Query 032696
Match_columns 135
No_of_seqs 27 out of 29
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 04:46:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032696.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032696hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08507 COPI_assoc: COPI asso 99.4 1.3E-12 2.8E-17 95.8 9.7 80 46-129 5-84 (136)
2 PF06151 Trehalose_recp: Treha 76.5 18 0.00038 31.8 8.1 36 75-110 90-126 (414)
3 PRK14756 hypothetical protein; 43.5 40 0.00086 20.7 3.1 21 47-67 7-27 (29)
4 PHA03281 envelope glycoprotein 38.9 1E+02 0.0022 29.8 6.4 41 33-74 546-586 (642)
5 COG3768 Predicted membrane pro 33.7 1.9E+02 0.0042 26.1 7.0 62 49-110 67-131 (350)
6 PF13705 TRC8_N: TRC8 N-termin 32.7 55 0.0012 30.5 3.7 75 40-122 174-248 (508)
7 TIGR00769 AAA ADP/ATP carrier 31.9 2.8E+02 0.0061 24.9 7.8 71 46-116 44-133 (472)
8 PF10805 DUF2730: Protein of u 28.1 84 0.0018 22.6 3.3 30 99-130 2-32 (106)
9 COG5074 t-SNARE complex subuni 27.4 35 0.00076 29.8 1.4 15 81-95 251-265 (280)
10 PF11163 DUF2947: Protein of u 26.8 24 0.00052 28.2 0.3 23 94-117 108-130 (153)
11 PLN00039 photosystem II reacti 26.6 40 0.00086 25.8 1.4 17 91-107 82-98 (111)
12 KOG2412 Nuclear-export-signal 26.2 23 0.0005 33.6 0.1 26 75-100 468-498 (591)
13 PRK13610 photosystem II reacti 26.0 41 0.00089 25.9 1.4 17 91-107 88-104 (113)
14 PF07444 Ycf66_N: Ycf66 protei 26.0 2.6E+02 0.0056 20.2 6.7 43 47-89 5-48 (84)
15 TIGR03047 PS_II_psb28 photosys 25.9 42 0.00091 25.6 1.4 18 90-107 80-97 (109)
16 KOG2675 Adenylate cyclase-asso 25.5 68 0.0015 29.9 3.0 20 51-70 265-284 (480)
17 PRK13612 photosystem II reacti 25.4 43 0.00094 25.7 1.4 17 91-107 84-100 (113)
18 PF11712 Vma12: Endoplasmic re 23.2 2.6E+02 0.0057 20.7 5.2 14 84-97 115-128 (142)
19 CHL00128 psbW photosystem II p 23.1 51 0.0011 25.3 1.4 18 90-107 83-100 (113)
20 PRK13611 photosystem II reacti 22.4 54 0.0012 24.9 1.4 17 91-107 77-93 (104)
21 KOG1908 Ribonuclease inhibitor 22.4 79 0.0017 25.7 2.4 12 15-26 3-14 (165)
22 PF05805 L6_membrane: L6 membr 21.7 92 0.002 25.6 2.7 23 44-66 7-29 (195)
23 PF02293 AmiS_UreI: AmiS/UreI 21.1 4.4E+02 0.0096 21.2 6.7 69 47-132 90-159 (166)
24 PF03912 Psb28: Psb28 protein; 20.9 56 0.0012 24.9 1.3 12 96-107 86-97 (108)
25 PF04588 HIG_1_N: Hypoxia indu 20.6 2.5E+02 0.0053 18.0 4.9 40 55-94 10-52 (54)
No 1
>PF08507 COPI_assoc: COPI associated protein; InterPro: IPR013714 Proteins in this family co-localise with COPI vesicle coat proteins []. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with TVP18 [].
Probab=99.43 E-value=1.3e-12 Score=95.80 Aligned_cols=80 Identities=21% Similarity=0.407 Sum_probs=66.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 032696 46 CYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQILYVLY 125 (135)
Q Consensus 46 ~fs~vTal~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQIFvAvm 125 (135)
.+.+++.++|+++++..+++.+.+ .++-+.++++|.+++++++.++|.+|.++.|++++|+.|.|||+++||+++|
T Consensus 5 ~~r~~~~~~~~~~i~~gi~~l~~~----~~~~~~i~~~Y~i~fg~ll~~~E~~~~~i~~~~~FL~~~~GRGlfyif~G~l 80 (136)
T PF08507_consen 5 IFRILNIIAGILLILAGILSLFNS----FSFSSFILGVYCILFGLLLILAEFRWPFIRKYFGFLYSYIGRGLFYIFLGTL 80 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHHHhccHHHHHhHhHHHhHHHHHHHHHHHHHH
Confidence 455566666666677777776665 3334778999999999999999999999999999999999999999999999
Q ss_pred HHHh
Q 032696 126 YRLI 129 (135)
Q Consensus 126 T~~~ 129 (135)
+...
