Query 025974
Match_columns 245
No_of_seqs 97 out of 99
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 11:41:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025974hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00059 PsbP domain-containin 100.0 1.6E-37 3.5E-42 281.8 15.1 134 102-245 125-285 (286)
2 PLN00042 photosystem II oxygen 100.0 3.1E-33 6.6E-38 252.6 17.0 131 102-244 106-259 (260)
3 PLN00067 PsbP domain-containin 100.0 4.3E-32 9.3E-37 245.3 17.0 114 119-244 141-263 (263)
4 PF01789 PsbP: PsbP; InterPro 100.0 4E-32 8.6E-37 227.9 11.4 132 102-244 39-174 (175)
5 PLN00066 PsbP domain-containin 100.0 9E-28 1.9E-32 217.6 14.4 105 125-245 145-259 (262)
6 PLN03152 hypothetical protein; 99.9 3.4E-26 7.3E-31 203.9 10.9 103 124-245 126-241 (241)
7 PF08786 DUF1795: Domain of un 97.4 0.0046 9.9E-08 49.3 11.8 114 113-242 9-130 (130)
8 PF10738 Lpp-LpqN: Probable li 95.0 0.69 1.5E-05 40.3 12.6 129 102-244 39-173 (175)
9 COG5435 Uncharacterized conser 82.2 15 0.00033 31.8 9.4 120 111-244 14-141 (147)
10 PF10518 TAT_signal: TAT (twin 46.7 12 0.00027 23.2 1.2 15 75-89 2-16 (26)
11 TIGR02811 formate_TAT formate 38.8 17 0.00037 27.2 1.2 17 72-88 6-22 (66)
12 PF09935 DUF2167: Protein of u 34.9 1.3E+02 0.0029 27.9 6.5 114 126-244 55-181 (239)
13 PF10399 UCR_Fe-S_N: Ubiquitin 34.6 24 0.00053 24.3 1.3 10 73-82 7-16 (41)
14 COG4290 Guanyl-specific ribonu 33.5 33 0.00072 29.8 2.3 26 184-209 104-129 (152)
15 COG3540 PhoD Phosphodiesterase 32.8 54 0.0012 33.6 3.9 75 74-150 2-91 (522)
16 PF08006 DUF1700: Protein of u 31.3 25 0.00054 29.7 1.2 19 143-161 46-64 (181)
17 PF07526 POX: Associated with 21.6 52 0.0011 27.9 1.4 29 215-244 81-109 (140)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=1.6e-37 Score=281.77 Aligned_cols=134 Identities=19% Similarity=0.347 Sum_probs=118.2
Q ss_pred cCcc--cccccCCcceeEEEecCCCCCCceEEEEEecCCC-CccccccCCChHHHHHHHhhccccCC---CCCCCCceEE
Q 025974 102 NDWQ--LGAGEPNGFKSITAFYPQEASSSSVSVVITGLGP-DFTRMESFGKVEAFADTLVSGLDRSW---RRPPGVAAKL 175 (245)
Q Consensus 102 ~~W~--~~~G~~sg~k~V~AF~P~~~~~eNVSVVITpv~~-DftsL~sfG~p~eVae~Lv~~v~rs~---~appg~~AkL 175 (245)
.||+ .+.|.|..|||++ +.+|||||+|++++. ++++|++||+|+||||+|+++++.+. +.+.|++++|
T Consensus 125 ~GWi~V~~~G~DVvFrD~I------e~~ENVSV~ISs~sss~~~sLeDLGsP~eVgerLlkqvLa~f~str~GsgReaeL 198 (286)
T PLN00059 125 QNWIQVRGAGADIFFRDPV------VLDENLSVEFSSPSSSKYTSLEDLGSPEEVGKRVLRQYLTEFMSTRLGVKREANI 198 (286)
T ss_pred CCCeEeccCCCceEEeccC------ccccceEEEEecCCcccCCChHHcCCHHHHHHHHHHHHhcccccccCCCCcceEE
Confidence 8999 4778898999987 999999999999974 46899999999999999999987321 1224799999
Q ss_pred Eeceec-----cceEEEEEEEeCCC----------------CCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHH
Q 025974 176 IDCKAS-----KGFYYIEYTLQNPG----------------ESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSN 234 (245)
Q Consensus 176 IdA~~r-----k~YY~lEYtvq~P~----------------~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~ 234 (245)
|+|.+| +.||+|||++++|+ ++.||++|+|+|.| ||||||++|+||+||+|+++.
