Query 034210
Match_columns 101
No_of_seqs 100 out of 170
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 11:00:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034210hhsearch_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 8.6E-30 1.9E-34 185.4 5.3 99 1-101 4-102 (230)
2 COG5407 SEC63 Preprotein trans 99.7 2E-18 4.4E-23 137.0 3.1 94 3-101 6-101 (610)
3 PF03579 SHP: Small hydrophobi 80.6 1.9 4.1E-05 25.8 2.4 20 6-25 10-29 (64)
4 PF12955 DUF3844: Domain of un 59.2 14 0.0003 24.3 3.1 31 5-35 63-93 (103)
5 PRK10873 hypothetical protein; 55.1 16 0.00034 24.8 3.0 20 70-89 105-124 (131)
6 PF07172 GRP: Glycine rich pro 54.3 17 0.00038 23.3 2.9 22 67-89 3-24 (95)
7 PRK13240 pbsY photosystem II p 53.4 17 0.00038 19.9 2.4 23 70-92 10-32 (40)
8 KOG0510 Ankyrin repeat protein 51.5 31 0.00068 30.5 4.7 25 8-32 505-529 (929)
9 PF08592 DUF1772: Domain of un 51.1 52 0.0011 21.3 4.9 74 7-83 62-137 (139)
10 PF06459 RR_TM4-6: Ryanodine R 49.9 27 0.00059 26.7 3.8 30 67-97 172-202 (274)
11 PF15176 LRR19-TM: Leucine-ric 49.7 23 0.00051 23.3 3.0 27 4-30 10-36 (102)
12 PF03967 PRCH: Photosynthetic 49.0 28 0.00061 24.1 3.4 21 70-90 13-33 (136)
13 PF06422 PDR_CDR: CDR ABC tran 47.5 27 0.00059 22.4 3.1 22 67-89 48-69 (103)
14 PF12273 RCR: Chitin synthesis 46.4 15 0.00032 24.5 1.7 25 11-35 2-26 (130)
15 PF11027 DUF2615: Protein of u 46.1 26 0.00056 23.1 2.8 19 70-88 54-72 (103)
16 PF06298 PsbY: Photosystem II 46.0 31 0.00068 18.5 2.6 19 70-88 10-28 (36)
17 PF15128 T_cell_tran_alt: T-ce 44.5 41 0.0009 21.6 3.4 17 70-86 26-42 (92)
18 PF04911 ATP-synt_J: ATP synth 43.7 20 0.00044 21.0 1.8 15 10-24 10-24 (54)
19 COG3924 Predicted membrane pro 42.7 19 0.00041 22.5 1.6 15 70-84 18-32 (80)
20 CHL00196 psbY photosystem II p 38.5 49 0.0011 17.7 2.6 19 70-88 10-28 (36)
21 COG2991 Uncharacterized protei 38.3 53 0.0011 20.5 3.1 14 42-55 43-57 (77)
22 TIGR02736 cbb3_Q_epsi cytochro 38.0 39 0.00084 19.9 2.4 24 11-34 2-25 (56)
23 COG3083 Predicted hydrolase of 38.0 23 0.00049 29.8 1.9 25 10-34 60-84 (600)
24 PF06930 DUF1282: Protein of u 35.2 1.5E+02 0.0032 20.3 5.7 26 6-31 15-40 (170)
25 TIGR03778 VPDSG_CTERM VPDSG-CT 34.3 42 0.00091 16.7 1.8 18 6-23 3-20 (26)
26 PHA00024 IX minor coat protein 33.1 69 0.0015 16.8 2.6 15 71-85 9-23 (33)
27 PF03311 Cornichon: Cornichon 31.9 1.4E+02 0.0029 20.1 4.6 24 8-31 3-27 (128)
28 PF07672 MFS_Mycoplasma: Mycop 31.5 95 0.0021 23.8 4.2 24 11-34 40-63 (267)
29 PF01542 HCV_core: Hepatitis C 31.0 33 0.00071 21.2 1.3 19 8-26 56-74 (75)
30 PF12686 DUF3800: Protein of u 30.6 3.1 6.7E-05 28.8 -3.8 17 4-20 4-28 (235)
31 PRK10726 hypothetical protein; 30.4 55 0.0012 21.6 2.4 22 10-31 54-75 (105)
32 PF07423 DUF1510: Protein of u 28.7 72 0.0016 23.6 3.1 19 70-88 16-34 (217)
33 PF09125 COX2-transmemb: Cytoc 28.4 90 0.0019 16.9 2.6 19 11-29 16-34 (38)
34 PF06596 PsbX: Photosystem II 28.1 68 0.0015 17.5 2.2 12 20-31 17-28 (39)
35 KOG0863 20S proteasome, regula 28.0 21 0.00045 27.1 0.1 9 1-9 134-142 (264)
36 COG2363 Uncharacterized small 27.9 67 0.0015 21.9 2.6 19 70-88 103-121 (124)
37 COG1288 Predicted membrane pro 27.9 2.5E+02 0.0054 23.4 6.2 25 8-32 215-239 (481)
38 PF14004 DUF4227: Protein of u 27.7 1E+02 0.0022 18.9 3.1 30 70-101 8-37 (71)
39 KOG2174 Leptin receptor gene-r 27.5 47 0.001 22.8 1.8 24 9-32 30-53 (131)
40 KOG2292 Oligosaccharyltransfer 27.1 67 0.0014 27.5 2.9 31 70-101 22-54 (751)
41 PF09878 DUF2105: Predicted me 27.0 46 0.00099 24.6 1.7 24 7-30 164-187 (212)
42 COG0713 NuoK NADH:ubiquinone o 26.7 44 0.00095 21.9 1.5 17 4-20 54-70 (100)
43 PHA02955 hypothetical protein; 26.6 57 0.0012 24.2 2.2 28 8-35 176-203 (213)
44 PF13198 DUF4014: Protein of u 26.2 84 0.0018 19.4 2.5 22 10-31 17-38 (72)
45 TIGR01150 puhA photosynthetic 26.1 82 0.0018 23.9 3.0 22 70-91 13-34 (252)
46 PF15156 CLN6: Ceroid-lipofusc 26.0 51 0.0011 24.9 1.9 18 7-24 201-218 (284)
47 COG4420 Predicted membrane pro 25.9 86 0.0019 22.9 3.0 25 77-101 62-87 (191)
48 cd00226 PRCH Photosynthetic re 25.8 83 0.0018 23.8 3.0 21 70-90 13-33 (246)
49 PF05616 Neisseria_TspB: Neiss 25.5 75 0.0016 26.4 2.9 21 68-88 478-498 (502)
50 PF10192 GpcrRhopsn4: Rhodopsi 25.4 66 0.0014 23.7 2.4 28 4-31 23-50 (257)
51 PF01544 CorA: CorA-like Mg2+ 25.2 52 0.0011 23.8 1.8 15 15-29 236-250 (292)
52 PHA03049 IMV membrane protein; 24.6 1.7E+02 0.0038 17.8 3.9 24 71-94 5-28 (68)
53 PF15383 TMEM237: Transmembran 24.5 31 0.00067 26.0 0.5 17 67-83 230-246 (253)
54 PF04834 Adeno_E3_14_5: Early 23.6 1.2E+02 0.0025 19.9 3.0 27 2-28 12-38 (97)
55 PF15145 DUF4577: Domain of un 23.6 81 0.0017 21.3 2.3 26 70-95 67-92 (128)
56 PF04133 Vps55: Vacuolar prote 23.0 80 0.0017 21.1 2.2 21 8-28 23-43 (120)
57 PF02012 BNR: BNR/Asp-box repe 22.7 45 0.00098 13.6 0.6 7 5-11 4-10 (12)
58 PF12084 DUF3561: Protein of u 22.4 98 0.0021 20.5 2.5 22 10-31 57-78 (107)
59 PF02060 ISK_Channel: Slow vol 22.1 1.4E+02 0.0031 20.4 3.3 30 71-101 46-78 (129)
60 PF14373 Imm_superinfect: Supe 21.9 1.6E+02 0.0034 16.3 3.3 16 72-87 23-38 (43)
61 PF02468 PsbN: Photosystem II 21.7 1.1E+02 0.0024 17.0 2.3 25 14-38 6-30 (43)
