Query 025928
Match_columns 246
No_of_seqs 176 out of 270
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 11:09:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025928.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025928hhsearch_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 3.2E-75 6.9E-80 519.4 20.8 241 1-246 1-260 (260)
2 PLN00059 PsbP domain-containin 100.0 6.6E-42 1.4E-46 305.4 16.1 192 27-245 57-284 (286)
3 PLN00067 PsbP domain-containin 100.0 3.4E-38 7.3E-43 281.3 16.6 176 51-245 42-263 (263)
4 PF01789 PsbP: PsbP; InterPro 100.0 3.4E-35 7.3E-40 249.8 9.9 143 87-246 16-175 (175)
5 PLN00066 PsbP domain-containin 100.0 2.8E-34 6.1E-39 258.0 15.0 177 49-245 42-258 (262)
6 PLN03152 hypothetical protein; 99.9 3.2E-26 6.8E-31 200.3 10.5 176 51-245 30-240 (241)
7 PF08786 DUF1795: Domain of un 96.1 0.024 5.2E-07 45.5 7.3 30 213-243 101-130 (130)
8 PF07174 FAP: Fibronectin-atta 91.6 1.1 2.4E-05 41.4 8.5 113 99-223 116-244 (297)
9 COG5435 Uncharacterized conser 77.7 25 0.00055 29.7 9.2 34 211-245 108-141 (147)
10 PLN00058 photosystem II reacti 76.7 4 8.6E-05 32.2 3.8 25 49-74 46-70 (103)
11 PF10518 TAT_signal: TAT (twin 72.3 3.6 7.9E-05 24.6 2.1 15 52-66 2-16 (26)
12 PF05757 PsbQ: Oxygen evolving 71.9 1.3 2.8E-05 39.2 0.1 33 30-66 11-43 (202)
13 PF10738 Lpp-LpqN: Probable li 65.6 63 0.0014 27.9 9.2 129 101-246 32-174 (175)
14 PRK11615 hypothetical protein; 57.7 1.3E+02 0.0029 26.3 11.0 123 99-245 47-184 (185)
15 COG4784 Putative Zn-dependent 51.5 68 0.0015 31.2 7.5 44 196-245 371-414 (479)
16 PF12712 DUF3805: Domain of un 38.7 32 0.00068 29.1 2.9 111 99-245 8-130 (153)
17 TIGR02811 formate_TAT formate 33.1 41 0.00088 24.5 2.4 13 51-63 8-20 (66)
18 PF12318 FAD-SLDH: Membrane bo 32.4 31 0.00067 29.4 1.9 20 152-171 102-121 (168)
19 TIGR01409 TAT_signal_seq Tat ( 31.8 47 0.001 20.0 2.2 13 52-64 1-13 (29)
20 smart00564 PQQ beta-propeller 31.6 36 0.00078 20.0 1.7 20 211-230 13-32 (33)
21 TIGR03741 PRTRC_E PRTRC system 28.9 1.6E+02 0.0034 23.5 5.2 32 133-164 24-64 (104)
22 smart00456 WW Domain with 2 co 27.1 52 0.0011 19.5 1.8 19 212-230 11-29 (32)
23 PF10916 DUF2712: Protein of u 26.7 2E+02 0.0043 24.4 5.7 47 98-150 33-81 (146)
24 PRK10882 hydrogenase 2 protein 26.2 75 0.0016 30.1 3.5 17 149-165 203-219 (328)
25 PF10399 UCR_Fe-S_N: Ubiquitin 24.5 74 0.0016 21.1 2.3 11 51-61 8-18 (41)
26 PF12559 Inhibitor_I10: Serine 22.4 36 0.00077 24.3 0.4 11 101-111 44-54 (56)
27 cd00201 WW Two conserved trypt 20.9 83 0.0018 18.2 1.8 19 212-230 10-28 (31)
28 PF07123 PsbW: Photosystem II 20.5 1.1E+02 0.0025 25.6 3.1 45 34-80 43-88 (138)
No 1
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=3.2e-75 Score=519.43 Aligned_cols=241 Identities=77% Similarity=1.203 Sum_probs=224.5
Q ss_pred CcchhhhhhccccCCCccccc---ccccccCCCCCceeeecccccccccccCccchhHHHHHHHHHHHhhhcCCCcchhc
Q 025928 1 MASTQCFLHHHALSTTPARTS---SSQRHVSNIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAAVGSKVSPADAA 77 (246)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~c~a~~~~~~~~~~~~~~RR~~L~~~a~~aa~~~~~~pa~aa 77 (246)
||||+||||||+++++....+ ++++.+..+++++++|++|++. .+.++||.+|++++|++++++.+.|++||
T Consensus 1 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~srr~~l~~~~ga~a~~~~~~pa~aa 75 (260)
T PLN00042 1 MASTACFLHQSALKSAAALASSSSASARAVSASRPSQVVCRAQEED-----NSAVSRRAALALLAGAAAAGAKVSPANAA 75 (260)
T ss_pred CcchhhhhhcccccchhhhcccccccccccCCCCCcceeeeccccc-----cccccHHHHHHHHHHHHHhhcccCchhhh
Confidence 999999999999954433211 3578899999999999999773 34689999999999988899999999999
Q ss_pred ccccccccCCCCCCCCceecCCCceEEecCCCCCcCCccCCCCceEEeecCCCCCCceEEEEecCCCCCccccCChHHHH
Q 025928 78 YGESANVFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFL 157 (246)
Q Consensus 78 ~~e~a~vfg~pk~~~~f~~y~~dgYsf~yP~~W~~~~~~~~~G~d~~f~D~~~~~~nVsV~Vsp~~~~sI~dlGsPeef~ 157 (246)
|||+|||||+||++++|++|++|||+|+||++|+++++.+++|+|++|+|+++.++||+|+|+|+++++|+|||+|||||
T Consensus 76 y~~~anvfg~~k~~~gF~~y~~dgY~FlyP~~W~~~ke~~~~G~dv~f~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~l 155 (260)
T PLN00042 76 YGESANVFGKPKTNTGFLPYNGDGFKLLVPSKWNPSKEREFPGQVLRFEDNFDATSNLSVMVTPTDKKSITDYGSPEEFL 155 (260)
T ss_pred hcchhhccCCCCCCCCCeEeeCCCeEEecCCCCccccccccCCceEEeeccccccccEEEEEecCCcCCHhhcCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhcCCCCCCCCCCCccccceeeeecccC----CceEEEEEEeecCCCc------------cCCeEEEEEe
Q 025928 158 SKVDYLLGKQAYSGKTSSEGGFDPDAVATANILEASVR----PPYYFLSVLTRTADGD------------EGGKLYICKA 221 (246)
Q Consensus 158 ~~v~~~L~~~~~~~~~~~~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~~~------------~~GrLYtl~a 221 (246)
++|+++|++|++.++|.+|+||+||++++++||++++| ++||+|||.+++++++ .|||||||++
