Query 032589
Match_columns 137
No_of_seqs 27 out of 29
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 03:24:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032589.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032589hhsearch_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 7.7E-13 1.7E-17 97.2 9.6 77 46-126 5-81 (136)
2 PF06151 Trehalose_recp: Treha 77.8 15 0.00033 32.3 8.2 36 75-110 90-126 (414)
3 PRK14756 hypothetical protein; 48.3 30 0.00066 21.2 3.1 21 47-67 7-27 (29)
4 PHA03281 envelope glycoprotein 39.1 99 0.0021 29.9 6.4 41 33-74 546-586 (642)
5 COG3768 Predicted membrane pro 37.3 1.6E+02 0.0034 26.7 7.0 62 49-110 67-131 (350)
6 TIGR00769 AAA ADP/ATP carrier 36.4 2.1E+02 0.0046 25.7 7.8 43 74-116 74-133 (472)
7 PF13705 TRC8_N: TRC8 N-termin 34.6 51 0.0011 30.8 3.8 75 40-122 174-248 (508)
8 COG5074 t-SNARE complex subuni 31.0 28 0.00061 30.4 1.4 15 81-95 251-265 (280)
9 PF11163 DUF2947: Protein of u 29.5 20 0.00044 28.7 0.3 23 94-117 108-130 (153)
10 KOG2412 Nuclear-export-signal 28.6 20 0.00043 34.1 0.1 26 75-100 468-498 (591)
11 PF07444 Ycf66_N: Ycf66 protei 28.4 2.3E+02 0.005 20.5 6.7 35 47-81 5-40 (84)
12 PF11712 Vma12: Endoplasmic re 27.7 1.9E+02 0.0042 21.5 5.2 14 84-97 115-128 (142)
13 PLN00039 photosystem II reacti 27.1 39 0.00084 25.9 1.4 18 90-107 81-98 (111)
14 PRK13610 photosystem II reacti 26.6 40 0.00086 26.1 1.4 17 91-107 88-104 (113)
15 TIGR03047 PS_II_psb28 photosys 26.4 41 0.00088 25.8 1.4 19 89-107 79-97 (109)
16 PRK13612 photosystem II reacti 25.9 42 0.00091 25.8 1.4 17 91-107 84-100 (113)
17 PF02293 AmiS_UreI: AmiS/UreI 25.3 3E+02 0.0066 22.2 6.3 66 47-129 90-157 (166)
18 PF04588 HIG_1_N: Hypoxia indu 24.1 2.1E+02 0.0045 18.4 4.9 40 55-94 10-52 (54)
19 PF05805 L6_membrane: L6 membr 23.5 80 0.0017 26.0 2.7 23 44-66 7-29 (195)
20 CHL00128 psbW photosystem II p 23.5 49 0.0011 25.5 1.4 18 90-107 83-100 (113)
21 PRK13611 photosystem II reacti 22.8 53 0.0011 25.0 1.4 17 91-107 77-93 (104)
22 PF03912 Psb28: Psb28 protein; 21.3 54 0.0012 25.0 1.3 12 96-107 86-97 (108)
23 KOG2675 Adenylate cyclase-asso 20.9 95 0.0021 29.1 2.9 20 51-70 265-284 (480)
24 PF11628 TCR_zetazeta: T-cell 20.3 83 0.0018 19.8 1.7 18 75-92 6-23 (33)
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=99.44 E-value=7.7e-13 Score=97.18 Aligned_cols=77 Identities=22% Similarity=0.427 Sum_probs=64.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 032589 46 CYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQILEFYA 125 (137)
Q Consensus 46 ~fs~vTa~~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQIFvA~m 125 (137)
.+.+++.++|+++++..+++.+.+ .++-+.++++|.++++++++++|.+|.++.|++++|..|.|||+++||+++|
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 H
Q 032589 126 L 126 (137)
Q Consensus 126 T 126 (137)
+
T Consensus 81 ~ 81 (136)
T PF08507_consen 81 C 81 (136)
T ss_pred H
Confidence 8
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=77.79 E-value=15 Score=32.26 Aligned_cols=36 Identities=14% Similarity=0.291 Sum_probs=30.5
Q ss_pred cccch-hhhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032589 75 DIFDG-IFRCYAVVIAFFVALAETEWQFVLKFTKVLE 110 (137)
Q Consensus 75 dif~G-I~RcYaV~iA~fVvlaETEW~~i~kF~kvLe 110 (137)
+-..+ +|-+...++.++....=.+|..+|+-|.-.|
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=48.29 E-value=30 Score=21.24 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHh
Q 032589 47 YSVLTSLTALLCLAVNVLSAI 67 (137)
Q Consensus 47 fs~vTa~~AlLCi~vNvlSav 67 (137)
||++|.+.||..|++..+.++
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=39.12 E-value=99 Score=29.90 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=28.0
Q ss_pred CCCCCCceEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcc
Q 032589 33 LRNRADPLLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGS 74 (137)
Q Consensus 33 ~~~~~DplL~vcr~fs~vTa~~AlLCi~vNvlSavrsf~~~~ 74 (137)
...+.-|+++-.-..+-+ ++.||||+++..+-..+.|++..
