Query 021662
Match_columns 309
No_of_seqs 50 out of 52
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:43:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021662hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10160 Tmemb_40: Predicted m 100.0 1E-103 3E-108 728.8 27.1 257 40-296 2-261 (261)
2 KOG4536 Predicted membrane pro 100.0 6.5E-95 1.4E-99 678.7 26.4 277 31-309 21-315 (347)
3 KOG4193 G protein-coupled rece 70.6 11 0.00023 40.2 6.5 71 36-106 458-535 (610)
4 cd00927 Cyt_c_Oxidase_VIc Cyto 66.6 2.6 5.6E-05 33.4 0.8 25 279-306 45-69 (70)
5 PF10192 GpcrRhopsn4: Rhodopsi 60.6 1.4E+02 0.0031 27.6 16.2 161 75-242 54-223 (257)
6 PF03189 Otopetrin: Otopetrin; 59.4 1.4E+02 0.0031 30.4 11.8 190 39-239 229-431 (441)
7 PF02937 COX6C: Cytochrome c o 51.9 5 0.00011 31.8 0.1 25 279-306 47-71 (73)
8 PF00124 Photo_RC: Photosynthe 49.9 59 0.0013 31.6 6.9 78 9-106 42-119 (257)
9 PF10160 Tmemb_40: Predicted m 48.9 94 0.002 30.3 8.1 96 109-204 76-177 (261)
10 PF09586 YfhO: Bacterial membr 48.6 3.6E+02 0.0077 28.8 13.1 89 48-139 144-232 (843)
11 PLN00056 photosystem Q(B) prot 47.7 43 0.00093 33.8 5.8 88 9-106 79-166 (353)
12 PRK13825 conjugal transfer pro 44.9 50 0.0011 33.1 5.9 71 157-238 48-118 (388)
13 TIGR00756 PPR pentatricopeptid 42.0 15 0.00033 22.0 1.2 31 274-304 2-32 (35)
14 KOG4536 Predicted membrane pro 40.9 33 0.00072 34.2 3.8 79 58-136 57-137 (347)
15 PF13041 PPR_2: PPR repeat fam 40.4 18 0.00038 24.8 1.4 31 274-304 5-35 (50)
16 PF01535 PPR: PPR repeat; Int 38.4 19 0.00041 21.5 1.2 30 274-303 2-31 (31)
17 PF12273 RCR: Chitin synthesis 34.9 32 0.00068 28.9 2.4 13 72-84 23-35 (130)
18 TIGR00939 2a57 Equilibrative N 34.4 2.6E+02 0.0057 28.2 9.1 29 189-217 172-200 (437)
19 PF04235 DUF418: Protein of un 29.5 2.5E+02 0.0054 23.8 7.0 138 144-289 10-153 (163)
20 PF13812 PPR_3: Pentatricopept 26.7 39 0.00085 20.6 1.2 30 274-303 3-32 (34)
21 TIGR01151 psbA photosystem II, 26.2 1.5E+02 0.0034 30.0 5.8 85 12-106 82-166 (360)
22 PF08285 DPM3: Dolichol-phosph 21.5 2E+02 0.0044 23.6 4.7 53 194-249 6-62 (91)
23 PF10271 Tmp39: Putative trans 21.0 6.4E+02 0.014 26.2 9.1 25 24-49 17-41 (423)
24 PF01529 zf-DHHC: DHHC palmito 20.2 4.3E+02 0.0094 22.2 6.7 14 35-48 74-88 (174)
No 1
>PF10160 Tmemb_40: Predicted membrane protein; InterPro: IPR018781 This entry represents 280 amino acid region found in a group of proteins conserved from plants to humans. These are predicted to be membrane proteins, but apart from that their function is unknown.
Probab=100.00 E-value=1.4e-103 Score=728.82 Aligned_cols=257 Identities=42% Similarity=0.766 Sum_probs=251.0
Q ss_pred cccccccceehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHHHHHHHHHHHHHHHhHhhcccccCc-hhHHHH
Q 021662 40 ESVRQCHGVLYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYYALLWLACVLNLAWCSLQGWQCSAG-KEVAWN 118 (309)
Q Consensus 40 ~w~~~c~g~~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY~ll~~v~llnl~rc~vsm~~~t~~-~~~~wn 118 (309)
+|+++|||++||+++++||++|++||++|+||+++|||+||||||+|||+++|+++++|++||++|||||+|+ ++++||
T Consensus 2 ~~~~~~~v~~~d~~l~vPn~lFllfL~~~~~~s~~KL~~~~SpI~~tyY~llw~v~llnl~rc~vsm~~~~~~~~~~~d~ 81 (261)
T PF10160_consen 2 RWIGGSRVRIWDVVLLVPNLLFLLFLAWRLRKSRRKLRHTRSPIFITYYALLWVVALLNLARCFVSMWVCSPGKGGIADK 81 (261)
T ss_pred cccccCceEehHHHHHHHHHHHHHHHHHhchHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCccchhHHH
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999875 589999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccc-cceeecCC-CCCCccchhHH
Q 021662 119 LLSLFTVAAVLYLEISLMAFLLQESYASGLETLARTFIISGIIVGVDMLLKVIYVFGFG-FPLFIDVD-STHRMKWGFWI 196 (309)
Q Consensus 119 iLwl~trf~lL~lEvSvvvFgl~g~~~~s~~sl~Rtl~iS~lia~~d~l~kaiy~f~~g-vplf~~~~-~~~hgg~~FW~ 196 (309)
++|+++||+||++|+||++||+||||+|||||||||+++|++++++|+++|++|+|++| +|++.+++ .++||||+||+
T Consensus 82 ~lW~ilrfflL~lEvSvvvFgL~fghlds~~Si~r~l~iT~~is~~~s~~Q~ilef~~~d~~l~~~~~~~~~hgg~~fW~ 161 (261)
T PF10160_consen 82 VLWNILRFFLLSLEVSVVVFGLQFGHLDSRSSIKRTLLITGLISLADSLTQAILEFGFGDVPLFIENFDLFGHGGWGFWF 161 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHheeecCcccccCCCCCcCCcCCeehHH
