF04854 DUF624: Protein of un 23.2 1.8E+02 0.004 17.5 4.5 38 98-136 21-62 (77)
17 COG3965 Predicted Co/Zn/Cd cat 23.0 3.9E+02 0.0085 21.3 9.7 77 21-103 99-176 (314)
18 PF09734 Tau95: RNA polymerase 23.0 59 0.0013 25.6 1.9 60 4-74 232-291 (310)
19 PF03988 DUF347: Repeat of Unk 22.6 1.7E+02 0.0037 16.9 4.3 45 22-73 5-49 (55)
20 PF07960 CBP4: CBP4; InterPro 21.0 68 0.0015 22.4 1.6 26 47-72 2-29 (128)
21 COG4779 FepG ABC-type enteroba 20.5 1.2E+02 0.0026 24.4 3.0 26 18-43 291-316 (346)
22 PF02909 TetR_C: Tetracyclin r 20.3 2.7E+02 0.0058 18.3 5.7 57 5-61 12-78 (139)
23 PRK09477 napH quinol dehydroge 20.1 4.1E+02 0.009 20.4 7.2 81 48-129 9-108 (271)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=99.96 E-value=2.4e-28 Score=184.60 Aligned_cols=124 Identities=32% Similarity=0.557 Sum_probs=117.5
Q ss_pred HhhCchHHHHHHHHHHH-HHHHHHHHhhhC-----CCchhHHHHHHHHHHhhhcccchhhHHHHHHHhhccCCChHHHHH
Q 032451 16 LQVHPLRTKAITAGVLA-GCSDAIAQKISG-----VKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKGRDNKSVAK 89 (140)
Q Consensus 16 l~~~Pl~t~~~t~~~l~-~~gD~laQ~~~~-----~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~~~~~~~~~ 89 (140)
...+|+.+++++++.+. .+||+++|.++. .+++|+.|++||+++|+++.||.+|+||+.||+.+|.++..++++
T Consensus 46 ~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p~~~~~~~~~ 125 (222)
T KOG1944|consen 46 FSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKKLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFPKKTLITVVK 125 (222)
T ss_pred hhhhhHHHHHHHHHHHHHHhchhhhhhhhhhcccccccccHHHHHHHHhhhhheeccchhHHHHHHHHHccCccHHHHHH
Confidence 46789999999999888 999999999863 367999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHhcCCChHHHHHHHHhhCHHHHHhCccC
Q 032451 90 KVLLEQLIFSPWINFLFMTYFGLVVEGKPWGSVMKKVRKDYPAVQFTSWKV 140 (140)
Q Consensus 90 Kvl~Dq~i~~P~~~~~f~~~~~~~leg~~~~~~~~~~k~~~~~~~~~~w~v 140 (140)
|++.||++++|+.+.+|+.+++ ++||++.+++.+++++++||++++||++
T Consensus 126 kvl~dql~~~P~~~~~ff~~~~-~legk~~~~~~~~~~~~~~p~l~~~~~~ 175 (222)
T KOG1944|consen 126 KVLLDQLVFAPLFIVVFFLLMG-LLEGKTNEEAKAKLKRKFWPTLKANWMV 175 (222)
T ss_pred HHHHhhhhhchHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHhhhhee
Confidence 9999999999999999999999 9999999999999999999999999985
No 2
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=98.01 E-value=1.8e-06 Score=53.59 Aligned_cols=30 Identities=37% Similarity=0.841 Sum_probs=28.1
Q ss_pred HHHHhcCCChHHHHHHHHhhCHHHHHhCccC
Q 032451 110 FGLVVEGKPWGSVMKKVRKDYPAVQFTSWKV 140 (140)
Q Consensus 110 ~~~~leg~~~~~~~~~~k~~~~~~~~~~w~v 140 (140)
|+ ++||+|++++++++|++|+++++++|++
T Consensus 1 Mg-~l~g~s~~~~~~~l~~~~~~~~~~~~~~ 30 (68)
T PF04117_consen 1 MG-LLEGKSWEEIKEKLKRDYWPTLKASWKF 30 (68)
T ss_pred CC-cccCCCHHHHHHHHHHHHHHHHHHHhHh
Confidence 56 8999999999999999999999999975
No 3
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=61.86 E-value=51 Score=25.31 Aligned_cols=80 Identities=13% Similarity=0.138 Sum_probs=53.4
Q ss_pred HHHHHHHHHHhhhcccchhhHHH--HHHH--hh---ccCCChHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHhcCCC--
Q 032451 50 LKRLLLLMLFDFGYGVPFGHFLN--KFLD--AI---FKGRDNKSVAKKVLLEQLIFSPWINFLFM--TYFGLVVEGKP-- 118 (140)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~~~wy--~~L~--~~---~~~~~~~~~~~Kvl~Dq~i~~P~~~~~f~--~~~~~~leg~~-- 118 (140)
+||+...++...++.||..+.|. ..|. +. +|..+....+.-++....+..+.+..... ...+ ++-|+-
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~-l~~GR~fC 82 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGTIPLSDPLITLQILLAGHSPPTNALIGALIIVAFYA-LFGGRAFC 82 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCCccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHH-HHhcccce
Confidence 68999999999988999888876 3443 33 33466777787777777777676655533 3335 566653
Q ss_pred --------hHHHHHHHHhhC
Q 032451 119 --------WGSVMKKVRKDY 130 (140)
Q Consensus 119 --------~~~~~~~~k~~~ 130 (140)
++|..++++++.
