Query 028350
Match_columns 210
No_of_seqs 88 out of 90
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:08:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028350.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028350hhsearch_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 1.7E-30 3.7E-35 230.1 13.4 147 40-209 32-205 (260)
2 PLN00059 PsbP domain-containin 99.9 1.2E-22 2.5E-27 181.6 11.7 127 74-208 76-216 (286)
3 PF01789 PsbP: PsbP; InterPro 99.9 4.1E-22 8.9E-27 163.4 8.8 104 98-208 16-122 (175)
4 PLN00067 PsbP domain-containin 99.8 9.2E-18 2E-22 149.4 13.1 167 11-209 3-213 (263)
5 PLN00066 PsbP domain-containin 99.7 1.9E-16 4.2E-21 141.0 12.7 132 72-209 42-215 (262)
6 PLN03152 hypothetical protein; 99.0 9.9E-10 2.1E-14 97.1 7.0 97 102-209 75-194 (241)
7 PF12712 DUF3805: Domain of un 81.8 5.5 0.00012 33.9 6.4 89 106-206 2-93 (153)
8 PF10738 Lpp-LpqN: Probable li 54.3 38 0.00082 29.0 5.8 59 114-179 32-92 (175)
9 TIGR02811 formate_TAT formate 52.4 7.5 0.00016 28.5 1.1 16 72-87 6-21 (66)
10 PF08786 DUF1795: Domain of un 52.3 28 0.00061 26.9 4.3 52 116-180 3-54 (130)
11 PF10518 TAT_signal: TAT (twin 47.4 16 0.00034 22.2 1.8 14 75-88 2-15 (26)
12 PF07174 FAP: Fibronectin-atta 38.2 20 0.00043 33.5 1.8 94 106-206 110-224 (297)
13 PF08802 CytB6-F_Fe-S: Cytochr 37.5 20 0.00044 24.2 1.3 18 75-92 6-23 (39)
14 PF08006 DUF1700: Protein of u 32.9 23 0.00051 29.2 1.2 20 161-180 45-64 (181)
15 PRK10882 hydrogenase 2 protein 30.6 40 0.00087 31.4 2.5 14 75-88 1-14 (328)
16 COG3540 PhoD Phosphodiesterase 24.3 65 0.0014 32.4 2.8 14 75-88 3-16 (522)
17 PLN02999 photosystem II oxygen 22.6 40 0.00087 29.8 0.9 39 75-115 41-79 (190)
No 1
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=99.97 E-value=1.7e-30 Score=230.09 Aligned_cols=147 Identities=22% Similarity=0.352 Sum_probs=114.5
Q ss_pred ccceeeeeeeccccchhhhhhhhccccccccccchhhHHHHHHHHHHHhh----ccccchhhhhhh--------ccCcee
Q 028350 40 QYKKQFVFCCKKQEQEDDARTLNRFRIEEQDDDSRTKRREVMFQLAFTAC----SFPAIVSYALAA--------NEDLRV 107 (210)
Q Consensus 40 ~~~k~~~~~c~~~~~~~~~~~~~~~~~~e~~~~~~~~RR~aL~~~a~aa~----~~pa~a~~a~AA--------~~gF~~ 107 (210)
..+.+. +.|++|.++.+ .++||.+|++++++++ +.|+.++++++| ++||.+
T Consensus 32 ~~~~~~-~~~~~~~~~~~----------------~~srr~~l~~~~ga~a~~~~~~pa~aay~~~anvfg~~k~~~gF~~ 94 (260)
T PLN00042 32 ASRPSQ-VVCRAQEEDNS----------------AVSRRAALALLAGAAAAGAKVSPANAAYGESANVFGKPKTNTGFLP 94 (260)
T ss_pred CCCCcc-eeeeccccccc----------------cccHHHHHHHHHHHHHhhcccCchhhhhcchhhccCCCCCCCCCeE
