Query 033409
Match_columns 120
No_of_seqs 100 out of 179
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 13:33:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033409.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033409hhsearch_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 6.4E-31 1.4E-35 200.8 5.5 108 1-110 4-111 (230)
2 COG5407 SEC63 Preprotein trans 99.8 1.5E-21 3.2E-26 162.5 4.5 103 3-110 6-110 (610)
3 COG2991 Uncharacterized protei 71.3 7.2 0.00016 25.5 3.4 16 41-56 42-58 (77)
4 PF03579 SHP: Small hydrophobi 70.2 4.6 0.0001 25.3 2.3 21 6-26 10-30 (64)
5 PF08592 DUF1772: Domain of un 63.9 21 0.00045 24.3 4.9 75 8-83 63-137 (139)
6 PF03622 IBV_3B: IBV 3B protei 59.3 4.4 9.5E-05 25.5 0.7 17 86-103 23-39 (64)
7 PF06210 DUF1003: Protein of u 46.2 33 0.00072 23.7 3.5 7 96-102 28-34 (108)
8 PF00226 DnaJ: DnaJ domain; I 45.3 5.6 0.00012 23.8 -0.5 12 99-110 1-12 (64)
9 PF06298 PsbY: Photosystem II 44.1 19 0.00042 20.3 1.7 16 70-85 10-25 (36)
10 COG4420 Predicted membrane pro 41.6 28 0.0006 26.7 2.7 26 77-102 62-88 (191)
11 cd06257 DnaJ DnaJ domain or J- 40.5 9 0.00019 21.9 -0.1 9 99-107 1-9 (55)
12 PF12955 DUF3844: Domain of un 36.5 41 0.00088 23.2 2.7 30 5-34 63-92 (103)
13 CHL00196 psbY photosystem II p 35.9 31 0.00068 19.5 1.7 15 71-85 11-25 (36)
14 PF03311 Cornichon: Cornichon 35.9 1.5E+02 0.0033 20.7 6.5 44 70-113 62-110 (128)
15 COG1288 Predicted membrane pro 35.4 1.2E+02 0.0027 26.3 5.9 20 70-89 275-294 (481)
16 KOG3672 Histidine acid phospha 34.8 31 0.00067 29.6 2.2 54 45-106 249-303 (487)
17 PRK13240 pbsY photosystem II p 33.3 36 0.00077 19.7 1.7 17 71-87 11-27 (40)
18 KOG0510 Ankyrin repeat protein 33.1 81 0.0018 29.4 4.7 26 8-33 505-530 (929)
19 PF05478 Prominin: Prominin; 32.5 68 0.0015 29.2 4.2 19 13-31 96-114 (806)
20 PF04583 Baculo_p74: Baculovir 31.6 37 0.00081 27.0 2.1 24 74-102 105-128 (249)
21 smart00271 DnaJ DnaJ molecular 31.0 16 0.00034 21.3 -0.0 10 99-108 2-11 (60)
22 PF15176 LRR19-TM: Leucine-ric 30.9 59 0.0013 22.5 2.7 27 4-30 10-36 (102)
23 PF06459 RR_TM4-6: Ryanodine R 30.5 56 0.0012 26.2 3.0 31 64-95 168-200 (274)
24 PF06422 PDR_CDR: CDR ABC tran 30.2 64 0.0014 21.7 2.9 22 67-89 48-69 (103)
25 PF11027 DUF2615: Protein of u 29.4 65 0.0014 22.2 2.8 19 70-88 54-72 (103)
26 PF03967 PRCH: Photosynthetic 29.0 78 0.0017 23.0 3.2 22 70-91 13-34 (136)
27 PF04911 ATP-synt_J: ATP synth 28.7 45 0.00097 20.5 1.7 15 10-24 10-24 (54)
28 COG3924 Predicted membrane pro 28.7 42 0.00091 22.0 1.6 15 70-84 18-32 (80)
29 PRK13183 psbN photosystem II r 27.8 78 0.0017 18.8 2.5 32 71-102 9-42 (46)
30 PF07172 GRP: Glycine rich pro 27.2 84 0.0018 21.1 3.0 20 70-89 5-24 (95)
31 PF12273 RCR: Chitin synthesis 25.8 47 0.001 23.1 1.6 24 11-34 2-25 (130)
32 PF14004 DUF4227: Protein of u 25.7 84 0.0018 20.2 2.6 31 70-102 8-38 (71)
33 PF09878 DUF2105: Predicted me 25.1 37 0.00081 26.3 1.0 24 7-30 164-187 (212)
34 CHL00020 psbN photosystem II p 24.8 72 0.0016 18.7 2.0 31 72-102 7-39 (43)
