Query 023424
Match_columns 282
No_of_seqs 178 out of 274
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:55:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023424.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023424hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00067 PsbP domain-containin 100.0 5.8E-67 1.3E-71 477.1 21.2 217 64-282 42-258 (263)
2 PLN00042 photosystem II oxygen 100.0 1.8E-49 3.8E-54 363.0 18.5 206 35-282 28-254 (260)
3 PLN00066 PsbP domain-containin 100.0 1.8E-48 3.8E-53 358.1 19.4 210 58-282 38-253 (262)
4 PLN00059 PsbP domain-containin 100.0 2.5E-41 5.3E-46 309.4 15.4 179 61-282 73-279 (286)
5 PLN03152 hypothetical protein; 100.0 7.9E-39 1.7E-43 286.3 13.7 203 60-282 26-235 (241)
6 PF01789 PsbP: PsbP; InterPro 100.0 2.5E-36 5.4E-41 262.3 11.6 145 107-282 20-169 (175)
7 PF08786 DUF1795: Domain of un 97.3 0.0043 9.4E-08 51.0 11.3 120 132-280 3-125 (130)
8 PRK11615 hypothetical protein; 86.5 19 0.00042 32.4 12.3 124 130-275 49-172 (185)
9 COG5435 Uncharacterized conser 79.4 24 0.00052 30.8 9.8 109 132-269 10-123 (147)
10 PF10518 TAT_signal: TAT (twin 79.0 2.4 5.1E-05 26.3 2.6 15 65-79 2-16 (26)
11 TIGR02811 formate_TAT formate 75.4 4 8.7E-05 30.7 3.5 15 64-78 8-22 (66)
12 TIGR01409 TAT_signal_seq Tat ( 66.3 6.2 0.00013 24.7 2.4 15 65-79 1-15 (29)
13 COG3212 Predicted membrane pro 63.4 29 0.00063 29.9 6.7 51 197-268 84-134 (144)
14 PF05757 PsbQ: Oxygen evolving 56.9 3.6 7.9E-05 37.4 0.0 12 61-72 25-36 (202)
15 PF07174 FAP: Fibronectin-atta 56.7 1.2E+02 0.0027 29.1 10.1 22 129-150 117-138 (297)
16 smart00564 PQQ beta-propeller 48.2 23 0.00051 21.5 2.8 22 252-273 11-32 (33)
17 COG4784 Putative Zn-dependent 41.7 55 0.0012 32.7 5.5 19 129-147 295-313 (479)
18 PF07009 DUF1312: Protein of u 39.6 40 0.00087 27.3 3.6 45 226-270 32-81 (113)
19 PF10738 Lpp-LpqN: Probable li 39.5 2.4E+02 0.0052 25.0 8.7 41 130-182 32-77 (175)
20 PF09211 DUF1958: Domain of un 35.0 38 0.00083 25.6 2.6 38 218-261 3-45 (65)
21 PF10399 UCR_Fe-S_N: Ubiquitin 31.6 38 0.00083 23.2 1.9 10 63-72 7-16 (41)
22 PF15495 Fimbrillin_C: Major f 28.2 1.4E+02 0.003 23.3 4.8 40 227-266 5-45 (85)
23 PF08166 NUC202: NUC202 domain 27.3 22 0.00047 26.7 0.1 26 8-33 23-48 (61)
24 PF01011 PQQ: PQQ enzyme repea 25.7 45 0.00098 21.5 1.4 24 252-275 5-28 (38)
25 PLN02729 PSII-Q subunit 23.8 71 0.0015 29.5 2.8 47 26-77 12-61 (220)
26 PF05137 PilN: Fimbrial assemb 23.1 1.8E+02 0.0038 21.0 4.4 27 214-240 51-77 (78)
27 PF08006 DUF1700: Protein of u 22.1 44 0.00095 29.0 1.1 20 189-208 44-63 (181)
28 smart00456 WW Domain with 2 co 21.3 62 0.0013 19.8 1.4 19 256-274 12-30 (32)
29 PF09478 CBM49: Carbohydrate b 21.1 1.8E+02 0.0039 22.0 4.1 32 226-259 12-43 (80)
No 1
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=5.8e-67 Score=477.13 Aligned_cols=217 Identities=81% Similarity=1.276 Sum_probs=206.7
Q ss_pred cchhHHHHHHhhhhhHhhhhcCCCCccccccccccccCCCCCCCCCceEEecCCCCCccccCCCCCCeEEEcCCCCccce
Q 023424 64 PILRREILKGLAVIPVTLIINKEPPYSEAREVEVGSYLPPSPTDPSFVFFKASPKDTPALRAGNVQPYQFVLPPSWKQMR 143 (282)
Q Consensus 64 ~~sRR~~L~~~a~~aa~~~~~~~~~~a~A~~~~~g~~~p~~~~~~gf~~y~~~~~~tp~~~~~~~dgY~F~yP~gW~~~~ 143 (282)
.++||++|+|+++..+ ++...++++.|.|+++|.|||+.++++||+.|.+++++||+||+|++.||+|+||+||++++
T Consensus 42 ~~~rr~~~~~~~~~~~--~~~~~~~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~ 119 (263)
T PLN00067 42 VIHRRELLLGLALAPL--ILIAPEPPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTR 119 (263)
T ss_pred hhHHHHHHhhhhhhhh--hhccCCchhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCcc
Confidence 5789999999887753 33445678999999999999999999999999999999999999999999999999999999
Q ss_pred eccccCCCcCCCCCCCCcceEEEeeCCCceEEEEEecCcccCCCCCCCccccCCHHHHHHhhcccccCCCCCCCceEEee
Q 023424 144 VANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVASPLIRLTNKPNASIEEIGSPEKVIASLGPFVTGNSYDPDELIETS 223 (282)
Q Consensus 144 v~~~~sG~~~~p~~~~~~~dv~F~d~~~enVsVvVsP~~~L~~~~~~sI~dlGspeev~~~l~~~~~~~~~~~a~Ll~a~ 223 (282)
|+++++||||||+|+|||+|++|+|+.+|||+|||+|+.+|+++++++|+|||+|++|+++|++.++++++++++||+++
T Consensus 120 Vs~~~sGnycqp~c~~p~~dv~F~D~~dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~v~g~~~~~~eLLeAs 199 (263)
T PLN00067 120 VANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPFVTGNSYDPDELLETS 199 (263)
T ss_pred ccccccCccccccccCCCceEEEeCCCCCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHHhhcCCCCCcceEEee
Confidence 99999999999999999999999999999999999999999988899999999999999999999999999999999999
Q ss_pred EEEeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeEEEEEeeeCcccccchhhhccccC
Q 023424 224 VEKVGDQMYYNYLLETPFALTGTHNLAKATAKGSTVVLFVASANDKQWAGVTESFENHA 282 (282)
Q Consensus 224 ~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkLYtl~a~a~ekrW~k~~~~lr~~a 282 (282)
+++.||++||+|||.+++++++||+|+++||++||||||++++||+||+|+++.|++|+
T Consensus 200 ~re~dGktYY~~E~~tp~a~~gRHnLataTV~~GkLYtf~asanEkRW~K~k~~l~~V~ 258 (263)
T PLN00067 200 VEKIGDQTYYKYVLETPFALTGSHNLAKATAKGNTVVLFVVSASDKQWQSSEKTLKAIL 258 (263)
T ss_pred eEeeCCeEEEEEEEEecCCCCCceEEEEEEEECCEEEEEEecCCHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999874
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=1.8e-49 Score=363.00 Aligned_cols=206 Identities=26% Similarity=0.375 Sum_probs=169.9
Q ss_pred cccCCCCCchhhhhhhhhhccCCCCCCCCcchhHHHHHHhhhhhHhhhhcCCCCccccccccccccCCCCCCCCCceEEe
Q 023424 35 SASNGRKPSNKIQRALTAFHQKGNECTRTPILRREILKGLAVIPVTLIINKEPPYSEAREVEVGSYLPPSPTDPSFVFFK 114 (282)
Q Consensus 35 ~a~~~~~~s~~~~~~~~~~~~~~~~~~~~~~sRR~~L~~~a~~aa~~~~~~~~~~a~A~~~~~g~~~p~~~~~~gf~~y~ 114 (282)
++.+..++++..||++ +. ....++||.+|+.+++++| +++...|+.+|++ +.+++|+++++++||.+|.
