Query 030310
Match_columns 179
No_of_seqs 132 out of 157
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 11:47:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030310.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030310hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00042 photosystem II oxygen 100.0 3.6E-62 7.7E-67 421.9 13.5 172 1-177 1-175 (260)
2 PLN00059 PsbP domain-containin 99.9 1.6E-27 3.4E-32 208.0 11.0 121 29-171 59-184 (286)
3 PLN00067 PsbP domain-containin 99.9 7.6E-22 1.7E-26 171.5 11.4 114 51-171 42-188 (263)
4 PF01789 PsbP: PsbP; InterPro 99.8 1.4E-20 3E-25 151.3 6.8 88 74-168 3-93 (175)
5 PLN00066 PsbP domain-containin 99.7 9.2E-18 2E-22 146.1 11.4 119 49-176 42-194 (262)
6 PLN03152 hypothetical protein; 98.3 6.1E-07 1.3E-11 77.8 4.9 109 51-165 30-166 (241)
7 PF05757 PsbQ: Oxygen evolving 76.0 0.86 1.9E-05 39.0 0.0 32 31-66 12-43 (202)
8 PF10518 TAT_signal: TAT (twin 66.7 6.1 0.00013 23.4 2.2 16 52-67 2-17 (26)
9 PLN00058 photosystem II reacti 51.1 17 0.00037 28.4 2.9 31 50-81 47-77 (103)
10 PF08006 DUF1700: Protein of u 46.0 10 0.00022 30.6 1.0 19 143-161 43-61 (181)
11 PF06525 SoxE: Sulfocyanin (So 42.0 12 0.00026 32.2 0.9 58 96-162 75-137 (196)
12 PF07174 FAP: Fibronectin-atta 41.2 17 0.00038 33.1 1.8 29 98-126 115-144 (297)
13 PF12712 DUF3805: Domain of un 39.3 35 0.00076 28.4 3.2 43 94-141 4-47 (153)
14 PF13561 adh_short_C2: Enoyl-( 34.6 21 0.00046 28.8 1.2 29 145-173 203-233 (241)
15 PF00861 Ribosomal_L18p: Ribos 34.5 88 0.0019 24.2 4.6 43 128-170 39-86 (119)
16 PF12318 FAD-SLDH: Membrane bo 34.1 32 0.00068 28.3 2.2 8 52-59 2-9 (168)
17 cd01129 PulE-GspE PulE/GspE Th 33.0 80 0.0017 27.2 4.6 56 120-175 27-91 (264)
18 PF10916 DUF2712: Protein of u 29.9 1.5E+02 0.0032 24.7 5.4 44 99-148 34-79 (146)
19 COG4709 Predicted membrane pro 29.1 33 0.00071 29.7 1.5 31 144-174 44-75 (195)
20 TIGR02525 plasmid_TraJ plasmid 27.0 77 0.0017 29.2 3.6 42 134-175 119-160 (372)
21 TIGR02811 formate_TAT formate 25.4 60 0.0013 23.1 2.1 13 51-63 8-20 (66)
22 PF04674 Phi_1: Phosphate-indu 24.7 58 0.0013 29.3 2.3 34 82-115 221-267 (273)
23 PF07123 PsbW: Photosystem II 22.0 1.1E+02 0.0024 25.2 3.2 10 34-43 43-52 (138)
24 PRK10882 hydrogenase 2 protein 21.5 1.2E+02 0.0025 27.7 3.7 13 53-65 2-14 (328)
25 PF10399 UCR_Fe-S_N: Ubiquitin 20.4 99 0.0021 20.2 2.2 13 51-63 8-20 (41)
No 1
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=3.6e-62 Score=421.87 Aligned_cols=172 Identities=76% Similarity=1.163 Sum_probs=160.5
Q ss_pred CcchhhhhhccccCCCccccc---ccccccCCCCCceeeeecccccccccCCcchhhHHHHHHHHHHHhhhccCCccccc
Q 030310 1 MASTQCFLHHHALSTTPARTS---SSQRHVSNIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAAVGSKVSPADAA 77 (179)
Q Consensus 1 ma~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~c~a~~~~~~~~~~~~~~RR~aL~~~~gaaa~~s~~~pa~Aa 77 (179)
