Query 033371
Match_columns 120
No_of_seqs 120 out of 945
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 13:04:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033371.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033371hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944 Peroxisomal membrane p 99.9 1.8E-23 3.8E-28 154.6 9.9 105 16-120 46-156 (222)
2 TIGR02230 ATPase_gene1 F0F1-AT 59.1 40 0.00086 22.0 5.2 35 49-83 38-74 (100)
3 PF00140 Sigma70_r1_2: Sigma-7 56.5 7.2 0.00016 20.6 1.2 18 7-24 2-19 (37)
4 COG1284 Uncharacterized conser 54.8 56 0.0012 25.3 6.3 57 19-75 111-186 (289)
5 PF09105 SelB-wing_1: Elongati 54.8 12 0.00027 21.4 2.0 23 36-58 5-28 (61)
6 PF10929 DUF2811: Protein of u 53.0 28 0.0006 20.5 3.3 29 36-64 12-40 (57)
7 smart00337 BCL BCL (B-Cell lym 47.8 72 0.0016 20.3 5.4 28 35-63 35-62 (100)
8 PF03988 DUF347: Repeat of Unk 46.0 57 0.0012 18.6 4.9 46 21-73 4-49 (55)
9 KOG0769 Predicted mitochondria 43.8 80 0.0017 24.6 5.4 46 36-81 48-93 (308)
10 TIGR02163 napH_ ferredoxin-typ 36.2 1.4E+02 0.003 22.3 5.8 68 49-116 3-79 (255)
11 PRK09609 hypothetical protein; 32.8 2.5E+02 0.0054 22.2 6.9 54 27-82 58-111 (312)
12 PF09734 Tau95: RNA polymerase 31.6 25 0.00055 27.0 1.2 60 4-74 232-291 (310)
13 COG0534 NorM Na+-driven multid 29.9 3E+02 0.0065 22.3 10.9 92 23-115 65-161 (455)
14 PF06027 DUF914: Eukaryotic pr 27.9 1.5E+02 0.0033 23.4 5.0 45 25-70 173-217 (334)
15 PF10960 DUF2762: Protein of u 27.4 96 0.0021 18.9 3.0 24 87-110 4-27 (71)
16 PF09645 F-112: F-112 protein; 27.4 41 0.00088 22.0 1.4 26 33-58 23-49 (110)
17 PF02909 TetR_C: Tetracyclin r 26.2 1.9E+02 0.004 18.7 5.8 40 4-43 11-55 (139)
18 PF01306 LacY_symp: LacY proto 21.9 1.7E+02 0.0038 23.8 4.4 31 33-63 123-153 (412)
19 TIGR02838 spore_V_AC stage V s 20.0 3E+02 0.0066 19.1 4.7 76 17-95 12-102 (141)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=99.90 E-value=1.8e-23 Score=154.64 Aligned_cols=105 Identities=34% Similarity=0.574 Sum_probs=97.9
Q ss_pred HhcCchhHHHHHHHHHH-hHHHHHHHHHhc-----CCcchHHHHHHHHHHhhhchhhhHhHHHHHhhhhcCCCChHHHHH
Q 033371 16 LQVHPLRTKAITAGVLA-GCSDAIAQKISG-----VKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKGRDNKSVAK 89 (120)
Q Consensus 16 l~~~Pl~t~~~t~~~l~-~~gD~laQ~~~~-----~~~~d~~R~~~~~~~G~~~~gp~~~~wy~~L~~~~~~~~~~~~~~ 89 (120)
...+|+.+++++++.+. .+||+++|.++. .+++|+.|++||+++|+++.||.+|+||+.||+.+|.++..++++
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 46788888999988888 999999999964 257899999999999988999999999999999999999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHhcCCCCCC
Q 033371 90 KVLLEQLIFSPWINFLFMTYFGLVENHGVQS 120 (120)
Q Consensus 90 Kvl~Dq~i~~P~~~~~f~~~~~~leg~~~~~ 120 (120)
|++.||++++|+.+.+|+.+++++||++.+|
T Consensus 126 kvl~dql~~~P~~~~~ff~~~~~legk~~~~ 156 (222)
T KOG1944|consen 126 KVLLDQLVFAPLFIVVFFLLMGLLEGKTNEE 156 (222)
T ss_pred HHHHhhhhhchHHHHHHHHHHHHHcCCCHHH
Confidence 9999999999999999999999999999765
No 2
>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=59.05 E-value=40 Score=22.05 Aligned_cols=35 Identities=14% Similarity=0.120 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHhhhchhhhHhHHH--HHhhhhcCCCC
Q 033371 49 QLKRLLLLMLFDFGYGVPFGHFLN--KFLDAIFKGRD 83 (120)
Q Consensus 49 d~~R~~~~~~~G~~~~gp~~~~wy--~~L~~~~~~~~ 83 (120)
-++....+..+|..+..|++-.-| .+||+.+++..
