Query 032691
Match_columns 135
No_of_seqs 44 out of 46
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 04:43:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00092 photosystem I reactio 100.0 2.2E-65 4.7E-70 392.2 9.3 135 1-135 1-137 (137)
2 PF07123 PsbW: Photosystem II 100.0 6.1E-60 1.3E-64 362.6 9.1 135 1-135 1-138 (138)
3 PLN00077 photosystem II reacti 100.0 6.2E-58 1.3E-62 348.1 8.4 125 1-135 1-128 (128)
4 PLN00082 photosystem II reacti 100.0 2.3E-39 5E-44 224.8 4.1 64 72-135 3-67 (67)
5 PRK07352 F0F1 ATP synthase sub 78.5 2.3 4.9E-05 32.3 2.9 33 93-125 12-44 (174)
6 PRK14472 F0F1 ATP synthase sub 62.8 6.2 0.00014 30.0 2.2 32 93-124 11-42 (175)
7 PRK13453 F0F1 ATP synthase sub 62.2 5.3 0.00011 30.6 1.7 32 93-124 11-42 (173)
8 CHL00019 atpF ATP synthase CF0 59.2 9.7 0.00021 29.2 2.7 31 95-125 19-49 (184)
9 PLN00090 photosystem II reacti 41.8 49 0.0011 25.5 4.0 57 73-133 48-110 (113)
10 PRK13455 F0F1 ATP synthase sub 39.0 59 0.0013 24.9 4.2 37 74-120 10-46 (184)
11 PRK06654 fliL flagellar basal 38.2 43 0.00092 27.3 3.4 30 90-119 17-50 (181)
12 PF01679 Pmp3: Proteolipid mem 37.6 15 0.00033 24.1 0.7 22 101-122 30-51 (51)
13 PF15168 TRIQK: Triple QxxK/R 36.5 38 0.00082 24.8 2.6 25 101-125 49-73 (79)
14 PRK13460 F0F1 ATP synthase sub 35.3 29 0.00063 26.3 2.0 29 96-124 12-40 (173)
15 PF14373 Imm_superinfect: Supe 31.6 35 0.00076 22.0 1.6 20 98-117 22-42 (43)
16 COG3376 HoxN High-affinity nic 30.4 54 0.0012 29.4 3.1 43 77-119 289-333 (342)
17 PF11862 DUF3382: Domain of un 28.0 70 0.0015 22.8 2.8 47 66-115 9-55 (101)
18 PRK11689 aromatic amino acid e 27.0 90 0.0019 24.9 3.6 29 101-129 154-182 (295)
19 PF13829 DUF4191: Domain of un 24.5 73 0.0016 26.8 2.7 22 99-120 23-44 (224)
20 PRK13454 F0F1 ATP synthase sub 24.5 68 0.0015 24.9 2.4 20 101-120 32-51 (181)
21 PRK07352 F0F1 ATP synthase sub 24.2 64 0.0014 24.4 2.2 37 89-125 12-48 (174)
22 PF02468 PsbN: Photosystem II 24.1 73 0.0016 20.8 2.1 16 104-121 12-27 (43)
23 COG4499 Predicted membrane pro 21.8 83 0.0018 29.1 2.7 22 103-124 225-246 (434)
24 PF14017 DUF4233: Protein of u 21.0 44 0.00096 24.7 0.7 26 106-131 81-106 (107)
25 COG4567 Response regulator con 20.9 44 0.00095 27.7 0.7 23 72-95 48-70 (182)
26 KOG0475 Cl- channel CLC-3 and 20.9 75 0.0016 30.9 2.3 22 101-122 308-329 (696)
27 PF07297 DPM2: Dolichol phosph 20.3 1.1E+02 0.0023 22.0 2.5 26 99-124 2-27 (78)
28 PF00662 Oxidored_q1_N: NADH-U 20.3 75 0.0016 20.4 1.6 41 85-125 6-46 (62)
29 PF01252 Peptidase_A8: Signal 20.1 1.3E+02 0.0027 22.6 3.0 36 88-123 37-78 (150)
No 1
>PLN00092 photosystem I reaction center subunit V (PsaG); Provisional
Probab=100.00 E-value=2.2e-65 Score=392.16 Aligned_cols=135 Identities=78% Similarity=1.191 Sum_probs=130.1
Q ss_pred CceeeccccccceecceecccCcccccCCCccCccccc-ccceeeeeeccCCCccccccccchhHHHHHHHHHhccc-cc
Q 032691 1 MAAITASVGTSSITRSVLVHKPSIVASSSPVLGLPAMA-VKGKVRCSMEEKPSKQESKTNVGMSASLLAAACAATMS-SP 78 (135)
Q Consensus 1 Mati~a~~~t~s~~ra~~~~~~~~~~ss~pv~GLP~m~-~~~~vrCs~~~K~~~~~~~~~~g~~asl~Aaa~aa~~a-~P 78 (135)
||||+|+++|++++|++++||+++++|++||+|||+|+ |+|||||++|+||+.+++..++||+|+++|++++++++ +|