T Consensus 28 ~~~~~~~~~~~~~~~~-----~~---~~~~~srr~~l~~~~ga~a--~~~~~~pa~aay~-~~anvfg~~k~~~gF~~y~ 96 (260)
T PLN00042 28 RAVSASRPSQVVCRAQ-----EE---DNSAVSRRAALALLAGAAA--AGAKVSPANAAYG-ESANVFGKPKTNTGFLPYN 96 (260)
T ss_pred cccCCCCCcceeeecc-----cc---ccccccHHHHHHHHHHHHH--hhcccCchhhhhc-chhhccCCCCCCCCCeEee
Confidence 3345555555555553 22 1235889999877776654 4566677777775 6789999999999999998
Q ss_pred cCCCCCccccCCCCCCeEEEcCCCCccceeccccCCCcCCCCCCCCcceEEEee--CCCceEEEEEecCcccCCCCCCCc
Q 023424 115 ASPKDTPALRAGNVQPYQFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFED--EKQGKVQVVASPLIRLTNKPNASI 192 (282)
Q Consensus 115 ~~~~~tp~~~~~~~dgY~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d--~~~enVsVvVsP~~~L~~~~~~sI 192 (282)
+ |||+|+||++|+++++.+ +||+|++|+| +.++||+|+|+|++ +++|
T Consensus 97 ~-------------dgY~FlyP~~W~~~ke~~------------~~G~dv~f~D~~~~~eNVSV~Ispt~------k~sI 145 (260)
T PLN00042 97 G-------------DGFKLLVPSKWNPSKERE------------FPGQVLRFEDNFDATSNLSVMVTPTD------KKSI 145 (260)
T ss_pred C-------------CCeEEecCCCCccccccc------------cCCceEEeeccccccccEEEEEecCC------cCCH
Confidence 5 999999999999998765 6789999999 89999999999998 6899
Q ss_pred cccCCHHH----HHHhhcccccCCC-----C------CCCceEEeeEEEeCCeEEEEEEEEeccCC---CCceEEEEEEE
Q 023424 193 EEIGSPEK----VIASLGPFVTGNS-----Y------DPDELIETSVEKVGDQMYYNYLLETPFAL---TGTHNLAKATA 254 (282)
Q Consensus 193 ~dlGspee----v~~~l~~~~~~~~-----~------~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~---~~rH~LasatV 254 (282)
+|||+||| |++.|+++++.++ + .+++||+++++++||++||+|||.+++++ ++||+|+++||
T Consensus 146 ~dlGsPee~l~~vgylL~kq~~a~~t~s~~Gf~p~~vata~Lleas~re~dGk~YY~lE~~~~~ad~d~~~RH~LatatV 225 (260)
T PLN00042 146 TDYGSPEEFLSKVSYLLGKQAYSGETASEGGFDANAVATAAVLESSTQEVGGKPYYYLSVLTRTADGDEGGKHQLITATV 225 (260)
T ss_pred hhcCCHHHHHHHHHHHHHhhhccCccccccCcCcccccceeEEEeeeEEeCCeEEEEEEEEEecCCCCCCCceEEEEEEE
Confidence 99999999 6667777776522 2 36799999999999999999999999997 78999999999
Q ss_pred eCCeEEEEEeeeCcccccch-hhhccccC
Q 023424 255 KGSTVVLFVASANDKQWAGV-TESFENHA 282 (282)
Q Consensus 255 ~~GkLYtl~a~a~ekrW~k~-~~~lr~~a 282 (282)
++||||||++|+||+||+|+ ++.|++++
T Consensus 226 ~~GkLYtl~aqa~EkRW~K~~~k~l~~v~ 254 (260)
T PLN00042 226 SDGKLYICKAQAGDKRWFKGARKFVEGAA 254 (260)
T ss_pred ECCEEEEEEecCchhhhhHHHHHHHHHHH
Confidence 99999999999999999999 44677663
No 3
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=100.00 E-value=1.8e-48 Score=358.11 Aligned_cols=210 Identities=26% Similarity=0.481 Sum_probs=182.8
Q ss_pred CCCCCCcchhHHHHHHhhhhhHhhhhcCCCCcccc-ccccccccCCC-CCCCCCceEEecCCCCC--ccccCCCCCCeEE
Q 023424 58 NECTRTPILRREILKGLAVIPVTLIINKEPPYSEA-REVEVGSYLPP-SPTDPSFVFFKASPKDT--PALRAGNVQPYQF 133 (282)
Q Consensus 58 ~~~~~~~~sRR~~L~~~a~~aa~~~~~~~~~~a~A-~~~~~g~~~p~-~~~~~gf~~y~~~~~~t--p~~~~~~~dgY~F 133 (282)
++++...++||.+|+++++++...+++...+..+| +++.+|++++. .++..||..|+.++.++ +|++|..+.+|+|
T Consensus 38 ~~~~~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F 117 (262)
T PLN00066 38 TEDVATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSF 117 (262)
T ss_pred hhhhcchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEE
Confidence 55566788999999876666322222332333334 89999998775 56678999999988888 8999999999999
Q ss_pred EcCCCCccceeccccCCCcCCCCCCCCcceEEEeeCCCceEEEEEecCcccCCC--CCCCccccCCHHHHHHhhcccccC
Q 023424 134 VLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVASPLIRLTNK--PNASIEEIGSPEKVIASLGPFVTG 211 (282)