T Consensus 38 ~~~~l~~~g~IG~~~v~pil~G~~lG~WLD~~~~t~~ 74 (100)
T TIGR02230 38 IWEGLGMFGLIGWSVAIPTLLGVAVGIWLDRHYPSPF 74 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc
Confidence 456667788999999999988777 89999998754
No 3
>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=56.50 E-value=7.2 Score=20.56 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=14.2
Q ss_pred HHHHHHHHHHhcCchhHH
Q 033371 7 EAWRKYLIQLQVHPLRTK 24 (120)
Q Consensus 7 ~l~~~Y~~~l~~~Pl~t~ 24 (120)
...+.|.+.+.++|++|.
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 456889999999999984
No 4
>COG1284 Uncharacterized conserved protein [Function unknown]
Probab=54.83 E-value=56 Score=25.26 Aligned_cols=57 Identities=23% Similarity=0.244 Sum_probs=38.8
Q ss_pred CchhHHHHHHHHHHhHH--------------HHHHHHHhcCCcchHHHHHHH-----HHHhhhchhhhHhHHHHHh
Q 033371 19 HPLRTKAITAGVLAGCS--------------DAIAQKISGVKKLQLKRLLLL-----MLFDFGYGVPFGHFLNKFL 75 (120)
Q Consensus 19 ~Pl~t~~~t~~~l~~~g--------------D~laQ~~~~~~~~d~~R~~~~-----~~~G~~~~gp~~~~wy~~L 75 (120)
++.+-.++.+|++.++| |++||.++++...+..+++-+ .+.+.++.+++-+.+|..+
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 55666799999998876 999999988777777665322 2333334456666677544
No 5
>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=54.79 E-value=12 Score=21.39 Aligned_cols=23 Identities=17% Similarity=0.057 Sum_probs=15.5
Q ss_pred HHHHHHH-hcCCcchHHHHHHHHH
Q 033371 36 DAIAQKI-SGVKKLQLKRLLLLML 58 (120)
Q Consensus 36 D~laQ~~-~~~~~~d~~R~~~~~~ 58 (120)
.++||.+ +.++.+||+....-+.
T Consensus 5 kilaqiiqehregldwqeaatras 28 (61)
T PF09105_consen 5 KILAQIIQEHREGLDWQEAATRAS 28 (61)
T ss_dssp HHHHHHHHC-TT-EEHHHHHHHHT
T ss_pred HHHHHHHHHHHccCcHHHHHHHhh
Confidence 5789999 4578899987655443
No 6
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=52.98 E-value=28 Score=20.50 Aligned_cols=29 Identities=21% Similarity=0.133 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCcchHHHHHHHHHHhhhch
Q 033371 36 DAIAQKISGVKKLQLKRLLLLMLFDFGYG 64 (120)
Q Consensus 36 D~laQ~~~~~~~~d~~R~~~~~~~G~~~~ 64 (120)
+.+.+.++.-+.+|-.|.+.-++-|+++.