Confidence 99999999999999999999999999999999999999999999999999999999999 89998765 44589999999
Q ss_pred HHHHHHHHHHHHHHHhccccccccCCCCchhHHHHHHHHHHHHHHHHHHHhhhcCCcceeEEechhhHHHHHhhhHHHHH
Q 021662 197 IHELLLTAVYGFILFVHFSKWREKLPSRPAFYHYVVVMFVVSAVAFLVVSLAGTGAAFGIWLYNLTVICYHSLYLPLLYA 276 (309)
Q Consensus 197 ~ss~~f~lVY~~I~~LP~t~~rerLPar~SFY~Yv~iL~lLN~~q~~Gs~Ll~~~~~~GlClvd~Tt~~Yfaly~PLlY~ 276 (309)
+||++|++||++|++||++|||+|||+|||||+||++|++||++|++||+|+++|+++|+|+||+|+++|||+|+|++|+
T Consensus 162 ~~s~~f~~vY~~I~~L~~~r~r~~LPar~SFY~Y~~~L~~LN~~q~~Gs~Ll~~~~~~Glc~~d~t~~~Yfa~y~PllY~ 241 (261)
T PF10160_consen 162 ISSLVFALVYGFILILTPLRWRDRLPARPSFYRYVGILFLLNLLQSIGSGLLGYGASFGLCLVDLTTFLYFALYPPLLYV 241 (261)
T ss_pred HHHHHHHHHHHHHHHHHhccccccCCCCccHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeccHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcccccccchhhhh
Q 021662 277 TFLADFFQEENFLLDNAYYS 296 (309)
Q Consensus 277 TFLadFF~~e~~~~~~~yYS 296 (309)
|||||||||||.|+||.|||
T Consensus 242 TFL~~fF~~~d~~L~~~Yys 261 (261)
T PF10160_consen 242 TFLADFFQEEDVHLENVYYS 261 (261)
T ss_pred HHHHHHhCccccCCCCCCCC
Confidence 99999999999999999997
No 2
>KOG4536 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=6.5e-95 Score=678.69 Aligned_cols=277 Identities=45% Similarity=0.785 Sum_probs=261.9
Q ss_pred CCcccccCcc--ccccccc-e---ehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHHHHHHHHHHHHHHHhHh
Q 021662 31 FPVKSIGGNE--SVRQCHG-V---LYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYYALLWLACVLNLAWCSL 104 (309)
Q Consensus 31 ~~~~~~~~~~--w~~~c~g-~---~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY~ll~~v~llnl~rc~v 104 (309)
.||.|-+|++ |+++||| + +||+++++||++|++||++|+|++++|||++|||||+|||++||+++++|+|||++
T Consensus 21 ~Pn~s~~~~~~~~vyk~~G~frvrywd~vllipnilFl~fL~~k~~s~~~Klr~~~SpI~iafy~lv~vvsLvniarc~~ 100 (347)
T KOG4536|consen 21 APNSSAPGRCLLWVYKCHGTFRVRYWDTVLLIPNILFLAFLAYKAKSSLSKLRNRRSPIMIAFYGLVWVVSLVNIARCCL 100 (347)
T ss_pred CCCCcCCCcceEEEEecCCcceehhhhHHHHHHHHHHHHHHHHhchhHHHHhhcCCChhHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999988 9999999 5 99999999999999999999999999999999999999999999999999999999
Q ss_pred hc-ccccCchhHHHHHHHHHHHHHHHHHHHHHHHHH----HhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 021662 105 QG-WQCSAGKEVAWNLLSLFTVAAVLYLEISLMAFL----LQESYASGLETLARTFIISGIIVGVDMLLKVIYVFGFGFP 179 (309)
Q Consensus 105 sm-~~~t~~~~~~wniLwl~trf~lL~lEvSvvvFg----l~g~~~~s~~sl~Rtl~iS~lia~~d~l~kaiy~f~~gvp 179 (309)
|| |+||||+|++||++|.++|||.++.|+++.++| -|||..|++++++||+++|+.++++|.++|++|.+++|+|
T Consensus 101 smt~s~t~g~e~~dkvlW~i~~fF~ls~el~~~v~glaFg~~~n~~Si~~aL~~T~liS~~~~a~q~~le~~y~d~~~~p 180 (347)
T KOG4536|consen 101 SMTWSCTPGKEVADKVLWNILTFFTLSGELFLEVSGLAFGFQGNYASIAEALTRTFLISGAYSALQLLLEAIYLDGFGVP 180 (347)
T ss_pred hceeeccCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHhhHHHHHHHHHHheeeccccCc
Confidence 99 889999999999999999999888887777755 4567888899999999999999999999999999999999
Q ss_pred eeecCCCCCCccchhHHHHHHHHHHHHHHHHHhcc--ccccccCCCCchhHHHHHHHHHHHHHHHHHHHhhhcCCcceeE
Q 021662 180 LFIDVDSTHRMKWGFWIIHELLLTAVYGFILFVHF--SKWREKLPSRPAFYHYVVVMFVVSAVAFLVVSLAGTGAAFGIW 257 (309)
Q Consensus 180 lf~~~~~~~hgg~~FW~~ss~~f~lVY~~I~~LP~--t~~rerLPar~SFY~Yv~iL~lLN~~q~~Gs~Ll~~~~~~GlC 257 (309)
++.| +++ |||..||+.+|..+++||.+++++|. +|||+|||+|||||+|+++|++||.+|++||+|+++|+++|+|
T Consensus 181 l~fd-i~~-~gg~~fWl~ss~~l~Lvy~~~milp~~~~k~r~kLPsr~sFy~Y~~im~~Ln~Lq~~gsal~~f~~~~Glc 258 (347)
T KOG4536|consen 181 LFFD-INE-HGGRFFWLWSSHKLLLVYSYGMILPMYNSKWREKLPSRPSFYVYIGIMAALNLLQLLGSALTAFDAHFGLC 258 (347)
T ss_pred eeee-ecc-cCcEEEehHHHHHHHHHHHHHheeeccchhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHhcccccceE
Confidence 9554 356 79999999999999999999999987 5667789999999999999999999999999999999999999
Q ss_pred EechhhHHHHHhhhHHHHHHHHHhhhcccccccchhh-hhhhhc-cc---cCCCCCC
Q 021662 258 LYNLTVICYHSLYLPLLYATFLADFFQEENFLLDNAY-YSEMKD-AG---FFDADWE 309 (309)
Q Consensus 258 lvd~Tt~~Yfaly~PLlY~TFLadFF~~e~~~~~~~y-YSemkD-ag---~fd~dw~ 309 (309)
+||+||+|||++|+|++|+|||||||||||.++||.| |||||| || +||+|||
T Consensus 259 ~vgitt~~Yf~fy~PliYvtFLr~ff~~ep~nl~~~~~yre~kd~aGa~~~~da~y~ 315 (347)
