Query 034079
Match_columns 104
No_of_seqs 104 out of 179
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 09:33:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034079.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034079hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0721 Molecular chaperone (D 100.0 2.8E-31 6.1E-36 191.2 5.4 102 1-104 4-105 (230)
2 COG5407 SEC63 Preprotein trans 99.8 4E-21 8.7E-26 150.8 4.3 97 3-104 6-104 (610)
3 COG2991 Uncharacterized protei 76.8 4.4 9.6E-05 24.9 3.3 15 41-55 42-57 (77)
4 PF03579 SHP: Small hydrophobi 75.7 2.8 6.1E-05 24.7 2.1 20 6-25 10-29 (64)
5 PF03622 IBV_3B: IBV 3B protei 73.6 1.9 4.2E-05 25.5 1.1 17 86-103 23-39 (64)
6 PF08592 DUF1772: Domain of un 72.5 10 0.00022 24.7 4.5 75 8-83 63-137 (139)
7 KOG3672 Histidine acid phospha 65.4 4 8.7E-05 32.8 1.6 52 45-104 249-301 (487)
8 COG4420 Predicted membrane pro 54.9 16 0.00034 26.4 3.0 7 96-102 82-88 (191)
9 KOG0510 Ankyrin repeat protein 49.2 32 0.00069 30.3 4.4 25 8-32 505-529 (929)
10 PF06298 PsbY: Photosystem II 45.9 33 0.00072 18.2 2.7 17 71-87 11-27 (36)
11 PF12955 DUF3844: Domain of un 43.8 29 0.00064 22.6 2.7 30 5-34 63-92 (103)
12 PRK13240 pbsY photosystem II p 42.8 22 0.00047 19.3 1.7 17 72-88 12-28 (40)
13 PF06210 DUF1003: Protein of u 42.1 46 0.00099 21.7 3.5 7 96-102 28-34 (108)
14 PF11027 DUF2615: Protein of u 41.8 32 0.0007 22.4 2.7 19 70-88 54-72 (103)
15 PF03967 PRCH: Photosynthetic 41.4 42 0.00091 23.0 3.3 22 70-91 13-34 (136)
16 COG3924 Predicted membrane pro 40.0 22 0.00048 21.9 1.6 15 70-84 18-32 (80)
17 PF04911 ATP-synt_J: ATP synth 39.0 24 0.00053 20.4 1.6 15 10-24 10-24 (54)
18 CHL00196 psbY photosystem II p 38.4 53 0.0011 17.4 2.7 17 71-87 11-27 (36)
19 PF04583 Baculo_p74: Baculovir 37.7 37 0.00081 25.5 2.8 23 75-102 106-128 (249)
20 PF14004 DUF4227: Protein of u 37.1 84 0.0018 19.1 3.9 31 70-102 8-38 (71)
21 PF15176 LRR19-TM: Leucine-ric 36.7 43 0.00092 21.8 2.6 27 4-30 10-36 (102)
22 PF07172 GRP: Glycine rich pro 36.3 53 0.0011 20.9 3.0 20 70-89 5-24 (95)
23 COG1288 Predicted membrane pro 34.2 1.9E+02 0.0042 23.8 6.5 20 70-89 275-294 (481)
24 PF06459 RR_TM4-6: Ryanodine R 33.5 52 0.0011 25.0 3.1 28 67-95 172-200 (274)
25 PF06422 PDR_CDR: CDR ABC tran 33.4 61 0.0013 20.6 3.0 20 70-89 50-69 (103)
26 PRK13183 psbN photosystem II r 33.2 56 0.0012 18.3 2.4 31 72-102 10-42 (46)
27 PF12686 DUF3800: Protein of u 32.7 3 6.6E-05 28.8 -3.5 16 4-19 4-27 (235)
28 PF09878 DUF2105: Predicted me 32.7 23 0.00049 25.9 1.0 23 7-29 164-186 (212)
29 TIGR03778 VPDSG_CTERM VPDSG-CT 32.4 43 0.00093 16.5 1.6 18 6-23 3-20 (26)
30 PF12273 RCR: Chitin synthesis 31.9 29 0.00064 22.9 1.4 24 11-34 2-25 (130)
31 KOG0863 20S proteasome, regula 31.4 16 0.00036 27.3 0.1 10 1-10 134-143 (264)
32 PF02468 PsbN: Photosystem II 29.8 1E+02 0.0023 16.9 3.2 26 77-102 12-39 (43)
33 CHL00020 psbN photosystem II p 29.5 52 0.0011 18.1 1.8 29 74-102 9-39 (43)
34 COG0713 NuoK NADH:ubiquinone o 27.9 36 0.00077 22.1 1.2 17 4-20 54-70 (100)
35 PRK14584 hmsS hemin storage sy 27.3 77 0.0017 22.1 2.9 19 70-88 18-36 (153)
36 PF15128 T_cell_tran_alt: T-ce 26.3 1.3E+02 0.0028 19.1 3.4 18 70-87 26-43 (92)
37 PHA00024 IX minor coat protein 25.4 1.1E+02 0.0024 15.8 2.8 16 71-86 9-24 (33)
38 PF04505 Dispanin: Interferon- 24.8 72 0.0016 19.5 2.1 19 14-32 19-39 (82)
39 PF03311 Cornichon: Cornichon 24.7 1.9E+02 0.0041 19.2 4.3 24 8-31 3-27 (128)
40 PF01542 HCV_core: Hepatitis C 24.7 57 0.0012 19.9 1.6 19 8-26 56-74 (75)
41 COG3083 Predicted hydrolase of 24.4 50 0.0011 27.7 1.7 24 11-34 61-84 (600)
42 TIGR01150 puhA photosynthetic 24.3 94 0.002 23.4 3.0 21 70-90 13-33 (252)
43 TIGR02736 cbb3_Q_epsi cytochro 24.0 79 0.0017 18.4 2.0 23 11-33 2-24 (56)
44 PF05478 Prominin: Prominin; 23.7 1.1E+02 0.0025 26.4 3.8 18 14-31 97-114 (806)
45 cd00226 PRCH Photosynthetic re 23.7 98 0.0021 23.3 3.0 20 70-89 13-32 (246)
46 PF15105 TMEM61: TMEM61 protei 23.0 90 0.0019 22.4 2.6 26 77-102 66-91 (198)
47 PF09125 COX2-transmemb: Cytoc 23.0 1.1E+02 0.0024 16.3 2.3 19 10-28 15-33 (38)
48 PF14373 Imm_superinfect: Supe 22.2 1.5E+02 0.0032 16.2 2.9 16 71-86 22-37 (43)
49 PRK10726 hypothetical protein; 22.1 83 0.0018 20.6 2.1 13 72-84 90-102 (105)
50 KOG0140 Medium-chain acyl-CoA 21.7 35 0.00076 27.0 0.3 9 1-9 51-59 (408)
51 PF07672 MFS_Mycoplasma: Mycop 21.6 1.5E+02 0.0033 22.5 3.7 24 11-34 40-63 (267)
52 PF06596 PsbX: Photosystem II 21.6 89 0.0019 16.8 1.8 12 20-31 17-28 (39)
53 PF05434 Tmemb_9: TMEM9; Inte 21.5 15 0.00032 25.5 -1.6 14 72-85 57-70 (149)
54 COG5264 VTC1 Vacuolar transpor 21.1 1.4E+02 0.003 20.2 3.1 25 74-99 73-98 (126)