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 55666777778899999999999888753
No 7
>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=47.84 E-value=72 Score=20.34 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=19.1
Q ss_pred HHHHHHHHhcCCcchHHHHHHHHHHhhhc
Q 033371 35 SDAIAQKISGVKKLQLKRLLLLMLFDFGY 63 (120)
Q Consensus 35 gD~laQ~~~~~~~~d~~R~~~~~~~G~~~ 63 (120)
..+..+.++. ..++|.|.+.+..+|..+
T Consensus 35 ~~Va~~lf~d-g~inWGRIval~~F~~~l 62 (100)
T smart00337 35 GEVATELFSD-GNINWGRVVALLSFGGAL 62 (100)
T ss_pred HHHHHHHHcc-CCCCHHHHHHHHHHHHHH
Confidence 3444443332 449999999999998864
No 8
>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=46.02 E-value=57 Score=18.65 Aligned_cols=46 Identities=17% Similarity=0.182 Sum_probs=31.1
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHhcCCcchHHHHHHHHHHhhhchhhhHhHHHH
Q 033371 21 LRTKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNK 73 (120)
Q Consensus 21 l~t~~~t~~~l~~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~~gp~~~~wy~ 73 (120)
++++.++...--..||.++|. .++.......++..++.. ....||+
T Consensus 4 W~a~ilt~~lGt~~~D~l~~~------lglg~~~~~~~~~~~l~~-~~~~~~~ 49 (55)
T PF03988_consen 4 WIAKILTTTLGTTAGDFLSKT------LGLGYLISTLIFAALLAV-VLALWYR 49 (55)
T ss_pred HHHHHHHHHhHHHHHHHHHhc------cCccHHHHHHHHHHHHHH-HHHHHHH
Confidence 467888899999999999984 455566666666665444 3445543
No 9
>KOG0769 consensus Predicted mitochondrial carrier protein [Energy production and conversion]
Probab=43.83 E-value=80 Score=24.64 Aligned_cols=46 Identities=15% Similarity=0.026 Sum_probs=28.8
Q ss_pred HHHHHHHhcCCcchHHHHHHHHHHhhhchhhhHhHHHHHhhhhcCC
Q 033371 36 DAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKG 81 (120)
Q Consensus 36 D~laQ~~~~~~~~d~~R~~~~~~~G~~~~gp~~~~wy~~L~~~~~~ 81 (120)
|+++|.+.++.-.-+.|-+--...+.++.-.+.+|||..+.+..-+
T Consensus 48 dvm~eiik~eg~lsLYqGl~p~~~~t~iSnFVYFY~y~~~k~~~~~ 93 (308)
T KOG0769|consen 48 DVMWEIIKEEGVLSLYQGLGPVLVSTFISNFVYFYTYSYFKAVASK 93 (308)
T ss_pred HHHHHHHhccchHHHhccccHHHHHHHHhhhHhhhhHHHHHHHHhc
Confidence 4444444332234455556666777777778889999999766543
No 10
>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=36.17 E-value=1.4e+02 Score=22.33 Aligned_cols=68 Identities=13% Similarity=0.111 Sum_probs=44.9
Q ss_pred hHHHHHHHHHHhhhchhhhHhHHH--HHhh--hh---cCCCChHHHHHHHHHHHHhHHHHHHHHHH--HHHHHhcCC
Q 033371 49 QLKRLLLLMLFDFGYGVPFGHFLN--KFLD--AI---FKGRDNKSVAKKVLLEQLIFSPWINFLFM--TYFGLVENH 116 (120)
Q Consensus 49 d~~R~~~~~~~G~~~~gp~~~~wy--~~L~--~~---~~~~~~~~~~~Kvl~Dq~i~~P~~~~~f~--~~~~~leg~ 116 (120)
-+||+...++...++.||....|. ..|. +. +|......++.-++....+..+.+..... ...+++-|+
T Consensus 3 ~~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~l~~GR 79 (255)
T TIGR02163 3 ILRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGTIPLSDPLITLQILLAGHSPPTNALIGALIIVAFYALFGGR 79 (255)
T ss_pred HHHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCCccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhcc
Confidence 368999999999988899888775 3333 22 34456677777777777766666655543 333555554
No 11
>PRK09609 hypothetical protein; Provisional
Probab=32.82 E-value=2.5e+02 Score=22.18 Aligned_cols=54 Identities=20% Similarity=0.124 Sum_probs=42.7
Q ss_pred HHHHHHhHHHHHHHHHhcCCcchHHHHHHHHHHhhhchhhhHhHHHHHhhhhcCCC
Q 033371 27 TAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKFLDAIFKGR 82 (120)
Q Consensus 27 t~~~l~~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~~gp~~~~wy~~L~~~~~~~ 82 (120)
.+++..+++|++.-.+.+ ..+.+.=++.-++.|. +.|-+..+.|+.+.+++.++
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 356677788999866654 5788888888888887 58988888899999988763
No 12
>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=31.58 E-value=25 Score=26.99 Aligned_cols=60 Identities=18% Similarity=0.297 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHhcCchhHHHHHHHHHHhHHHHHHHHHhcCCcchHHHHHHHHHHhhhchhhhHhHHHHH
