Query 032703
Match_columns 135
No_of_seqs 149 out of 932
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 04:52:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032703.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032703hhsearch_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 5.1E-26 1.1E-30 172.8 11.1 117 16-134 46-168 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 96.8 0.00017 3.7E-09 44.9 -1.0 24 111-135 1-24 (68)
3 TIGR02163 napH_ ferredoxin-typ 63.1 32 0.0007 26.5 6.3 79 50-130 4-101 (255)
4 COG1284 Uncharacterized conser 55.5 95 0.0021 24.7 7.8 57 19-75 111-186 (289)
5 KOG0769 Predicted mitochondria 53.6 39 0.00085 27.0 5.2 70 35-104 47-125 (308)
6 PF00140 Sigma70_r1_2: Sigma-7 48.1 9.9 0.00021 20.5 0.9 18 7-24 2-19 (37)
7 COG0534 NorM Na+-driven multid 46.9 1.7E+02 0.0037 24.4 11.7 93 23-117 65-161 (455)
8 smart00337 BCL BCL (B-Cell lym 43.1 66 0.0014 21.1 4.5 28 35-63 35-62 (100)
9 PF03818 MadM: Malonate/sodium 36.9 99 0.0021 18.8 6.4 34 11-44 3-36 (60)
10 PF03988 DUF347: Repeat of Unk 36.6 90 0.002 18.3 5.3 45 22-73 5-49 (55)
11 PF06027 DUF914: Eukaryotic pr 35.8 1E+02 0.0023 25.0 5.4 50 19-69 165-216 (334)
12 PRK09609 hypothetical protein; 32.9 1.7E+02 0.0038 23.6 6.1 53 27-81 58-110 (312)
13 PRK09477 napH quinol dehydroge 32.1 2.2E+02 0.0047 22.1 6.5 81 48-130 9-108 (271)
14 PF10929 DUF2811: Protein of u 31.0 95 0.0021 18.7 3.3 28 36-63 12-39 (57)
15 PF08628 Nexin_C: Sorting nexi 29.6 1.3E+02 0.0028 19.9 4.3 45 89-134 10-54 (113)
16 TIGR02230 ATPase_gene1 F0F1-AT 26.6 2E+02 0.0044 19.2 5.3 33 50-82 39-73 (100)
17 PF14490 HHH_4: Helix-hairpin- 26.4 20 0.00043 23.3 -0.2 55 4-59 24-82 (94)
18 PF10960 DUF2762: Protein of u 26.3 96 0.0021 19.4 2.9 25 88-112 4-28 (71)
19 PF03698 UPF0180: Uncharacteri 25.7 52 0.0011 21.1 1.7 17 115-131 63-79 (80)
20 PF11547 E3_UbLigase_EDD: E3 u 24.0 88 0.0019 18.3 2.2 19 111-130 17-35 (53)
21 PF11043 DUF2856: Protein of u 24.0 51 0.0011 21.4 1.4 17 115-131 14-30 (97)
22 cd06845 Bcl-2_like Apoptosis r 23.2 1.6E+02 0.0034 20.3 3.9 17 46-62 83-99 (144)
23 COG3037 SgaT Uncharacterized p 22.9 85 0.0018 26.8 2.8 37 88-124 6-42 (481)
24 PRK12997 PTS system ascorbate- 22.8 1.5E+02 0.0032 25.4 4.2 35 91-125 9-43 (466)
25 PRK09548 PTS system ascorbate- 22.2 1.2E+02 0.0026 26.8 3.7 32 94-125 12-43 (602)
26 PF09734 Tau95: RNA polymerase 21.6 69 0.0015 25.3 2.0 61 3-74 231-291 (310)
27 PF09105 SelB-wing_1: Elongati 21.6 1.1E+02 0.0023 17.9 2.3 21 36-56 5-26 (61)
28 PF01306 LacY_symp: LacY proto 20.1 2.1E+02 0.0046 23.9 4.6 31 33-63 123-153 (412)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=99.93 E-value=5.1e-26 Score=172.84 Aligned_cols=117 Identities=36% Similarity=0.527 Sum_probs=110.0
Q ss_pred HhhCchHHHHHHHHHHH-HHHHHHHHHHhcc-----ccchhHHHHHHHHHhhhhhhhhHHHHHHHhhhhccCCCCHHHHH
Q 032703 16 LQQHPLRTKAITAGVLS-AISDIVAQKLTGI-----QKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKGKKDTSTVA 89 (135)
Q Consensus 16 l~~~Pl~tk~it~~~l~-~~gD~laQ~~~~~-----~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~~~~~~~~~ 89 (135)
...+|+.+++++++.+. .+||+++|.++.+ +.+|+.|++||+++|+++.||.+|+||+.||+.+|. ++..+++
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 45689899999888888 9999999998753 468999999999999999999999999999999999 8999999
