Query 025092
Match_columns 258
No_of_seqs 190 out of 312
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 02:37:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025092hhsearch_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 3.8E-79 8.3E-84 545.1 23.1 252 1-258 1-260 (260)
2 PLN00059 PsbP domain-containin 100.0 4.2E-44 9.1E-49 319.3 19.0 203 27-257 57-284 (286)
3 PLN00067 PsbP domain-containin 100.0 1.9E-41 4.1E-46 302.3 18.7 185 51-257 42-263 (263)
4 PF01789 PsbP: PsbP; InterPro 100.0 8.3E-39 1.8E-43 273.5 11.8 154 86-258 15-175 (175)
5 PLN00066 PsbP domain-containin 100.0 1.2E-37 2.6E-42 280.1 17.0 180 49-257 42-258 (262)
6 PLN03152 hypothetical protein; 100.0 3E-28 6.4E-33 212.8 12.5 184 51-257 30-240 (241)
7 PF08786 DUF1795: Domain of un 97.1 0.0056 1.2E-07 49.5 10.2 56 196-255 74-130 (130)
8 PF07174 FAP: Fibronectin-atta 90.6 5.1 0.00011 37.1 11.7 142 94-246 110-276 (297)
9 PRK11615 hypothetical protein; 88.1 17 0.00037 31.7 16.1 132 99-257 47-184 (185)
10 COG5435 Uncharacterized conser 86.9 11 0.00024 31.8 10.4 66 186-257 75-141 (147)
11 COG4784 Putative Zn-dependent 75.8 12 0.00025 36.3 7.4 41 215-257 373-414 (479)
12 PF10518 TAT_signal: TAT (twin 69.8 4.2 9.1E-05 24.2 2.0 14 52-65 2-15 (26)
13 PF10738 Lpp-LpqN: Probable li 65.2 91 0.002 26.9 14.0 132 101-258 32-174 (175)
14 PLN00058 photosystem II reacti 65.1 9.5 0.0002 30.0 3.6 17 49-65 46-62 (103)
15 PF05757 PsbQ: Oxygen evolving 63.5 2.3 5.1E-05 37.7 0.0 33 29-65 10-42 (202)
16 smart00564 PQQ beta-propeller 49.7 22 0.00048 20.9 2.8 24 219-242 9-32 (33)
17 PF12712 DUF3805: Domain of un 43.6 31 0.00066 29.1 3.5 123 99-257 8-130 (153)
18 TIGR01409 TAT_signal_seq Tat ( 33.2 40 0.00088 20.2 2.0 13 52-64 1-13 (29)
19 TIGR02811 formate_TAT formate 33.2 38 0.00082 24.6 2.2 14 50-63 7-20 (66)
20 PF12318 FAD-SLDH: Membrane bo 33.1 29 0.00062 29.7 1.8 12 160-171 110-121 (168)
21 PF07123 PsbW: Photosystem II 28.5 63 0.0014 27.0 3.0 46 34-81 43-89 (138)
22 PF10399 UCR_Fe-S_N: Ubiquitin 25.1 67 0.0014 21.3 2.1 13 50-62 7-19 (41)
23 PF01011 PQQ: PQQ enzyme repea 22.7 47 0.001 20.8 1.0 23 221-243 5-27 (38)
24 PF05984 Cytomega_UL20A: Cytom 22.6 61 0.0013 25.0 1.8 14 52-65 1-14 (100)
25 PLN00077 photosystem II reacti 22.2 80 0.0017 25.9 2.5 48 31-81 31-78 (128)
26 PF12559 Inhibitor_I10: Serine 21.2 38 0.00083 24.1 0.4 11 101-111 44-54 (56)
No 1
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=3.8e-79 Score=545.08 Aligned_cols=252 Identities=78% Similarity=1.208 Sum_probs=238.4
Q ss_pred CcchhhhhhccccCCCccccc----ccccccCCCCCceeeeccccccccccCCccchhHHHHHHHHHHHhhccCCCcchh
Q 025092 1 MASTQCFLHHHALSTTPARTS----SSQRHVSNIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAAVGSKVSPADA 76 (258)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~RR~~L~~~a~aaa~~~~~~pa~A 76 (258)
||||+||||||+++++. +.+ +++|.....++++++|++|++. .+.++||.+|+++++++++++.+.|+.|
T Consensus 1 ~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~srr~~l~~~~ga~a~~~~~~pa~a 74 (260)
T PLN00042 1 MASTACFLHQSALKSAA-ALASSSSASARAVSASRPSQVVCRAQEED-----NSAVSRRAALALLAGAAAAGAKVSPANA 74 (260)
T ss_pred Ccchhhhhhcccccchh-hhcccccccccccCCCCCcceeeeccccc-----cccccHHHHHHHHHHHHHhhcccCchhh
Confidence 99999999999995443 332 4688899999999999999773 3468999999999999888999999999
Q ss_pred hccccccccCCCCCCCCceeccCCceEEecCCCCccCccccCCCceEEeecCCCCCCcEEEEEecCCCCccccCCChHHH
Q 025092 77 AYGESANVFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEF 156 (258)
Q Consensus 77 a~ge~a~~f~~p~~~~~f~~y~~dgYsf~yP~~W~~~~e~~~~G~dv~f~d~~~~~~nVsV~v~p~~~~sI~d~Gspeev 156 (258)
+|||+||+||+||+++||++|++|||+|+||++|++++|.+++|+|++|+|+++.++||+|+|+|+++++|+|||+||||