T Consensus 81 ~~~~ 84 (136)
T PF08507_consen 81 CLGQ 84 (136)
T ss_pred HHhh
Confidence 8754
No 2
>PF06151 Trehalose_recp: Trehalose receptor; InterPro: IPR009318 In Drosophila, taste is perceived by gustatory neurons located in sensilla distributed on several different appendages throughout the body of the animal. This family represents the taste receptor sensitive to trehalose [,].
Probab=76.45 E-value=18 Score=31.82 Aligned_cols=36 Identities=14% Similarity=0.291 Sum_probs=30.4
Q ss_pred cccch-hhhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032696 75 DIFDG-IFRCYAVVIAFFVALAETEWQFVLKFTKVLE 110 (135)
Q Consensus 75 dif~G-I~RcYaV~iA~fVvlaETEW~~i~kF~kvLe 110 (135)
+-..+ +|-+...++.++....=.+|..+|+-|.-.|
T Consensus 90 ~~~~~liFy~~~~~~~i~Fl~LAr~Wp~lm~~W~~vE 126 (414)
T PF06151_consen 90 NNIASLIFYVVCLLISILFLRLARRWPQLMREWSRVE 126 (414)
T ss_pred eehhhhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 44455 6889999999888888999999999998876
No 3
>PRK14756 hypothetical protein; Provisional
Probab=43.47 E-value=40 Score=20.69 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHh
Q 032696 47 YSVLTSLTALLCLAVNVLSAI 67 (135)
Q Consensus 47 fs~vTal~AlLCi~vNvlSav 67 (135)
||.+|.+.||..|++..+.|+
T Consensus 7 ~SL~tTvvaL~~Iva~~~ta~ 27 (29)
T PRK14756 7 FSLVTTIIVLGLIVAVGLTAA 27 (29)
T ss_pred hhHHHHHHHHHHHHHHHHHHh
Confidence 789999999998888766553
No 4
>PHA03281 envelope glycoprotein E; Provisional
Probab=38.93 E-value=1e+02 Score=29.80 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=27.8
Q ss_pred CCCCCCceEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcc
Q 032696 33 LRNRADPLLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGS 74 (135)
Q Consensus 33 ~~~~~DplL~vcr~fs~vTal~AlLCi~vNvlSavrsf~~~~ 74 (135)
...+.-|++.-.-..+-+ ++.||||+++-.+-..+.|++..
T Consensus 546 s~~~~~p~~~y~~l~~~~-a~~~ll~l~~~~~c~~~~~~~~~ 586 (642)
T PHA03281 546 SEPGTFPFKRYAAITGGF-AALALLCLAIALICTAKKFGHKA 586 (642)
T ss_pred cccCCCCeEeehhhhhhh-HHHHHHHHHHHHHHHHHHhhhhe
Confidence 345567777654333322 46789999999998888887653
No 5
>COG3768 Predicted membrane protein [Function unknown]
Probab=33.73 E-value=1.9e+02 Score=26.08 Aligned_cols=62 Identities=19% Similarity=0.187 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHH---HhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032696 49 VLTSLTALLCLAVNVLS---AIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLE 110 (135)
Q Consensus 49 ~vTal~AlLCi~vNvlS---avrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLe 110 (135)
.+++...|+|.+|-.-| ..+.|....-++=|..=+-++++.++|..+=|||-.++|+-++.+
T Consensus 67 ~~~a~~vLf~~Av~~q~~qwi~d~~qr~dWl~~~a~~v~~l~vlagv~~v~rEw~rl~rL~~r~~ 131 (350)
T COG3768 67 MLGAGGVLFSLAVGLQSVQWIRDLFQRADWLGLGAAAVGALIVLAGVGSVVREWRRLVRLRQRQH 131 (350)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677778887775544 345564444566566667788888999999999999999987653
No 6
>PF13705 TRC8_N: TRC8 N-terminal domain
Probab=32.69 E-value=55 Score=30.49 Aligned_cols=75 Identities=24% Similarity=0.346 Sum_probs=45.5
Q ss_pred eEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhhHHH
Q 032696 40 LLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQ 119 (135)
Q Consensus 40 lL~vcr~fs~vTal~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQ 119 (135)
++.++.+-...|++..+--+.-|.....+.-| .-+.-+.|.||. ..++|+||.++-==.-..-||..|=..|
T Consensus 174 l~~~~~~a~~~~~~~v~~~~~~~~~~~~~~v~---~~~~~~~~~~Gl-----~~l~~~~W~rL~vP~vl~vFWl~~f~~q 245 (508)
T PF13705_consen 174 LLIVHNFALWLTILEVLYFILSNYPVPYRFVK---TAYRHMYENYGL-----QALVESLWNRLRVPEVLRVFWLTRFAVQ 245 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCccchHHHHH---HHHHHHHHHhhH-----HHHHHHHHhhhcchhhHHHHHHHHHHHH
Confidence 34444444444444444444444443333321 223455677764 5789999999866666667999999999
Q ss_pred HHH
Q 032696 120 ILY 122 (135)
Q Consensus 120 IFv 122 (135)
+..