T Consensus 199 VsA~~Re~~DGktYY~lEY~Vks~~~~n~~~~~~qdr~~~~~w~RH~LA~v~V~n----GkLYTL~~qtpE~RW~kvk~~ 274 (286)
T PLN00059 199 LSTSSRVADDGKLYYQVEVNIKSYANNNELAVMPQDRVARLEWNRRYLAVLGVEN----DRLYSIRLQTPEKVFLEEEKD 274 (286)
T ss_pred EEeeeEEccCCcEEEEEEEEEEcCcccccccccccccccccccceeeEEEEEEeC----CEEEEEEcCCcHHHHHHHHHH
Confidence 999999 56999999999972 23899999999988 599999999999999999999
Q ss_pred HHHHhcceeeC
Q 025974 235 IEKAVASFRFI 245 (245)
Q Consensus 235 f~~vVdSF~v~ 245 (245)
|++|++||+|+
T Consensus 275 f~~V~dSF~V~ 285 (286)
T PLN00059 275 LRRVMDSFRVE 285 (286)
T ss_pred HHHHHhheeec
Confidence 99999999985
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=3.1e-33 Score=252.63 Aligned_cols=131 Identities=20% Similarity=0.269 Sum_probs=107.9
Q ss_pred cCcc---c--ccccCCcceeEEEecCCCCCCceEEEEEecCCCCccccccCCChHH----HHHHHhhccccCC-C----C
Q 025974 102 NDWQ---L--GAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEA----FADTLVSGLDRSW-R----R 167 (245)
Q Consensus 102 ~~W~---~--~~G~~sg~k~V~AF~P~~~~~eNVSVVITpv~~DftsL~sfG~p~e----Vae~Lv~~v~rs~-~----a 167 (245)
++|+ + ..|++..|+|.+ +.++||||+|+|+ |+++|++||+|+| |++.|.+.+.... . .
T Consensus 106 ~~W~~~ke~~~~G~dv~f~D~~------~~~eNVSV~Ispt--~k~sI~dlGsPee~l~~vgylL~kq~~a~~t~s~~Gf 177 (260)
T PLN00042 106 SKWNPSKEREFPGQVLRFEDNF------DATSNLSVMVTPT--DKKSITDYGSPEEFLSKVSYLLGKQAYSGETASEGGF 177 (260)
T ss_pred CCCccccccccCCceEEeeccc------cccccEEEEEecC--CcCCHhhcCCHHHHHHHHHHHHHhhhccCccccccCc
Confidence 8997 2 236666777765 8999999999988 4579999999999 7878887764221 0 0
Q ss_pred CCCC--ceEEEeceec----cceEEEEEEEeCCC--CCceeEEEEEEeecCCccceEEEEeccccchhhHHH-HHHHHHH
Q 025974 168 PPGV--AAKLIDCKAS----KGFYYIEYTLQNPG--ESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKY-GSNIEKA 238 (245)
Q Consensus 168 ppg~--~AkLIdA~~r----k~YY~lEYtvq~P~--~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kv-k~~f~~v 238 (245)
.|++ +|+||++++| ++||+|||.+++|+ +..||+|++|+|.+ ||||||++|+||+||.|+ ++.|+.|
T Consensus 178 ~p~~vata~Lleas~re~dGk~YY~lE~~~~~ad~d~~~RH~LatatV~~----GkLYtl~aqa~EkRW~K~~~k~l~~v 253 (260)
T PLN00042 178 DANAVATAAVLESSTQEVGGKPYYYLSVLTRTADGDEGGKHQLITATVSD----GKLYICKAQAGDKRWFKGARKFVEGA 253 (260)
T ss_pred CcccccceeEEEeeeEEeCCeEEEEEEEEEecCCCCCCCceEEEEEEEEC----CEEEEEEecCchhhhhHHHHHHHHHH
Confidence 1332 7899999999 67999999999996 35799999999976 599999999999999998 6689999
Q ss_pred hcceee
Q 025974 239 VASFRF 244 (245)
Q Consensus 239 VdSF~v 244 (245)
++||+|
T Consensus 254 ~~SFsV 259 (260)
T PLN00042 254 ASSFSV 259 (260)
T ss_pred Hhceec
Confidence 999997
No 3
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=4.3e-32 Score=245.27 Aligned_cols=114 Identities=14% Similarity=0.160 Sum_probs=102.6
Q ss_pred EecCCCCCCceEEEEEecCC-----CCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEeceec----cceEEEEE