T Consensus 156 ~~vgylL~kq~~a~~t~s~~Gf~p~~vata~Lleas~re~dGk~YY~lE~~~~~ad~d~~~RH~LatatV~~GkLYtl~a 235 (260)
T PLN00042 156 SKVSYLLGKQAYSGETASEGGFDANAVATAAVLESSTQEVGGKPYYYLSVLTRTADGDEGGKHQLITATVSDGKLYICKA 235 (260)
T ss_pred HHHHHHHHhhhccCccccccCcCcccccceeEEEeeeEEeCCeEEEEEEEEEecCCCCCCCceEEEEEEEECCEEEEEEe
Confidence 99999999999999999999999999999999999998 9999999999999753 4899999999
Q ss_pred eeCCccccchhhHhHHHhhcccccC
Q 025928 222 QAGDKRWFKGTRKYVESTASSFSVA 246 (246)
Q Consensus 222 qa~e~rW~k~~~~~l~~v~~SF~V~ 246 (246)
|+||+||+|+.+++|++|++||+||
T Consensus 236 qa~EkRW~K~~~k~l~~v~~SFsVa 260 (260)
T PLN00042 236 QAGDKRWFKGARKFVEGAASSFSVA 260 (260)
T ss_pred cCchhhhhHHHHHHHHHHHhceecC
Confidence 9999999998776799999999997
No 2
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=6.6e-42 Score=305.36 Aligned_cols=192 Identities=23% Similarity=0.322 Sum_probs=150.4
Q ss_pred cCCCCCceeeecccccccccccCccchhHHHHHHHHHHHhhhcCCCcchhcccccccccCCCCCCCCceecCCCceEEec
Q 025928 27 VSNIKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAAVGSKVSPADAAYGESANVFGKPKTNTDFLPYNGDGFKLSI 106 (246)
Q Consensus 27 ~~~~~~~~~~c~a~~~~~~~~~~~~~~RR~~L~~~a~~aa~~~~~~pa~aa~~e~a~vfg~pk~~~~f~~y~~dgYsf~y 106 (246)
..+-+|-.+.|..+... ..+++||.+|+..+..+.+.....-...|++ .|+++..|++ +.|||+|+|
T Consensus 57 ~~~~~~~~~~~~~~~~~-----~~~~~rr~~~~~~l~~~~~~~s~~~~~~a~a-------~~~~l~~y~D-~~DGY~FlY 123 (286)
T PLN00059 57 AKPDSPVAINCLTDAKQ-----VCAVGRRKSMMMGLLMSGLIVSEANLPTAFA-------SIPVFREYID-TFDGYSFKY 123 (286)
T ss_pred cCCCCCeeeecccchhh-----hhhhhhhhhhHHHHHHHHHHHHhhcCchhhc-------CCcccceeEc-CCCCeEEeC
Confidence 34455566788888331 3489999997643322322222111112333 3556777777 789999999
Q ss_pred CCCCCcCCccCCCCceEEeecCCCCCCceEEEEecC---CCCCccccCChHHHHHHHHHHHHhhhhcCC--CCCCCCCCC
Q 025928 107 PSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPT---DKKSITDYGSPEEFLSKVDYLLGKQAYSGK--TSSEGGFDP 181 (246)
Q Consensus 107 P~~W~~~~~~~~~G~d~~f~D~~~~~~nVsV~Vsp~---~~~sI~dlGsPeef~~~v~~~L~~~~~~~~--~~~~~g~~~ 181 (246)
|.+|++++. .|+|++|+|+++.+|||+|+|+|+ ++++|+|||+|+| ||++|++++++++ +..++|+
T Consensus 124 P~GWi~V~~---~G~DVvFrD~Ie~~ENVSV~ISs~sss~~~sLeDLGsP~e----VgerLlkqvLa~f~str~GsgR-- 194 (286)
T PLN00059 124 PQNWIQVRG---AGADIFFRDPVVLDENLSVEFSSPSSSKYTSLEDLGSPEE----VGKRVLRQYLTEFMSTRLGVKR-- 194 (286)
T ss_pred CCCCeEecc---CCCceEEeccCccccceEEEEecCCcccCCChHHcCCHHH----HHHHHHHHHhcccccccCCCCc--
Confidence 999988873 499999999999999999999988 4899999999999 9999999999975 2233343
Q ss_pred ccccceeeeecccC-----CceEEEEEEeecCC---------C-----------------ccCCeEEEEEeeeCCccccc
Q 025928 182 DAVATANILEASVR-----PPYYFLSVLTRTAD---------G-----------------DEGGKLYICKAQAGDKRWFK 230 (246)
Q Consensus 182 ~~v~~a~ll~a~~r-----~~YY~~Ey~~~~~~---------~-----------------~~~GrLYtl~aqa~e~rW~k 230 (246)
+++||++.+| ++||+|||.++++. + .+|||||||++|+||+||.|
T Consensus 195 ----eaeLVsA~~Re~~DGktYY~lEY~Vks~~~~n~~~~~~qdr~~~~~w~RH~LA~v~V~nGkLYTL~~qtpE~RW~k 270 (286)
T PLN00059 195 ----EANILSTSSRVADDGKLYYQVEVNIKSYANNNELAVMPQDRVARLEWNRRYLAVLGVENDRLYSIRLQTPEKVFLE 270 (286)
T ss_pred ----ceEEEEeeeEEccCCcEEEEEEEEEEcCcccccccccccccccccccceeeEEEEEEeCCEEEEEEcCCcHHHHHH
Confidence 8999999987 99999999999961 1 25999999999999999999
Q ss_pred hhhHhHHHhhccccc
Q 025928 231 GTRKYVESTASSFSV 245 (246)
Q Consensus 231 ~~~~~l~~v~~SF~V 245 (246)
+++. |++|++||+|
T Consensus 271 vk~~-f~~V~dSF~V 284 (286)
T PLN00059 271 EEKD-LRRVMDSFRV 284 (286)
T ss_pred HHHH-HHHHHhheee
Confidence 9886 9999999998
No 3
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=3.4e-38 Score=281.35 Aligned_cols=176 Identities=23% Similarity=0.373 Sum_probs=132.6
Q ss_pred cchhHHHHHHHHHHHhh-hcCCCcchhcccccccccCCC-CCCCCceecC-------------CCceEEecCCCCCcCCc
Q 025928 51 AVSRRLALTVLIGAAAV-GSKVSPADAAYGESANVFGKP-KTNTDFLPYN-------------GDGFKLSIPSKWNPSKE 115 (246)
Q Consensus 51 ~~~RR~~L~~~a~~aa~-~~~~~pa~aa~~e~a~vfg~p-k~~~~f~~y~-------------~dgYsf~yP~~W~~~~~ 115 (246)
...||++|.+++++..+ .....|+.|..-|. +.+-.| ....+|..|. ..||+|+||.+|+++++
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 57899999887765433 22233444333332 222222 1234565554 47999999999999998
Q ss_pred cC------------CCCceEEeecCCCCCCceEEEEecC------CCCCccccCChHHHHHHHHHHHHhhhhcCCCCCCC
Q 025928 116 RE------------FPGQVLRYEDNFDSNSNVSVIITPT------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEG 177 (246)
Q Consensus 116 ~~------------~~G~d~~f~D~~~~~~nVsV~Vsp~------~~~sI~dlGsPeef~~~v~~~L~~~~~~~~~~~~~ 177 (246)
.+ ++|+|++|+|++ ++||+|+|+|+ ++++|+|||+||+| ++.|++.+.+ ++
T Consensus 121 s~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeV----l~~Lg~~v~g-----~~ 189 (263)
T PLN00067 121 ANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKL----IASLGPFVTG-----NS 189 (263)