T Consensus 246 ~~~ 248 (508)
T PF13705_consen 246 LYI 248 (508)
T ss_pred Hhe
Confidence 866
No 7
>TIGR00769 AAA ADP/ATP carrier protein family. These proteins are members of the ATP:ADP Antiporter (AAA) Family (TC 2.A.12), which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers.
Probab=31.86 E-value=2.8e+02 Score=24.93 Aligned_cols=71 Identities=10% Similarity=0.154 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHHHHH--HHHHHhhhccCcccccchhhhHHHHHHHHHHHHH---h--------------hhHHHHHHHH
Q 032696 46 CYSVLTSLTALLCLAV--NVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALA---E--------------TEWQFVLKFT 106 (135)
Q Consensus 46 ~fs~vTal~AlLCi~v--NvlSavrsf~~~~dif~GI~RcYaV~iA~fVvla---E--------------TEW~~i~kF~ 106 (135)
..+++...+-+-|.++ =+++..-+--..+++|..+.+.+...+.+|-.+. + +=-..+..++
T Consensus 44 ~i~fLk~~~~lp~~~~~~~ly~~l~~~~~~~~lf~~~~~~F~~~f~lF~~vl~p~~~~~~p~~~~~~~~~~~~~~~~~~i 123 (472)
T TIGR00769 44 IIPFLKTWVVVPMAVIFMLIYTKLSNILSKEALFYTVISPFLGFFALFAFVIYPLSDLLHPTALADKLLSLLPPGFMGFI 123 (472)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHhHHHHHHHHHHHHHHHHHHHhcchhhcCCcHHHHHHHhhcchhhHHHH
Confidence 4555555443333333 2222222222236899999999999998887772 1 1123466788
Q ss_pred HHHHHHhhhh
Q 032696 107 KVLEYWVARG 116 (135)
Q Consensus 107 kvLeyW~gRG 116 (135)
.++.+|..+.
T Consensus 124 ~~~~~W~~~~ 133 (472)
T TIGR00769 124 AILRIWSFAL 133 (472)
T ss_pred HHHhhhhHHH
Confidence 9999999985
No 8
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=28.10 E-value=84 Score=22.64 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHhhhh-HHHHHHHHHHHHhh
Q 032696 99 WQFVLKFTKVLEYWVARG-MLQILYVLYYRLIL 130 (135)
Q Consensus 99 W~~i~kF~kvLeyW~gRG-mLQIFvAvmT~~~~ 130 (135)
|++|.|.|.+ .|.+=| ...+|.+.|++.|.