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHhcccCCC
Q 032703 90 KKVVLEQLTSSPWNNLMFMIYYGVVVEGKLILHNIINFTFGRWNH 134 (135)
Q Consensus 90 ~Kv~~DQ~i~~P~~~~~f~~~~~~~leg~~~~~~~~~lr~~~w~~ 134 (135)
+|++.||++++|+++.+||.+++ ++||++.+++.++++++|||+
T Consensus 125 ~kvl~dql~~~P~~~~~ff~~~~-~legk~~~~~~~~~~~~~~p~ 168 (222)
T KOG1944|consen 125 KKVLLDQLVFAPLFIVVFFLLMG-LLEGKTNEEAKAKLKRKFWPT 168 (222)
T ss_pred HHHHHhhhhhchHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999 999999999999999999986
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=96.83 E-value=0.00017 Score=44.88 Aligned_cols=24 Identities=21% Similarity=0.277 Sum_probs=21.7
Q ss_pred HHHHhcCCCHHHHHHHHhcccCCCC
Q 032703 111 YGVVVEGKLILHNIINFTFGRWNHW 135 (135)
Q Consensus 111 ~~~~leg~~~~~~~~~lr~~~w~~~ 135 (135)
|+ ++||+|++++++++|++||+++
T Consensus 1 Mg-~l~g~s~~~~~~~l~~~~~~~~ 24 (68)
T PF04117_consen 1 MG-LLEGKSWEEIKEKLKRDYWPTL 24 (68)
T ss_pred CC-cccCCCHHHHHHHHHHHHHHHH
Confidence 46 8999999999999999999863
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=63.11 E-value=32 Score=26.50 Aligned_cols=79 Identities=16% Similarity=0.217 Sum_probs=53.0
Q ss_pred hHHHHHHHHHhhhhhhhhHHHHH--HHhh--hh---ccCCCCHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHhcCC--
Q 032703 50 LRRLLLKVLFGCAYLGPFGHFLH--LILD--KI---FKGKKDTSTVAKKVVLEQLTSSPWNNLMFM--IYYGVVVEGK-- 118 (135)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~~~wy--~~L~--~~---~~~~~~~~~~~~Kv~~DQ~i~~P~~~~~f~--~~~~~~leg~-- 118 (135)
+||+...++...++.||....|. ..|. +. +|. .+...++.-++....+..+.+..... ...+ ++-|+
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 68999999999998999877775 3333 22 334 57777777777777766666554433 3345 66665
Q ss_pred --------CHHHHHHHHhcc
Q 032703 119 --------LILHNIINFTFG 130 (135)
Q Consensus 119 --------~~~~~~~~lr~~ 130 (135)
.++|..++++++
T Consensus 82 CgwiCP~g~~~el~~~l~~k 101 (255)
T TIGR02163 82 CSWVCPVNLVTDFAAWLRRK 101 (255)
T ss_pred eeccCCchHHHHHHHHHHHh
Confidence 567777766654
No 4
>COG1284 Uncharacterized conserved protein [Function unknown]
Probab=55.50 E-value=95 Score=24.67 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=39.3
Q ss_pred CchHHHHHHHHHHHHHH--------------HHHHHHHhccccchhHHHHH-----HHHHhhhhhhhhHHHHHHHh
Q 032703 19 HPLRTKAITAGVLSAIS--------------DIVAQKLTGIQKLQLRRLLL-----KVLFGCAYLGPFGHFLHLIL 75 (135)
Q Consensus 19 ~Pl~tk~it~~~l~~~g--------------D~laQ~~~~~~~~D~~R~~~-----~~~~G~~~~gP~~~~wy~~L 75 (135)
++.+-.++-+|++.|+| |++||.++++..++..+++- ..+.++++.+|+-+..|..+
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 56667899999998886 99999999877777776542 22334443446666666544
No 5
>KOG0769 consensus Predicted mitochondrial carrier protein [Energy production and conversion]
Probab=53.57 E-value=39 Score=26.95 Aligned_cols=70 Identities=17% Similarity=0.038 Sum_probs=38.5
Q ss_pred HHHHHHHHhccccchhHHHHHHHHHhhhhhhhhHHHHHHHhhhhccCCC---------CHHHHHHHHHHHHHhHHHHHH
Q 032703 35 SDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKGKK---------DTSTVAKKVVLEQLTSSPWNN 104 (135)
Q Consensus 35 gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~~~---------~~~~~~~Kv~~DQ~i~~P~~~ 104 (135)
.|++.|.+.+..-.-..|-+.-...+.+++--+-+|||.++.+....++ ++.-.+.-=.++++.-.|+..