62 COG3771 Predicted membrane pro 21.6 1.1E+02 0.0024 19.8 2.5 17 72-88 51-67 (97)
63 COG4036 Predicted membrane pro 21.1 59 0.0013 23.8 1.3 23 7-29 166-188 (224)
64 PF04505 Dispanin: Interferon- 20.2 77 0.0017 19.5 1.6 20 14-33 19-40 (82)
65 PF10731 Anophelin: Thrombin i 20.2 1.4E+02 0.003 17.9 2.6 17 84-100 18-35 (65)
66 PRK15127 multidrug efflux syst 20.1 84 0.0018 28.1 2.4 25 14-38 1012-1036(1049)
67 PF02667 SCFA_trans: Short cha 20.1 2.1E+02 0.0045 23.6 4.4 21 70-90 252-272 (453)
No 1
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=8.6e-30 Score=185.36 Aligned_cols=99 Identities=25% Similarity=0.483 Sum_probs=81.9
Q ss_pred CcccccCCCchhHHHHHHHhhhhhhhHHHhhhccccccccccccccCccccchHHHHHHhhhhcCcchhHHHHHHHHHHH
Q 034210 1 MAATEENSQLFPIFILTIMALPLVPYTILKLCHAFSKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVI 80 (101)
Q Consensus 1 ~~~YDE~g~tfp~Fvlt~l~lvLiP~T~~~l~~~~~~~~~~~~~~~~~c~~~~~~i~~~~kr~~~~~~~~~i~li~GW~l 80 (101)
|.||||+|+|||||+||+++++|+|+||.+|++.........+|+|.+|.+.+.+..+.+++ +..++ |++++++||++
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 DYEYDESGNTFPYFLLSFLAIILLPMTYLLIPRNPEPPKRKEECQCHGCDKKRRKKAKVSPK-SISTK-RKVFLVVGWAV 81 (230)
T ss_pred ccccccccCccHHHHHHHHHHHHHHHHHHHhccccchhhhhhHHhhhhhhhhhhhhcccCcc-cchhH-HHHHHHHHHHH
Confidence 57999999999999999999999999999998643322224679999999876654333332 22256 99999999999
Q ss_pred HHHHHHHHHhcccccccCCCC
Q 034210 81 MIILIYYIKSTSREFLSHSAY 101 (101)
Q Consensus 81 ~~~L~y~i~~t~~~~~~~~~~ 101 (101)
+++|+|+|++++++.+.||||
T Consensus 82 ~~fL~y~i~~~~~~~~~fDPy 102 (230)
T KOG0721|consen 82 IAFLIYKIMNSRRERQKFDPY 102 (230)
T ss_pred HHHHHHHHhhhhHHhhcCCcH
Confidence 999999999999999999998
No 2
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=99.72 E-value=2e-18 Score=137.03 Aligned_cols=94 Identities=21% Similarity=0.388 Sum_probs=74.0
Q ss_pred ccccCCCchhHHHHHHHhhhhhhhHHHhhhccc-cccccccccccCccccchHHHHHHhhhhcCcchhHHHHHHHHHHHH
Q 034210 3 ATEENSQLFPIFILTIMALPLVPYTILKLCHAF-SKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIM 81 (101)
Q Consensus 3 ~YDE~g~tfp~Fvlt~l~lvLiP~T~~~l~~~~-~~~~~~~~~~~~~c~~~~~~i~~~~kr~~~~~~~~~i~li~GW~l~ 81 (101)
||||+|.+||+|+|+.+.++..|+||..+-+.. +++....+|.|+.|..+...+ +|| + +.+.|++++++||+++
T Consensus 6 eYDE~g~~~p~fvL~gl~~vvlpmTY~~i~gpsaSKe~~~vr~~~q~~Rpkdknv--~rK--S-If~lR~If~ivgWl~i 80 (610)
T COG5407 6 EYDESGLASPYFVLSGLVPVVLPMTYDLIEGPSASKELRRVRCACQGCRPKDKNV--SRK--S-IFKLRKIFTIVGWLVI 80 (610)
T ss_pred ccccccccchHHHHhhhhheeeeeehhheeCCcccchhhcchhhhhhcCccccch--hhh--H-HHhhhHHHHHHHHHHH
Confidence 899999999999999999999999998876553 223335779999888644432 111 2 3233999999999999
Q ss_pred HHHHHHHHhccccc-ccCCCC
Q 034210 82 IILIYYIKSTSREF-LSHSAY 101 (101)
Q Consensus 82 ~~L~y~i~~t~~~~-~~~~~~ 101 (101)
+||.++|.+.+.+. .-||||
T Consensus 81 ~~L~~~I~~~k~~~~~~fDPy 101 (610)
T COG5407 81 SYLISNIRTLKIEYRRGFDPY 101 (610)
T ss_pred HHHHHHHHHHHHHHHcCCChH
Confidence 99999999988874 489998
No 3
>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=80.58 E-value=1.9 Score=25.77 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=14.7
Q ss_pred cCCCchhHHHHHHHhhhhhh
Q 034210 6 ENSQLFPIFILTIMALPLVP 25 (101)
Q Consensus 6 E~g~tfp~Fvlt~l~lvLiP 25 (101)
-.|++||||-|.+..+.++-
T Consensus 10 FtskFW~YFtLi~M~lti~~ 29 (64)
T PF03579_consen 10 FTSKFWTYFTLIFMMLTIGF 29 (64)
T ss_pred eccccchHHHHHHHHHHHHH
Confidence 46899999988776555443
No 4
>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=59.16 E-value=14 Score=24.33 Aligned_cols=31 Identities=19% Similarity=0.048 Sum_probs=26.8
Q ss_pred ccCCCchhHHHHHHHhhhhhhhHHHhhhccc
Q 034210 5 EENSQLFPIFILTIMALPLVPYTILKLCHAF 35 (101)
Q Consensus 5 DE~g~tfp~Fvlt~l~lvLiP~T~~~l~~~~ 35 (101)
|=+.++|.|+-.|+++++++-..+..|+..-
T Consensus 63 DvS~~F~L~~~~ti~lv~~~~~~I~lL~svG 93 (103)
T PF12955_consen 63 DVSVPFWLFAGFTIALVVLVAGAIGLLFSVG 93 (103)
T ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 6688899999999999999999999987653
No 5
>PRK10873 hypothetical protein; Provisional
Probab=55.07 E-value=16 Score=24.84 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYIK 89 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~ 89 (101)
-=+.+++||+++++-+.+.+
T Consensus 105 GG~~li~GWl~la~~a~~~~ 124 (131)
T PRK10873 105 GGVSFLAGWALMLIGALRLK 124 (131)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 56788899999998877754
No 6
>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=54.25 E-value=17 Score=23.33 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=15.3
Q ss_pred chhHHHHHHHHHHHHHHHHHHHH
Q 034210 67 STCSNLSLVLLWVIMIILIYYIK 89 (101)
Q Consensus 67 ~~~~~i~li~GW~l~~~L~y~i~ 89 (101)
+| ..++|.+.+|+++++..-++
T Consensus 3 SK-~~llL~l~LA~lLlisSeva 24 (95)
T PF07172_consen 3 SK-AFLLLGLLLAALLLISSEVA 24 (95)
T ss_pred hh-HHHHHHHHHHHHHHHHhhhh
Confidence 45 66777777888877766554
No 7
>PRK13240 pbsY photosystem II protein Y; Reviewed
Probab=53.36 E-value=17 Score=19.93 Aligned_cols=23 Identities=9% Similarity=0.010 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Q 034210 70 SNLSLVLLWVIMIILIYYIKSTS 92 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~t~ 92 (101)
--+++.+||+++-+.---+.+..
