Query 031930
Match_columns 150
No_of_seqs 162 out of 1046
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 07:19:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031930.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031930hhsearch_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 7.8E-33 1.7E-37 211.9 12.8 133 16-150 46-184 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.2 4.3E-12 9.2E-17 80.2 1.2 39 111-150 1-39 (68)
3 PF10929 DUF2811: Protein of u 61.5 16 0.00036 22.0 3.4 30 35-64 11-40 (57)
4 TIGR02163 napH_ ferredoxin-typ 47.8 87 0.0019 24.4 6.5 80 50-131 4-102 (255)
5 PF00140 Sigma70_r1_2: Sigma-7 45.4 13 0.00028 20.1 1.1 18 7-24 2-19 (37)
6 PF03988 DUF347: Repeat of Unk 45.3 64 0.0014 19.0 5.0 45 22-73 5-49 (55)
7 COG1284 Uncharacterized conser 38.9 1.3E+02 0.0029 24.0 6.4 57 19-75 111-186 (289)
8 KOG0769 Predicted mitochondria 36.2 1.1E+02 0.0025 24.5 5.4 71 35-105 47-126 (308)
9 PF06027 DUF914: Eukaryotic pr 34.0 1.2E+02 0.0025 24.9 5.4 51 19-70 165-217 (334)
10 PF09734 Tau95: RNA polymerase 32.0 26 0.00057 28.0 1.4 60 4-74 232-291 (310)
11 TIGR02230 ATPase_gene1 F0F1-AT 31.5 1.5E+02 0.0031 20.0 4.7 33 50-82 39-73 (100)
12 COG0534 NorM Na+-driven multid 29.6 3.4E+02 0.0074 22.8 10.8 81 23-103 65-149 (455)
13 PF07960 CBP4: CBP4; InterPro 27.6 35 0.00075 24.1 1.2 26 47-72 2-29 (128)
14 PRK09609 hypothetical protein; 25.6 2.7E+02 0.0058 22.7 6.0 53 27-81 58-110 (312)
15 PF11998 DUF3493: Protein of u 25.3 1.9E+02 0.0041 18.4 4.8 49 47-97 13-61 (75)
16 smart00337 BCL BCL (B-Cell lym 23.8 2.2E+02 0.0048 18.7 4.6 28 35-63 35-62 (100)
17 PF03818 MadM: Malonate/sodium 22.4 2E+02 0.0043 17.6 6.4 34 11-44 3-36 (60)
18 PF02909 TetR_C: Tetracyclin r 20.7 2.7E+02 0.0059 18.6 5.4 41 4-44 11-56 (139)
19 PF09105 SelB-wing_1: Elongati 20.6 89 0.0019 18.3 1.8 22 36-57 5-27 (61)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=7.8e-33 Score=211.95 Aligned_cols=133 Identities=35% Similarity=0.551 Sum_probs=126.1
Q ss_pred HhhCchhHHHHHHHHHH-HHHHHHHHhHhcC-----CchhhHHHHHHHHHhhhhhchhhhHHHHHHHhhcCCCCchHHHH
Q 031930 16 LQQHPLRTKAITAGVLS-AISDIVAQKLTGI-----QKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKGKKDTSTVA 89 (150)
Q Consensus 16 l~~~Pl~t~~~ts~~l~-~~gD~~aQ~~~~~-----~~~D~~R~~~~~~~G~~~~gP~~h~wy~~L~~~~~~~~~~~~~~ 89 (150)
...+|+++++++++.+. .+||+++|.++.+ +.+|+.|++||+++|+++.||..|+||+.||+.+|. ++..+++
T Consensus 46 ~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p~-~~~~~~~ 124 (222)
T KOG1944|consen 46 FSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKKLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFPK-KTLITVV 124 (222)
T ss_pred hhhhhHHHHHHHHHHHHHHhchhhhhhhhhhcccccccccHHHHHHHHhhhhheeccchhHHHHHHHHHccC-ccHHHHH
Confidence 46789999999998888 9999999999742 578999999999999999999999999999999999 7999999
Q ss_pred HHHHHhhhccchHHHHHHHHHHHHHhcCCChHHHHHHHHhcCHHHHhhCcccchhhhhhcC
Q 031930 90 KKVVLEQLTSSPWNNLMFMIYYGVVVEGRPWRDVKTKIKKDYPTVQYTSWTVLLLSLIVFW 150 (150)
Q Consensus 90 ~Kv~~Dq~v~~P~~~~~f~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~~~~vWp~~q~i~~ 150 (150)
+|++.||++++|+.+.+|+..++ ++||++.+++.++++++++|++++||++||++|+|||
