Query 033508
Match_columns 118
No_of_seqs 27 out of 29
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:05:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033508hhsearch_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 99.1 6.5E-10 1.4E-14 80.0 7.2 68 46-117 5-72 (136)
2 PF06151 Trehalose_recp: Treha 80.8 12 0.00025 32.3 8.1 36 75-110 90-126 (414)
3 PRK14756 hypothetical protein; 53.3 23 0.0005 21.2 3.1 21 47-67 7-27 (29)
4 PHA03281 envelope glycoprotein 42.3 86 0.0019 29.6 6.4 41 33-74 546-586 (642)
5 TIGR00769 AAA ADP/ATP carrier 42.1 1.6E+02 0.0034 26.0 7.7 43 74-116 74-133 (472)
6 COG3768 Predicted membrane pro 40.8 1.4E+02 0.003 26.5 7.1 61 49-109 67-130 (350)
7 PF11163 DUF2947: Protein of u 35.1 14 0.00031 28.9 0.3 18 94-111 108-125 (153)
8 COG5074 t-SNARE complex subuni 33.0 25 0.00055 30.0 1.4 15 81-95 251-265 (280)
9 KOG2412 Nuclear-export-signal 31.7 16 0.00035 34.0 0.1 26 75-100 468-498 (591)
10 PF11712 Vma12: Endoplasmic re 31.6 1.6E+02 0.0034 21.4 5.3 23 84-107 115-137 (142)
11 PF07444 Ycf66_N: Ycf66 protei 30.6 2E+02 0.0043 20.4 6.6 27 47-73 5-31 (84)
12 PLN00039 photosystem II reacti 30.3 32 0.00069 25.8 1.4 18 90-107 81-98 (111)
13 PF13705 TRC8_N: TRC8 N-termin 29.9 52 0.0011 30.0 3.0 68 40-115 174-241 (508)
14 PRK13610 photosystem II reacti 29.8 33 0.00071 25.9 1.4 17 91-107 88-104 (113)
15 TIGR03047 PS_II_psb28 photosys 29.5 34 0.00073 25.6 1.4 19 89-107 79-97 (109)
16 PRK13612 photosystem II reacti 29.0 35 0.00075 25.7 1.4 18 90-107 83-100 (113)
17 PF05805 L6_membrane: L6 membr 27.5 62 0.0014 26.1 2.7 24 44-67 7-30 (195)
18 PF04588 HIG_1_N: Hypoxia indu 27.1 1.7E+02 0.0036 18.4 4.9 40 55-94 10-52 (54)
19 CHL00128 psbW photosystem II p 26.4 41 0.00089 25.3 1.4 19 89-107 82-100 (113)
20 PRK13611 photosystem II reacti 25.6 44 0.00095 24.9 1.4 17 91-107 77-93 (104)
21 PF03912 Psb28: Psb28 protein; 24.1 45 0.00098 24.9 1.3 12 96-107 86-97 (108)
22 PF11628 TCR_zetazeta: T-cell 23.2 69 0.0015 19.7 1.7 18 75-92 6-23 (33)
23 PF04750 Far-17a_AIG1: FAR-17a 22.7 1.1E+02 0.0025 22.5 3.2 53 42-94 30-85 (201)
24 PHA02815 hypothetical protein; 22.6 1.9E+02 0.004 20.1 4.0 25 86-110 7-31 (64)
25 PHA01399 membrane protein P6 22.3 4E+02 0.0087 22.4 6.6 57 50-113 30-87 (242)
26 KOG2675 Adenylate cyclase-asso 21.7 92 0.002 28.6 2.9 20 51-70 265-284 (480)
27 KOG3419 Mitochondrial/chloropl 21.5 50 0.0011 25.0 1.1 10 109-118 59-68 (112)
28 KOG1908 Ribonuclease inhibitor 21.5 86 0.0019 25.0 2.5 12 15-26 3-14 (165)
29 PRK00040 rpsP 30S ribosomal pr 21.1 52 0.0011 22.6 1.0 11 108-118 56-66 (75)
30 KOG3030 Lipid phosphate phosph 20.5 1.4E+02 0.0031 25.4 3.7 33 59-93 225-258 (317)
31 PF08551 DUF1751: Eukaryotic i 20.4 1E+02 0.0022 21.4 2.5 47 44-93 48-96 (99)
32 PF06459 RR_TM4-6: Ryanodine R 20.3 81 0.0017 26.3 2.2 19 43-61 246-264 (274)
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=99.05 E-value=6.5e-10 Score=80.01 Aligned_cols=68 Identities=24% Similarity=0.472 Sum_probs=56.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccC
Q 033508 46 CYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARVL 117 (118)