T KOG4536|consen 259 LVGITTVCYFAFYLPLIYVTFLRDFFQEEPLNLENVYCYREMKDAAGAAGFFDADYE 315 (347)
T ss_pred EechhHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhHHhhhhhccCCCCccccCc
Confidence 9999999999999999999999999999999999999 999999 77 9999997
No 3
>KOG4193 consensus G protein-coupled receptors [Signal transduction mechanisms]
Probab=70.57 E-value=11 Score=40.18 Aligned_cols=71 Identities=14% Similarity=0.119 Sum_probs=58.8
Q ss_pred ccCccccccccceehh-----hHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHH--HHHHHHHHHHHHHHHhHhhc
Q 021662 36 IGGNESVRQCHGVLYD-----AALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMIS--YYALLWLACVLNLAWCSLQG 106 (309)
Q Consensus 36 ~~~~~w~~~c~g~~wD-----v~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~t--yY~ll~~v~llnl~rc~vsm 106 (309)
.+..||++...+++|= .++++-|+.+++--++|+.+...+++...++...+ +-..+-+..++++.|++-=+
T Consensus 458 ~~~~CWl~~~~~~~~~F~GPv~~ii~~Ni~~Fv~t~~~l~~~~~~~~~~~~~~~~~~~~~~~l~L~~lLGlTW~fgi~ 535 (610)
T KOG4193|consen 458 TPRVCWLDTQNGFIWSFLGPVTLIILVNIVMFVVTLKKLLRRLSKLQPIASKLENISLIRSALALLFLLGLTWIFGIF 535 (610)
T ss_pred cCCceEEecCCceEEEEehHHHHHHHHHHHHHHHHHHHHhhcccccCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344899999999987 77888999999999999999999999998887776 66677777788888876544
No 4
>cd00927 Cyt_c_Oxidase_VIc Cytochrome c oxidase subunit VIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIc subunit is found only in eukaryotes and its specific function remains unclear. It has been reported that the relative concentrations of some nuclear encoded CcO subunits, including subunit VIc, compared to those of the mitochondrial encoded subunits, are altered significantly during the progression of prostate cancer.
Probab=66.62 E-value=2.6 Score=33.42 Aligned_cols=25 Identities=32% Similarity=0.752 Sum_probs=20.1
Q ss_pred HHhhhcccccccchhhhhhhhccccCCC
Q 021662 279 LADFFQEENFLLDNAYYSEMKDAGFFDA 306 (309)
Q Consensus 279 LadFF~~e~~~~~~~yYSemkDag~fd~ 306 (309)
-+||+++=|+.-+ +.+||++|+|+.
T Consensus 45 YadFYknYD~~kd---FerM~~~G~f~S 69 (70)
T cd00927 45 YADFYKTYDAMKD---FERMRKAGLFQS 69 (70)
T ss_pred HHHHHHccChHHH---HHHHHHcCCccc
Confidence 3678888886555 799999999975
No 5
>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=60.61 E-value=1.4e+02 Score=27.64 Aligned_cols=161 Identities=15% Similarity=0.076 Sum_probs=78.4
Q ss_pred ccccCCchHHHHHHHHHHHHHHHHHHHhHhhccc-ccCchhHHHHHHHHHHHHHHHHHHHHHHHHH--H-hhcccchhHH
Q 021662 75 KLCNGRSYIMISYYALLWLACVLNLAWCSLQGWQ-CSAGKEVAWNLLSLFTVAAVLYLEISLMAFL--L-QESYASGLET 150 (309)
Q Consensus 75 KL~~t~SpI~~tyY~ll~~v~llnl~rc~vsm~~-~t~~~~~~wniLwl~trf~lL~lEvSvvvFg--l-~g~~~~s~~s 150 (309)
|-|+..++++..+.+.+.+-. +++.-....... ..+|.+ ...+..+-+.+-...|...+.-+ + +|- .-++..
T Consensus 54 ~~~~~~h~~~~l~~~~l~l~~-~s~~l~~ih~~~ya~nG~G--~~~l~~~g~i~~~~s~~~~~lLLllla~Gw-Ti~~~~ 129 (257)
T PF10192_consen 54 KKRGLMHPVYKLFSAALLLQF-LSLLLNLIHYIVYAYNGVG--IPFLKVLGQIFDILSQILFLLLLLLLAKGW-TITRSR 129 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHccCCC--chhHHHHHHHHHHHHHHHHHHHHHHHHccc-ccccCc
Confidence 335566677666555444433 333333333322 223322 34566666666666776655543 2 442 222333
Q ss_pred HH-----HHHHHHHHHHHHHHHHHHHHhhccccceeecCCCCCCccchhHHHHHHHHHHHHHHHHHhccccccccCCCCc
Q 021662 151 LA-----RTFIISGIIVGVDMLLKVIYVFGFGFPLFIDVDSTHRMKWGFWIIHELLLTAVYGFILFVHFSKWREKLPSRP 225 (309)
Q Consensus 151 l~-----Rtl~iS~lia~~d~l~kaiy~f~~gvplf~~~~~~~hgg~~FW~~ss~~f~lVY~~I~~LP~t~~rerLPar~ 225 (309)
++ .+..+..+.+.++.++...+....-.|.-..+++....|+..=...-+... | ++.....|.-.||=|.|+
T Consensus 130 ~s~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~d~~~~~~~y~s~pGy~li~lri~~~~--~-F~~~~~~t~~~~~~~~k~ 206 (257)
T PF10192_consen 130 LSQSNSVKLIVFIILYVVLQVILFIWENRFYFDPHSYLYFYDSWPGYILIALRIVLAI--W-FIYGLYQTISKEKDPEKR 206 (257)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHhccCCcccceeecccHHHHHHHHHHHHHHH--H-HHHHHHHHHHHhcCHHHH
Confidence 32 223333333334444432212222223222222222567766544433322 2 333445577778899999
Q ss_pred hhHHHHHHHHHHHHHHH
Q 021662 226 AFYHYVVVMFVVSAVAF 242 (309)
Q Consensus 226 SFY~Yv~iL~lLN~~q~ 242 (309)
.||.--++.+.+-.+..