Q 025974 119 AFYPQEASSSSVSVVITGLG-----PDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCKAS----KGFYYIEY 189 (245)
Q Consensus 119 AF~P~~~~~eNVSVVITpv~-----~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLIdA~~r----k~YY~lEY 189 (245)
.|.. +.++||||||+||+ +| ++|++||+|++|+++|.+.++ .++++.++||||.+| ++||+|||
T Consensus 141 ~F~D--~~dgnVSVIVSPV~r~t~k~~-~sIeDlGsPeeVl~~Lg~~v~----g~~~~~~eLLeAs~re~dGktYY~~E~ 213 (263)
T PLN00067 141 KFED--EKQGKVQVVASPLIRLTNKPN-ATIEEIGSPEKLIASLGPFVT----GNSYDPDELLETSVEKIGDQTYYKYVL 213 (263)
T ss_pred EEeC--CCCCCEEEEEecccccccCCC-CChHHccCHHHHHHHhhHHhh----cCCCCCcceEEeeeEeeCCeEEEEEEE
Confidence 4543 55889999999984 45 699999999999999999987 568999999999999 67999999
Q ss_pred EEeCCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 190 TLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 190 tvq~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
.+..+++ .||+|+++++.+ |||||+++|+||+||.|+++.|++|++||+|
T Consensus 214 ~tp~a~~-gRHnLataTV~~----GkLYtf~asanEkRW~K~k~~l~~V~dSFsV 263 (263)
T PLN00067 214 ETPFALT-GSHNLAKATAKG----NTVVLFVVSASDKQWQSSEKTLKAILDSFQA 263 (263)
T ss_pred EecCCCC-CceEEEEEEEEC----CEEEEEEecCCHHHHHHHHHHHHHHHHhccC
Confidence 9999985 799999988865 5999999999999999999999999999986
No 4
>PF01789 PsbP: PsbP; InterPro: IPR002683 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbP. Both PsbP and PsbQ (IPR008797 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [, ]. The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity []. PsbP is encoded in the nuclear genome in plants.; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 2VU4_A 1V2B_A 2LNJ_A 2XB3_A.
Probab=99.97 E-value=4e-32 Score=227.88 Aligned_cols=132 Identities=32% Similarity=0.502 Sum_probs=112.6
Q ss_pred cCcccccccCCcceeEEEecCCCCCCceEEEEEecCCCCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEeceec
Q 025974 102 NDWQLGAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCKAS 181 (245)
Q Consensus 102 ~~W~~~~G~~sg~k~V~AF~P~~~~~eNVSVVITpv~~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLIdA~~r 181 (245)
+||....+ .| ..+.|.++...++||+|+|+|++.+| +|++||+|++||++|++.++++ ...++.++||++.+|
T Consensus 39 ~gW~~~~~--~G--~~v~f~d~~~~~~nvsV~v~p~~~~~-sl~~lGs~~~va~~l~~~~~~~--~~~~~~a~li~a~~~ 111 (175)
T PF01789_consen 39 SGWEEVDV--SG--ADVVFRDPIDADENVSVVVSPVPKDF-SLEDLGSPEEVAERLLNGELAS--PGSGREAELISASER 111 (175)
T ss_dssp TTEEEEES--TT--EEEEEEETTETTSEEEEEEEE-STS--SGGGG-SHHHHHHHHHHHCCCH--CTSSEEEEEEEEEEE
T ss_pred CCCeecCC--CC--eEEEEECcccccceEEEEEEecCCcC-chhhcCCHHHHHHHHhhhhccc--ccCCcceEEEEeeee
Confidence 89975444 34 34578999999999999999999997 9999999999999999998733 112399999999999