||||+||||||+++++....+ ++++.++..++++++|++|++. .+.++||.+|++++|+++++++++|+++|
T Consensus 1 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~srr~~l~~~~ga~a~~~~~~pa~aa 75 (260)
T PLN00042 1 MASTACFLHQSALKSAAALASSSSASARAVSASRPSQVVCRAQEED-----NSAVSRRAALALLAGAAAAGAKVSPANAA 75 (260)
T ss_pred CcchhhhhhcccccchhhhcccccccccccCCCCCcceeeeccccc-----cccccHHHHHHHHHHHHHhhcccCchhhh
Confidence 999999999999955443211 4578899999999999999773 34689999999999999999999999999
Q ss_pred ccccccccCCCCCCCCcccccCCCeeEecCCCCCCCceeeeCCceEEeeeCCCCCCceEEEEecCCCCCcccCCChHHHH
Q 030310 78 YGESANVFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFL 157 (179)
Q Consensus 78 yge~anvFg~p~~~~~F~~y~~DGYsFlyPs~Wnpskev~~~G~dv~f~D~~~~~eNvsV~ispt~kksI~DlGsPee~~ 157 (179)
|||+|||||+||+++||++|++|||+|+||+||||++|++++|+|++|||+|+++|||+|+|+|++|++|+|||+||||+
T Consensus 76 y~~~anvfg~~k~~~gF~~y~~dgY~FlyP~~W~~~ke~~~~G~dv~f~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~l 155 (260)
T PLN00042 76 YGESANVFGKPKTNTGFLPYNGDGFKLLVPSKWNPSKEREFPGQVLRFEDNFDATSNLSVMVTPTDKKSITDYGSPEEFL 155 (260)
T ss_pred hcchhhccCCCCCCCCCeEeeCCCeEEecCCCCccccccccCCceEEeeccccccccEEEEEecCCcCCHhhcCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhcccCcccc
Q 030310 158 SKVDYLLGKQAYSGKTSSEV 177 (179)
Q Consensus 158 ~~Vgy~L~kq~~~g~t~seg 177 (179)
++|+|+|+||+|+|+|+|||
T Consensus 156 ~~vgylL~kq~~a~~t~s~~ 175 (260)
T PLN00042 156 SKVSYLLGKQAYSGETASEG 175 (260)
T ss_pred HHHHHHHHhhhccCcccccc
Confidence 99999999999999999986
No 2
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.95 E-value=1.6e-27 Score=207.97 Aligned_cols=121 Identities=24% Similarity=0.354 Sum_probs=97.2
Q ss_pred CCCCceeeeecc-cccccccCCcchhhHHHHHHHHH-HHhhhccCCcccccccccccccCCCCCCCCcccccCCCeeEec
Q 030310 29 NIKPTQIVCRAQ-KQAVQEDDGSAVSRRLALTVLIG-AAAVGSKVSPADAAYGESANVFGKPKTNTDFLPYNGDGFKLSI 106 (179)
Q Consensus 29 ~~~~~~~~c~a~-~~~~~~~~~~~~~RR~aL~~~~g-aaa~~s~~~pa~Aayge~anvFg~p~~~~~F~~y~~DGYsFly 106 (179)
.-+|..+.|..| ++ ..+++||++|+..+- +..+.+.++ ...|++ .|++++.|+| +.|||+|+|
T Consensus 59 ~~~~~~~~~~~~~~~------~~~~~rr~~~~~~l~~~~~~~s~~~-~~~a~a-------~~~~l~~y~D-~~DGY~FlY 123 (286)
T PLN00059 59 PDSPVAINCLTDAKQ------VCAVGRRKSMMMGLLMSGLIVSEAN-LPTAFA-------SIPVFREYID-TFDGYSFKY 123 (286)
T ss_pred CCCCeeeecccchhh------hhhhhhhhhhHHHHHHHHHHHHhhc-Cchhhc-------CCcccceeEc-CCCCeEEeC
Confidence 345566888888 34 448999999764442 333333332 234444 4668899999 899999999
Q ss_pred CCCCCCCceeeeCCceEEeeeCCCCCCceEEEEecCC---CCCcccCCChHHHHHHHHHHHHhhhhcc
Q 030310 107 PSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTD---KKSITDYGSPEEFLSKVDYLLGKQAYSG 171 (179)
Q Consensus 107 Ps~Wnpskev~~~G~dv~f~D~~~~~eNvsV~ispt~---kksI~DlGsPee~~~~Vgy~L~kq~~~g 171 (179)
|+|| +||+..|+|++|||+|+.+|||+|+|+|+. +++|+|||+|+| |||+|.||+++.