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 3444444433233344455555666677777778999999987654421 111222223456666677654
No 6
>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=48.08 E-value=9.9 Score=20.53 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=14.2
Q ss_pred HHHHHHHHHHhhCchHHH
Q 032703 7 KGLQQYLIQLQQHPLRTK 24 (135)
Q Consensus 7 ~~~~~Y~~~l~~~Pl~tk 24 (135)
...+.|.+.+.++|++|.
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 456899999999999875
No 7
>COG0534 NorM Na+-driven multidrug efflux pump [Defense mechanisms]
Probab=46.93 E-value=1.7e+02 Score=24.37 Aligned_cols=93 Identities=19% Similarity=0.309 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhhhhhh-hhHHHHHHHhh---hhccCCCCHHHHHHHHHHHHHh
Q 032703 23 TKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLG-PFGHFLHLILD---KIFKGKKDTSTVAKKVVLEQLT 98 (135)
Q Consensus 23 tk~it~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~g-P~~~~wy~~L~---~~~~~~~~~~~~~~Kv~~DQ~i 98 (135)
.-++..++-.+++=++||.+-.++.-+.+|+.+.+++-.++.| ++.-..+-+.| +.+..+.+......+=+-=..+
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 3456778888999999999987777888899888888666666 44444444444 4444322333333333333334
Q ss_pred HHHHHHHHHHHHHHHHhcC
Q 032703 99 SSPWNNLMFMIYYGVVVEG 117 (135)
Q Consensus 99 ~~P~~~~~f~~~~~~~leg 117 (135)
..|.. ..+++..+ .+++
T Consensus 145 ~~~~~-~~~~~~~~-~lr~ 161 (455)
T COG0534 145 GAPFA-LLSFVLSG-ILRG 161 (455)
T ss_pred HHHHH-HHHHHHHH-HHHh
Confidence 44443 33344444 4543
No 8
>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=43.08 E-value=66 Score=21.06 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=20.0
Q ss_pred HHHHHHHHhccccchhHHHHHHHHHhhhh
Q 032703 35 SDIVAQKLTGIQKLQLRRLLLKVLFGCAY 63 (135)
Q Consensus 35 gD~laQ~~~~~~~~D~~R~~~~~~~G~~~ 63 (135)
..+..+.+ ++..++|.|.+.+..||+.+
T Consensus 35 ~~Va~~lf-~dg~inWGRIval~~F~~~l 62 (100)
T smart00337 35 GEVATELF-SDGNINWGRVVALLSFGGAL 62 (100)
T ss_pred HHHHHHHH-ccCCCCHHHHHHHHHHHHHH
Confidence 44444444 44669999999999998874
No 9
>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=36.88 E-value=99 Score=18.80 Aligned_cols=34 Identities=24% Similarity=0.188 Sum_probs=30.5
Q ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhc
Q 032703 11 QYLIQLQQHPLRTKAITAGVLSAISDIVAQKLTG 44 (135)
Q Consensus 11 ~Y~~~l~~~Pl~tk~it~~~l~~~gD~laQ~~~~ 44 (135)
.-.+.++++.++|....-|+++.++..++-++.+
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 4567889999999999999999999999988875
No 10
>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=36.58 E-value=90 Score=18.25 Aligned_cols=45 Identities=16% Similarity=0.201 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhhhhhhhhHHHHHH
Q 032703 22 RTKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHL 73 (135)
Q Consensus 22 ~tk~it~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~ 73 (135)
+++.+|...-..+||.++|. .+........+++.++...+ -.||+
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 56788899999999999994 45556666666666645543 34553
No 11
>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=35.80 E-value=1e+02 Score=24.95 Aligned_cols=50 Identities=24% Similarity=0.262 Sum_probs=32.6
Q ss_pred CchH--HHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhhhhhhhhHH
Q 032703 19 HPLR--TKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGH 69 (135)
Q Consensus 19 ~Pl~--tk~it~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~ 69 (135)
+|++ -=++.+++++++++++...+.++.+. ..=...++++|.++.||...