T Consensus 207 ~Fy~~f~~~~~lWFl~~ 223 (257)
T PF10192_consen 207 KFYLPFGIIFSLWFLSL 223 (257)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99998887777666543
No 6
>PF03189 Otopetrin: Otopetrin; InterPro: IPR004878 The otopetrins are a group of proteins that are restricted to the metazoa. The structure of otopetrin-1 (Q80VM9 from SWISSPROT) shows it to have 12 transmembrane domains, with three conserved sub-domains (OD-1 to OD-III) []. Otopetrins modulate calcium homeostasis and influx of calcium in response to extracellular ATP. The otopetrins are required for normal formation of otoconia/otoliths in the inner ear. Otoconia are minute biomineral particles embedded in a gelatinous membrane that overlies the sensory epithelium in the inner ear. Gravity and acceleration cause the octoconia to deflect the stereocilia of sensory hair cells. Otoconia are required for normal processing of information regarding spatial orientation and acceleration.
Probab=59.39 E-value=1.4e+02 Score=30.41 Aligned_cols=190 Identities=10% Similarity=0.131 Sum_probs=107.6
Q ss_pred ccccccccce----ehhhHHHhhHHH-HHHHHHHhhhhhhhccccCCchHHHHHHHHHHHHHHHHHHHhHhhccc--c--
Q 021662 39 NESVRQCHGV----LYDAALVVPTVL-FVLYLVVHAKKNLTKLCNGRSYIMISYYALLWLACVLNLAWCSLQGWQ--C-- 109 (309)
Q Consensus 39 ~~w~~~c~g~----~wDv~LlvPn~L-FllFL~~~~~~s~~KL~~t~SpI~~tyY~ll~~v~llnl~rc~vsm~~--~-- 109 (309)
+.+=..|+|. .--+++++-.+. +.+|.+..-++ +.+..--.++-.+-..+..++++..+-|..||-. -
T Consensus 229 ~~~~vdc~~a~~Glf~Gil~lv~tii~lilf~v~~~~~---~~~~~A~~~~~i~~~~l~~l~~~a~i~g~~~~r~l~~~~ 305 (441)
T PF03189_consen 229 HHISVDCSGASKGLFLGILVLVATIIVLILFFVLINDP---EYSELAILLVYIFELVLYSLSILAVIIGIYRMRKLKFSS 305 (441)
T ss_pred CceeEEeCCcchhHHHHHHHHHHHHHHhehhhheecCC---chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Confidence 3355677765 444554444443 44455554332 2222223455666677788888888888888743 1
Q ss_pred cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccc--cceeecCCCC
Q 021662 110 SAGKEVAWNLLSLFTVAAVLYLEISLMAFLLQESYASGLETLARTFIISGIIVGVDMLLKVIYVFGFG--FPLFIDVDST 187 (309)
Q Consensus 110 t~~~~~~wniLwl~trf~lL~lEvSvvvFgl~g~~~~s~~sl~Rtl~iS~lia~~d~l~kaiy~f~~g--vplf~~~~~~ 187 (309)
...++.+|.+|=+..=+|....-+--++=+.. .+..+......++++++..++..+|..++.--- -+.-.++...
T Consensus 306 ~~~~~~LD~iLL~va~~G~~ly~~fsIia~~~---~~~~~~~~~l~l~~~ll~iiQv~~QtlFIl~a~rR~~~~~~~~~~ 382 (441)
T PF03189_consen 306 KNPGRSLDVILLVVAAFGEFLYSYFSIIAGIF---TDPHGSLNWLNLIYSLLRIIQVTLQTLFILDASRRRCSSEEQQRR 382 (441)
T ss_pred cCccccHhHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCcChHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccc
Confidence 23467889999888877766555433332222 222333566778999999999999998776321 1111111111
Q ss_pred CCcc--chhHHHHHHHHHHHHHHHHHhccccccccCCCCchhHHHHHHHHHHHH
Q 021662 188 HRMK--WGFWIIHELLLTAVYGFILFVHFSKWREKLPSRPAFYHYVVVMFVVSA 239 (309)
Q Consensus 188 ~hgg--~~FW~~ss~~f~lVY~~I~~LP~t~~rerLPar~SFY~Yv~iL~lLN~ 239 (309)
.-|| ..|-++..+.+.+++.+-. .|. +.-|-...||-+..=-.+.|.
T Consensus 383 kpgrq~itFLl~~N~~lw~~~tf~~----~~~-~~~~~~~~~yg~~~W~~i~~~ 431 (441)
T PF03189_consen 383 KPGRQIITFLLVCNISLWIINTFEA----KKA-GFNPVQIEFYGFWAWTIITHI 431 (441)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhc----ccc-cCChhHHHHhCccHHHHHHHH
Confidence 1122 3366666666666665533 222 346888888855444444443
No 7
>PF02937 COX6C: Cytochrome c oxidase subunit VIc; InterPro: IPR004204 Cytochrome c oxidase, a 13 subunit complex, 1.9.3.1 from EC is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG4_I 2DYS_V 3ASO_I 2EIK_V 2EIM_I 1OCC_V 1V54_V 1OCO_V 3ASN_V 2EIL_I ....
Probab=51.95 E-value=5 Score=31.79 Aligned_cols=25 Identities=36% Similarity=0.775 Sum_probs=15.5
Q ss_pred HHhhhcccccccchhhhhhhhccccCCC
Q 021662 279 LADFFQEENFLLDNAYYSEMKDAGFFDA 306 (309)
Q Consensus 279 LadFF~~e~~~~~~~yYSemkDag~fd~ 306 (309)
-+||+++=|+.-+ +.||+++|+|..