Q Consensus 46 ~fs~vTa~~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGm 117 (118)
.+.+++.++|+++++..+++.+.+ .++-+.++++|.++++++++++|.+|.++.|++++|+.|.|||+
T Consensus 5 ~~r~~~~~~~~~~i~~gi~~l~~~----~~~~~~i~~~Y~i~fg~ll~~~E~~~~~i~~~~~FL~~~~GRGl 72 (136)
T PF08507_consen 5 IFRILNIIAGILLILAGILSLFNS----FSFSSFILGVYCILFGLLLILAEFRWPFIRKYFGFLYSYIGRGL 72 (136)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHHHhccHHHHHhHhHHHhHHHHHH
Confidence 455666666666777777777665 33447789999999999999999999999999999999999996
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=80.79 E-value=12 Score=32.27 Aligned_cols=36 Identities=14% Similarity=0.291 Sum_probs=30.5
Q ss_pred cccch-hhhhHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 033508 75 DIFDG-IFRCYAVVIAFFVALAETEWQFVLKFTKVLE 110 (118)
Q Consensus 75 dif~G-I~RcYaV~iA~fVvlaETEW~~i~kF~kvLe 110 (118)
+-..+ +|-+...++.++....=.+|..+|+-|.-.|
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 6889999999888889999999999998876
No 3
>PRK14756 hypothetical protein; Provisional
Probab=53.28 E-value=23 Score=21.24 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHh
Q 033508 47 YSVLTSLTALLCLAVNVLSAI 67 (118)
Q Consensus 47 fs~vTa~~AlLCi~vNvlSav 67 (118)
||.+|.+.||..|++..+.|+
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=42.34 E-value=86 Score=29.65 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=28.0
Q ss_pred CCCCCCceEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcc
Q 033508 33 LRNRADPLLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGS 74 (118)
Q Consensus 33 ~~~~~DplL~vcr~fs~vTa~~AlLCi~vNvlSavrsf~~~~ 74 (118)
...+.-|+++---..+-+ ++.||||+++..+-..+.|++..
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 345567777654433322 46789999999998888887653
No 5
>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=42.09 E-value=1.6e+02 Score=25.97 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=32.3
Q ss_pred ccccchhhhhHHHHHHHHHHHH---h--------------hhHHHHHHHHHHHHHHHhcc
Q 033508 74 SDIFDGIFRCYAVVIAFFVALA---E--------------TEWQFVLKFTKVLEYWVARV 116 (118)
Q Consensus 74 ~dif~GI~RcYaV~iA~fVvla---E--------------TEW~~i~kF~kvLeyW~gRG 116 (118)
+++|.-+.+.+...+.+|-.+. + +=-..+..++.++.+|..+.
T Consensus 74 ~~lf~~~~~~F~~~f~lF~~vl~p~~~~~~p~~~~~~~~~~~~~~~~~~i~~~~~W~~~~ 133 (472)
T TIGR00769 74 EALFYTVISPFLGFFALFAFVIYPLSDLLHPTALADKLLSLLPPGFMGFIAILRIWSFAL 133 (472)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHhcchhhcCCcHHHHHHHhhcchhhHHHHHHHhhhhHHH
Confidence 6899999999999999888772 1 11223667888999998764
No 6
>COG3768 Predicted membrane protein [Function unknown]
Probab=40.77 E-value=1.4e+02 Score=26.49 Aligned_cols=61 Identities=20% Similarity=0.188 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHH---HhhhccCcccccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 033508 49 VLTSLTALLCLAVNVLS---AIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVL 109 (118)
Q Consensus 49 ~vTa~~AlLCi~vNvlS---avrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvL 109 (118)
.+++...|+|.+|-.-| ..+.|....-++=|..=+-++++.++|..+=|||-.++|+-++.