T Consensus 165 ~~i~GDll~l~~a~lya~~nV~~E~~v~~~~~-~~~lg~~Glfg~ii~~iq~~ 216 (334)
T PF06027_consen 165 NPILGDLLALLGAILYAVSNVLEEKLVKKAPR-VEFLGMLGLFGFIISGIQLA 216 (334)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHhcccCCH-HHHHHHHHHHHHHHHHHHHH
Confidence 4554 23678899999999987776653221 11245677788887777654
No 12
>PRK09609 hypothetical protein; Provisional
Probab=32.92 E-value=1.7e+02 Score=23.63 Aligned_cols=53 Identities=17% Similarity=0.212 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhhhhhhhhHHHHHHHhhhhccC
Q 032703 27 TAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLILDKIFKG 81 (135)
Q Consensus 27 t~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~L~~~~~~ 81 (135)
.+++..+++|++.-.+.+ ..+.+.=++.-++.|.+ .|-+..+.|+.+.+.|..
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 356677889999977754 68888888888877765 888888888888888865
No 13
>PRK09477 napH quinol dehydrogenase membrane component; Provisional
Probab=32.13 E-value=2.2e+02 Score=22.06 Aligned_cols=81 Identities=16% Similarity=0.125 Sum_probs=44.7
Q ss_pred chhHHHHHHHHHhhhhhhhhHHHHH--HHhh-----hhccCCCCHHHHHHHHHHHHHhHHHHHHHH--HHHHHHHHhcCC
Q 032703 48 LQLRRLLLKVLFGCAYLGPFGHFLH--LILD-----KIFKGKKDTSTVAKKVVLEQLTSSPWNNLM--FMIYYGVVVEGK 118 (135)
Q Consensus 48 ~D~~R~~~~~~~G~~~~gP~~~~wy--~~L~-----~~~~~~~~~~~~~~Kv~~DQ~i~~P~~~~~--f~~~~~~~leg~ 118 (135)
.-.||+...++.+.++.+|....|. ..+. ..+|- .+...++.-++....+..+..... .+...+ ++-|+
T Consensus 9 ~~~R~~~q~~~~~lf~~~~~~~~~~~~g~~~~s~~~~~~~~-~dp~~~~q~~~a~~~~~~~~l~g~~iv~~~~~-l~~GR 86 (271)
T PRK09477 9 LILRRLSQLSILALFLSGPWFGVWILKGNLSSSLLFDTIPL-TDPLATLQSLAAGHLPATVALIGALIITVFYA-LAGGR 86 (271)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcceeEEecchHHHhcCCccc-cCHHHHHHHHHhcChhHHHHHHHHHHHHHHHH-HHhcc
Confidence 3678899999999988888776661 2222 12333 445555554444444433332211 122334 55665
Q ss_pred ----------CHHHHHHHHhcc
Q 032703 119 ----------LILHNIINFTFG 130 (135)
Q Consensus 119 ----------~~~~~~~~lr~~ 130 (135)
.++|..++++++
T Consensus 87 ~fCgwiCP~g~l~e~~~~l~~k 108 (271)
T PRK09477 87 AFCSWVCPVNLVTDLANWLRRK 108 (271)
T ss_pred cceeeeCCchhHHHHHHHHHHH
Confidence 567777766654
No 14
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=31.02 E-value=95 Score=18.68 Aligned_cols=28 Identities=14% Similarity=0.131 Sum_probs=19.6
Q ss_pred HHHHHHHhccccchhHHHHHHHHHhhhh
Q 032703 36 DIVAQKLTGIQKLQLRRLLLKVLFGCAY 63 (135)
Q Consensus 36 D~laQ~~~~~~~~D~~R~~~~~~~G~~~ 63 (135)
+.+.+.++....+|-.|....++-|+++
T Consensus 12 ~~m~~fie~hP~WDQ~Rl~~aALa~FL~ 39 (57)
T PF10929_consen 12 QAMKDFIETHPNWDQYRLFQAALAGFLL 39 (57)
T ss_pred HHHHHHHHcCCCchHHHHHHHHHHHHHH
Confidence 4455556666778888888888777764
No 15
>PF08628 Nexin_C: Sorting nexin C terminal; InterPro: IPR013937 This region is found at the C terminus of proteins belonging to the nexin family. It is found on proteins which also contain IPR001683 from INTERPRO.