T Consensus 2 ~~~~~~~w~i--i~a~~~~~~~~~~~~l~~~~a 32 (106)
T PF10805_consen 2 WEFIKKNWGI--IWAVFGIAGGIFWLWLRRTYA 32 (106)
T ss_pred hHHHHhCcHH--HHHHHHHHHHHHHHHHHHhhc
Confidence 7888888888 566655 55677777777654
No 9
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=27.39 E-value=35 Score=29.76 Aligned_cols=15 Identities=20% Similarity=0.820 Sum_probs=12.0
Q ss_pred hhHHHHHHHHHHHHH
Q 032696 81 FRCYAVVIAFFVALA 95 (135)
Q Consensus 81 ~RcYaV~iA~fVvla 95 (135)
.|||+|+|.++++++
T Consensus 251 i~c~gI~~iii~viv 265 (280)
T COG5074 251 IRCYGICFIIIIVIV 265 (280)
T ss_pred eehhhhHHHHHHHHH
Confidence 589999988877654
No 10
>PF11163 DUF2947: Protein of unknown function (DUF2947); InterPro: IPR021334 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=26.78 E-value=24 Score=28.19 Aligned_cols=23 Identities=22% Similarity=0.447 Sum_probs=17.9
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhhH
Q 032696 94 LAETEWQFVLKFTKVLEYWVARGM 117 (135)
Q Consensus 94 laETEW~~i~kF~kvLeyW~gRGm 117 (135)
++||.|+-+.|-||-+-|- .-|+
T Consensus 108 iiET~W~vFkr~WknFLF~-ddGp 130 (153)
T PF11163_consen 108 IIETRWDVFKRNWKNFLFY-DDGP 130 (153)
T ss_pred EEEeehHHHHHHHHHHhcc-cCcc
Confidence 5799999999999987654 3443
No 11
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=26.61 E-value=40 Score=25.82 Aligned_cols=17 Identities=24% Similarity=0.681 Sum_probs=12.8
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032696 91 FVALAETEWQFVLKFTK 107 (135)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (135)
++.=-|.||+++|+|-.
T Consensus 82 y~m~s~~~WdRFMRFMe 98 (111)
T PLN00039 82 YVMRSPREWDRFMRFME 98 (111)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34445889999999964
No 12
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=26.18 E-value=23 Score=33.62 Aligned_cols=26 Identities=35% Similarity=0.569 Sum_probs=22.8
Q ss_pred ccc----chhhhHHHHHHHHHH-HHHhhhHH
Q 032696 75 DIF----DGIFRCYAVVIAFFV-ALAETEWQ 100 (135)
Q Consensus 75 dif----~GI~RcYaV~iA~fV-vlaETEW~ 100 (135)
|.| +||+|.||.+|.+=. ..+=|+|+
T Consensus 468 d~YleRm~Gi~rLYAAIi~l~~p~~~~~~~h 498 (591)
T KOG2412|consen 468 DAYLERMDGIMRLYAAIIQLDIPVGNATNVH 498 (591)
T ss_pred chHHHHhHhHHHHHHHHHHhcccccCCCCCC
Confidence 788 899999999999887 78888877
No 13
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=26.05 E-value=41 Score=25.91 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=12.5
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032696 91 FVALAETEWQFVLKFTK 107 (135)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (135)
++.=-|.||+++|+|-.
T Consensus 88 y~m~s~~~WdRFMRFMe 104 (113)
T PRK13610 88 YNWNSEEAFERFMRFAS 104 (113)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 33445889999999954
No 14
>PF07444 Ycf66_N: Ycf66 protein N-terminus; InterPro: IPR010004 This entry represents Ycf66, a protein that is restricted to the chloroplasts of simple plants and algae. It is also found in the cyanobacteria. The function is unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=26.04 E-value=2.6e+02 Score=20.20 Aligned_cols=43 Identities=21% Similarity=0.239 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhccCc-ccccchhhhHHHHHHH
Q 032696 47 YSVLTSLTALLCLAVNVLSAIRSFKNG-SDIFDGIFRCYAVVIA 89 (135)
Q Consensus 47 fs~vTal~AlLCi~vNvlSavrsf~~~-~dif~GI~RcYaV~iA 89 (135)
|+.-+.++.++-++...+-..|.++.. ++.+|=++=.-+.+.+
T Consensus 5 ~~~~~iLgi~l~~~~~~Ly~lr~~~Pev~Rd~D~~fs~vgLl~g 48 (84)
T PF07444_consen 5 FGPSYILGIILILGGLALYFLRFFRPEVSRDYDIFFSSVGLLYG 48 (84)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHCcchhhhhhHHHHHHHHHHH
Confidence 456677888888889999999999877 4444433333333333
No 15
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=25.94 E-value=42 Score=25.63 Aligned_cols=18 Identities=22% Similarity=0.720 Sum_probs=13.5
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 032696 90 FFVALAETEWQFVLKFTK 107 (135)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (135)
.++.=-|.||+++|+|-.