35 PF07672 MFS_Mycoplasma: Mycop 24.5 1.2E+02 0.0027 24.3 3.9 24 11-34 40-63 (267)
36 PF04341 DUF485: Protein of un 24.1 1.1E+02 0.0024 20.0 3.1 25 70-100 59-83 (91)
37 PF02560 Cyanate_lyase: Cyanat 24.0 46 0.00099 21.7 1.1 21 97-117 12-32 (73)
38 PF12686 DUF3800: Protein of u 23.7 5.8 0.00013 28.7 -3.5 16 4-19 4-27 (235)
39 PF02468 PsbN: Photosystem II 23.4 1.4E+02 0.0031 17.4 3.1 27 76-102 11-39 (43)
40 cd00559 Cyanase_C Cyanase C-te 23.1 47 0.001 21.4 1.1 22 96-117 7-28 (69)
41 TIGR02736 cbb3_Q_epsi cytochro 21.0 1E+02 0.0022 19.0 2.2 24 11-34 2-25 (56)
42 PF01542 HCV_core: Hepatitis C 20.8 63 0.0014 20.9 1.3 19 8-26 56-74 (75)
43 COG3083 Predicted hydrolase of 20.1 69 0.0015 28.4 1.8 24 11-34 61-84 (600)
No 1
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=6.4e-31 Score=200.78 Aligned_cols=108 Identities=24% Similarity=0.446 Sum_probs=87.1
Q ss_pred CCccccCCCchhHHHHHHHhhhhhhhhHHhhhcccccccccccccCccchhhHHHHHHHhhhhcCcchhHHHHHHHHHHH
Q 033409 1 MAATEENSQLFPIFILTIMALPLVPYTILKLCHAFSKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVI 80 (120)
Q Consensus 1 ~~~YDE~g~tfpyFvLt~l~lvLIP~T~~~l~~~~~~~~~~~~c~c~~c~~~~~~i~~~~kr~~~~~~~~~l~lv~GW~l 80 (120)
|.||||+|+|||||+||+++++|+|+||.+|++...+.....+|||.+|+..+...++..+ + .++..+++++++||++
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 5799999999999999999999999999999853222222458999999987754333322 2 3333399999999999
Q ss_pred HHHHHHHHHhcccccCccchhhHhHhhhhh
Q 033409 81 MIILIYYIKSTSREHTRFGTWGLRFRYKES 110 (120)
Q Consensus 81 ~~~L~y~i~~~~~~~~~fDPYeIL~~~~~~ 110 (120)
+++|+|+|++.+++.+.|||||||++...+
T Consensus 82 ~~fL~y~i~~~~~~~~~fDPyEILGl~pga 111 (230)
T KOG0721|consen 82 IAFLIYKIMNSRRERQKFDPYEILGLDPGA 111 (230)
T ss_pred HHHHHHHHhhhhHHhhcCCcHHhhCCCCCC
Confidence 999999999999888999999999997643
No 2
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=99.84 E-value=1.5e-21 Score=162.46 Aligned_cols=103 Identities=18% Similarity=0.322 Sum_probs=81.1
Q ss_pred ccccCCCchhHHHHHHHhhhhhhhhHHhhhcccccc-cccccccCccchhhHHHHHHHhhhhcCcchhHHHHHHHHHHHH
Q 033409 3 ATEENSQLFPIFILTIMALPLVPYTILKLCHAFSKK-IKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIM 81 (120)
Q Consensus 3 ~YDE~g~tfpyFvLt~l~lvLIP~T~~~l~~~~~~~-~~~~~c~c~~c~~~~~~i~~~~kr~~~~~~~~~l~lv~GW~l~ 81 (120)
||||+|.+||||+|+.+.++..|+||..+-+....+ ....+|.|+.|..+.++ .+|| + +.++|++++++||+++
T Consensus 6 eYDE~g~~~p~fvL~gl~~vvlpmTY~~i~gpsaSKe~~~vr~~~q~~Rpkdkn--v~rK--S-If~lR~If~ivgWl~i 80 (610)
T COG5407 6 EYDESGLASPYFVLSGLVPVVLPMTYDLIEGPSASKELRRVRCACQGCRPKDKN--VSRK--S-IFKLRKIFTIVGWLVI 80 (610)
T ss_pred ccccccccchHHHHhhhhheeeeeehhheeCCcccchhhcchhhhhhcCccccc--hhhh--H-HHhhhHHHHHHHHHHH
Confidence 899999999999999999999999998875553222 22557888888754432 2222 3 2224999999999999
Q ss_pred HHHHHHHHhccccc-CccchhhHhHhhhhh
Q 033409 82 IILIYYIKSTSREH-TRFGTWGLRFRYKES 110 (120)
Q Consensus 82 ~~L~y~i~~~~~~~-~~fDPYeIL~~~~~~ 110 (120)
++|.|+|.+.+.+. +.|||||||+|.+..