Confidence 334444 45599887554 2899999998888743 367778888886 599999
Q ss_pred eeeCCCceEEEcCCCCcCCCC-CCCCcceeEEecCCCCCCcceEEEEecCCCCcccccccCCHHHHHHHH----hhcc--
Q 028350 108 YTDELNKFEISIPQDWQLGAG-EPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTL----VSGL-- 180 (210)
Q Consensus 108 Y~D~~dGFsf~yPs~W~~~~g-e~sG~K~V~af~p~~~~~sNVsViiTpi~tDftsI~sFGspeefae~L----V~~v-- 180 (210)
|+ +|||+|+||++|+++++ +++| ++++|+|+.++++||+|+|+| +|+++|++||+||||+++| .+.+
T Consensus 95 y~--~dgY~FlyP~~W~~~ke~~~~G--~dv~f~D~~~~~eNVSV~Isp--t~k~sI~dlGsPee~l~~vgylL~kq~~a 168 (260)
T PLN00042 95 YN--GDGFKLLVPSKWNPSKEREFPG--QVLRFEDNFDATSNLSVMVTP--TDKKSITDYGSPEEFLSKVSYLLGKQAYS 168 (260)
T ss_pred ee--CCCeEEecCCCCccccccccCC--ceEEeeccccccccEEEEEec--CCcCCHhhcCCHHHHHHHHHHHHHhhhcc
Confidence 98 69999999999999976 5688 899999999999999999988 6889999999999976664 3322
Q ss_pred --cCCC-CCCCCC--ceEEEeceec--CC-cEEEEee
Q 028350 181 --DRSW-RRPPGV--AAKLIDCKAS--KG-ICIFFSI 209 (210)
Q Consensus 181 --drs~-~rpP~q--~akLiDa~~r--~g-~YY~~~~ 209 (210)
+++. -+.|++ .++|||++++ +| .||+|.+
T Consensus 169 ~~t~s~~Gf~p~~vata~Lleas~re~dGk~YY~lE~ 205 (260)
T PLN00042 169 GETASEGGFDANAVATAAVLESSTQEVGGKPYYYLSV 205 (260)
T ss_pred CccccccCcCcccccceeEEEeeeEEeCCeEEEEEEE
Confidence 1110 113665 5789999998 45 6999765
No 2
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.88 E-value=1.2e-22 Score=181.58 Aligned_cols=127 Identities=19% Similarity=0.271 Sum_probs=103.0
Q ss_pred hhhHHHHHH--HHHHHhhccccchhhhhhhccCceeeeeCCCceEEEcCCCCcCCCCCCCCcceeEEecCCCCCCcceEE
Q 028350 74 RTKRREVMF--QLAFTACSFPAIVSYALAANEDLRVYTDELNKFEISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSV 151 (210)
Q Consensus 74 ~~~RR~aL~--~~a~aa~~~pa~a~~a~AA~~gF~~Y~D~~dGFsf~yPs~W~~~~ge~sG~K~V~af~p~~~~~sNVsV 151 (210)
.+.||++|+ ++++.+..+-+..+.|+|++.+|++|.|..|||+|+||.+|....+ .| +-+.|-|....+.||+|
T Consensus 76 ~~~rr~~~~~~l~~~~~~~s~~~~~~a~a~~~~l~~y~D~~DGY~FlYP~GWi~V~~--~G--~DVvFrD~Ie~~ENVSV 151 (286)
T PLN00059 76 AVGRRKSMMMGLLMSGLIVSEANLPTAFASIPVFREYIDTFDGYSFKYPQNWIQVRG--AG--ADIFFRDPVVLDENLSV 151 (286)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcCchhhcCCcccceeEcCCCCeEEeCCCCCeEecc--CC--CceEEeccCccccceEE
Confidence 389999965 3333344444556678888999999999999999999999998875 35 45568888899999999
Q ss_pred EEecCCC-CcccccccCCHHHHHHHHhhcccCCCCCCC-------CCceEEEeceec---CC-cEEEEe
Q 028350 152 VITGLGP-DFTRMESFGKVEAFADTLVSGLDRSWRRPP-------GVAAKLIDCKAS---KG-ICIFFS 208 (210)