55 PF11057 Cortexin: Cortexin of 20.9 75 0.0016 19.7 1.6 19 5-23 25-43 (81)
56 PF02937 COX6C: Cytochrome c o 20.8 72 0.0016 19.4 1.5 33 70-102 19-58 (73)
57 PF04341 DUF485: Protein of un 20.8 1.3E+02 0.0028 18.6 2.8 18 70-87 59-76 (91)
58 PRK07899 rpsA 30S ribosomal pr 20.6 42 0.00091 27.4 0.6 9 2-10 385-393 (486)
59 PF14475 Mso1_Sec1_bdg: Sec1-b 20.4 29 0.00063 18.9 -0.3 11 3-13 29-39 (41)
60 PHA02955 hypothetical protein; 20.2 79 0.0017 23.3 1.9 28 8-35 176-203 (213)
61 PF05461 ApoL: Apolipoprotein 20.2 50 0.0011 25.5 0.9 14 15-28 111-124 (313)
62 PRK10873 hypothetical protein; 20.1 1.2E+02 0.0026 20.4 2.6 20 70-89 105-124 (131)
No 1
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.8e-31 Score=191.18 Aligned_cols=102 Identities=25% Similarity=0.466 Sum_probs=82.4
Q ss_pred CCccccCCCchhHHHHHHHhhhhhhhhhhhhhccccccccccccccccchhhHHHHHHHhhhccCcchhHHHHHHHHHHH
Q 034079 1 MAATEENSQLFPIFILTIMALPLVPYTILKLCHAFSKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVI 80 (104)
Q Consensus 1 ~~~YDE~g~~f~yFvlt~l~lvLiP~T~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~k~~~~~~~~~~i~lv~gW~l 80 (104)
|.||||+|+|||||+||+++++++|+||.++++...+.....+|||.+|.+++...++..+ + .++..+++++++||++
T Consensus 4 ~~eYDE~g~tf~yflls~~~~i~~P~Ty~~i~~~~~~~~~~~~c~c~~c~~~r~~~~~~~~-k-~~~~~~~i~lv~~W~v 81 (230)
T KOG0721|consen 4 DYEYDESGNTFPYFLLSFLAIILLPMTYLLIPRNPEPPKRKEECQCHGCDKKRRKKAKVSP-K-SISTKRKVFLVVGWAV 81 (230)
T ss_pred ccccccccCccHHHHHHHHHHHHHHHHHHHhccccchhhhhhHHhhhhhhhhhhhhcccCc-c-cchhHHHHHHHHHHHH
Confidence 5799999999999999999999999999999853222222468999999887654333322 2 3333399999999999
Q ss_pred HHHHHHHHHhcccccCccCCcccC
Q 034079 81 MIILIYYIKSTSREVWNMGPQIQI 104 (104)
Q Consensus 81 ~~~L~y~i~~~~~~~~~fDPyei~ 104 (104)
+++|+|+|++++++.+.||||||+
T Consensus 82 ~~fL~y~i~~~~~~~~~fDPyEIL 105 (230)
T KOG0721|consen 82 IAFLIYKIMNSRRERQKFDPYEIL 105 (230)
T ss_pred HHHHHHHHhhhhHHhhcCCcHHhh
Confidence 999999999999888999999996
No 2
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=99.82 E-value=4e-21 Score=150.80 Aligned_cols=97 Identities=21% Similarity=0.364 Sum_probs=76.7
Q ss_pred ccccCCCchhHHHHHHHhhhhhhhhhhhhhcccccc-ccccccccccchhhHHHHHHHhhhccCcchhHHHHHHHHHHHH
Q 034079 3 ATEENSQLFPIFILTIMALPLVPYTILKLCHAFSKK-IKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIM 81 (104)
Q Consensus 3 ~YDE~g~~f~yFvlt~l~lvLiP~T~~~l~~~~~~~-~~~~~~~~~~~~~~~~~i~~~~k~~~~~~~~~~i~lv~gW~l~ 81 (104)
||||+|.+||||+|+.+.++..|+||..+-+....+ ....+|.|+.|..+..+ .+|| +.++. |++++++||.++
T Consensus 6 eYDE~g~~~p~fvL~gl~~vvlpmTY~~i~gpsaSKe~~~vr~~~q~~Rpkdkn--v~rK--SIf~l-R~If~ivgWl~i 80 (610)
T COG5407 6 EYDESGLASPYFVLSGLVPVVLPMTYDLIEGPSASKELRRVRCACQGCRPKDKN--VSRK--SIFKL-RKIFTIVGWLVI 80 (610)
T ss_pred ccccccccchHHHHhhhhheeeeeehhheeCCcccchhhcchhhhhhcCccccc--hhhh--HHHhh-hHHHHHHHHHHH
Confidence 899999999999999999999999998886553332 33567888888754432 2222 32234 999999999999
Q ss_pred HHHHHHHHhccccc-CccCCcccC
Q 034079 82 IILIYYIKSTSREV-WNMGPQIQI 104 (104)
Q Consensus 82 ~~L~y~i~~~~~~~-~~fDPyei~ 104 (104)
++|.|+|.+.+.+. +.||||||+
T Consensus 81 ~~L~~~I~~~k~~~~~~fDPyEIL 104 (610)
T COG5407 81 SYLISNIRTLKIEYRRGFDPYEIL 104 (610)
T ss_pred HHHHHHHHHHHHHHHcCCChHHhh
Confidence 99999999777776 899999996
No 3
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.82 E-value=4.4 Score=24.92 Aligned_cols=15 Identities=27% Similarity=0.749 Sum_probs=8.3
Q ss_pred cccccccc-chhhHHH
Q 034079 41 TIHCQCSD-CARSGKY 55 (104)
Q Consensus 41 ~~~~~~~~-~~~~~~~ 55 (104)
++.|.|+. |..+.++
T Consensus 42 ~K~CdC~~pCDt~~~k 57 (77)
T COG2991 42 EKVCDCDEPCDTHKKK 57 (77)
T ss_pred chhcCCCCchHHHHHh
Confidence 34577765 5554443
No 4
>PF03579 SHP: Small hydrophobic protein; InterPro: IPR005327 The small hydrophobic integral membrane protein, SH (previously designated 1A) is found to have a variety of glycosylated forms [, ]. This protein is a component of the mature respiratory syncytial virion [] where it may form complexes and appears to play a structural role.; GO: 0016020 membrane, 0016021 integral to membrane, 0048222 glycoprotein network
Probab=75.75 E-value=2.8 Score=24.71 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=14.2
Q ss_pred cCCCchhHHHHHHHhhhhhh
Q 034079 6 ENSQLFPIFILTIMALPLVP 25 (104)
Q Consensus 6 E~g~~f~yFvlt~l~lvLiP 25 (104)
-+|.+||||-|.+..+.++-
T Consensus 10 FtskFW~YFtLi~M~lti~~ 29 (64)
T PF03579_consen 10 FTSKFWTYFTLIFMMLTIGF 29 (64)
T ss_pred eccccchHHHHHHHHHHHHH
Confidence 36899999987766554443
No 5
>PF03622 IBV_3B: IBV 3B protein ; InterPro: IPR005295 These proteins are the product of ORF 3B from Infectious bronchitis virus). Currently, the function of this protein remains unknown [].