Q 033371 4 IVKEAWRKYLIQLQVHPLRTKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHFLNKF 74 (120)
Q Consensus 4 ~~~~l~~~Y~~~l~~~Pl~t~~~t~~~l~~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~~gp~~~~wy~~ 74 (120)
....+.+.-+.++++||+.|+-..-.-+-..+ .....++++...+|-+ -.||+-..|-++
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 45677888899999999988764433331111 4567778888888877 499998888654
No 13
>COG0534 NorM Na+-driven multidrug efflux pump [Defense mechanisms]
Probab=29.90 E-value=3e+02 Score=22.26 Aligned_cols=92 Identities=22% Similarity=0.169 Sum_probs=54.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHhcCCcchHHHHHHHHHHhhhchh-hhHhHHHHH---hhhhcCCC-ChHHHHHHHHHHHHh
Q 033371 23 TKAITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGV-PFGHFLNKF---LDAIFKGR-DNKSVAKKVLLEQLI 97 (120)
Q Consensus 23 t~~~t~~~l~~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~~g-p~~~~wy~~---L~~~~~~~-~~~~~~~Kvl~Dq~i 97 (120)
.-++..++..+++=++||.+-.++.-+.+|+.+.+++-.++.| ++.-..+-+ +=+.+.++ +.....++=+-=..+
T Consensus 65 ~~~~~~gl~~g~~~liaq~~Ga~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~~~v~~~a~~Yl~i~~~ 144 (455)
T COG0534 65 IIAIFIGLGTGTTVLVAQAIGAGDRKKAKRVLGQGLLLALLLGLLLAILLLFFAEPLLRLLGAPAEVLELAAEYLRIILL 144 (455)
T ss_pred HHHHHHHHHHhHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHhHHHHHHHHHHHHHH
Confidence 3466778888999999999966677788888888888655566 443333333 33444432 233333333333333
Q ss_pred HHHHHHHHHHHHHHHhcC
Q 033371 98 FSPWINFLFMTYFGLVEN 115 (120)
Q Consensus 98 ~~P~~~~~f~~~~~~leg 115 (120)
..|. ...++...+.+++
T Consensus 145 ~~~~-~~~~~~~~~~lr~ 161 (455)
T COG0534 145 GAPF-ALLSFVLSGILRG 161 (455)
T ss_pred HHHH-HHHHHHHHHHHHh
Confidence 3443 4555555566654
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=27.95 E-value=1.5e+02 Score=23.36 Aligned_cols=45 Identities=20% Similarity=0.162 Sum_probs=28.7
Q ss_pred HHHHHHHHhHHHHHHHHHhcCCcchHHHHHHHHHHhhhchhhhHhH
Q 033371 25 AITAGVLAGCSDAIAQKISGVKKLQLKRLLLLMLFDFGYGVPFGHF 70 (120)
Q Consensus 25 ~~t~~~l~~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~~gp~~~~ 70 (120)
++.+++++++.+++...+-++.+. ..=...+.++|.++.+|....
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 578888999999887776442221 112456667777777766543
No 15
>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=27.43 E-value=96 Score=18.92 Aligned_cols=24 Identities=25% Similarity=0.281 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHH
Q 033371 87 VAKKVLLEQLIFSPWINFLFMTYF 110 (120)
Q Consensus 87 ~~~Kvl~Dq~i~~P~~~~~f~~~~ 110 (120)
-+.|+++.|.+|+-+++..++...
T Consensus 4 ei~k~~~sQG~fA~LFv~Ll~yvl 27 (71)
T PF10960_consen 4 EIIKLALSQGIFAVLFVWLLFYVL 27 (71)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHH
Confidence 467899999999999877766543
No 16
>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.
Probab=27.35 E-value=41 Score=22.03 Aligned_cols=26 Identities=23% Similarity=0.195 Sum_probs=16.6
Q ss_pred hHHHHHHHHH-hcCCcchHHHHHHHHH
Q 033371 33 GCSDAIAQKI-SGVKKLQLKRLLLLML 58 (120)
Q Consensus 33 ~~gD~laQ~~-~~~~~~d~~R~~~~~~ 58 (120)
.+-|++||.= .....++..|++|+.+
T Consensus 23 t~eDIlaqfeIS~s~Ay~I~~~lr~iC 49 (110)
T PF09645_consen 23 TLEDILAQFEISYSRAYNIQRVLRKIC 49 (110)
T ss_dssp -HHHHHHHH---HHHHHHHHHHHHHHH
T ss_pred cHHHHHHHhccchhhhhHHHHHHHHHH
Confidence 3568888873 4445678888888765
No 17
>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=26.24 E-value=1.9e+02 Score=18.65 Aligned_cols=40 Identities=18% Similarity=0.189 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhcCchhHHHHHHH-----HHHhHHHHHHHHHh
Q 033371 4 IVKEAWRKYLIQLQVHPLRTKAITAG-----VLAGCSDAIAQKIS 43 (120)
Q Consensus 4 ~~~~l~~~Y~~~l~~~Pl~t~~~t~~-----~l~~~gD~laQ~~~ 43 (120)
-++.+...|.+.+.+||.....+... .-...-|.+-|.+.