Q Consensus 152 iiTpi~t-DftsI~sFGspeefae~LV~~vdrs~~rpP-------~q~akLiDa~~r---~g-~YY~~~ 208 (210)
+|++++. ++++|++||+|+|||+.|++.+ ..|| ++.++||+|.+| +| .||+|-
T Consensus 152 ~ISs~sss~~~sLeDLGsP~eVgerLlkqv----La~f~str~GsgReaeLVsA~~Re~~DGktYY~lE 216 (286)
T PLN00059 152 EFSSPSSSKYTSLEDLGSPEEVGKRVLRQY----LTEFMSTRLGVKREANILSTSSRVADDGKLYYQVE 216 (286)
T ss_pred EEecCCcccCCChHHcCCHHHHHHHHHHHH----hcccccccCCCCcceEEEEeeeEEccCCcEEEEEE
Confidence 9998753 5889999999999999999988 4432 589999999987 45 599943
No 3
>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=99.87 E-value=4.1e-22 Score=163.39 Aligned_cols=104 Identities=25% Similarity=0.358 Sum_probs=85.1
Q ss_pred hhhhccCceeeeeCCCceEEEcCCCCcCCCCCCCCcceeEEecCCCCCCcceEEEEecCCCCcccccccCCHHHHHHHHh
Q 028350 98 ALAANEDLRVYTDELNKFEISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLV 177 (210)
Q Consensus 98 a~AA~~gF~~Y~D~~dGFsf~yPs~W~~~~ge~sG~K~V~af~p~~~~~sNVsViiTpi~tDftsI~sFGspeefae~LV 177 (210)
++...++|++|.|+++||+|.||++|++... +| .++.|.|+.+...||+|+|+|++.++ +|++||+|++|++.|+
T Consensus 16 ~~~~~~~~~~y~d~~~~y~f~~P~gW~~~~~--~G--~~v~f~d~~~~~~nvsV~v~p~~~~~-sl~~lGs~~~va~~l~ 90 (175)
T PF01789_consen 16 AAEASTGFQPYTDSDDGYSFLYPSGWEEVDV--SG--ADVVFRDPIDADENVSVVVSPVPKDF-SLEDLGSPEEVAERLL 90 (175)
T ss_dssp STT--SSEEEEEECTTTEEEEEETTEEEEES--TT--EEEEEEETTETTSEEEEEEEE-STS--SGGGG-SHHHHHHHHH
T ss_pred cccCCCCceEEEcCCCCEEEECCCCCeecCC--CC--eEEEEECcccccceEEEEEEecCCcC-chhhcCCHHHHHHHHh
Confidence 3455899999999999999999999976655 67 78889999999999999999998888 9999999999999999
Q ss_pred hcccCCCCCCCCCceEEEeceec--CC-cEEEEe
Q 028350 178 SGLDRSWRRPPGVAAKLIDCKAS--KG-ICIFFS 208 (210)
Q Consensus 178 ~~vdrs~~rpP~q~akLiDa~~r--~g-~YY~~~ 208 (210)
+.+++++... +.++||++.++ +| .||.|.
T Consensus 91 ~~~~~~~~~~--~~a~li~a~~~~~~g~~yY~~E 122 (175)
T PF01789_consen 91 NGELASPGSG--REAELISASEREVDGKTYYEYE 122 (175)
T ss_dssp HHCCCHCTSS--EEEEEEEEEEEEETTEEEEEEE
T ss_pred hhhcccccCC--cceEEEEeeeeecCCccEEEEE
Confidence 9995444431 89999999998 45 488753
No 4
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.76 E-value=9.2e-18 Score=149.40 Aligned_cols=167 Identities=14% Similarity=0.153 Sum_probs=111.3
Q ss_pred ccccCccccccCCCCcceeeeeccCCCCCccceeeeeeeccccchhhhhhhhccccccccccchhhHHHHHHHHHHHh-h
Q 028350 11 MASISPLHTWSQRPHHASFTAFSNNKGTNQYKKQFVFCCKKQEQEDDARTLNRFRIEEQDDDSRTKRREVMFQLAFTA-C 89 (210)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~c~~~~~~~~~~~~~~~~~~e~~~~~~~~RR~aL~~~a~aa-~ 89 (210)
.++.+|+..|-..+.++.++.-.. .+..+--..| . .....+.||++|.+++++. .