T Consensus 75 ay~~~anvfg~~k~~~gF~~y~~dgY~FlyP~~W~~~ke~~~~G~dv~f~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~ 154 (260)
T PLN00042 75 AYGESANVFGKPKTNTGFLPYNGDGFKLLVPSKWNPSKEREFPGQVLRFEDNFDATSNLSVMVTPTDKKSITDYGSPEEF 154 (260)
T ss_pred hhcchhhccCCCCCCCCCeEeeCCCeEEecCCCCccccccccCCceEEeeccccccccEEEEEecCCcCCHhhcCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhcCCCCCCCCCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEE
Q 025092 157 LSKVDYLLGKQAYSGKTSSEGGFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICK 232 (258)
Q Consensus 157 a~~v~~~L~~~~~~~~t~s~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~ 232 (258)
+++|+++|+++++.++|.+|+||+||++++++||++++| ++||+|||.++++||||++||+|+++||+|||||||+
T Consensus 155 l~~vgylL~kq~~a~~t~s~~Gf~p~~vata~Lleas~re~dGk~YY~lE~~~~~ad~d~~~RH~LatatV~~GkLYtl~ 234 (260)
T PLN00042 155 LSKVSYLLGKQAYSGETASEGGFDANAVATAAVLESSTQEVGGKPYYYLSVLTRTADGDEGGKHQLITATVSDGKLYICK 234 (260)
T ss_pred HHHHHHHHHhhhccCccccccCcCcccccceeEEEeeeEEeCCeEEEEEEEEEecCCCCCCCceEEEEEEEECCEEEEEE
Confidence 999999999999999999999999999999999999998 9999999999999999999999999999999999999
Q ss_pred eEeccccccchhHHHHHHHhhccccC
Q 025092 233 AQAGDKRWFKGTRKYVESTASSFSVA 258 (258)
Q Consensus 233 ~qa~e~rW~k~~~~~l~~vv~SF~V~ 258 (258)
+|+||+||+|+.+++|++|++||+||
T Consensus 235 aqa~EkRW~K~~~k~l~~v~~SFsVa 260 (260)
T PLN00042 235 AQAGDKRWFKGARKFVEGAASSFSVA 260 (260)
T ss_pred ecCchhhhhHHHHHHHHHHHhceecC
Confidence 99999999998777799999999997
No 2
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=4.2e-44 Score=319.34 Aligned_cols=203 Identities=24% Similarity=0.312 Sum_probs=157.9
Q ss_pred cCCCCCceeeeccccccccccCCccchhHHHHHHHH-HHHhhccCCCcchhhccccccccCCCCCCCCceecc--CCceE
Q 025092 27 VSNIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLI-GAAAVGSKVSPADAAYGESANVFGKPKTNTDFLPYN--GDGFK 103 (258)
Q Consensus 27 ~~~~~~~~~~c~~~~~~~~~~~~~~~~RR~~L~~~a-~aaa~~~~~~pa~Aa~ge~a~~f~~p~~~~~f~~y~--~dgYs 103 (258)
..+-+|-.+.|..+... ..+++||.+|+..+ .+..+.+.+ .....|+.|+ ||+.|. .|||+
T Consensus 57 ~~~~~~~~~~~~~~~~~-----~~~~~rr~~~~~~l~~~~~~~s~~--------~~~~a~a~~~---~l~~y~D~~DGY~ 120 (286)
T PLN00059 57 AKPDSPVAINCLTDAKQ-----VCAVGRRKSMMMGLLMSGLIVSEA--------NLPTAFASIP---VFREYIDTFDGYS 120 (286)
T ss_pred cCCCCCeeeecccchhh-----hhhhhhhhhhHHHHHHHHHHHHhh--------cCchhhcCCc---ccceeEcCCCCeE
Confidence 34455566788888331 34799999965333 222221111 1112233443 566665 89999
Q ss_pred EecCCCCccCccccCCCceEEeecCCCCCCcEEEEEecC---CCCccccCCChHHHHHHHHHHHHhhhhcCCCCCCCCCC
Q 025092 104 LSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPT---DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEGGFD 180 (258)
Q Consensus 104 f~yP~~W~~~~e~~~~G~dv~f~d~~~~~~nVsV~v~p~---~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~~g~~ 180 (258)
|+||.||++++ ..|+|++|+|+++.+|||+|+|+|+ ++++|+|||+|+| ||++|.+++++++ ++++
T Consensus 121 FlYP~GWi~V~---~~G~DVvFrD~Ie~~ENVSV~ISs~sss~~~sLeDLGsP~e----VgerLlkqvLa~f---~str- 189 (286)
T PLN00059 121 FKYPQNWIQVR---GAGADIFFRDPVVLDENLSVEFSSPSSSKYTSLEDLGSPEE----VGKRVLRQYLTEF---MSTR- 189 (286)
T ss_pred EeCCCCCeEec---cCCCceEEeccCccccceEEEEecCCcccCCChHHcCCHHH----HHHHHHHHHhccc---cccc-
Confidence 99999998655 4699999999999999999999988 4899999999999 8889999999875 2222
Q ss_pred ccccccceeeecccC-----CCeEEEEEEEEcCC---------C-----CCCcceEEEEEEEeCCEEEEEEeEecccccc
Q 025092 181 PDAVATANILEASVR-----PPYYFLSVLTRTAD---------G-----DEGGKHQLITATVKGGKLYICKAQAGDKRWF 241 (258)
Q Consensus 181 ~~~v~~a~ll~a~~r-----~~YY~~Ey~~~~~~---------g-----~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~ 241 (258)
+|.-++++||++++| ++||+|||.+++++ . .||.||+|++++|.|||||||++|+||+||.