T ss_pred cccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHH----HHHhhHHhhc-----CC
Confidence 74 456999999965 68999999998 56899999999995 5555554444 22
Q ss_pred CCCCccccceeeeecccC----CceEEEEEEeecCCCc---------cCCeEEEEEeeeCCccccchhhHhHHHhhcccc
Q 025928 178 GFDPDAVATANILEASVR----PPYYFLSVLTRTADGD---------EGGKLYICKAQAGDKRWFKGTRKYVESTASSFS 244 (246)
Q Consensus 178 g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~~~---------~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~ 244 (246)
++ .++||+++++ ++||+|||.++.+++. +|||||||++|++|+||+|+++. |++|++||+
T Consensus 190 ~~------~~eLLeAs~re~dGktYY~~E~~tp~a~~gRHnLataTV~~GkLYtf~asanEkRW~K~k~~-l~~V~dSFs 262 (263)
T PLN00067 190 YD------PDELLETSVEKIGDQTYYKYVLETPFALTGSHNLAKATAKGNTVVLFVVSASDKQWQSSEKT-LKAILDSFQ 262 (263)
T ss_pred CC------CcceEEeeeEeeCCeEEEEEEEEecCCCCCceEEEEEEEECCEEEEEEecCCHHHHHHHHHH-HHHHHHhcc
Confidence 32 5589999998 9999999999988653 59999999999999999998875 999999998
Q ss_pred c
Q 025928 245 V 245 (246)
Q Consensus 245 V 245 (246)
|
T Consensus 263 V 263 (263)
T PLN00067 263 A 263 (263)
T ss_pred C
Confidence 7
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=3.4e-35 Score=249.79 Aligned_cols=143 Identities=34% Similarity=0.584 Sum_probs=118.5
Q ss_pred CCCCCCCceec--CCCceEEecCCCCCcCCccCCCCceEEeecCCCCCCceEEEEecCCCC-CccccCChHHHHHHHHHH
Q 025928 87 KPKTNTDFLPY--NGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKK-SITDYGSPEEFLSKVDYL 163 (246)
Q Consensus 87 ~pk~~~~f~~y--~~dgYsf~yP~~W~~~~~~~~~G~d~~f~D~~~~~~nVsV~Vsp~~~~-sI~dlGsPeef~~~v~~~ 163 (246)
.++...+|.+| .++||+|+||++|++++. .|++++|+|+++.++||+|+|+|+... +|+|||+|++ +++.
T Consensus 16 ~~~~~~~~~~y~d~~~~y~f~~P~gW~~~~~---~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~----va~~ 88 (175)
T PF01789_consen 16 AAEASTGFQPYTDSDDGYSFLYPSGWEEVDV---SGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEE----VAER 88 (175)
T ss_dssp STT--SSEEEEEECTTTEEEEEETTEEEEES---TTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHH----HHHH
T ss_pred cccCCCCceEEEcCCCCEEEECCCCCeecCC---CCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHH----HHHH
Confidence 34456778888 689999999999965544 699999999999999999999999555 9999999999 8888
Q ss_pred HHhhhhcCCCCCCCCCCCccccceeeeecccC----CceEEEEEEeecCC-Cc---------cCCeEEEEEeeeCCcccc
Q 025928 164 LGKQAYSGKTSSEGGFDPDAVATANILEASVR----PPYYFLSVLTRTAD-GD---------EGGKLYICKAQAGDKRWF 229 (246)
Q Consensus 164 L~~~~~~~~~~~~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~-~~---------~~GrLYtl~aqa~e~rW~ 229 (246)
|.+..+..+ +++ +.++||++.++ ++||+|||.++.++ +. .|||||+|++|++|+||+
T Consensus 89 l~~~~~~~~---~~~------~~a~li~a~~~~~~g~~yY~~Ey~~~~~~~~~rh~l~~~tv~~g~lY~l~~~a~e~~w~ 159 (175)
T PF01789_consen 89 LLNGELASP---GSG------REAELISASEREVDGKTYYEYEYTVQSPNEGRRHNLAVVTVKNGKLYTLTAQAPESRWD 159 (175)
T ss_dssp HHHHCCCHC---TSS------EEEEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEHHHHH
T ss_pred Hhhhhcccc---cCC------cceEEEEeeeeecCCccEEEEEEEeccCCCcccEEEEEEEEECCEEEEEEEEcCHHHHH
Confidence 888766644 323 38899999998 89999999999887 32 599999999999999999
Q ss_pred chhhHhHHHhhcccccC
Q 025928 230 KGTRKYVESTASSFSVA 246 (246)
Q Consensus 230 k~~~~~l~~v~~SF~V~ 246 (246)
|++++ |++|++||+|+
T Consensus 160 k~~~~-l~~iv~SF~v~ 175 (175)
T PF01789_consen 160 KVEPK-LRKIVDSFRVY 175 (175)
T ss_dssp TCHHH-HHHHHHC-EE-
T ss_pred HHHHH-HHHHHhcEEeC
Confidence 99886 99999999985
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=100.00 E-value=2.8e-34 Score=257.95 Aligned_cols=177 Identities=24% Similarity=0.380 Sum_probs=136.1
Q ss_pred CccchhHHHHHHHHHHHhh--hcCCCcchhc-cccccc-ccC--CCCCCCCceecCC---------------CceEEecC
Q 025928 49 GSAVSRRLALTVLIGAAAV--GSKVSPADAA-YGESAN-VFG--KPKTNTDFLPYNG---------------DGFKLSIP 107 (246)
Q Consensus 49 ~~~~~RR~~L~~~a~~aa~--~~~~~pa~aa-~~e~a~-vfg--~pk~~~~f~~y~~---------------dgYsf~yP 107 (246)
...++||.+|+.++.++.+ .+.+.++.|+ +|..|+ |+| .|. ..+|+.|.. .+|+|+||
T Consensus 42 ~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~-~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP 120 (262)
T PLN00066 42 ATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPD-ENGWRTYRRPEGKSGGHGVGWSEITPYSFKVP 120 (262)
T ss_pred cchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCcc-ccceEEEecCccccCcCCCCccccCCeEEECC
Confidence 4578999999866554333 2334444445 787765 666 443 478888872 57999999
Q ss_pred CCCCcCCccC----CCCceEEeecCCCCCCceEEEEecC--------CCCCccccCChHHHHHHHHHHHHhhhhcCCCCC
Q 025928 108 SKWNPSKERE----FPGQVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSS 175 (246)
Q Consensus 108 ~~W~~~~~~~----~~G~d~~f~D~~~~~~nVsV~Vsp~--------~~~sI~dlGsPeef~~~v~~~L~~~~~~~~~~~ 175 (246)