T Consensus 1 MAtitas~~t~~~~ra~~~~k~~~~~s~~~vlGLPam~~~~g~v~Cs~e~k~~~~~~~~~~g~~asl~Aaa~a~a~~a~P 80 (137)
T PLN00092 1 MATITASTPTTSLVRAALVHKPSVGITSSPVLGLPAMAKKKGRVRCSMEEKPSVQDKSSNMGMGASLMAAACAVAMSASP 80 (137)
T ss_pred CceEeccCccccchhhhhcccCCcccccCcccCCchhcccCceeEEecccCccccccccccchhHHHHHHHHHHHhhcCc
Confidence 99999999999999999999999999999999999999 57999999999999988899999999999999775555 99
Q ss_pred chhhhhhcccCCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcCCCCCCCCCCC
Q 032691 79 AMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSLDEDEESGLSL 135 (135)
Q Consensus 79 A~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l~edddSGLsL 135 (135)
|||||||||||||||||||||||+|||||+|||+|||++||+|+++++|||||||||
T Consensus 81 A~AlVDeRlsteGTGlplGlsn~~LgwIL~gVf~lIWslYf~~~~~l~edeDSGLsL 137 (137)
T PLN00092 81 AMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWSLYFVYTSTLEEDEESGLSL 137 (137)
T ss_pred HHHHHHHhhcCCCccccccccCcchhhHHHhHHHHHHHHHheeecccCccccccccC
Confidence 999999999999999999999999999999999999999999999999999999997
No 2
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 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 PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=100.00 E-value=6.1e-60 Score=362.57 Aligned_cols=135 Identities=67% Similarity=1.022 Sum_probs=127.4
Q ss_pred Cceeecccc-ccceecceecccCcccccCCCccCcccccccceeeeeeccCCCccccc-cccchhHHHHHHHHH-hcccc
Q 032691 1 MAAITASVG-TSSITRSVLVHKPSIVASSSPVLGLPAMAVKGKVRCSMEEKPSKQESK-TNVGMSASLLAAACA-ATMSS 77 (135)
Q Consensus 1 Mati~a~~~-t~s~~ra~~~~~~~~~~ss~pv~GLP~m~~~~~vrCs~~~K~~~~~~~-~~~g~~asl~Aaa~a-a~~a~ 77 (135)
||+|++++. |+++.|+...+++.....++|++|||+|++|.||+|++|+|+++++.. .++||++++++++++ +++++
T Consensus 1 MAti~a~~~~t~~~~ra~~~~~~~~~~~~~~~~glp~~~~r~~v~cs~~~~~~~~~~~~~~~~~~a~~~aa~~a~~a~a~ 80 (138)
T PF07123_consen 1 MATIAASASVTSVVARALLRSSSSAAASSSPVLGLPAMRARRRVRCSAEKKPSTVAAVNSQKGMGAALLAAAAATAATAS 80 (138)
T ss_pred CceeeecccchhhhhhhhhccCcccceecccccCCCccccccceEEEeccCccchhhhhhhcchhHHHHHHHHHHHhhcC
Confidence 999999998 999999999999989999999999999999999999999999876554 788999999998866 67799
Q ss_pred cchhhhhhcccCCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcCCCCCCCCCCC
Q 032691 78 PAMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSLDEDEESGLSL 135 (135)
Q Consensus 78 PA~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l~edddSGLsL 135 (135)
||||||||||||||||||||||||+|||||+|||+|||+|||+|+|+|+|||||||||
T Consensus 81 PA~ALVDeRlsteGTGL~lGlsn~~LgwIL~gVf~lIWslY~~~~~~l~ededSGLsL 138 (138)
T PF07123_consen 81 PALALVDERLSTEGTGLPLGLSNNLLGWILLGVFGLIWSLYFVYTSTLDEDEDSGLSL 138 (138)
T ss_pred cHHHHHHHHhcCCCccccccccCchhHHHHHHHHHHHHHHHHhhccccCCCcccCcCC
Confidence 9999999999999999999999999999999999999999999999999999999997
No 3
>PLN00077 photosystem II reaction centre W protein; Provisional
Probab=100.00 E-value=6.2e-58 Score=348.09 Aligned_cols=125 Identities=56% Similarity=0.931 Sum_probs=115.1
Q ss_pred CceeeccccccceecceecccCcccccCCCccCccccc-ccceeeeeeccCCCccccccccchhHHHHHHHH-Hhccccc