T Consensus 125 ~kvl~dql~~~P~~~~~ff~~~~-~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF 184 (222)
T KOG1944|consen 125 KKVLLDQLVFAPLFIVVFFLLMG-LLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINF 184 (222)
T ss_pred HHHHHhhhhhchHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeee
Confidence 99999999999999999999999 9999999999999999999999999999999999996
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=99.20 E-value=4.3e-12 Score=80.22 Aligned_cols=39 Identities=33% Similarity=0.700 Sum_probs=37.2
Q ss_pred HHHHhcCCChHHHHHHHHhcCHHHHhhCcccchhhhhhcC
Q 031930 111 YGVVVEGRPWRDVKTKIKKDYPTVQYTSWTVLLLSLIVFW 150 (150)
Q Consensus 111 ~~~~l~g~~~~~~~~~~~~~~~~~~~~~~~vWp~~q~i~~ 150 (150)
|+ ++||+|++++++++|++++++++++|++|||+|++||
T Consensus 1 Mg-~l~g~s~~~~~~~l~~~~~~~~~~~~~~Wp~~~~vnF 39 (68)
T PF04117_consen 1 MG-LLEGKSWEEIKEKLKRDYWPTLKASWKFWPPAQIVNF 39 (68)
T ss_pred CC-cccCCCHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHh
Confidence 46 8999999999999999999999999999999999986
No 3
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=61.51 E-value=16 Score=22.04 Aligned_cols=30 Identities=13% Similarity=0.102 Sum_probs=24.0
Q ss_pred HHHHHHhHhcCCchhhHHHHHHHHHhhhhh
Q 031930 35 SDIVAQKLTGIQKLQLRRLLLKVLFGCAYL 64 (150)
Q Consensus 35 gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~ 64 (150)
=+.+.+.++..+.+|-.|.+.-++-|+++.
T Consensus 11 ~~~m~~fie~hP~WDQ~Rl~~aALa~FL~Q 40 (57)
T PF10929_consen 11 HQAMKDFIETHPNWDQYRLFQAALAGFLLQ 40 (57)
T ss_pred HHHHHHHHHcCCCchHHHHHHHHHHHHHHH
Confidence 355667777788999999999999998754
No 4
>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=47.76 E-value=87 Score=24.36 Aligned_cols=80 Identities=18% Similarity=0.274 Sum_probs=52.2
Q ss_pred hHHHHHHHHHhhhhhchhhhHHH--HHHH--hh---cCCCCchHHHHHHHHHhhhccchHHHHHHH--HHHHHHhcCCC-
Q 031930 50 LRRLLLKVLFGCAYLGPFGHFLH--LILD--KI---FKGKKDTSTVAKKVVLEQLTSSPWNNLMFM--IYYGVVVEGRP- 119 (150)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~h~wy--~~L~--~~---~~~~~~~~~~~~Kv~~Dq~v~~P~~~~~f~--~~~~~~l~g~~- 119 (150)
+||+...++...++.||..+.|. ..|. +. +|. .++...+.-++....+..+.+..... ...+ ++-|+-
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~~~l-~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~-l~~GR~f 81 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGTIPL-SDPLITLQILLAGHSPPTNALIGALIIVAFYA-LFGGRAF 81 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCCccC-cCHHHHHHHHHhcChhhHHHHHHHHHHHHHHH-HHhcccc
Confidence 68999999999988899887775 2332 22 344 46677777777777776666655533 3335 666662
Q ss_pred ---------hHHHHHHHHhcC
Q 031930 120 ---------WRDVKTKIKKDY 131 (150)
Q Consensus 120 ---------~~~~~~~~~~~~ 131 (150)
++|..++++++.
T Consensus 82 CgwiCP~g~~~el~~~l~~k~ 102 (255)
T TIGR02163 82 CSWVCPVNLVTDFAAWLRRKL 102 (255)
T ss_pred eeccCCchHHHHHHHHHHHhh
Confidence 566666665543
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=45.44 E-value=13 Score=20.12 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhhCchhHH
Q 031930 7 KGLQQYLIQLQQHPLRTK 24 (150)
Q Consensus 7 ~~~~~Y~~~l~~~Pl~t~ 24 (150)
..++.|.+.+.++|++|.