Probab=29.62 E-value=1.3e+02 Score=19.87 Aligned_cols=45 Identities=11% Similarity=0.024 Sum_probs=23.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHhcccCCC
Q 032703 89 AKKVVLEQLTSSPWNNLMFMIYYGVVVEGKLILHNIINFTFGRWNH 134 (135)
Q Consensus 89 ~~Kv~~DQ~i~~P~~~~~f~~~~~~~leg~~~~~~~~~lr~~~w~~ 134 (135)
+.|.++.|++.+-+---+-=.+.. +.+...+.+.+..+++.+||.
T Consensus 10 ~l~~~l~~~~g~tI~r~i~~~v~~-l~se~~v~~~i~~l~~~lwP~ 54 (113)
T PF08628_consen 10 VLQQILRQTFGSTIERKIRDQVEW-LTSEEQVARYIQLLRESLWPN 54 (113)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHH-HcCHHHHHHHHHHHHHhhCCC
Confidence 334445555444443222222323 555566677777777777763
No 16
>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=26.62 E-value=2e+02 Score=19.20 Aligned_cols=33 Identities=18% Similarity=0.091 Sum_probs=26.7
Q ss_pred hHHHHHHHHHhhhhhhhhHHHHH--HHhhhhccCC
Q 032703 50 LRRLLLKVLFGCAYLGPFGHFLH--LILDKIFKGK 82 (135)
Q Consensus 50 ~~R~~~~~~~G~~~~gP~~~~wy--~~L~~~~~~~ 82 (135)
++....++.+|.-+.+|+.---| .+||+.+++.
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 55666788999988999887777 6899999873
No 17
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=26.41 E-value=20 Score=23.29 Aligned_cols=55 Identities=29% Similarity=0.366 Sum_probs=34.4
Q ss_pred HHHHHHHHHH----HHHhhCchHHHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHH
Q 032703 4 IAKKGLQQYL----IQLQQHPLRTKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLF 59 (135)
Q Consensus 4 ~~~~~~~~Y~----~~l~~~Pl~tk~it~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~ 59 (135)
...++++.|. +.++++|+.--.-.-|+-+-..|-+|+.+ +-..-|.+|......+
T Consensus 24 ~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~-g~~~~d~~Ri~A~i~~ 82 (94)
T PF14490_consen 24 LAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL-GIEPDDPRRIRAAILY 82 (94)
T ss_dssp HHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT-T--TT-HHHHHHHHHH
T ss_pred HHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc-CCCCCCHHHHHHHHHH
Confidence 3456666665 47889997644433588899999999986 4366788887655443
No 18
>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=26.35 E-value=96 Score=19.40 Aligned_cols=25 Identities=12% Similarity=-0.057 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHH
Q 032703 88 VAKKVVLEQLTSSPWNNLMFMIYYG 112 (135)
Q Consensus 88 ~~~Kv~~DQ~i~~P~~~~~f~~~~~ 112 (135)
-+.|+++.|-+||-++...++..+-
T Consensus 4 ei~k~~~sQG~fA~LFv~Ll~yvlK 28 (71)
T PF10960_consen 4 EIIKLALSQGIFAVLFVWLLFYVLK 28 (71)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHH
Confidence 4678999999999988777765544
No 19
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=25.72 E-value=52 Score=21.13 Aligned_cols=17 Identities=6% Similarity=-0.144 Sum_probs=14.1
Q ss_pred hcCCCHHHHHHHHhccc
Q 032703 115 VEGKLILHNIINFTFGR 131 (135)
Q Consensus 115 leg~~~~~~~~~lr~~~ 131 (135)
.+|+|.+|+.++++++.