Probab=73.63 E-value=1.9 Score=25.49 Aligned_cols=17 Identities=12% Similarity=-0.099 Sum_probs=11.3
Q ss_pred HHHHhcccccCccCCccc
Q 034079 86 YYIKSTSREVWNMGPQIQ 103 (104)
Q Consensus 86 y~i~~~~~~~~~fDPyei 103 (104)
+.|+ +.-+..+|||||.
T Consensus 23 q~IS-svl~t~iFDPFE~ 39 (64)
T PF03622_consen 23 QHIS-SVLNTEIFDPFEV 39 (64)
T ss_pred HHHH-HHHhhhhcCCeeE
Confidence 5555 3335578999985
No 6
>PF08592 DUF1772: Domain of unknown function (DUF1772); InterPro: IPR013901 This entry represents proteins of unknown function.
Probab=72.53 E-value=10 Score=24.66 Aligned_cols=75 Identities=9% Similarity=0.279 Sum_probs=38.5
Q ss_pred CCchhHHHHHHHhhhhhhhhhhhhhccccccccccccccccchhhHHHHHHHhhhccCcchhHHHHHHHHHHHHHH
Q 034079 8 SQLFPIFILTIMALPLVPYTILKLCHAFSKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIMII 83 (104)
Q Consensus 8 g~~f~yFvlt~l~lvLiP~T~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~k~~~~~~~~~~i~lv~gW~l~~~ 83 (104)
+....+.+.+.+.+-.+|.|....... ++.-..-+-+........+..++.++|..+.+..|.++-++++++..+
T Consensus 63 ~~~~~~~~a~~~~~~~~~~T~~~~~P~-N~~l~~~~~~~~~~~~~~~~~~~l~~~W~~~n~vR~~~~~~a~~~~~~ 137 (139)
T PF08592_consen 63 AARLLWLAAAALLLSIIPFTFLVNVPI-NNRLAAWDIESSPEEAPADWVRALLDRWGRLNLVRTVLSLVAFLLLLI 137 (139)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhHH-HHHHHHccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555666667899998775322 111000000001112222334555555666654488888888887653
No 7
>KOG3672 consensus Histidine acid phosphatase [General function prediction only]
Probab=65.42 E-value=4 Score=32.84 Aligned_cols=52 Identities=15% Similarity=0.137 Sum_probs=28.2
Q ss_pred ccccchhhHHHHHHHhhh-ccCcchhHHHHHHHHHHHHHHHHHHHHhcccccCccCCcccC
Q 034079 45 QCSDCARSGKYRKSIFKR-ISNFSTCSNLSLVLLWVIMIILIYYIKSTSREVWNMGPQIQI 104 (104)
Q Consensus 45 ~~~~~~~~~~~i~~~~k~-~~~~~~~~~i~lv~gW~l~~~L~y~i~~~~~~~~~fDPyei~ 104 (104)
+| .|+.+...++....+ -..+.+ +....+.-|.=.+.+ .....+.||||+.|
T Consensus 249 ~C-~Cp~~~~~r~~~e~~~~~q~lk-~~~~dv~~~~~~~~~------~~~p~~~~~pf~~I 301 (487)
T KOG3672|consen 249 QC-ACPIHKSIRRIYEEEHLQQFLK-MKSDDVADEEKKFLS------FPQPAASFDPFQMI 301 (487)
T ss_pred cc-cchHHHHHHHHHHHHHHHHHHh-cchHHHHhhhcceee------ecccccccCchhHH
Confidence 66 377766665544431 111133 334566677655443 22344679999865
No 8
>COG4420 Predicted membrane protein [Function unknown]
Probab=54.89 E-value=16 Score=26.42 Aligned_cols=7 Identities=14% Similarity=0.069 Sum_probs=5.8
Q ss_pred CccCCcc
Q 034079 96 WNMGPQI 102 (104)
Q Consensus 96 ~~fDPye 102 (104)
..||||-
T Consensus 82 ~~wDpyP 88 (191)
T COG4420 82 LAWDPYP 88 (191)
T ss_pred CcCCCcc
Confidence 6799995
No 9
>KOG0510 consensus Ankyrin repeat protein [General function prediction only]
Probab=49.23 E-value=32 Score=30.25 Aligned_cols=25 Identities=36% Similarity=0.369 Sum_probs=19.8
Q ss_pred CCchhHHHHHHHhhhhhhhhhhhhh
Q 034079 8 SQLFPIFILTIMALPLVPYTILKLC 32 (104)
Q Consensus 8 g~~f~yFvlt~l~lvLiP~T~~~l~ 32 (104)
|--|.++-|-+++++++|+|++.+-
T Consensus 505 g~~~~~~nL~~Y~lFlv~lT~Yv~~ 529 (929)
T KOG0510|consen 505 GKYFHLNNLLIYSLFLVSLTIYVLL 529 (929)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345666789999999999998873
No 10
>PF06298 PsbY: Photosystem II protein Y (PsbY); InterPro: IPR009388 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 PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants []. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea []. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.; GO: 0030145 manganese ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0016021 integral to membrane
Probab=45.94 E-value=33 Score=18.18 Aligned_cols=17 Identities=12% Similarity=0.016 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034079 71 NLSLVLLWVIMIILIYY 87 (104)
Q Consensus 71 ~i~lv~gW~l~~~L~y~ 87 (104)
-+++.+||+++-..---
T Consensus 11 Pil~A~gWa~fNIg~~A 27 (36)
T PF06298_consen 11 PILPAAGWALFNIGRAA 27 (36)
T ss_pred HHHHHHHHHHHHhHHHH
Confidence 35566799998666433
No 11
>PF12955 DUF3844: Domain of unknown function (DUF3844); InterPro: IPR024382 This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins thought to be located in the endoplasmic reticulum.
Probab=43.78 E-value=29 Score=22.60 Aligned_cols=30 Identities=20% Similarity=0.108 Sum_probs=25.1
Q ss_pred ccCCCchhHHHHHHHhhhhhhhhhhhhhcc
Q 034079 5 EENSQLFPIFILTIMALPLVPYTILKLCHA 34 (104)
Q Consensus 5 DE~g~~f~yFvlt~l~lvLiP~T~~~l~~~ 34 (104)
|=+.++|.++-.|+++++++-..+..|+..
T Consensus 63 DvS~~F~L~~~~ti~lv~~~~~~I~lL~sv 92 (103)
T PF12955_consen 63 DVSVPFWLFAGFTIALVVLVAGAIGLLFSV 92 (103)
T ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 667888888889999999998888888655
No 12
>PRK13240 pbsY photosystem II protein Y; Reviewed
Probab=42.83 E-value=22 Score=19.33 Aligned_cols=17 Identities=12% Similarity=0.020 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034079 72 LSLVLLWVIMIILIYYI 88 (104)
Q Consensus 72 i~lv~gW~l~~~L~y~i 88 (104)
+++.+||+++-..---+
T Consensus 12 il~A~~Wa~fNIg~~Al 28 (40)
T PRK13240 12 ILAAAGWAVFNIGKAAR 28 (40)
T ss_pred HHHHHHHHHHHhhHHHH
Confidence 56678999987664443
No 13
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=42.10 E-value=46 Score=21.71 Aligned_cols=7 Identities=14% Similarity=-0.012 Sum_probs=5.4
Q ss_pred CccCCcc
Q 034079 96 WNMGPQI 102 (104)
Q Consensus 96 ~~fDPye 102 (104)
..||||-
T Consensus 28 ~~fDpyP 34 (108)
T PF06210_consen 28 PAFDPYP 34 (108)
T ss_pred CCCCCcc
Confidence 4699984
No 14
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=41.82 E-value=32 Score=22.42 Aligned_cols=19 Identities=21% Similarity=0.831 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYI 88 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i 88 (104)
...+++++|.++|++.|..