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~-------------~------~~~~~~~rr~~~~~~~~~~~~ 58 (263)
T PLN00067 3 TASLSPLSLSFSVSSSTSASSSAS-----SPLAVASSVS-------------P------RAAVVIHRRELLLGLALAPLI 58 (263)
T ss_pred cccccccccccccCcccccccccc-----CCcccccccc-------------c------cccchhHHHHHHhhhhhhhhh
Confidence 357899999988888776542111 0111111111 1 1123478999999998873 2
Q ss_pred ccccc-hhhhhhh-----------ccCceeee-----------eCCCceEEEcCCCCcCCCCC-------------CCCc
Q 028350 90 SFPAI-VSYALAA-----------NEDLRVYT-----------DELNKFEISIPQDWQLGAGE-------------PNGF 133 (210)
Q Consensus 90 ~~pa~-a~~a~AA-----------~~gF~~Y~-----------D~~dGFsf~yPs~W~~~~ge-------------~sG~ 133 (210)
+.... .+.|.+. ..||--|. +.=.||+|+||.+|++.+.. .++
T Consensus 59 ~~~~~~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~Vs~~~sGnycqp~c~~p~- 137 (263)
T PLN00067 59 LIAPEPPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTRVANILSGNYCQPKCAEPW- 137 (263)
T ss_pred hccCCchhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCccccccccCccccccccCCC-
Confidence 22211 1111111 34666664 23369999999999976431 233
Q ss_pred ceeEEecCCCCCCcceEEEEecCC--C--CcccccccCCHHHHHHHHhhcccCCCCCCCCCceEEEeceec--CC-cEEE
Q 028350 134 KSITAFYPQEASSSSVSVVITGLG--P--DFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLIDCKAS--KG-ICIF 206 (210)
Q Consensus 134 K~V~af~p~~~~~sNVsViiTpi~--t--DftsI~sFGspeefae~LV~~vdrs~~rpP~q~akLiDa~~r--~g-~YY~ 206 (210)
..++|+++. +.||+|||.|+. + +.++|++||+||+|+++|...+. ..|++.++|||+.++ +| .||+
T Consensus 138 -~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~v~----g~~~~~~eLLeAs~re~dGktYY~ 210 (263)
T PLN00067 138 -VEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPFVT----GNSYDPDELLETSVEKIGDQTYYK 210 (263)
T ss_pred -ceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHHhh----cCCCCCcceEEeeeEeeCCeEEEE
Confidence 688999966 449999999974 2 33699999999999999998885 358888999999998 45 5999
Q ss_pred Eee
Q 028350 207 FSI 209 (210)
Q Consensus 207 ~~~ 209 (210)
|.+
T Consensus 211 ~E~ 213 (263)
T PLN00067 211 YVL 213 (263)
T ss_pred EEE
Confidence 876
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.70 E-value=1.9e-16 Score=140.98 Aligned_cols=132 Identities=19% Similarity=0.277 Sum_probs=98.2
Q ss_pred cchhhHHHHHHHHHHHh----hccccchh---hhh----------hhccCceeeeeCC-------------CceEEEcCC
Q 028350 72 DSRTKRREVMFQLAFTA----CSFPAIVS---YAL----------AANEDLRVYTDEL-------------NKFEISIPQ 121 (210)
Q Consensus 72 ~~~~~RR~aL~~~a~aa----~~~pa~a~---~a~----------AA~~gF~~Y~D~~-------------dGFsf~yPs 121 (210)
...++||.+|+.+++++ .++|+.+. .+. +...||.+|.-+. ..|+|+||.