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 232238999999987 99999999999962 2 2689999999999999999999999999999
Q ss_pred chhHHHHHHHhhcccc
Q 025092 242 KGTRKYVESTASSFSV 257 (258)
Q Consensus 242 k~~~~~l~~vv~SF~V 257 (258)
|+++. |++|++||+|
T Consensus 270 kvk~~-f~~V~dSF~V 284 (286)
T PLN00059 270 EEEKD-LRRVMDSFRV 284 (286)
T ss_pred HHHHH-HHHHHhheee
Confidence 98886 9999999998
No 3
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=1.9e-41 Score=302.33 Aligned_cols=185 Identities=25% Similarity=0.437 Sum_probs=143.9
Q ss_pred cchhHHHHHHHHHHHhhcc-CCCcchhhccccccccCCC-CCCCCceecc-------------CCceEEecCCCCccCcc
Q 025092 51 AVSRRLALTVLIGAAAVGS-KVSPADAAYGESANVFGKP-KTNTDFLPYN-------------GDGFKLSIPSKWNPSKE 115 (258)
Q Consensus 51 ~~~RR~~L~~~a~aaa~~~-~~~pa~Aa~ge~a~~f~~p-~~~~~f~~y~-------------~dgYsf~yP~~W~~~~e 115 (258)
.+.||++|.+++.+.++.. ...|+.|...|. +.|-.| .+.+||..|. ..||+|+||.+|+++++
T Consensus 42 ~~~rr~~~~~~~~~~~~~~~~~~~~~~~~~~v-~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~V 120 (263)
T PLN00067 42 VIHRRELLLGLALAPLILIAPEPPAEAREVEV-GSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTRV 120 (263)
T ss_pred hhHHHHHHhhhhhhhhhhccCCchhhhheehh-hcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCccc
Confidence 5789999988877644332 233444433332 222211 1345666555 57999999999999988
Q ss_pred cc------------CCCceEEeecCCCCCCcEEEEEecC------CCCccccCCChHHHHHHHHHHHHhhhhcCCCCCCC
Q 025092 116 RE------------FPGQVLRYEDNFDSNSNVSVIITPT------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEG 177 (258)
Q Consensus 116 ~~------------~~G~dv~f~d~~~~~~nVsV~v~p~------~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~~ 177 (258)
.+ .+|+|++|+|++ ++||+|+|+|+ ++++|+|||+|++|+++ |++.+..+
T Consensus 121 s~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~----Lg~~v~g~------ 188 (263)
T PLN00067 121 ANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKLIAS----LGPFVTGN------ 188 (263)
T ss_pred cccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHHHHH----hhHHhhcC------
Confidence 64 345999999965 67999999998 56899999999996655 55555542
Q ss_pred CCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccccccchhHHHHHHHhh
Q 025092 178 GFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTAS 253 (258)
Q Consensus 178 g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~k~~~~~l~~vv~ 253 (258)
++ +.++||+++++ ++||+|||.+++++ ++||+|+++||++||||||++|++|+||+|+++. |++|++
T Consensus 189 ~~-----~~~eLLeAs~re~dGktYY~~E~~tp~a~---~gRHnLataTV~~GkLYtf~asanEkRW~K~k~~-l~~V~d 259 (263)
T PLN00067 189 SY-----DPDELLETSVEKIGDQTYYKYVLETPFAL---TGSHNLAKATAKGNTVVLFVVSASDKQWQSSEKT-LKAILD 259 (263)
T ss_pred CC-----CCcceEEeeeEeeCCeEEEEEEEEecCCC---CCceEEEEEEEECCEEEEEEecCCHHHHHHHHHH-HHHHHH
Confidence 22 25689999998 99999999999998 6899999999999999999999999999998775 999999
Q ss_pred cccc
Q 025092 254 SFSV 257 (258)
Q Consensus 254 SF~V 257 (258)
||+|
T Consensus 260 SFsV 263 (263)
T PLN00067 260 SFQA 263 (263)
T ss_pred hccC
Confidence 9987
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=100.00 E-value=8.3e-39 Score=273.51 Aligned_cols=154 Identities=36% Similarity=0.605 Sum_probs=127.8
Q ss_pred CCCCCCCCceec--cCCceEEecCCCCccCccccCCCceEEeecCCCCCCcEEEEEecCCCC-ccccCCChHHHHHHHHH
Q 025092 86 GKPKTNTDFLPY--NGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKK-SITDYGSPEEFLSKVDY 162 (258)
Q Consensus 86 ~~p~~~~~f~~y--~~dgYsf~yP~~W~~~~e~~~~G~dv~f~d~~~~~~nVsV~v~p~~~~-sI~d~Gspeeva~~v~~ 162 (258)
+.++...||.+| ..+||+|.||++|+ +.+..|++++|+|+++..+||+|+|+|+... +|+|||+|++ +++
T Consensus 15 ~~~~~~~~~~~y~d~~~~y~f~~P~gW~---~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~----va~ 87 (175)
T PF01789_consen 15 CAAEASTGFQPYTDSDDGYSFLYPSGWE---EVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEE----VAE 87 (175)
T ss_dssp -STT--SSEEEEEECTTTEEEEEETTEE---EEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHH----HHH
T ss_pred hcccCCCCceEEEcCCCCEEEECCCCCe---ecCCCCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHH----HHH
Confidence 344467899999 58999999999996 4444899999999999999999999999554 9999999999 455
Q ss_pred HHHhhhhcCCCCCCCCCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccc
Q 025092 163 LLGKQAYSGKTSSEGGFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDK 238 (258)
Q Consensus 163 ~L~~~~~~~~t~s~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~ 238 (258)
.|.+..+..+ +++ +.++||++.++ ++||+|||.+++++ ++.||+|++++++|||||+|++|++|+
T Consensus 88 ~l~~~~~~~~---~~~------~~a~li~a~~~~~~g~~yY~~Ey~~~~~~--~~~rh~l~~~tv~~g~lY~l~~~a~e~ 156 (175)