T Consensus 54 ~~~~~~~~w~~~A~~ly~~ 72 (103)
T PF11027_consen 54 SMFMMMMLWMVLAMALYLL 72 (103)
T ss_pred cHHHHHHHHHHHHHHHHHc
Confidence 5677888999999999987
No 15
>PF03967 PRCH: Photosynthetic reaction centre, H-chain N-terminal region; InterPro: IPR015810 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors []. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) []. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [, , ]. The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits []. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain []. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. This entry represents the N-terminal domain of the photosynthetic reaction centre H subunit, which includes the transmembrane domain and part of the cytoplasmic domain [].; GO: 0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0019684 photosynthesis, light reaction, 0030077 plasma membrane light-harvesting complex; PDB: 1RZZ_H 1PST_H 2J8D_H 3DUQ_H 1FNP_H 1KBY_H 1E14_H 2HG3_H 1UMX_H 1YST_H ....
Probab=41.37 E-value=42 Score=22.98 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 034079 70 SNLSLVLLWVIMIILIYYIKST 91 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~~~ 91 (104)
--++|-+.|+.|+.|+|+....
T Consensus 13 Aql~lyaFwiFFagLi~YLrrE 34 (136)
T PF03967_consen 13 AQLVLYAFWIFFAGLIYYLRRE 34 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4466778999999999998533
No 16
>COG3924 Predicted membrane protein [Function unknown]
Probab=40.02 E-value=22 Score=21.90 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIIL 84 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L 84 (104)
-.++.++||.+.+|+
T Consensus 18 LtllYl~gW~v~AYl 32 (80)
T COG3924 18 LTLLYLAGWLVAAYL 32 (80)
T ss_pred HHHHHHHHHHHHHhC
Confidence 456777899999987
No 17
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=38.96 E-value=24 Score=20.38 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=11.8
Q ss_pred chhHHHHHHHhhhhh
Q 034079 10 LFPIFILTIMALPLV 24 (104)
Q Consensus 10 ~f~yFvlt~l~lvLi 24 (104)
+||||+.+.+.+.+|
T Consensus 10 ~wPFf~ag~iv~ygv 24 (54)
T PF04911_consen 10 MWPFFAAGAIVYYGV 24 (54)
T ss_pred hhHHHHHHHHHHHHH
Confidence 699999988766655
No 18
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=38.45 E-value=53 Score=17.40 Aligned_cols=17 Identities=12% Similarity=0.106 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034079 71 NLSLVLLWVIMIILIYY 87 (104)
Q Consensus 71 ~i~lv~gW~l~~~L~y~ 87 (104)
=+++.+||+++-..---
T Consensus 11 Pil~A~~Wa~fNIg~~A 27 (36)
T CHL00196 11 PVLAAASWALFNIGRLA 27 (36)
T ss_pred HHHHHHHHHHHHhHHHH
Confidence 35667799998655433
No 19
>PF04583 Baculo_p74: Baculoviridae p74 conserved region; InterPro: IPR007663 Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts. GFP tagging experiments implicate p74 as an ODV envelope protein [, ].; GO: 0019058 viral infectious cycle
Probab=37.69 E-value=37 Score=25.51 Aligned_cols=23 Identities=17% Similarity=0.109 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHhcccccCccCCcc
Q 034079 75 VLLWVIMIILIYYIKSTSREVWNMGPQI 102 (104)
Q Consensus 75 v~gW~l~~~L~y~i~~~~~~~~~fDPye 102 (104)
|+||+|++..+--+ -...||||-
T Consensus 106 Vvgi~Li~~ti~Dl-----vL~~WDPfG 128 (249)
T PF04583_consen 106 VVGIVLIFLTIADL-----VLMFWDPFG 128 (249)
T ss_pred HHHHHHHHHHHHHH-----HHHhcCccc
Confidence 46887776654322 125799983
No 20
>PF14004 DUF4227: Protein of unknown function (DUF4227)
Probab=37.13 E-value=84 Score=19.06 Aligned_cols=31 Identities=10% Similarity=-0.143 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccCccCCcc
Q 034079 70 SNLSLVLLWVIMIILIYYIKSTSREVWNMGPQI 102 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~~~~~~~~~fDPye 102 (104)
|.++|-.|=.+++|-+..-- ..+...+|||+
T Consensus 8 k~~~LF~~~T~lfYy~~~w~--~~~~~~~hrY~ 38 (71)
T PF14004_consen 8 KFFLLFTGCTLLFYYAILWV--SDEYEPYHRYD 38 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHHhccCCCCC
Confidence 55666555555555443322 23456788886
No 21
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=36.72 E-value=43 Score=21.84 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=17.9
Q ss_pred cccCCCchhHHHHHHHhhhhhhhhhhh
Q 034079 4 TEENSQLFPIFILTIMALPLVPYTILK 30 (104)
Q Consensus 4 YDE~g~~f~yFvlt~l~lvLiP~T~~~ 30 (104)
-.++|..|+|.+.-+++.+.+-+-+..
T Consensus 10 ~~~~g~sW~~LVGVv~~al~~SlLIal 36 (102)
T PF15176_consen 10 PGEGGRSWPFLVGVVVTALVTSLLIAL 36 (102)
T ss_pred CCCCCcccHhHHHHHHHHHHHHHHHHH
Confidence 357899999987666555555444433
No 22
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=36.32 E-value=53 Score=20.91 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYIK 89 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~ 89 (104)
+.++|.+.+|+++++..-++
T Consensus 5 ~~llL~l~LA~lLlisSeva 24 (95)
T PF07172_consen 5 AFLLLGLLLAALLLISSEVA 24 (95)
T ss_pred HHHHHHHHHHHHHHHHhhhh
Confidence 56666677777777766554
No 23
>COG1288 Predicted membrane protein [Function unknown]
Probab=34.23 E-value=1.9e+02 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYIK 89 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~ 89 (104)
++++|.+.=+.+..++|-+.
T Consensus 275 ~klvL~lf~l~f~~mI~GV~ 294 (481)
T COG1288 275 DKLVLLLFTLTFVIMIWGVI 294 (481)
T ss_pred hhHHHHHHHHHHHHHHHHhh
Confidence 55555555555556666554
No 24
>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=33.48 E-value=52 Score=24.98 Aligned_cols=28 Identities=29% Similarity=0.462 Sum_probs=20.1
Q ss_pred chhHHHHHHHHHHHHHHHH-HHHHhccccc
Q 034079 67 STCSNLSLVLLWVIMIILI-YYIKSTSREV 95 (104)
Q Consensus 67 ~~~~~i~lv~gW~l~~~L~-y~i~~~~~~~ 95 (104)
+. |.+.|+++-++-++|. |||+....+.