T Consensus 81 ~~L~~~I~~~k~~~~~~fDPyEILGI~~~t 110 (610)
T COG5407 81 SYLISNIRTLKIEYRRGFDPYEILGIDQDT 110 (610)
T ss_pred HHHHHHHHHHHHHHHcCCChHHhhcccCCC
Confidence 99999999877776 899999999998753
No 3
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.32 E-value=7.2 Score=25.50 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=8.9
Q ss_pred cccccCcc-chhhHHHH
Q 033409 41 TIHCQCSD-CARSGKYR 56 (120)
Q Consensus 41 ~~~c~c~~-c~~~~~~i 56 (120)
++.|.|+. |..+.++.
T Consensus 42 ~K~CdC~~pCDt~~~kl 58 (77)
T COG2991 42 EKVCDCDEPCDTHKKKL 58 (77)
T ss_pred chhcCCCCchHHHHHhH
Confidence 44587765 55544443
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=70.17 E-value=4.6 Score=25.33 Aligned_cols=21 Identities=24% Similarity=0.391 Sum_probs=15.1
Q ss_pred cCCCchhHHHHHHHhhhhhhh
Q 033409 6 ENSQLFPIFILTIMALPLVPY 26 (120)
Q Consensus 6 E~g~tfpyFvLt~l~lvLIP~ 26 (120)
-.|.+||||-|.+..+.++-+
T Consensus 10 FtskFW~YFtLi~M~lti~~~ 30 (64)
T PF03579_consen 10 FTSKFWTYFTLIFMMLTIGFF 30 (64)
T ss_pred eccccchHHHHHHHHHHHHHH
Confidence 368999999887766555443
No 5
>PF08592 DUF1772: Domain of unknown function (DUF1772); InterPro: IPR013901 This entry represents proteins of unknown function.
Probab=63.86 E-value=21 Score=24.34 Aligned_cols=75 Identities=9% Similarity=0.279 Sum_probs=38.1
Q ss_pred CCchhHHHHHHHhhhhhhhhHHhhhcccccccccccccCccchhhHHHHHHHhhhhcCcchhHHHHHHHHHHHHHH
Q 033409 8 SQLFPIFILTIMALPLVPYTILKLCHAFSKKIKTIHCQCSDCARSGKYRKSIFKRISNFSTCSNLSLVLLWVIMII 83 (120)
Q Consensus 8 g~tfpyFvLt~l~lvLIP~T~~~l~~~~~~~~~~~~c~c~~c~~~~~~i~~~~kr~~~~~~~~~l~lv~GW~l~~~ 83 (120)
+..+.+.+.+.+.+-.+|.|....... .+.-..-+-+-.+.....+..++.++|..+.+..|.++-++||++..+
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 344445555666677899998775222 111000000000111122233555555666644488888888887753
No 6
>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=59.34 E-value=4.4 Score=25.52 Aligned_cols=17 Identities=12% Similarity=0.167 Sum_probs=11.4
Q ss_pred HHHHhcccccCccchhhH
Q 033409 86 YYIKSTSREHTRFGTWGL 103 (120)
Q Consensus 86 y~i~~~~~~~~~fDPYeI 103 (120)
+.|+ ..-+..+|||||.
T Consensus 23 q~IS-svl~t~iFDPFE~ 39 (64)
T PF03622_consen 23 QHIS-SVLNTEIFDPFEV 39 (64)
T ss_pred HHHH-HHHhhhhcCCeeE
Confidence 5554 3345578999985
No 7
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=46.21 E-value=33 Score=23.67 Aligned_cols=7 Identities=14% Similarity=0.439 Sum_probs=5.3
Q ss_pred Cccchhh
Q 033409 96 TRFGTWG 102 (120)
Q Consensus 96 ~~fDPYe 102 (120)
..||||-
T Consensus 28 ~~fDpyP 34 (108)
T PF06210_consen 28 PAFDPYP 34 (108)
T ss_pred CCCCCcc
Confidence 4699965
No 8
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=45.28 E-value=5.6 Score=23.83 Aligned_cols=12 Identities=0% Similarity=-0.078 Sum_probs=9.4
Q ss_pred chhhHhHhhhhh
Q 033409 99 GTWGLRFRYKES 110 (120)
Q Consensus 99 DPYeIL~~~~~~ 110 (120)
|||+||++-..+
T Consensus 1 ~~y~iLgl~~~~ 12 (64)
T PF00226_consen 1 NPYEILGLPPDA 12 (64)
T ss_dssp HHHHHCTSTTTS
T ss_pred ChHHHCCCCCCC
Confidence 799999987544
No 9
>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=44.08 E-value=19 Score=20.30 Aligned_cols=16 Identities=13% Similarity=0.065 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 033409 70 SNLSLVLLWVIMIILI 85 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~ 85 (120)
--+++.+||+++-..-
T Consensus 10 ~Pil~A~gWa~fNIg~ 25 (36)
T PF06298_consen 10 LPILPAAGWALFNIGR 25 (36)
T ss_pred HHHHHHHHHHHHHhHH