T PF01789_consen 88 RLLNGELASP---GSG------REAELISASEREVDGKTYYEYEYTVQSPN--EGRRHNLAVVTVKNGKLYTLTAQAPES 156 (175)
T ss_dssp HHHHHCCCHC---TSS------EEEEEEEEEEEEETTEEEEEEEEEEEETT--EEEEEEEEEEEEETTEEEEEEEEEEHH
T ss_pred HHhhhhcccc---cCC------cceEEEEeeeeecCCccEEEEEEEeccCC--CcccEEEEEEEEECCEEEEEEEEcCHH
Confidence 5766655543 222 48899999998 89999999999987 468999999999999999999999999
Q ss_pred cccchhHHHHHHHhhccccC
Q 025092 239 RWFKGTRKYVESTASSFSVA 258 (258)
Q Consensus 239 rW~k~~~~~l~~vv~SF~V~ 258 (258)
||+|++++ |++|++||+|+
T Consensus 157 ~w~k~~~~-l~~iv~SF~v~ 175 (175)
T PF01789_consen 157 RWDKVEPK-LRKIVDSFRVY 175 (175)
T ss_dssp HHHTCHHH-HHHHHHC-EE-
T ss_pred HHHHHHHH-HHHHHhcEEeC
Confidence 99998886 99999999985
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=100.00 E-value=1.2e-37 Score=280.14 Aligned_cols=180 Identities=26% Similarity=0.451 Sum_probs=143.6
Q ss_pred CccchhHHHHHHHHHHHhhccCCCcch--hh-cccccccc---CCCCCCCCceeccC---------------CceEEecC
Q 025092 49 GSAVSRRLALTVLIGAAAVGSKVSPAD--AA-YGESANVF---GKPKTNTDFLPYNG---------------DGFKLSIP 107 (258)
Q Consensus 49 ~~~~~RR~~L~~~a~aaa~~~~~~pa~--Aa-~ge~a~~f---~~p~~~~~f~~y~~---------------dgYsf~yP 107 (258)
...++||.+|+.++.++.++....|+. |+ +|..|+.. +.| +..||+.|.. .+|+|+||
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 457899999987665543333334544 44 89888764 555 5699999981 57999999
Q ss_pred CCCccCcccc----CCCceEEeecCCCCCCcEEEEEecC--------CCCccccCCChHHHHHHHHHHHHhhhhcCCCCC
Q 025092 108 SKWNPSKERE----FPGQVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSS 175 (258)
Q Consensus 108 ~~W~~~~e~~----~~G~dv~f~d~~~~~~nVsV~v~p~--------~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s 175 (258)
.+|+++.+.+ .+|+|++|.| +.++||+|+|+|+ ++++|+|||+||+|++ .|+++++..+
T Consensus 121 ~GW~ev~VS~~d~gg~~vd~Rf~~--~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~----~l~~~v~g~~--- 191 (262)
T PLN00066 121 QGWEEVPVSIADLGGTEIDLRFAS--DKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVIS----GFGPELIGEP--- 191 (262)
T ss_pred CCCeEeecccccCCCCceEEEecc--CCCccEEEEEeccccccccccCCCChHHcCCHHHHHH----HHHHHhcCCC---
Confidence 9999877652 2446666666 5789999999998 6889999999999655 5666655432
Q ss_pred CCCCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccccccchhHHHHHHH
Q 025092 176 EGGFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVEST 251 (258)
Q Consensus 176 ~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~k~~~~~l~~v 251 (258)
. ++++|++++++ ++||+||| . +|+|+++||.+||||+|++|+||+||+|++++ |++|
T Consensus 192 ------~--~e~eLl~a~~re~dGktYY~~E~-----~-----rH~LasaTV~~GrLYt~~asape~rW~k~~~~-lr~v 252 (262)
T PLN00066 192 ------V--EEGKVLSMEVAEHSGRTYYQFEL-----P-----PHTLVTATAAGNRVYIFSVTANGLQWKRHYKD-LKRI 252 (262)
T ss_pred ------c--cccceeEeeeeecCCcEEEEEEE-----e-----CceEEEEEEECCEEEEEEeecchHhhHHHHHH-HHHH
Confidence 1 36789999887 99999999 2 89999999999999999999999999998886 9999
Q ss_pred hhcccc
Q 025092 252 ASSFSV 257 (258)
Q Consensus 252 v~SF~V 257 (258)
++||+|
T Consensus 253 ~dSF~V 258 (262)
T PLN00066 253 AKSFRV 258 (262)
T ss_pred hhceee
Confidence 999997
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.95 E-value=3e-28 Score=212.75 Aligned_cols=184 Identities=26% Similarity=0.388 Sum_probs=126.3
Q ss_pred cchhHHHHHHHHHH-HhhccCCCcchhhcccccc----ccCCCCCCCCceeccCCceEEecCCCCccCccccC--CC---
Q 025092 51 AVSRRLALTVLIGA-AAVGSKVSPADAAYGESAN----VFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREF--PG--- 120 (258)
Q Consensus 51 ~~~RR~~L~~~a~a-aa~~~~~~pa~Aa~ge~a~----~f~~p~~~~~f~~y~~dgYsf~yP~~W~~~~e~~~--~G--- 120 (258)
..+||+.++-.+.+ +.....-.|..-..++..+ +.+...+...|..|.++||++.||.+|...-|.+- .|
T Consensus 30 ~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~~g~gf~~~~pp~f~di~e~~~~~~g~~~ 109 (241)
T PLN03152 30 GASRRDFILHTASLCASSLAAQNPLPPSLADPSKPSKPLLSGIANTKSWFQFYGDGFSIRVPPSFEDIMEPEDYNAGLSL 109 (241)
T ss_pred cccccceeeehhHHHHhhhhcCCCCCccccCCCCCCCchheeeecchhhhhhhCCceEEeCCCChhhhcChhhcccccce
Confidence 45677776533322 1111222343333344322 12222367789999999999999999986655431 12
Q ss_pred ---------ceEEeecCCCCCCcEEEEEecC--------CCCccccCCChHHHHHHHHHHHHhhhhcCCCCCCCCCCccc
Q 025092 121 ---------QVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEGGFDPDA 183 (258)
Q Consensus 121 ---------~dv~f~d~~~~~~nVsV~v~p~--------~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~~g~~~~~ 183 (258)
-..||.. .|.+|||||+|+|+ +.++|+|||+|+| |++.|. +. ++.+-.+
T Consensus 110 yg~~akp~~~~aRf~s-~D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~E----Vgkv~v-----P~---g~~~~sa- 175 (241)