T Consensus 67 ~~~a~~vLf~~Av~~q~~qwi~d~~qr~dWl~~~a~~v~~l~vlagv~~v~rEw~rl~rL~~r~ 130 (350)
T COG3768 67 MLGAGGVLFSLAVGLQSVQWIRDLFQRADWLGLGAAAVGALIVLAGVGSVVREWRRLVRLRQRQ 130 (350)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677777887775544 34556444456666666778888999999999999999987764
No 7
>PF11163 DUF2947: Protein of unknown function (DUF2947); InterPro: IPR021334 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=35.05 E-value=14 Score=28.86 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=15.7
Q ss_pred HHhhhHHHHHHHHHHHHH
Q 033508 94 LAETEWQFVLKFTKVLEY 111 (118)
Q Consensus 94 laETEW~~i~kF~kvLey 111 (118)
++||.|+-|.|-||-+-|
T Consensus 108 iiET~W~vFkr~WknFLF 125 (153)
T PF11163_consen 108 IIETRWDVFKRNWKNFLF 125 (153)
T ss_pred EEEeehHHHHHHHHHHhc
Confidence 579999999999997755
No 8
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=33.05 E-value=25 Score=30.04 Aligned_cols=15 Identities=20% Similarity=0.820 Sum_probs=12.0
Q ss_pred hhhHHHHHHHHHHHH
Q 033508 81 FRCYAVVIAFFVALA 95 (118)
Q Consensus 81 ~RcYaV~iA~fVvla 95 (118)
.|||+|+|.++++++
T Consensus 251 i~c~gI~~iii~viv 265 (280)
T COG5074 251 IRCYGICFIIIIVIV 265 (280)
T ss_pred eehhhhHHHHHHHHH
Confidence 589999988877654
No 9
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=31.71 E-value=16 Score=34.01 Aligned_cols=26 Identities=35% Similarity=0.569 Sum_probs=23.3
Q ss_pred ccc----chhhhhHHHHHHHHH-HHHhhhHH
Q 033508 75 DIF----DGIFRCYAVVIAFFV-ALAETEWQ 100 (118)
Q Consensus 75 dif----~GI~RcYaV~iA~fV-vlaETEW~ 100 (118)
|.| +||+|.||.+|.+=. +.+=|+|+
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 899999999999888 88888888
No 10
>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=31.62 E-value=1.6e+02 Score=21.39 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHH
Q 033508 84 YAVVIAFFVALAETEWQFVLKFTK 107 (118)
Q Consensus 84 YaV~iA~fVvlaETEW~~i~kF~k 107 (118)
-+++.|++|.+||+ |=++.+++|
T Consensus 115 lgl~~al~vlvAEv-~l~~~y~~k 137 (142)
T PF11712_consen 115 LGLFGALLVLVAEV-VLYIRYLRK 137 (142)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHhh
Confidence 46778889999997 333444433
No 11
>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=30.57 E-value=2e+02 Score=20.35 Aligned_cols=27 Identities=22% Similarity=0.205 Sum_probs=22.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhccCc
Q 033508 47 YSVLTSLTALLCLAVNVLSAIRSFKNG 73 (118)
Q Consensus 47 fs~vTa~~AlLCi~vNvlSavrsf~~~ 73 (118)
|+.-+.++.++-++...+-..|.++..
T Consensus 5 ~~~~~iLgi~l~~~~~~Ly~lr~~~Pe 31 (84)
T PF07444_consen 5 FGPSYILGIILILGGLALYFLRFFRPE 31 (84)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHCcc
Confidence 456677888888889999999999877
No 12
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=30.28 E-value=32 Score=25.80 Aligned_cols=18 Identities=22% Similarity=0.582 Sum_probs=13.4
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 033508 90 FFVALAETEWQFVLKFTK 107 (118)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (118)
.++.=-|.||+++|+|-.