Q Consensus 134 ~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d~~~enVsVvVsP~~~L~~~--~~~sI~dlGspeev~~~l~~~~~~ 211 (282)
+||+||++++|+++..| -+++|++|.|+.++||+|+|+|+.||+++ ++++|+|||+||+|++.|++++++
T Consensus 118 ~yP~GW~ev~VS~~d~g--------g~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~g 189 (262)
T PLN00066 118 KVPQGWEEVPVSIADLG--------GTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELIG 189 (262)
T ss_pred ECCCCCeEeecccccCC--------CCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhcC
Confidence 99999999999988544 14899999999999999999999999876 899999999999999999999999
Q ss_pred CCCCCCceEEeeEEEeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeEEEEEeeeCcccccchhhhccccC
Q 023424 212 NSYDPDELIETSVEKVGDQMYYNYLLETPFALTGTHNLAKATAKGSTVVLFVASANDKQWAGVTESFENHA 282 (282)
Q Consensus 212 ~~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkLYtl~a~a~ekrW~k~~~~lr~~a 282 (282)
.+.++++|+++++++.+|++||+||| .+|+|++|||++||||+|++++||+||+|++++|++|+
T Consensus 190 ~~~~e~eLl~a~~re~dGktYY~~E~-------~rH~LasaTV~~GrLYt~~asape~rW~k~~~~lr~v~ 253 (262)
T PLN00066 190 EPVEEGKVLSMEVAEHSGRTYYQFEL-------PPHTLVTATAAGNRVYIFSVTANGLQWKRHYKDLKRIA 253 (262)
T ss_pred CCccccceeEeeeeecCCcEEEEEEE-------eCceEEEEEEECCEEEEEEeecchHhhHHHHHHHHHHh
Confidence 88899999999999999999999999 27999999999999999999999999999999999874
No 4
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=2.5e-41 Score=309.35 Aligned_cols=179 Identities=18% Similarity=0.226 Sum_probs=147.9
Q ss_pred CCCcchhHHHHHHhhhhhHhhhhcCC-CCccccccccccccCCCCCCCCCceEEecCCCCCccccCCCCCCeEEEcCCCC
Q 023424 61 TRTPILRREILKGLAVIPVTLIINKE-PPYSEAREVEVGSYLPPSPTDPSFVFFKASPKDTPALRAGNVQPYQFVLPPSW 139 (282)
Q Consensus 61 ~~~~~sRR~~L~~~a~~aa~~~~~~~-~~~a~A~~~~~g~~~p~~~~~~gf~~y~~~~~~tp~~~~~~~dgY~F~yP~gW 139 (282)
..+.+.||.++ .++++.++++.+.+ .++++|+ .+||..|.+ ..|||+|+||.||
T Consensus 73 ~~~~~~rr~~~-~~~l~~~~~~~s~~~~~~a~a~-------------~~~l~~y~D-----------~~DGY~FlYP~GW 127 (286)
T PLN00059 73 QVCAVGRRKSM-MMGLLMSGLIVSEANLPTAFAS-------------IPVFREYID-----------TFDGYSFKYPQNW 127 (286)
T ss_pred hhhhhhhhhhh-HHHHHHHHHHHHhhcCchhhcC-------------CcccceeEc-----------CCCCeEEeCCCCC
Confidence 44678999886 23333333443332 2344442 138999995 5699999999999
Q ss_pred ccceeccccCCCcCCCCCCCCcceEEEee--CCCceEEEEEecCcccCCCCCCCccccCCHHHHHHhhcccccC------
Q 023424 140 KQMRVANILSGNYCQPKCAEPWVEVKFED--EKQGKVQVVASPLIRLTNKPNASIEEIGSPEKVIASLGPFVTG------ 211 (282)
Q Consensus 140 ~~~~v~~~~sG~~~~p~~~~~~~dv~F~d--~~~enVsVvVsP~~~L~~~~~~sI~dlGspeev~~~l~~~~~~------ 211 (282)
.++... |+|++|+| +.+|||+|+|+|+.. .++++|+|||+|+||+++|++++++
T Consensus 128 i~V~~~---------------G~DVvFrD~Ie~~ENVSV~ISs~ss---s~~~sLeDLGsP~eVgerLlkqvLa~f~str 189 (286)
T PLN00059 128 IQVRGA---------------GADIFFRDPVVLDENLSVEFSSPSS---SKYTSLEDLGSPEEVGKRVLRQYLTEFMSTR 189 (286)
T ss_pred eEeccC---------------CCceEEeccCccccceEEEEecCCc---ccCCChHHcCCHHHHHHHHHHHHhccccccc
Confidence 999843 49999999 999999999998761 1279999999999999999999887
Q ss_pred -CCCCCCceEEeeEEEe-CCeEEEEEEEEeccC-----------------CCCceEEEEEEEeCCeEEEEEeeeCccccc
Q 023424 212 -NSYDPDELIETSVEKV-GDQMYYNYLLETPFA-----------------LTGTHNLAKATAKGSTVVLFVASANDKQWA 272 (282)
Q Consensus 212 -~~~~~a~Ll~a~~r~~-dG~tYY~yE~~~~~~-----------------~~~rH~LasatV~~GkLYtl~a~a~ekrW~ 272 (282)
+++++++||++++|+. ||++||+|||.+.+. +|.||+|++++|.+||||||++|+||+||.