T Consensus 172 Nl-r~lALflAFaINFILLFYKVs~~~~~~ 200 (274)
T PF06459_consen 172 NL-RFLALFLAFAINFILLFYKVSTSPPEE 200 (274)
T ss_pred HH-HHHHHHHHHHHHHHHHHHHhccCCccc
Confidence 55 8899999888866555 8887555443
No 25
>PF06422 PDR_CDR: CDR ABC transporter; InterPro: IPR010929 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). In yeast, the PDR and CDR ABC transporters display extensive sequence homology, and confer resistance to several anti-fungal compounds by actively transporting their substrates out of the cell. These transporters have two homologous halves, each with an N-terminal intracellular hydrophilic region that contains an ATP-binding site, followed by a C-terminal membrane-associated region containing six transmembrane segments []. This entry represents a domain of the PDR/CDR ABC transporter comprising extracellular loop 3, transmembrane segment 6 and a linker region.; GO: 0005524 ATP binding, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane
Probab=33.42 E-value=61 Score=20.64 Aligned_cols=20 Identities=15% Similarity=0.482 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYIK 89 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~ 89 (104)
||+-+++||.+++++++.+.
T Consensus 50 RN~GIli~f~i~f~~~~~~~ 69 (103)
T PF06422_consen 50 RNFGILIAFWIFFIVLTLLA 69 (103)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 78888888877777766653
No 26
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=33.18 E-value=56 Score=18.27 Aligned_cols=31 Identities=13% Similarity=0.100 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHH-Hhccccc-CccCCcc
Q 034079 72 LSLVLLWVIMIILIYYI-KSTSREV-WNMGPQI 102 (104)
Q Consensus 72 i~lv~gW~l~~~L~y~i-~~~~~~~-~~fDPye 102 (104)
+.+.++=+++.+..|.+ +...+.+ +.=||||
T Consensus 10 ~~i~i~~lL~~~TgyaiYtaFGppSk~LrDPFe 42 (46)
T PRK13183 10 LAITILAILLALTGFGIYTAFGPPSKELDDPFD 42 (46)
T ss_pred HHHHHHHHHHHHhhheeeeccCCcccccCCchh
Confidence 33444445555666665 3345555 6789987
No 27
>PF12686 DUF3800: Protein of unknown function (DUF3800); InterPro: IPR024524 This family of proteins is functionally uncharacterised. Some family members possess a DE motif at their N terminus and a QXXD motif at their C terminus that may be functionally important.
Probab=32.71 E-value=3 Score=28.81 Aligned_cols=16 Identities=25% Similarity=0.395 Sum_probs=12.6
Q ss_pred cccCCC--------chhHHHHHHH
Q 034079 4 TEENSQ--------LFPIFILTIM 19 (104)
Q Consensus 4 YDE~g~--------~f~yFvlt~l 19 (104)
.||||+ .-|||+++.+
T Consensus 4 iDESG~~~~~~~~~~~~~fvl~gv 27 (235)
T PF12686_consen 4 IDESGNTGPNYSDKNSPYFVLGGV 27 (235)
T ss_pred EeCCCCCCCCcCCCCCCEEEEEEE
Confidence 499998 4899987765
No 28
>PF09878 DUF2105: Predicted membrane protein (DUF2105); InterPro: IPR019212 This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Probab=32.66 E-value=23 Score=25.89 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=20.6
Q ss_pred CCCchhHHHHHHHhhhhhhhhhh
Q 034079 7 NSQLFPIFILTIMALPLVPYTIL 29 (104)
Q Consensus 7 ~g~~f~yFvlt~l~lvLiP~T~~ 29 (104)
||-+|.++++.|+.+++.|--+.
T Consensus 164 SGiaWalWi~gF~~Ff~~P~~Wl 186 (212)
T PF09878_consen 164 SGIAWALWIAGFIGFFLFPQYWL 186 (212)
T ss_pred hhHHHHHHHHHHHHHHHhHHHHH
Confidence 78899999999999999997653
No 29
>TIGR03778 VPDSG_CTERM VPDSG-CTERM exosortase interaction domain. Through in silico analysis, we previously described the PEP-CTERM/exosortase system (PubMed:16930487). This model describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C-terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif (TIGR02595) of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria.
Probab=32.38 E-value=43 Score=16.47 Aligned_cols=18 Identities=11% Similarity=0.220 Sum_probs=12.5
Q ss_pred cCCCchhHHHHHHHhhhh
Q 034079 6 ENSQLFPIFILTIMALPL 23 (104)
Q Consensus 6 E~g~~f~yFvlt~l~lvL 23 (104)
++|+|..-+.+++++++.
T Consensus 3 DsGST~~Ll~~~l~~l~~ 20 (26)
T TIGR03778 3 DSGSTLALLGLGLLGLLG 20 (26)
T ss_pred CchhHHHHHHHHHHHHHH
Confidence 467787777777766654
No 30
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=31.87 E-value=29 Score=22.87 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=12.0
Q ss_pred hhHHHHHHHhhhhhhhhhhhhhcc
Q 034079 11 FPIFILTIMALPLVPYTILKLCHA 34 (104)
Q Consensus 11 f~yFvlt~l~lvLiP~T~~~l~~~ 34 (104)
|.+|++-+++++++=+...+..++
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rR 25 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRR 25 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHH
Confidence 455655555555554444444333
No 31
>KOG0863 consensus 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones]
Probab=31.42 E-value=16 Score=27.33 Aligned_cols=10 Identities=20% Similarity=0.272 Sum_probs=8.0
Q ss_pred CCccccCCCc
Q 034079 1 MAATEENSQL 10 (104)
Q Consensus 1 ~~~YDE~g~~ 10 (104)
|++|||+|--
T Consensus 134 v~gYDe~G~h 143 (264)
T KOG0863|consen 134 VAGYDESGPH 143 (264)
T ss_pred EEeecCCCce
Confidence 6889999954
No 32
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 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 PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=29.75 E-value=1e+02 Score=16.90 Aligned_cols=26 Identities=15% Similarity=-0.004 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHH-Hhccccc-CccCCcc
Q 034079 77 LWVIMIILIYYI-KSTSREV-WNMGPQI 102 (104)
Q Consensus 77 gW~l~~~L~y~i-~~~~~~~-~~fDPye 102 (104)
+=+++....|.+ ....+.+ +.=||||
T Consensus 12 ~~~lv~~Tgy~iYtaFGppSk~LrDPfe 39 (43)
T PF02468_consen 12 SCLLVSITGYAIYTAFGPPSKELRDPFE 39 (43)
T ss_pred HHHHHHHHhhhhhheeCCCccccCCccc
Confidence 334444444544 2344445 6789987
No 33
>CHL00020 psbN photosystem II protein N
Probab=29.46 E-value=52 Score=18.12 Aligned_cols=29 Identities=7% Similarity=0.025 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHH-Hhccccc-CccCCcc
Q 034079 74 LVLLWVIMIILIYYI-KSTSREV-WNMGPQI 102 (104)
Q Consensus 74 lv~gW~l~~~L~y~i-~~~~~~~-~~fDPye 102 (104)
+.++=+++....|.+ +...+.+ +.=||||
T Consensus 9 i~i~~ll~~~Tgy~iYtaFGppSk~LrDPfe 39 (43)
T CHL00020 9 IFISGLLVSFTGYALYTAFGQPSKQLRDPFE 39 (43)
T ss_pred HHHHHHHHHhhheeeeeccCCchhccCCchh
Confidence 333444555555665 3344455 6789987
No 34
>COG0713 NuoK NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Energy production and conversion]
Probab=27.90 E-value=36 Score=22.13 Aligned_cols=17 Identities=35% Similarity=0.733 Sum_probs=13.7
Q ss_pred cccCCCchhHHHHHHHh
Q 034079 4 TEENSQLFPIFILTIMA 20 (104)
Q Consensus 4 YDE~g~~f~yFvlt~l~ 20 (104)
+|-+||.|.+|++|+-+
T Consensus 54 ~~~~gQvfaifvitvAA 70 (100)
T COG0713 54 GDLDGQVFAIFVITVAA 70 (100)
T ss_pred ccccchHHHHHHHHHHH
Confidence 35589999999998754
No 35
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=27.29 E-value=77 Score=22.09 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYI 88 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i 88 (104)
-.++-+++|+.|+|+.++.