Q ss_pred ----cceEEEEEEEeCCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 182 ----KGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 182 ----k~YY~lEYtvq~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
+.||+|||+++.|++..||+++++++.+ ||||||++|+||+||+|+++.|++|++||+|
T Consensus 112 ~~~g~~yY~~Ey~~~~~~~~~rh~l~~~tv~~----g~lY~l~~~a~e~~w~k~~~~l~~iv~SF~v 174 (175)
T PF01789_consen 112 EVDGKTYYEYEYTVQSPNEGRRHNLAVVTVKN----GKLYTLTAQAPESRWDKVEPKLRKIVDSFRV 174 (175)
T ss_dssp EETTEEEEEEEEEEEETTEEEEEEEEEEEEET----TEEEEEEEEEEHHHHHTCHHHHHHHHHC-EE
T ss_pred ecCCccEEEEEEEeccCCCcccEEEEEEEEEC----CEEEEEEEEcCHHHHHHHHHHHHHHHhcEEe
Confidence 4699999999999866899999999975 5999999999999999999999999999997
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.95 E-value=9e-28 Score=217.56 Aligned_cols=105 Identities=18% Similarity=0.265 Sum_probs=95.3
Q ss_pred CCCceEEEEEecCC------CCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEeceec----cceEEEEEEEeCC
Q 025974 125 ASSSSVSVVITGLG------PDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCKAS----KGFYYIEYTLQNP 194 (245)
Q Consensus 125 ~~~eNVSVVITpv~------~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLIdA~~r----k~YY~lEYtvq~P 194 (245)
..++||+|+|+|++ .+.++|++||+|++|++.|.+.++ .++.+.++||++.++ ++||.|||
T Consensus 145 ~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~----g~~~~e~eLl~a~~re~dGktYY~~E~----- 215 (262)
T PLN00066 145 DKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELI----GEPVEEGKVLSMEVAEHSGRTYYQFEL----- 215 (262)
T ss_pred CCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhc----CCCccccceeEeeeeecCCcEEEEEEE-----
Confidence 57899999999996 244799999999999999999876 557789999999998 67999999
Q ss_pred CCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceeeC
Q 025974 195 GESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRFI 245 (245)
Q Consensus 195 ~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v~ 245 (245)
.||+|++|+|.+ ||||||++|+||+||.|+++.|+.|++||+|+
T Consensus 216 ---~rH~LasaTV~~----GrLYt~~asape~rW~k~~~~lr~v~dSF~V~ 259 (262)
T PLN00066 216 ---PPHTLVTATAAG----NRVYIFSVTANGLQWKRHYKDLKRIAKSFRVV 259 (262)
T ss_pred ---eCceEEEEEEEC----CEEEEEEeecchHhhHHHHHHHHHHhhceeee
Confidence 289999999986 59999999999999999999999999999985
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.93 E-value=3.4e-26 Score=203.91 Aligned_cols=103 Identities=20% Similarity=0.343 Sum_probs=86.4
Q ss_pred CCCCceEEEEEecCC-------CCccccccCCChHHHHHHHhhccccCCCCCCC---CceEEEecee-c--cceEEEEEE
Q 025974 124 EASSSSVSVVITGLG-------PDFTRMESFGKVEAFADTLVSGLDRSWRRPPG---VAAKLIDCKA-S--KGFYYIEYT 190 (245)
Q Consensus 124 ~~~~eNVSVVITpv~-------~DftsL~sfG~p~eVae~Lv~~v~rs~~appg---~~AkLIdA~~-r--k~YY~lEYt 190 (245)
...+|||||+|+|++ .+ ++|.+||+|+|||+.|+. +| +.++.++.++ . |+||+|||.