T Consensus 190 ~GsgReaeLVsA~~Re~~DGktYY~lEY~Vks~~~~n~~~~~~qdr~~~~~w~RH~LA~v~V~nGkLYTL~~qtpE~RW~ 269 (286)
T PLN00059 190 LGVKREANILSTSSRVADDGKLYYQVEVNIKSYANNNELAVMPQDRVARLEWNRRYLAVLGVENDRLYSIRLQTPEKVFL 269 (286)
T ss_pred CCCCcceEEEEeeeEEccCCcEEEEEEEEEEcCcccccccccccccccccccceeeEEEEEEeCCEEEEEEcCCcHHHHH
Confidence 3468999999999977 999999999999984 469999999999999999999999999999
Q ss_pred chhhhccccC
Q 023424 273 GVTESFENHA 282 (282)
Q Consensus 273 k~~~~lr~~a 282 (282)
|+++.|++++
T Consensus 270 kvk~~f~~V~ 279 (286)
T PLN00059 270 EEEKDLRRVM 279 (286)
T ss_pred HHHHHHHHHH
Confidence 9999999873
No 5
>PLN03152 hypothetical protein; Provisional
Probab=100.00 E-value=7.9e-39 Score=286.33 Aligned_cols=203 Identities=18% Similarity=0.224 Sum_probs=163.3
Q ss_pred CCCCcchhHHHHHHhhhhhHhhhhcC-CCCcccccccc-ccccCCCCCCCCCceEEecCCCCCccccCCCCCCeEEEcCC
Q 023424 60 CTRTPILRREILKGLAVIPVTLIINK-EPPYSEAREVE-VGSYLPPSPTDPSFVFFKASPKDTPALRAGNVQPYQFVLPP 137 (282)
Q Consensus 60 ~~~~~~sRR~~L~~~a~~aa~~~~~~-~~~~a~A~~~~-~g~~~p~~~~~~gf~~y~~~~~~tp~~~~~~~dgY~F~yP~ 137 (282)
.+.|..+||+++++++.+++..+.+. ..+++.|.... ...++....++..|++|++ +||++.||+
T Consensus 26 ~~~~~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~~g-------------~gf~~~~pp 92 (241)
T PLN03152 26 LSRCGASRRDFILHTASLCASSLAAQNPLPPSLADPSKPSKPLLSGIANTKSWFQFYG-------------DGFSIRVPP 92 (241)
T ss_pred cccccccccceeeehhHHHHhhhhcCCCCCccccCCCCCCCchheeeecchhhhhhhC-------------CceEEeCCC
Confidence 36788999999999998886543322 12344443222 2334556778889999997 999999999
Q ss_pred CCccceeccc-cCC-CcCCCCCCCCcceEEEee-CCCceEEEEEecCcccC--CCCCCCccccCCHHHHHHhhcccccCC
Q 023424 138 SWKQMRVANI-LSG-NYCQPKCAEPWVEVKFED-EKQGKVQVVASPLIRLT--NKPNASIEEIGSPEKVIASLGPFVTGN 212 (282)
Q Consensus 138 gW~~~~v~~~-~sG-~~~~p~~~~~~~dv~F~d-~~~enVsVvVsP~~~L~--~~~~~sI~dlGspeev~~~l~~~~~~~ 212 (282)
+|+++.+.+. ..| .++.++.+.....+||.+ |++|||||+|+|+++|| +.++++|+|||+|+||++.|+|.- +
T Consensus 93 ~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~EVgkv~vP~g--~ 170 (241)
T PLN03152 93 SFEDIMEPEDYNAGLSLYGDKAKPRTFAARFASPDGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKEAAKIFVPGG--A 170 (241)
T ss_pred ChhhhcChhhcccccceecCCCCCcceeeeecCCCCCceEEEEEecCccccccccccCChhHcCCHHHHHHhhCCCc--c
Confidence 9999987654 445 677778777889999999 99999999999999876 789999999999999999998731 1
Q ss_pred CCCCCceEEeeEEEeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeEEEEEeeeCcccccchhhhccccC
Q 023424 213 SYDPDELIETSVEKVGDQMYYNYLLETPFALTGTHNLAKATAKGSTVVLFVASANDKQWAGVTESFENHA 282 (282)
Q Consensus 213 ~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkLYtl~a~a~ekrW~k~~~~lr~~a 282 (282)
....+.+++. +++.||++||+|||.++ +||+|++|||++||||||+++++|+||+|++++|++++
T Consensus 171 ~~~saR~iel-~~E~dGKtYY~lEy~v~----~RH~LaTVaVsrGKLYTl~aSt~EkRW~Kvk~kfr~aa 235 (241)
T PLN03152 171 TLYSARTIKV-KEEEGIRTYYFYEFGRD----EQHVALVATVNSGKAYIAGATAPESKWDDDGVKLRSAA 235 (241)
T ss_pred cccccceeee-eeecCCceeEEEEEEeC----CcEEEEEEEEcCCeEEEEecCCchhchHHHHHHHHHHH
Confidence 0112344444 45889999999999986 89999999999999999999999999999999999874
No 6
>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=100.00 E-value=2.5e-36 Score=262.27 Aligned_cols=145 Identities=28% Similarity=0.454 Sum_probs=129.4
Q ss_pred CCCceEEecCCCCCccccCCCCCCeEEEcCCCCccceeccccCCCcCCCCCCCCcceEEEee--CCCceEEEEEecCccc
Q 023424 107 DPSFVFFKASPKDTPALRAGNVQPYQFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFED--EKQGKVQVVASPLIRL 184 (282)
Q Consensus 107 ~~gf~~y~~~~~~tp~~~~~~~dgY~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d--~~~enVsVvVsP~~~L 184 (282)
..||.+|.++ .+||+|.||.+|+++.+. |+|++|+| +.++||+|+|+|+.+
T Consensus 20 ~~~~~~y~d~-----------~~~y~f~~P~gW~~~~~~---------------G~~v~f~d~~~~~~nvsV~v~p~~~- 72 (175)
T PF01789_consen 20 STGFQPYTDS-----------DDGYSFLYPSGWEEVDVS---------------GADVVFRDPIDADENVSVVVSPVPK- 72 (175)
T ss_dssp -SSEEEEEEC-----------TTTEEEEEETTEEEEEST---------------TEEEEEEETTETTSEEEEEEEE-ST-
T ss_pred CCCceEEEcC-----------CCCEEEECCCCCeecCCC---------------CeEEEEECcccccceEEEEEEecCC-
Confidence 4799999863 489999999999888763 49999999 789999999999994
Q ss_pred CCCCCCCccccCCHHHHHHhhcccccCCCC--CCCceEEeeEEEeCCeEEEEEEEEeccCC-CCceEEEEEEEeCCeEEE
Q 023424 185 TNKPNASIEEIGSPEKVIASLGPFVTGNSY--DPDELIETSVEKVGDQMYYNYLLETPFAL-TGTHNLAKATAKGSTVVL 261 (282)
Q Consensus 185 ~~~~~~sI~dlGspeev~~~l~~~~~~~~~--~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~-~~rH~LasatV~~GkLYt 261 (282)
.++|+|||+|++|+++|++..++..+ +.++||++.+++.+|++||+|||.++.++ +.||+|+++||.+||||+
T Consensus 73 ----~~sl~~lGs~~~va~~l~~~~~~~~~~~~~a~li~a~~~~~~g~~yY~~Ey~~~~~~~~~rh~l~~~tv~~g~lY~ 148 (175)
T PF01789_consen 73 ----DFSLEDLGSPEEVAERLLNGELASPGSGREAELISASEREVDGKTYYEYEYTVQSPNEGRRHNLAVVTVKNGKLYT 148 (175)
T ss_dssp ----S-SGGGG-SHHHHHHHHHHHCCCHCTSSEEEEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEE
T ss_pred ----cCchhhcCCHHHHHHHHhhhhcccccCCcceEEEEeeeeecCCccEEEEEEEeccCCCcccEEEEEEEEECCEEEE
Confidence 55999999999999999998877443 88999999999999999999999999988 889999999999999999
Q ss_pred EEeeeCcccccchhhhccccC
Q 023424 262 FVASANDKQWAGVTESFENHA 282 (282)
Q Consensus 262 l~a~a~ekrW~k~~~~lr~~a 282 (282)
|+++++|+||+|++++|++|+
T Consensus 149 l~~~a~e~~w~k~~~~l~~iv 169 (175)
T PF01789_consen 149 LTAQAPESRWDKVEPKLRKIV 169 (175)
T ss_dssp EEEEEEHHHHHTCHHHHHHHH
T ss_pred EEEEcCHHHHHHHHHHHHHHH
Confidence 999999999999999999863
No 7
>PF08786 DUF1795: Domain of unknown function (DUF1795); InterPro: IPR014894 This is a bacterial protein of unknown function. It forms an antiparallel beta sheet structure and contains some alpha helical regions. ; PDB: 1TU1_A 3LYD_A.