T Consensus 42 ~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~ 121 (262)
T PLN00066 42 ATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQ 121 (262)
T ss_pred cchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCC
Confidence 44579999999666652 22444333 111 2258899998654 679999999
Q ss_pred CCcCCC---CCCCCcceeEEecCCCCCCcceEEEEecCC------CCcccccccCCHHHHHHHHhhcccCCCCCCCCCce
Q 028350 122 DWQLGA---GEPNGFKSITAFYPQEASSSSVSVVITGLG------PDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAA 192 (210)
Q Consensus 122 ~W~~~~---ge~sG~K~V~af~p~~~~~sNVsViiTpi~------tDftsI~sFGspeefae~LV~~vdrs~~rpP~q~a 192 (210)
+|.+.. -+..|.-.+++|.. ..+.||+|+|.|+. .++++|+++|+||+|++.|+..+ ..+|.+.+
T Consensus 122 GW~ev~VS~~d~gg~~vd~Rf~~--~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v----~g~~~~e~ 195 (262)
T PLN00066 122 GWEEVPVSIADLGGTEIDLRFAS--DKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPEL----IGEPVEEG 195 (262)
T ss_pred CCeEeecccccCCCCceEEEecc--CCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHh----cCCCcccc
Confidence 999552 22234447788887 47889999999985 37889999999999999999987 45577789
Q ss_pred EEEeceec--CC-cEEEEee
Q 028350 193 KLIDCKAS--KG-ICIFFSI 209 (210)
Q Consensus 193 kLiDa~~r--~g-~YY~~~~ 209 (210)
+||++.++ +| .||.|.+
T Consensus 196 eLl~a~~re~dGktYY~~E~ 215 (262)
T PLN00066 196 KVLSMEVAEHSGRTYYQFEL 215 (262)
T ss_pred ceeEeeeeecCCcEEEEEEE
Confidence 99999987 45 6999875
No 6
>PLN03152 hypothetical protein; Provisional
Probab=98.98 E-value=9.9e-10 Score=97.07 Aligned_cols=97 Identities=21% Similarity=0.304 Sum_probs=70.8
Q ss_pred ccCceeeeeCCCceEEEcCCCCcCCCC-C-C-C-----C----cceeEEecCCCCCCcceEEEEecCC------CCcccc
Q 028350 102 NEDLRVYTDELNKFEISIPQDWQLGAG-E-P-N-----G----FKSITAFYPQEASSSSVSVVITGLG------PDFTRM 163 (210)
Q Consensus 102 ~~gF~~Y~D~~dGFsf~yPs~W~~~~g-e-~-s-----G----~K~V~af~p~~~~~sNVsViiTpi~------tDftsI 163 (210)
.+....|. ++||++-||-++...-+ + + . | -+++.+=+...|...||||+|.|+. .+.++|
T Consensus 75 t~~w~~~~--g~gf~~~~pp~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~D~sEnVSVVIspv~~LK~tfle~kDL 152 (241)
T PLN03152 75 TKSWFQFY--GDGFSIRVPPSFEDIMEPEDYNAGLSLYGDKAKPRTFAARFASPDGSEVLSVVIRPSNQLKITFLEAKDI 152 (241)
T ss_pred chhhhhhh--CCceEEeCCCChhhhcChhhcccccceecCCCCCcceeeeecCCCCCceEEEEEecCccccccccccCCh
Confidence 45666777 99999999999986633 1 0 1 1 2255555566688999999999975 478899
Q ss_pred cccCCHHHHHHHHhhcccCCCCCCCC---CceEEEeceec-CC-cEEEEee
Q 028350 164 ESFGKVEAFADTLVSGLDRSWRRPPG---VAAKLIDCKAS-KG-ICIFFSI 209 (210)
Q Consensus 164 ~sFGspeefae~LV~~vdrs~~rpP~---q~akLiDa~~r-~g-~YY~~~~ 209 (210)
++||+|+||++.+| |++ +.+++++.++. +| .||+|..