Confidence 3455677999986653
No 10
>COG4420 Predicted membrane protein [Function unknown]
Probab=41.58 E-value=28 Score=26.67 Aligned_cols=26 Identities=8% Similarity=0.202 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHhccccc-Cccchhh
Q 033409 77 LWVIMIILIYYIKSTSREH-TRFGTWG 102 (120)
Q Consensus 77 GW~l~~~L~y~i~~~~~~~-~~fDPYe 102 (120)
+|..+++++|-+-+...-. ..||||-
T Consensus 62 l~~~~~ll~Wi~lNl~~~~~~~wDpyP 88 (191)
T COG4420 62 LTFTLLLLLWIVLNLFLVPGLAWDPYP 88 (191)
T ss_pred HHHHHHHHHHHHHHHhhhcCCcCCCcc
Confidence 3333444444433333322 6799985
No 11
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=40.52 E-value=9 Score=21.93 Aligned_cols=9 Identities=0% Similarity=-0.267 Sum_probs=7.7
Q ss_pred chhhHhHhh
Q 033409 99 GTWGLRFRY 107 (120)
Q Consensus 99 DPYeIL~~~ 107 (120)
|||++|++-
T Consensus 1 ~~y~vLgl~ 9 (55)
T cd06257 1 DYYDILGVP 9 (55)
T ss_pred ChHHHcCCC
Confidence 799999875
No 12
>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=36.53 E-value=41 Score=23.24 Aligned_cols=30 Identities=20% Similarity=0.108 Sum_probs=25.0
Q ss_pred ccCCCchhHHHHHHHhhhhhhhhHHhhhcc
Q 033409 5 EENSQLFPIFILTIMALPLVPYTILKLCHA 34 (120)
Q Consensus 5 DE~g~tfpyFvLt~l~lvLIP~T~~~l~~~ 34 (120)
|=+.++|.++-.|+++++++-..+..|+..
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 13
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=35.89 E-value=31 Score=19.47 Aligned_cols=15 Identities=13% Similarity=0.169 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHH
Q 033409 71 NLSLVLLWVIMIILI 85 (120)
Q Consensus 71 ~l~lv~GW~l~~~L~ 85 (120)
-+++.+||+++-..-
T Consensus 11 Pil~A~~Wa~fNIg~ 25 (36)
T CHL00196 11 PVLAAASWALFNIGR 25 (36)
T ss_pred HHHHHHHHHHHHhHH
Confidence 356678999986543
No 14
>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=35.88 E-value=1.5e+02 Score=20.74 Aligned_cols=44 Identities=18% Similarity=0.128 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHH-----HHHHHHhcccccCccchhhHhHhhhhhhhh
Q 033409 70 SNLSLVLLWVIMII-----LIYYIKSTSREHTRFGTWGLRFRYKESISE 113 (120)
Q Consensus 70 ~~l~lv~GW~l~~~-----L~y~i~~~~~~~~~fDPYeIL~~~~~~~~~ 113 (120)
..+.++.||-+.+. ++|.+....+....+||=||-...+..-.|
T Consensus 62 ~~l~ll~g~w~~~llnlPl~~y~~~~~~~~~~l~D~T~If~~L~~~kk~ 110 (128)
T PF03311_consen 62 CLLFLLTGHWFLFLLNLPLLAYHIYRYFRRQHLYDPTEIFNQLKREKKE 110 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccHHHHHHHHHHHHHH
Confidence 34444555554433 455554333334569999998775544444
No 15
>COG1288 Predicted membrane protein [Function unknown]
Probab=35.40 E-value=1.2e+02 Score=26.31 Aligned_cols=20 Identities=25% Similarity=0.507 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 033409 70 SNLSLVLLWVIMIILIYYIK 89 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i~ 89 (120)
++++|.+.=+.+..++|-+.
T Consensus 275 ~klvL~lf~l~f~~mI~GV~ 294 (481)
T COG1288 275 DKLVLLLFTLTFVIMIWGVI 294 (481)
T ss_pred hhHHHHHHHHHHHHHHHHhh
Confidence 45555544455555666554
No 16
>KOG3672 consensus Histidine acid phosphatase [General function prediction only]
Probab=34.77 E-value=31 Score=29.57 Aligned_cols=54 Identities=13% Similarity=0.076 Sum_probs=28.7
Q ss_pred cCccchhhHHHHHHHhhhhc-CcchhHHHHHHHHHHHHHHHHHHHHhcccccCccchhhHhHh
Q 033409 45 QCSDCARSGKYRKSIFKRIS-NFSTCSNLSLVLLWVIMIILIYYIKSTSREHTRFGTWGLRFR 106 (120)
Q Consensus 45 ~c~~c~~~~~~i~~~~kr~~-~~~~~~~l~lv~GW~l~~~L~y~i~~~~~~~~~fDPYeIL~~ 106 (120)
+| .|+.+...++....+-. .+.+ +....+.-|.-.+.+ .....+.||||+.-..