.+|.++++.+ -+|+|++|.| +.++||+|+|+|+ ++++|+|||+||+ |++.|+++++..+
T Consensus 121 ~GW~ev~VS~~d~gg~~vd~Rf~~--~~~~nvsVvVspv~rla~~~~~~~sI~dLGspee----Vi~~l~~~v~g~~--- 191 (262)
T PLN00066 121 QGWEEVPVSIADLGGTEIDLRFAS--DKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEK----VISGFGPELIGEP--- 191 (262)
T ss_pred CCCeEeecccccCCCCceEEEecc--CCCccEEEEEeccccccccccCCCChHHcCCHHH----HHHHHHHHhcCCC---
Confidence 9999888763 2456777776 5789999999998 6889999999999 6777777666532
Q ss_pred CCCCCCccccceeeeecccC----CceEEEEEEeecCC---CccCCeEEEEEeeeCCccccchhhHhHHHhhccccc
Q 025928 176 EGGFDPDAVATANILEASVR----PPYYFLSVLTRTAD---GDEGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 245 (246)
Q Consensus 176 ~~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~---~~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V 245 (246)
. +.++||+++++ ++||+||| .++.. ...|||||||++|+||+||+|++++ |++|++||+|
T Consensus 192 --~------~e~eLl~a~~re~dGktYY~~E~-~rH~LasaTV~~GrLYt~~asape~rW~k~~~~-lr~v~dSF~V 258 (262)
T PLN00066 192 --V------EEGKVLSMEVAEHSGRTYYQFEL-PPHTLVTATAAGNRVYIFSVTANGLQWKRHYKD-LKRIAKSFRV 258 (262)
T ss_pred --c------cccceeEeeeeecCCcEEEEEEE-eCceEEEEEEECCEEEEEEeecchHhhHHHHHH-HHHHhhceee
Confidence 1 26789999887 99999999 22221 2379999999999999999999886 9999999997
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.93 E-value=3.2e-26 Score=200.26 Aligned_cols=176 Identities=25% Similarity=0.399 Sum_probs=121.5
Q ss_pred cchhHHHHHHHHHHHh-hhcCCCcchhccccccc----ccCCCCCCCCceecCCCceEEecCCCCCcCCccC-C------
Q 025928 51 AVSRRLALTVLIGAAA-VGSKVSPADAAYGESAN----VFGKPKTNTDFLPYNGDGFKLSIPSKWNPSKERE-F------ 118 (246)
Q Consensus 51 ~~~RR~~L~~~a~~aa-~~~~~~pa~aa~~e~a~----vfg~pk~~~~f~~y~~dgYsf~yP~~W~~~~~~~-~------ 118 (246)
..+||+.++-.+.+.+ ....-.|..-++++..+ +.+.-.+.+.|..|.++||++.||.++...-|.+ +
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 3557777654332222 12223444444555432 3333345778999999999999999998776543 1
Q ss_pred CC-------ceEEeecCCCCCCceEEEEecC--------CCCCccccCChHHHHHHHHHHHHhhhhcCCCCCCCCCC-Cc
Q 025928 119 PG-------QVLRYEDNFDSNSNVSVIITPT--------DKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEGGFD-PD 182 (246)
Q Consensus 119 ~G-------~d~~f~D~~~~~~nVsV~Vsp~--------~~~sI~dlGsPeef~~~v~~~L~~~~~~~~~~~~~g~~-~~ 182 (246)
.| -..||..+ |.+|||||+|+|+ +.++|+|||+|+| ||+.|. +. ++.. .+
T Consensus 110 yg~~akp~~~~aRf~s~-D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~E----Vgkv~v-----P~----g~~~~sa 175 (241)
T PLN03152 110 YGDKAKPRTFAARFASP-DGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKE----AAKIFV-----PG----GATLYSA 175 (241)
T ss_pred ecCCCCCcceeeeecCC-CCCceEEEEEecCccccccccccCChhHcCCHHH----HHHhhC-----CC----ccccccc
Confidence 12 24577754 7899999999997 7899999999999 897664 22 1100 11
Q ss_pred cccceeeeecccC--CceEEEEEEeecCC-----CccCCeEEEEEeeeCCccccchhhHhHHHhhccccc
Q 025928 183 AVATANILEASVR--PPYYFLSVLTRTAD-----GDEGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 245 (246)
Q Consensus 183 ~v~~a~ll~a~~r--~~YY~~Ey~~~~~~-----~~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V 245 (246)
+.+++-+ +. ++||+|||.++.-+ ...+||||||+++++|+||+|++++ |+++++||+|
T Consensus 176 --R~iel~~--E~dGKtYY~lEy~v~~RH~LaTVaVsrGKLYTl~aSt~EkRW~Kvk~k-fr~aa~SFsV 240 (241)
T PLN03152 176 --RTIKVKE--EEGIRTYYFYEFGRDEQHVALVATVNSGKAYIAGATAPESKWDDDGVK-LRSAAISLTV 240 (241)
T ss_pred --ceeeeee--ecCCceeEEEEEEeCCcEEEEEEEEcCCeEEEEecCCchhchHHHHHH-HHHHHhheee
Confidence 1334411 22 99999999987222 1369999999999999999999998 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=96.14 E-value=0.024 Score=45.46 Aligned_cols=30 Identities=17% Similarity=0.078 Sum_probs=25.9
Q ss_pred CCeEEEEEeeeCCccccchhhHhHHHhhccc
Q 025928 213 GGKLYICKAQAGDKRWFKGTRKYVESTASSF 243 (246)
Q Consensus 213 ~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF 243 (246)
++++|+|+.+++....+.... .++.+++||
T Consensus 101 ~~~~l~~T~t~~~~~~~~~~~-~~~~i~~Sf 130 (130)
T PF08786_consen 101 GRRVLVFTYTAPGPFTEEQRA-HWEAILKSF 130 (130)
T ss_dssp -CCEEEEEEEEECCCHHHHHH-HHHHHHCT-
T ss_pred CCEEEEEEEEcCCCCCHHHHH-HHHHHHhcC
Confidence 589999999999999999776 599999998
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=91.62 E-value=1.1 Score=41.43 Aligned_cols=113 Identities=19% Similarity=0.293 Sum_probs=54.8
Q ss_pred CCceEEecCCCCCcCCccCC-CCceEEeecCCCC---------CCceEEEEecCCCCCccccCChHHHHHHHHHHHHhh-
Q 025928 99 GDGFKLSIPSKWNPSKEREF-PGQVLRYEDNFDS---------NSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQ- 167 (246)
Q Consensus 99 ~dgYsf~yP~~W~~~~~~~~-~G~d~~f~D~~~~---------~~nVsV~Vsp~~~~sI~dlGsPeef~~~v~~~L~~~- 167 (246)
.-||+|.+|.+|..+....+ .|+.+.-+-..+. .+.-+|++..+|.| =|-+.|.=-.+.+.+|+..