T Consensus 124 P~GW---i~V~~~G~DVvFrD~Ie~~ENVSV~ISs~sss~~~sLeDLGsP~e----VgerLlkqvLa~ 184 (286)
T PLN00059 124 PQNW---IQVRGAGADIFFRDPVVLDENLSVEFSSPSSSKYTSLEDLGSPEE----VGKRVLRQYLTE 184 (286)
T ss_pred CCCC---eEeccCCCceEEeccCccccceEEEEecCCcccCCChHHcCCHHH----HHHHHHHHHhcc
Confidence 9999 999999999999999999999999999874 899999999999 999999999873
No 3
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.87 E-value=7.6e-22 Score=171.46 Aligned_cols=114 Identities=21% Similarity=0.352 Sum_probs=84.0
Q ss_pred chhhHHHHHHHHHHHhhhccCCcccccccc-cccccCCC-CCCCCccccc-------------CCCeeEecCCCCCCCce
Q 030310 51 AVSRRLALTVLIGAAAVGSKVSPADAAYGE-SANVFGKP-KTNTDFLPYN-------------GDGFKLSIPSKWNPSKE 115 (179)
Q Consensus 51 ~~~RR~aL~~~~gaaa~~s~~~pa~Aayge-~anvFg~p-~~~~~F~~y~-------------~DGYsFlyPs~Wnpske 115 (179)
.+.||+.|.+++.+..++.. .+..+...| +...|.+| ....+|..|. ..||+|+||++|+++++
T Consensus 42 ~~~rr~~~~~~~~~~~~~~~-~~~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~V 120 (263)
T PLN00067 42 VIHRRELLLGLALAPLILIA-PEPPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTRV 120 (263)
T ss_pred hhHHHHHHhhhhhhhhhhcc-CCchhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCccc
Confidence 57899999887755444333 333443444 47888876 5678888876 78999999999965555
Q ss_pred e------------eeCCceEEeeeCCCCCCceEEEEecC------CCCCcccCCChHHHHHHHHHHHHhhhhcc
Q 030310 116 R------------EFPGQVLRYEDNFDSNSNVSVIITPT------DKKSITDYGSPEEFLSKVDYLLGKQAYSG 171 (179)
Q Consensus 116 v------------~~~G~dv~f~D~~~~~eNvsV~ispt------~kksI~DlGsPee~~~~Vgy~L~kq~~~g 171 (179)
- +++|+|++|||++ ++||+|+|+|+ ++++|+|||+|||| ++.||+.+..|
T Consensus 121 s~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeV----l~~Lg~~v~g~ 188 (263)
T PLN00067 121 ANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKL----IASLGPFVTGN 188 (263)
T ss_pred cccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHH----HHHhhHHhhcC
Confidence 3 2346999999955 67999999997 66999999999995 55555555553
No 4
>PF01789 PsbP: PsbP; InterPro: IPR002683 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 []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbP. Both PsbP and PsbQ (IPR008797 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [, ]. The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity []. PsbP is encoded in the nuclear genome in plants.; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 2VU4_A 1V2B_A 2LNJ_A 2XB3_A.
Probab=99.82 E-value=1.4e-20 Score=151.32 Aligned_cols=88 Identities=40% Similarity=0.613 Sum_probs=63.4
Q ss_pred ccccccccccccCCCCCCCCcccc--cCCCeeEecCCCCCCCceeeeCCceEEeeeCCCCCCceEEEEecCCCC-CcccC
Q 030310 74 ADAAYGESANVFGKPKTNTDFLPY--NGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKK-SITDY 150 (179)
Q Consensus 74 a~Aayge~anvFg~p~~~~~F~~y--~~DGYsFlyPs~Wnpskev~~~G~dv~f~D~~~~~eNvsV~ispt~kk-sI~Dl 150 (179)
+.++++..+|+++..++..+|++| ..|||+|+||++| ++++++|+|++|+|+++..+||+|+|+|+.++ +|+||
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~y~d~~~~y~f~~P~gW---~~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~l 79 (175)
T PF01789_consen 3 ALAALLSSANVACAAEASTGFQPYTDSDDGYSFLYPSGW---EEVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDL 79 (175)
T ss_dssp -------------STT--SSEEEEEECTTTEEEEEETTE---EEEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG
T ss_pred eeEEeeccchhhhcccCCCCceEEEcCCCCEEEECCCCC---eecCCCCeEEEEECcccccceEEEEEEecCCcCchhhc
Confidence 445666666777777777888888 7999999999999 99999999999999999999999999999666 99999
Q ss_pred CChHHHHHHHHHHHHhhh
Q 030310 151 GSPEEFLSKVDYLLGKQA 168 (179)
Q Consensus 151 GsPee~~~~Vgy~L~kq~ 168 (179)
|+|+| |++.|.++.