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 345567777654433332 46789999999988888887653
No 5
>COG3768 Predicted membrane protein [Function unknown]
Probab=37.27 E-value=1.6e+02 Score=26.71 Aligned_cols=62 Identities=19% Similarity=0.187 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHH---HhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 032589 49 VLTSLTALLCLAVNVLS---AIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLE 110 (137)
Q Consensus 49 ~vTa~~AlLCi~vNvlS---avrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLe 110 (137)
.+++...|+|.+|-.-| ..+.|....-++=|..=+-++++.++|..+=|||-.++|+-++..
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 36677777887775544 345564444566666667788889999999999999999987653
No 6
>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=36.39 E-value=2.1e+02 Score=25.73 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=33.1
Q ss_pred ccccchhhhHHHHHHHHHHHHH-----------------hhhHHHHHHHHHHHHHHHhhh
Q 032589 74 SDIFDGIFRCYAVVIAFFVALA-----------------ETEWQFVLKFTKVLEYWVARG 116 (137)
Q Consensus 74 ~dif~GI~RcYaV~iA~fVvla-----------------ETEW~~i~kF~kvLeyW~gRG 116 (137)
+++|.-+.+.+...+.+|-.+. ++=-..+..++.++.+|..+.
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 6899999999999998888772 111223667888999999985
No 7
>PF13705 TRC8_N: TRC8 N-terminal domain
Probab=34.62 E-value=51 Score=30.80 Aligned_cols=75 Identities=24% Similarity=0.337 Sum_probs=45.6
Q ss_pred eEEehhhhHHHHHHHHHHHHHHHHHHHhhhccCcccccchhhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhhHH
Q 032589 40 LLVVCRCYSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDGIFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQ 119 (137)
Q Consensus 40 lL~vcr~fs~vTa~~AlLCi~vNvlSavrsf~~~~dif~GI~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQ 119 (137)
++.++.+-...|++..+--+.-|.....+.-+ .-+.-+.|.||. ..++|+||.++-==.-..-||..|=..|
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 34444444444444444444444444333221 223455677764 5789999999866666667999999999
Q ss_pred HHH
Q 032589 120 ILE 122 (137)
Q Consensus 120 IFv 122 (137)
+..
T Consensus 246 ~~~ 248 (508)
T PF13705_consen 246 LYI 248 (508)
T ss_pred Hhe
Confidence 866
No 8
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=30.96 E-value=28 Score=30.42 Aligned_cols=15 Identities=20% Similarity=0.820 Sum_probs=12.1
Q ss_pred hhHHHHHHHHHHHHH
Q 032589 81 FRCYAVVIAFFVALA 95 (137)
Q Consensus 81 ~RcYaV~iA~fVvla 95 (137)
.|||+|+|.++++++
T Consensus 251 i~c~gI~~iii~viv 265 (280)
T COG5074 251 IRCYGICFIIIIVIV 265 (280)
T ss_pred eehhhhHHHHHHHHH
Confidence 589999988877654
No 9
>PF11163 DUF2947: Protein of unknown function (DUF2947); InterPro: IPR021334 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=29.49 E-value=20 Score=28.69 Aligned_cols=23 Identities=22% Similarity=0.447 Sum_probs=18.2
Q ss_pred HHhhhHHHHHHHHHHHHHHHhhhh
Q 032589 94 LAETEWQFVLKFTKVLEYWVARGM 117 (137)
Q Consensus 94 laETEW~~i~kF~kvLeyW~gRGm 117 (137)
++||.|+-|.|-||-+-|- .-|+
T Consensus 108 iiET~W~vFkr~WknFLF~-ddGp 130 (153)
T PF11163_consen 108 IIETRWDVFKRNWKNFLFY-DDGP 130 (153)
T ss_pred EEEeehHHHHHHHHHHhcc-cCcc
Confidence 5799999999999987664 3444
No 10
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=28.58 E-value=20 Score=34.14 Aligned_cols=26 Identities=35% Similarity=0.569 Sum_probs=22.7
Q ss_pred ccc----chhhhHHHHHHHHHH-HHHhhhHH
Q 032589 75 DIF----DGIFRCYAVVIAFFV-ALAETEWQ 100 (137)
Q Consensus 75 dif----~GI~RcYaV~iA~fV-vlaETEW~ 100 (137)
|.| +||+|.||.+|.+=. +.+=|+|+