T Consensus 47 YadFYknYD~~k~---fe~M~~~G~fqS 71 (73)
T PF02937_consen 47 YADFYKNYDPMKD---FEEMRKAGIFQS 71 (73)
T ss_dssp HHHHHHT--HHHH---HHHHHHTT--SS
T ss_pred HHHHHHccChHHH---HHHHHhcCCccc
Confidence 3677877775544 789999999974
No 8
>PF00124 Photo_RC: Photosynthetic reaction centre protein; InterPro: IPR000484 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 describes the photosynthetic reaction centre L and M subunits, and the homologous D1 (PsbA) and D2 (PsbD) photosystem II (PSII) reaction centre proteins from cyanobacteria, algae and plants. The D1 and D2 proteins only show approximately 15% sequence homology with the L and M subunits, however the conserved amino acids correspond to the binding sites of the phytochemically active cofactors. As a result, the reaction centres (RCs) of purple photosynthetic bacteria and PSII display considerable structural similarity in terms of cofactor organisation. The D1 and D2 proteins occur as a heterodimer that form the reaction core of PSII, a multisubunit protein-pigment complex containing over forty different cofactors, which are anchored in the cell membrane in cyanobacteria, and in the thylakoid membrane in algae and plants. Upon absorption of light energy, the D1/D2 heterodimer undergoes charge separation, and the electrons are transferred from the primary donor (chlorophyll a) via pheophytin to the primary acceptor quinone Qa, then to the secondary acceptor Qb, which like the bacterial system, culminates in the production of ATP. However, PSII has an additional function over the bacterial system. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose [, ].; GO: 0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0009772 photosynthetic electron transport in photosystem II, 0019684 photosynthesis, light reaction; PDB: 2GMR_L 3A0B_D 3ARC_d 3A0H_d 1IZL_J 2AXT_A 1S5L_A 3KZI_A 3PRQ_A 4FBY_G ....
Probab=49.88 E-value=59 Score=31.56 Aligned_cols=78 Identities=18% Similarity=0.301 Sum_probs=57.7
Q ss_pred eeeeeeccceeeecCCCcccCCCCcccccCccccccccceehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHH
Q 021662 9 TINVTTASESFSVSLPPIAELPFPVKSIGGNESVRQCHGVLYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYY 88 (309)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~c~g~~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY 88 (309)
++++...+.++..++||+.| |=+|-.+-+--.+-++.+.+-+-++|+ | -..|-+|-.+|=
T Consensus 42 ~~al~PP~~~yGL~~~PL~e------------------GG~w~~~~f~~~~s~~~W~~R~~e~ar-~-LGmg~hva~AFs 101 (257)
T PF00124_consen 42 WLALEPPPPEYGLSFPPLWE------------------GGWWQIIGFFLTISFLSWWLRQYERAR-K-LGMGPHVAWAFS 101 (257)
T ss_dssp T-EBSSSSGGGTTSTSTGGG------------------THHHHHHHHHHHHHHHHHHHHHHHHHH-H-TTSTSHHHHHHH
T ss_pred EEeccCCCHHHccceeeccC------------------CceEEehhHHHHHHHHHHHHHHHHhhh-H-hcccchHhHHHH
Confidence 45666777777777888877 445666666666666666665555443 3 456669999999
Q ss_pred HHHHHHHHHHHHHhHhhc
Q 021662 89 ALLWLACVLNLAWCSLQG 106 (309)
Q Consensus 89 ~ll~~v~llnl~rc~vsm 106 (309)
+-+|+...+.++|=++|-
T Consensus 102 aaI~~~~~l~~irPi~mG 119 (257)
T PF00124_consen 102 AAIWAYLVLGFIRPILMG 119 (257)
T ss_dssp HHHHHHHHHHTHHHHHHT
T ss_pred HHHHHHHHHHhhcccccc
Confidence 999999999999999987
No 9
>PF10160 Tmemb_40: Predicted membrane protein; InterPro: IPR018781 This entry represents 280 amino acid region found in a group of proteins conserved from plants to humans. These are predicted to be membrane proteins, but apart from that their function is unknown.
Probab=48.86 E-value=94 Score=30.28 Aligned_cols=96 Identities=19% Similarity=0.125 Sum_probs=75.2
Q ss_pred ccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHh-hccccceeecCCCC
Q 021662 109 CSAGKEVAWNLLSLFTVAAVLYLEISLMAFLLQESYASGLETLARTFIISGIIVGVDMLLKVIYV-FGFGFPLFIDVDST 187 (309)
Q Consensus 109 ~t~~~~~~wniLwl~trf~lL~lEvSvvvFgl~g~~~~s~~sl~Rtl~iS~lia~~d~l~kaiy~-f~~gvplf~~~~~~ 187 (309)
.+..++++||++.++.=+.=+++=+-.+.||-..+..+=|..+.-|-+|+++-+.++.+++-.+. .-.-+-.+...++|
T Consensus 76 ~~~~d~~lW~ilrfflL~lEvSvvvFgL~fghlds~~Si~r~l~iT~~is~~~s~~Q~ilef~~~d~~l~~~~~~~~~hg 155 (261)
T PF10160_consen 76 GGIADKVLWNILRFFLLSLEVSVVVFGLQFGHLDSRSSIKRTLLITGLISLADSLTQAILEFGFGDVPLFIENFDLFGHG 155 (261)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHheeecCcccccCCCCCcCCcC
Confidence 34689999999999999999999999999999888888899999999999999999999998776 22223334444544
Q ss_pred CCccch-----hHHHHHHHHHH
Q 021662 188 HRMKWG-----FWIIHELLLTA 204 (309)
Q Consensus 188 ~hgg~~-----FW~~ss~~f~l 204 (309)
.++=|. |-.+...++.+
T Consensus 156 g~~fW~~~s~~f~~vY~~I~~L 177 (261)
T PF10160_consen 156 GWGFWFISSLVFALVYGFILIL 177 (261)
T ss_pred CeehHHHHHHHHHHHHHHHHHH
Confidence 466665 55555555554
No 10
>PF09586 YfhO: Bacterial membrane protein YfhO; InterPro: IPR018580 The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system []. Some members of this family have been annotated as putative ABC transporter permease proteins.
