Query psy12548
Match_columns 151
No_of_seqs 129 out of 954
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 22:09:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12548hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3071|consensus 100.0 4.8E-33 1E-37 231.4 7.7 116 1-116 150-268 (274)
2 PF01151 ELO: GNS1/SUR4 family 100.0 6.4E-32 1.4E-36 221.3 8.8 112 1-114 129-250 (250)
3 PTZ00251 fatty acid elongase; 100.0 8.2E-29 1.8E-33 206.2 6.8 111 1-114 150-270 (272)
4 KOG3072|consensus 99.9 3.3E-23 7.2E-28 172.4 6.6 105 3-110 159-269 (282)
5 KOG3071|consensus 74.6 3 6.4E-05 35.4 2.9 75 48-122 193-270 (274)
6 COG4858 Uncharacterized membra 34.7 1.1E+02 0.0025 25.0 5.4 25 30-54 140-166 (226)
7 PRK00753 psbL photosystem II r 33.7 58 0.0013 19.6 2.7 24 80-103 15-38 (39)
8 CHL00038 psbL photosystem II p 32.4 77 0.0017 19.1 3.0 24 80-103 14-37 (38)
9 KOG3187|consensus 28.7 1.1E+02 0.0024 25.2 4.5 37 18-55 106-142 (223)
10 PF12643 MazG-like: MazG-like 27.6 90 0.002 22.3 3.4 27 19-45 34-60 (98)
11 PF02419 PsbL: PsbL protein; 27.6 1.3E+02 0.0027 18.1 3.4 24 81-104 14-37 (37)
12 KOG3030|consensus 26.8 4.2E+02 0.009 22.9 9.5 55 12-79 181-236 (317)
13 PF01102 Glycophorin_A: Glycop 25.1 1.2E+02 0.0027 22.6 3.8 27 84-110 69-95 (122)
14 PF11030 Nucleocapsid-N: Nucle 23.7 43 0.00092 25.7 1.1 18 132-149 138-155 (167)
15 PTZ00046 rifin; Provisional 22.5 52 0.0011 29.0 1.6 20 85-111 326-345 (358)
16 TIGR01477 RIFIN variant surfac 21.3 57 0.0012 28.7 1.6 19 86-111 322-340 (353)
No 1
>KOG3071|consensus
Probab=99.98 E-value=4.8e-33 Score=231.44 Aligned_cols=116 Identities=46% Similarity=0.772 Sum_probs=106.8
Q ss_pred CceEEEeeEEEccCcchhhHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhhhhhhhhhhhhhheeee-ecc-cCC
Q psy12548 1 MPMVSWGAAKYYPGGHGTFIGTINSFVHVIMYTYYALAALGDQWQKYLWWKKYITTLQLLQFCIAFIHSSQL-LFT-DCG 78 (151)
Q Consensus 1 m~~~~W~~~~~~~~g~~~~~~~lNs~VHviMY~YY~lsa~g~~~~~~l~wK~~IT~lQivQF~i~~~~~~~~-~~~-~C~ 78 (151)
|++++|..+++.++|+..+.+.+|++||+|||+||+++|+||++++++|||+++|.+|++||++..+|..+. ++. ||.