T Consensus 81 ~y~m~s~~~WdRFMRFMe 98 (111)
T PLN00039 81 KYVMRSPREWDRFMRFME 98 (111)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344456889999999964
No 13
>PF13705 TRC8_N: TRC8 N-terminal domain
Probab=29.87 E-value=52 Score=30.05 Aligned_cols=68 Identities=25% Similarity=0.378 Sum_probs=36.1
Q ss_pred eEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhc
Q 033508 40 LLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVAR 115 (118)
Q Consensus 40 lL~vcr~fs~vTa~~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gR 115 (118)
++.++.+-...|++..+--+.-|.....+.-| .-+.-+.|.||. ..++|+||.++-==.-..-||..|
T Consensus 174 l~~~~~~a~~~~~~~v~~~~~~~~~~~~~~v~---~~~~~~~~~~Gl-----~~l~~~~W~rL~vP~vl~vFWl~~ 241 (508)
T PF13705_consen 174 LLIVHNFALWLTILEVLYFILSNYPVPYRFVK---TAYRHMYENYGL-----QALVESLWNRLRVPEVLRVFWLTR 241 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCccchHHHHH---HHHHHHHHHhhH-----HHHHHHHHhhhcchhhHHHHHHHH
Confidence 34444444444444444444444444333321 222445666764 578999999875444444567654
No 14
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=29.77 E-value=33 Score=25.91 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=12.7
Q ss_pred HHHHHhhhHHHHHHHHH
Q 033508 91 FVALAETEWQFVLKFTK 107 (118)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (118)
++.=-|.||++||+|-.
T Consensus 88 y~m~s~~~WdRFMRFMe 104 (113)
T PRK13610 88 YNWNSEEAFERFMRFAS 104 (113)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34446889999999964
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=29.53 E-value=34 Score=25.61 Aligned_cols=19 Identities=26% Similarity=0.725 Sum_probs=14.1
Q ss_pred HHHHHHHhhhHHHHHHHHH
Q 033508 89 AFFVALAETEWQFVLKFTK 107 (118)
Q Consensus 89 A~fVvlaETEW~~i~kF~k 107 (118)
|.++.=-|.||+++|+|-.
T Consensus 79 a~y~m~s~~~WdRFMRFme 97 (109)
T TIGR03047 79 AVYIMKSEDEWDRFMRFME 97 (109)
T ss_pred EEEEECCHHHHHHHHHHHH
Confidence 3444556889999999965
No 16
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=28.98 E-value=35 Score=25.68 Aligned_cols=18 Identities=22% Similarity=0.624 Sum_probs=13.2
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 033508 90 FFVALAETEWQFVLKFTK 107 (118)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (118)
.++.=-|.||+++|+|-.
T Consensus 83 ~y~m~s~~~WdRFMRFMe 100 (113)
T PRK13612 83 TYIWKSEQEWDRFMRFME 100 (113)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344446889999999964
No 17
>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=27.47 E-value=62 Score=26.06 Aligned_cols=24 Identities=33% Similarity=0.551 Sum_probs=20.1
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHh
Q 033508 44 CRCYSVLTSLTALLCLAVNVLSAI 67 (118)
Q Consensus 44 cr~fs~vTa~~AlLCi~vNvlSav 67 (118)
-||..+.-...|++|+++|.+=-+
T Consensus 7 arclG~sLl~Lal~~iiaNilL~F 30 (195)
T PF05805_consen 7 ARCLGFSLLPLALLCIIANILLFF 30 (195)
T ss_pred hhhhhhHHHHHHHHHHHHHHheec
Confidence 378888888999999999999433
No 18
>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=27.07 E-value=1.7e+02 Score=18.41 Aligned_cols=40 Identities=15% Similarity=0.221 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhhhccCcccccch-h--hhhHHHHHHHHHHH
Q 033508 55 ALLCLAVNVLSAIRSFKNGSDIFDG-I--FRCYAVVIAFFVAL 94 (118)
Q Consensus 55 AlLCi~vNvlSavrsf~~~~dif~G-I--~RcYaV~iA~fVvl 94 (118)
+++.++.=+....++|+.++..-.- + .|+|+=.+++...+
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 3444444477788888877433333 3 69998877777655
No 19
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=26.43 E-value=41 Score=25.30 Aligned_cols=19 Identities=16% Similarity=0.579 Sum_probs=13.9
Q ss_pred HHHHHHHhhhHHHHHHHHH
Q 033508 89 AFFVALAETEWQFVLKFTK 107 (118)
Q Consensus 89 A~fVvlaETEW~~i~kF~k 107 (118)
|.++.=-|.||+++|+|-.