T Consensus 63 A~G~T~eEI~~~v~~rl 79 (80)
T PF03698_consen 63 ASGLTAEEIVQEVEERL 79 (80)
T ss_pred cCCCCHHHHHHHHHHhh
Confidence 37999999999998763
No 20
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=24.02 E-value=88 Score=18.26 Aligned_cols=19 Identities=21% Similarity=-0.005 Sum_probs=14.7
Q ss_pred HHHHhcCCCHHHHHHHHhcc
Q 032703 111 YGVVVEGKLILHNIINFTFG 130 (135)
Q Consensus 111 ~~~~leg~~~~~~~~~lr~~ 130 (135)
.. +|+|||-+-|+.++++.
T Consensus 17 q~-VLqgksR~vIirELqrT 35 (53)
T PF11547_consen 17 QV-VLQGKSRNVIIRELQRT 35 (53)
T ss_dssp HH-HSTTS-HHHHHHHHHHT
T ss_pred HH-HHcCCcHHHHHHHHHHh
Confidence 45 89999999999888764
No 21
>PF11043 DUF2856: Protein of unknown function (DUF2856); InterPro: IPR020500 This phage protein modulates the activity of the host recBCD nuclease and thus protects the linear double stranded DNA from exonuclease degradation [].
Probab=24.01 E-value=51 Score=21.38 Aligned_cols=17 Identities=12% Similarity=0.083 Sum_probs=14.4
Q ss_pred hcCCCHHHHHHHHhccc
Q 032703 115 VEGKLILHNIINFTFGR 131 (135)
Q Consensus 115 leg~~~~~~~~~lr~~~ 131 (135)
..|.|.+|+.+++|++|
T Consensus 14 CSGnSvsEVL~~~k~N~ 30 (97)
T PF11043_consen 14 CSGNSVSEVLDNIKNNY 30 (97)
T ss_pred ccCccHHHHHHHHHHHH
Confidence 46889999999999876
No 22
>cd06845 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting
Probab=23.21 E-value=1.6e+02 Score=20.34 Aligned_cols=17 Identities=18% Similarity=0.307 Sum_probs=13.8
Q ss_pred ccchhHHHHHHHHHhhh
Q 032703 46 QKLQLRRLLLKVLFGCA 62 (135)
Q Consensus 46 ~~~D~~R~~~~~~~G~~ 62 (135)
..++|.|.+.+..||..
T Consensus 83 g~inWGRIval~~f~~~ 99 (144)
T cd06845 83 GGINWGRIVALFAFGGR 99 (144)
T ss_pred CCCChHHHHHHHHHHHH
Confidence 47899998888888765
No 23
>COG3037 SgaT Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.93 E-value=85 Score=26.83 Aligned_cols=37 Identities=14% Similarity=0.116 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCHHHHH
Q 032703 88 VAKKVVLEQLTSSPWNNLMFMIYYGVVVEGKLILHNI 124 (135)
Q Consensus 88 ~~~Kv~~DQ~i~~P~~~~~f~~~~~~~leg~~~~~~~ 124 (135)
.......||++--|-.+..+++..++++++|+..++.