T Consensus 126 ~D~sEnVSVVIspv~~LK~tfle~-kDLtDLGsp~EVgkv~vP---------~g~~~~saR~iel~~E~dGKtYY~lEy~ 195 (241)
T PLN03152 126 PDGSEVLSVVIRPSNQLKITFLEA-KDITDLGSLKEAAKIFVP---------GGATLYSARTIKVKEEEGIRTYYFYEFG 195 (241)
T ss_pred CCCCceEEEEEecCcccccccccc-CChhHcCCHHHHHHhhCC---------CcccccccceeeeeeecCCceeEEEEEE
Confidence 345899999999997 55 899999999999977753 22 1344444332 2 789999999
Q ss_pred EeCCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceeeC
Q 025974 191 LQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRFI 245 (245)
Q Consensus 191 vq~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v~ 245 (245)
++ .||++++|+|.+ |||||+++|++|+||+|++++|+++++||+|+
T Consensus 196 v~-----~RH~LaTVaVsr----GKLYTl~aSt~EkRW~Kvk~kfr~aa~SFsV~ 241 (241)
T PLN03152 196 RD-----EQHVALVATVNS----GKAYIAGATAPESKWDDDGVKLRSAAISLTVL 241 (241)
T ss_pred eC-----CcEEEEEEEEcC----CeEEEEecCCchhchHHHHHHHHHHHhheeeC
Confidence 86 599999999987 59999999999999999999999999999986
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=97.37 E-value=0.0046 Score=49.29 Aligned_cols=114 Identities=16% Similarity=0.212 Sum_probs=74.2
Q ss_pred ccee--EEEecCCCC--CCceEEEEEecCCCCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEeceec----cce
Q 025974 113 GFKS--ITAFYPQEA--SSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCKAS----KGF 184 (245)
Q Consensus 113 g~k~--V~AF~P~~~--~~eNVSVVITpv~~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLIdA~~r----k~Y 184 (245)
|++| +.+|-++.. ...|+.|.-.+++++ .+.++..++.++.+-+ --..-++++.+.- ..-
T Consensus 9 ~~~D~t~nv~~~~~~~~~~~slvIsR~~l~~g-------~tl~~~~~~q~~~l~~-----~l~~~~~~~~~~~~l~~~~a 76 (130)
T PF08786_consen 9 GWQDRTMNVLVLPDSGGSGPSLVISRDPLPDG-------ETLEDYLQRQLAQLRK-----QLPGFQLVERQPITLGGRPA 76 (130)
T ss_dssp TSEE--BEEEEE--BTTB-EEEEEEEE---TT-------S-HHHHHHHHHHHHHC-----CSTT-EEEEEEEEEETTEEE
T ss_pred cceeceEEEEEccCCCCCcceEEEEeccCCCC-------CCHHHHHHHHHHHHHh-----hCCCcEEEeeEEEEeCCCCe
Confidence 4444 345544433 356666666677776 3678888888887631 1223344443333 368
Q ss_pred EEEEEEEeCCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcce
Q 025974 185 YYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASF 242 (245)
Q Consensus 185 Y~lEYtvq~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF 242 (245)
+.+||+...++. .-|-.-++.+-. | +++|+||..++..-.+..+..++.+++||
T Consensus 77 ~~l~~~~~~~g~-~v~Q~q~~~~~~-~--~~~l~~T~t~~~~~~~~~~~~~~~i~~Sf 130 (130)
T PF08786_consen 77 RELEYSFRSGGQ-PVYQRQAAVLLP-G--RRVLVFTYTAPGPFTEEQRAHWEAILKSF 130 (130)
T ss_dssp EEEEEEEEETTC-EEEEEEEEEEEC----CCEEEEEEEEECCCHHHHHHHHHHHHCT-
T ss_pred EEEEEEEeeCCE-EEEEEEEEEEEC-C--CEEEEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 999999998885 566666655433 2 59999999999999999999999999998
No 8
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=95.05 E-value=0.69 Score=40.35 Aligned_cols=129 Identities=16% Similarity=0.117 Sum_probs=85.4
Q ss_pred cCccc-ccccCCcceeEEEecCC-CCCCceEEEEEecCCCCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEece
Q 025974 102 NDWQL-GAGEPNGFKSITAFYPQ-EASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCK 179 (245)
Q Consensus 102 ~~W~~-~~G~~sg~k~V~AF~P~-~~~~eNVSVVITpv~~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLIdA~ 179 (245)
.||+. ........-.+++.-.. +.-..|+-|++..+..|| +|+|+.+.=-..+. .-||-+ .+++.