T Consensus 10 ~Pil~A~~Wa~fNIg~~Al~Q~q 32 (40)
T PRK13240 10 APILAAAGWAVFNIGKAAREQFQ 32 (40)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHH
Confidence 34567789999966654444433
No 8
>KOG0510 consensus Ankyrin repeat protein [General function prediction only]
Probab=51.53 E-value=31 Score=30.53 Aligned_cols=25 Identities=36% Similarity=0.369 Sum_probs=19.9
Q ss_pred CCchhHHHHHHHhhhhhhhHHHhhh
Q 034210 8 SQLFPIFILTIMALPLVPYTILKLC 32 (101)
Q Consensus 8 g~tfp~Fvlt~l~lvLiP~T~~~l~ 32 (101)
|--|.++-|-+++++++|+|++.+-
T Consensus 505 g~~~~~~nL~~Y~lFlv~lT~Yv~~ 529 (929)
T KOG0510|consen 505 GKYFHLNNLLIYSLFLVSLTIYVLL 529 (929)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345666688999999999998874
No 9
>PF08592 DUF1772: Domain of unknown function (DUF1772); InterPro: IPR013901 This entry represents proteins of unknown function.
Probab=51.09 E-value=52 Score=21.29 Aligned_cols=74 Identities=9% Similarity=0.311 Sum_probs=35.2
Q ss_pred CCCchhHHHHHHHhhhhhhhHHHhhhcccccccc--ccccccCccccchHHHHHHhhhhcCcchhHHHHHHHHHHHHHH
Q 034210 7 NSQLFPIFILTIMALPLVPYTILKLCHAFSKKIK--TIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIMII 83 (101)
Q Consensus 7 ~g~tfp~Fvlt~l~lvLiP~T~~~l~~~~~~~~~--~~~~~~~~c~~~~~~i~~~~kr~~~~~~~~~i~li~GW~l~~~ 83 (101)
.+..+.+.+.+.+.+-.+|.|+...-.. .+.-. ...-..+.- ..+.+++..+|=.+.+.+|.++-++||++..+
T Consensus 62 ~~~~~~~~~a~~~~~~~~~~T~~~~~P~-N~~l~~~~~~~~~~~~--~~~~~~~l~~~W~~~n~vR~~~~~~a~~~~~~ 137 (139)
T PF08592_consen 62 PAARLLWLAAAALLLSIIPFTFLVNVPI-NNRLAAWDIESSPEEA--PADWVRALLDRWGRLNLVRTVLSLVAFLLLLI 137 (139)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHhhHH-HHHHHHcccccccccc--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555666777999998875222 11100 000011111 12222333332223344488888888887643
No 10
>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=49.95 E-value=27 Score=26.66 Aligned_cols=30 Identities=27% Similarity=0.380 Sum_probs=22.6
Q ss_pred chhHHHHHHHHHHHHHHHH-HHHHhccccccc
Q 034210 67 STCSNLSLVLLWVIMIILI-YYIKSTSREFLS 97 (101)
Q Consensus 67 ~~~~~i~li~GW~l~~~L~-y~i~~t~~~~~~ 97 (101)
|- |.++|+++-++-++|. |||+....+..+
T Consensus 172 Nl-r~lALflAFaINFILLFYKVs~~~~~~~e 202 (274)
T PF06459_consen 172 NL-RFLALFLAFAINFILLFYKVSTSPPEEEE 202 (274)
T ss_pred HH-HHHHHHHHHHHHHHHHHHHhccCCccccc
Confidence 45 9999999999876555 898887765443
No 11
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=49.70 E-value=23 Score=23.28 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=19.1
Q ss_pred cccCCCchhHHHHHHHhhhhhhhHHHh
Q 034210 4 TEENSQLFPIFILTIMALPLVPYTILK 30 (101)
Q Consensus 4 YDE~g~tfp~Fvlt~l~lvLiP~T~~~ 30 (101)
-.++|..|||.|.-+++.+.+-+-|..
T Consensus 10 ~~~~g~sW~~LVGVv~~al~~SlLIal 36 (102)
T PF15176_consen 10 PGEGGRSWPFLVGVVVTALVTSLLIAL 36 (102)
T ss_pred CCCCCcccHhHHHHHHHHHHHHHHHHH
Confidence 357899999988777666665555544
No 12
>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=48.97 E-value=28 Score=24.05 Aligned_cols=21 Identities=33% Similarity=0.825 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 034210 70 SNLSLVLLWVIMIILIYYIKS 90 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~ 90 (101)
--++|-+-|+.|+.|+|+...
T Consensus 13 Aql~lyaFwiFFagLi~YLrr 33 (136)
T PF03967_consen 13 AQLVLYAFWIFFAGLIYYLRR 33 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 446778899999999988743
No 13
>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=47.52 E-value=27 Score=22.45 Aligned_cols=22 Identities=14% Similarity=0.383 Sum_probs=16.9
Q ss_pred chhHHHHHHHHHHHHHHHHHHHH
Q 034210 67 STCSNLSLVLLWVIMIILIYYIK 89 (101)
Q Consensus 67 ~~~~~i~li~GW~l~~~L~y~i~ 89 (101)
.+ ||+-+++||.+++++++-+.
T Consensus 48 ~W-RN~GIli~f~i~f~~~~~~~ 69 (103)
T PF06422_consen 48 RW-RNFGILIAFWIFFIVLTLLA 69 (103)
T ss_pred hh-hhHHHHHHHHHHHHHHHHHH
Confidence 35 89999999988877766654
No 14
>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=46.36 E-value=15 Score=24.47 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=14.0
Q ss_pred hhHHHHHHHhhhhhhhHHHhhhccc
Q 034210 11 FPIFILTIMALPLVPYTILKLCHAF 35 (101)
Q Consensus 11 fp~Fvlt~l~lvLiP~T~~~l~~~~ 35 (101)
|.+|++-+++++|+=+.+++..|+.
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR 26 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRR 26 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666666555555555554443
No 15
>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=46.11 E-value=26 Score=23.07 Aligned_cols=19 Identities=21% Similarity=0.831 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i 88 (101)
...++++.|.++|.+.|..