T Consensus 18 D~~lT~~aW~gfi~l~~~~ 36 (153)
T PRK14584 18 DIILTALAWFGFLFLLVRG 36 (153)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6677788999999999886
No 36
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=26.34 E-value=1.3e+02 Score=19.13 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYY 87 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~ 87 (104)
.++-+++||.++..++-.
T Consensus 26 ~ifkllL~WlvlsLl~I~ 43 (92)
T PF15128_consen 26 QIFKLLLGWLVLSLLAIH 43 (92)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 556688899988766543
No 37
>PHA00024 IX minor coat protein
Probab=25.42 E-value=1.1e+02 Score=15.84 Aligned_cols=16 Identities=13% Similarity=0.299 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHH
Q 034079 71 NLSLVLLWVIMIILIY 86 (104)
Q Consensus 71 ~i~lv~gW~l~~~L~y 86 (104)
.-..++||++..-+.+
T Consensus 9 fgA~ilG~~l~~~Il~ 24 (33)
T PHA00024 9 FGAYILGWALFYGILV 24 (33)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3457789999855443
No 38
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=24.79 E-value=72 Score=19.53 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=10.0
Q ss_pred HHHHHHhhhh--hhhhhhhhh
Q 034079 14 FILTIMALPL--VPYTILKLC 32 (104)
Q Consensus 14 Fvlt~l~lvL--iP~T~~~l~ 32 (104)
..+++++++. .|+.+.-+.
T Consensus 19 l~~sI~s~l~Cc~PlGi~Ai~ 39 (82)
T PF04505_consen 19 LVLSIFSTLCCCWPLGIVAIV 39 (82)
T ss_pred eeHHHHHHHHHHhhHHHHHhe
Confidence 3444444444 477765553
No 39
>PF03311 Cornichon: Cornichon protein; InterPro: IPR003377 The drosophila cornichon protein (gene: cni) [] is required in the germline for dorsal-ventral signalling. The dorsal-ventral pattern formation involves a reorganisation of the microtubule network correlated with the movement of the oocyte nucleus, and depending on the initial correct establishment of the anterior-posterior axis via a signal from the oocyte produced by cornichon and gurken and received by torpedo protein in the follicle cells. The biochemical function of the cornichon protein is currently not known. It is a protein of 144 residues that seems to contain three transmembrane regions. ; GO: 0035556 intracellular signal transduction, 0016020 membrane
Probab=24.68 E-value=1.9e+02 Score=19.18 Aligned_cols=24 Identities=13% Similarity=0.303 Sum_probs=13.8
Q ss_pred CCchhHHHHHHHh-hhhhhhhhhhh
Q 034079 8 SQLFPIFILTIMA-LPLVPYTILKL 31 (104)
Q Consensus 8 g~~f~yFvlt~l~-lvLiP~T~~~l 31 (104)
++.+..|+++++. .+++-++.+.+
T Consensus 3 ~~~~~~~i~alll~~~ll~~~vy~i 27 (128)
T PF03311_consen 3 FDFIVLWILALLLTAALLFIVVYFI 27 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566666655 55555555554
No 40
>PF01542 HCV_core: Hepatitis C virus core protein; InterPro: IPR002521 The Hepatitis C virus (HCV) is a small (50 nm in size), enveloped, single-stranded, positive sense RNA virus. It is the only known member of the hepacivirus genus in the family Flaviviridae. There are six major genotypes of the hepatitis C virus, which are identified numerically (e.g., genotype 1, genotype 2, etc.). Although Hepatitis A virus, Hepatitis B virus, and Hepatitis C virus have similar names, because they all cause liver inflammation, these are distinctly different viruses both genetically and clinically. HCV has a positive sense RNA genome that consists of a single open reading frame of 9600 nucleotides. At the 5' and 3' ends of the RNA are the UTR regions that are not translated into proteins but are important to translation and replication of the viral RNA. The 5' UTR has a ribosome binding site (IRES - Internal ribosome entry site) that starts the translation of a 3000 amino acid containing protein that is later cut by cellular and viral proteases into 10 active structural and non-structural smaller proteins. The HCV core protein is located at the N terminus of the polyprotein and is followed by the signal sequence located between the core protein and the E1 envelope glycoprotein. This signal sequence targets the nascent HCV polyprotein to the endoplasmic reticulum (ER), allowing the translocation of E1 to the ER lumen. Cleavage by a signal peptidase in the ER lumen releases the N-terminal end of E1, leaving the 191-amino acids (aa) core protein anchored by its C-terminal signal peptide [, ]. This 191aa polypeptide, also known as p23, is the immature form of the core protein; p23 is further processed by an intramembrane protease, the signal peptide peptidase (SPP), that removes the ER anchor , releasing p21, the N-terminal 179aa mature form of the core protein []. Core protein (p21) is responsible for packaging viral RNA to form a viral nucleocapsid, and it also promotes virion budding []. Two domains have been identified in the mature form of the HCV core protein, based on predicted structural and functional characteristics []. Domain I, corresponding to the N-terminal region of approximately 120 aa, is a highly basic domain that is probably involved in the recruitment of viral RNA during particle morphogenesis. Domain II, located between aa 120 and aa 175, is a hydrophobic region predicted to form one or two alpha-helices that are probably involved in the association of core with the ER membrane and lipid droplets. This entry represents domain II and domain III (ER anchor sequence) of the core protein p23. ; GO: 0005198 structural molecule activity
Probab=24.66 E-value=57 Score=19.89 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=16.0
Q ss_pred CCchhHHHHHHHhhhhhhh
Q 034079 8 SQLFPIFILTIMALPLVPY 26 (104)
Q Consensus 8 g~~f~yFvlt~l~lvLiP~ 26 (104)
|=-|..|++++++++..|.
T Consensus 56 gcsfsIFllaLlSc~~~p~ 74 (75)
T PF01542_consen 56 GCSFSIFLLALLSCLTVPA 74 (75)
T ss_pred CccHHHHHHHHHHhccccC
Confidence 5568899999999998874
No 41
>COG3083 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]
Probab=24.38 E-value=50 Score=27.66 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=20.2
Q ss_pred hhHHHHHHHhhhhhhhhhhhhhcc
Q 034079 11 FPIFILTIMALPLVPYTILKLCHA 34 (104)
Q Consensus 11 f~yFvlt~l~lvLiP~T~~~l~~~ 34 (104)
|.|++.+..++++.|+|...++++
T Consensus 61 FsflvFA~yLlvlfpltfiv~s~r 84 (600)
T COG3083 61 FSFLVFALYLLVLFPLTFIVLSQR 84 (600)
T ss_pred HHHHHHHHHHHHHhhhhhhcccHH
Confidence 678889999999999998777655
No 42
>TIGR01150 puhA photosynthetic reaction center, subunit H, bacterial. This model describes the photosynthetic reaction center H subunit in non-oxygenic photosynthetic bacteria. The reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in the form of NADH. Ultimately, the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is an organic acid rather than water. Much of our current functional understanding of photosynthesis comes from the structural determination
Probab=24.26 E-value=94 Score=23.41 Aligned_cols=21 Identities=29% Similarity=0.825 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 034079 70 SNLSLVLLWVIMIILIYYIKS 90 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~~ 90 (104)
--+.|-+.|+.|+.|+|+...