T PLN03152 110 YGDKAKPRTFAARFAS-PDGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKE----AAKIFV-----PG---GATLYSA- 175 (241)
T ss_pred ecCCCCCcceeeeecC-CCCCceEEEEEecCccccccccccCChhHcCCHHH----HHHhhC-----CC---ccccccc-
Confidence 2356665 37899999999997 7899999999999 554443 32 1101011
Q ss_pred cccceeeecccCCCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccccccchhHHHHHHHhhcccc
Q 025092 184 VATANILEASVRPPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 257 (258)
Q Consensus 184 v~~a~ll~a~~r~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~k~~~~~l~~vv~SF~V 257 (258)
+.+++-+...-++||+|||.+. +||+|++|+|.+||||||+++++|+||+|++++ |+++++||+|
T Consensus 176 -R~iel~~E~dGKtYY~lEy~v~-------~RH~LaTVaVsrGKLYTl~aSt~EkRW~Kvk~k-fr~aa~SFsV 240 (241)
T PLN03152 176 -RTIKVKEEEGIRTYYFYEFGRD-------EQHVALVATVNSGKAYIAGATAPESKWDDDGVK-LRSAAISLTV 240 (241)
T ss_pred -ceeeeeeecCCceeEEEEEEeC-------CcEEEEEEEEcCCeEEEEecCCchhchHHHHHH-HHHHHhheee
Confidence 1334422111199999999973 499999999999999999999999999999998 9999999997
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=97.14 E-value=0.0056 Score=49.45 Aligned_cols=56 Identities=16% Similarity=0.006 Sum_probs=44.8
Q ss_pred CCeEEEEEEEEcCCCCCCcceEEEEEEEeC-CEEEEEEeEeccccccchhHHHHHHHhhcc
Q 025092 196 PPYYFLSVLTRTADGDEGGKHQLITATVKG-GKLYICKAQAGDKRWFKGTRKYVESTASSF 255 (258)
Q Consensus 196 ~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~-gkLYtl~~qa~e~rW~k~~~~~l~~vv~SF 255 (258)
.+-+.++|.-...+ ..-|+..++...+ ++||+++.+++....+..... ++.|++||
T Consensus 74 ~~a~~l~~~~~~~g---~~v~Q~q~~~~~~~~~~l~~T~t~~~~~~~~~~~~-~~~i~~Sf 130 (130)
T PF08786_consen 74 RPARELEYSFRSGG---QPVYQRQAAVLLPGRRVLVFTYTAPGPFTEEQRAH-WEAILKSF 130 (130)
T ss_dssp EEEEEEEEEEEETT---CEEEEEEEEEEEC-CCEEEEEEEEECCCHHHHHHH-HHHHHCT-
T ss_pred CCeEEEEEEEeeCC---EEEEEEEEEEEECCCEEEEEEEEcCCCCCHHHHHH-HHHHHhcC
Confidence 45566666665444 5688888888887 999999999999999987774 99999998
No 8
>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=90.59 E-value=5.1 Score=37.14 Aligned_cols=142 Identities=15% Similarity=0.177 Sum_probs=65.8
Q ss_pred ceecc-CCceEEecCCCCccCccccC-CCceEEeecCCCC---------CCcEEEEEecCCCCccccC-CChHHHHHHHH
Q 025092 94 FLPYN-GDGFKLSIPSKWNPSKEREF-PGQVLRYEDNFDS---------NSNVSVIITPTDKKSITDY-GSPEEFLSKVD 161 (258)
Q Consensus 94 f~~y~-~dgYsf~yP~~W~~~~e~~~-~G~dv~f~d~~~~---------~~nVsV~v~p~~~~sI~d~-Gspeeva~~v~ 161 (258)
.+-++ ..||+|.+|.||+.+..... .|+.+.-+-..++ .+.-+|++..+|.+=...- -+-...+-.++
T Consensus 110 grvdn~~gGFS~vvP~GW~~Sda~~L~yG~alls~~~~~~~~~~~~~p~andt~v~lgrld~kl~a~ae~dn~kaa~rl~ 189 (297)
T PF07174_consen 110 GRVDNAAGGFSYVVPAGWVESDASHLDYGSALLSKQTGEPPMPGQPPPVANDTSVVLGRLDLKLFASAEPDNTKAAVRLA 189 (297)
T ss_pred ccccccccceEEeccCCccccccceeecceeeeccCCCCCCCCCCCCCcCCCceEEeccccccccccccCChHHHHHHHh
Confidence 34334 67999999999986554332 4665554422211 1233455555433222111 01122222233
Q ss_pred HHHHhhhhcCCCCCCCCCCccccccceeeecccC---CCeEEEEEEEEc-CCCCCCcceEEEEEEE---------eCCEE
Q 025092 162 YLLGKQAYSGKTSSEGGFDPDAVATANILEASVR---PPYYFLSVLTRT-ADGDEGGKHQLITATV---------KGGKL 228 (258)
Q Consensus 162 ~~L~~~~~~~~t~s~~g~~~~~v~~a~ll~a~~r---~~YY~~Ey~~~~-~~g~e~~rH~L~~~tv---------~~gkL 228 (258)
..+++++.- . .|+| .|+ +...|++.-. ..||...|.=.. ++ +.-.-.+++. ..-|-
T Consensus 190 sdmgeffmp-~---pg~r-inq--~~~~l~~~g~~g~asyyevkf~d~~kp~----gqiw~~vvg~p~~~~~~~~~~~rw 258 (297)
T PF07174_consen 190 SDMGEFFMP-Y---PGTR-INQ--ETTPLDANGMPGSASYYEVKFTDANKPN----GQIWAGVVGSPVAPGTPRGTPQRW 258 (297)
T ss_pred ccccceecc-C---CCcc-ccc--cccccccCCcccceeEEEEEeccCCCCC----CceEEEeecCcCCCCCCCCCCceE
Confidence 333333322 1 2333 554 4456665544 667766665211 22 2222233332 11266
Q ss_pred EEEEeEeccccccchhHH
Q 025092 229 YICKAQAGDKRWFKGTRK 246 (258)
Q Consensus 229 Ytl~~qa~e~rW~k~~~~ 246 (258)
|.+=+.....--+|.+.+
T Consensus 259 fvvwlgt~~~pvd~~~a~ 276 (297)
T PF07174_consen 259 FVVWLGTANNPVDKGAAK 276 (297)
T ss_pred EEEEecCCCCCCCHHHHH
Confidence 666666665555665444
No 9
>PRK11615 hypothetical protein; Provisional
Probab=88.11 E-value=17 Score=31.73 Aligned_cols=132 Identities=12% Similarity=0.148 Sum_probs=80.2
Q ss_pred CCceEEecCCCCccCcccc-CCC-ceEEeecCCCCCCcEEEEEecCCCCccccCCChHHHHHHHHHHHHhhhhcCCCCCC
Q 025092 99 GDGFKLSIPSKWNPSKERE-FPG-QVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSE 176 (258)
Q Consensus 99 ~dgYsf~yP~~W~~~~e~~-~~G-~dv~f~d~~~~~~nVsV~v~p~~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~ 176 (258)
+.+.+|.+|.++....... ..+ .--+|-|+ ....+ |+|++-| .+.++++.++.+|..+--.