Probab=97.30 E-value=0.0043 Score=51.00 Aligned_cols=120 Identities=14% Similarity=0.113 Sum_probs=78.2
Q ss_pred EEEcCCCCccceeccccCCCcCCCCCCCCcceEEEeeCCCceEEEEEe--cCcccCCCCCCCccccCCHHHHHHhhcccc
Q 023424 132 QFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVAS--PLIRLTNKPNASIEEIGSPEKVIASLGPFV 209 (282)
Q Consensus 132 ~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d~~~enVsVvVs--P~~~L~~~~~~sI~dlGspeev~~~l~~~~ 209 (282)
+|.+|.+|++..+. -+++.|......+++|+ ++. ...+ +++..++.+..+
T Consensus 3 ~~~lP~~~~D~t~n-----------------v~~~~~~~~~~~slvIsR~~l~-----~g~t------l~~~~~~q~~~l 54 (130)
T PF08786_consen 3 SLTLPDGWQDRTMN-----------------VLVLPDSGGSGPSLVISRDPLP-----DGET------LEDYLQRQLAQL 54 (130)
T ss_dssp EEEEETTSEE--BE-----------------EEEE--BTTB-EEEEEEEE--------TTS-------HHHHHHHHHHHH
T ss_pred eEeCCCcceeceEE-----------------EEEccCCCCCcceEEEEeccCC-----CCCC------HHHHHHHHHHHH
Confidence 57899999998653 36666654445555554 555 2444 444444433322
Q ss_pred cCCCCCCCceEEeeEEEeCCeEEEEEEEEeccCCCCceEEEEEEEeC-CeEEEEEeeeCcccccchhhhccc
Q 023424 210 TGNSYDPDELIETSVEKVGDQMYYNYLLETPFALTGTHNLAKATAKG-STVVLFVASANDKQWAGVTESFEN 280 (282)
Q Consensus 210 ~~~~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~-GkLYtl~a~a~ekrW~k~~~~lr~ 280 (282)
......-++++...-+.+|.+-+.++|........-|+..++..-+ +++|+|+.+++.......+..+..
T Consensus 55 -~~~l~~~~~~~~~~~~l~~~~a~~l~~~~~~~g~~v~Q~q~~~~~~~~~~l~~T~t~~~~~~~~~~~~~~~ 125 (130)
T PF08786_consen 55 -RKQLPGFQLVERQPITLGGRPARELEYSFRSGGQPVYQRQAAVLLPGRRVLVFTYTAPGPFTEEQRAHWEA 125 (130)
T ss_dssp -HCCSTT-EEEEEEEEEETTEEEEEEEEEEEETTCEEEEEEEEEEEC-CCEEEEEEEEECCCHHHHHHHHHH
T ss_pred -HhhCCCcEEEeeEEEEeCCCCeEEEEEEEeeCCEEEEEEEEEEEECCCEEEEEEEEcCCCCCHHHHHHHHH
Confidence 2334556888887888899999999999887667789888888888 999999999988877776665543
No 8
>PRK11615 hypothetical protein; Provisional
Probab=86.47 E-value=19 Score=32.36 Aligned_cols=124 Identities=7% Similarity=-0.017 Sum_probs=75.0
Q ss_pred CeEEEcCCCCccceeccccCCCcCCCCCCCCcceEEEeeCCCceEEEEEecCcccCCCCCCCccccCCHHHHHHhhcccc
Q 023424 130 PYQFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVASPLIRLTNKPNASIEEIGSPEKVIASLGPFV 209 (282)
Q Consensus 130 gY~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d~~~enVsVvVsP~~~L~~~~~~sI~dlGspeev~~~l~~~~ 209 (282)
..+|.+|.|+.+..... || ....=-+|.|.....+-+||-+ +.+=++ .+..+.+|..+-
T Consensus 49 Kl~FtLPag~sdqsgk~---Gt-------q~nn~~vYad~tg~kavIVi~g--------D~~~~~---Ld~la~rl~~qQ 107 (185)
T PRK11615 49 KLSFTLPADMSDQSGKL---GT-------QANNMHVYADATGQKAVIVILG--------DDTNED---LAVLAKRLEDQQ 107 (185)
T ss_pred EEEEEcCCccccccccc---cc-------cccceEEEEcCCCCEEEEEEeC--------CCChhh---HHHHHHHHHHHH
Confidence 68999999999764322 32 1124456777555554433321 122222 355566775543
Q ss_pred cCCCCCCCceEEeeEEEeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeEEEEEeeeCcccccchh
Q 023424 210 TGNSYDPDELIETSVEKVGDQMYYNYLLETPFALTGTHNLAKATAKGSTVVLFVASANDKQWAGVT 275 (282)
Q Consensus 210 ~~~~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkLYtl~a~a~ekrW~k~~ 275 (282)
-. ....-.++.-..-+++|+.++.++-........--+-+..+..++||-++.+..|.+-=.+.+
T Consensus 108 r~-rdp~lqvvsnK~i~i~G~~~qQLDS~~t~~Gqk~~SSvvL~~v~~rl~tlQitlpA~nqqqaq 172 (185)
T PRK11615 108 RS-RDPQLQVVTNKAIELKGHKLQQLDSIISAKGQTAYSSVVLGKVDNQLLTMQITLPADNQQQAQ 172 (185)
T ss_pred Hh-hCcCceeecceeEEECCeeeEEeeeeeecCCceEEEEEEEEeeCCeEEEEEEecCCCCHHHHH
Confidence 21 122334556666677999999999877755333444555788999999999998876544433
No 9
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=79.41 E-value=24 Score=30.76 Aligned_cols=109 Identities=19% Similarity=0.205 Sum_probs=62.4
Q ss_pred EEEcCCCCccceeccccCCCcCCCCCCCCcceEEEeeCCCceEEEEEe--cCcccCCCCCCCccccCCHHHHHHhhcccc
Q 023424 132 QFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVAS--PLIRLTNKPNASIEEIGSPEKVIASLGPFV 209 (282)
Q Consensus 132 ~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d~~~enVsVvVs--P~~~L~~~~~~sI~dlGspeev~~~l~~~~ 209 (282)
.|.+|..|++..+.. ..+.+++..-++.+|+ |+. ....+.+|=. +-+..+-+++
T Consensus 10 ~l~lP~~w~DrSvNv-----------------f~~~~~gt~~~sfvIsRd~~~-----~g~~~~~y~~--rql~~l~k~L 65 (147)
T COG5435 10 TLELPAAWQDRSVNV-----------------FVSGDNGTSGFSFVISRDPLE-----PGDTFPEYVQ--RQLALLRKQL 65 (147)
T ss_pred eEcCcchhccceEEE-----------------EEecCCCcceeEEEEecCCCC-----CCCcHHHHHH--HHHHHHHhhC
Confidence 589999999987653 4444566677888887 443 2444444411 1122222222
Q ss_pred cCCCCCCCceEEeeEEEeCCeEEEEEEEEecc--CCCC-ceEEEEEEEeCCeEEEEEeeeCcc
Q 023424 210 TGNSYDPDELIETSVEKVGDQMYYNYLLETPF--ALTG-THNLAKATAKGSTVVLFVASANDK 269 (282)
Q Consensus 210 ~~~~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~--~~~~-rH~LasatV~~GkLYtl~a~a~ek 269 (282)
..=++..-.+-+++|..--..+|.-.. .+++ -|++.++.-.++++-+|+++++-.