T Consensus 80 Gs~~~----va~~l~~~~ 93 (175)
T PF01789_consen 80 GSPEE----VAERLLNGE 93 (175)
T ss_dssp -SHHH----HHHHHHHHC
T ss_pred CCHHH----HHHHHhhhh
Confidence 99999 566665543
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.75 E-value=9.2e-18 Score=146.11 Aligned_cols=119 Identities=26% Similarity=0.394 Sum_probs=83.3
Q ss_pred CcchhhHHHHHHHHHHHhh--hccCCccccc-cccccc-c--cCCCCCCCCccccc---------------CCCeeEecC
Q 030310 49 GSAVSRRLALTVLIGAAAV--GSKVSPADAA-YGESAN-V--FGKPKTNTDFLPYN---------------GDGFKLSIP 107 (179)
Q Consensus 49 ~~~~~RR~aL~~~~gaaa~--~s~~~pa~Aa-yge~an-v--Fg~p~~~~~F~~y~---------------~DGYsFlyP 107 (179)
...++||.+|+.++.++.+ ++...++.|+ ||-.|. + |..| ...+|..|. ...|+|+||
T Consensus 42 ~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~-~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP 120 (262)
T PLN00066 42 ATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEP-DENGWRTYRRPEGKSGGHGVGWSEITPYSFKVP 120 (262)
T ss_pred cchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCc-cccceEEEecCccccCcCCCCccccCCeEEECC
Confidence 4478999999876655333 3333344444 775432 2 1222 224555554 478999999
Q ss_pred CCCCCCceeeeC-----CceEEeeeCCCCCCceEEEEecC--------CCCCcccCCChHHHHHHHHHHHHhhhhcccCc
Q 030310 108 SKWNPSKEREFP-----GQVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTS 174 (179)
Q Consensus 108 s~Wnpskev~~~-----G~dv~f~D~~~~~eNvsV~ispt--------~kksI~DlGsPee~~~~Vgy~L~kq~~~g~t~ 174 (179)
++| +|+.+. |.++.||+..+..+||+|+|+|+ ++++|+|||+||| |++.|+++++ |.+.
T Consensus 121 ~GW---~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspee----Vi~~l~~~v~-g~~~ 192 (262)
T PLN00066 121 QGW---EEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEK----VISGFGPELI-GEPV 192 (262)
T ss_pred CCC---eEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHH----HHHHHHHHhc-CCCc
Confidence 999 999887 66677777779999999999997 7999999999999 5566666643 5554
Q ss_pred cc
Q 030310 175 SE 176 (179)
Q Consensus 175 se 176 (179)
.|
T Consensus 193 ~e 194 (262)
T PLN00066 193 EE 194 (262)
T ss_pred cc
Confidence 44
No 6
>PLN03152 hypothetical protein; Provisional
Probab=98.33 E-value=6.1e-07 Score=77.77 Aligned_cols=109 Identities=23% Similarity=0.449 Sum_probs=66.9
Q ss_pred chhhHHHHHHHHH--HHhhhccCCccccccccccc----ccCCCCCCCCcccccCCCeeEecCCCCCCCcee-eeC-C--
Q 030310 51 AVSRRLALTVLIG--AAAVGSKVSPADAAYGESAN----VFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKER-EFP-G-- 120 (179)
Q Consensus 51 ~~~RR~aL~~~~g--aaa~~s~~~pa~Aayge~an----vFg~p~~~~~F~~y~~DGYsFlyPs~Wnpskev-~~~-G-- 120 (179)
..+||+.+.-.+. +.++. .-.|...++++..+ +-+.-.|.+.+-.|-+|||+.-||..+...-|- ++. |
T Consensus 30 ~~~~r~~~~~t~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~~g~gf~~~~pp~f~di~e~~~~~~g~~ 108 (241)
T PLN03152 30 GASRRDFILHTASLCASSLA-AQNPLPPSLADPSKPSKPLLSGIANTKSWFQFYGDGFSIRVPPSFEDIMEPEDYNAGLS 108 (241)
T ss_pred cccccceeeehhHHHHhhhh-cCCCCCccccCCCCCCCchheeeecchhhhhhhCCceEEeCCCChhhhcChhhcccccc
Confidence 3557766533222 22222 33555566666522 222223445555566999999999999333222 111 1
Q ss_pred ----------ceEEeeeCCCCCCceEEEEecC--------CCCCcccCCChHHHHHHHHHHHH
Q 030310 121 ----------QVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLG 165 (179)
Q Consensus 121 ----------~dv~f~D~~~~~eNvsV~ispt--------~kksI~DlGsPee~~~~Vgy~L~ 165 (179)
-..|| +--|.+|||||+|+|+ ++|+|+|||+|+| ||++|.