T Consensus 47 dGKl~FtLPag~sdqsgk~Gtq~nn~~vYad~--tg~ka-vIVi~gD--------~~~~~Ld~la~rl~~qQr~------ 109 (185)
T PRK11615 47 DGKLSFTLPADMSDQSGKLGTQANNMHVYADA--TGQKA-VIVILGD--------DTNEDLAVLAKRLEDQQRS------ 109 (185)
T ss_pred ccEEEEEcCCccccccccccccccceEEEEcC--CCCEE-EEEEeCC--------CChhhHHHHHHHHHHHHHh------
Confidence 7789999999997332111 111 23477774 23333 3333211 3345556677788776433
Q ss_pred CCCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccccccchhHHHHHHHh
Q 025092 177 GGFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTA 252 (258)
Q Consensus 177 ~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~k~~~~~l~~vv 252 (258)
++|+. .++..+.. +.++.++-.+...+ ..--+-++++..|+||-+|.+..|.+.-.+.... .+.|+
T Consensus 110 --rdp~l----qvvsnK~i~i~G~~~qQLDS~~t~~G---qk~~SSvvL~~v~~rl~tlQitlpA~nqqqaq~~-ae~ii 179 (185)
T PRK11615 110 --RDPQL----QVVTNKAIELKGHKLQQLDSIISAKG---QTAYSSVVLGKVDNQLLTMQITLPADNQQQAQTT-AENII 179 (185)
T ss_pred --hCcCc----eeecceeEEECCeeeEEeeeeeecCC---ceEEEEEEEEeeCCeEEEEEEecCCCCHHHHHHH-HHHHH
Confidence 24552 23333322 77788887755443 2233444566679999999999999887776664 89999
Q ss_pred hcccc
Q 025092 253 SSFSV 257 (258)
Q Consensus 253 ~SF~V 257 (258)
++..+
T Consensus 180 ~tl~~ 184 (185)
T PRK11615 180 NTLVI 184 (185)
T ss_pred hheec
Confidence 88765
No 10
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=86.92 E-value=11 Score=31.84 Aligned_cols=66 Identities=15% Similarity=0.063 Sum_probs=43.0
Q ss_pred cceeeecccCCCeEEEEEEEEcCCCCCCcceEEEEEEE-eCCEEEEEEeEeccccccchhHHHHHHHhhcccc
Q 025092 186 TANILEASVRPPYYFLSVLTRTADGDEGGKHQLITATV-KGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 257 (258)
Q Consensus 186 ~a~ll~a~~r~~YY~~Ey~~~~~~g~e~~rH~L~~~tv-~~gkLYtl~~qa~e~rW~k~~~~~l~~vv~SF~V 257 (258)
++++-.......+|.+-+. +. |+++-....+.+ .++++-+++++++-.-=++ .++...+++.||..
T Consensus 75 e~~v~~~aa~~~~y~w~~~---~~--~~r~v~q~~~~i~~g~~vLifT~Tt~~~ftp~-q~~~~~~~I~Sf~p 141 (147)
T COG5435 75 EIEVGGAAAPLLDYQWTSP---EG--EQRRVQQRQVFIERGDTVLIFTLTTPGEFTPS-QKKAWEQVIQSFVP 141 (147)
T ss_pred ccccCccccceeEEEeecC---CC--CCceEEEEEeecccCCeEEEEEecCCCCCCHH-HHHHHHHHHHhcCC
Confidence 3333333344666776664 22 245554455555 5779999999998777676 44469999999974
No 11
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=75.85 E-value=12 Score=36.26 Aligned_cols=41 Identities=17% Similarity=0.190 Sum_probs=28.4
Q ss_pred ceEEEEEEE-eCCEEEEEEeEeccccccchhHHHHHHHhhcccc
Q 025092 215 KHQLITATV-KGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 257 (258)
Q Consensus 215 rH~L~~~tv-~~gkLYtl~~qa~e~rW~k~~~~~l~~vv~SF~V 257 (258)
|-++=++.+ .+++.|.+-.-+|--.-.- ++. +..+..|||.
T Consensus 373 ~w~fdvaVI~~g~rvyrfltavp~gs~~l-~~~-a~sv~~SFR~ 414 (479)
T COG4784 373 RWQFDVAVIRAGDRVYRFLTAVPKGSTAL-EPR-ANSVRRSFRP 414 (479)
T ss_pred cccceEEEEEeCCEEEEEEEecccCcchh-hHH-HHHHHhhccc
Confidence 444444555 4789999888777655544 554 8999999985
No 12
>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=69.75 E-value=4.2 Score=24.22 Aligned_cols=14 Identities=43% Similarity=0.249 Sum_probs=10.6
Q ss_pred chhHHHHHHHHHHH
Q 025092 52 VSRRLALTVLIGAA 65 (258)
Q Consensus 52 ~~RR~~L~~~a~aa 65 (258)
++||+.|.+.++++
T Consensus 2 ~sRR~fLk~~~a~~ 15 (26)
T PF10518_consen 2 LSRRQFLKGGAAAA 15 (26)
T ss_pred CcHHHHHHHHHHHH
Confidence 68999998666543
No 13
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=65.23 E-value=91 Score=26.92 Aligned_cols=132 Identities=18% Similarity=0.207 Sum_probs=68.3
Q ss_pred ceEEecCCCCccCccccCCCceEEeecC-C--CCCCcEEEEEecCCCCccccCCChHHHHHHHHHHHHhhhhcCCCCCCC
Q 025092 101 GFKLSIPSKWNPSKEREFPGQVLRYEDN-F--DSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEG 177 (258)
Q Consensus 101 gYsf~yP~~W~~~~e~~~~G~dv~f~d~-~--~~~~nVsV~v~p~~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~~ 177 (258)
--++-.|.||.+....+++..-....++ . ...-|+.|+|..+ ..+| +|+|+++. ++.=.+ .+.