T Consensus 66 -----pgy~~~~~~e~~v~~~aa~~~~y~w~~~~~~~r~v~q~~~~i~~g~~vLifT~Tt~~~ 123 (147)
T COG5435 66 -----PGYELHHRREIEVGGAAAPLLDYQWTSPEGEQRRVQQRQVFIERGDTVLIFTLTTPGE 123 (147)
T ss_pred -----CCeEEeeccccccCccccceeEEEeecCCCCCceEEEEEeecccCCeEEEEEecCCCC
Confidence 223566655666777654444444433 2333 355555555777888998888643
No 10
>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=78.98 E-value=2.4 Score=26.25 Aligned_cols=15 Identities=40% Similarity=0.541 Sum_probs=11.6
Q ss_pred chhHHHHHHhhhhhH
Q 023424 65 ILRREILKGLAVIPV 79 (282)
Q Consensus 65 ~sRR~~L~~~a~~aa 79 (282)
.+||++|.+.+++++
T Consensus 2 ~sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAA 16 (26)
T ss_pred CcHHHHHHHHHHHHH
Confidence 589999987776654
No 11
>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=75.40 E-value=4 Score=30.73 Aligned_cols=15 Identities=47% Similarity=0.601 Sum_probs=11.2
Q ss_pred cchhHHHHHHhhhhh
Q 023424 64 PILRREILKGLAVIP 78 (282)
Q Consensus 64 ~~sRR~~L~~~a~~a 78 (282)
..+||+||.++++++
T Consensus 8 ~~sRR~Flk~lg~~a 22 (66)
T TIGR02811 8 DPSRRDLLKGLGVGA 22 (66)
T ss_pred CccHHHHHHHHHHHH
Confidence 578999998766543
No 12
>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.
Probab=66.35 E-value=6.2 Score=24.74 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=10.8
Q ss_pred chhHHHHHHhhhhhH
Q 023424 65 ILRREILKGLAVIPV 79 (282)
Q Consensus 65 ~sRR~~L~~~a~~aa 79 (282)
.+||++|...+..++
T Consensus 1 ~sRR~Flk~~~~~~a 15 (29)
T TIGR01409 1 LSRRDFLKGAAAAGA 15 (29)
T ss_pred CchhhhHHHHHHHHH
Confidence 479999977665544
No 13
>COG3212 Predicted membrane protein [Function unknown]
Probab=63.38 E-value=29 Score=29.86 Aligned_cols=51 Identities=14% Similarity=0.077 Sum_probs=34.3
Q ss_pred CHHHHHHhhcccccCCCCCCCceEEeeEEEeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeEEEEEeeeCc
Q 023424 197 SPEKVIASLGPFVTGNSYDPDELIETSVEKVGDQMYYNYLLETPFALTGTHNLAKATAKGSTVVLFVASAND 268 (282)
Q Consensus 197 speev~~~l~~~~~~~~~~~a~Ll~a~~r~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkLYtl~a~a~e 268 (282)
+.+++.+.-++++-| ++.+..-.+.+|+.+|..|+..+ +|+-|.+.+-|..
T Consensus 84 s~~ea~~iAl~~~~G------~v~dieLe~~~g~~vYevei~~~---------------d~~e~ev~iDA~T 134 (144)
T COG3212 84 SLEEAKEIALKRVPG------KVDDIELEEDNGRLVYEVEIVKD---------------DGQEYEVEIDAKT 134 (144)
T ss_pred CHHHHHHHHHHHCCC------ceeEEEEeccCCEEEEEEEEEeC---------------CCcEEEEEEecCC
Confidence 455555554444322 77787778889999999998854 4666666666543
No 14
>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=56.88 E-value=3.6 Score=37.42 Aligned_cols=12 Identities=25% Similarity=0.407 Sum_probs=0.0
Q ss_pred CCCcchhHHHHH
Q 023424 61 TRTPILRREILK 72 (282)
Q Consensus 61 ~~~~~sRR~~L~ 72 (282)
.+...+||.+|.
T Consensus 25 ~~~~~~RRa~l~ 36 (202)
T PF05757_consen 25 AQQQTSRRAVLG 36 (202)
T ss_dssp ------------
T ss_pred ccccccHHHHHH
Confidence 334678998874
No 15
>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=56.69 E-value=1.2e+02 Score=29.12 Aligned_cols=22 Identities=18% Similarity=0.602 Sum_probs=17.2
Q ss_pred CCeEEEcCCCCccceeccccCC
Q 023424 129 QPYQFVLPPSWKQMRVANILSG 150 (282)
Q Consensus 129 dgY~F~yP~gW~~~~v~~~~sG 150 (282)
-||+|++|.||++..-..-.+|
T Consensus 117 gGFS~vvP~GW~~Sda~~L~yG 138 (297)
T PF07174_consen 117 GGFSYVVPAGWVESDASHLDYG 138 (297)
T ss_pred cceEEeccCCccccccceeecc
Confidence 4999999999998875544555
No 16
>smart00564 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases.