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 356889999999999874
No 6
>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=45.27 E-value=64 Score=19.01 Aligned_cols=45 Identities=16% Similarity=0.201 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHhhhhhchhhhHHHH
Q 031930 22 RTKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHL 73 (150)
Q Consensus 22 ~t~~~ts~~l~~~gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~wy~ 73 (150)
.++.+++.+-...||.++|. .+........+++..+...+ -.||+
T Consensus 5 ~a~ilt~~lGt~~~D~l~~~------lglg~~~~~~~~~~~l~~~~-~~~~~ 49 (55)
T PF03988_consen 5 IAKILTTTLGTTAGDFLSKT------LGLGYLISTLIFAALLAVVL-ALWYR 49 (55)
T ss_pred HHHHHHHHhHHHHHHHHHhc------cCccHHHHHHHHHHHHHHHH-HHHHH
Confidence 57888999999999999994 44555555556665544443 35543
No 7
>COG1284 Uncharacterized conserved protein [Function unknown]
Probab=38.95 E-value=1.3e+02 Score=24.03 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=38.1
Q ss_pred CchhHHHHHHHHHHHHH--------------HHHHHhHhcCCchhhHHHHH-----HHHHhhhhhchhhhHHHHHH
Q 031930 19 HPLRTKAITAGVLSAIS--------------DIVAQKLTGIQKLQLRRLLL-----KVLFGCAYLGPFGHFLHLIL 75 (150)
Q Consensus 19 ~Pl~t~~~ts~~l~~~g--------------D~~aQ~~~~~~~~D~~R~~~-----~~~~G~~~~gP~~h~wy~~L 75 (150)
++.+-.++-+|++.|+| |++||.++++..+|.-++.- ..+.++++.+|.-+..|..+
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 56667899999998876 99999998877666665532 22333333445666666443
No 8
>KOG0769 consensus Predicted mitochondrial carrier protein [Energy production and conversion]
Probab=36.21 E-value=1.1e+02 Score=24.54 Aligned_cols=71 Identities=17% Similarity=0.046 Sum_probs=37.8
Q ss_pred HHHHHHhHhcCCchhhHHHHHHHHHhhhhhchhhhHHHHHHHhhcCCCC---------chHHHHHHHHHhhhccchHHHH
Q 031930 35 SDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKGKK---------DTSTVAKKVVLEQLTSSPWNNL 105 (150)
Q Consensus 35 gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~wy~~L~~~~~~~~---------~~~~~~~Kv~~Dq~v~~P~~~~ 105 (150)
.|+++|.+.++.-...-|-+--...+.|++--+.+|||.++.+....+. +..-.+.-=.++++.-.|+...
T Consensus 47 ~dvm~eiik~eg~lsLYqGl~p~~~~t~iSnFVYFY~y~~~k~~~~~~~~s~s~~t~~~Lllga~AGsinvl~T~Plwvv 126 (308)
T KOG0769|consen 47 SDVMWEIIKEEGVLSLYQGLGPVLVSTFISNFVYFYTYSYFKAVASKGKLSQSSGTKADLLLGAAAGSINVLLTTPLWVV 126 (308)
T ss_pred HHHHHHHHhccchHHHhccccHHHHHHHHhhhHhhhhHHHHHHHHhcCCCcCCcchHHHHHHHHHHhhhHHHhcChHHHH
Confidence 3444444433333334444445556666666778899999987653310 1111222233566677777544
No 9
>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=34.00 E-value=1.2e+02 Score=24.92 Aligned_cols=51 Identities=24% Similarity=0.263 Sum_probs=34.1
Q ss_pred Cchh--HHHHHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHhhhhhchhhhH
Q 031930 19 HPLR--TKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHF 70 (150)
Q Consensus 19 ~Pl~--t~~~ts~~l~~~gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~ 70 (150)
+|++ .=++.+++++|+++++-..+.++.+. ..=...++++|.++.||....