Q 032691 1 MAAITASVGTSSITRSVLVHKPSIVASSSPVLGLPAMA-VKGKVRCSMEEKPSKQESKTNVGMSASLLAAAC-AATMSSP 78 (135)
Q Consensus 1 Mati~a~~~t~s~~ra~~~~~~~~~~ss~pv~GLP~m~-~~~~vrCs~~~K~~~~~~~~~~g~~asl~Aaa~-aa~~a~P 78 (135)
||||+|+++|++++|++ .+.||+|||+|+ |++||||+||+|++++ +..++||+++++++++ ++++++|
T Consensus 1 mat~~as~~t~~~~raa---------~s~pvlGLP~l~~~~~~v~Cs~e~k~~~~-~~~~~~~~asl~a~~~a~~a~a~P 70 (128)
T PLN00077 1 MATVSAAAATCVVARAA---------AARPVLGLPQLRARSERVRCSYEKKAANK-ADVNKLAGASLLVTSAATMAYAHP 70 (128)
T ss_pred Ccceeccccchhhhhhh---------hcCcccCchhhhccCCceEEecccCcccc-cccccchhHHHHHHHHHHHhcccc
Confidence 99999999999999997 245799999999 6799999999999864 6678999999999886 5889999
Q ss_pred chhhhhhcccCCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcCCCC-CCCCCCC
Q 032691 79 AMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSLDED-EESGLSL 135 (135)
Q Consensus 79 A~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l~ed-ddSGLsL 135 (135)
|||||||||||||||||||||||+|||||+|||+|||++||+|+|+++|| |||||||
T Consensus 71 A~AlVDeRlsteGtGl~lGlsn~~LgwIL~gVf~liw~ly~~~~~~l~~~edDsGLsL 128 (128)
T PLN00077 71 AFALVDERMSTEGTGLSLGLSNNLLGWILLGVFGLIWSLYTTYTSDLPEDEEDSGLSL 128 (128)
T ss_pred HHHHHhHhhcCCCccccccccCchhhHHHHhHHHHHHHHHhheecccCCccccccccC
Confidence 99999999999999999999999999999999999999999999999775 4599997
No 4
>PLN00082 photosystem II reaction centre W protein (PsbW); Provisional
Probab=100.00 E-value=2.3e-39 Score=224.79 Aligned_cols=64 Identities=63% Similarity=1.053 Sum_probs=61.7
Q ss_pred HhcccccchhhhhhcccCCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcCCC-CCCCCCCC
Q 032691 72 AATMSSPAMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSLDE-DEESGLSL 135 (135)
Q Consensus 72 aa~~a~PA~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l~e-dddSGLsL 135 (135)
++++++||+||||||||||||||||||||++|||||+|||++||++||+|+++++| ||||||||
T Consensus 3 ~~a~a~PA~AlVDeRlsteGtGl~lGls~~~LgwIL~gvf~liw~ly~~~~~~l~~~deDsGLsL 67 (67)
T PLN00082 3 TMAYAHPALALVDERLSTEGTGLGLGVSNGKLTWILVGVTALIWALYFSYSSTLPEGDDDSGLSL 67 (67)
T ss_pred hhhhcCcHHHHHHHHhcCCCccccccccCchhhhHHHHHHHHHHHHHhheecccCCCCcccCccC
Confidence 46788999999999999999999999999999999999999999999999999987 99999997
No 5
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=78.46 E-value=2.3 Score=32.31 Aligned_cols=33 Identities=33% Similarity=0.209 Sum_probs=26.7
Q ss_pred CcccccccchhHHHHHHHHHHHHHHHHhhcCcC
Q 032691 93 GLPFGLSNNLLGWILLGVFGLIWALYIPYASSL 125 (135)
Q Consensus 93 Gl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l 125 (135)
|=+||+|.+.+-|-++-.+.++|.||++..+.+
T Consensus 12 ~~~~~~~~~~~~~~iinflIl~~lL~~fl~kpI 44 (174)
T PRK07352 12 EGGFGLNLNLLETNLINLAIVIGLLYYFGRGFL 44 (174)
T ss_pred cCCCCCchhHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 446899999998988888888999888765543
No 6
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=62.80 E-value=6.2 Score=29.96 Aligned_cols=32 Identities=13% Similarity=0.066 Sum_probs=25.8
Q ss_pred CcccccccchhHHHHHHHHHHHHHHHHhhcCc
Q 032691 93 GLPFGLSNNLLGWILLGVFGLIWALYIPYASS 124 (135)
Q Consensus 93 Gl~lGlsn~~LgwILlgVf~liW~ly~~~~~~ 124 (135)
|=.|+++.+.+.|.++-.+.|+|.|+++..+.