T Consensus 32 ~v~lP~P~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL----~G~~-Dp~e~l~~-a~~d~~-~l~------- 97 (175)
T PF10738_consen 32 TVSLPTPPGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKL----TGDF-DPAEALEH-APADAQ-NLP------- 97 (175)
T ss_pred EEeccCCcCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEec----cCCC-CHHHHHHh-chhhHh-hCc-------
Confidence 3577889999876655554433333222 1 2245777777654 1355 57777662 221111 111
Q ss_pred CCCccccccceeeecccC----CCeEEEEEEEEcCCCCCCcce--EEEEEEEeCCE--EEEEEeEeccccccchhHHHHH
Q 025092 178 GFDPDAVATANILEASVR----PPYYFLSVLTRTADGDEGGKH--QLITATVKGGK--LYICKAQAGDKRWFKGTRKYVE 249 (258)
Q Consensus 178 g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~g~e~~rH--~L~~~tv~~gk--LYtl~~qa~e~rW~k~~~~~l~ 249 (258)
|+ +.++.+.- -.=+.+|-.-+. +| ..+| +..++.-.++. |..|++++.+.+=....+. .+
T Consensus 98 g~--------~~~~~s~~~~~GfpS~~i~GtY~~-~g--~~~~~~~r~VV~~~~~~~Ylvqltvt~~~~qa~~~~~a-~~ 165 (175)
T PF10738_consen 98 GF--------RELDGSPSDFSGFPSSQIEGTYDK-DG--MRLHTSQRTVVIPGDDQRYLVQLTVTTTADQAVALADA-TE 165 (175)
T ss_pred Cc--------ccccCCccccCCCceeEEEEEEee-CC--EEeEeEEEEEEEeCCCcEEEEEEEeeccccchhhhhhH-HH
Confidence 11 11121111 112344422222 22 2344 33333334554 4456777888888877775 99
Q ss_pred HHhhccccC
Q 025092 250 STASSFSVA 258 (258)
Q Consensus 250 ~vv~SF~V~ 258 (258)
.|++.|+|+
T Consensus 166 aI~~g~~It 174 (175)
T PF10738_consen 166 AIDEGFTIT 174 (175)
T ss_pred HHHcCCEec
Confidence 999999984
No 14
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=65.08 E-value=9.5 Score=29.98 Aligned_cols=17 Identities=29% Similarity=0.169 Sum_probs=11.7
Q ss_pred CccchhHHHHHHHHHHH
Q 025092 49 GSAVSRRLALTVLIGAA 65 (258)
Q Consensus 49 ~~~~~RR~~L~~~a~aa 65 (258)
++..+||.++..+++++
T Consensus 46 e~~~gRR~~mfaaaAaa 62 (103)
T PLN00058 46 QSTTMRRDLMFTAAAAA 62 (103)
T ss_pred cchhhHHHHHHHHHHHH
Confidence 35678999987655443
No 15
>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=63.48 E-value=2.3 Score=37.65 Aligned_cols=33 Identities=30% Similarity=0.388 Sum_probs=0.0
Q ss_pred CCCCceeeeccccccccccCCccchhHHHHHHHHHHH
Q 025092 29 NIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAA 65 (258)
Q Consensus 29 ~~~~~~~~c~~~~~~~~~~~~~~~~RR~~L~~~a~aa 65 (258)
+.+...++|+++... .+...+||.+|.++++++
T Consensus 10 ~~~r~~~~vra~~~~----~~~~~~RRa~l~~l~a~~ 42 (202)
T PF05757_consen 10 ASRRAGVVVRASQSP----AQQQTSRRAVLGSLLAAA 42 (202)
T ss_dssp -------------------------------------
T ss_pred ccccccceeccccCc----ccccccHHHHHHHHHHHH
Confidence 344556668888622 133568999987555443
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=49.71 E-value=22 Score=20.94 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=19.4
Q ss_pred EEEEEeCCEEEEEEeEeccccccc
Q 025092 219 ITATVKGGKLYICKAQAGDKRWFK 242 (258)
Q Consensus 219 ~~~tv~~gkLYtl~~qa~e~rW~k 242 (258)
..++-.+|+||.+....++.+|..
T Consensus 9 v~~~~~~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 9 VYVGSTDGTLYALDAKTGEILWTY 32 (33)
T ss_pred EEEEcCCCEEEEEEcccCcEEEEc
Confidence 334556899999999999999963
No 17
>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=43.59 E-value=31 Score=29.06 Aligned_cols=123 Identities=17% Similarity=0.225 Sum_probs=58.2
Q ss_pred CCceEEecCCCCccCccccCCCceEEeecCCCCCCcEEEEEecCCCCccccCCChHHHHHHHHHHHHhhhhcCCCCCCCC
Q 025092 99 GDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEGG 178 (258)
Q Consensus 99 ~dgYsf~yP~~W~~~~e~~~~G~dv~f~d~~~~~~nVsV~v~p~~~~sI~d~Gspeeva~~v~~~L~~~~~~~~t~s~~g 178 (258)
+.=|++.||.+|.+-... .| -..|.||..=.+|..+..-.- ++-.-..++ .++.+...
T Consensus 8 g~WFS~~YP~~W~EfED~--E~-sflFYnp~~WTGNfRISayk~-----~~~~ygk~~--------i~~EL~en------ 65 (153)
T PF12712_consen 8 GAWFSMEYPADWNEFEDG--EG-SFLFYNPDQWTGNFRISAYKG-----GSAQYGKEC--------IRQELKEN------ 65 (153)
T ss_dssp GG-EEEEE-TT-EEE-----TT-EEEEE-SSS---EEEEEEEE-------STTHHHHH--------HHHHHHH-------
T ss_pred CceEEEecCCCcchhccC--Cc-ceEEEChHHhcCceEEEEEec-----ccccchHHH--------HHHHHHhC------
Confidence 345999999999643211 12 357888888888887664320 011112333 33333321
Q ss_pred CCccccccceeeecccCCCeEEEEEEEEcCCCCCCcceEEEEEEEeCCEEEEEEeEeccccccchhHHHHHHHhhcccc
Q 025092 179 FDPDAVATANILEASVRPPYYFLSVLTRTADGDEGGKHQLITATVKGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 257 (258)
Q Consensus 179 ~~~~~v~~a~ll~a~~r~~YY~~Ey~~~~~~g~e~~rH~L~~~tv~~gkLYtl~~qa~e~rW~k~~~~~l~~vv~SF~V 257 (258)
+ .+++++...-.--|.-|.-- .+|..+..|.. +|-.++..|.|..+.+-..=.+ ..+.|+.|..|
T Consensus 66 --~----~a~~vkvg~~~caYs~E~f~--eeg~~YtsH~W--vtg~~~~sfeCSFTv~kg~~~~----~aE~iiasL~v 130 (153)
T PF12712_consen 66 --P----SAKLVKVGNWECAYSKEMFQ--EEGAYYTSHLW--VTGEGDVSFECSFTVPKGESVK----EAEEIIASLEV 130 (153)
T ss_dssp --T----T-EEEEETTEEEEEEEEEEE--ETTEEEEEEEE--EEEETTEEEEEEEEEETT---H----HHHHHHHH-EE