T Consensus 11 ~l~~~a~~~r~~~~~hP~~~~~~~~~~~~~p~~l~~~e~~l~~L~ 55 (139)
T PF02909_consen 11 RLRALARAYRAALLRHPWLAELLLARPPPGPNALRLMEAMLRALR 55 (139)
T ss_dssp HHHHHHHHHHHHHHTSTTHHHHHHTSSCTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCcCHHHHHHhcCCCChhHHHHHHHHHHHHH
Confidence 36778899999999999988877665 33344455555554
No 18
>PF01306 LacY_symp: LacY proton/sugar symporter; InterPro: IPR022814 In bacteria there are a number of families of transport proteins, including symporters and antiporters, that mediate the intake of a variety of sugars with the concomitant uptake of hydrogen ions (proton symporters) []. The lacY family of Escherichia coli and Klebsiella pneumoniae are proton/beta-galactoside symporters, which, like most sugar transporters, are integral membrane proteins with 12 predicted transmembrane (TM) regions. Also similar to the lacY family are the rafinose (rafB) and sucrose (cscB) permeases from E. coli []. This entry also includes bacterial phenylproprionate permease.; PDB: 1PV7_B 1PV6_A 2Y5Y_B 2CFQ_A 2V8N_B 2CFP_A.
Probab=21.89 E-value=1.7e+02 Score=23.75 Aligned_cols=31 Identities=19% Similarity=0.223 Sum_probs=24.4
Q ss_pred hHHHHHHHHHhcCCcchHHHHHHHHHHhhhc
Q 033371 33 GCSDAIAQKISGVKKLQLKRLLLLMLFDFGY 63 (120)
Q Consensus 33 ~~gD~laQ~~~~~~~~d~~R~~~~~~~G~~~ 63 (120)
++.|..+++..++..+|+.|.-....+|..+
T Consensus 123 ~~~Ea~~er~sr~~~feYG~~R~wGSig~ai 153 (412)
T PF01306_consen 123 PLSEAYAERVSRRNGFEYGRARMWGSIGFAI 153 (412)
T ss_dssp HHHHHHHHHHHHHHSS-HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhcCCcchHHHHhhHHHHH
Confidence 6779999999888899999987777777543
No 19
>TIGR02838 spore_V_AC stage V sporulation protein AC. This model describes stage V sporulation protein AC, a paralog of stage V sporulation protein AE. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sproulation defect.
Probab=20.04 E-value=3e+02 Score=19.11 Aligned_cols=76 Identities=9% Similarity=-0.015 Sum_probs=41.6
Q ss_pred hcCchhHHHHHH----HHHHhHHHHHHHHHhcCCcch----HH-HHHHHHHHhhhchhhhHhHHHHHhhhhcCC------
Q 033371 17 QVHPLRTKAITA----GVLAGCSDAIAQKISGVKKLQ----LK-RLLLLMLFDFGYGVPFGHFLNKFLDAIFKG------ 81 (120)
Q Consensus 17 ~~~Pl~t~~~t~----~~l~~~gD~laQ~~~~~~~~d----~~-R~~~~~~~G~~~~gp~~~~wy~~L~~~~~~------ 81 (120)
-|+|++.|++-+ |.++.+|.++-+......+++ .. -+..+...|.+..| .-+|+.|-++-..
T Consensus 12 Pk~~~~~n~l~AFlvGG~IC~iGQ~l~d~~~~~~~lt~~~a~~~~~~~lV~lgaiLtg---lGiYd~l~~faGAGa~VPI 88 (141)
T TIGR02838 12 PKPPYLKNCVMAFLVGGLICLIGQLISDFYLRYFQFSEKTAGSPTSATLIFISALLTG---LGVYDKIAQFAGAGSIVPI 88 (141)
T ss_pred CCCcHHHHHHHHHHhCcHHHHHHHHHHHHHHHhccCChhhcccchhhHHHHHHHHHhc---ccccHHHHHHcCCCceeec
Confidence 367888888765 455555555554443212233 22 34455555654332 3578888766532
Q ss_pred CChHHHHHHHHHHH
Q 033371 82 RDNKSVAKKVLLEQ 95 (120)
Q Consensus 82 ~~~~~~~~Kvl~Dq 95 (120)
+++.+.+.+-.++.
T Consensus 89 TGFansl~s~AiE~ 102 (141)
T TIGR02838 89 TGFANAMASPALEH 102 (141)
T ss_pred cchHHHHHHHHHHH
Confidence 56666666655543
Done!