T Consensus 116 ~gGFS~vvP~GW~~Sda~~L~yG~alls~~~~~~~~~~~~~p~andt~v~lgrld~k---l~a~ae~dn~kaa~rl~sdm 192 (297)
T PF07174_consen 116 AGGFSYVVPAGWVESDASHLDYGSALLSKQTGEPPMPGQPPPVANDTSVVLGRLDLK---LFASAEPDNTKAAVRLASDM 192 (297)
T ss_pred ccceEEeccCCccccccceeecceeeeccCCCCCCCCCCCCCcCCCceEEecccccc---ccccccCChHHHHHHHhccc
Confidence 56999999999976654433 5666655422111 12334555554332 2322222112345555432
Q ss_pred --hhcCCCCCCCCCCCccccceeeeecccC---CceEEEEEEeecCCCccCCeEEEEEeee
Q 025928 168 --AYSGKTSSEGGFDPDAVATANILEASVR---PPYYFLSVLTRTADGDEGGKLYICKAQA 223 (246)
Q Consensus 168 --~~~~~~~~~~g~~~~~v~~a~ll~a~~r---~~YY~~Ey~~~~~~~~~~GrLYtl~aqa 223 (246)
+|-+. . |.+-|+ +..-|++.-- ..||...|. -. ...||++|+-.+..
T Consensus 193 geffmp~---p-g~rinq--~~~~l~~~g~~g~asyyevkf~--d~-~kp~gqiw~~vvg~ 244 (297)
T PF07174_consen 193 GEFFMPY---P-GTRINQ--ETTPLDANGMPGSASYYEVKFT--DA-NKPNGQIWAGVVGS 244 (297)
T ss_pred cceeccC---C-Cccccc--cccccccCCcccceeEEEEEec--cC-CCCCCceEEEeecC
Confidence 12222 2 223444 2234554433 667744332 11 12477777777665
No 9
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=77.67 E-value=25 Score=29.73 Aligned_cols=34 Identities=15% Similarity=0.103 Sum_probs=27.9
Q ss_pred ccCCeEEEEEeeeCCccccchhhHhHHHhhccccc
Q 025928 211 DEGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 245 (246)
Q Consensus 211 ~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V 245 (246)
.+++++-+|+++++-.-=++.+. .+.+++.||..
T Consensus 108 ~~g~~vLifT~Tt~~~ftp~q~~-~~~~~I~Sf~p 141 (147)
T COG5435 108 ERGDTVLIFTLTTPGEFTPSQKK-AWEQVIQSFVP 141 (147)
T ss_pred ccCCeEEEEEecCCCCCCHHHHH-HHHHHHHhcCC
Confidence 36889999999998877677555 59999999974
No 10
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=76.69 E-value=4 Score=32.16 Aligned_cols=25 Identities=32% Similarity=0.146 Sum_probs=15.1
Q ss_pred CccchhHHHHHHHHHHHhhhcCCCcc
Q 025928 49 GSAVSRRLALTVLIGAAAVGSKVSPA 74 (246)
Q Consensus 49 ~~~~~RR~~L~~~a~~aa~~~~~~pa 74 (246)
++..+||+++..+++ +++.+....+
T Consensus 46 e~~~gRR~~mfaaaA-aav~s~a~~A 70 (103)
T PLN00058 46 QSTTMRRDLMFTAAA-AAVCSLAKVA 70 (103)
T ss_pred cchhhHHHHHHHHHH-HHHHhhhHHH
Confidence 356799999986553 4444433443
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=72.28 E-value=3.6 Score=24.59 Aligned_cols=15 Identities=47% Similarity=0.286 Sum_probs=11.0
Q ss_pred chhHHHHHHHHHHHh
Q 025928 52 VSRRLALTVLIGAAA 66 (246)
Q Consensus 52 ~~RR~~L~~~a~~aa 66 (246)
++||+.|...+++++
T Consensus 2 ~sRR~fLk~~~a~~a 16 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAA 16 (26)
T ss_pred CcHHHHHHHHHHHHH
Confidence 689999987665544
No 12
>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=71.92 E-value=1.3 Score=39.22 Aligned_cols=33 Identities=30% Similarity=0.383 Sum_probs=0.0
Q ss_pred CCCceeeecccccccccccCccchhHHHHHHHHHHHh
Q 025928 30 IKPTQIVCRAQKQAVQEDDGSAVSRRLALTVLIGAAA 66 (246)
Q Consensus 30 ~~~~~~~c~a~~~~~~~~~~~~~~RR~~L~~~a~~aa 66 (246)
.+...++|+++.... +...+||.+|.+++++++
T Consensus 11 ~~r~~~~vra~~~~~----~~~~~RRa~l~~l~a~~~ 43 (202)
T PF05757_consen 11 SRRAGVVVRASQSPA----QQQTSRRAVLGSLLAAAL 43 (202)
T ss_dssp -------------------------------------
T ss_pred cccccceeccccCcc----cccccHHHHHHHHHHHHH
Confidence 344566788886221 335789999874444433
No 13
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=65.63 E-value=63 Score=27.86 Aligned_cols=129 Identities=16% Similarity=0.175 Sum_probs=64.9
Q ss_pred ceEEecCCCCCcCCccCCCCceEEeecC---CCCCCceEEEEecCCCCCccccCChHHHHHHHHHHHHh--hhhc--CCC
Q 025928 101 GFKLSIPSKWNPSKEREFPGQVLRYEDN---FDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGK--QAYS--GKT 173 (246)
Q Consensus 101 gYsf~yP~~W~~~~~~~~~G~d~~f~D~---~~~~~nVsV~Vsp~~~~sI~dlGsPeef~~~v~~~L~~--~~~~--~~~ 173 (246)
.-++-.|.+|.+....+++..-...-|+ ....-|+.|+|..+. .+| +|+|+|+..-..+.. .|.. +..