T Consensus 39 ~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL~G~~-------Dp~e~l~~a~~d~~----~l~g~~--~~~~s 105 (175)
T PF10738_consen 39 PGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKLTGDF-------DPAEALEHAPADAQ----NLPGFR--ELDGS 105 (175)
T ss_pred cCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEeccCCC-------CHHHHHHhchhhHh----hCcCcc--cccCC
Confidence 89994 55556566677766552 233789999999998887 46666553322221 224444 33332
Q ss_pred ec--c--ceEEEEEEEeCCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 180 AS--K--GFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 180 ~r--k--~YY~lEYtvq~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
.- . .-+.+|.+-..++- +||...-+.|.-++-.--|..||+++.+..-....+..+.|++.|+|
T Consensus 106 ~~~~~GfpS~~i~GtY~~~g~-~~~~~~r~VV~~~~~~~Ylvqltvt~~~~qa~~~~~a~~aI~~g~~I 173 (175)
T PF10738_consen 106 PSDFSGFPSSQIEGTYDKDGM-RLHTSQRTVVIPGDDQRYLVQLTVTTTADQAVALADATEAIDEGFTI 173 (175)
T ss_pred ccccCCCceeEEEEEEeeCCE-EeEeEEEEEEEeCCCcEEEEEEEeeccccchhhhhhHHHHHHcCCEe
Confidence 22 2 25788866666663 67776664444434334677899999999999999999999999997
No 9
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=82.16 E-value=15 Score=31.82 Aligned_cols=120 Identities=17% Similarity=0.278 Sum_probs=74.2
Q ss_pred CCccee--EEEecCCCCCCceEEEEEe--cCCCCccccccCCChHHHHHHHhhccccCCCCCCCCceEEEe-ceec-cce
Q 025974 111 PNGFKS--ITAFYPQEASSSSVSVVIT--GLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLID-CKAS-KGF 184 (245)
Q Consensus 111 ~sg~k~--V~AF~P~~~~~eNVSVVIT--pv~~DftsL~sfG~p~eVae~Lv~~v~rs~~appg~~AkLId-A~~r-k~Y 184 (245)
+.+++| |-+|--+.....-+|.+|| ++++| . +-.++.++.|..+-+ .=||-+.+=-. ..-- .--
T Consensus 14 P~~w~DrSvNvf~~~~~gt~~~sfvIsRd~~~~g-~------~~~~y~~rql~~l~k---~Lpgy~~~~~~e~~v~~~aa 83 (147)
T COG5435 14 PAAWQDRSVNVFVSGDNGTSGFSFVISRDPLEPG-D------TFPEYVQRQLALLRK---QLPGYELHHRREIEVGGAAA 83 (147)
T ss_pred cchhccceEEEEEecCCCcceeEEEEecCCCCCC-C------cHHHHHHHHHHHHHh---hCCCeEEeeccccccCcccc
Confidence 445555 4456555555667777777 45444 2 346677777776531 11332222111 0000 235
Q ss_pred EEEEEEEeCC-CCCceeEEEE-EEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 185 YYIEYTLQNP-GESRKHLFSA-IGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 185 Y~lEYtvq~P-~~~~RH~la~-Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
-.+||.-+.| .++ |-.... +.+.++ .++-+||+.++-.--++-+.....+|.||..