T Consensus 6 ~~~~~~~~~il~~PAiLlGli~liGy~llkK~~~~ii 42 (481)
T COG3037 6 TIFNFFINNILTEPAILLGLITLIGYILLKKPASKII 42 (481)
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHHHHHHhcCCcccee
Confidence 4567889999999999999999999999999877753
No 24
>PRK12997 PTS system ascorbate-specific transporter subunit IIC; Reviewed
Probab=22.76 E-value=1.5e+02 Score=25.35 Aligned_cols=35 Identities=11% Similarity=0.203 Sum_probs=29.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHhcCCCHHHHHH
Q 032703 91 KVVLEQLTSSPWNNLMFMIYYGVVVEGKLILHNII 125 (135)
Q Consensus 91 Kv~~DQ~i~~P~~~~~f~~~~~~~leg~~~~~~~~ 125 (135)
...+++.+..|.++...++..++++++++++|+.+
T Consensus 9 ~fiv~~iLg~pailigli~~iGL~l~kkk~~kai~ 43 (466)
T PRK12997 9 NFFIQNILGTPAILVGLIVLIGYILLKKSFSDVIT 43 (466)
T ss_pred HHHHhhhccCchHHHHHHHHHHHHHcCCCHHHHHH
Confidence 34567788999999999999996699999998754
No 25
>PRK09548 PTS system ascorbate-specific transporter subunits IICB; Provisional
Probab=22.19 E-value=1.2e+02 Score=26.75 Aligned_cols=32 Identities=16% Similarity=-0.005 Sum_probs=27.5
Q ss_pred HHHHhHHHHHHHHHHHHHHHHhcCCCHHHHHH
Q 032703 94 LEQLTSSPWNNLMFMIYYGVVVEGKLILHNII 125 (135)
Q Consensus 94 ~DQ~i~~P~~~~~f~~~~~~~leg~~~~~~~~ 125 (135)
+++.+-.|..+...++..|+++++|+++|+..
T Consensus 12 ~~~il~~pailiGlia~iGlllqkK~~~~ii~ 43 (602)
T PRK09548 12 FSQVIGKAPLLLGLVACIGYLLLKKDTTTIIK 43 (602)
T ss_pred HHHHhcccHHHHHHHHHHHHHHcCCCHhHHHH
Confidence 46788889888899999999999999999753
No 26
>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=21.58 E-value=69 Score=25.27 Aligned_cols=61 Identities=16% Similarity=0.229 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHhhhhhhhhHHHHHHH
Q 032703 3 SIAKKGLQQYLIQLQQHPLRTKAITAGVLSAISDIVAQKLTGIQKLQLRRLLLKVLFGCAYLGPFGHFLHLI 74 (135)
Q Consensus 3 ~~~~~~~~~Y~~~l~~~Pl~tk~it~~~l~~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~~gP~~~~wy~~ 74 (135)
.....+.+.-.+++++||+.|+-..-.-+-..+ .....++.+...+|-+. .||+-..|-++
T Consensus 231 ~~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~----------~~~~~k~~l~~v~Y~f~-~GPwr~~~vr~ 291 (310)
T PF09734_consen 231 PVLQELIQELKKLFEERPIWTRRALLNHLPKSG----------SQSKLKRALPYVAYYFK-NGPWRDCWVRF 291 (310)
T ss_pred hhHHHHHHHHHHHHhcCCccCHHHHHHhhhhcc----------cHHHHHHHHHhhEEEEe-cCcccceeEec
Confidence 345667788889999999988764433222111 44667788888888876 99998888654
No 27
>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=21.56 E-value=1.1e+02 Score=17.94 Aligned_cols=21 Identities=19% Similarity=0.234 Sum_probs=14.2
Q ss_pred HHHHHHHhc-cccchhHHHHHH
Q 032703 36 DIVAQKLTG-IQKLQLRRLLLK 56 (135)
Q Consensus 36 D~laQ~~~~-~~~~D~~R~~~~ 56 (135)
.++||.+++ ++..||.....-
T Consensus 5 kilaqiiqehregldwqeaatr 26 (61)
T PF09105_consen 5 KILAQIIQEHREGLDWQEAATR 26 (61)
T ss_dssp HHHHHHHHC-TT-EEHHHHHHH
T ss_pred HHHHHHHHHHHccCcHHHHHHH
Confidence 578999874 567888865443
No 28
>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=20.05 E-value=2.1e+02 Score=23.89 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhccccchhHHHHHHHHHhhhh
Q 032703 33 AISDIVAQKLTGIQKLQLRRLLLKVLFGCAY 63 (135)
Q Consensus 33 ~~gD~laQ~~~~~~~~D~~R~~~~~~~G~~~ 63 (135)
++.|..+++..+++.+|+.|.-..+++|..+
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 7889999999988899999987777777543
Done!