T Consensus 11 ~~~~~~~~~~~~~~~i~Flil~~lL~~~l~kp 42 (175)
T PRK14472 11 GGLLSPNPGLIFWTAVTFVIVLLILKKIAWGP 42 (175)
T ss_pred CCccCCCHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 33689999999999999999999996665443
No 7
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=62.21 E-value=5.3 Score=30.55 Aligned_cols=32 Identities=16% Similarity=-0.058 Sum_probs=25.7
Q ss_pred CcccccccchhHHHHHHHHHHHHHHHHhhcCc
Q 032691 93 GLPFGLSNNLLGWILLGVFGLIWALYIPYASS 124 (135)
Q Consensus 93 Gl~lGlsn~~LgwILlgVf~liW~ly~~~~~~ 124 (135)
|-.+|++...+.|.++-++.|+|.|+.+..+.
T Consensus 11 ~~~~~~~~~t~~~~iInFliL~~lL~~~l~~p 42 (173)
T PRK13453 11 GAAGGVEWGTVIVTVLTFIVLLALLKKFAWGP 42 (173)
T ss_pred HhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55678888889999999999999996665443
No 8
>CHL00019 atpF ATP synthase CF0 B subunit
Probab=59.15 E-value=9.7 Score=29.21 Aligned_cols=31 Identities=19% Similarity=0.224 Sum_probs=24.7
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHhhcCcC
Q 032691 95 PFGLSNNLLGWILLGVFGLIWALYIPYASSL 125 (135)
Q Consensus 95 ~lGlsn~~LgwILlgVf~liW~ly~~~~~~l 125 (135)
.||+|.+.+.|-++-...++|.||++..+.+
T Consensus 19 ~f~~n~~~~~~~~Inflill~lL~~fl~kPI 49 (184)
T CHL00019 19 SFGFNTDILETNLINLSVVLGVLIYFGKGVL 49 (184)
T ss_pred ccCCcchHHHHHHHHHHHHHHHHHHHhHhHH
Confidence 5899998888878888889999888665543
No 9
>PLN00090 photosystem II reaction center M protein; Provisional
Probab=41.79 E-value=49 Score=25.50 Aligned_cols=57 Identities=18% Similarity=0.349 Sum_probs=37.9
Q ss_pred hcccccchhh--hhhcccCCCCCcccccccchhHHHHHHHHHHHHHHH--HhhcCcC--CCCCCCCC
Q 032691 73 ATMSSPAMAL--VDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALY--IPYASSL--DEDEESGL 133 (135)
Q Consensus 73 a~~a~PA~AL--VDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly--~~~~~~l--~edddSGL 133 (135)
++.+.||+|+ +-|.|-|.- +.+.-|.||+|-.-.|.+|=..| ..|.++. ++.+|.|.