T Consensus 153 tDLGsp~EVgkv~v---------P~g~~~~saR~iel~~E~dGKtYY~lEy 194 (241)
T PLN03152 153 TDLGSLKEAAKIFV---------PGGATLYSARTIKVKEEEGIRTYYFYEF 194 (241)
T ss_pred hHcCCHHHHHHhhC---------CCcccccccceeeeeeecCCceeEEEEE
Confidence 99999999997666 454 36777776654 45 5998653
No 7
>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=81.82 E-value=5.5 Score=33.94 Aligned_cols=89 Identities=15% Similarity=0.095 Sum_probs=43.8
Q ss_pred eeeeeCCCceEEEcCCCCcCCC-CCCCCcceeEEecCCCCCCcceEEEEecCCCCcccccccCCHHHHHHHHhhcccCCC
Q 028350 106 RVYTDELNKFEISIPQDWQLGA-GEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSW 184 (210)
Q Consensus 106 ~~Y~D~~dGFsf~yPs~W~~~~-ge~sG~K~V~af~p~~~~~sNVsViiTpi~tDftsI~sFGspeefae~LV~~vdrs~ 184 (210)
.-|..++-=|++.||++|...+ |+ | ..+ |+.|..-+-|.++..-. =++-+-..+++..-++.-...-
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfED~E--~--sfl-FYnp~~WTGNfRISayk-------~~~~~ygk~~i~~EL~en~~a~ 69 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFEDGE--G--SFL-FYNPDQWTGNFRISAYK-------GGSAQYGKECIRQELKENPSAK 69 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE---T--T--EEE-EE-SSS---EEEEEEEE---------STTHHHHHHHHHHHH-TT-E
T ss_pred CcccCCCceEEEecCCCcchhccCC--c--ceE-EEChHHhcCceEEEEEe-------cccccchHHHHHHHHHhCCCcc
Confidence 3567677789999999998775 33 3 344 55555567787776522 1222335677766666542100
Q ss_pred C--CCCCCceEEEeceecCCcEEE
Q 028350 185 R--RPPGVAAKLIDCKASKGICIF 206 (210)
Q Consensus 185 ~--rpP~q~akLiDa~~r~g~YY~ 206 (210)
+ -...+-|...++.+.+|.||+
T Consensus 70 ~vkvg~~~caYs~E~f~eeg~~Yt 93 (153)
T PF12712_consen 70 LVKVGNWECAYSKEMFQEEGAYYT 93 (153)
T ss_dssp EEEETTEEEEEEEEEEEETTEEEE
T ss_pred eEEeccEEEEEEhhhhhccCeeEE
Confidence 0 012233444555566888886
No 8
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=54.29 E-value=38 Score=28.95 Aligned_cols=59 Identities=12% Similarity=0.210 Sum_probs=39.5
Q ss_pred ceEEEcCCCCcCCCC-CCCCcceeEEecCCC-CCCcceEEEEecCCCCcccccccCCHHHHHHHHhhc
Q 028350 114 KFEISIPQDWQLGAG-EPNGFKSITAFYPQE-ASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSG 179 (210)
Q Consensus 114 GFsf~yPs~W~~~~g-e~sG~K~V~af~p~~-~~~sNVsViiTpi~tDftsI~sFGspeefae~LV~~ 179 (210)
--++-+|.+|..... ..+..-.+++..... .-..|+.|+|..+..|| +|+|+++.=...