T Consensus 54 ~~~~~~~~w~~~A~~ly~~ 72 (103)
T PF11027_consen 54 SMFMMMMLWMVLAMALYLL 72 (103)
T ss_pred cHHHHHHHHHHHHHHHHHc
Confidence 5678888999999999876
No 16
>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=45.96 E-value=31 Score=18.51 Aligned_cols=19 Identities=11% Similarity=0.027 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i 88 (101)
.-+++.+||+++=..---+
T Consensus 10 ~Pil~A~gWa~fNIg~~Al 28 (36)
T PF06298_consen 10 LPILPAAGWALFNIGRAAL 28 (36)
T ss_pred HHHHHHHHHHHHHhHHHHH
Confidence 3456677999986554333
No 17
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=44.50 E-value=41 Score=21.56 Aligned_cols=17 Identities=24% Similarity=0.594 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIY 86 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y 86 (101)
..+-+++||+++..++-
T Consensus 26 ~ifkllL~WlvlsLl~I 42 (92)
T PF15128_consen 26 QIFKLLLGWLVLSLLAI 42 (92)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 56678889999876653
No 18
>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=43.69 E-value=20 Score=20.96 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=11.9
Q ss_pred chhHHHHHHHhhhhh
Q 034210 10 LFPIFILTIMALPLV 24 (101)
Q Consensus 10 tfp~Fvlt~l~lvLi 24 (101)
+||||+.+.+.+.+|
T Consensus 10 ~wPFf~ag~iv~ygv 24 (54)
T PF04911_consen 10 MWPFFAAGAIVYYGV 24 (54)
T ss_pred hhHHHHHHHHHHHHH
Confidence 699999988766655
No 19
>COG3924 Predicted membrane protein [Function unknown]
Probab=42.65 E-value=19 Score=22.47 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIIL 84 (101)
Q Consensus 70 ~~i~li~GW~l~~~L 84 (101)
-.++.++||.+.||+
T Consensus 18 LtllYl~gW~v~AYl 32 (80)
T COG3924 18 LTLLYLAGWLVAAYL 32 (80)
T ss_pred HHHHHHHHHHHHHhC
Confidence 456677899999987
No 20
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=38.53 E-value=49 Score=17.74 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i 88 (101)
--+++.+||+++=..---+
T Consensus 10 ~Pil~A~~Wa~fNIg~~Al 28 (36)
T CHL00196 10 APVLAAASWALFNIGRLAI 28 (36)
T ss_pred HHHHHHHHHHHHHhHHHHH
Confidence 3456778999985543333
No 21
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.26 E-value=53 Score=20.46 Aligned_cols=14 Identities=29% Similarity=0.805 Sum_probs=6.9
Q ss_pred cccccCc-cccchHH
Q 034210 42 IHCQCSD-CARSGKY 55 (101)
Q Consensus 42 ~~~~~~~-c~~~~~~ 55 (101)
..|.|+. |..+.++
T Consensus 43 K~CdC~~pCDt~~~k 57 (77)
T COG2991 43 KVCDCDEPCDTHKKK 57 (77)
T ss_pred hhcCCCCchHHHHHh
Confidence 4477754 4443333
No 22
>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=37.99 E-value=39 Score=19.89 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=15.4
Q ss_pred hhHHHHHHHhhhhhhhHHHhhhcc
Q 034210 11 FPIFILTIMALPLVPYTILKLCHA 34 (101)
Q Consensus 11 fp~Fvlt~l~lvLiP~T~~~l~~~ 34 (101)
+.||.+|+++.|++=-=++.++|.
T Consensus 2 y~yf~~ti~lvv~LYgY~yhLYrs 25 (56)
T TIGR02736 2 YAYFAFTLLLVIFLYAYIYHLYRS 25 (56)
T ss_pred cchHHHHHHHHHHHHHHHHHhhhh
Confidence 357777777777774555556554
No 23
>COG3083 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]
Probab=37.98 E-value=23 Score=29.84 Aligned_cols=25 Identities=24% Similarity=0.518 Sum_probs=20.8
Q ss_pred chhHHHHHHHhhhhhhhHHHhhhcc
Q 034210 10 LFPIFILTIMALPLVPYTILKLCHA 34 (101)
Q Consensus 10 tfp~Fvlt~l~lvLiP~T~~~l~~~ 34 (101)
-|.|++.+.+++|+.|+|+...+++
T Consensus 60 hFsflvFA~yLlvlfpltfiv~s~r 84 (600)
T COG3083 60 HFSFLVFALYLLVLFPLTFIVLSQR 84 (600)
T ss_pred HHHHHHHHHHHHHHhhhhhhcccHH
Confidence 3778999999999999998776544
No 24
>PF06930 DUF1282: Protein of unknown function (DUF1282); InterPro: IPR009698 This entry represents several hypothetical proteins of around 200 residues in length. The function of is unknown although a number of the members are thought to be putative membrane proteins.
Probab=35.15 E-value=1.5e+02 Score=20.32 Aligned_cols=26 Identities=15% Similarity=0.542 Sum_probs=18.0
Q ss_pred cCCCchhHHHHHHHhhhhhhhHHHhh
Q 034210 6 ENSQLFPIFILTIMALPLVPYTILKL 31 (101)
Q Consensus 6 E~g~tfp~Fvlt~l~lvLiP~T~~~l 31 (101)
|+...+..|+.-++.+.++|..+...
T Consensus 15 ~~~~~~~~~~~~~l~~~l~~~~~~~~ 40 (170)
T PF06930_consen 15 EHESSWALYLVHVLLLALIPVVCFFI 40 (170)
T ss_pred cCCchhHHHHHHHHHHHHHHHHHHHH
Confidence 33444556788888888988776555
No 25
>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=34.28 E-value=42 Score=16.73 Aligned_cols=18 Identities=11% Similarity=0.220 Sum_probs=12.4
Q ss_pred cCCCchhHHHHHHHhhhh
Q 034210 6 ENSQLFPIFILTIMALPL 23 (101)
Q Consensus 6 E~g~tfp~Fvlt~l~lvL 23 (101)
++|.|..-+.+++++++.
T Consensus 3 DsGST~~Ll~~~l~~l~~ 20 (26)
T TIGR03778 3 DSGSTLALLGLGLLGLLG 20 (26)
T ss_pred CchhHHHHHHHHHHHHHH
Confidence 467787777777766654
No 26
>PHA00024 IX minor coat protein
Probab=33.12 E-value=69 Score=16.85 Aligned_cols=15 Identities=13% Similarity=0.344 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHH
Q 034210 71 NLSLVLLWVIMIILI 85 (101)
Q Consensus 71 ~i~li~GW~l~~~L~ 85 (101)
.-+.++||++..-+.
T Consensus 9 fgA~ilG~~l~~~Il 23 (33)
T PHA00024 9 FGAYILGWALFYGIL 23 (33)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345788999985443
No 27
>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=31.85 E-value=1.4e+02 Score=20.05 Aligned_cols=24 Identities=13% Similarity=0.303 Sum_probs=15.1
Q ss_pred CCchhHHHHHHHh-hhhhhhHHHhh
Q 034210 8 SQLFPIFILTIMA-LPLVPYTILKL 31 (101)
Q Consensus 8 g~tfp~Fvlt~l~-lvLiP~T~~~l 31 (101)
++.+..|+++++. .+++=++.+.+
T Consensus 3 ~~~~~~~i~alll~~~ll~~~vy~i 27 (128)
T PF03311_consen 3 FDFIVLWILALLLTAALLFIVVYFI 27 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556567777665 66666666665
No 28
>PF07672 MFS_Mycoplasma: Mycoplasma MFS transporter; InterPro: IPR011699 These proteins share some similarity with members of the Major Facilitator Superfamily (MFS).