T Consensus 13 Aq~~ly~FwiFFA~Li~YLrr 33 (252)
T TIGR01150 13 AQLVIYAFWIFLAGLIYYLRR 33 (252)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 345677899999999999853
No 43
>TIGR02736 cbb3_Q_epsi cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial. Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase systems, so this family is assumed to represent the epsilonproteobacterial variant of CcoQ.
Probab=24.01 E-value=79 Score=18.37 Aligned_cols=23 Identities=17% Similarity=0.353 Sum_probs=12.4
Q ss_pred hhHHHHHHHhhhhhhhhhhhhhc
Q 034079 11 FPIFILTIMALPLVPYTILKLCH 33 (104)
Q Consensus 11 f~yFvlt~l~lvLiP~T~~~l~~ 33 (104)
+.||++|++..+++=--++-+++
T Consensus 2 y~yf~~ti~lvv~LYgY~yhLYr 24 (56)
T TIGR02736 2 YAYFAFTLLLVIFLYAYIYHLYR 24 (56)
T ss_pred cchHHHHHHHHHHHHHHHHHhhh
Confidence 35777777666665333334443
No 44
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=23.69 E-value=1.1e+02 Score=26.36 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=12.9
Q ss_pred HHHHHHhhhhhhhhhhhh
Q 034079 14 FILTIMALPLVPYTILKL 31 (104)
Q Consensus 14 Fvlt~l~lvLiP~T~~~l 31 (104)
.++.++.++++|++-..+
T Consensus 97 ~~i~ll~~il~P~vg~~f 114 (806)
T PF05478_consen 97 AVIGLLFIILMPLVGLCF 114 (806)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 356777778889886554
No 45
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=23.66 E-value=98 Score=23.27 Aligned_cols=20 Identities=30% Similarity=0.850 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYIK 89 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~ 89 (104)
--++|-+.|+.|+.|+|+..
T Consensus 13 A~~~l~~Fw~ffa~Li~YL~ 32 (246)
T cd00226 13 AQLVIYAFWIFFAGLIYYLR 32 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 44667789999999999985
No 46
>PF15105 TMEM61: TMEM61 protein family
Probab=23.04 E-value=90 Score=22.38 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhcccccCccCCcc
Q 034079 77 LWVIMIILIYYIKSTSREVWNMGPQI 102 (104)
Q Consensus 77 gW~l~~~L~y~i~~~~~~~~~fDPye 102 (104)
|-.|++-|.+.|....+..-.||||-
T Consensus 66 GlLLl~GLLWSikas~~~~pr~d~y~ 91 (198)
T PF15105_consen 66 GLLLLFGLLWSIKASTRGPPRWDPYH 91 (198)
T ss_pred HHHHHHHHHhhhhcccCCCCCCCccc
Confidence 55556666788865656556799994
No 47
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=22.96 E-value=1.1e+02 Score=16.32 Aligned_cols=19 Identities=11% Similarity=0.116 Sum_probs=13.9
Q ss_pred chhHHHHHHHhhhhhhhhh
Q 034079 10 LFPIFILTIMALPLVPYTI 28 (104)
Q Consensus 10 ~f~yFvlt~l~lvLiP~T~ 28 (104)
-|..|.++++.++++-.-|
T Consensus 15 ~Wi~F~l~mi~vFi~li~y 33 (38)
T PF09125_consen 15 GWIAFALAMILVFIALIGY 33 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 3888998888777765544
No 48
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=22.23 E-value=1.5e+02 Score=16.15 Aligned_cols=16 Identities=25% Similarity=0.252 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHH
Q 034079 71 NLSLVLLWVIMIILIY 86 (104)
Q Consensus 71 ~i~lv~gW~l~~~L~y 86 (104)
.+=+.+||.+++.++-
T Consensus 22 ~~Nl~lGWT~iGWv~a 37 (43)
T PF14373_consen 22 LLNLLLGWTGIGWVAA 37 (43)
T ss_pred hHHHHHHhHHHHHHHH
Confidence 3345567777766643
No 49
>PRK10726 hypothetical protein; Provisional
Probab=22.14 E-value=83 Score=20.58 Aligned_cols=13 Identities=23% Similarity=0.516 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHH
Q 034079 72 LSLVLLWVIMIIL 84 (104)
Q Consensus 72 i~lv~gW~l~~~L 84 (104)
.+..+-|.++.+|
T Consensus 90 ~V~~lFwllF~~L 102 (105)
T PRK10726 90 TVGCLFWLLFSWL 102 (105)
T ss_pred HHHHHHHHHHHHH
Confidence 3445578888766
No 50
>KOG0140 consensus Medium-chain acyl-CoA dehydrogenase [Lipid transport and metabolism]
Probab=21.69 E-value=35 Score=26.96 Aligned_cols=9 Identities=11% Similarity=0.250 Sum_probs=6.3
Q ss_pred CCccccCCC
Q 034079 1 MAATEENSQ 9 (104)
Q Consensus 1 ~~~YDE~g~ 9 (104)
|||||++|+
T Consensus 51 aae~Dk~ge 59 (408)
T KOG0140|consen 51 AAEYDKSGE 59 (408)
T ss_pred hhhhcccCC
Confidence 577777774
No 51
>PF07672 MFS_Mycoplasma: Mycoplasma MFS transporter; InterPro: IPR011699 These proteins share some similarity with members of the Major Facilitator Superfamily (MFS).
Probab=21.63 E-value=1.5e+02 Score=22.49 Aligned_cols=24 Identities=8% Similarity=0.271 Sum_probs=18.0
Q ss_pred hhHHHHHHHhhhhhhhhhhhhhcc
Q 034079 11 FPIFILTIMALPLVPYTILKLCHA 34 (104)
Q Consensus 11 f~yFvlt~l~lvLiP~T~~~l~~~ 34 (104)
|-+-+..+.+++++|+-++.+.+.
T Consensus 40 W~~I~si~~lL~~IpLIly~ifGk 63 (267)
T PF07672_consen 40 WQWILSIFILLIFIPLILYIIFGK 63 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 556666777888999998887544
No 52
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 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 []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=21.61 E-value=89 Score=16.83 Aligned_cols=12 Identities=8% Similarity=0.238 Sum_probs=9.1
Q ss_pred hhhhhhhhhhhh
Q 034079 20 ALPLVPYTILKL 31 (104)
Q Consensus 20 ~lvLiP~T~~~l 31 (104)
.+|++|.+.-.+
T Consensus 17 ~iVv~~i~~ali 28 (39)
T PF06596_consen 17 VIVVIPIAGALI 28 (39)
T ss_dssp -HHHHHHHHHHH
T ss_pred hhhhhhhhhheE
Confidence 378999998766
No 53
>PF05434 Tmemb_9: TMEM9; InterPro: IPR008853 This family contains several eukaryotic transmembrane proteins which are homologous to Homo sapiens transmembrane protein 9 Q9P0T7 from SWISSPROT. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to H. sapiens and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localised to the late endosomes and lysosomes []. Members of this family contain CXCXC repeats IPR004153 from INTERPRO in their N-terminal region.; GO: 0016021 integral to membrane
Probab=21.50 E-value=15 Score=25.54 Aligned_cols=14 Identities=29% Similarity=0.971 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHHHH
Q 034079 72 LSLVLLWVIMIILI 85 (104)
Q Consensus 72 i~lv~gW~l~~~L~ 85 (104)
+++++.|++.+.+.