T Consensus 32 ~v~lP~P~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL~G~~-------Dp~e~l~~a~~d 92 (175)
T PF10738_consen 32 TVSLPTPPGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKLTGDF-------DPAEALEHAPAD 92 (175)
T ss_pred EEeccCCcCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEeccCCC-------CHHHHHHhchhh
Confidence 357888999998765 344434577666522 23899999998887677 577776654333
No 9
>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=52.36 E-value=7.5 Score=28.46 Aligned_cols=16 Identities=19% Similarity=0.364 Sum_probs=11.7
Q ss_pred cchhhHHHHHHHHHHH
Q 028350 72 DSRTKRREVMFQLAFT 87 (210)
Q Consensus 72 ~~~~~RR~aL~~~a~a 87 (210)
+..++||.+|.+++++
T Consensus 6 ~~~~sRR~Flk~lg~~ 21 (66)
T TIGR02811 6 KADPSRRDLLKGLGVG 21 (66)
T ss_pred cCCccHHHHHHHHHHH
Confidence 3457999999876664
No 10
>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=52.28 E-value=28 Score=26.87 Aligned_cols=52 Identities=15% Similarity=0.290 Sum_probs=32.0
Q ss_pred EEEcCCCCcCCCCCCCCcceeEEecCCCCCCcceEEEEecCCCCcccccccCCHHHHHHHHhhcc
Q 028350 116 EISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGL 180 (210)
Q Consensus 116 sf~yPs~W~~~~ge~sG~K~V~af~p~~~~~sNVsViiTpi~tDftsI~sFGspeefae~LV~~v 180 (210)
+|..|.+|+...= .|+.+.+++....|+.|.-.+++.+ .+++++++..++.+
T Consensus 3 ~~~lP~~~~D~t~------nv~~~~~~~~~~~slvIsR~~l~~g-------~tl~~~~~~q~~~l 54 (130)
T PF08786_consen 3 SLTLPDGWQDRTM------NVLVLPDSGGSGPSLVISRDPLPDG-------ETLEDYLQRQLAQL 54 (130)
T ss_dssp EEEEETTSEE--B------EEEEE--BTTB-EEEEEEEE---TT-------S-HHHHHHHHHHHH
T ss_pred eEeCCCcceeceE------EEEEccCCCCCcceEEEEeccCCCC-------CCHHHHHHHHHHHH
Confidence 5778999986432 4777776666677888777776554 37788888888877
No 11
>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=47.38 E-value=16 Score=22.23 Aligned_cols=14 Identities=29% Similarity=0.173 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHHHh
Q 028350 75 TKRREVMFQLAFTA 88 (210)
Q Consensus 75 ~~RR~aL~~~a~aa 88 (210)
++||++|-..++++
T Consensus 2 ~sRR~fLk~~~a~~ 15 (26)
T PF10518_consen 2 LSRRQFLKGGAAAA 15 (26)
T ss_pred CcHHHHHHHHHHHH
Confidence 68999998777764
No 12
>PF07174 FAP: Fibronectin-attachment protein (FAP); InterPro: IPR010801 This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix [].; GO: 0050840 extracellular matrix binding, 0005576 extracellular region
Probab=38.17 E-value=20 Score=33.50 Aligned_cols=94 Identities=16% Similarity=0.199 Sum_probs=51.1
Q ss_pred eeeeeCCCceEEEcCCCCcCCCC-CCC-CcceeEEe--c--C-CCCC---CcceEEEEecCCCCcccccccCCH----HH
Q 028350 106 RVYTDELNKFEISIPQDWQLGAG-EPN-GFKSITAF--Y--P-QEAS---SSSVSVVITGLGPDFTRMESFGKV----EA 171 (210)
Q Consensus 106 ~~Y~D~~dGFsf~yPs~W~~~~g-e~s-G~K~V~af--~--p-~~~~---~sNVsViiTpi~tDftsI~sFGsp----ee 171 (210)
-++.|..-||+|++|.+|..++. +.. | +++-- - | ..++ ..|=.+++-+- -|. +=|-+. ..
T Consensus 110 grvdn~~gGFS~vvP~GW~~Sda~~L~yG--~alls~~~~~~~~~~~~~p~andt~v~lgr-ld~---kl~a~ae~dn~k 183 (297)
T PF07174_consen 110 GRVDNAAGGFSYVVPAGWVESDASHLDYG--SALLSKQTGEPPMPGQPPPVANDTSVVLGR-LDL---KLFASAEPDNTK 183 (297)
T ss_pred ccccccccceEEeccCCccccccceeecc--eeeeccCCCCCCCCCCCCCcCCCceEEecc-ccc---cccccccCChHH
Confidence 36777888999999999998854 422 3 22211 1 1 1111 23555555221 133 333332 34
Q ss_pred HHHHHhhcccCCCCC-----CCCCceEEEeceecCC--cEEE
Q 028350 172 FADTLVSGLDRSWRR-----PPGVAAKLIDCKASKG--ICIF 206 (210)
Q Consensus 172 fae~LV~~vdrs~~r-----pP~q~akLiDa~~r~g--~YY~ 206 (210)
-|-.|-..|- ...- .=+|....+|+..-.| -||.