T Consensus 150 m~~~~~~~l~~~~~g~~~~~~~lNs~VHviMY~YYflsa~G~~v~~~lWWkky~t~vQlvqf~~~~~~~~~~~~~~~~c~ 229 (274)
T KOG3071|consen 150 MAFLSYLWLKFYGGGHGFFAILLNSFVHVIMYGYYFLSAFGPRVQWYLWWKKYITIVQLVQFLILFVHTLYVHLFKPGCC 229 (274)
T ss_pred HHHhhhheeEEeCCceeeeeeehhhhHHHHHHHHHHHHhhCcCccccchHHHHHHHHHHHHHHHHHHHHhheeeecCCCC
Confidence 678999999999999999999999999999999999999999999999999999999999999999999887 664 899
Q ss_pred CChH-HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy12548 79 YPRW-SVYFTLPNAIFFYYLFSDFYNKAYGSSTPKGKGK 116 (151)
Q Consensus 79 ~~~~-~~~~~~~~~~s~l~LF~~Fy~~sY~k~~~~~~~k 116 (151)
+|.+ ....+..+..+|++||.|||+++|.|++++++++
T Consensus 230 ~~~~~~~~~~~~~~~~~l~LF~nFY~~tY~k~~~~~~~~ 268 (274)
T KOG3071|consen 230 FGIGAWAFNGSVINVSFLLLFSNFYIKTYKKPKKKKAKK 268 (274)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchhh
Confidence 9998 6667688999999999999999999876665555
No 2
>PF01151 ELO: GNS1/SUR4 family; InterPro: IPR002076 This group of eukaryotic integral membrane proteins are evolutionary related, but exact function has not yet clearly been established. The proteins have from 290 to 435 amino acid residues. Structurally, they seem to be formed of three sections: a N-terminal region with two transmembrane domains, a central hydrophilic loop and a C-terminal region that contains from one to three transmembrane domains. Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis []. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 (P40319 from SWISSPROT) affects plasma membrane H+-ATPase activity, and may act on a glucose-signalling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1 []. ; GO: 0016021 integral to membrane
Probab=99.97 E-value=6.4e-32 Score=221.28 Aligned_cols=112 Identities=46% Similarity=0.879 Sum_probs=101.4
Q ss_pred CceEEEeeEEEccCcchhhHHHHHHHHHHHHHHHHHHHhcCCc-chhhhhhhhhhhhhhhhhhhhhhhheeeeecc----
Q psy12548 1 MPMVSWGAAKYYPGGHGTFIGTINSFVHVIMYTYYALAALGDQ-WQKYLWWKKYITTLQLLQFCIAFIHSSQLLFT---- 75 (151)
Q Consensus 1 m~~~~W~~~~~~~~g~~~~~~~lNs~VHviMY~YY~lsa~g~~-~~~~l~wK~~IT~lQivQF~i~~~~~~~~~~~---- 75 (151)
|++.+|..+++.++|+.++.+++|++||++||+||+++|+|.| .| .||||+||.+||+||++++++....++.
T Consensus 129 ~~~~~w~~~~~~~~~~~~~~~~~N~~VH~iMY~YY~l~a~g~~~~~--~~~k~~IT~~Qi~QF~~~~~~~~~~~~~~~~~ 206 (250)
T PF01151_consen 129 TLLYCWISYKYGPGGQIWFIAALNSFVHVIMYSYYFLSALGIRKVP--RWWKKYITSLQIVQFVIGIVHTVYALYYYFFP 206 (250)
T ss_pred hhhhhhheeeeccccchhHHHHHHHHHHHHHHHHHHHHhcccccch--hHHHHHHhHHhhhhhHHHHHHHHHHhheeccC
Confidence 4678999999999999999999999999999999999999976 33 5999999999999999999988777665
Q ss_pred --cC---CCChHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCC
Q psy12548 76 --DC---GYPRWSVYFTLPNAIFFYYLFSDFYNKAYGSSTPKGK 114 (151)
Q Consensus 76 --~C---~~~~~~~~~~~~~~~s~l~LF~~Fy~~sY~k~~~~~~ 114 (151)
+| ++|.....++..+++++++||.|||+++|.+++++||
T Consensus 207 ~~~C~~~~~~~~~~~~~~~~~~s~l~LF~~Fy~~~Y~~~~~~k~ 250 (250)
T PF01151_consen 207 GGDCDTSGYPKFNAILGLVYYVSYLYLFINFYIKSYIKKKKKKK 250 (250)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCC
Confidence 79 6778889999999999999999999999999877765
No 3
>PTZ00251 fatty acid elongase; Provisional