Probab=48.62 E-value=3.6e+02 Score=28.81 Aligned_cols=89 Identities=12% Similarity=0.252 Sum_probs=50.7
Q ss_pred eehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHHHHHHHHHHHHHHHhHhhcccccCchhHHHHHHHHHHHHH
Q 021662 48 VLYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYYALLWLACVLNLAWCSLQGWQCSAGKEVAWNLLSLFTVAA 127 (309)
Q Consensus 48 ~~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY~ll~~v~llnl~rc~vsm~~~t~~~~~~wniLwl~trf~ 127 (309)
++-|.++++|-++.-+=-+.|-||...=.-..---++.-| ...+..++..++..++... . ......++-++-+.-..
T Consensus 144 ~fld~~i~lPL~llgie~~~~~~k~~~~~~~~~l~~i~nf-Yf~ym~~if~~iY~~~r~~-~-~~~k~~~~~~~~~~~~~ 220 (843)
T PF09586_consen 144 MFLDAMILLPLLLLGIERLLKEKKWWLFIISLALALISNF-YFAYMICIFLVIYFLIRYF-F-KNWKNFFKKILRFIGSS 220 (843)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHHHH
Confidence 4679999999887766555554432111100000122223 3456677777777777664 2 33334445556666677
Q ss_pred HHHHHHHHHHHH
Q 021662 128 VLYLEISLMAFL 139 (309)
Q Consensus 128 lL~lEvSvvvFg 139 (309)
.+.+=+|.++++
T Consensus 221 ilg~~lsa~~ll 232 (843)
T PF09586_consen 221 ILGVGLSAFLLL 232 (843)
T ss_pred HHHHHHHHHHHH
Confidence 778888887764
No 11
>PLN00056 photosystem Q(B) protein; Provisional
Probab=47.69 E-value=43 Score=33.76 Aligned_cols=88 Identities=17% Similarity=0.109 Sum_probs=65.6
Q ss_pred eeeeeeccceeeecCCCcccCCCCcccccCccccccccceehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHH
Q 021662 9 TINVTTASESFSVSLPPIAELPFPVKSIGGNESVRQCHGVLYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYY 88 (309)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~c~g~~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY 88 (309)
++.+.+.+.+...++||+-|- ..-.+|+++. =+|..+-+--.+-++.+.+-+-..| |--..|-+|-.+|=
T Consensus 79 ~~av~PP~~~yGL~~~PLwea------~~~~ewl~~G--G~wqii~f~~~~s~~~W~~R~~e~a--r~LGMg~hia~AFs 148 (353)
T PLN00056 79 SGAIIPTSAAIGLHFYPIWEA------ASVDEWLYNG--GPYELIVLHFLLGVACYMGREWELS--FRLGMRPWIAVAYS 148 (353)
T ss_pred eEEecCCchhhccccCCcccc------ccchhhhhCC--CcHHHHHHHHHHHHHHHHHHHHHHH--HHhCCchhHhHHHH
Confidence 567778888889999999882 2334588764 3687776666666666666555544 33456669999999
Q ss_pred HHHHHHHHHHHHHhHhhc
Q 021662 89 ALLWLACVLNLAWCSLQG 106 (309)
Q Consensus 89 ~ll~~v~llnl~rc~vsm 106 (309)
.-+|+...+.++|=++|-
T Consensus 149 aaI~a~~~l~lIrPilmG 166 (353)
T PLN00056 149 APVAAATAVFLIYPIGQG 166 (353)
T ss_pred HHHHHHHHhheeeecccc
Confidence 999999999999999987
No 12
>PRK13825 conjugal transfer protein TraB; Provisional
Probab=44.89 E-value=50 Score=33.05 Aligned_cols=71 Identities=13% Similarity=0.215 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHhhccccceeecCCCCCCccchhHHHHHHHHHHHHHHHHHhccccccccCCCCchhHHHHHHHHH
Q 021662 157 ISGIIVGVDMLLKVIYVFGFGFPLFIDVDSTHRMKWGFWIIHELLLTAVYGFILFVHFSKWREKLPSRPAFYHYVVVMFV 236 (309)
Q Consensus 157 iS~lia~~d~l~kaiy~f~~gvplf~~~~~~~hgg~~FW~~ss~~f~lVY~~I~~LP~t~~rerLPar~SFY~Yv~iL~l 236 (309)
...++++.+-+. +....-+|+.-|..++. +-|+.+|..+|+.|++++... +++- ++++.+.+|++.+.+
T Consensus 48 ~a~~~~~~y~l~-~~~~~~~~~~~f~~~~~--~~g~~~w~~~~~~~~~~~~~~----~~~~----~~~~~~~r~~~~~~l 116 (388)
T PRK13825 48 AAALVSAGYFLA-ASRGLPQGVAAFFGSDL--WPGLALWLAASLSFVLVHAAL----WTAP----RGRARALRYLLAAVL 116 (388)
T ss_pred HHHHHHHHHHHH-HhccccchhhhhccchH--HHHHHHHHHHHHHHHHHHHhh----cccc----ccccHHHHHHHHHHH
Confidence 344455544444 23444455555554442 348899999999999988765 2211 567888999888776
Q ss_pred HH
Q 021662 237 VS 238 (309)
Q Consensus 237 LN 238 (309)
..
T Consensus 117 ~~ 118 (388)
T PRK13825 117 MA 118 (388)
T ss_pred Hh
Confidence 54
No 13
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=41.99 E-value=15 Score=22.00 Aligned_cols=31 Identities=16% Similarity=0.254 Sum_probs=26.7
Q ss_pred HHHHHHHhhhcccccccchhhhhhhhccccC
Q 021662 274 LYATFLADFFQEENFLLDNAYYSEMKDAGFF 304 (309)
Q Consensus 274 lY~TFLadFF~~e~~~~~~~yYSemkDag~f 304 (309)
.|-+.++.|-+..+++.-...|.+|+++|.-
T Consensus 2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~ 32 (35)
T TIGR00756 2 TYNTLIDGLCKAGRVEEALELFKEMLERGIE 32 (35)
T ss_pred cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence 3678889999999988888999999999864
No 14
>KOG4536 consensus Predicted membrane protein [Function unknown]
Probab=40.94 E-value=33 Score=34.16 Aligned_cols=79 Identities=18% Similarity=0.249 Sum_probs=46.1
Q ss_pred HHHHHHHHHHhhhhhhhccccCCchHHHHHHHHHHHHHHHHHHHhH-hhcccc-cCchhHHHHHHHHHHHHHHHHHHHHH
Q 021662 58 TVLFVLYLVVHAKKNLTKLCNGRSYIMISYYALLWLACVLNLAWCS-LQGWQC-SAGKEVAWNLLSLFTVAAVLYLEISL 135 (309)
Q Consensus 58 n~LFllFL~~~~~~s~~KL~~t~SpI~~tyY~ll~~v~llnl~rc~-vsm~~~-t~~~~~~wniLwl~trf~lL~lEvSv 135 (309)
-++|+++=+-+.++-+|-=|+-==--+--.--++-++.+.--+=.. +||+-. +-.+++.|||+-+|+..+++++|+|.