Probab=48.21 E-value=23 Score=21.47 Aligned_cols=22 Identities=14% Similarity=0.231 Sum_probs=18.7
Q ss_pred EEEeCCeEEEEEeeeCcccccc
Q 023424 252 ATAKGSTVVLFVASANDKQWAG 273 (282)
Q Consensus 252 atV~~GkLYtl~a~a~ekrW~k 273 (282)
++-.+|+||.+.+...+.+|..
T Consensus 11 ~~~~~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 11 VGSTDGTLYALDAKTGEILWTY 32 (33)
T ss_pred EEcCCCEEEEEEcccCcEEEEc
Confidence 4556899999999999999963
No 17
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=41.65 E-value=55 Score=32.71 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=16.0
Q ss_pred CCeEEEcCCCCccceeccc
Q 023424 129 QPYQFVLPPSWKQMRVANI 147 (282)
Q Consensus 129 dgY~F~yP~gW~~~~v~~~ 147 (282)
-|++|.||.||+-+...++
T Consensus 295 Lg~tf~~P~Gf~IdN~~~A 313 (479)
T COG4784 295 LGVTFDVPDGFKIDNSAEA 313 (479)
T ss_pred cceEEecCCceEecCchHH
Confidence 4999999999998876555
No 18
>PF07009 DUF1312: Protein of unknown function (DUF1312); InterPro: IPR010739 This family consists of several bacterial proteins of around 120 residues in length. The function of this family is unknown.; PDB: 4ESN_B 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2KPP_A 3LD7_C.
Probab=39.56 E-value=40 Score=27.34 Aligned_cols=45 Identities=16% Similarity=0.076 Sum_probs=30.6
Q ss_pred EeCCeEEEEEEEEeccCC-----CCceEEEEEEEeCCeEEEEEeeeCccc
Q 023424 226 KVGDQMYYNYLLETPFAL-----TGTHNLAKATAKGSTVVLFVASANDKQ 270 (282)
Q Consensus 226 ~~dG~tYY~yE~~~~~~~-----~~rH~LasatV~~GkLYtl~a~a~ekr 270 (282)
..+|+.|+.|.+.....+ .+......+-+.+|+++...+.||++-
T Consensus 32 ~~~g~~~~~i~L~~~~~~~~i~i~~~~g~~~i~i~~g~vrv~~s~Cpdki 81 (113)
T PF07009_consen 32 YVDGKEVKRIPLDKVNEDKTIEIDGDGGYNTIEIKDGKVRVIESDCPDKI 81 (113)
T ss_dssp EETTEEEEEEETTS-BSEEEEEEETTTCEEEEEEETTEEEEEEESTSS-H
T ss_pred EECCEEEEEEECCCCCCCEEEEEecCCcEEEEEEECCEEEEEECCCCCcc
Confidence 458999987754431111 133445678899999999999999874
No 19
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=39.48 E-value=2.4e+02 Score=25.00 Aligned_cols=41 Identities=24% Similarity=0.419 Sum_probs=24.5
Q ss_pred CeEEEcCCCCccceeccccCCCcCCCCCCCCcceEEEee-----CCCceEEEEEecCc
Q 023424 130 PYQFVLPPSWKQMRVANILSGNYCQPKCAEPWVEVKFED-----EKQGKVQVVASPLI 182 (282)
Q Consensus 130 gY~F~yP~gW~~~~v~~~~sG~~~~p~~~~~~~dv~F~d-----~~~enVsVvVsP~~ 182 (282)
.-++-.|+||....-.+ .++.-....+ .-.-|+.|+|..+.
T Consensus 32 ~v~lP~P~GW~~~~~~~------------~~~a~~vi~~~~~~~~~~Pnavv~V~kL~ 77 (175)
T PF10738_consen 32 TVSLPTPPGWEPAPDPN------------PPWAYAVIVDPQADGGFPPNAVVTVSKLT 77 (175)
T ss_pred EEeccCCcCcccCCCCC------------CCceEEEEEeccccCCCCCceEEEEEecc
Confidence 45577899999975443 1222333322 33457888888766
No 20
>PF09211 DUF1958: Domain of unknown function (DUF1958); InterPro: IPR015294 Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. Penicillin-binding protein 4 (PBP4) functions as a transpeptidase, and belongs to MEROPS peptidase family S11 (clan SE). PBP4 acts co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents []. This entry represents the C-terminal domain PBP4.; PDB: 1TVF_A 3HUN_A 3HUM_B.
Probab=35.00 E-value=38 Score=25.61 Aligned_cols=38 Identities=18% Similarity=0.331 Sum_probs=24.2
Q ss_pred ceEEeeEEEeCCeEEEE----EEEEeccCCCCceEE-EEEEEeCCeEEE
Q 023424 218 ELIETSVEKVGDQMYYN----YLLETPFALTGTHNL-AKATAKGSTVVL 261 (282)
Q Consensus 218 ~Ll~a~~r~~dG~tYY~----yE~~~~~~~~~rH~L-asatV~~GkLYt 261 (282)
+||++.+.++||++||. |... + +..= -...|.+|+|++
T Consensus 3 KvLskG~h~IdGk~y~v~kDlYd~V-p-----K~~~~~~~~v~dg~v~v 45 (65)
T PF09211_consen 3 KVLSKGEHTIDGKKYYVKKDLYDVV-P-----KGKKPYKLKVKDGKVHV 45 (65)
T ss_dssp EEE-SEEEEETTEEEEESS-EEEEE-E-----TT--GSEEEEETTEEEE
T ss_pred ccccCccEEECCEEEEecCChhhhc-c-----CCCccceEEEeCCEEEE
Confidence 68999999999999983 3322 1 1211 256677788776
No 21
>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=31.64 E-value=38 Score=23.24 Aligned_cols=10 Identities=30% Similarity=0.421 Sum_probs=5.9
Q ss_pred CcchhHHHHH
Q 023424 63 TPILRREILK 72 (282)
Q Consensus 63 ~~~sRR~~L~ 72 (282)
...+||++|.
T Consensus 7 ~~~~RRdFL~ 16 (41)
T PF10399_consen 7 VDPTRRDFLT 16 (41)
T ss_dssp ---HHHHHHH
T ss_pred CCchHHHHHH
Confidence 4578999984
No 22
>PF15495 Fimbrillin_C: Major fimbrial subunit protein type IV, Fimbrillin, C-terminal
Probab=28.21 E-value=1.4e+02 Score=23.27 Aligned_cols=40 Identities=13% Similarity=0.125 Sum_probs=27.4
Q ss_pred eCCeEEEEEEEEe-ccCCCCceEEEEEEEeCCeEEEEEeee
Q 023424 227 VGDQMYYNYLLET-PFALTGTHNLAKATAKGSTVVLFVASA 266 (282)
Q Consensus 227 ~dG~tYY~yE~~~-~~~~~~rH~LasatV~~GkLYtl~a~a 266 (282)
.+|..||.+.+.- +........+.-..|-++..|.|+++.