Probab=99.95 E-value=8.2e-29 Score=206.18 Aligned_cols=111 Identities=27% Similarity=0.371 Sum_probs=88.1
Q ss_pred CceEEEeeEEEccCcchhh-HHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhhhhhhhhhhhhhheeeeec-----
Q psy12548 1 MPMVSWGAAKYYPGGHGTF-IGTINSFVHVIMYTYYALAALGDQWQKYLWWKKYITTLQLLQFCIAFIHSSQLLF----- 74 (151)
Q Consensus 1 m~~~~W~~~~~~~~g~~~~-~~~lNs~VHviMY~YY~lsa~g~~~~~~l~wK~~IT~lQivQF~i~~~~~~~~~~----- 74 (151)
|++.+|..+ .++++..+ ++++|++||++||+||+++|+|++.+ .-||||+||.+||+||+++++|....++
T Consensus 150 ~~~~~w~~~--~~g~~~~~~~~~lNs~VH~iMY~YY~lsa~g~~~~-~~~~kk~IT~lQi~Qfv~~~~~~~~~~~~~~~~ 226 (272)
T PTZ00251 150 IFLYAWMSY--QQGSSIWICAAAMNYFVHSIMYFYFALSEAGFKKL-VKPFAMYITLLQITQMVGGLFVSGYVIVQKLTK 226 (272)
T ss_pred HHHHHHHHH--hCCCcHHHHHHHHHHHHHHHHHHHHHHHhcCCchh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 345677765 34444443 59999999999999999999999732 1259999999999999999988766553
Q ss_pred ---ccCCCCh-HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCC
Q psy12548 75 ---TDCGYPR-WSVYFTLPNAIFFYYLFSDFYNKAYGSSTPKGK 114 (151)
Q Consensus 75 ---~~C~~~~-~~~~~~~~~~~s~l~LF~~Fy~~sY~k~~~~~~ 114 (151)
.+|+++. ........++++|++||.|||+++|+++|++++
T Consensus 227 ~~~~~C~~~~~~~~~~~~~~~~s~l~LF~~Fy~~~Y~~~~~~~~ 270 (272)
T PTZ00251 227 GDPKGCSGTTMATARGQLMIYIFNFYLFSEMFVKGYVLPRKAKA 270 (272)
T ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Confidence 2598877 666777789999999999999999998755543
No 4
>KOG3072|consensus
Probab=99.88 E-value=3.3e-23 Score=172.36 Aligned_cols=105 Identities=27% Similarity=0.430 Sum_probs=88.6
Q ss_pred eEEEeeEEEccCcchhhHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhhhhhhhhhhhhhheeeeec------cc
Q psy12548 3 MVSWGAAKYYPGGHGTFIGTINSFVHVIMYTYYALAALGDQWQKYLWWKKYITTLQLLQFCIAFIHSSQLLF------TD 76 (151)
Q Consensus 3 ~~~W~~~~~~~~g~~~~~~~lNs~VHviMY~YY~lsa~g~~~~~~l~wK~~IT~lQivQF~i~~~~~~~~~~------~~ 76 (151)
+..|.++.-.. +.++|++.+|.+||++||+||+++|+|+|+|+ +..+.||.+||+||++++........ .+
T Consensus 159 iy~~~~y~~~~-a~~rw~i~mNy~vHa~MY~YY~lrsl~ir~Pk--~vam~iTtlQi~Qm~i~~~i~~~v~~~~~~~~~~ 235 (282)
T KOG3072|consen 159 IYAWHSYIEKV-AWGRWFIWMNYLVHAFMYSYYALRSLGIRLPK--SVAMAITTLQIVQMVIGCYIGTHVYYVKHTHQLL 235 (282)
T ss_pred eeeeeecccCC-cCceEEEEEehhHHHHHHHHHHHHHcCCCCCh--HHHHHHHHHHHHHHHHHHheeeEEEEEEecCCee
Confidence 45666666543 34689999999999999999999999999997 56999999999999999864443322 13
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy12548 77 CGYPRWSVYFTLPNAIFFYYLFSDFYNKAYGSST 110 (151)
Q Consensus 77 C~~~~~~~~~~~~~~~s~l~LF~~Fy~~sY~k~~ 110 (151)
|+.+..+..++.+++++|++||.|||+++|+++.
T Consensus 236 c~~s~~~~~l~~~my~syfvLf~~Ff~~aYi~~g 269 (282)
T KOG3072|consen 236 CQQSYKNLSLCFLMYISYFVLFANFFYQAYIKKG 269 (282)
T ss_pred eeeeccchhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9998888999999999999999999999999985
No 5
>KOG3071|consensus
Probab=74.60 E-value=3 Score=35.35 Aligned_cols=75 Identities=17% Similarity=0.169 Sum_probs=49.5
Q ss_pred hhhhh-hhhhhhhhhhhhhhhheeeeecccCCCC--hHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCcccc
Q psy12548 48 LWWKK-YITTLQLLQFCIAFIHSSQLLFTDCGYP--RWSVYFTLPNAIFFYYLFSDFYNKAYGSSTPKGKGKDGKEVA 122 (151)