T Consensus 32 ~v~lP~P~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL~----G~~-Dp~e~l~~a~~d~~~l~g~~~~~~s~ 106 (175)
T PF10738_consen 32 TVSLPTPPGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKLT----GDF-DPAEALEHAPADAQNLPGFRELDGSP 106 (175)
T ss_pred EEeccCCcCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEecc----CCC-CHHHHHHhchhhHhhCcCcccccCCc
Confidence 3577889999988766665544433222 123568888888762 244 577754432221111 1110 000
Q ss_pred CCCCCCCCccccceeeeecccCCceEEEEEE-eecCC----CccCC--eEEEEEeeeCCccccchhhHhHHHhhcccccC
Q 025928 174 SSEGGFDPDAVATANILEASVRPPYYFLSVL-TRTAD----GDEGG--KLYICKAQAGDKRWFKGTRKYVESTASSFSVA 246 (246)
Q Consensus 174 ~~~~g~~~~~v~~a~ll~a~~r~~YY~~Ey~-~~~~~----~~~~G--rLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V~ 246 (246)
.-=+|| .+.+| ...|.-+=. ..... ...++ .|-.|++++.+.+=....+. .+.|++.|+|+
T Consensus 107 ~~~~Gf------pS~~i-----~GtY~~~g~~~~~~~r~VV~~~~~~~Ylvqltvt~~~~qa~~~~~a-~~aI~~g~~It 174 (175)
T PF10738_consen 107 SDFSGF------PSSQI-----EGTYDKDGMRLHTSQRTVVIPGDDQRYLVQLTVTTTADQAVALADA-TEAIDEGFTIT 174 (175)
T ss_pred cccCCC------ceeEE-----EEEEeeCCEEeEeEEEEEEEeCCCcEEEEEEEeeccccchhhhhhH-HHHHHcCCEec
Confidence 001122 11111 111211100 00000 01133 55578888888888887774 99999999984
No 14
>PRK11615 hypothetical protein; Provisional
Probab=57.71 E-value=1.3e+02 Score=26.35 Aligned_cols=123 Identities=13% Similarity=0.171 Sum_probs=77.6
Q ss_pred CCceEEecCCCCCcCCccC-CCC-ceEEeecCCCCCCceEEEEecCCCCCccccCChHHHHHHHHHHHHhhhhcCCCCCC
Q 025928 99 GDGFKLSIPSKWNPSKERE-FPG-QVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSE 176 (246)
Q Consensus 99 ~dgYsf~yP~~W~~~~~~~-~~G-~d~~f~D~~~~~~nVsV~Vsp~~~~sI~dlGsPeef~~~v~~~L~~~~~~~~~~~~ 176 (246)
+...+|.+|.++....... ..+ .--+|-|+ .+.=.|+|++-| .+.++|+-++.+|..|-..
T Consensus 47 dGKl~FtLPag~sdqsgk~Gtq~nn~~vYad~---tg~kavIVi~gD--------~~~~~Ld~la~rl~~qQr~------ 109 (185)
T PRK11615 47 DGKLSFTLPADMSDQSGKLGTQANNMHVYADA---TGQKAVIVILGD--------DTNEDLAVLAKRLEDQQRS------ 109 (185)
T ss_pred ccEEEEEcCCccccccccccccccceEEEEcC---CCCEEEEEEeCC--------CChhhHHHHHHHHHHHHHh------
Confidence 5679999999997432211 112 23467774 233344444322 4556677788888876433
Q ss_pred CCCCCccccceeeeecccC----CceEEEEEEeecCCC---------ccCCeEEEEEeeeCCccccchhhHhHHHhhccc
Q 025928 177 GGFDPDAVATANILEASVR----PPYYFLSVLTRTADG---------DEGGKLYICKAQAGDKRWFKGTRKYVESTASSF 243 (246)
Q Consensus 177 ~g~~~~~v~~a~ll~a~~r----~~YY~~Ey~~~~~~~---------~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF 243 (246)
+.|+- +++..+.. +.+++++-.+...++ .-|+||-+|.+..|.+.-.+.+.. -+.|+++.
T Consensus 110 --rdp~l----qvvsnK~i~i~G~~~qQLDS~~t~~Gqk~~SSvvL~~v~~rl~tlQitlpA~nqqqaq~~-ae~ii~tl 182 (185)
T PRK11615 110 --RDPQL----QVVTNKAIELKGHKLQQLDSIISAKGQTAYSSVVLGKVDNQLLTMQITLPADNQQQAQTT-AENIINTL 182 (185)
T ss_pred --hCcCc----eeecceeEEECCeeeEEeeeeeecCCceEEEEEEEEeeCCeEEEEEEecCCCCHHHHHHH-HHHHHhhe
Confidence 23441 12222222 788888876655543 248999999999999887776664 89999887
Q ss_pred cc
Q 025928 244 SV 245 (246)
Q Consensus 244 ~V 245 (246)
.+
T Consensus 183 ~~ 184 (185)
T PRK11615 183 VI 184 (185)
T ss_pred ec
Confidence 65
No 15
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=51.51 E-value=68 Score=31.23 Aligned_cols=44 Identities=14% Similarity=0.128 Sum_probs=29.6
Q ss_pred CceEEEEEEeecCCCccCCeEEEEEeeeCCccccchhhHhHHHhhccccc
Q 025928 196 PPYYFLSVLTRTADGDEGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 245 (246)
Q Consensus 196 ~~YY~~Ey~~~~~~~~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V 245 (246)
..-|+|++.+-. .|+|.|.|-.-.+--.-.- ++. ...+..|||.