T Consensus 48 aa~a~pafa~dsivealpt~t----~~~EVNiLafIATaLFIlIPTaFLLILYVQT~Sr~~g~~gg~ 110 (113)
T PLN00090 48 AAIAAPAFALDSIVEALPTNT----LALEVQFGAYLAVALGTFLPCLFLINLFIQTESRKAGRAGGI 110 (113)
T ss_pred HHhcccHhHHHHHHHHcCccc----eeeehHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCC
Confidence 4567788886 346676653 46678899999888777775544 3466665 55566664
No 10
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=38.95 E-value=59 Score=24.88 Aligned_cols=37 Identities=32% Similarity=0.347 Sum_probs=22.1
Q ss_pred cccccchhhhhhcccCCCCCcccccccchhHHHHHHHHHHHHHHHHh
Q 032691 74 TMSSPAMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIP 120 (135)
Q Consensus 74 ~~a~PA~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~ 120 (135)
.++.||+|- +| |+ |++++..+ |..+-.+.++|.|+++
T Consensus 10 ~~~~~~~~~-------~g-~~-~~~~~t~~-~~~inflil~~iL~~f 46 (184)
T PRK13455 10 LAASPALAA-------GG-PF-FSLSNTDF-VVTLAFLLFIGILVYF 46 (184)
T ss_pred HccchHhhc-------CC-CC-CCCcchHH-HHHHHHHHHHHHHHHH
Confidence 455666664 22 44 67777666 6666666666666655
No 11
>PRK06654 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=38.23 E-value=43 Score=27.28 Aligned_cols=30 Identities=27% Similarity=0.714 Sum_probs=24.9
Q ss_pred CCCCcccccccc----hhHHHHHHHHHHHHHHHH
Q 032691 90 EGTGLPFGLSNN----LLGWILLGVFGLIWALYI 119 (135)
Q Consensus 90 eGTGl~lGlsn~----~LgwILlgVf~liW~ly~ 119 (135)
.+-|--.|+... +|.||.++++++|+..--
T Consensus 17 ~~~~~~~g~~p~~~~k~l~~~~i~~~a~i~i~~v 50 (181)
T PRK06654 17 APDGRKVGLLPDVIIKILQWVAIGLFAVIFIVTV 50 (181)
T ss_pred cCCcCccCcChHHHHHHHHHHHHHHHHHHHHhhh
Confidence 344667899999 999999999999997644
No 12
>PF01679 Pmp3: Proteolipid membrane potential modulator; InterPro: IPR000612 Proteolipid membrane potential modulator is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants. Proteins in this entry include the PMP3 as well as several other proteins that have been shown [] to be evolutionary related. These are small proteins of from 52 to 140 amino-acid resiudes that contain two transmembrane domains and belong to the UPF0057 (PMP3) protein family.; GO: 0016021 integral to membrane
Probab=37.63 E-value=15 Score=24.10 Aligned_cols=22 Identities=45% Similarity=0.536 Sum_probs=16.7
Q ss_pred chhHHHHHHHHHHHHHHHHhhc
Q 032691 101 NLLGWILLGVFGLIWALYIPYA 122 (135)
Q Consensus 101 ~~LgwILlgVf~liW~ly~~~~ 122 (135)
|.+-+++.-+++.||++|.+|+
T Consensus 30 nl~Ltl~g~iPg~ihA~y~i~~ 51 (51)
T PF01679_consen 30 NLLLTLLGWIPGVIHALYVIYK 51 (51)
T ss_pred HHHHHHHHHHHHHHHeeEEEeC
Confidence 3455666678999999998764
No 13
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=36.49 E-value=38 Score=24.78 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=19.4
Q ss_pred chhHHHHHHHHHHHHHHHHhhcCcC
Q 032691 101 NLLGWILLGVFGLIWALYIPYASSL 125 (135)
Q Consensus 101 ~~LgwILlgVf~liW~ly~~~~~~l 125 (135)
.-.+|+|.+++.+..++|..+.=.+
T Consensus 49 kev~l~l~ail~lL~a~Ya~fyl~l 73 (79)
T PF15168_consen 49 KEVALVLAAILVLLLAFYAFFYLNL 73 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3467899999999999887665444
No 14
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=35.34 E-value=29 Score=26.35 Aligned_cols=29 Identities=14% Similarity=0.208 Sum_probs=21.7
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhhcCc
Q 032691 96 FGLSNNLLGWILLGVFGLIWALYIPYASS 124 (135)
Q Consensus 96 lGlsn~~LgwILlgVf~liW~ly~~~~~~ 124 (135)
|.++.+.+.|.++....|+|.|+++..+.