T Consensus 57 Fl~fL~~k~~s~~~Klr~~~SpI~iafy~lv~vvsLvniarc~~smt~s~t~g~e~~dkvlW~i~~fF~ls~el~~~v~g 136 (347)
T KOG4536|consen 57 FLAFLAYKAKSSLSKLRNRRSPIMIAFYGLVWVVSLVNIARCCLSMTWSCTPGKEVADKVLWNILTFFTLSGELFLEVSG 136 (347)
T ss_pred HHHHHHHhchhHHHHhhcCCChhHHHHHHHHHHHHHHHHHHHHHhceeeccCchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777655444433322222111122222233333333333333 677764 46889999999999999999999986
Q ss_pred H
Q 021662 136 M 136 (309)
Q Consensus 136 v 136 (309)
+
T Consensus 137 l 137 (347)
T KOG4536|consen 137 L 137 (347)
T ss_pred H
Confidence 4
No 15
>PF13041 PPR_2: PPR repeat family
Probab=40.44 E-value=18 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=27.7
Q ss_pred HHHHHHHhhhcccccccchhhhhhhhccccC
Q 021662 274 LYATFLADFFQEENFLLDNAYYSEMKDAGFF 304 (309)
Q Consensus 274 lY~TFLadFF~~e~~~~~~~yYSemkDag~f 304 (309)
.|-+.++.|.+..+++.-.-.|+||++.|.-
T Consensus 5 ~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~ 35 (50)
T PF13041_consen 5 TYNTLISGYCKAGKFEEALKLFKEMKKRGIK 35 (50)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHcCCC
Confidence 4788999999999999888999999999864
No 16
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=38.37 E-value=19 Score=21.46 Aligned_cols=30 Identities=17% Similarity=0.449 Sum_probs=25.8
Q ss_pred HHHHHHHhhhcccccccchhhhhhhhcccc
Q 021662 274 LYATFLADFFQEENFLLDNAYYSEMKDAGF 303 (309)
Q Consensus 274 lY~TFLadFF~~e~~~~~~~yYSemkDag~ 303 (309)
.|-+.++.|-+..+++.-..-|.||++.|+
T Consensus 2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 2 TYNSLISGYCKMGQFEEALEVFDEMRERGI 31 (31)
T ss_pred cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence 477888889999998888889999999885
No 17
>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=34.91 E-value=32 Score=28.94 Aligned_cols=13 Identities=23% Similarity=0.138 Sum_probs=6.8
Q ss_pred hhhccccCCchHH
Q 021662 72 NLTKLCNGRSYIM 84 (309)
Q Consensus 72 s~~KL~~t~SpI~ 84 (309)
++||.|.+..|+.
T Consensus 23 ~rRR~r~G~~P~~ 35 (130)
T PF12273_consen 23 NRRRRRRGLQPIY 35 (130)
T ss_pred HHHHhhcCCCCcC
Confidence 4444444666664
No 18
>TIGR00939 2a57 Equilibrative Nucleoside Transporter (ENT).
Probab=34.45 E-value=2.6e+02 Score=28.21 Aligned_cols=29 Identities=7% Similarity=0.060 Sum_probs=21.9
Q ss_pred CccchhHHHHHHHHHHHHHHHHHhccccc
Q 021662 189 RMKWGFWIIHELLLTAVYGFILFVHFSKW 217 (309)
Q Consensus 189 hgg~~FW~~ss~~f~lVY~~I~~LP~t~~ 217 (309)
++...|-.++.++-.+....-..+++.++
T Consensus 172 ~~a~~YF~~a~~v~l~~i~~~~~l~k~~~ 200 (437)
T TIGR00939 172 KSALGYFGTPCVVQLICIVCYLLLPKLPF 200 (437)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHhcCHH
Confidence 67888888888877777776667776655
No 19
>PF04235 DUF418: Protein of unknown function (DUF418); InterPro: IPR007349 Tihs is a probable integral membrane protein. It is usually found associated with (IPR007299 from INTERPRO).
Probab=29.50 E-value=2.5e+02 Score=23.82 Aligned_cols=138 Identities=14% Similarity=0.063 Sum_probs=73.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccceeecCC-CCCCccchhHHHHHHHHHHHHHHHHHhccccccccCC
Q 021662 144 YASGLETLARTFIISGIIVGVDMLLKVIYVFGFGFPLFIDVD-STHRMKWGFWIIHELLLTAVYGFILFVHFSKWREKLP 222 (309)
Q Consensus 144 ~~~s~~sl~Rtl~iS~lia~~d~l~kaiy~f~~gvplf~~~~-~~~hgg~~FW~~ss~~f~lVY~~I~~LP~t~~rerLP 222 (309)
-...+.-.+|++.++..++..-.+..+ ........+ ..++..-..-.+.....++.|..++++=..+-+.+
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~y~~l~~ll~~~~~~~-- 81 (163)
T PF04235_consen 10 PEEHRKLLRRLLLIGLAVGLPLALLSA------ASWLSAWPSPPAAHLSSVLYMLGGPLLALGYVALLILLCQKRPRQ-- 81 (163)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHH------HHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcc--
Confidence 344577888999988888775444433 001111111 11233444556677777888877665543222211
Q ss_pred CCchhHHHHHHHHHHH-HHHHHHHHhhhcCCcceeEE-echhhHHHHHh---hhHHHHHHHHHhhhcccccc
Q 021662 223 SRPAFYHYVVVMFVVS-AVAFLVVSLAGTGAAFGIWL-YNLTVICYHSL---YLPLLYATFLADFFQEENFL 289 (309)
Q Consensus 223 ar~SFY~Yv~iL~lLN-~~q~~Gs~Ll~~~~~~GlCl-vd~Tt~~Yfal---y~PLlY~TFLadFF~~e~~~ 289 (309)
.=-....+++=|++=| ..|++-+..+.++.+.|+-- .+.......+. -..++..+.-.++|+--|.|
T Consensus 82 ~~~~~l~~~GrmaLT~Yi~qsii~~~lf~~~~l~l~~~~~~~~~~~~~~~i~~~q~~~s~~W~~~f~~GPlE 153 (163)
T PF04235_consen 82 RLLRPLAAVGRMALTNYILQSIIGTLLFYGYGLGLFGHLSPAQSLLIALGIWVVQLLFSYLWLRRFRRGPLE 153 (163)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcHH
Confidence 0135566777777644 67888887777665555211 12222222221 22455566666777766643
No 20
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=26.68 E-value=39 Score=20.57 Aligned_cols=30 Identities=20% Similarity=0.280 Sum_probs=25.5
Q ss_pred HHHHHHHhhhcccccccchhhhhhhhcccc
Q 021662 274 LYATFLADFFQEENFLLDNAYYSEMKDAGF 303 (309)
Q Consensus 274 lY~TFLadFF~~e~~~~~~~yYSemkDag~ 303 (309)
.|-+.++-+.+..+++.-.-.+++|++.|.