T Consensus 109 ~yg~~akp~~~~aRf-~s~D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~E----Vgkv~v 166 (241)
T PLN03152 109 LYGDKAKPRTFAARF-ASPDGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKE----AAKIFV 166 (241)
T ss_pred eecCCCCCcceeeee-cCCCCCceEEEEEecCccccccccccCChhHcCCHHH----HHHhhC
Confidence 12333 2346799999999996 7999999999999 677665
No 7
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 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 []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=75.95 E-value=0.86 Score=39.01 Aligned_cols=32 Identities=31% Similarity=0.414 Sum_probs=0.0
Q ss_pred CCceeeeecccccccccCCcchhhHHHHHHHHHHHh
Q 030310 31 KPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAA 66 (179)
Q Consensus 31 ~~~~~~c~a~~~~~~~~~~~~~~RR~aL~~~~gaaa 66 (179)
+...++||++.... ....+||.+|.+++++++
T Consensus 12 ~r~~~~vra~~~~~----~~~~~RRa~l~~l~a~~~ 43 (202)
T PF05757_consen 12 RRAGVVVRASQSPA----QQQTSRRAVLGSLLAAAL 43 (202)
T ss_dssp ------------------------------------
T ss_pred ccccceeccccCcc----cccccHHHHHHHHHHHHH
Confidence 44556688886211 235689999986665544
No 8
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=66.71 E-value=6.1 Score=23.36 Aligned_cols=16 Identities=44% Similarity=0.270 Sum_probs=11.9
Q ss_pred hhhHHHHHHHHHHHhh
Q 030310 52 VSRRLALTVLIGAAAV 67 (179)
Q Consensus 52 ~~RR~aL~~~~gaaa~ 67 (179)
.+||+.|-+.+++++.
T Consensus 2 ~sRR~fLk~~~a~~a~ 17 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAA 17 (26)
T ss_pred CcHHHHHHHHHHHHHH
Confidence 5799999877765543
No 9
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=51.06 E-value=17 Score=28.40 Aligned_cols=31 Identities=35% Similarity=0.148 Sum_probs=16.5
Q ss_pred cchhhHHHHHHHHHHHhhhccCCccccccccc
Q 030310 50 SAVSRRLALTVLIGAAAVGSKVSPADAAYGES 81 (179)
Q Consensus 50 ~~~~RR~aL~~~~gaaa~~s~~~pa~Aayge~ 81 (179)
+...||.+|...+ ++++.+....+.+.+.|+
T Consensus 47 ~~~gRR~~mfaaa-Aaav~s~a~~A~a~~~ep 77 (103)
T PLN00058 47 STTMRRDLMFTAA-AAAVCSLAKVAMAEEEEP 77 (103)
T ss_pred chhhHHHHHHHHH-HHHHHhhhHHHhhcccCC
Confidence 3567888886544 344444444444434343
No 10
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=46.02 E-value=10 Score=30.60 Aligned_cols=19 Identities=26% Similarity=0.557 Sum_probs=15.1
Q ss_pred CCCCcccCCChHHHHHHHH
Q 030310 143 DKKSITDYGSPEEFLSKVD 161 (179)
Q Consensus 143 ~kksI~DlGsPee~~~~Vg 161 (179)
+.+=++|||+|+|+++++-
T Consensus 43 Eeeii~~LG~P~~iA~~i~ 61 (181)
T PF08006_consen 43 EEEIIAELGSPKEIAREIL 61 (181)
T ss_pred HHHHHHHcCCHHHHHHHHH
Confidence 4556789999999887764
No 11
>PF06525 SoxE: Sulfocyanin (SoxE); InterPro: IPR010532 Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterised as functionally different are the rusticyanins.