T Consensus 82 a~y~m~s~~~WdRFMRFMe 100 (113)
T CHL00128 82 AIYIMKNPEAWDRFMRFME 100 (113)
T ss_pred EEEEECCHHHHHHHHHHHH
Confidence 3444556889999999964
No 20
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=25.64 E-value=44 Score=24.86 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=12.9
Q ss_pred HHHHHhhhHHHHHHHHH
Q 033508 91 FVALAETEWQFVLKFTK 107 (118)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (118)
++.--|.||+++|+|-.
T Consensus 77 y~m~s~~~wdRFMRFme 93 (104)
T PRK13611 77 YDMETEAEWDRFLRFME 93 (104)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 44446889999999964
No 21
>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=24.07 E-value=45 Score=24.88 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=10.2
Q ss_pred hhhHHHHHHHHH
Q 033508 96 ETEWQFVLKFTK 107 (118)
Q Consensus 96 ETEW~~i~kF~k 107 (118)
+-||+++|+|-.
T Consensus 86 ~~~WdRFMRFMe 97 (108)
T PF03912_consen 86 EEEWDRFMRFME 97 (108)
T ss_dssp SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 679999999964
No 22
>PF11628 TCR_zetazeta: T-cell surface glycoprotein CD3 zeta chain; InterPro: IPR021663 The TCR complex of T-lymphocytes consists of either a TCR alpha/beta or TCR gamma/delta heterodimer co-expressed at the cell surface with the invariant subunits of CD3 labelled gamma, delta, epsilon, zeta, and eta []. The zeta subunit forms either homodimers or heterodimers with eta [], but eta homodimers have not been observed. The structure of the zetazeta transmembrane dimer consists of a left-handed coiled coil with polar contacts. Two aspartic acids are critical for zetazeta dimerisation and assembly with TCR []. The high affinity immunoglobulin epsilon receptor (IgE Fc receptor) subunit gamma associates with a variety of FcR alpha chains to form a functional signaling complex. The gamma subunit has a critical role in allowing the IgE Fc receptor to reach the cell surface and regulates several aspects of the immune response []. This family includes both CD3 zeta subunits and IgE Fc receptor gamma subunits. The gamma chain of the high affinity Fc receptor for IgE has significant structural homology to CD3 zeta and the related CD3 eta subunit and can facilitate T cell receptor expression and signaling in the absence of CD3 zeta and CD3 eta [].; PDB: 2HAC_B.
Probab=23.16 E-value=69 Score=19.65 Aligned_cols=18 Identities=33% Similarity=0.628 Sum_probs=15.0
Q ss_pred cccchhhhhHHHHHHHHH
Q 033508 75 DIFDGIFRCYAVVIAFFV 92 (118)
Q Consensus 75 dif~GI~RcYaV~iA~fV 92 (118)
+|-|||+=.|||++-.+.