Probab=31.51 E-value=95 Score=23.76 Aligned_cols=24 Identities=8% Similarity=0.271 Sum_probs=19.4
Q ss_pred hhHHHHHHHhhhhhhhHHHhhhcc
Q 034210 11 FPIFILTIMALPLVPYTILKLCHA 34 (101)
Q Consensus 11 fp~Fvlt~l~lvLiP~T~~~l~~~ 34 (101)
|-+-+..+.+++++|+-++.+.+.
T Consensus 40 W~~I~si~~lL~~IpLIly~ifGk 63 (267)
T PF07672_consen 40 WQWILSIFILLIFIPLILYIIFGK 63 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 667777788899999999888644
No 29
>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=30.99 E-value=33 Score=21.18 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=15.7
Q ss_pred CCchhHHHHHHHhhhhhhh
Q 034210 8 SQLFPIFILTIMALPLVPY 26 (101)
Q Consensus 8 g~tfp~Fvlt~l~lvLiP~ 26 (101)
|=-|-.|++++++++..|.
T Consensus 56 gcsfsIFllaLlSc~~~p~ 74 (75)
T PF01542_consen 56 GCSFSIFLLALLSCLTVPA 74 (75)
T ss_pred CccHHHHHHHHHHhccccC
Confidence 4568899999999998874
No 30
>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=30.60 E-value=3.1 Score=28.81 Aligned_cols=17 Identities=24% Similarity=0.389 Sum_probs=12.9
Q ss_pred cccCCCc--------hhHHHHHHHh
Q 034210 4 TEENSQL--------FPIFILTIMA 20 (101)
Q Consensus 4 YDE~g~t--------fp~Fvlt~l~ 20 (101)
-||||++ -|||+++.+.
T Consensus 4 iDESG~~~~~~~~~~~~~fvl~gv~ 28 (235)
T PF12686_consen 4 IDESGNTGPNYSDKNSPYFVLGGVI 28 (235)
T ss_pred EeCCCCCCCCcCCCCCCEEEEEEEE
Confidence 4999984 7999877653
No 31
>PRK10726 hypothetical protein; Provisional
Probab=30.39 E-value=55 Score=21.63 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=13.6
Q ss_pred chhHHHHHHHhhhhhhhHHHhh
Q 034210 10 LFPIFILTIMALPLVPYTILKL 31 (101)
Q Consensus 10 tfp~Fvlt~l~lvLiP~T~~~l 31 (101)
|||||+.-+=.-||+=..++.+
T Consensus 54 TWPFFLALmPvsVlvGi~l~~L 75 (105)
T PRK10726 54 TWPFFLALMPVSVLVGIALHSL 75 (105)
T ss_pred HHHHHHHHhHHHHHHHHHHHHH
Confidence 5777766555556665555555
No 32
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=28.69 E-value=72 Score=23.60 Aligned_cols=19 Identities=21% Similarity=0.551 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i 88 (101)
-|++|++.=+|+++++|.+
T Consensus 16 LNiaI~IV~lLIiiva~~l 34 (217)
T PF07423_consen 16 LNIAIGIVSLLIIIVAYQL 34 (217)
T ss_pred HHHHHHHHHHHHHHHhhhh
Confidence 4555555445555555554
No 33
>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=28.41 E-value=90 Score=16.86 Aligned_cols=19 Identities=11% Similarity=0.170 Sum_probs=14.4
Q ss_pred hhHHHHHHHhhhhhhhHHH
Q 034210 11 FPIFILTIMALPLVPYTIL 29 (101)
Q Consensus 11 fp~Fvlt~l~lvLiP~T~~ 29 (101)
|..|.++++.++++-.-|.
T Consensus 16 Wi~F~l~mi~vFi~li~yt 34 (38)
T PF09125_consen 16 WIAFALAMILVFIALIGYT 34 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8899999888877755443
No 34
>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=28.08 E-value=68 Score=17.48 Aligned_cols=12 Identities=8% Similarity=0.238 Sum_probs=9.4
Q ss_pred hhhhhhhHHHhh
Q 034210 20 ALPLVPYTILKL 31 (101)
Q Consensus 20 ~lvLiP~T~~~l 31 (101)
.+|++|.+.-.+
T Consensus 17 ~iVv~~i~~ali 28 (39)
T PF06596_consen 17 VIVVIPIAGALI 28 (39)
T ss_dssp -HHHHHHHHHHH
T ss_pred hhhhhhhhhheE
Confidence 488999998776
No 35
>KOG0863 consensus 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones]
Probab=28.04 E-value=21 Score=27.07 Aligned_cols=9 Identities=22% Similarity=0.372 Sum_probs=7.7
Q ss_pred CcccccCCC
Q 034210 1 MAATEENSQ 9 (101)
Q Consensus 1 ~~~YDE~g~ 9 (101)
|+.|||+|.
T Consensus 134 v~gYDe~G~ 142 (264)
T KOG0863|consen 134 VAGYDESGP 142 (264)
T ss_pred EEeecCCCc
Confidence 688999995
No 36
>COG2363 Uncharacterized small membrane protein [Function unknown]
Probab=27.86 E-value=67 Score=21.85 Aligned_cols=19 Identities=11% Similarity=0.371 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 034210 70 SNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i 88 (101)
--+..++||+++++=+++-
T Consensus 103 GG~~fi~GW~~l~~~a~~~ 121 (124)
T COG2363 103 GGVLFIAGWLLLAIGAFRS 121 (124)
T ss_pred chHHHHHHHHHHHHHHHhh
Confidence 4466778999999887764
No 37
>COG1288 Predicted membrane protein [Function unknown]
Probab=27.85 E-value=2.5e+02 Score=23.36 Aligned_cols=25 Identities=12% Similarity=0.147 Sum_probs=12.9
Q ss_pred CCchhHHHHHHHhhhhhhhHHHhhh
Q 034210 8 SQLFPIFILTIMALPLVPYTILKLC 32 (101)
Q Consensus 8 g~tfp~Fvlt~l~lvLiP~T~~~l~ 32 (101)
|-.|-..++-+..++-+-.+|.+..