T Consensus 5 ~~G~~YY~~~I~h~d~~~~~~~~~~~y~IvRNn~Y~l~I~~ 45 (85)
T PF15495_consen 5 ENGVCYYYYWINHNDNNNPATMGQGEYGIVRNNVYKLTITS 45 (85)
T ss_pred eCCEEEEEEEecCCCCCcccccccceeceEeccEEEEEEEe
Confidence 4899999998875 111122234555688889999999874
No 23
>PF08166 NUC202: NUC202 domain; InterPro: IPR012980 This domain is found in a novel family of nucleolar proteins [].
Probab=27.31 E-value=22 Score=26.65 Aligned_cols=26 Identities=38% Similarity=0.598 Sum_probs=21.9
Q ss_pred ccceeeeeccCChhhhccccCCCCcc
Q 023424 8 SREVLEVSRFCSPEMAASLTTPLSPK 33 (282)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (282)
+-.+++||+||+--+-..|..|..|-
T Consensus 23 ~~~~Lq~ss~~~EaLl~~Li~d~~P~ 48 (61)
T PF08166_consen 23 SSGVLQVSSFCSEALLTHLIHDRTPP 48 (61)
T ss_pred ccCcccccchhHHHHHHHHcCCCCCC
Confidence 45789999999999999998887764
No 24
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=25.65 E-value=45 Score=21.53 Aligned_cols=24 Identities=13% Similarity=0.093 Sum_probs=20.3
Q ss_pred EEEeCCeEEEEEeeeCcccccchh
Q 023424 252 ATAKGSTVVLFVASANDKQWAGVT 275 (282)
Q Consensus 252 atV~~GkLYtl~a~a~ekrW~k~~ 275 (282)
++..+|.||.+.+..++..|....
T Consensus 5 ~~~~~g~l~AlD~~TG~~~W~~~~ 28 (38)
T PF01011_consen 5 VGTPDGYLYALDAKTGKVLWKFQT 28 (38)
T ss_dssp EETTTSEEEEEETTTTSEEEEEES
T ss_pred EeCCCCEEEEEECCCCCEEEeeeC
Confidence 446799999999999999998643
No 25
>PLN02729 PSII-Q subunit
Probab=23.82 E-value=71 Score=29.54 Aligned_cols=47 Identities=26% Similarity=0.236 Sum_probs=23.2
Q ss_pred ccCCCCccccccCCCCC---chhhhhhhhhhccCCCCCCCCcchhHHHHHHhhhh
Q 023424 26 LTTPLSPKFSASNGRKP---SNKIQRALTAFHQKGNECTRTPILRREILKGLAVI 77 (282)
Q Consensus 26 ~~~~~~~~~~a~~~~~~---s~~~~~~~~~~~~~~~~~~~~~~sRR~~L~~~a~~ 77 (282)
-|.|.-||.+-. ++. .+-+-+.-++.+|...++ ...+||.+| |++++
T Consensus 12 ~~~~~~~~~~~~--~~~~~~~~~~g~l~~~~~~~~~~~--~~~~rr~~l-gl~a~ 61 (220)
T PLN02729 12 ETLPAIPKLRNL--QRTRKRGKIIGFLCKKAENFQEDS--FQTTRRLAL-GLASI 61 (220)
T ss_pred cccccchhhhcc--hhhhhhhhhhhHhhhhhhhcccch--hhhhHHHHH-HHHHH
Confidence 355777777643 222 222222233334433333 367899776 55543
No 26
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=23.06 E-value=1.8e+02 Score=21.00 Aligned_cols=27 Identities=7% Similarity=0.121 Sum_probs=21.4
Q ss_pred CCCCceEEeeEEEeCCeEEEEEEEEec
Q 023424 214 YDPDELIETSVEKVGDQMYYNYLLETP 240 (282)
Q Consensus 214 ~~~a~Ll~a~~r~~dG~tYY~yE~~~~ 240 (282)
....++.+....+.+|..+|.|++...
T Consensus 51 f~~v~l~~~~~~~~~~~~~~~F~i~~~ 77 (78)
T PF05137_consen 51 FSDVSLSSISRQEGDGNSLVSFTITAK 77 (78)
T ss_pred ccceEEEEEEeeccCCCceEEEEEEEE
Confidence 456788888888878888999998753
No 27
>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=22.07 E-value=44 Score=28.96 Aligned_cols=20 Identities=25% Similarity=0.418 Sum_probs=16.3
Q ss_pred CCCccccCCHHHHHHhhccc
Q 023424 189 NASIEEIGSPEKVIASLGPF 208 (282)
Q Consensus 189 ~~sI~dlGspeev~~~l~~~ 208 (282)
..-+++||+|+++++.+...
T Consensus 44 eeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 44 EEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHh
Confidence 56679999999999887653
No 28
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=21.35 E-value=62 Score=19.82 Aligned_cols=19 Identities=11% Similarity=0.316 Sum_probs=15.1
Q ss_pred CCeEEEEEeeeCcccccch
Q 023424 256 GSTVVLFVASANDKQWAGV 274 (282)
Q Consensus 256 ~GkLYtl~a~a~ekrW~k~ 274 (282)
+|+.|-++..+.+++|.+-
T Consensus 12 ~g~~yy~n~~t~~s~W~~P 30 (32)
T smart00456 12 DGRPYYYNHETKETQWEKP 30 (32)
T ss_pred CCCEEEEECCCCCEEcCCC
Confidence 4788888888888988753
No 29
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=21.05 E-value=1.8e+02 Score=21.97 Aligned_cols=32 Identities=13% Similarity=0.176 Sum_probs=22.6
Q ss_pred EeCCeEEEEEEEEeccCCCCceEEEEEEEeCCeE
Q 023424 226 KVGDQMYYNYLLETPFALTGTHNLAKATAKGSTV 259 (282)
Q Consensus 226 ~~dG~tYY~yE~~~~~~~~~rH~LasatV~~GkL 259 (282)
..+|++||.|+..+. +.+.|.+..+.+.-..|
T Consensus 12 ~~~g~~y~qy~v~I~--N~~~~~I~~~~i~~~~l 43 (80)
T PF09478_consen 12 TENGQTYTQYDVTIT--NNGSKPIKSLKISIDNL 43 (80)
T ss_pred EeCCEEEEEEEEEEE--ECCCCeEEEEEEEECcc
Confidence 468999999998887 45667666665544444
Done!