T Consensus 80 ~y~m~s~~~WdRFMRFme 97 (109)
T TIGR03047 80 VYIMKSEDEWDRFMRFME 97 (109)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344456889999999964
No 16
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=25.53 E-value=68 Score=29.92 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHhhhc
Q 032696 51 TSLTALLCLAVNVLSAIRSF 70 (135)
Q Consensus 51 Tal~AlLCi~vNvlSavrsf 70 (135)
.+|.|=|--.-++-|.+|+-
T Consensus 265 ~AlFaqlNqGe~iTsgLkkV 284 (480)
T KOG2675|consen 265 GALFAQLNQGEGITSGLKKV 284 (480)
T ss_pred HHHHHHHhccchhhhhhhhC
Confidence 34555555555666666654
No 17
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=25.44 E-value=43 Score=25.70 Aligned_cols=17 Identities=24% Similarity=0.704 Sum_probs=12.7
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032696 91 FVALAETEWQFVLKFTK 107 (135)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (135)
++.=-|.||+++|+|-.
T Consensus 84 y~m~s~~~WdRFMRFMe 100 (113)
T PRK13612 84 YIWKSEQEWDRFMRFME 100 (113)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34445889999999964
No 18
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=23.22 E-value=2.6e+02 Score=20.68 Aligned_cols=14 Identities=29% Similarity=0.342 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHhh
Q 032696 84 YAVVIAFFVALAET 97 (135)
Q Consensus 84 YaV~iA~fVvlaET 97 (135)
-+++.|++|.+||+
T Consensus 115 lgl~~al~vlvAEv 128 (142)
T PF11712_consen 115 LGLFGALLVLVAEV 128 (142)
T ss_pred HHHHHHHHHHHHHH
Confidence 46778888999997
No 19
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=23.11 E-value=51 Score=25.32 Aligned_cols=18 Identities=11% Similarity=0.567 Sum_probs=13.3
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 032696 90 FFVALAETEWQFVLKFTK 107 (135)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (135)
.++.=-|.||+++|+|-.
T Consensus 83 ~y~m~s~~~WdRFMRFMe 100 (113)
T CHL00128 83 IYIMKNPEAWDRFMRFME 100 (113)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344456889999999964
No 20
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=22.43 E-value=54 Score=24.89 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=12.7
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032696 91 FVALAETEWQFVLKFTK 107 (135)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (135)
++.--|.||+++|+|-.
T Consensus 77 y~m~s~~~wdRFMRFme 93 (104)
T PRK13611 77 YDMETEAEWDRFLRFME 93 (104)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34445889999999964
No 21
>KOG1908 consensus Ribonuclease inhibitor type leucine-rich repeat proteins [RNA processing and modification]
Probab=22.35 E-value=79 Score=25.71 Aligned_cols=12 Identities=33% Similarity=0.603 Sum_probs=7.6
Q ss_pred CCCCCCCCCCCC
Q 032696 15 PPQPQPPPPPAR 26 (135)
Q Consensus 15 ~~~p~~~~~~~~ 26 (135)
+|+||||++++.
T Consensus 3 A~p~~~~sh~Aa 14 (165)
T KOG1908|consen 3 APPEAPPSHGAA 14 (165)
T ss_pred CCCCCCCCCCCc
Confidence 456677776664
No 22
>PF05805 L6_membrane: L6 membrane protein; InterPro: IPR008661 This family consists of several eukaryotic L6 membrane proteins. L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily it has now been found that that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 family []. Several members of this family have been implicated in Homo sapiens cancer [, ].; GO: 0016021 integral to membrane
Probab=21.69 E-value=92 Score=25.64 Aligned_cols=23 Identities=35% Similarity=0.560 Sum_probs=19.7
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHH
Q 032696 44 CRCYSVLTSLTALLCLAVNVLSA 66 (135)
Q Consensus 44 cr~fs~vTal~AlLCi~vNvlSa 66 (135)
-||..+.-...|++|+++|.+--
T Consensus 7 arclG~sLl~Lal~~iiaNilL~ 29 (195)
T PF05805_consen 7 ARCLGFSLLPLALLCIIANILLF 29 (195)
T ss_pred hhhhhhHHHHHHHHHHHHHHhee
Confidence 37888888899999999999943
No 23
>PF02293 AmiS_UreI: AmiS/UreI family transporter; InterPro: IPR003211 Helicobacter pylori is a Gram-negative, ureolytic bacteria that can colonise the human stomach. It does not survive in a medium with a pH less than 4.0 unless urea is present, preferring a neutral pH. Gastric juice urea is able to rapidly access intrabacterial urease when the periplasmic pH falls below approximately 6.2 owing to pH-gating of a urea channel, UreI. UreI is a six-transmembrane segment protein that is homologous to the amiS genes of the amidase gene cluster and to UreI of Helicobacter hepaticus and Streptococcus salivarius. UreI in H. pylori and H. hepaticus can transport urea only at acidic pH, whereas that of S. salivarius is open at both neutral and acidic pH []. The amiS gene encodes an 18kDa protein with a high content of hydrophobic residues. It has six transmembrane helices. AmiB and AmiS resemble two components of an ABC transporter system []. This family includes UreI and proton gated urea channel as well as putative amide transporters [].; GO: 0006810 transport, 0016020 membrane
Probab=21.14 E-value=4.4e+02 Score=21.19 Aligned_cols=69 Identities=29% Similarity=0.340 Sum_probs=45.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhccCcccccch-hhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 032696 47 YSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDG-IFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQILYVLY 125 (135)
Q Consensus 47 fs~vTal~AlLCi~vNvlSavrsf~~~~dif~G-I~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQIFvAvm 125 (135)
||...+++|+... +.+|.+..|.--| |-=.+++++.+|-++.-.+- .+.||. |.+.|++++.