T Consensus 57 vVIivl~Vi~lLvl 70 (149)
T PF05434_consen 57 VVIIVLWVIGLLVL 70 (149)
T ss_pred EEEEeHHHHHHHHH
Confidence 33444454443333
No 54
>COG5264 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=21.12 E-value=1.4e+02 Score=20.18 Aligned_cols=25 Identities=8% Similarity=0.090 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHhccccc-CccC
Q 034079 74 LVLLWVIMIILIYYIKSTSREV-WNMG 99 (104)
Q Consensus 74 lv~gW~l~~~L~y~i~~~~~~~-~~fD 99 (104)
.+..|+++.|+ ++.+.+..-. +.||
T Consensus 73 f~~~ya~~lY~-kRa~~Ir~R~~~pyD 98 (126)
T COG5264 73 FCGFYALMLYL-KRAVNIRQRSAGPYD 98 (126)
T ss_pred HHHHHHHHHHH-HHHHHHHhcCCCCCc
Confidence 34589999888 7877776654 6665
No 55
>PF11057 Cortexin: Cortexin of kidney; InterPro: IPR020066 Cortexin is a neuron-specific, 82-residue membrane protein which is found especially in vertebrate brain cortex tissue. It may mediate extracellular or intracellular signalling of cortical neurons during forebrain development. Cortexin is present at significant levels in the foetal brain, suggesting that it may be important to neurons of both the developing and adult cerebral cortex. Cortexin has a conserved single membrane-spanning region in the middle of each sequence []. In humans, there is selective expression of Cortexin 3 (CTXN3) in the kidney as well as the brain []. This entry contains Cortexins 1, 2 and 3.; GO: 0031224 intrinsic to membrane
Probab=20.95 E-value=75 Score=19.70 Aligned_cols=19 Identities=26% Similarity=0.226 Sum_probs=12.2
Q ss_pred ccCCCchhHHHHHHHhhhh
Q 034079 5 EENSQLFPIFILTIMALPL 23 (104)
Q Consensus 5 DE~g~~f~yFvlt~l~lvL 23 (104)
-|++.+|.|.++-++.+++
T Consensus 25 ~eqkt~faFV~~L~~fL~~ 43 (81)
T PF11057_consen 25 LEQKTAFAFVGLLCLFLGL 43 (81)
T ss_pred cccceeehHHHHHHHHHHH
Confidence 3788888887655444433
No 56
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=20.84 E-value=72 Score=19.38 Aligned_cols=33 Identities=9% Similarity=0.188 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccc------cc-CccCCcc
Q 034079 70 SNLSLVLLWVIMIILIYYIKSTSR------EV-WNMGPQI 102 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~~~~~------~~-~~fDPye 102 (104)
+++++.+.=.+.+..+++....++ |- +.|||++
T Consensus 19 ~~i~~a~~ls~~~~~~~kf~v~~pRKk~YadFYknYD~~k 58 (73)
T PF02937_consen 19 RHIVVAFVLSLGVAAAYKFGVAEPRKKAYADFYKNYDPMK 58 (73)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHT--HHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHccChHH
Confidence 445444444445555555422221 33 6789874
No 57
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=20.78 E-value=1.3e+02 Score=18.63 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYY 87 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~ 87 (104)
-...++++|++..+-+.+
T Consensus 59 g~~~~~~~~~l~~~Yv~~ 76 (91)
T PF04341_consen 59 GLGQIVFAWVLTWLYVRR 76 (91)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 445566788887766555
No 58
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=20.63 E-value=42 Score=27.45 Aligned_cols=9 Identities=22% Similarity=0.320 Sum_probs=7.8
Q ss_pred CccccCCCc
Q 034079 2 AATEENSQL 10 (104)
Q Consensus 2 ~~YDE~g~~ 10 (104)
|+|||+|+.
T Consensus 385 ~~~~~~~~~ 393 (486)
T PRK07899 385 AEYDEQGNY 393 (486)
T ss_pred cccccCCCc
Confidence 789999974
No 59
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=20.39 E-value=29 Score=18.92 Aligned_cols=11 Identities=27% Similarity=0.301 Sum_probs=8.4
Q ss_pred ccccCCCchhH
Q 034079 3 ATEENSQLFPI 13 (104)
Q Consensus 3 ~YDE~g~~f~y 13 (104)
=|+|.|+.||=
T Consensus 29 yY~~k~~~~P~ 39 (41)
T PF14475_consen 29 YYTEKGRPFPG 39 (41)
T ss_pred HHHHcCCCCCC
Confidence 48888888873
No 60
>PHA02955 hypothetical protein; Provisional
Probab=20.22 E-value=79 Score=23.27 Aligned_cols=28 Identities=18% Similarity=0.145 Sum_probs=20.8
Q ss_pred CCchhHHHHHHHhhhhhhhhhhhhhccc
Q 034079 8 SQLFPIFILTIMALPLVPYTILKLCHAF 35 (104)
Q Consensus 8 g~~f~yFvlt~l~lvLiP~T~~~l~~~~ 35 (104)
|..+|+|++....++++-+.++.++|..
T Consensus 176 g~~~~w~ii~~v~ii~~~v~l~yikR~i 203 (213)
T PHA02955 176 SFSIKWFIIYIVLCLLILIILGYIYRTV 203 (213)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHh
Confidence 5577888888888877777777776553
No 61
>PF05461 ApoL: Apolipoprotein L; InterPro: IPR008405 Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia []. The various functions of apoL are still not entirely clear. Apolipoprotein L-I has been identified as a trypanolytic agent [] and displays similar phylogenetic distribution to the programmed cell death protein Bcl-2 and BH-3 domain-containing proteins, suggesting a possible role in apoptosis [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region
Probab=20.20 E-value=50 Score=25.46 Aligned_cols=14 Identities=50% Similarity=0.795 Sum_probs=12.6
Q ss_pred HHHHHhhhhhhhhh
Q 034079 15 ILTIMALPLVPYTI 28 (104)
Q Consensus 15 vlt~l~lvLiP~T~ 28 (104)
++|+++++|.|.|.
T Consensus 111 ilsIlGLaLAPvT~ 124 (313)
T PF05461_consen 111 ILSILGLALAPVTA 124 (313)
T ss_pred HHHHHhHHhccccc
Confidence 68999999999984
No 62
>PRK10873 hypothetical protein; Provisional
Probab=20.10 E-value=1.2e+02 Score=20.35 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034079 70 SNLSLVLLWVIMIILIYYIK 89 (104)
Q Consensus 70 ~~i~lv~gW~l~~~L~y~i~ 89 (104)
-=+.+++||+++++-+.+.+
T Consensus 105 GG~~li~GWl~la~~a~~~~ 124 (131)
T PRK10873 105 GGVSFLAGWALMLIGALRLK 124 (131)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 66788899999998877653
Done!