T Consensus 3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 3 TYNALLRACAKAGDPDAALQLFDEMKEQGV 32 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence 367788889988888888899999999885
No 21
>TIGR01151 psbA photosystem II, DI subunit (also called Q(B)). This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemi
Probab=26.20 E-value=1.5e+02 Score=30.01 Aligned_cols=85 Identities=19% Similarity=0.125 Sum_probs=60.9
Q ss_pred eeeccceeeecCCCcccCCCCcccccCccccccccceehhhHHHhhHHHHHHHHHHhhhhhhhccccCCchHHHHHHHHH
Q 021662 12 VTTASESFSVSLPPIAELPFPVKSIGGNESVRQCHGVLYDAALVVPTVLFVLYLVVHAKKNLTKLCNGRSYIMISYYALL 91 (309)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~c~g~~wDv~LlvPn~LFllFL~~~~~~s~~KL~~t~SpI~~tyY~ll 91 (309)
|.+.+.+...++||+.|-. .-.+|+++. =+|..+-+--.+-++.+.+-+-.++ |--..|-+|-.+|=.-+
T Consensus 82 v~PP~~~yGL~~~PLwEa~------~~~ewL~~G--G~wqii~f~~~~sv~~W~~R~~e~A--r~LGMg~hia~AFsaaI 151 (360)
T TIGR01151 82 VVPSSNAIGLHFYPIWEAA------SLDEWLYNG--GPYQLIVFHFLLGVACYMGREWELS--YRLGMRPWICVAYSAPV 151 (360)
T ss_pred ecCCchhhccccCcccccc------cchhhhhcC--CCHHHHHHHHHHHHHHHHHHHHHHH--HHhCCchhHhHHHHHHH
Confidence 4455778888899988722 234588764 3677766655555555555554443 33456679999999999
Q ss_pred HHHHHHHHHHhHhhc
Q 021662 92 WLACVLNLAWCSLQG 106 (309)
Q Consensus 92 ~~v~llnl~rc~vsm 106 (309)
|+...+.++|=+.|-
T Consensus 152 ~a~~~l~lIrPilmG 166 (360)
T TIGR01151 152 AAATAVFLIYPIGQG 166 (360)
T ss_pred HHHHHhheeeecccc
Confidence 999999999999987
No 22
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=21.47 E-value=2e+02 Score=23.58 Aligned_cols=53 Identities=26% Similarity=0.369 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHHHHHHHH----hccccccccCCCCchhHHHHHHHHHHHHHHHHHHHhhh
Q 021662 194 FWIIHELLLTAVYGFILF----VHFSKWREKLPSRPAFYHYVVVMFVVSAVAFLVVSLAG 249 (309)
Q Consensus 194 FW~~ss~~f~lVY~~I~~----LP~t~~rerLPar~SFY~Yv~iL~lLN~~q~~Gs~Ll~ 249 (309)
=|+....+++++|..... +|..++++-+|.=| .|..+++-...+..+|=++.-
T Consensus 6 ~~l~~~~~l~~~w~~l~~~~~~~~~~~~~~ii~~lP---~~~Lv~fG~Ysl~~lgy~v~t 62 (91)
T PF08285_consen 6 QWLSALLLLSALWLALLLGLLPLPPEPQQEIIPYLP---FYALVSFGCYSLFTLGYGVAT 62 (91)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCchhHHHHHHHhh---HHHHHHHHHHHHHHHHHhhhc
Confidence 377888888888888776 55556777654444 588888888888887766654
No 23
>PF10271 Tmp39: Putative transmembrane protein; InterPro: IPR019397 This is a family of putative, eukaryote, transmembrane proteins but the function is unknown.
Probab=20.97 E-value=6.4e+02 Score=26.20 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=17.0
Q ss_pred CCcccCCCCcccccCcccccccccee
Q 021662 24 PPIAELPFPVKSIGGNESVRQCHGVL 49 (309)
Q Consensus 24 ~~~~~~~~~~~~~~~~~w~~~c~g~~ 49 (309)
||....|+|.+... +++++||.=+.
T Consensus 17 ~~~kH~~~P~lp~~-~~l~FE~~~f~ 41 (423)
T PF10271_consen 17 PPPKHIPIPELPVD-GELLFELLLFF 41 (423)
T ss_pred CCCCCCCCCCCCCc-chHHHHHHHHH
Confidence 34445567777777 78999996553
No 24
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.24 E-value=4.3e+02 Score=22.15 Aligned_cols=14 Identities=14% Similarity=0.235 Sum_probs=10.5
Q ss_pred cccCcc-ccccccce
Q 021662 35 SIGGNE-SVRQCHGV 48 (309)
Q Consensus 35 ~~~~~~-w~~~c~g~ 48 (309)
--.|+| |++.|.|.
T Consensus 74 ~~DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 74 RFDHHCPWLGNCIGR 88 (174)
T ss_pred cccccchhhcccccc
Confidence 345666 99999985
Done!