Probab=42.03 E-value=12 Score=32.19 Aligned_cols=58 Identities=17% Similarity=0.327 Sum_probs=30.1
Q ss_pred cccCCCee-----EecCCCCCCCceeeeCCceEEeeeCCCCCCceEEEEecCCCCCcccCCChHHHHHHHHH
Q 030310 96 PYNGDGFK-----LSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDY 162 (179)
Q Consensus 96 ~y~~DGYs-----FlyPs~Wnpskev~~~G~dv~f~D~~~~~eNvsV~ispt~kksI~DlGsPee~~~~Vgy 162 (179)
.|+++||+ +++|.|| . +.+.|.+.-.-.-|+.|+..++..-.-.++|+-.+++..+|+
T Consensus 75 ~~nfnGts~G~m~i~VPAGw---~------V~i~f~N~~~l~Hnl~iv~~~~~~p~~~~i~~DgkIl~~~G~ 137 (196)
T PF06525_consen 75 PFNFNGTSNGQMTIYVPAGW---N------VQITFTNQESLPHNLVIVQNDTPTPNNPPISSDGKILLYVGA 137 (196)
T ss_pred ceeeecccCCcEEEEEcCCC---E------EEEEEEcCCCCCeeEEEEeCCCCCCCccccCCCCceeeeccC
Confidence 33456665 4899999 2 356666643223366666555533333344443343334444
No 12
>PF07174 FAP: Fibronectin-attachment protein (FAP); InterPro: IPR010801 This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix [].; GO: 0050840 extracellular matrix binding, 0005576 extracellular region
Probab=41.24 E-value=17 Score=33.06 Aligned_cols=29 Identities=24% Similarity=0.546 Sum_probs=20.8
Q ss_pred cCCCeeEecCCCCCCCceeeeC-CceEEee
Q 030310 98 NGDGFKLSIPSKWNPSKEREFP-GQVLRYE 126 (179)
Q Consensus 98 ~~DGYsFlyPs~Wnpskev~~~-G~dv~f~ 126 (179)
...||+|++|.||..|..-+.. |+.+.=+
T Consensus 115 ~~gGFS~vvP~GW~~Sda~~L~yG~alls~ 144 (297)
T PF07174_consen 115 AAGGFSYVVPAGWVESDASHLDYGSALLSK 144 (297)
T ss_pred cccceEEeccCCccccccceeecceeeecc
Confidence 4889999999999666554444 6665554
No 13
>PF12712 DUF3805: Domain of unknown function (DUF3805); InterPro: IPR024315 This entry represents an N-terminal domain found in a family of bacterial proteins, whose function is unknown. In two related Bacteroides species, the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.; PDB: 3HLZ_A.
Probab=39.29 E-value=35 Score=28.40 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=23.0
Q ss_pred cccccCCCeeEecCCCCCCCceeeeCCce-EEeeeCCCCCCceEEEEec
Q 030310 94 FLPYNGDGFKLSIPSKWNPSKEREFPGQV-LRYEDNFDSNSNVSVIITP 141 (179)
Q Consensus 94 F~~y~~DGYsFlyPs~Wnpskev~~~G~d-v~f~D~~~~~eNvsV~isp 141 (179)
|++ .+.=|++.||.+| -|.+ +|-+ ..|-|+-.-+-|.++..-.
T Consensus 4 fiS-pg~WFS~~YP~~W---~EfE-D~E~sflFYnp~~WTGNfRISayk 47 (153)
T PF12712_consen 4 FIS-PGAWFSMEYPADW---NEFE-DGEGSFLFYNPDQWTGNFRISAYK 47 (153)
T ss_dssp EE--GGG-EEEEE-TT----EEE----TTEEEEE-SSS---EEEEEEEE
T ss_pred ccC-CCceEEEecCCCc---chhc-cCCcceEEEChHHhcCceEEEEEe
Confidence 565 5667999999999 8876 5433 4466777778898876654
No 14
>PF13561 adh_short_C2: Enoyl-(Acyl carrier protein) reductase; PDB: 2UV8_B 3HMJ_A 2VKZ_C 1O5I_A 2P91_C 2OP0_A 2OL4_B 1NHW_A 1NNU_B 2O2Y_B ....
Probab=34.57 E-value=21 Score=28.78 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=24.1
Q ss_pred CCcccCCChHHHHHHHHHHHHhh--hhcccC
Q 030310 145 KSITDYGSPEEFLSKVDYLLGKQ--AYSGKT 173 (179)
Q Consensus 145 ksI~DlGsPee~~~~Vgy~L~kq--~~~g~t 173 (179)
.-+..+|+|||+++-|-||+..+ .+.|++
T Consensus 203 ~pl~r~~~~~evA~~v~fL~s~~a~~itG~~ 233 (241)
T PF13561_consen 203 IPLGRLGTPEEVANAVLFLASDAASYITGQV 233 (241)
T ss_dssp STTSSHBEHHHHHHHHHHHHSGGGTTGTSEE
T ss_pred hccCCCcCHHHHHHHHHHHhCccccCccCCe
Confidence 45567899999999999999987 677765
No 15
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=34.46 E-value=88 Score=24.16 Aligned_cols=43 Identities=26% Similarity=0.258 Sum_probs=31.7
Q ss_pred CCCCCCceEEEEecCCCCCcccCC-C----hHHHHHHHHHHHHhhhhc
Q 030310 128 NFDSNSNVSVIITPTDKKSITDYG-S----PEEFLSKVDYLLGKQAYS 170 (179)
Q Consensus 128 ~~~~~eNvsV~ispt~kksI~DlG-s----Pee~~~~Vgy~L~kq~~~ 170 (179)
+++...+..+....|-.+.|.++| . =-+.+..||++|++.+..