T Consensus 6 YiLDgiL~iYgiiiT~L~ 23 (33)
T PF11628_consen 6 YILDGILFIYGIIITALY 23 (33)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred eeHHHHHHHHHHHHHHHH
Confidence 577999999999987654
No 23
>PF04750 Far-17a_AIG1: FAR-17a/AIG1-like protein; InterPro: IPR006838 This entry includes the hamster androgen-induced FAR-17a protein (Q60534 from SWISSPROT) []. The function of these proteins is unknown but it is thought to have a central role in the fusion process during myogenesis, within the somatic mesoderm. This entry also includes homologous regions from a number of other metazoan proteins.; GO: 0016021 integral to membrane
Probab=22.75 E-value=1.1e+02 Score=22.52 Aligned_cols=53 Identities=17% Similarity=0.226 Sum_probs=36.4
Q ss_pred EehhhhHHHHHHHHHHHHHHHHHHHhhhccCcc--ccc-chhhhhHHHHHHHHHHH
Q 033508 42 VVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGS--DIF-DGIFRCYAVVIAFFVAL 94 (118)
Q Consensus 42 ~vcr~fs~vTa~~AlLCi~vNvlSavrsf~~~~--dif-~GI~RcYaV~iA~fVvl 94 (118)
....-|.++|-++..++++...++.+..++..+ ..+ +-++..-+.-++++|.+
T Consensus 30 ~~gg~~~fLT~~~~~~~~~~~~~~~~~d~~~~~~l~~~~~~~~~~~~~pl~~~V~~ 85 (201)
T PF04750_consen 30 SYGGRFKFLTNWSLVLQTIYFILALLCDLFSSRKLRKLRDWLFYSLAFPLEFIVTV 85 (201)
T ss_pred hhcCcceehhHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcchh
Confidence 344678999999999999999999999774442 222 44555555555555443
No 24
>PHA02815 hypothetical protein; Provisional
Probab=22.56 E-value=1.9e+02 Score=20.12 Aligned_cols=25 Identities=12% Similarity=0.409 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHH
Q 033508 86 VVIAFFVALAETEWQFVLKFTKVLE 110 (118)
Q Consensus 86 V~iA~fVvlaETEW~~i~kF~kvLe 110 (118)
|+|.+|..+-=-.|+++++||.-++
T Consensus 7 I~~~~ylLl~Lv~wsyv~~~~~~iK 31 (64)
T PHA02815 7 IVISLYLLFQLVNCFYLFKLFNKIK 31 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777777789999999997654
No 25
>PHA01399 membrane protein P6
Probab=22.34 E-value=4e+02 Score=22.43 Aligned_cols=57 Identities=23% Similarity=0.556 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCcccccchhhhhHHHHHHHHHHHHhhhHHHHHHHHHHHHH-HH
Q 033508 50 LTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEY-WV 113 (118)
Q Consensus 50 vTa~~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLey-W~ 113 (118)
+.++-|++-+.-...|.+-+| -+.||+-| +|+. +++.++--.|-++-.|.-++++ |.
T Consensus 30 v~~ika~vk~ikkivsvi~~f--iskifs~i----g~il-~~il~~~~awf~fpa~IAIIKNLWE 87 (242)
T PHA01399 30 VKAIKAIVKIIKKIVSVILDF--ISKIFSKI----GIIL-IIILIIIAAWFFFPAFAAFLQSAWA 87 (242)
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHhc----cHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555566666666 34455433 2221 1122222356666667666666 63
No 26
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=21.68 E-value=92 Score=28.57 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHhhhc
Q 033508 51 TSLTALLCLAVNVLSAIRSF 70 (118)
Q Consensus 51 Ta~~AlLCi~vNvlSavrsf 70 (118)
.||.|=|--.-++-|.+|+-
T Consensus 265 ~AlFaqlNqGe~iTsgLkkV 284 (480)
T KOG2675|consen 265 GALFAQLNQGEGITSGLKKV 284 (480)
T ss_pred HHHHHHHhccchhhhhhhhC
Confidence 34555555555666666654
No 27
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=21.47 E-value=50 Score=25.02 Aligned_cols=10 Identities=30% Similarity=0.817 Sum_probs=8.1
Q ss_pred HHHHHhccCC
Q 033508 109 LEYWVARVLQ 118 (118)
Q Consensus 109 LeyW~gRGm~ 118 (118)
++||+|.|-|
T Consensus 59 ikyWl~~GAq 68 (112)
T KOG3419|consen 59 IKYWLGVGAQ 68 (112)
T ss_pred HHHHHhcCCc
Confidence 5799999865
No 28
>KOG1908 consensus Ribonuclease inhibitor type leucine-rich repeat proteins [RNA processing and modification]
Probab=21.47 E-value=86 Score=24.99 Aligned_cols=12 Identities=33% Similarity=0.603 Sum_probs=7.5
Q ss_pred CCCCCCCCCCCC
Q 033508 15 PPQPQPPPPPAR 26 (118)
Q Consensus 15 ~~~p~~~~~~~~ 26 (118)
+|+||||++++.