T Consensus 215 G~~~Riv~~v~~~~~~i~y~~~Ya~ 239 (481)
T COG1288 215 GMGLRIVVWVVFTLISIIYVYWYAS 239 (481)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555545554543
No 38
>PF14004 DUF4227: Protein of unknown function (DUF4227)
Probab=27.71 E-value=1e+02 Score=18.90 Aligned_cols=30 Identities=13% Similarity=0.093 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccCCCC
Q 034210 70 SNLSLVLLWVIMIILIYYIKSTSREFLSHSAY 101 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~t~~~~~~~~~~ 101 (101)
+.++|-+|=.+++|-+..-- ..+...||||
T Consensus 8 k~~~LF~~~T~lfYy~~~w~--~~~~~~~hrY 37 (71)
T PF14004_consen 8 KFFLLFTGCTLLFYYAILWV--SDEYEPYHRY 37 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHHhccCCCC
Confidence 55666666666666544432 3445566665
No 39
>KOG2174 consensus Leptin receptor gene-related protein [Signal transduction mechanisms]
Probab=27.49 E-value=47 Score=22.76 Aligned_cols=24 Identities=17% Similarity=0.502 Sum_probs=20.9
Q ss_pred CchhHHHHHHHhhhhhhhHHHhhh
Q 034210 9 QLFPIFILTIMALPLVPYTILKLC 32 (101)
Q Consensus 9 ~tfp~Fvlt~l~lvLiP~T~~~l~ 32 (101)
+-||-|++.++.+.-+|.++.--+
T Consensus 30 nwwPlf~~~~yvl~PiP~l~f~a~ 53 (131)
T KOG2174|consen 30 NWWPLFVILFYVLSPIPNLLFIAG 53 (131)
T ss_pred chHHHHHHHHHHhcCCchHHhccc
Confidence 889999999999999998885543
No 40
>KOG2292 consensus Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones]
Probab=27.15 E-value=67 Score=27.54 Aligned_cols=31 Identities=19% Similarity=0.102 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccc--cccCCCC
Q 034210 70 SNLSLVLLWVIMIILIYYIKSTSRE--FLSHSAY 101 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~t~~~--~~~~~~~ 101 (101)
+.+++++.|++- +-.-.-+..+-| -.|||||
T Consensus 22 ~~~IL~l~~v~~-fssRLFaVirfESiIHEFDP~ 54 (751)
T KOG2292|consen 22 KLLILVLAAVLS-FSSRLFAVIRFESIIHEFDPW 54 (751)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHhhccCch
Confidence 566667777654 332333444444 4599997
No 41
>PF09878 DUF2105: Predicted membrane protein (DUF2105); InterPro: IPR019212 This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Probab=27.00 E-value=46 Score=24.56 Aligned_cols=24 Identities=17% Similarity=0.288 Sum_probs=21.2
Q ss_pred CCCchhHHHHHHHhhhhhhhHHHh
Q 034210 7 NSQLFPIFILTIMALPLVPYTILK 30 (101)
Q Consensus 7 ~g~tfp~Fvlt~l~lvLiP~T~~~ 30 (101)
||-.|.+++++|+.+++.|--+..
T Consensus 164 SGiaWalWi~gF~~Ff~~P~~Wl~ 187 (212)
T PF09878_consen 164 SGIAWALWIAGFIGFFLFPQYWLL 187 (212)
T ss_pred hhHHHHHHHHHHHHHHHhHHHHHH
Confidence 788999999999999999976544
No 42
>COG0713 NuoK NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Energy production and conversion]
Probab=26.71 E-value=44 Score=21.93 Aligned_cols=17 Identities=35% Similarity=0.733 Sum_probs=13.9
Q ss_pred cccCCCchhHHHHHHHh
Q 034210 4 TEENSQLFPIFILTIMA 20 (101)
Q Consensus 4 YDE~g~tfp~Fvlt~l~ 20 (101)
+|-+||.|.+|++|+-+
T Consensus 54 ~~~~gQvfaifvitvAA 70 (100)
T COG0713 54 GDLDGQVFAIFVITVAA 70 (100)
T ss_pred ccccchHHHHHHHHHHH
Confidence 35589999999999854
No 43
>PHA02955 hypothetical protein; Provisional
Probab=26.64 E-value=57 Score=24.19 Aligned_cols=28 Identities=18% Similarity=0.145 Sum_probs=21.7
Q ss_pred CCchhHHHHHHHhhhhhhhHHHhhhccc
Q 034210 8 SQLFPIFILTIMALPLVPYTILKLCHAF 35 (101)
Q Consensus 8 g~tfp~Fvlt~l~lvLiP~T~~~l~~~~ 35 (101)
|..+|+|++....++++-+.+++++|..
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 5577889988888888877777776654
No 44
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=26.17 E-value=84 Score=19.40 Aligned_cols=22 Identities=23% Similarity=0.297 Sum_probs=15.7
Q ss_pred chhHHHHHHHhhhhhhhHHHhh
Q 034210 10 LFPIFILTIMALPLVPYTILKL 31 (101)
Q Consensus 10 tfp~Fvlt~l~lvLiP~T~~~l 31 (101)
.|.||++-++.++.|..-+..+
T Consensus 17 efLF~ilfIvlmipI~pll~~~ 38 (72)
T PF13198_consen 17 EFLFFILFIVLMIPISPLLFVW 38 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4789998888887765555444
No 45
>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=26.11 E-value=82 Score=23.92 Aligned_cols=22 Identities=27% Similarity=0.786 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 034210 70 SNLSLVLLWVIMIILIYYIKST 91 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~t 91 (101)
--++|-+-|+.|+.|+|+...-
T Consensus 13 Aq~~ly~FwiFFA~Li~YLrrE 34 (252)
T TIGR01150 13 AQLVIYAFWIFLAGLIYYLRRE 34 (252)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4467788999999999987543
No 46
>PF15156 CLN6: Ceroid-lipofuscinosis neuronal protein 6
Probab=26.00 E-value=51 Score=24.95 Aligned_cols=18 Identities=33% Similarity=0.659 Sum_probs=16.1
Q ss_pred CCCchhHHHHHHHhhhhh
Q 034210 7 NSQLFPIFILTIMALPLV 24 (101)
Q Consensus 7 ~g~tfp~Fvlt~l~lvLi 24 (101)
+||.|.-|++||.++..+
T Consensus 201 EGQifilfifTffaM~a~ 218 (284)
T PF15156_consen 201 EGQIFILFIFTFFAMLAL 218 (284)
T ss_pred cCeeeHHHHHHHHHHHHH
Confidence 699999999999998765
No 47
>COG4420 Predicted membrane protein [Function unknown]
Probab=25.87 E-value=86 Score=22.86 Aligned_cols=25 Identities=16% Similarity=0.268 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHhcccc-cccCCCC
Q 034210 77 LWVIMIILIYYIKSTSRE-FLSHSAY 101 (101)
Q Consensus 77 GW~l~~~L~y~i~~t~~~-~~~~~~~ 101 (101)
+|..++++++-+-|..-- .-.+|||
T Consensus 62 l~~~~~ll~Wi~lNl~~~~~~~wDpy 87 (191)
T COG4420 62 LTFTLLLLLWIVLNLFLVPGLAWDPY 87 (191)
T ss_pred HHHHHHHHHHHHHHHhhhcCCcCCCc
Confidence 444444555555455443 3788888
No 48
>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=25.83 E-value=83 Score=23.81 Aligned_cols=21 Identities=29% Similarity=0.806 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 034210 70 SNLSLVLLWVIMIILIYYIKS 90 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~ 90 (101)
--++|-+-|+.||.|+|+...
T Consensus 13 A~~~l~~Fw~ffa~Li~YL~~ 33 (246)
T cd00226 13 AQLVIYAFWIFFAGLIYYLRR 33 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 446778899999999988753
No 49
>PF05616 Neisseria_TspB: Neisseria meningitidis TspB protein; InterPro: IPR008708 This family consists mainly of Neisseria meningitidis TspB virulence factor proteins.
Probab=25.49 E-value=75 Score=26.45 Aligned_cols=21 Identities=10% Similarity=0.241 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 034210 68 TCSNLSLVLLWVIMIILIYYI 88 (101)
Q Consensus 68 ~~~~i~li~GW~l~~~L~y~i 88 (101)
++|-++|+++|++.+++++.-
T Consensus 478 kiRPlVI~laii~AaFivf~s 498 (502)
T PF05616_consen 478 KIRPLVIALAIIMAAFIVFGS 498 (502)
T ss_pred HHhHHHHHHHHHHHHHHhhhh
Confidence 348899999999999998863
No 50
>PF10192 GpcrRhopsn4: Rhodopsin-like GPCR transmembrane domain; InterPro: IPR019336 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans [].