Q Consensus 48 l~wK~-~IT~lQivQF~i~~~~~~~~~~~~C~~~--~~~~~~~~~~~~s~l~LF~~Fy~~sY~k~~~~~~~k~~~~~~ 122 (151)
.+|+. +-|-+|++||+..++...+.....--.| .............+.+.|.--|.+=|.+.=+|+++++.|+.+
T Consensus 193 v~~~lWWkky~t~vQlvqf~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~l~LF~nFY~~tY~k~~~~~~~~~~ 270 (274)
T KOG3071|consen 193 VQWYLWWKKYITIVQLVQFLILFVHTLYVHLFKPGCCFGIGAWAFNGSVINVSFLLLFSNFYIKTYKKPKKKKAKKKA 270 (274)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHhheeeecCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchhhhh
Confidence 47888 8999999999998876443222211122 232232344557889999999999999987776666444433
No 6
>COG4858 Uncharacterized membrane-bound protein conserved in bacteria [Function unknown]
Probab=34.67 E-value=1.1e+02 Score=24.96 Aligned_cols=25 Identities=36% Similarity=0.521 Sum_probs=12.7
Q ss_pred HHH--HHHHHHhcCCcchhhhhhhhhh
Q psy12548 30 IMY--TYYALAALGDQWQKYLWWKKYI 54 (151)
Q Consensus 30 iMY--~YY~lsa~g~~~~~~l~wK~~I 54 (151)
.|| .||+-+-.|-+-++.-|||-.+
T Consensus 140 amy~my~y~yr~~ad~sqr~~~~K~~l 166 (226)
T COG4858 140 AMYIMYYYAYRMRADNSQRPGTWKYLL 166 (226)
T ss_pred HHHHHHHHHHHhhcccccCCchHHHHH
Confidence 355 3455555554444444677443
No 7
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=33.72 E-value=58 Score=19.64 Aligned_cols=24 Identities=29% Similarity=0.431 Sum_probs=19.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHH
Q psy12548 80 PRWSVYFTLPNAIFFYYLFSDFYN 103 (151)
Q Consensus 80 ~~~~~~~~~~~~~s~l~LF~~Fy~ 103 (151)
.+..++++.+..+...+||.++|.
T Consensus 15 NRTSLy~GlLlifvl~vLFssYff 38 (39)
T PRK00753 15 NRTSLYLGLLLVFVLGILFSSYFF 38 (39)
T ss_pred chhhHHHHHHHHHHHHHHHHhhcc
Confidence 466678888888899999999874
No 8
>CHL00038 psbL photosystem II protein L
Probab=32.36 E-value=77 Score=19.06 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=19.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHH
Q psy12548 80 PRWSVYFTLPNAIFFYYLFSDFYN 103 (151)
Q Consensus 80 ~~~~~~~~~~~~~s~l~LF~~Fy~ 103 (151)
.+..++++.+......+||.++|.
T Consensus 14 NRTSLy~GLLlifvl~vlfssyff 37 (38)
T CHL00038 14 NRTSLYWGLLLIFVLAVLFSNYFF 37 (38)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhc
Confidence 456678888888889999999875
No 9
>KOG3187|consensus
Probab=28.70 E-value=1.1e+02 Score=25.22 Aligned_cols=37 Identities=32% Similarity=0.582 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhh
Q psy12548 18 TFIGTINSFVHVIMYTYYALAALGDQWQKYLWWKKYIT 55 (151)
Q Consensus 18 ~~~~~lNs~VHviMY~YY~lsa~g~~~~~~l~wK~~IT 55 (151)
.....+=+..-.+=|+||+++.++- .|+.+.|-||=+
T Consensus 106 ~~l~~~ws~tEIiRY~fY~f~~~~~-~p~~l~wlRYt~ 142 (223)
T KOG3187|consen 106 FFLLIAWSLTEIIRYSFYAFNLLGV-LPKLLTWLRYTL 142 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CchhhhHhhhhh
Confidence 3444566788888999999999987 667677777744
No 10
>PF12643 MazG-like: MazG-like family
Probab=27.60 E-value=90 Score=22.30 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhcCCcch
Q psy12548 19 FIGTINSFVHVIMYTYYALAALGDQWQ 45 (151)
Q Consensus 19 ~~~~lNs~VHviMY~YY~lsa~g~~~~ 45 (151)
--.+.+.+.++++|+|-+...+|..+.