T Consensus 84 ~~~~y~w~~~~~~~-r~v~q~~~~i~~g---~~vLifT~Tt~~~ftp~q~~~~~~~I~Sf~p 141 (147)
T COG5435 84 PLLDYQWTSPEGEQ-RRVQQRQVFIERG---DTVLIFTLTTPGEFTPSQKKAWEQVIQSFVP 141 (147)
T ss_pred ceeEEEeecCCCCC-ceEEEEEeecccC---CeEEEEEecCCCCCCHHHHHHHHHHHHhcCC
Confidence 6677777775 443 444333 455554 6999999999999999999999999999964
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=46.67 E-value=12 Score=23.19 Aligned_cols=15 Identities=27% Similarity=0.173 Sum_probs=11.7
Q ss_pred hhHHHHHHHhhhhhh
Q 025974 75 TKRREVMFQLAFTAC 89 (245)
Q Consensus 75 ~~RR~~Ll~~~~~a~ 89 (245)
+.||++|.+.+++++
T Consensus 2 ~sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAA 16 (26)
T ss_pred CcHHHHHHHHHHHHH
Confidence 679999987777653
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=38.80 E-value=17 Score=27.21 Aligned_cols=17 Identities=24% Similarity=0.389 Sum_probs=12.5
Q ss_pred CCchhHHHHHHHhhhhh
Q 025974 72 DSRTKRREVMFQLAFTA 88 (245)
Q Consensus 72 ~~~~~RR~~Ll~~~~~a 88 (245)
+..+.||.+|.++++++
T Consensus 6 ~~~~sRR~Flk~lg~~a 22 (66)
T TIGR02811 6 KADPSRRDLLKGLGVGA 22 (66)
T ss_pred cCCccHHHHHHHHHHHH
Confidence 34578999998766644
No 12
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=34.94 E-value=1.3e+02 Score=27.85 Aligned_cols=114 Identities=11% Similarity=0.189 Sum_probs=73.7
Q ss_pred CCceEEEEEecCCCCcccccc--CCChHHHHHHHhhccccC--CCC----CC----C-CceEEEeceeccceEEEEEEEe
Q 025974 126 SSSSVSVVITGLGPDFTRMES--FGKVEAFADTLVSGLDRS--WRR----PP----G-VAAKLIDCKASKGFYYIEYTLQ 192 (245)
Q Consensus 126 ~~eNVSVVITpv~~DftsL~s--fG~p~eVae~Lv~~v~rs--~~a----pp----g-~~AkLIdA~~rk~YY~lEYtvq 192 (245)
.+.+-.|+|+-.+.++-+-.+ ==++++.=+.+-...... .++ |+ | ...=-+|+..++-+|-.|-...
T Consensus 55 ~~~~W~v~~~y~~~GyVkDdda~~id~d~LL~~~k~~t~e~N~eR~~~G~~~l~l~GW~~~P~YD~~t~~L~Wa~~~~~~ 134 (239)
T PF09935_consen 55 DDEDWFVVFEYEDSGYVKDDDAKNIDYDELLKSMKEGTEESNKERKKRGYPPLHLVGWAEPPHYDAATHRLYWAKELKFG 134 (239)
T ss_pred CCCCEEEEEEEcCCCceecchhhhCCHHHHHHHHHHhHHhhhHHHHhcCCCceEEeccccCCccCccccEEEEEEeeecC
Confidence 567777888777666655444 223444444433322100 000 01 1 1111256666777888887776
Q ss_pred CCCCCceeEEEEEEeecCCccceEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 193 NPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 193 ~P~~~~RH~la~Vav~~nG~~grLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
...+ .--|+.+.+++|.| ..+||.-+..+.-+.++..++++++.+++
T Consensus 135 ~~~~-~~vNYn~r~LGR~G----~~~l~lV~~~~~l~~~k~~~~~lL~~~~f 181 (239)
T PF09935_consen 135 GDPE-NTVNYNTRVLGREG----VLSLNLVADPDQLPAVKPEAQALLSAVEF 181 (239)
T ss_pred CCCC-ceEEEEEEEeecce----EEEEEEecCHHHHHHHHHHHHHHHhhccC
Confidence 6432 47899999999975 78999999999999999999999987764
No 13
>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=34.65 E-value=24 Score=24.29 Aligned_cols=10 Identities=20% Similarity=0.391 Sum_probs=5.7
Q ss_pred CchhHHHHHH
Q 025974 73 SRTKRREVMF 82 (245)
Q Consensus 73 ~~~~RR~~Ll 82 (245)
....||.+|.