T Consensus 165 ~~i~GDll~l~~a~lya~~nV~~E~~v~~~~~-~~~lg~~Glfg~ii~~iq~~i 217 (334)
T PF06027_consen 165 NPILGDLLALLGAILYAVSNVLEEKLVKKAPR-VEFLGMLGLFGFIISGIQLAI 217 (334)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHhcccCCH-HHHHHHHHHHHHHHHHHHHHh
Confidence 4444 23678899999999987777653221 223567778888888877653
No 10
>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=32.04 E-value=26 Score=27.98 Aligned_cols=60 Identities=17% Similarity=0.231 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHhhhhhchhhhHHHHH
Q 031930 4 IAKKGLQQYLIQLQQHPLRTKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLI 74 (150)
Q Consensus 4 ~~~~~~~~Y~~~l~~~Pl~t~~~ts~~l~~~gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~wy~~ 74 (150)
......+.-++++++||+.|+-..-.-+-..+ .....++++....|-+. .||+-..|-++
T Consensus 232 ~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~----------~~~~~k~~l~~v~Y~f~-~GPwr~~~vr~ 291 (310)
T PF09734_consen 232 VLQELIQELKKLFEERPIWTRRALLNHLPKSG----------SQSKLKRALPYVAYYFK-NGPWRDCWVRF 291 (310)
T ss_pred hHHHHHHHHHHHHhcCCccCHHHHHHhhhhcc----------cHHHHHHHHHhhEEEEe-cCcccceeEec
Confidence 44567888899999999998865443332221 45677788888888875 99999888764
No 11
>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=31.45 E-value=1.5e+02 Score=20.01 Aligned_cols=33 Identities=18% Similarity=0.091 Sum_probs=26.7
Q ss_pred hHHHHHHHHHhhhhhchhhhHHH--HHHHhhcCCC
Q 031930 50 LRRLLLKVLFGCAYLGPFGHFLH--LILDKIFKGK 82 (150)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~h~wy--~~L~~~~~~~ 82 (150)
++....+..+|.-+.+|+.---| .+||+.++++
T Consensus 39 ~~~l~~~g~IG~~~v~pil~G~~lG~WLD~~~~t~ 73 (100)
T TIGR02230 39 WEGLGMFGLIGWSVAIPTLLGVAVGIWLDRHYPSP 73 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Confidence 55666788999998999887666 6899999873
No 12
>COG0534 NorM Na+-driven multidrug efflux pump [Defense mechanisms]
Probab=29.62 E-value=3.4e+02 Score=22.83 Aligned_cols=81 Identities=19% Similarity=0.251 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHhhhhhc-hhhhHHHHHHH---hhcCCCCchHHHHHHHHHhhhc
Q 031930 23 TKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLG-PFGHFLHLILD---KIFKGKKDTSTVAKKVVLEQLT 98 (150)
Q Consensus 23 t~~~ts~~l~~~gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~g-P~~h~wy~~L~---~~~~~~~~~~~~~~Kv~~Dq~v 98 (150)
.-++..|+-.+++=++||.+-.++.-+.+|+.+.+++-.++.| ++.-..+-+.| +.+..+.+......+=+-=...
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 3456778888999999999977677888899888888666666 44433333334 4444422333344433333344
Q ss_pred cchHH
Q 031930 99 SSPWN 103 (150)
Q Consensus 99 ~~P~~ 103 (150)
..|..
T Consensus 145 ~~~~~ 149 (455)
T COG0534 145 GAPFA 149 (455)
T ss_pred HHHHH
Confidence 44443
No 13
>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=27.63 E-value=35 Score=24.11 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=19.4
Q ss_pred chhhHHHHHHHHHhhhhh--chhhhHHH
Q 031930 47 KLQLRRLLLKVLFGCAYL--GPFGHFLH 72 (150)
Q Consensus 47 ~~D~~R~~~~~~~G~~~~--gP~~h~wy 72 (150)
...|.|..+|.++|+++. ||++..|-
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 457899999999998765 66665443
No 14
>PRK09609 hypothetical protein; Provisional
Probab=25.60 E-value=2.7e+02 Score=22.75 Aligned_cols=53 Identities=17% Similarity=0.212 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHhHhcCCchhhHHHHHHHHHhhhhhchhhhHHHHHHHhhcCC
Q 031930 27 TAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKG 81 (150)
Q Consensus 27 ts~~l~~~gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~wy~~L~~~~~~ 81 (150)
.+++..+++|++.=.+.+ ..+.+-=++.-++.|.. .|-+..+.|+.+.+.|..
T Consensus 58 ~G~ivG~lsDLLs~li~p-G~ffPgFTLsa~l~GlI-~Glf~~~~fk~~~~~f~~ 110 (312)
T PRK09609 58 VGFFTGLLSDLISFLFVP-GVYHPYYTLAAMVYGFI-PGIVGWFFFKFGKKFFGK 110 (312)
T ss_pred HHHHHHHHHHHHHHHhcC-CccCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhH
Confidence 456777889999977654 67888888888877774 888888888999888876
No 15
>PF11998 DUF3493: Protein of unknown function (DUF3493); InterPro: IPR021883 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.