T Consensus 249 ~C-~Cp~~~~~r~~~e~~~~~q~lk-~~~~dv~~~~~~~~~------~~~p~~~~~pf~~ID~ 303 (487)
T KOG3672|consen 249 QC-ACPIHKSIRRIYEEEHLQQFLK-MKSDDVADEEKKFLS------FPQPAASFDPFQMIDV 303 (487)
T ss_pred cc-cchHHHHHHHHHHHHHHHHHHh-cchHHHHhhhcceee------ecccccccCchhHHHH
Confidence 56 37776655544443111 1123 334566677666444 2234467999987544
No 17
>PRK13240 pbsY photosystem II protein Y; Reviewed
Probab=33.30 E-value=36 Score=19.65 Aligned_cols=17 Identities=12% Similarity=0.049 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHH
Q 033409 71 NLSLVLLWVIMIILIYY 87 (120)
Q Consensus 71 ~l~lv~GW~l~~~L~y~ 87 (120)
=+++.+||+++-..---
T Consensus 11 Pil~A~~Wa~fNIg~~A 27 (40)
T PRK13240 11 PILAAAGWAVFNIGKAA 27 (40)
T ss_pred HHHHHHHHHHHHhhHHH
Confidence 35667899998665433
No 18
>KOG0510 consensus Ankyrin repeat protein [General function prediction only]
Probab=33.10 E-value=81 Score=29.41 Aligned_cols=26 Identities=35% Similarity=0.327 Sum_probs=20.5
Q ss_pred CCchhHHHHHHHhhhhhhhhHHhhhc
Q 033409 8 SQLFPIFILTIMALPLVPYTILKLCH 33 (120)
Q Consensus 8 g~tfpyFvLt~l~lvLIP~T~~~l~~ 33 (120)
|--|.++-|-+++++++|+|++.+-.
T Consensus 505 g~~~~~~nL~~Y~lFlv~lT~Yv~~~ 530 (929)
T KOG0510|consen 505 GKYFHLNNLLIYSLFLVSLTIYVLLI 530 (929)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33466677899999999999988743
No 19
>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=32.49 E-value=68 Score=29.20 Aligned_cols=19 Identities=16% Similarity=0.296 Sum_probs=13.5
Q ss_pred HHHHHHHhhhhhhhhHHhh
Q 033409 13 IFILTIMALPLVPYTILKL 31 (120)
Q Consensus 13 yFvLt~l~lvLIP~T~~~l 31 (120)
..++.++.++++|++-..+
T Consensus 96 ~~~i~ll~~il~P~vg~~f 114 (806)
T PF05478_consen 96 CAVIGLLFIILMPLVGLCF 114 (806)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3456777788899986555
No 20
>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=31.55 E-value=37 Score=26.98 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHhcccccCccchhh
Q 033409 74 LVLLWVIMIILIYYIKSTSREHTRFGTWG 102 (120)
Q Consensus 74 lv~GW~l~~~L~y~i~~~~~~~~~fDPYe 102 (120)
=|+||++++..+--+ -...||||-
T Consensus 105 SVvgi~Li~~ti~Dl-----vL~~WDPfG 128 (249)
T PF04583_consen 105 SVVGIVLIFLTIADL-----VLMFWDPFG 128 (249)
T ss_pred HHHHHHHHHHHHHHH-----HHHhcCccc
Confidence 346888876664322 125799984
No 21
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=31.01 E-value=16 Score=21.29 Aligned_cols=10 Identities=0% Similarity=-0.180 Sum_probs=8.4
Q ss_pred chhhHhHhhh
Q 033409 99 GTWGLRFRYK 108 (120)
Q Consensus 99 DPYeIL~~~~ 108 (120)
|||+||++-.
T Consensus 2 ~~y~vLgl~~ 11 (60)
T smart00271 2 DYYEILGVPR 11 (60)
T ss_pred CHHHHcCCCC
Confidence 8999999854
No 22
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=30.92 E-value=59 Score=22.47 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=18.2
Q ss_pred cccCCCchhHHHHHHHhhhhhhhhHHh
Q 033409 4 TEENSQLFPIFILTIMALPLVPYTILK 30 (120)
Q Consensus 4 YDE~g~tfpyFvLt~l~lvLIP~T~~~ 30 (120)
-.++|..|+|.|.-+++.+.+-+-+..