T Consensus 7 ~~~~RRdFL~ 16 (41)
T PF10399_consen 7 VDPTRRDFLT 16 (41)
T ss_dssp ---HHHHHHH
T ss_pred CCchHHHHHH
Confidence 3478898883
No 14
>COG4290 Guanyl-specific ribonuclease Sa [Nucleotide transport and metabolism]
Probab=33.55 E-value=33 Score=29.81 Aligned_cols=26 Identities=31% Similarity=0.444 Sum_probs=19.8
Q ss_pred eEEEEEEEeCCCCCceeEEEEEEeec
Q 025974 184 FYYIEYTLQNPGESRKHLFSAIGMAS 209 (245)
Q Consensus 184 YY~lEYtvq~P~~~~RH~la~Vav~~ 209 (245)
=|+=||||+.|+...|-..=+|+-+-
T Consensus 104 gYYREYTVeTpG~sdRGarRIV~GGd 129 (152)
T COG4290 104 GYYREYTVETPGLSDRGARRIVTGGD 129 (152)
T ss_pred CcceeeEeeCCCcccCCceeEeeCCC
Confidence 35569999999988777777766543
No 15
>COG3540 PhoD Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]
Probab=32.81 E-value=54 Score=33.63 Aligned_cols=75 Identities=20% Similarity=0.274 Sum_probs=38.7
Q ss_pred chhHHHHHHHhhhhh--hcccc-hhhhHhHh-cCcc-----cccccCCcceeEEEec---CCCCC---CceEEEEEecCC
Q 025974 74 RTKRREVMFQLAFTA--CSFPA-IVSYALAA-NDWQ-----LGAGEPNGFKSITAFY---PQEAS---SSSVSVVITGLG 138 (245)
Q Consensus 74 ~~~RR~~Ll~~~~~a--~~~p~-~~~~a~Ae-~~W~-----~~~G~~sg~k~V~AF~---P~~~~---~eNVSVVITpv~ 138 (245)
.++||.+|.+.|.++ ++.++ .+..+.+. ++-. |..| |..--+|++|. |+... ..-|.+-|+.-
T Consensus 2 ~l~RR~fl~~~a~~aG~la~a~~~~~~a~a~f~~rpaF~~GVaSG-Dp~~~svviWTRl~P~p~~~g~~v~V~wEvs~~- 79 (522)
T COG3540 2 TLKRRQFLQGAAVTAGGLAIASGLAAPAIARFSGRPAFTHGVASG-DPTATSVVIWTRLDPEPLNGGRPVPVIWEVSTD- 79 (522)
T ss_pred cchHHHHHhhhhhhhhhhhhhhccccccccccCCCCccccccccC-CCCCCeEEEEEccCCccccCCCCcceEEEecCC-
Confidence 378999999866655 22221 11222222 2322 5566 44455666664 43333 33344444433
Q ss_pred CCccccccCCCh
Q 025974 139 PDFTRMESFGKV 150 (245)
Q Consensus 139 ~DftsL~sfG~p 150 (245)
++|++|-..|++
T Consensus 80 ~~f~~ivr~gt~ 91 (522)
T COG3540 80 ENFSNIVRKGTV 91 (522)
T ss_pred ccHHHHHhcCCc
Confidence 677766666654
No 16
>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=31.32 E-value=25 Score=29.72 Aligned_cols=19 Identities=11% Similarity=0.288 Sum_probs=16.4
Q ss_pred ccccCCChHHHHHHHhhcc
Q 025974 143 RMESFGKVEAFADTLVSGL 161 (245)
Q Consensus 143 sL~sfG~p~eVae~Lv~~v 161 (245)
=+++||+|+++|..++...
T Consensus 46 ii~~LG~P~~iA~~i~~~~ 64 (181)
T PF08006_consen 46 IIAELGSPKEIAREILAEY 64 (181)
T ss_pred HHHHcCCHHHHHHHHHHhh
Confidence 4789999999999998763
No 17
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=21.64 E-value=52 Score=27.86 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=22.4
Q ss_pred eEEEEeccccchhhHHHHHHHHHHhcceee
Q 025974 215 RLYTVTGQFVEEESEKYGSNIEKAVASFRF 244 (245)
Q Consensus 215 rLYTltaq~~E~rW~Kvk~~f~~vVdSF~v 244 (245)
||.++ .+-.|+|..+|.++++.||.||.-
T Consensus 81 KLl~m-L~eVd~RY~qY~~Qmq~VvssFe~ 109 (140)
T PF07526_consen 81 KLLSM-LDEVDRRYRQYYDQMQAVVSSFEA 109 (140)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44443 455788999999999999999953
Done!