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 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=28.45 E-value=2.3e+02 Score=20.48 Aligned_cols=35 Identities=26% Similarity=0.267 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhccCc-ccccchhh
Q 032589 47 YSVLTSLTALLCLAVNVLSAIRSFKNG-SDIFDGIF 81 (137)
Q Consensus 47 fs~vTa~~AlLCi~vNvlSavrsf~~~-~dif~GI~ 81 (137)
|+.-+.++.++-++...+-..|.++.. ++.+|=+|
T Consensus 5 ~~~~~iLgi~l~~~~~~Ly~lr~~~Pev~Rd~D~~f 40 (84)
T PF07444_consen 5 FGPSYILGIILILGGLALYFLRFFRPEVSRDYDIFF 40 (84)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHCcchhhhhhHHH
Confidence 456677888888889999999999876 44333333
No 12
>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=27.73 E-value=1.9e+02 Score=21.46 Aligned_cols=14 Identities=29% Similarity=0.342 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHhh
Q 032589 84 YAVVIAFFVALAET 97 (137)
Q Consensus 84 YaV~iA~fVvlaET 97 (137)
-+++.|++|.+||+
T Consensus 115 lgl~~al~vlvAEv 128 (142)
T PF11712_consen 115 LGLFGALLVLVAEV 128 (142)
T ss_pred HHHHHHHHHHHHHH
Confidence 46778888999997
No 13
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=27.05 E-value=39 Score=25.95 Aligned_cols=18 Identities=22% Similarity=0.582 Sum_probs=13.3
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 032589 90 FFVALAETEWQFVLKFTK 107 (137)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (137)
.++.=-|.||+++|+|-.
T Consensus 81 ~y~m~s~~~WdRFMRFMe 98 (111)
T PLN00039 81 KYVMRSPREWDRFMRFME 98 (111)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344446889999999964
No 14
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=26.62 E-value=40 Score=26.06 Aligned_cols=17 Identities=12% Similarity=0.321 Sum_probs=12.6
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032589 91 FVALAETEWQFVLKFTK 107 (137)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (137)
++.=-|.||++||+|-.
T Consensus 88 y~m~s~~~WdRFMRFMe 104 (113)
T PRK13610 88 YNWNSEEAFERFMRFAS 104 (113)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34445889999999954
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=26.38 E-value=41 Score=25.76 Aligned_cols=19 Identities=26% Similarity=0.725 Sum_probs=13.9
Q ss_pred HHHHHHHhhhHHHHHHHHH
Q 032589 89 AFFVALAETEWQFVLKFTK 107 (137)
Q Consensus 89 A~fVvlaETEW~~i~kF~k 107 (137)
|.++.=-|.||+++|+|-.
T Consensus 79 a~y~m~s~~~WdRFMRFme 97 (109)
T TIGR03047 79 AVYIMKSEDEWDRFMRFME 97 (109)
T ss_pred EEEEECCHHHHHHHHHHHH
Confidence 3344556889999999964
No 16
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=25.88 E-value=42 Score=25.83 Aligned_cols=17 Identities=24% Similarity=0.704 Sum_probs=12.8
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032589 91 FVALAETEWQFVLKFTK 107 (137)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (137)
++.=-|.||+++|+|-.
T Consensus 84 y~m~s~~~WdRFMRFMe 100 (113)
T PRK13612 84 YIWKSEQEWDRFMRFME 100 (113)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34445889999999964
No 17
>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=25.32 E-value=3e+02 Score=22.17 Aligned_cols=66 Identities=32% Similarity=0.378 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhccCcccccch-hhhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 032589 47 YSVLTSLTALLCLAVNVLSAIRSFKNGSDIFDG-IFRCYAVVIAFFVALAETEWQFVLKFTKVLEYWVARGMLQILEFYA 125 (137)
Q Consensus 47 fs~vTa~~AlLCi~vNvlSavrsf~~~~dif~G-I~RcYaV~iA~fVvlaETEW~~i~kF~kvLeyW~gRGmLQIFvA~m 125 (137)
||...++.|+... +.+|.+..|.--| |-=.+++++.+|-++.-.+- .+.||. |.+.|++++.