T Consensus 371 A~~w~fdvaVI~----~g~rvyrfltavp~gs~~l-~~~-a~sv~~SFR~ 414 (479)
T COG4784 371 ADRWQFDVAVIR----AGDRVYRFLTAVPKGSTAL-EPR-ANSVRRSFRP 414 (479)
T ss_pred cccccceEEEEE----eCCEEEEEEEecccCcchh-hHH-HHHHHhhccc
Confidence 444666655433 4889999887776555444 454 8889999985
No 16
>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=38.74 E-value=32 Score=29.05 Aligned_cols=111 Identities=19% Similarity=0.281 Sum_probs=51.2
Q ss_pred CCceEEecCCCCCcCCccCCCCceEEeecCCCCCCceEEEEecCCCCCccccCChHHHHHHHHHHHHhhhhcCCCCCCCC
Q 025928 99 GDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPTDKKSITDYGSPEEFLSKVDYLLGKQAYSGKTSSEGG 178 (246)
Q Consensus 99 ~dgYsf~yP~~W~~~~~~~~~G~d~~f~D~~~~~~nVsV~Vsp~~~~sI~dlGsPeef~~~v~~~L~~~~~~~~~~~~~g 178 (246)
+.=|++.||.+|..-...+ |- ..|-|+..=++|..+..-.- |+.. -+...+++.+... .
T Consensus 8 g~WFS~~YP~~W~EfED~E--~s-flFYnp~~WTGNfRISayk~--------~~~~-----ygk~~i~~EL~en----~- 66 (153)
T PF12712_consen 8 GAWFSMEYPADWNEFEDGE--GS-FLFYNPDQWTGNFRISAYKG--------GSAQ-----YGKECIRQELKEN----P- 66 (153)
T ss_dssp GG-EEEEE-TT-EEE---T--TE-EEEE-SSS---EEEEEEEE----------STT-----HHHHHHHHHHHH-----T-
T ss_pred CceEEEecCCCcchhccCC--cc-eEEEChHHhcCceEEEEEec--------cccc-----chHHHHHHHHHhC----C-
Confidence 4559999999996443221 33 44556777788988654331 1222 2455555555533 1
Q ss_pred CCCccccceeeeecccC------------CceEEEEEEeecCCCccCCeEEEEEeeeCCccccchhhHhHHHhhccccc
Q 025928 179 FDPDAVATANILEASVR------------PPYYFLSVLTRTADGDEGGKLYICKAQAGDKRWFKGTRKYVESTASSFSV 245 (246)
Q Consensus 179 ~~~~~v~~a~ll~a~~r------------~~YY~~Ey~~~~~~~~~~GrLYtl~aqa~e~rW~k~~~~~l~~v~~SF~V 245 (246)
.|.+++...- ..||+=-+=+. -.++..|.|.-+.+-..=.+ ..+.|+.|..|
T Consensus 67 -------~a~~vkvg~~~caYs~E~f~eeg~~YtsH~Wvt----g~~~~sfeCSFTv~kg~~~~----~aE~iiasL~v 130 (153)
T PF12712_consen 67 -------SAKLVKVGNWECAYSKEMFQEEGAYYTSHLWVT----GEGDVSFECSFTVPKGESVK----EAEEIIASLEV 130 (153)
T ss_dssp -------T-EEEEETTEEEEEEEEEEEETTEEEEEEEEEE----EETTEEEEEEEEEETT---H----HHHHHHHH-EE
T ss_pred -------CcceEEeccEEEEEEhhhhhccCeeEEEEEEEE----ecCceEEEEEEEccCCCCcc----hHHHHHhhhee
Confidence 1233433332 45553322221 25778898888876443222 25667777654
No 17
>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=33.05 E-value=41 Score=24.52 Aligned_cols=13 Identities=38% Similarity=0.036 Sum_probs=9.6
Q ss_pred cchhHHHHHHHHH
Q 025928 51 AVSRRLALTVLIG 63 (246)
Q Consensus 51 ~~~RR~~L~~~a~ 63 (246)
.++||++|.++++
T Consensus 8 ~~sRR~Flk~lg~ 20 (66)
T TIGR02811 8 DPSRRDLLKGLGV 20 (66)
T ss_pred CccHHHHHHHHHH
Confidence 5799999975443
No 18
>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=32.36 E-value=31 Score=29.45 Aligned_cols=20 Identities=20% Similarity=0.321 Sum_probs=13.7
Q ss_pred ChHHHHHHHHHHHHhhhhcC
Q 025928 152 SPEEFLSKVDYLLGKQAYSG 171 (246)
Q Consensus 152 sPeef~~~v~~~L~~~~~~~ 171 (246)
.++.-+..++..++.-||.|
T Consensus 102 ~~~~~l~~~a~~Ii~aWY~G 121 (168)
T PF12318_consen 102 APDAALQDLARAIISAWYLG 121 (168)
T ss_pred cchhhHHHHHHHHHHHeeeE
Confidence 44333555888888889885
No 19
>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=31.82 E-value=47 Score=20.02 Aligned_cols=13 Identities=38% Similarity=0.227 Sum_probs=9.0
Q ss_pred chhHHHHHHHHHH
Q 025928 52 VSRRLALTVLIGA 64 (246)
Q Consensus 52 ~~RR~~L~~~a~~ 64 (246)
++||+.|...+.+
T Consensus 1 ~sRR~Flk~~~~~ 13 (29)
T TIGR01409 1 LSRRDFLKGAAAA 13 (29)
T ss_pred CchhhhHHHHHHH
Confidence 4799999765433
No 20
>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=31.63 E-value=36 Score=19.98 Aligned_cols=20 Identities=30% Similarity=0.610 Sum_probs=17.3
Q ss_pred ccCCeEEEEEeeeCCccccc
Q 025928 211 DEGGKLYICKAQAGDKRWFK 230 (246)
Q Consensus 211 ~~~GrLYtl~aqa~e~rW~k 230 (246)
..+|+||.+.+..++.+|..
T Consensus 13 ~~~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 13 STDGTLYALDAKTGEILWTY 32 (33)
T ss_pred cCCCEEEEEEcccCcEEEEc
Confidence 35799999999999999964
No 21
>TIGR03741 PRTRC_E PRTRC system protein E. A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. This model does not include the low-complexity region.