T Consensus 10 ~~~~g~sW~~LVGVv~~al~~SlLIal 36 (102)
T PF15176_consen 10 PGEGGRSWPFLVGVVVTALVTSLLIAL 36 (102)
T ss_pred CCCCCcccHhHHHHHHHHHHHHHHHHH
Confidence 357899999987666665555444443
No 23
>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=30.50 E-value=56 Score=26.18 Aligned_cols=31 Identities=32% Similarity=0.555 Sum_probs=21.8
Q ss_pred cCc-chhHHHHHHHHHHHHHHHH-HHHHhccccc
Q 033409 64 SNF-STCSNLSLVLLWVIMIILI-YYIKSTSREH 95 (120)
Q Consensus 64 ~~~-~~~~~l~lv~GW~l~~~L~-y~i~~~~~~~ 95 (120)
+++ +. |.++|+++-++-++|. |||+....+.
T Consensus 168 RNFYNl-r~lALflAFaINFILLFYKVs~~~~~~ 200 (274)
T PF06459_consen 168 RNFYNL-RFLALFLAFAINFILLFYKVSTSPPEE 200 (274)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHhccCCccc
Confidence 344 55 8999999998876655 8887555443
No 24
>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=30.16 E-value=64 Score=21.70 Aligned_cols=22 Identities=14% Similarity=0.383 Sum_probs=16.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHH
Q 033409 67 STCSNLSLVLLWVIMIILIYYIK 89 (120)
Q Consensus 67 ~~~~~l~lv~GW~l~~~L~y~i~ 89 (120)
.+ ||+-+++||.+++++++-+.
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 88888888888877777663
No 25
>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=29.40 E-value=65 Score=22.23 Aligned_cols=19 Identities=21% Similarity=0.831 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 033409 70 SNLSLVLLWVIMIILIYYI 88 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i 88 (120)
...+++++|.++|++.|..
T Consensus 54 ~~~~~~~~w~~~A~~ly~~ 72 (103)
T PF11027_consen 54 SMFMMMMLWMVLAMALYLL 72 (103)
T ss_pred cHHHHHHHHHHHHHHHHHc
Confidence 5677888999999999887
No 26
>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=29.00 E-value=78 Score=22.98 Aligned_cols=22 Identities=32% Similarity=0.786 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 033409 70 SNLSLVLLWVIMIILIYYIKST 91 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i~~~ 91 (120)
--++|-+.|+.|+.|+|.....
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 27
>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=28.70 E-value=45 Score=20.49 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=11.5
Q ss_pred chhHHHHHHHhhhhh
Q 033409 10 LFPIFILTIMALPLV 24 (120)
Q Consensus 10 tfpyFvLt~l~lvLI 24 (120)
.||||+.+.+.+.+|
T Consensus 10 ~wPFf~ag~iv~ygv 24 (54)
T PF04911_consen 10 MWPFFAAGAIVYYGV 24 (54)
T ss_pred hhHHHHHHHHHHHHH
Confidence 699999988665554
No 28
>COG3924 Predicted membrane protein [Function unknown]
Probab=28.65 E-value=42 Score=21.99 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHH
Q 033409 70 SNLSLVLLWVIMIIL 84 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L 84 (120)
-.++.++||.+.+|+
T Consensus 18 LtllYl~gW~v~AYl 32 (80)
T COG3924 18 LTLLYLAGWLVAAYL 32 (80)
T ss_pred HHHHHHHHHHHHHhC
Confidence 445677899999988
No 29
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=27.82 E-value=78 Score=18.80 Aligned_cols=32 Identities=9% Similarity=0.178 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHH-Hhccccc-Cccchhh
Q 033409 71 NLSLVLLWVIMIILIYYI-KSTSREH-TRFGTWG 102 (120)
Q Consensus 71 ~l~lv~GW~l~~~L~y~i-~~~~~~~-~~fDPYe 102 (120)
.+.+.++=+++++..|-+ .+..+.+ +.=||||
T Consensus 9 ~~~i~i~~lL~~~TgyaiYtaFGppSk~LrDPFe 42 (46)
T PRK13183 9 SLAITILAILLALTGFGIYTAFGPPSKELDDPFD 42 (46)
T ss_pred HHHHHHHHHHHHHhhheeeeccCCcccccCCchh
Confidence 344444555556666666 3344445 6789987
No 30
>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=27.21 E-value=84 Score=21.13 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 033409 70 SNLSLVLLWVIMIILIYYIK 89 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i~ 89 (120)