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 5555555555443 4445444555455 57899999999777665554 555654 5567888888
Q ss_pred Hh-hc
Q 032589 126 LA-AS 129 (137)
Q Consensus 126 Ta-~~ 129 (137)
|+ .|
T Consensus 153 T~wiP 157 (166)
T PF02293_consen 153 TAWIP 157 (166)
T ss_pred HHHHH
Confidence 83 44
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=24.12 E-value=2.1e+02 Score=18.43 Aligned_cols=40 Identities=15% Similarity=0.221 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhhhccCcccccch-h--hhHHHHHHHHHHHH
Q 032589 55 ALLCLAVNVLSAIRSFKNGSDIFDG-I--FRCYAVVIAFFVAL 94 (137)
Q Consensus 55 AlLCi~vNvlSavrsf~~~~dif~G-I--~RcYaV~iA~fVvl 94 (137)
++++++.=+....++|+.++..-.. + .|+|+=.+++...+
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 3444444467778888876433333 3 69998877776655
No 19
>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=23.53 E-value=80 Score=26.03 Aligned_cols=23 Identities=35% Similarity=0.560 Sum_probs=19.7
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHH
Q 032589 44 CRCYSVLTSLTALLCLAVNVLSA 66 (137)
Q Consensus 44 cr~fs~vTa~~AlLCi~vNvlSa 66 (137)
-||..+.-...|++|+++|.+-.
T Consensus 7 arclG~sLl~Lal~~iiaNilL~ 29 (195)
T PF05805_consen 7 ARCLGFSLLPLALLCIIANILLF 29 (195)
T ss_pred hhhhhhHHHHHHHHHHHHHHhee
Confidence 37888888899999999999943
No 20
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=23.52 E-value=49 Score=25.45 Aligned_cols=18 Identities=11% Similarity=0.567 Sum_probs=13.4
Q ss_pred HHHHHHhhhHHHHHHHHH
Q 032589 90 FFVALAETEWQFVLKFTK 107 (137)
Q Consensus 90 ~fVvlaETEW~~i~kF~k 107 (137)
.++.=-|-||+++|+|-.
T Consensus 83 ~y~m~s~~~WdRFMRFMe 100 (113)
T CHL00128 83 IYIMKNPEAWDRFMRFME 100 (113)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 344456889999999964
No 21
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=22.75 E-value=53 Score=25.00 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=12.8
Q ss_pred HHHHHhhhHHHHHHHHH
Q 032589 91 FVALAETEWQFVLKFTK 107 (137)
Q Consensus 91 fVvlaETEW~~i~kF~k 107 (137)
++.--|.||+++|+|-.
T Consensus 77 y~m~s~~~wdRFMRFme 93 (104)
T PRK13611 77 YDMETEAEWDRFLRFME 93 (104)
T ss_pred EEECCHHHHHHHHHHHH
Confidence 34446889999999964
No 22
>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=21.29 E-value=54 Score=25.02 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=10.1
Q ss_pred hhhHHHHHHHHH
Q 032589 96 ETEWQFVLKFTK 107 (137)
Q Consensus 96 ETEW~~i~kF~k 107 (137)
+-||+++|+|-.
T Consensus 86 ~~~WdRFMRFMe 97 (108)
T PF03912_consen 86 EEEWDRFMRFME 97 (108)
T ss_dssp SHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 679999999964
No 23
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=20.95 E-value=95 Score=29.10 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHhhhc
Q 032589 51 TSLTALLCLAVNVLSAIRSF 70 (137)
Q Consensus 51 Ta~~AlLCi~vNvlSavrsf 70 (137)
.+|.|=|--.-++-|.+|+-
T Consensus 265 ~AlFaqlNqGe~iTsgLkkV 284 (480)
T KOG2675|consen 265 GALFAQLNQGEGITSGLKKV 284 (480)
T ss_pred HHHHHHHhccchhhhhhhhC
Confidence 44555555555666666654
No 24
>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=20.27 E-value=83 Score=19.76 Aligned_cols=18 Identities=33% Similarity=0.628 Sum_probs=14.8
Q ss_pred cccchhhhHHHHHHHHHH
Q 032589 75 DIFDGIFRCYAVVIAFFV 92 (137)
Q Consensus 75 dif~GI~RcYaV~iA~fV 92 (137)
+|-|||+=.|||++-.+.
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
Done!