T Consensus 39 ii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~ 86 (119)
T PF00861_consen 39 IIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALE 86 (119)
T ss_dssp EEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHH
T ss_pred EEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHH
Confidence 455556666677777677888876 2 257889999999999875
No 16
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=34.07 E-value=32 Score=28.27 Aligned_cols=8 Identities=50% Similarity=0.609 Sum_probs=5.9
Q ss_pred hhhHHHHH
Q 030310 52 VSRRLALT 59 (179)
Q Consensus 52 ~~RR~aL~ 59 (179)
.+||.+|+
T Consensus 2 ~sRR~~L~ 9 (168)
T PF12318_consen 2 LSRRRLLA 9 (168)
T ss_pred CcHHHHHH
Confidence 46888883
No 17
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=33.01 E-value=80 Score=27.20 Aligned_cols=56 Identities=21% Similarity=0.186 Sum_probs=34.3
Q ss_pred CceEEeeeCCCCC---CceEEEEecCC--CCCcccCCChHHHHHHHHHHHHhh----hhcccCcc
Q 030310 120 GQVLRYEDNFDSN---SNVSVIITPTD--KKSITDYGSPEEFLSKVDYLLGKQ----AYSGKTSS 175 (179)
Q Consensus 120 G~dv~f~D~~~~~---eNvsV~ispt~--kksI~DlGsPee~~~~Vgy~L~kq----~~~g~t~s 175 (179)
|..++|+=..-++ +.+.+++.+.+ -.+++|||-+++.++.+-.++.+. +++|.|-|
T Consensus 27 ~~~~~~Rv~~~p~~~G~~~~iR~~~~~~~~~~l~~lg~~~~~~~~l~~~~~~~~GlilisG~tGS 91 (264)
T cd01129 27 GREIDLRVSTLPTIYGESVVLRILDKKNQILDLEKLGLKPENLEIFRKLLEKPHGIILVTGPTGS 91 (264)
T ss_pred CcEEEEEEEEeecCCCCEEEEEEeCCccCCCCHHHcCCCHHHHHHHHHHHhcCCCEEEEECCCCC
Confidence 3334444333333 57888887754 368999999998777776555422 35555543
No 18
>PF10916 DUF2712: Protein of unknown function (DUF2712); InterPro: IPR020208 This entry represents a group of uncharacterised proteins.
Probab=29.86 E-value=1.5e+02 Score=24.68 Aligned_cols=44 Identities=20% Similarity=0.189 Sum_probs=31.3
Q ss_pred CCCeeEecCCCCCCCceeeeCCceEEeeeCCCCCCceEEEEecC--CCCCcc
Q 030310 99 GDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPT--DKKSIT 148 (179)
Q Consensus 99 ~DGYsFlyPs~Wnpskev~~~G~dv~f~D~~~~~eNvsV~ispt--~kksI~ 148 (179)
.=+|.|.+|..- .. .+-+-|||..-...++--|.+... .|.+|.
T Consensus 34 ~i~F~F~i~~~~---an---sys~~ryRqTt~t~n~WKV~l~~StEGkGTi~ 79 (146)
T PF10916_consen 34 NIPFSFTIKPNQ---AN---SYSGSRYRQTTSTNNPWKVNLTYSTEGKGTIY 79 (146)
T ss_pred CCceEEEeCCcc---cc---cccCceeeccCCCCCccEEeccccccccceEE
Confidence 457899998876 33 567788888888877777777643 565654
No 19
>COG4709 Predicted membrane protein [Function unknown]
Probab=29.08 E-value=33 Score=29.67 Aligned_cols=31 Identities=19% Similarity=0.147 Sum_probs=22.0
Q ss_pred CCCcccCCChHHHHHHHH-HHHHhhhhcccCc
Q 030310 144 KKSITDYGSPEEFLSKVD-YLLGKQAYSGKTS 174 (179)
Q Consensus 144 kksI~DlGsPee~~~~Vg-y~L~kq~~~g~t~ 174 (179)
.+=+.|||+|+|++..+- ..++|+.-.-+|.