T Consensus 83 gwiCP~g~~~el~~~l~~k~ 102 (255)
T TIGR02163 83 SWVCPVNLVTDFAAWLRRKL 102 (255)
T ss_pred eccCCchHHHHHHHHHHHhh
Confidence 366666666543
No 4
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=55.78 E-value=22 Score=21.19 Aligned_cols=29 Identities=21% Similarity=0.133 Sum_probs=22.9
Q ss_pred HHHHHhhhCCCchhHHHHHHHHHHhhhcc
Q 032451 36 DAIAQKISGVKKLQLKRLLLLMLFDFGYG 64 (140)
Q Consensus 36 D~laQ~~~~~~~~D~~R~~~~~~~G~~~~ 64 (140)
+.+.+.+|....||-.|.+.-++-|+++.
T Consensus 12 ~~m~~fie~hP~WDQ~Rl~~aALa~FL~Q 40 (57)
T PF10929_consen 12 QAMKDFIETHPNWDQYRLFQAALAGFLLQ 40 (57)
T ss_pred HHHHHHHHcCCCchHHHHHHHHHHHHHHH
Confidence 45666677778899999999999988754
No 5
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=48.91 E-value=9 Score=20.51 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhhCchHHH
Q 032451 7 EAWRKYLIQLQVHPLRTK 24 (140)
Q Consensus 7 ~~~~~Y~~~l~~~Pl~t~ 24 (140)
..++.|.+...++|++|.
T Consensus 2 D~l~~Yl~ei~~~~LLt~ 19 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTA 19 (37)
T ss_dssp HHHHHHHHHHHHS-EETT
T ss_pred cHHHHHHHHHcCCCCCCH
Confidence 457889999999999874
No 6
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=45.19 E-value=69 Score=21.31 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhhcccchhhHHH--HHHHhhccCCC
Q 032451 50 LKRLLLLMLFDFGYGVPFGHFLN--KFLDAIFKGRD 83 (140)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~~~wy--~~L~~~~~~~~ 83 (140)
++....+..+|.-+.+|+.-.-| .|||+.+++..
T Consensus 39 ~~~l~~~g~IG~~~v~pil~G~~lG~WLD~~~~t~~ 74 (100)
T TIGR02230 39 WEGLGMFGLIGWSVAIPTLLGVAVGIWLDRHYPSPF 74 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc
Confidence 45666688999999999887777 69999998744
No 7
>COG1284 Uncharacterized conserved protein [Function unknown]
Probab=43.68 E-value=1.6e+02 Score=23.25 Aligned_cols=57 Identities=23% Similarity=0.244 Sum_probs=37.1
Q ss_pred CchHHHHHHHHHHHHHH--------------HHHHHhhhCCCchhHHHHHHH-----HHHhhhcccchhhHHHHHH
Q 032451 19 HPLRTKAITAGVLAGCS--------------DAIAQKISGVKKLQLKRLLLL-----MLFDFGYGVPFGHFLNKFL 75 (140)
Q Consensus 19 ~Pl~t~~~t~~~l~~~g--------------D~laQ~~~~~~~~D~~R~~~~-----~~~G~~~~gP~~~~wy~~L 75 (140)
++.+-.++.+|++.|+| |++||.++++..++..++.-+ .+.++++.+|+-+..|..+
T Consensus 111 ~~~ll~aifgG~l~G~G~glv~r~ggStGGtdIlA~~l~kk~g~~iG~~ll~vd~~i~~~a~~~~~~~~~~lytli 186 (289)
T COG1284 111 IDPLLAALFGGLLLGIGLGLVFRHGGSTGGTDILALILNKKFGISVGKILLLVDGFILLIAALVFGPLPNALYTLL 186 (289)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHcCCChhhhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 56667999999999887 999999976666666554322 2223333445666666443
No 8
>KOG0769 consensus Predicted mitochondrial carrier protein [Energy production and conversion]
Probab=41.44 E-value=80 Score=25.08 Aligned_cols=69 Identities=17% Similarity=0.031 Sum_probs=37.2
Q ss_pred HHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhHHHHHHHhhccCC----------ChHHHHHHHHHHHHhHHHHHH
Q 032451 35 SDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKGR----------DNKSVAKKVLLEQLIFSPWIN 103 (140)
Q Consensus 35 gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~~----------~~~~~~~Kvl~Dq~i~~P~~~ 103 (140)
.|+++|.+.+..-....|-+--...+.|++--+.++||+.+.+....+ ++.-.+.--.+++++-.|++.