T Consensus 184 aa~rl~sdmg-effmp~pg~rinq~~~~l~~~g~~g~asyye 224 (297)
T PF07174_consen 184 AAVRLASDMG-EFFMPYPGTRINQETTPLDANGMPGSASYYE 224 (297)
T ss_pred HHHHHhcccc-ceeccCCCccccccccccccCCcccceeEEE
Confidence 4555666552 1111 2567888888766655 5887
No 13
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=37.47 E-value=20 Score=24.19 Aligned_cols=18 Identities=33% Similarity=0.366 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHHhhccc
Q 028350 75 TKRREVMFQLAFTACSFP 92 (210)
Q Consensus 75 ~~RR~aL~~~a~aa~~~p 92 (210)
.+||++|..+.+.+++.+
T Consensus 6 m~RR~lmN~ll~Gava~~ 23 (39)
T PF08802_consen 6 MSRRQLMNLLLGGAVAVP 23 (39)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHhhHHHH
Confidence 799999988777654434
No 14
>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=32.89 E-value=23 Score=29.15 Aligned_cols=20 Identities=10% Similarity=0.272 Sum_probs=16.9
Q ss_pred ccccccCCHHHHHHHHhhcc
Q 028350 161 TRMESFGKVEAFADTLVSGL 180 (210)
Q Consensus 161 tsI~sFGspeefae~LV~~v 180 (210)
.=++++|+|+++|.+++...
T Consensus 45 eii~~LG~P~~iA~~i~~~~ 64 (181)
T PF08006_consen 45 EIIAELGSPKEIAREILAEY 64 (181)
T ss_pred HHHHHcCCHHHHHHHHHHhh
Confidence 45789999999999998754
No 15
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=30.65 E-value=40 Score=31.39 Aligned_cols=14 Identities=21% Similarity=0.211 Sum_probs=10.0
Q ss_pred hhHHHHHHHHHHHh
Q 028350 75 TKRREVMFQLAFTA 88 (210)
Q Consensus 75 ~~RR~aL~~~a~aa 88 (210)
++||.+|..+++++
T Consensus 1 ~~RR~fl~~~~~~~ 14 (328)
T PRK10882 1 MNRRNFLKAASAGA 14 (328)
T ss_pred CCHHHHHHHHHHHH
Confidence 36999998766553
No 16
>COG3540 PhoD Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]
Probab=24.31 E-value=65 Score=32.37 Aligned_cols=14 Identities=43% Similarity=0.442 Sum_probs=11.0
Q ss_pred hhHHHHHHHHHHHh
Q 028350 75 TKRREVMFQLAFTA 88 (210)
Q Consensus 75 ~~RR~aL~~~a~aa 88 (210)
++||++|.++++++
T Consensus 3 l~RR~fl~~~a~~a 16 (522)
T COG3540 3 LKRRQFLQGAAVTA 16 (522)
T ss_pred chHHHHHhhhhhhh
Confidence 68999998866655
No 17
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=22.60 E-value=40 Score=29.79 Aligned_cols=39 Identities=18% Similarity=0.072 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHHHhhccccchhhhhhhccCceeeeeCCCce
Q 028350 75 TKRREVMFQLAFTACSFPAIVSYALAANEDLRVYTDELNKF 115 (210)
Q Consensus 75 ~~RR~aL~~~a~aa~~~pa~a~~a~AA~~gF~~Y~D~~dGF 115 (210)
..||..|+...+.........+.|.+.+.|-+.|. .++|
T Consensus 41 ~~rr~~~~~~l~~~~~~~~~~~~~~~e~~GtRsfL--Kerf 79 (190)
T PLN02999 41 FTRRRTLTSLITFTVIGGATSSALAQEKWGTRSFI--KEKY 79 (190)
T ss_pred HHHHHHHHHHHHHHHHhhccCcHHHHhhhhhHHHH--HHhc
Confidence 56888887554443344455677888899999999 7776
Done!