..++|.+.+|+++++..-++
T Consensus 5 ~~llL~l~LA~lLlisSeva 24 (95)
T PF07172_consen 5 AFLLLGLLLAALLLISSEVA 24 (95)
T ss_pred HHHHHHHHHHHHHHHHhhhh
Confidence 56666677777777765554
No 31
>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=25.84 E-value=47 Score=23.10 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=12.0
Q ss_pred hhHHHHHHHhhhhhhhhHHhhhcc
Q 033409 11 FPIFILTIMALPLVPYTILKLCHA 34 (120)
Q Consensus 11 fpyFvLt~l~lvLIP~T~~~l~~~ 34 (120)
|.+|++-+++++++-+...+..++
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 32
>PF14004 DUF4227: Protein of unknown function (DUF4227)
Probab=25.71 E-value=84 Score=20.21 Aligned_cols=31 Identities=10% Similarity=0.058 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccCccchhh
Q 033409 70 SNLSLVLLWVIMIILIYYIKSTSREHTRFGTWG 102 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i~~~~~~~~~fDPYe 102 (120)
|.++|-+|=.+++|-+..-- .++...+|||+
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 56666666665555444332 23446688875
No 33
>PF09878 DUF2105: Predicted membrane protein (DUF2105); InterPro: IPR019212 This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Probab=25.11 E-value=37 Score=26.26 Aligned_cols=24 Identities=17% Similarity=0.288 Sum_probs=21.1
Q ss_pred CCCchhHHHHHHHhhhhhhhhHHh
Q 033409 7 NSQLFPIFILTIMALPLVPYTILK 30 (120)
Q Consensus 7 ~g~tfpyFvLt~l~lvLIP~T~~~ 30 (120)
||-+|.++++.|+.+++.|--+..
T Consensus 164 SGiaWalWi~gF~~Ff~~P~~Wl~ 187 (212)
T PF09878_consen 164 SGIAWALWIAGFIGFFLFPQYWLL 187 (212)
T ss_pred hhHHHHHHHHHHHHHHHhHHHHHH
Confidence 788999999999999999976643
No 34
>CHL00020 psbN photosystem II protein N
Probab=24.83 E-value=72 Score=18.69 Aligned_cols=31 Identities=3% Similarity=0.091 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHH-Hhccccc-Cccchhh
Q 033409 72 LSLVLLWVIMIILIYYI-KSTSREH-TRFGTWG 102 (120)
Q Consensus 72 l~lv~GW~l~~~L~y~i-~~~~~~~-~~fDPYe 102 (120)
+.+.++=+++....|.+ .+..+.+ +.=||||
T Consensus 7 ~~i~i~~ll~~~Tgy~iYtaFGppSk~LrDPfe 39 (43)
T CHL00020 7 VAIFISGLLVSFTGYALYTAFGQPSKQLRDPFE 39 (43)
T ss_pred HHHHHHHHHHHhhheeeeeccCCchhccCCchh
Confidence 33444445555666665 3344444 6789987
No 35
>PF07672 MFS_Mycoplasma: Mycoplasma MFS transporter; InterPro: IPR011699 These proteins share some similarity with members of the Major Facilitator Superfamily (MFS).
Probab=24.53 E-value=1.2e+02 Score=24.30 Aligned_cols=24 Identities=8% Similarity=0.271 Sum_probs=18.6
Q ss_pred hhHHHHHHHhhhhhhhhHHhhhcc
Q 033409 11 FPIFILTIMALPLVPYTILKLCHA 34 (120)
Q Consensus 11 fpyFvLt~l~lvLIP~T~~~l~~~ 34 (120)
|-+-+..+.+++++|+-++.+.+.
T Consensus 40 W~~I~si~~lL~~IpLIly~ifGk 63 (267)
T PF07672_consen 40 WQWILSIFILLIFIPLILYIIFGK 63 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 666667777889999998887544
No 36
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=24.15 E-value=1.1e+02 Score=20.04 Aligned_cols=25 Identities=16% Similarity=0.373 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccCccch
Q 033409 70 SNLSLVLLWVIMIILIYYIKSTSREHTRFGT 100 (120)
Q Consensus 70 ~~l~lv~GW~l~~~L~y~i~~~~~~~~~fDP 100 (120)
-...++++|++..+-+.+.. +.|||
T Consensus 59 g~~~~~~~~~l~~~Yv~~An------~~~D~ 83 (91)
T PF04341_consen 59 GLGQIVFAWVLTWLYVRRAN------REFDP 83 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHc------cccCH
Confidence 45566678888877666532 34777
No 37
>PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A.
Probab=23.96 E-value=46 Score=21.67 Aligned_cols=21 Identities=14% Similarity=0.270 Sum_probs=16.5
Q ss_pred ccchhhHhHhhhhhhhhhhhc
Q 033409 97 RFGTWGLRFRYKESISETFHT 117 (120)
Q Consensus 97 ~fDPYeIL~~~~~~~~~~~~~ 117 (120)
+|-=||++++|-+++.+..|.