T Consensus 47 ~dvm~eiik~eg~lsLYqGl~p~~~~t~iSnFVYFY~y~~~k~~~~~~~~s~s~~t~~~Lllga~AGsinvl~T~Plwv 125 (308)
T KOG0769|consen 47 SDVMWEIIKEEGVLSLYQGLGPVLVSTFISNFVYFYTYSYFKAVASKGKLSQSSGTKADLLLGAAAGSINVLLTTPLWV 125 (308)
T ss_pred HHHHHHHHhccchHHHhccccHHHHHHHHhhhHhhhhHHHHHHHHhcCCCcCCcchHHHHHHHHHHhhhHHHhcChHHH
Confidence 344444443222334444444455666666667789999987765432 122223333456666677654
No 9
>PRK09609 hypothetical protein; Provisional
Probab=36.45 E-value=1.8e+02 Score=23.37 Aligned_cols=54 Identities=20% Similarity=0.124 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhHHHHHHHhhccCC
Q 032451 27 TAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKGR 82 (140)
Q Consensus 27 t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~~ 82 (140)
.+++..+++|++.-.+.+ ..+.+.=++.-++.|. +.|-+..+.|+.+.+.|.++
T Consensus 58 ~G~ivG~lsDLLs~li~p-G~ffPgFTLsa~l~Gl-I~Glf~~~~fk~~~~~f~~~ 111 (312)
T PRK09609 58 VGFFTGLLSDLISFLFVP-GVYHPYYTLAAMVYGF-IPGIVGWFFFKFGKKFFGKE 111 (312)
T ss_pred HHHHHHHHHHHHHHHhcC-CccCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhHH
Confidence 466777889999876654 6888888888888887 58888888889999988763
No 10
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=33.75 E-value=1.1e+02 Score=19.78 Aligned_cols=28 Identities=11% Similarity=0.201 Sum_probs=19.2
Q ss_pred HHHHHHhhhCCCchhHHHHHHHHHHhhhc
Q 032451 35 SDAIAQKISGVKKLQLKRLLLLMLFDFGY 63 (140)
Q Consensus 35 gD~laQ~~~~~~~~D~~R~~~~~~~G~~~ 63 (140)
..+..+.+ ++..++|.|.+.+..||..+
T Consensus 35 ~~Va~~lf-~dg~inWGRIval~~F~~~l 62 (100)
T smart00337 35 GEVATELF-SDGNINWGRVVALLSFGGAL 62 (100)
T ss_pred HHHHHHHH-ccCCCCHHHHHHHHHHHHHH
Confidence 33333333 33459999999999998863
No 11
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=31.30 E-value=44 Score=19.34 Aligned_cols=22 Identities=18% Similarity=0.092 Sum_probs=14.1
Q ss_pred HHHHHhh-hCCCchhHHHHHHHH
Q 032451 36 DAIAQKI-SGVKKLQLKRLLLLM 57 (140)
Q Consensus 36 D~laQ~~-~~~~~~D~~R~~~~~ 57 (140)
.++||.+ |.++.+||.....-+
T Consensus 5 kilaqiiqehregldwqeaatra 27 (61)
T PF09105_consen 5 KILAQIIQEHREGLDWQEAATRA 27 (61)
T ss_dssp HHHHHHHHC-TT-EEHHHHHHHH
T ss_pred HHHHHHHHHHHccCcHHHHHHHh
Confidence 5789998 456778888665433
No 12
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=28.18 E-value=87 Score=19.45 Aligned_cols=25 Identities=24% Similarity=0.255 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHH
Q 032451 87 VAKKVLLEQLIFSPWINFLFMTYFG 111 (140)
Q Consensus 87 ~~~Kvl~Dq~i~~P~~~~~f~~~~~ 111 (140)
-+.|+++.|-+||-+++.+++..+-
T Consensus 4 ei~k~~~sQG~fA~LFv~Ll~yvlK 28 (71)
T PF10960_consen 4 EIIKLALSQGIFAVLFVWLLFYVLK 28 (71)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHH
Confidence 4678999999999998888877665
No 13
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=26.06 E-value=59 Score=20.72 Aligned_cols=16 Identities=13% Similarity=0.266 Sum_probs=13.9
Q ss_pred cCCChHHHHHHHHhhC
Q 032451 115 EGKPWGSVMKKVRKDY 130 (140)
Q Consensus 115 eg~~~~~~~~~~k~~~ 130 (140)
+|+|.+|+.+.+++++
T Consensus 64 ~G~T~eEI~~~v~~rl 79 (80)
T PF03698_consen 64 SGLTAEEIVQEVEERL 79 (80)
T ss_pred CCCCHHHHHHHHHHhh
Confidence 6899999999998864
No 14
>PF06027 DUF914: Eukaryotic protein of unknown function (DUF914); InterPro: IPR009262 This family consists of several hypothetical proteins of unknown function. Some of the sequences in this family are annotated as putative membrane proteins.
Probab=25.39 E-value=1.7e+02 Score=23.62 Aligned_cols=45 Identities=20% Similarity=0.162 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhH
Q 032451 25 AITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHF 70 (140)
Q Consensus 25 ~~t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~ 70 (140)
++.+++++|+.+++...+-++.+. ..=...++++|+++.||....
T Consensus 173 ~l~~a~lya~~nV~~E~~v~~~~~-~~~lg~~Glfg~ii~~iq~~i 217 (334)
T PF06027_consen 173 ALLGAILYAVSNVLEEKLVKKAPR-VEFLGMLGLFGFIISGIQLAI 217 (334)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCH-HHHHHHHHHHHHHHHHHHHHh
Confidence 578888888888887665332211 112466677777777776543
No 15
>PF04835 Pox_A9: A9 protein conserved region; InterPro: IPR006920 This entry represents a family of Chordopoxvirus A9 proteins. Chordopoxvirus belongs to the family Poxviridae and is the cause of vertebrate infections [].
Probab=23.32 E-value=1.7e+02 Score=17.20 Aligned_cols=41 Identities=12% Similarity=0.070 Sum_probs=31.9
Q ss_pred hhHHHHHHHhhccCCChHHHHHHHHHHHHhHHHHHHHHHHH
Q 032451 68 GHFLNKFLDAIFKGRDNKSVAKKVLLEQLIFSPWINFLFMT 108 (140)
Q Consensus 68 ~~~wy~~L~~~~~~~~~~~~~~Kvl~Dq~i~~P~~~~~f~~ 108 (140)
=|....+-|..+.++++..++.|.++.-+++--+.+..++.
T Consensus 6 rH~~myfce~k~R~NsF~fViik~vismimylilGi~L~yi 46 (54)
T PF04835_consen 6 RHCFMYFCENKLRPNSFWFVIIKSVISMIMYLILGIALIYI 46 (54)
T ss_pred HHHHHHHHHhhcCCchHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 36667788888888999999999999988776666555543
No 16
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=23.22 E-value=1.8e+02 Score=17.50 Aligned_cols=38 Identities=8% Similarity=0.185 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHhcCC-C---hHHHHHHHHhhCHHHHHh
Q 032451 98 FSPWINFLFMTYFGLVVEGK-P---WGSVMKKVRKDYPAVQFT 136 (140)
Q Consensus 98 ~~P~~~~~f~~~~~~~leg~-~---~~~~~~~~k~~~~~~~~~ 136 (140)
..|...+.+.+... ..+++ + +++-++..|+++.+....