T Consensus 12 l~~~~~~~~~~~i~Flil~~iL~~~~~kp 40 (173)
T PRK13460 12 LDVNPGLVVWTLVTFLVVVLVLKKFAWDV 40 (173)
T ss_pred cCCcHhHHHHHHHHHHHHHHHHHHHhHHH
Confidence 45555689998888888999996665443
No 15
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=31.55 E-value=35 Score=21.96 Aligned_cols=20 Identities=65% Similarity=1.100 Sum_probs=14.9
Q ss_pred cccchhHHHHHH-HHHHHHHH
Q 032691 98 LSNNLLGWILLG-VFGLIWAL 117 (135)
Q Consensus 98 lsn~~LgwILlg-Vf~liW~l 117 (135)
+=|=.|||-++| +..|||++
T Consensus 22 ~~Nl~lGWT~iGWv~aLiwA~ 42 (43)
T PF14373_consen 22 LLNLLLGWTGIGWVAALIWAL 42 (43)
T ss_pred hHHHHHHhHHHHHHHHHHHhc
Confidence 346678998888 56788875
No 16
>COG3376 HoxN High-affinity nickel permease [Inorganic ion transport and metabolism]
Probab=30.44 E-value=54 Score=29.39 Aligned_cols=43 Identities=21% Similarity=0.496 Sum_probs=35.2
Q ss_pred ccchhhhhhcccCCCCCcc--cccccchhHHHHHHHHHHHHHHHH
Q 032691 77 SPAMALVDERMSTEGTGLP--FGLSNNLLGWILLGVFGLIWALYI 119 (135)
Q Consensus 77 ~PA~ALVDeRlsteGTGl~--lGlsn~~LgwILlgVf~liW~ly~ 119 (135)
..++-|+++.++=.|.=.. -.+|++.+|++++|+|.+-|..-+
T Consensus 289 iE~Lglia~~l~L~G~fW~~i~~l~~~~vGy~vV~~F~l~WliS~ 333 (342)
T COG3376 289 IELLGLIADKLNLSGGFWDQIGSLNFNYVGYYVVGLFALTWLISF 333 (342)
T ss_pred HHHHHHHHHHhcCcchHHHHHhccccchhHHHHHHHHHHHHHHHH
Confidence 5789999999998775111 268999999999999999998755
No 17
>PF11862 DUF3382: Domain of unknown function (DUF3382); InterPro: IPR021807 This entry represents the N-terminal domain of the LivHM type high-affinity branched-chain amino acid transport system permease proteins. The domain is about 100 amino acids in length, and is found associated with PF02653 from PFAM.
Probab=28.00 E-value=70 Score=22.78 Aligned_cols=47 Identities=23% Similarity=0.330 Sum_probs=30.7
Q ss_pred HHHHHHHhcccccchhhhhhcccCCCCCcccccccchhHHHHHHHHHHHH
Q 032691 66 LLAAACAATMSSPAMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIW 115 (135)
Q Consensus 66 l~Aaa~aa~~a~PA~ALVDeRlsteGTGl~lGlsn~~LgwILlgVf~liW 115 (135)
+.|+..+...+.|-+-+ |+.+||+.|.+.=-.+.+.|+...++...+
T Consensus 9 l~aall~lvl~~pi~Gl---~l~~~g~~L~~~~r~~~~~~~V~~~~~~~F 55 (101)
T PF11862_consen 9 LFAALLALVLFGPIVGL---KLDNQGGQLVLEPRWGLLAWWVAVAAAGRF 55 (101)
T ss_pred HHHHHHHHHHHHHheEE---EEecCCcEEEEEecchHHHHHHHHHHHHHH
Confidence 34444455666787766 455899999877776666666666665544
No 18
>PRK11689 aromatic amino acid exporter; Provisional
Probab=27.00 E-value=90 Score=24.94 Aligned_cols=29 Identities=24% Similarity=0.340 Sum_probs=22.5
Q ss_pred chhHHHHHHHHHHHHHHHHhhcCcCCCCC
Q 032691 101 NLLGWILLGVFGLIWALYIPYASSLDEDE 129 (135)
Q Consensus 101 ~~LgwILlgVf~liW~ly~~~~~~l~edd 129 (135)
+.+|.++.=.-.+.|++|.++.|.+.++.