T Consensus 12 iYR~yE~v~vYG~~~K~li~E 32 (73)
T PF02560_consen 12 IYRLYEIVQVYGPAIKALIHE 32 (73)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred EeeeehhhHhhCHHHHHHHHH
Confidence 455599999999888877763
No 38
>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=23.69 E-value=5.8 Score=28.70 Aligned_cols=16 Identities=25% Similarity=0.395 Sum_probs=12.7
Q ss_pred cccCCC--------chhHHHHHHH
Q 033409 4 TEENSQ--------LFPIFILTIM 19 (120)
Q Consensus 4 YDE~g~--------tfpyFvLt~l 19 (120)
.||+|+ .-|||+++.+
T Consensus 4 iDESG~~~~~~~~~~~~~fvl~gv 27 (235)
T PF12686_consen 4 IDESGNTGPNYSDKNSPYFVLGGV 27 (235)
T ss_pred EeCCCCCCCCcCCCCCCEEEEEEE
Confidence 499998 4899987765
No 39
>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=23.36 E-value=1.4e+02 Score=17.39 Aligned_cols=27 Identities=11% Similarity=0.091 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHH-Hhccccc-Cccchhh
Q 033409 76 LLWVIMIILIYYI-KSTSREH-TRFGTWG 102 (120)
Q Consensus 76 ~GW~l~~~L~y~i-~~~~~~~-~~fDPYe 102 (120)
++=+++....|-+ ....+.+ +.=||||
T Consensus 11 i~~~lv~~Tgy~iYtaFGppSk~LrDPfe 39 (43)
T PF02468_consen 11 ISCLLVSITGYAIYTAFGPPSKELRDPFE 39 (43)
T ss_pred HHHHHHHHHhhhhhheeCCCccccCCccc
Confidence 3444444444554 2344444 6779987
No 40
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=23.13 E-value=47 Score=21.36 Aligned_cols=22 Identities=9% Similarity=0.212 Sum_probs=17.7
Q ss_pred CccchhhHhHhhhhhhhhhhhc
Q 033409 96 TRFGTWGLRFRYKESISETFHT 117 (120)
Q Consensus 96 ~~fDPYeIL~~~~~~~~~~~~~ 117 (120)
.+|-=||++++|-+++.|..|.
T Consensus 7 ~iYRlyE~v~vYG~~~K~li~E 28 (69)
T cd00559 7 LIYRFYEIVQVYGPTLKALIHE 28 (69)
T ss_pred eeeehHHHHHHhhHHHHHHHHH
Confidence 3566799999999988887773
No 41
>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=21.03 E-value=1e+02 Score=19.03 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=13.9
Q ss_pred hhHHHHHHHhhhhhhhhHHhhhcc
Q 033409 11 FPIFILTIMALPLVPYTILKLCHA 34 (120)
Q Consensus 11 fpyFvLt~l~lvLIP~T~~~l~~~ 34 (120)
+.||++++++++++=-=++-+++.
T Consensus 2 y~yf~~ti~lvv~LYgY~yhLYrs 25 (56)
T TIGR02736 2 YAYFAFTLLLVIFLYAYIYHLYRS 25 (56)
T ss_pred cchHHHHHHHHHHHHHHHHHhhhh
Confidence 357777777666664444445443
No 42
>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=20.75 E-value=63 Score=20.94 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=15.9
Q ss_pred CCchhHHHHHHHhhhhhhh
Q 033409 8 SQLFPIFILTIMALPLVPY 26 (120)
Q Consensus 8 g~tfpyFvLt~l~lvLIP~ 26 (120)
|=-|..|++++++++..|.
T Consensus 56 gcsfsIFllaLlSc~~~p~ 74 (75)
T PF01542_consen 56 GCSFSIFLLALLSCLTVPA 74 (75)
T ss_pred CccHHHHHHHHHHhccccC
Confidence 5568899999999998874
No 43
>COG3083 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]
Probab=20.10 E-value=69 Score=28.38 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=20.3
Q ss_pred hhHHHHHHHhhhhhhhhHHhhhcc
Q 033409 11 FPIFILTIMALPLVPYTILKLCHA 34 (120)
Q Consensus 11 fpyFvLt~l~lvLIP~T~~~l~~~ 34 (120)
|.|++.+..++|+.|+|...+++.
T Consensus 61 FsflvFA~yLlvlfpltfiv~s~r 84 (600)
T COG3083 61 FSFLVFALYLLVLFPLTFIVLSQR 84 (600)
T ss_pred HHHHHHHHHHHHHhhhhhhcccHH
Confidence 678899999999999998776555
Done!