T Consensus 90 fsLFVAi~a~~~a-------~~~~~~~~d~~~~~~W~~Wa~LW~lfFl~l~L~k-~l~~~~---------g~~~i~~gi~ 152 (166)
T PF02293_consen 90 FSLFVAITALPYA-------ILSFSGAGDPWFAVIWLAWAVLWFLFFLLLALKK-PLGKFT---------GWLAIVEGIV 152 (166)
T ss_pred HHHHHHHHHHHHH-------HHHHcccccHHHHHHHHHHHHHHHHHHHHHhcCC-cchhHH---------HHHHHHHHHH
Confidence 4555555555443 4445544555555 57899999999776665554 555654 5567888888
Q ss_pred HHHhhhc
Q 032696 126 YRLILFY 132 (135)
Q Consensus 126 T~~~~~~ 132 (135)
|--+|.+
T Consensus 153 T~wiPg~ 159 (166)
T PF02293_consen 153 TAWIPGF 159 (166)
T ss_pred HHHHHHH
Confidence 8877764
No 24
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=20.88 E-value=56 Score=24.88 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=10.1
Q ss_pred hhhHHHHHHHHH
Q 032696 96 ETEWQFVLKFTK 107 (135)
Q Consensus 96 ETEW~~i~kF~k 107 (135)
+-||+++|+|-.
T Consensus 86 ~~~WdRFMRFMe 97 (108)
T PF03912_consen 86 EEEWDRFMRFME 97 (108)
T ss_dssp SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 679999999964
No 25
>PF04588 HIG_1_N: Hypoxia induced protein conserved region; InterPro: IPR007667 The hypoxia induced gene 1 (HIG1) or hypoglycemia/hypoxia inducible mitochondrial protein (HIMP1) is up-regulated by stresses of the microenvironment such as low oxygen or low glucose conditions. HIG1 is a mitochondrial inner membrane protein, which is ubiquitously expressed. It is predicted to be an integral membrane protein consisting of two hydrophobic helices, 21-23 residues in length that might tend to form a hairpin-like loop across the bilayer. HIG1 could be implied in apoptotic or cytoprotective signals. HIG1 is a member of a well conserved eukaryote protein family. The predicted transmembrane helice (TMH) and loop regions represent the most highly conserved regions in these proteins [, ]. The profile we developed covers the predicted TMH and loop regions. This domain is found in proteins thought to be involved in the response to hypoxia []. It is also found in altered inheritance of mitochondria proteins.; PDB: 2LOM_A 2LON_A.
Probab=20.57 E-value=2.5e+02 Score=18.01 Aligned_cols=40 Identities=15% Similarity=0.221 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhhhccCcccccch-h--hhHHHHHHHHHHHH
Q 032696 55 ALLCLAVNVLSAIRSFKNGSDIFDG-I--FRCYAVVIAFFVAL 94 (135)
Q Consensus 55 AlLCi~vNvlSavrsf~~~~dif~G-I--~RcYaV~iA~fVvl 94 (135)
++++++.=+....++|+.++..-.. + .|+|+=.+++...+
T Consensus 10 g~~~~~~~l~~g~~~~~~g~~~~s~klmr~RV~aQ~~tv~~l~ 52 (54)
T PF04588_consen 10 GMLATVGALAYGLYNFRRGNMKTSQKLMRARVYAQGLTVAALV 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHTSSS----SSSSS-SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444467778888877443344 3 69998777776654
Done!