T Consensus 154 ~~~G~~~~l~aa~~~A~~~v~~k~~~~~~ 182 (295)
T PRK11689 154 NPLSYGLAFIGAFIWAAYCNVTRKYARGK 182 (295)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 45676666677789999999999986544
No 19
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=24.49 E-value=73 Score=26.76 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=15.5
Q ss_pred ccchhHHHHHHHHHHHHHHHHh
Q 032691 99 SNNLLGWILLGVFGLIWALYIP 120 (135)
Q Consensus 99 sn~~LgwILlgVf~liW~ly~~ 120 (135)
+|+.++|+++++|..+-.++++
T Consensus 23 ~dp~l~~~ml~a~l~~~~v~v~ 44 (224)
T PF13829_consen 23 EDPKLPWLMLGAFLGPIAVFVL 44 (224)
T ss_pred HCcchHHHHHHHHHHHHHHHHH
Confidence 4778888888888766555443
No 20
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=24.46 E-value=68 Score=24.85 Aligned_cols=20 Identities=20% Similarity=0.461 Sum_probs=15.7
Q ss_pred chhHHHHHHHHHHHHHHHHh
Q 032691 101 NLLGWILLGVFGLIWALYIP 120 (135)
Q Consensus 101 ~~LgwILlgVf~liW~ly~~ 120 (135)
+.+.|.++.++.|+|.|..+
T Consensus 32 ~q~~~~lI~F~iL~~ll~k~ 51 (181)
T PRK13454 32 NQIFWLLVTLVAIYFVLTRV 51 (181)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 57889888888889988433
No 21
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=24.23 E-value=64 Score=24.43 Aligned_cols=37 Identities=19% Similarity=0.001 Sum_probs=28.9
Q ss_pred CCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcC
Q 032691 89 TEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSL 125 (135)
Q Consensus 89 teGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l 125 (135)
+.|-|+.+.+--.-+.|+++=++.|.|.+|=.-.+-+
T Consensus 12 ~~~~~~~~~~~~~~iinflIl~~lL~~fl~kpI~~~l 48 (174)
T PRK07352 12 EGGFGLNLNLLETNLINLAIVIGLLYYFGRGFLGKIL 48 (174)
T ss_pred cCCCCCchhHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 5677999998777788888889999998886554443
No 22
>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=24.15 E-value=73 Score=20.80 Aligned_cols=16 Identities=25% Similarity=0.787 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 032691 104 GWILLGVFGLIWALYIPY 121 (135)
Q Consensus 104 gwILlgVf~liW~ly~~~ 121 (135)
+.+|+|+.+ +++|..+
T Consensus 12 ~~~lv~~Tg--y~iYtaF 27 (43)
T PF02468_consen 12 SCLLVSITG--YAIYTAF 27 (43)
T ss_pred HHHHHHHHh--hhhhhee
Confidence 445566555 7788776
No 23
>COG4499 Predicted membrane protein [Function unknown]
Probab=21.81 E-value=83 Score=29.08 Aligned_cols=22 Identities=32% Similarity=0.544 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHHHHhhcCc
Q 032691 103 LGWILLGVFGLIWALYIPYASS 124 (135)
Q Consensus 103 LgwILlgVf~liW~ly~~~~~~ 124 (135)
+|+|.+-|..+||..|+.+...
T Consensus 225 iGliillvl~li~~~Y~~f~~~ 246 (434)
T COG4499 225 IGLIILLVLLLIYFTYYYFSNQ 246 (434)
T ss_pred HhHHHHHHHHHHHHHHHHHHcC
Confidence 4789999999999999887543
No 24
>PF14017 DUF4233: Protein of unknown function (DUF4233)
Probab=20.98 E-value=44 Score=24.72 Aligned_cols=26 Identities=12% Similarity=0.300 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHhhcCcCCCCCCC
Q 032691 106 ILLGVFGLIWALYIPYASSLDEDEES 131 (135)
Q Consensus 106 ILlgVf~liW~ly~~~~~~l~edddS 131 (135)
++-.+|+.+|..-....+++|+..+-
T Consensus 81 vvG~iF~~~W~~~l~lg~~i~~~~~~ 106 (107)
T PF14017_consen 81 VVGVIFAAVWWYALYLGRRIDRRMAR 106 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 44567899998877777887665443
No 25
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=20.94 E-value=44 Score=27.66 Aligned_cols=23 Identities=43% Similarity=0.720 Sum_probs=18.3
Q ss_pred HhcccccchhhhhhcccCCCCCcc
Q 032691 72 AATMSSPAMALVDERMSTEGTGLP 95 (135)
Q Consensus 72 aa~~a~PA~ALVDeRlsteGTGl~ 95 (135)
++-+..|+.|+||=||.. |-||.
T Consensus 48 ~art~~PayAvvDlkL~~-gsGL~ 70 (182)
T COG4567 48 AARTAPPAYAVVDLKLGD-GSGLA 70 (182)
T ss_pred HHhcCCCceEEEEeeecC-CCchH
Confidence 446778999999999977 76663
No 26
>KOG0475 consensus Cl- channel CLC-3 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism]
Probab=20.85 E-value=75 Score=30.93 Aligned_cols=22 Identities=41% Similarity=0.887 Sum_probs=19.5
Q ss_pred chhHHHHHHHHHHHHHHHHhhc
Q 032691 101 NLLGWILLGVFGLIWALYIPYA 122 (135)
Q Consensus 101 ~~LgwILlgVf~liW~ly~~~~ 122 (135)
+++-||++|+|+=+|..|+++.