Probab=25.45 E-value=66 Score=23.69 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=24.8
Q ss_pred cccCCCchhHHHHHHHhhhhhhhHHHhh
Q 034210 4 TEENSQLFPIFILTIMALPLVPYTILKL 31 (101)
Q Consensus 4 YDE~g~tfp~Fvlt~l~lvLiP~T~~~l 31 (101)
+||+|-.-.++++.++.+++.+......
T Consensus 23 ~de~gi~~~~~~~~~~y~vl~~~~~~~~ 50 (257)
T PF10192_consen 23 ADEQGILEIYLLFLLLYIVLSIISIYSI 50 (257)
T ss_pred hhhcCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 6999999999999999999999887665
No 51
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=25.20 E-value=52 Score=23.77 Aligned_cols=15 Identities=33% Similarity=0.660 Sum_probs=12.9
Q ss_pred HHHHHhhhhhhhHHH
Q 034210 15 ILTIMALPLVPYTIL 29 (101)
Q Consensus 15 vlt~l~lvLiP~T~~ 29 (101)
.||+++++.+|+|+.
T Consensus 236 ~LT~~t~iflPlt~i 250 (292)
T PF01544_consen 236 VLTIVTAIFLPLTFI 250 (292)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 589999999999963
No 52
>PHA03049 IMV membrane protein; Provisional
Probab=24.63 E-value=1.7e+02 Score=17.78 Aligned_cols=24 Identities=17% Similarity=0.308 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcccc
Q 034210 71 NLSLVLLWVIMIILIYYIKSTSRE 94 (101)
Q Consensus 71 ~i~li~GW~l~~~L~y~i~~t~~~ 94 (101)
.++++++=++++.++|-|-+-+++
T Consensus 5 ~~l~iICVaIi~lIvYgiYnkk~~ 28 (68)
T PHA03049 5 IILVIICVVIIGLIVYGIYNKKTT 28 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc
Confidence 456677788888888887554443
No 53
>PF15383 TMEM237: Transmembrane protein 237
Probab=24.53 E-value=31 Score=26.04 Aligned_cols=17 Identities=18% Similarity=0.454 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHHH
Q 034210 67 STCSNLSLVLLWVIMII 83 (101)
Q Consensus 67 ~~~~~i~li~GW~l~~~ 83 (101)
+.+|-++.++||+++++
T Consensus 230 n~~Ralla~lgWl~va~ 246 (253)
T PF15383_consen 230 NLVRALLAILGWLFVAL 246 (253)
T ss_pred hHHHHHHHHHHHHeeEc
Confidence 44588999999998864
No 54
>PF04834 Adeno_E3_14_5: Early E3 14.5 kDa protein; InterPro: IPR008131 The E3B 14.5 kDa was first identified in human adenovirus type 5. It is an integral membrane protein oriented with its C terminus in the cytoplasm. It functions to down-regulate the epidermal growth factor receptor and prevent tumour necrosis factor cytolysis. It achieves this through the interaction with E3 10.4 kDa protein [, ]. ; GO: 0009966 regulation of signal transduction, 0016021 integral to membrane
Probab=23.63 E-value=1.2e+02 Score=19.86 Aligned_cols=27 Identities=11% Similarity=0.127 Sum_probs=17.9
Q ss_pred cccccCCCchhHHHHHHHhhhhhhhHH
Q 034210 2 AATEENSQLFPIFILTIMALPLVPYTI 28 (101)
Q Consensus 2 ~~YDE~g~tfp~Fvlt~l~lvLiP~T~ 28 (101)
.+|||..++-.+++.++....+.=.|+
T Consensus 12 ~CY~~~~d~~~~Wl~~i~~~~v~~~t~ 38 (97)
T PF04834_consen 12 DCYDKKSDMPNYWLYAIGIVLVFCSTF 38 (97)
T ss_pred hhcccCCCCCHHHHHHHHHHHHHHHHH
Confidence 589999988666666655544444443
No 55
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=23.57 E-value=81 Score=21.33 Aligned_cols=26 Identities=15% Similarity=0.331 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccccc
Q 034210 70 SNLSLVLLWVIMIILIYYIKSTSREF 95 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~t~~~~ 95 (101)
-.+++++--+++.|.++.|.+|.+.+
T Consensus 67 lii~LivSLaLVsFvIFLiiQTgnkM 92 (128)
T PF15145_consen 67 LIIVLIVSLALVSFVIFLIIQTGNKM 92 (128)
T ss_pred HHHHHHHHHHHHHHHHHheeeccchH
Confidence 45667778899999999999888754
No 56
>PF04133 Vps55: Vacuolar protein sorting 55 ; InterPro: IPR007262 Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase. Both Vps55 and obesity receptor gene-related protein are important for functioning membrane trafficking to the vacuole/lysosome of eukaryotic cells [].
Probab=22.97 E-value=80 Score=21.14 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=19.2
Q ss_pred CCchhHHHHHHHhhhhhhhHH
Q 034210 8 SQLFPIFILTIMALPLVPYTI 28 (101)
Q Consensus 8 g~tfp~Fvlt~l~lvLiP~T~ 28 (101)
+|.||.|++-++.+.-+|..+
T Consensus 23 ~nw~PL~v~~~y~laPiP~~i 43 (120)
T PF04133_consen 23 KNWWPLFVVLFYVLAPIPNLI 43 (120)
T ss_pred cccHHHHHHHHHHHHhhhHHH
Confidence 689999999999999999887
No 57
>PF02012 BNR: BNR/Asp-box repeat; InterPro: IPR002860 Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [].; PDB: 2JKB_A 2VW0_A 2VW2_A 2VW1_A 2CN2_D 2CN3_B 2VK7_B 2VK5_A 2VK6_A 2BF6_A ....
Probab=22.66 E-value=45 Score=13.61 Aligned_cols=7 Identities=0% Similarity=0.344 Sum_probs=4.3
Q ss_pred ccCCCch
Q 034210 5 EENSQLF 11 (101)
Q Consensus 5 DE~g~tf 11 (101)
++.|+||
T Consensus 4 ~D~G~TW 10 (12)
T PF02012_consen 4 TDGGKTW 10 (12)
T ss_dssp SSTTSS-
T ss_pred CCCcccC
Confidence 5678887
No 58
>PF12084 DUF3561: Protein of unknown function (DUF3561); InterPro: IPR022721 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Probab=22.39 E-value=98 Score=20.53 Aligned_cols=22 Identities=18% Similarity=0.375 Sum_probs=13.8
Q ss_pred chhHHHHHHHhhhhhhhHHHhh
Q 034210 10 LFPIFILTIMALPLVPYTILKL 31 (101)
Q Consensus 10 tfp~Fvlt~l~lvLiP~T~~~l 31 (101)
|||||+.=+=..|++=..+..+
T Consensus 57 TWPFFLALmPvsVl~Gi~l~~l 78 (107)
T PF12084_consen 57 TWPFFLALMPVSVLIGIALSSL 78 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 6777766555566665555555
No 59
>PF02060 ISK_Channel: Slow voltage-gated potassium channel; InterPro: IPR000369 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Two types of beta subunit (KCNE and KCNAB) are presently known to associate with voltage-gated alpha subunits (Kv, KCNQ and eag-like). However, not all combinations of alpha and beta subunits are possible. The KCNE family of K+ channel subunits are membrane glycoproteins that possess a single transmembrane (TM) domain. They share no structural relationship with the alpha subunit proteins, which possess pore forming domains. The subunits appear to have a regulatory function, modulating the kinetics and voltage dependence of the alpha subunits of voltage-dependent K+ channels. KCNE subunits are formed from short polypeptides of ~130 amino acids, and are divided into five subfamilies: KCNE1 (MinK/IsK), KCNE2 (MiRP1), KCNE3 (MiRP2), KCNE4 (MiRP3) and KCNE1L (AMMECR2). ; GO: 0005249 voltage-gated potassium channel activity, 0006811 ion transport, 0016020 membrane; PDB: 2K21_A.