T Consensus 44 ~EI~~~LG~P~eiA~ei~s~~~~k~~~~~~~~ 75 (195)
T COG4709 44 EEIAKDLGDPKEIAAEILSERGIKKEEVKPTQ 75 (195)
T ss_pred HHHHHHhCCHHHHHHHHHHHccchHHhccCcc
Confidence 345789999999887765 6677776554443
No 20
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
Probab=27.05 E-value=77 Score=29.18 Aligned_cols=42 Identities=17% Similarity=0.316 Sum_probs=28.4
Q ss_pred ceEEEEecCCCCCcccCCChHHHHHHHHHHHHhhhhcccCcc
Q 030310 134 NVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSS 175 (179)
Q Consensus 134 NvsV~ispt~kksI~DlGsPee~~~~Vgy~L~kq~~~g~t~s 175 (179)
.+.+++.|.+..+++++|-|+++++.+-..-|--++.|.|-|
T Consensus 119 ~i~iR~~~~~~~~l~~lgl~~~~~~~l~~~~GlilI~G~TGS 160 (372)
T TIGR02525 119 SLTLRVIPSDIPDLKQMGIEPDLFNSLLPAAGLGLICGETGS 160 (372)
T ss_pred eEEEEeCCCcCCCHHHcCCCHHHHHHHHhcCCEEEEECCCCC
Confidence 566777777788999999999887665443333345555543
No 21
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=25.43 E-value=60 Score=23.10 Aligned_cols=13 Identities=38% Similarity=0.036 Sum_probs=9.3
Q ss_pred chhhHHHHHHHHH
Q 030310 51 AVSRRLALTVLIG 63 (179)
Q Consensus 51 ~~~RR~aL~~~~g 63 (179)
.++||..|.++++
T Consensus 8 ~~sRR~Flk~lg~ 20 (66)
T TIGR02811 8 DPSRRDLLKGLGV 20 (66)
T ss_pred CccHHHHHHHHHH
Confidence 4689998875544
No 22
>PF04674 Phi_1: Phosphate-induced protein 1 conserved region; InterPro: IPR006766 This entry represents a family of conserved plant proteins. A conserved region in these proteins was identified in a phosphate-induced protein of unknown function [].
Probab=24.67 E-value=58 Score=29.32 Aligned_cols=34 Identities=26% Similarity=0.683 Sum_probs=23.3
Q ss_pred ccccCC-------------CCCCCCcccccCCCeeEecCCCCCCCce
Q 030310 82 ANVFGK-------------PKTNTDFLPYNGDGFKLSIPSKWNPSKE 115 (179)
Q Consensus 82 anvFg~-------------p~~~~~F~~y~~DGYsFlyPs~Wnpske 115 (179)
+.+||+ +.+--.|.-+-..|=+||+|.-|||.+.
T Consensus 221 ~giyG~Gaypgy~G~l~vD~~tGaSyN~~G~~gRkfLlpa~wdP~t~ 267 (273)
T PF04674_consen 221 AGIYGSGAYPGYPGQLLVDPATGASYNANGVNGRKFLLPALWDPETS 267 (273)
T ss_pred cccccCCCCCCCCcceeecCCCCceeeccccCCceEEeecccCCCcC
Confidence 678986 2233334443367889999999999754
No 23
>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=21.99 E-value=1.1e+02 Score=25.18 Aligned_cols=10 Identities=30% Similarity=0.767 Sum_probs=7.6
Q ss_pred eeeeeccccc
Q 030310 34 QIVCRAQKQA 43 (179)
Q Consensus 34 ~~~c~a~~~~ 43 (179)
.+.|.++++.
T Consensus 43 ~v~cs~~~~~ 52 (138)
T PF07123_consen 43 RVRCSAEKKP 52 (138)
T ss_pred ceEEEeccCc
Confidence 5889988764
No 24
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=21.47 E-value=1.2e+02 Score=27.69 Aligned_cols=13 Identities=31% Similarity=0.248 Sum_probs=9.2
Q ss_pred hhHHHHHHHHHHH
Q 030310 53 SRRLALTVLIGAA 65 (179)
Q Consensus 53 ~RR~aL~~~~gaa 65 (179)
.||..|.++++++
T Consensus 2 ~RR~fl~~~~~~~ 14 (328)
T PRK10882 2 NRRNFLKAASAGA 14 (328)
T ss_pred CHHHHHHHHHHHH
Confidence 5999998765443
No 25
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=20.37 E-value=99 Score=20.24 Aligned_cols=13 Identities=31% Similarity=0.276 Sum_probs=7.3
Q ss_pred chhhHHHHHHHHH
Q 030310 51 AVSRRLALTVLIG 63 (179)
Q Consensus 51 ~~~RR~aL~~~~g 63 (179)
..+||..|....+
T Consensus 8 ~~~RRdFL~~at~ 20 (41)
T PF10399_consen 8 DPTRRDFLTIATS 20 (41)
T ss_dssp --HHHHHHHHHHH
T ss_pred CchHHHHHHHHHH
Confidence 5678888854443
Done!