T Consensus 21 igPA~~Al~~~~~~-~~~~~~~~~~~~~f~~~fk~nf~~~~~~ 62 (77)
T PF04854_consen 21 IGPATAALYYVVRK-WVRDEEDSYLFRDFWRAFKQNFKQSLLL 62 (77)
T ss_pred HHHHHHHHHHHHHH-HHcCCccChHHHHHHHHHHHHHHHHHHH
Confidence 45666677777776 66555 2 456666666666665443
No 17
>COG3965 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=23.05 E-value=3.9e+02 Score=21.28 Aligned_cols=77 Identities=9% Similarity=0.015 Sum_probs=50.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhHHH-HHHHhhccCCChHHHHHHHHHHHHhHH
Q 032451 21 LRTKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLN-KFLDAIFKGRDNKSVAKKVLLEQLIFS 99 (140)
Q Consensus 21 l~t~~~t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy-~~L~~~~~~~~~~~~~~Kvl~Dq~i~~ 99 (140)
++.-.+..+.+.+++|++ +|-+++|+.-...+.++... |...-+|+ +.++|..+..=...=.|+.++|-.+-+
T Consensus 99 ll~ll~lyAlinAl~~l~----dGGR~v~~~~ai~yt~~s~~--~Ca~~~~~~~r~nrr~~s~lIald~kqW~Mst~lS~ 172 (314)
T COG3965 99 LLALLCLYALINALGSLL----DGGREVEPGHAIAYTLVSVT--GCAAIAWKLRRLNRRLKSPLIALDTKQWLMSTCLSA 172 (314)
T ss_pred HHHHHHHHHHHHHHHHHh----cCCccccccHHHHHHHHHHH--HHHHHHHHHHhhhccCCCchhhhHHHHHHHHHHHHH
Confidence 555566667777777765 77677887777777777653 44445565 577887776545555677788877655
Q ss_pred HHHH
Q 032451 100 PWIN 103 (140)
Q Consensus 100 P~~~ 103 (140)
-+++
T Consensus 173 al~V 176 (314)
T COG3965 173 ALFV 176 (314)
T ss_pred HHHH
Confidence 5443
No 18
>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Probab=22.99 E-value=59 Score=25.59 Aligned_cols=60 Identities=18% Similarity=0.297 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhHHHHH
Q 032451 4 IVKEAWRKYLIQLQVHPLRTKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKF 74 (140)
Q Consensus 4 ~~~~~~~~Y~~~l~~~Pl~t~~~t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~ 74 (140)
......+.-.+++++||+-|+-..-.-+-..+ .....++++....|-+ -.||+-..|-++
T Consensus 232 ~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~----------~~~~~k~~l~~v~Y~f-~~GPwr~~~vr~ 291 (310)
T PF09734_consen 232 VLQELIQELKKLFEERPIWTRRALLNHLPKSG----------SQSKLKRALPYVAYYF-KNGPWRDCWVRF 291 (310)
T ss_pred hHHHHHHHHHHHHhcCCccCHHHHHHhhhhcc----------cHHHHHHHHHhhEEEE-ecCcccceeEec
Confidence 34567788889999999988754333222211 4567778899999987 599999988653
No 19
>PF03988 DUF347: Repeat of Unknown Function (DUF347) ; InterPro: IPR007136 This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.
Probab=22.58 E-value=1.7e+02 Score=16.92 Aligned_cols=45 Identities=18% Similarity=0.177 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCchhHHHHHHHHHHhhhcccchhhHHHH
Q 032451 22 RTKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNK 73 (140)
Q Consensus 22 ~t~~~t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~ 73 (140)
.++.+++..=...||.++|. .+........++..++... .-.||+
T Consensus 5 ~a~ilt~~lGt~~~D~l~~~------lglg~~~~~~~~~~~l~~~-~~~~~~ 49 (55)
T PF03988_consen 5 IAKILTTTLGTTAGDFLSKT------LGLGYLISTLIFAALLAVV-LALWYR 49 (55)
T ss_pred HHHHHHHHhHHHHHHHHHhc------cCccHHHHHHHHHHHHHHH-HHHHHH
Confidence 46788888889999999984 3444555555555544443 334543
No 20
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=21.01 E-value=68 Score=22.37 Aligned_cols=26 Identities=8% Similarity=-0.155 Sum_probs=19.5
Q ss_pred chhHHHHHHHHHHhhhcc--cchhhHHH
Q 032451 47 KLQLKRLLLLMLFDFGYG--VPFGHFLN 72 (140)
Q Consensus 47 ~~D~~R~~~~~~~G~~~~--gP~~~~wy 72 (140)
...|.|.++|.++|+++. ||.+..|-
T Consensus 2 ~~~w~~W~K~~~~G~~ii~~G~~l~~y~ 29 (128)
T PF07960_consen 2 PPNWRRWAKMLVAGAVIIGGGPALVKYT 29 (128)
T ss_pred CchHHHHHHHHHhcceeEeechHHheec
Confidence 357889999999998654 67766654
No 21
>COG4779 FepG ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]
Probab=20.49 E-value=1.2e+02 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=23.0
Q ss_pred hCchHHHHHHHHHHHHHHHHHHHhhh
Q 032451 18 VHPLRTKAITAGVLAGCSDAIAQKIS 43 (140)
Q Consensus 18 ~~Pl~t~~~t~~~l~~~gD~laQ~~~ 43 (140)
.-|++..+..++.+..++|+++|.+.