T Consensus 308 EL~pFi~LGifgGl~G~~~ir~ 329 (696)
T KOG0475|consen 308 ELLPFILLGIFGGLWGAFFIRL 329 (696)
T ss_pred cchHHHHHHHhhhHHHHHHHHH
Confidence 5678999999999999999864
No 27
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=20.29 E-value=1.1e+02 Score=22.03 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=21.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHhhcCc
Q 032691 99 SNNLLGWILLGVFGLIWALYIPYASS 124 (135)
Q Consensus 99 sn~~LgwILlgVf~liW~ly~~~~~~ 124 (135)
+|.++|..++.+-..++.-|++..=-
T Consensus 2 ~Dr~vG~~~l~~a~~vF~YYt~Wvll 27 (78)
T PF07297_consen 2 SDRLVGLLMLAVALSVFTYYTIWVLL 27 (78)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889999999999988888776533
No 28
>PF00662 Oxidored_q1_N: NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; InterPro: IPR001516 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This domain represents an N-terminal extension of IPR001750 from INTERPRO. It contains NADH-Ubiquinone chain 5 and eubacterial chain L; these are found in the NADH:ubiquinone oxidoreductase (complex I) which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0055114 oxidation-reduction process; PDB: 3RKO_L.
Probab=20.28 E-value=75 Score=20.39 Aligned_cols=41 Identities=20% Similarity=0.188 Sum_probs=32.5
Q ss_pred hcccCCCCCcccccccchhHHHHHHHHHHHHHHHHhhcCcC
Q 032691 85 ERMSTEGTGLPFGLSNNLLGWILLGVFGLIWALYIPYASSL 125 (135)
Q Consensus 85 eRlsteGTGl~lGlsn~~LgwILlgVf~liW~ly~~~~~~l 125 (135)
|.++..+..+++++.-..++.+++.+..+|+.+-..|...-
T Consensus 6 ~w~~~~~~~i~~~~~~D~ls~~f~~~v~~Is~~V~~yS~~Y 46 (62)
T PF00662_consen 6 EWFSLGSLNISFSFYLDPLSALFLLLVLFISSLVHIYSIGY 46 (62)
T ss_dssp EEEE-SS-EEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEeeeccEeEEEEEEEHHhHHHHHHHHHHhheeeeeccccc
Confidence 34566778899999999999999999999999988887765
No 29
>PF01252 Peptidase_A8: Signal peptidase (SPase) II This is family A8 in the peptidase classification. ; InterPro: IPR001872 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to the MEROPS peptidase family A8 (signal peptidase II family, clan AC). The catalytic residues have not been identified, but three conserved aspartates can be identified from sequence alignments. The type example is the Escherichia coli lipoprotein signal peptidase or SPase II (3.4.23.36 from EC). This enzyme recognises a conserved sequence and cuts in front of a cysteine residue to which a glyceride-fatty acid lipid is attached. SPase II is an integral membrane protein that is anchored in the membrane. Bacterial cell walls contain large amounts of murein lipoprotein, a small protein that is both N-terminally bound to lipid and attached to membrane peptidoglycan (murein) through the epsilon-amino group of its C-terminal lysine residue []. Secretion of this lipoprotein is facilitated by the action of the lipoprotein signal peptidases in this entry, located in the inner membrane [, ]. They enzyme are inhibited by globomycin and also by pepstatin, suggesting that they are aspartic peptidases [].; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane
Probab=20.13 E-value=1.3e+02 Score=22.56 Aligned_cols=36 Identities=28% Similarity=0.617 Sum_probs=22.6
Q ss_pred cCCCCCcccccccch------hHHHHHHHHHHHHHHHHhhcC
Q 032691 88 STEGTGLPFGLSNNL------LGWILLGVFGLIWALYIPYAS 123 (135)
Q Consensus 88 steGTGl~lGlsn~~------LgwILlgVf~liW~ly~~~~~ 123 (135)
..+-+|..||+.++. +.++++.++.+++.+|+...+
T Consensus 37 ~~~N~G~afg~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~ 78 (150)
T PF01252_consen 37 YVENTGAAFGLFSGLPGAIRKLFLLIISILAILFILYFLFKK 78 (150)
T ss_pred EEecCCceeecccccchhhHHHHHHHHHHHHHHHHHHHHHHc
Confidence 456788888988876 234445555566666555444
Done!