Probab=25.29 E-value=1.9e+02 Score=18.42 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=32.5
Q ss_pred chhhHHHHHHHHHhhhhhchhhhHHHHHHHhhcCCCCchHHHHHHHHHhhh
Q 031930 47 KLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKGKKDTSTVAKKVVLEQL 97 (150)
Q Consensus 47 ~~D~~R~~~~~~~G~~~~gP~~h~wy~~L~~~~~~~~~~~~~~~Kv~~Dq~ 97 (150)
.-.+-|.+|.++||++ .+--.---+-.+-+...+ ++....+.-+.+|-.
T Consensus 13 ~~aPfR~lR~f~y~a~-~aSa~iG~~i~~~rl~a~-~~l~~~l~nlaI~ig 61 (75)
T PF11998_consen 13 AQAPFRGLRRFFYGAF-GASAGIGLFIFLFRLIAG-PDLNEALPNLAIQIG 61 (75)
T ss_pred HHCchHHHHHHHHHHH-HHHHHHHHHHHHHHHHcC-ccHHHHhhhHhHHHH
Confidence 3456799999999997 444444555566666666 566666776766654
No 16
>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=23.76 E-value=2.2e+02 Score=18.65 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=19.3
Q ss_pred HHHHHHhHhcCCchhhHHHHHHHHHhhhh
Q 031930 35 SDIVAQKLTGIQKLQLRRLLLKVLFGCAY 63 (150)
Q Consensus 35 gD~~aQ~~~~~~~~D~~R~~~~~~~G~~~ 63 (150)
..+..+.+ ++..++|.|...+..+|..+
T Consensus 35 ~~Va~~lf-~dg~inWGRIval~~F~~~l 62 (100)
T smart00337 35 GEVATELF-SDGNINWGRVVALLSFGGAL 62 (100)
T ss_pred HHHHHHHH-ccCCCCHHHHHHHHHHHHHH
Confidence 33333433 34559999999999998863
No 17
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=22.39 E-value=2e+02 Score=17.56 Aligned_cols=34 Identities=24% Similarity=0.188 Sum_probs=30.6
Q ss_pred HHHHHHhhCchhHHHHHHHHHHHHHHHHHHhHhc
Q 031930 11 QYLIQLQQHPLRTKAITAGVLSAISDIVAQKLTG 44 (150)
Q Consensus 11 ~Y~~~l~~~Pl~t~~~ts~~l~~~gD~~aQ~~~~ 44 (150)
...+.++++.++|.-..-|+++-++..++-++.+
T Consensus 3 ~i~~vl~~ngLitaFa~vG~~m~~S~~lS~~LT~ 36 (60)
T PF03818_consen 3 MIEKVLTKNGLITAFAVVGIIMWVSYWLSKKLTR 36 (60)
T ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3467899999999999999999999999999876
No 18
>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=20.67 E-value=2.7e+02 Score=18.56 Aligned_cols=41 Identities=15% Similarity=0.162 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhhCchhHHHHHHH-----HHHHHHHHHHHhHhc
Q 031930 4 IAKKGLQQYLIQLQQHPLRTKAITAG-----VLSAISDIVAQKLTG 44 (150)
Q Consensus 4 ~~~~~~~~Y~~~l~~~Pl~t~~~ts~-----~l~~~gD~~aQ~~~~ 44 (150)
-++.+...|.+.+.+||-+...+.+. .-...-|.+.|.+..
T Consensus 11 ~l~~~a~~~r~~~~~hP~~~~~~~~~~~~~p~~l~~~e~~l~~L~~ 56 (139)
T PF02909_consen 11 RLRALARAYRAALLRHPWLAELLLARPPPGPNALRLMEAMLRALRD 56 (139)
T ss_dssp HHHHHHHHHHHHHHTSTTHHHHHHTSSCTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCcCHHHHHHhcCCCChhHHHHHHHHHHHHHH
Confidence 35678899999999999888777655 444556666666654
No 19
>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=20.55 E-value=89 Score=18.29 Aligned_cols=22 Identities=18% Similarity=0.225 Sum_probs=14.8
Q ss_pred HHHHHhHhc-CCchhhHHHHHHH
Q 031930 36 DIVAQKLTG-IQKLQLRRLLLKV 57 (150)
Q Consensus 36 D~~aQ~~~~-~~~~D~~R~~~~~ 57 (150)
.++||.+.+ ++.+||...+.-+
T Consensus 5 kilaqiiqehregldwqeaatra 27 (61)
T PF09105_consen 5 KILAQIIQEHREGLDWQEAATRA 27 (61)
T ss_dssp HHHHHHHHC-TT-EEHHHHHHHH
T ss_pred HHHHHHHHHHHccCcHHHHHHHh
Confidence 578999864 6788988665433
Done!