T Consensus 291 gv~L~~~almGa~LLlaADll~q~l~ 316 (346)
T COG4779 291 GVSLLAAALMGALLLLAADLLAQHLF 316 (346)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHhcc
Confidence 34688899999999999999999985
No 22
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=20.31 E-value=2.7e+02 Score=18.33 Aligned_cols=57 Identities=16% Similarity=0.185 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhhCchHHHHHHHH-----HHHHHHHHHHHhhhC-----CCchhHHHHHHHHHHhh
Q 032451 5 VKEAWRKYLIQLQVHPLRTKAITAG-----VLAGCSDAIAQKISG-----VKKLQLKRLLLLMLFDF 61 (140)
Q Consensus 5 ~~~~~~~Y~~~l~~~Pl~t~~~t~~-----~l~~~gD~laQ~~~~-----~~~~D~~R~~~~~~~G~ 61 (140)
++.+...|.+.+.+||-+...+... .-...-|-+.|.+.. ++......++...+.|+
T Consensus 12 l~~~a~~~r~~~~~hP~~~~~~~~~~~~~p~~l~~~e~~l~~L~~aG~~~~~a~~~~~~l~~~v~g~ 78 (139)
T PF02909_consen 12 LRALARAYRAALLRHPWLAELLLARPPPGPNALRLMEAMLRALRDAGFSPEEAARAYAALSSFVLGF 78 (139)
T ss_dssp HHHHHHHHHHHHHTSTTHHHHHHTSSCTSHHHHHHHHHHHHHHHHTTEEHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCcCHHHHHHhcCCCChhHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHH
Confidence 5678899999999999888877665 334455555555532 12333444444445554
No 23
>PRK09477 napH quinol dehydrogenase membrane component; Provisional
Probab=20.06 E-value=4.1e+02 Score=20.43 Aligned_cols=81 Identities=14% Similarity=0.135 Sum_probs=44.1
Q ss_pred hhHHHHHHHHHHhhhcccchhhHHH--HHHH--hh---ccCCChHHHHHHHHHHHHhHHHHHHHH--HHHHHHHHhcCCC
Q 032451 48 LQLKRLLLLMLFDFGYGVPFGHFLN--KFLD--AI---FKGRDNKSVAKKVLLEQLIFSPWINFL--FMTYFGLVVEGKP 118 (140)
Q Consensus 48 ~D~~R~~~~~~~G~~~~gP~~~~wy--~~L~--~~---~~~~~~~~~~~Kvl~Dq~i~~P~~~~~--f~~~~~~~leg~~ 118 (140)
.-.+|+...++.+.++.+|....|. ..+. +. +|-.+....+.-++.-..+..+..... .+...+ ++-|+-
T Consensus 9 ~~~R~~~q~~~~~lf~~~~~~~~~~~~g~~~~s~~~~~~~~~dp~~~~q~~~a~~~~~~~~l~g~~iv~~~~~-l~~GR~ 87 (271)
T PRK09477 9 LILRRLSQLSILALFLSGPWFGVWILKGNLSSSLLFDTIPLTDPLATLQSLAAGHLPATVALIGALIITVFYA-LAGGRA 87 (271)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcceeEEecchHHHhcCCccccCHHHHHHHHHhcChhHHHHHHHHHHHHHHHH-HHhccc
Confidence 4678889999999888889877662 2222 22 233445455544444444433332221 122334 555654
Q ss_pred ----------hHHHHHHHHhh
Q 032451 119 ----------WGSVMKKVRKD 129 (140)
Q Consensus 119 ----------~~~~~~~~k~~ 129 (140)
++|..++++++
T Consensus 88 fCgwiCP~g~l~e~~~~l~~k 108 (271)
T PRK09477 88 FCSWVCPVNLVTDLANWLRRK 108 (271)
T ss_pred ceeeeCCchhHHHHHHHHHHH
Confidence 46666666654
Done!