Probab=22.09 E-value=1.4e+02 Score=20.41 Aligned_cols=30 Identities=27% Similarity=0.528 Sum_probs=13.5
Q ss_pred HHHHHH---HHHHHHHHHHHHHhcccccccCCCC
Q 034210 71 NLSLVL---LWVIMIILIYYIKSTSREFLSHSAY 101 (101)
Q Consensus 71 ~i~li~---GW~l~~~L~y~i~~t~~~~~~~~~~ 101 (101)
.|++++ |-.+++.|+-.+.+-++|+. .|||
T Consensus 46 YIL~vmgfFgff~~gImlsyvRSKK~E~s-~DPy 78 (129)
T PF02060_consen 46 YILVVMGFFGFFTVGIMLSYVRSKKREHS-HDPY 78 (129)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH------TT
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhccc-cChH
Confidence 344444 45555666555554444544 4887
No 60
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=21.91 E-value=1.6e+02 Score=16.26 Aligned_cols=16 Identities=25% Similarity=0.314 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 034210 72 LSLVLLWVIMIILIYY 87 (101)
Q Consensus 72 i~li~GW~l~~~L~y~ 87 (101)
+=+.+||.+++.++-.
T Consensus 23 ~Nl~lGWT~iGWv~aL 38 (43)
T PF14373_consen 23 LNLLLGWTGIGWVAAL 38 (43)
T ss_pred HHHHHHhHHHHHHHHH
Confidence 3456688877666533
No 61
>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=21.67 E-value=1.1e+02 Score=16.97 Aligned_cols=25 Identities=20% Similarity=0.231 Sum_probs=16.7
Q ss_pred HHHHHHhhhhhhhHHHhhhcccccc
Q 034210 14 FILTIMALPLVPYTILKLCHAFSKK 38 (101)
Q Consensus 14 Fvlt~l~lvLiP~T~~~l~~~~~~~ 38 (101)
++..+++++|+-+|-+-+|..+-..
T Consensus 6 ~~~i~i~~~lv~~Tgy~iYtaFGpp 30 (43)
T PF02468_consen 6 VLAIFISCLLVSITGYAIYTAFGPP 30 (43)
T ss_pred eHHHHHHHHHHHHHhhhhhheeCCC
Confidence 3445567777888888888776433
No 62
>COG3771 Predicted membrane protein [Function unknown]
Probab=21.65 E-value=1.1e+02 Score=19.78 Aligned_cols=17 Identities=18% Similarity=0.405 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 034210 72 LSLVLLWVIMIILIYYI 88 (101)
Q Consensus 72 i~li~GW~l~~~L~y~i 88 (101)
+=+++||.+.+.+-.|+
T Consensus 51 ~G~~lgwli~g~fy~k~ 67 (97)
T COG3771 51 AGFALGWLICGLFYLKV 67 (97)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34678999998775443
No 63
>COG4036 Predicted membrane protein [Function unknown]
Probab=21.08 E-value=59 Score=23.79 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=20.5
Q ss_pred CCCchhHHHHHHHhhhhhhhHHH
Q 034210 7 NSQLFPIFILTIMALPLVPYTIL 29 (101)
Q Consensus 7 ~g~tfp~Fvlt~l~lvLiP~T~~ 29 (101)
||-+|.+++..|+.+++-|=-+.
T Consensus 166 SGi~WalWvaGF~~FF~~P~~WL 188 (224)
T COG4036 166 SGIGWALWVAGFSTFFLHPKAWL 188 (224)
T ss_pred chHHHHHHHHHHHHHHhcHHHHH
Confidence 78999999999999999997653
No 64
>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=20.22 E-value=77 Score=19.54 Aligned_cols=20 Identities=20% Similarity=0.369 Sum_probs=10.9
Q ss_pred HHHHHHhhhh--hhhHHHhhhc
Q 034210 14 FILTIMALPL--VPYTILKLCH 33 (101)
Q Consensus 14 Fvlt~l~lvL--iP~T~~~l~~ 33 (101)
..+++++++. .|+.+.-+..
T Consensus 19 l~~sI~s~l~Cc~PlGi~Ai~~ 40 (82)
T PF04505_consen 19 LVLSIFSTLCCCWPLGIVAIVY 40 (82)
T ss_pred eeHHHHHHHHHHhhHHHHHhee
Confidence 3344444444 4777766643
No 65
>PF10731 Anophelin: Thrombin inhibitor from mosquito; InterPro: IPR018932 Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Probab=20.22 E-value=1.4e+02 Score=17.94 Aligned_cols=17 Identities=12% Similarity=-0.050 Sum_probs=9.3
Q ss_pred HHHHHHhccc-ccccCCC
Q 034210 84 LIYYIKSTSR-EFLSHSA 100 (101)
Q Consensus 84 L~y~i~~t~~-~~~~~~~ 100 (101)
+++-..+-.+ +.++||.
T Consensus 18 ~vQ~APQYa~GeeP~YDE 35 (65)
T PF10731_consen 18 IVQSAPQYAPGEEPSYDE 35 (65)
T ss_pred HHhcCcccCCCCCCCcCc
Confidence 4455444444 5677773
No 66
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=20.09 E-value=84 Score=28.13 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=21.3
Q ss_pred HHHHHHhhhhhhhHHHhhhcccccc
Q 034210 14 FILTIMALPLVPYTILKLCHAFSKK 38 (101)
Q Consensus 14 Fvlt~l~lvLiP~T~~~l~~~~~~~ 38 (101)
.+.|+++++++|.-|..++|..+++
T Consensus 1012 ~~St~ltL~~vP~ly~~~~~~~~~~ 1036 (1049)
T PRK15127 1012 VTATVLAIFFVPVFFVVVRRRFSRK 1036 (1049)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 5678999999999999998876555
No 67
>PF02667 SCFA_trans: Short chain fatty acid transporter; InterPro: IPR006160 Members of this family may be short chain fatty acid transporters although there has been no experimental characterisation of this function.
Probab=20.08 E-value=2.1e+02 Score=23.63 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 034210 70 SNLSLVLLWVIMIILIYYIKS 90 (101)
Q Consensus 70 ~~i~li~GW~l~~~L~y~i~~ 90 (101)
+.+.+++|=..++|+++...+
T Consensus 252 ~~l~~lig~~g~~yl~~~f~~ 272 (453)
T PF02667_consen 252 RILSLLIGLLGLAYLVYYFAT 272 (453)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 556666676667777776554
Done!