T ss_pred --C----CcceEEeccEEEEEEhhhhh--ccCeeEEEEEE--EEecCceEEEEEEEccCCCCcc----hHHHHHhhhee
Confidence 1 23455555543335445442 12212335554 4567899999999987543332 36677777654
No 18
>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=33.17 E-value=40 Score=20.24 Aligned_cols=13 Identities=38% Similarity=0.227 Sum_probs=9.2
Q ss_pred chhHHHHHHHHHH
Q 025092 52 VSRRLALTVLIGA 64 (258)
Q Consensus 52 ~~RR~~L~~~a~a 64 (258)
++||+.|-..+.+
T Consensus 1 ~sRR~Flk~~~~~ 13 (29)
T TIGR01409 1 LSRRDFLKGAAAA 13 (29)
T ss_pred CchhhhHHHHHHH
Confidence 4799999765543
No 19
>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=33.15 E-value=38 Score=24.64 Aligned_cols=14 Identities=36% Similarity=0.060 Sum_probs=10.0
Q ss_pred ccchhHHHHHHHHH
Q 025092 50 SAVSRRLALTVLIG 63 (258)
Q Consensus 50 ~~~~RR~~L~~~a~ 63 (258)
..++||.+|.++++
T Consensus 7 ~~~sRR~Flk~lg~ 20 (66)
T TIGR02811 7 ADPSRRDLLKGLGV 20 (66)
T ss_pred CCccHHHHHHHHHH
Confidence 35799999875443
No 20
>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=33.09 E-value=29 Score=29.71 Aligned_cols=12 Identities=17% Similarity=0.152 Sum_probs=8.1
Q ss_pred HHHHHHhhhhcC
Q 025092 160 VDYLLGKQAYSG 171 (258)
Q Consensus 160 v~~~L~~~~~~~ 171 (258)
++..+..-|+.|
T Consensus 110 ~a~~Ii~aWY~G 121 (168)
T PF12318_consen 110 LARAIISAWYLG 121 (168)
T ss_pred HHHHHHHHeeeE
Confidence 556677777765
No 21
>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=28.51 E-value=63 Score=27.04 Aligned_cols=46 Identities=28% Similarity=0.279 Sum_probs=22.5
Q ss_pred eeeeccccccccccC-CccchhHHHHHHHHHHHhhccCCCcchhhcccc
Q 025092 34 QIVCRAQKQAVQEDD-GSAVSRRLALTVLIGAAAVGSKVSPADAAYGES 81 (258)
Q Consensus 34 ~~~c~~~~~~~~~~~-~~~~~RR~~L~~~a~aaa~~~~~~pa~Aa~ge~ 81 (258)
.++|.++++....+. ....+-..+|+.++ +++.....||.|...|-
T Consensus 43 ~v~cs~~~~~~~~~~~~~~~~~~a~~~aa~--~a~~a~a~PA~ALVDeR 89 (138)
T PF07123_consen 43 RVRCSAEKKPSTVAAVNSQKGMGAALLAAA--AATAATASPALALVDER 89 (138)
T ss_pred ceEEEeccCccchhhhhhhcchhHHHHHHH--HHHHhhcCcHHHHHHHH
Confidence 578999876432111 11122333333222 22233367998876654
No 22
>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=25.06 E-value=67 Score=21.26 Aligned_cols=13 Identities=31% Similarity=0.240 Sum_probs=7.1
Q ss_pred ccchhHHHHHHHH
Q 025092 50 SAVSRRLALTVLI 62 (258)
Q Consensus 50 ~~~~RR~~L~~~a 62 (258)
...+||.+|..+.
T Consensus 7 ~~~~RRdFL~~at 19 (41)
T PF10399_consen 7 VDPTRRDFLTIAT 19 (41)
T ss_dssp ---HHHHHHHHHH
T ss_pred CCchHHHHHHHHH
Confidence 3578999985433
No 23
>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=22.67 E-value=47 Score=20.78 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=19.3
Q ss_pred EEEeCCEEEEEEeEeccccccch
Q 025092 221 ATVKGGKLYICKAQAGDKRWFKG 243 (258)
Q Consensus 221 ~tv~~gkLYtl~~qa~e~rW~k~ 243 (258)
++-.+|.||.|.+..++..|...
T Consensus 5 ~~~~~g~l~AlD~~TG~~~W~~~ 27 (38)
T PF01011_consen 5 VGTPDGYLYALDAKTGKVLWKFQ 27 (38)
T ss_dssp EETTTSEEEEEETTTTSEEEEEE
T ss_pred EeCCCCEEEEEECCCCCEEEeee
Confidence 34568999999999999999863
No 24
>PF05984 Cytomega_UL20A: Cytomegalovirus UL20A protein; InterPro: IPR009245 This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein [].
Probab=22.60 E-value=61 Score=25.05 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=9.9
Q ss_pred chhHHHHHHHHHHH
Q 025092 52 VSRRLALTVLIGAA 65 (258)
Q Consensus 52 ~~RR~~L~~~a~aa 65 (258)
+.||.+|+++++..
T Consensus 1 MaRRlwiLslLAVt 14 (100)
T PF05984_consen 1 MARRLWILSLLAVT 14 (100)
T ss_pred CchhhHHHHHHHHH
Confidence 36999888776543
No 25
>PLN00077 photosystem II reaction centre W protein; Provisional
Probab=22.22 E-value=80 Score=25.89 Aligned_cols=48 Identities=23% Similarity=0.341 Sum_probs=24.1
Q ss_pred CCceeeeccccccccccCCccchhHHHHHHHHHHHhhccCCCcchhhcccc
Q 025092 31 KPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAAVGSKVSPADAAYGES 81 (258)
Q Consensus 31 ~~~~~~c~~~~~~~~~~~~~~~~RR~~L~~~a~aaa~~~~~~pa~Aa~ge~ 81 (258)
+...++|..+++.+.. +....-..+..++.+++.+....|+.|...|-
T Consensus 31 ~~~~v~Cs~e~k~~~~---~~~~~~~~asl~a~~~a~~a~a~PA~AlVDeR 78 (128)
T PLN00077 31 RSERVRCSYEKKAANK---ADVNKLAGASLLVTSAATMAYAHPAFALVDER 78 (128)
T ss_pred cCCceEEecccCcccc---cccccchhHHHHHHHHHHHhccccHHHHHhHh
Confidence 4467999999764321 11111111222222233345567988876654
No 26
>PF12559 Inhibitor_I10: Serine endopeptidase inhibitors; InterPro: IPR022217 This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation. ; PDB: 1IXU_A.
Probab=21.24 E-value=38 Score=24.05 Aligned_cols=11 Identities=36% Similarity=0.661 Sum_probs=4.0
Q ss_pred ceEEecCCCCc
Q 025092 101 GFKLSIPSKWN 111 (258)
Q Consensus 101 gYsf~yP~~W~ 111 (258)
..+..||++|.
T Consensus 44 ~~TlKyPSD~e 54 (56)
T PF12559_consen 44 IQTLKYPSDWE 54 (56)
T ss_dssp -----SS-SS-
T ss_pred CcceeCCCccc
Confidence 37899999995
Done!