T Consensus 34 ~e~i~deLAdvii~~ylLa~rLGid~~ 60 (98)
T PF12643_consen 34 QEAIKDELADVIIYCYLLADRLGIDFR 60 (98)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCHH
Confidence 357889999999999999999999843
No 11
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 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 PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=27.58 E-value=1.3e+02 Score=18.06 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHh
Q psy12548 81 RWSVYFTLPNAIFFYYLFSDFYNK 104 (151)
Q Consensus 81 ~~~~~~~~~~~~s~l~LF~~Fy~~ 104 (151)
+..++++.+..+..-+||.+++.+
T Consensus 14 RTSLY~GLllifvl~vLFssyffN 37 (37)
T PF02419_consen 14 RTSLYWGLLLIFVLAVLFSSYFFN 37 (37)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHhHHHHHHHHHHHHHHhhhhhcC
Confidence 445778888888889999998753
No 12
>KOG3030|consensus
Probab=26.82 E-value=4.2e+02 Score=22.90 Aligned_cols=55 Identities=24% Similarity=0.169 Sum_probs=28.6
Q ss_pred ccCcchhhHHHHHHHHHHHHHHH-HHHHhcCCcchhhhhhhhhhhhhhhhhhhhhhhheeeeecccCCC
Q psy12548 12 YPGGHGTFIGTINSFVHVIMYTY-YALAALGDQWQKYLWWKKYITTLQLLQFCIAFIHSSQLLFTDCGY 79 (151)
Q Consensus 12 ~~~g~~~~~~~lNs~VHviMY~Y-Y~lsa~g~~~~~~l~wK~~IT~lQivQF~i~~~~~~~~~~~~C~~ 79 (151)
.|+||+.+ ......|.+ |..+.+..+. +--+.--++||...++.....+-.=|++
T Consensus 181 FPSGHsS~------s~y~~~flalyl~~~~~~~~-------~~rllr~~l~f~~l~~A~~v~lSRV~DY 236 (317)
T KOG3030|consen 181 FPSGHSSF------SFYAMGFLALYLQARLFWFG-------RGRLLRPLLQFLPLMLALLVGLSRVSDY 236 (317)
T ss_pred CCCccHHH------HHHHHHHHHHHHHHHHhcCC-------CchhHHHHHHHHHHHHHHHHeeehhccc
Confidence 36777763 345667766 5555554432 1223334567776665443333333556
No 13
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=25.13 E-value=1.2e+02 Score=22.58 Aligned_cols=27 Identities=7% Similarity=0.183 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy12548 84 VYFTLPNAIFFYYLFSDFYNKAYGSST 110 (151)
Q Consensus 84 ~~~~~~~~~s~l~LF~~Fy~~sY~k~~ 110 (151)
+.++.+-++..++||.-|..++-+||.
T Consensus 69 Ii~gv~aGvIg~Illi~y~irR~~Kk~ 95 (122)
T PF01102_consen 69 IIFGVMAGVIGIILLISYCIRRLRKKS 95 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHS---
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 455666667778889999998776553
No 14
>PF11030 Nucleocapsid-N: Nucleocapsid protein N ; InterPro: IPR020253 This entry represents the nucleocapsid protein from bovine, porcine and equine toroviruses. It is the major structural component of virions associating with the virion genomic RNA.
Probab=23.73 E-value=43 Score=25.71 Aligned_cols=18 Identities=33% Similarity=0.650 Sum_probs=15.5
Q ss_pred ccCCCCeeecCCcccccc
Q psy12548 132 MNGHNGVALSNGKMETAK 149 (151)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~ 149 (151)
++||+.+++|+|.+||-+
T Consensus 138 vsghatveis~g~eds~~ 155 (167)
T PF11030_consen 138 VSGHATVEISNGTEDSNH 155 (167)
T ss_pred hccceEEEecCCCCCCCc
Confidence 488999999999999865
No 15
>PTZ00046 rifin; Provisional
Probab=22.48 E-value=52 Score=28.99 Aligned_cols=20 Identities=20% Similarity=0.305 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12548 85 YFTLPNAIFFYYLFSDFYNKAYGSSTP 111 (151)
Q Consensus 85 ~~~~~~~~s~l~LF~~Fy~~sY~k~~~ 111 (151)
.+.+++.+.||+| +|+|+|+
T Consensus 326 VIVLIMvIIYLIL-------RYRRKKK 345 (358)
T PTZ00046 326 VIVLIMVIIYLIL-------RYRRKKK 345 (358)
T ss_pred HHHHHHHHHHHHH-------Hhhhcch
Confidence 3344466666666 7876644
No 16
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=21.26 E-value=57 Score=28.72 Aligned_cols=19 Identities=21% Similarity=0.340 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCC
Q psy12548 86 FTLPNAIFFYYLFSDFYNKAYGSSTP 111 (151)
Q Consensus 86 ~~~~~~~s~l~LF~~Fy~~sY~k~~~ 111 (151)
+.+++.+.||+| +|+|||+
T Consensus 322 IVLIMvIIYLIL-------RYRRKKK 340 (353)
T TIGR01477 322 IVLIMVIIYLIL-------RYRRKKK 340 (353)
T ss_pred HHHHHHHHHHHH-------Hhhhcch
Confidence 334456666666 7876643
Done!