Probab=28.87 E-value=1.6e+02 Score=23.49 Aligned_cols=32 Identities=28% Similarity=0.401 Sum_probs=20.6
Q ss_pred CceEEEEecCC---CC------CccccCChHHHHHHHHHHH
Q 025928 133 SNVSVIITPTD---KK------SITDYGSPEEFLSKVDYLL 164 (246)
Q Consensus 133 ~nVsV~Vsp~~---~~------sI~dlGsPeef~~~v~~~L 164 (246)
+++.|+|.|.. .+ -+.=-|+|+|+-+.....|
T Consensus 24 d~l~V~v~P~~~~~~~d~~l~~Pl~L~gTp~ELD~gF~~ai 64 (104)
T TIGR03741 24 DKLTVTVTPTPKSGAKDGALTKPLVLTGTPAELDAGFAGAL 64 (104)
T ss_pred CEEEEEEeeccccccccccccCCeeeccCHHHHHHHHHHHH
Confidence 38999999972 22 1233499999655555443
No 22
>smart00456 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.
Probab=27.15 E-value=52 Score=19.53 Aligned_cols=19 Identities=21% Similarity=0.566 Sum_probs=16.5
Q ss_pred cCCeEEEEEeeeCCccccc
Q 025928 212 EGGKLYICKAQAGDKRWFK 230 (246)
Q Consensus 212 ~~GrLYtl~aqa~e~rW~k 230 (246)
.+|+.|-++..+.+.+|.+
T Consensus 11 ~~g~~yy~n~~t~~s~W~~ 29 (32)
T smart00456 11 PDGRPYYYNHETKETQWEK 29 (32)
T ss_pred CCCCEEEEECCCCCEEcCC
Confidence 4589999999999999976
No 23
>PF10916 DUF2712: Protein of unknown function (DUF2712); InterPro: IPR020208 This entry represents a group of uncharacterised proteins.
Probab=26.73 E-value=2e+02 Score=24.36 Aligned_cols=47 Identities=23% Similarity=0.241 Sum_probs=32.6
Q ss_pred CCCceEEecCCCCCcCCccCCCCceEEeecCCCCCCceEEEEecC--CCCCcccc
Q 025928 98 NGDGFKLSIPSKWNPSKEREFPGQVLRYEDNFDSNSNVSVIITPT--DKKSITDY 150 (246)
Q Consensus 98 ~~dgYsf~yP~~W~~~~~~~~~G~d~~f~D~~~~~~nVsV~Vsp~--~~~sI~dl 150 (246)
..=+|.|.+|..-..+ +-+.||+...+.+.+--|-+.-. .+.+|..|
T Consensus 33 n~i~F~F~i~~~~ans------ys~~ryRqTt~t~n~WKV~l~~StEGkGTi~tf 81 (146)
T PF10916_consen 33 NNIPFSFTIKPNQANS------YSGSRYRQTTSTNNPWKVNLTYSTEGKGTIYTF 81 (146)
T ss_pred cCCceEEEeCCccccc------ccCceeeccCCCCCccEEeccccccccceEEEE
Confidence 4568999999887322 55778988776666666666533 67777766
No 24
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=26.23 E-value=75 Score=30.06 Aligned_cols=17 Identities=29% Similarity=0.493 Sum_probs=11.4
Q ss_pred ccCChHHHHHHHHHHHH
Q 025928 149 DYGSPEEFLSKVDYLLG 165 (246)
Q Consensus 149 dlGsPeef~~~v~~~L~ 165 (246)
.||..+|+++.+-+++.
T Consensus 203 ~fG~~~el~~~a~~ri~ 219 (328)
T PRK10882 203 IFGTREELLAEAKRRLA 219 (328)
T ss_pred EeccHHHHHHHHHHHHH
Confidence 48888887666655554
No 25
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=24.53 E-value=74 Score=21.12 Aligned_cols=11 Identities=36% Similarity=0.332 Sum_probs=6.9
Q ss_pred cchhHHHHHHH
Q 025928 51 AVSRRLALTVL 61 (246)
Q Consensus 51 ~~~RR~~L~~~ 61 (246)
..+||+.|..+
T Consensus 8 ~~~RRdFL~~a 18 (41)
T PF10399_consen 8 DPTRRDFLTIA 18 (41)
T ss_dssp --HHHHHHHHH
T ss_pred CchHHHHHHHH
Confidence 57899999543
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=22.36 E-value=36 Score=24.29 Aligned_cols=11 Identities=36% Similarity=0.661 Sum_probs=4.0
Q ss_pred ceEEecCCCCC
Q 025928 101 GFKLSIPSKWN 111 (246)
Q Consensus 101 gYsf~yP~~W~ 111 (246)
..+++||++|.
T Consensus 44 ~~TlKyPSD~e 54 (56)
T PF12559_consen 44 IQTLKYPSDWE 54 (56)
T ss_dssp -----SS-SS-
T ss_pred CcceeCCCccc
Confidence 37999999994
No 27
>cd00201 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.
Probab=20.87 E-value=83 Score=18.25 Aligned_cols=19 Identities=16% Similarity=0.573 Sum_probs=16.1
Q ss_pred cCCeEEEEEeeeCCccccc
Q 025928 212 EGGKLYICKAQAGDKRWFK 230 (246)
Q Consensus 212 ~~GrLYtl~aqa~e~rW~k 230 (246)
.+|+.|-.+....+.+|.+
T Consensus 10 ~~g~~yy~n~~t~~s~W~~ 28 (31)
T cd00201 10 PDGRVYYYNHNTKETQWED 28 (31)
T ss_pred CCCCEEEEECCCCCEeCCC
Confidence 4588999999999999976
No 28
>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=20.53 E-value=1.1e+02 Score=25.56 Aligned_cols=45 Identities=31% Similarity=0.310 Sum_probs=21.0
Q ss_pred eeeeccccccccccc-CccchhHHHHHHHHHHHhhhcCCCcchhcccc
Q 025928 34 QIVCRAQKQAVQEDD-GSAVSRRLALTVLIGAAAVGSKVSPADAAYGE 80 (246)
Q Consensus 34 ~~~c~a~~~~~~~~~-~~~~~RR~~L~~~a~~aa~~~~~~pa~aa~~e 80 (246)
.++|.++++....+. ....+-..+++.+ ++++.....||.|.-.|
T Consensus 43 ~v~cs~~~~~~~~~~~~~~~~~~a~~~aa--~~a~~a~a~PA~ALVDe 88 (138)
T PF07123_consen 43 RVRCSAEKKPSTVAAVNSQKGMGAALLAA--AAATAATASPALALVDE 88 (138)
T ss_pred ceEEEeccCccchhhhhhhcchhHHHHHH--HHHHHhhcCcHHHHHHH
Confidence 588999977432111 0112222333322 23333446788765544
Done!