T Consensus 3 A~p~~~~sh~Aa 14 (165)
T KOG1908|consen 3 APPEAPPSHGAA 14 (165)
T ss_pred CCCCCCCCCCCc
Confidence 356677776664
No 29
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=21.10 E-value=52 Score=22.63 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=8.0
Q ss_pred HHHHHHhccCC
Q 033508 108 VLEYWVARVLQ 118 (118)
Q Consensus 108 vLeyW~gRGm~ 118 (118)
-++||++.|-|
T Consensus 56 ri~~Wl~~GAq 66 (75)
T PRK00040 56 RVLYWLGQGAQ 66 (75)
T ss_pred HHHHHHHCCCc
Confidence 35788888865
No 30
>KOG3030 consensus Lipid phosphate phosphatase and related enzymes of the PAP2 family [Lipid transport and metabolism]
Probab=20.54 E-value=1.4e+02 Score=25.35 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=22.8
Q ss_pred HHHHHHHHhhhccCc-ccccchhhhhHHHHHHHHHH
Q 033508 59 LAVNVLSAIRSFKNG-SDIFDGIFRCYAVVIAFFVA 93 (118)
Q Consensus 59 i~vNvlSavrsf~~~-~dif~GI~RcYaV~iA~fVv 93 (118)
.++=.+|=|..|||. +|++.|.+ -|+++|.++.
T Consensus 225 A~~v~lSRV~DYkHHwsDV~aG~l--iG~~~A~~~~ 258 (317)
T KOG3030|consen 225 ALLVGLSRVSDYKHHWSDVLAGAL--IGAFVAYFLY 258 (317)
T ss_pred HHHHeeehhcccccccHHHHHHHH--HHHHHHHHHH
Confidence 334457888899999 89999964 2555555543
No 31
>PF08551 DUF1751: Eukaryotic integral membrane protein (DUF1751); InterPro: IPR013861 This entry is found in eukaryotic integral membrane proteins. Q12239 from SWISSPROT, a Saccharomyces cerevisiae (Baker's yeast) protein, has been shown to localise COP II vesicles [].
Probab=20.44 E-value=1e+02 Score=21.39 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=28.5
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHhhhccCc--ccccchhhhhHHHHHHHHHH
Q 033508 44 CRCYSVLTSLTALLCLAVNVLSAIRSFKNG--SDIFDGIFRCYAVVIAFFVA 93 (118)
Q Consensus 44 cr~fs~vTa~~AlLCi~vNvlSavrsf~~~--~dif~GI~RcYaV~iA~fVv 93 (118)
.+++.+++.++.++..++..+.-.-+.+.. .-.++|- ++++.+++|+
T Consensus 48 lkFi~vv~~~tnl~~~~~~~~~y~i~~~~~~l~~~i~G~---~~~~~g~lVa 96 (99)
T PF08551_consen 48 LKFILVVNVITNLLTFLLYLLLYAITGNESYLFVPISGF---MGVLAGFLVA 96 (99)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHhCCCceeEEEecCc---HHhHhheEEE
Confidence 567777777777777666665555444333 1234443 6777776664
No 32
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=20.28 E-value=81 Score=26.27 Aligned_cols=19 Identities=26% Similarity=0.481 Sum_probs=16.6
Q ss_pred ehhhhHHHHHHHHHHHHHH
Q 033508 43 VCRCYSVLTSLTALLCLAV 61 (118)
Q Consensus 43 vcr~fs~vTa~~AlLCi~v 61 (118)
+.|||+++=.+.+++|++-
T Consensus 246 ~Lr~lAvlHtiiSf~clIg 264 (274)
T PF06459_consen 246 ALRILAVLHTIISFACLIG 264 (274)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3699999999999999863
Done!