Query 024710
Match_columns 264
No_of_seqs 135 out of 172
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:46:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024710hhsearch_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 2.8E-47 6E-52 347.3 20.7 182 73-264 75-285 (286)
2 PLN00042 photosystem II oxygen 100.0 3.6E-45 7.8E-50 333.0 20.4 190 60-263 38-259 (260)
3 PF01789 PsbP: PsbP; InterPro 100.0 1.2E-39 2.6E-44 279.4 13.9 152 101-263 19-174 (175)
4 PLN00067 PsbP domain-containin 100.0 2.2E-34 4.7E-39 262.2 19.8 177 73-263 41-263 (263)
5 PLN00066 PsbP domain-containin 100.0 1.3E-32 2.8E-37 251.7 18.8 174 73-264 43-259 (262)
6 PLN03152 hypothetical protein; 99.9 1.5E-27 3.3E-32 213.4 13.2 143 104-264 77-241 (241)
7 PF08786 DUF1795: Domain of un 97.6 0.0031 6.7E-08 51.3 13.2 124 116-261 3-130 (130)
8 PF10738 Lpp-LpqN: Probable li 94.7 1.2 2.5E-05 39.3 13.2 133 115-263 33-173 (175)
9 PF12712 DUF3805: Domain of un 92.7 1.5 3.1E-05 38.0 9.9 128 106-263 2-130 (153)
10 COG5435 Uncharacterized conser 92.0 2.4 5.1E-05 36.8 10.4 125 116-263 10-141 (147)
11 COG4784 Putative Zn-dependent 72.5 13 0.00028 36.9 7.1 23 106-128 288-310 (479)
12 PF07174 FAP: Fibronectin-atta 70.8 89 0.0019 30.0 11.9 136 105-249 109-272 (297)
13 PRK11615 hypothetical protein; 60.2 1.3E+02 0.0029 27.1 13.6 137 106-263 41-184 (185)
14 TIGR02811 formate_TAT formate 40.0 23 0.0005 26.6 2.1 15 73-87 7-21 (66)
15 PF10518 TAT_signal: TAT (twin 36.6 25 0.00054 21.7 1.5 14 75-88 2-15 (26)
16 PF08006 DUF1700: Protein of u 36.5 19 0.00041 30.9 1.3 20 161-180 45-64 (181)
17 PRK10882 hydrogenase 2 protein 23.3 76 0.0017 30.6 3.0 14 75-88 1-14 (328)
18 COG3540 PhoD Phosphodiesterase 21.8 1.6E+02 0.0034 30.6 4.9 40 130-170 47-92 (522)
19 PF05757 PsbQ: Oxygen evolving 20.3 34 0.00074 31.0 0.0 27 59-87 15-41 (202)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=2.8e-47 Score=347.33 Aligned_cols=182 Identities=19% Similarity=0.297 Sum_probs=154.3
Q ss_pred ccchhHHHHHHHH--HHhhhcccchhhhhhccCCceeeeeCCCceEEEccCCCccCC--CCCCCcceEEEeccCCCCCce
Q 024710 73 SRTKRREVMFQLA--FTACSFPAIVSYALAANEDLRVYTDELNKFEISIPQDWQLGA--GEPNGFKSITAFYPQEASSSS 148 (264)
Q Consensus 73 ~~~~RR~aLl~i~--~a~~a~~~~~s~A~A~~~gf~~y~D~~dGYsf~yPs~W~~~~--G~~~g~k~Vv~F~p~~~~~eN 148 (264)
+++.||++|+..+ +.++...+..++|+|+..||++|+|+.|||+|+||.||+..+ |+| ++|+|+++.+||
T Consensus 75 ~~~~rr~~~~~~l~~~~~~~s~~~~~~a~a~~~~l~~y~D~~DGY~FlYP~GWi~V~~~G~D------VvFrD~Ie~~EN 148 (286)
T PLN00059 75 CAVGRRKSMMMGLLMSGLIVSEANLPTAFASIPVFREYIDTFDGYSFKYPQNWIQVRGAGAD------IFFRDPVVLDEN 148 (286)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcCchhhcCCcccceeEcCCCCeEEeCCCCCeEeccCCCc------eEEeccCccccc
Confidence 8899999966333 333233333456788888999999999999999999999543 444 789999999999
Q ss_pred eEEEEecCCC-CccccccCCCHHHHHHHHHhcccccC---CCCCCCeeeEEEeeec---Cc--eEEEEEEEECC------
Q 024710 149 VSVVITGLGP-DFTRMESFGKVEAFADTLVSGLDRSW---RRPPGVAAKLIDCKAS---KG--FYYIEYTLQNP------ 213 (264)
Q Consensus 149 VSVvITpv~~-d~~sL~dfGsPeeva~~Lv~~l~~s~---~~~~~~~A~LldA~sr---~g--yY~~EY~v~~p------ 213 (264)
|||+|+|+++ ++++|+|||+|+|||++|+++++.++ +.+++++++||+|.+| +| ||+|||.++.+
T Consensus 149 VSV~ISs~sss~~~sLeDLGsP~eVgerLlkqvLa~f~str~GsgReaeLVsA~~Re~~DGktYY~lEY~Vks~~~~n~~ 228 (286)
T PLN00059 149 LSVEFSSPSSSKYTSLEDLGSPEEVGKRVLRQYLTEFMSTRLGVKREANILSTSSRVADDGKLYYQVEVNIKSYANNNEL 228 (286)
T ss_pred eEEEEecCCcccCCChHHcCCHHHHHHHHHHHHhcccccccCCCCcceEEEEeeeEEccCCcEEEEEEEEEEcCcccccc
Confidence 9999998864 67999999999999999999997543 3456899999999988 23 99999999996
Q ss_pred ----------CCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceeeC
Q 024710 214 ----------GESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRFI 264 (264)
Q Consensus 214 ----------~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v~ 264 (264)
.+|.||+|++|+|.| | |||||++|+||+||+|+++.|++||+||+|+
T Consensus 229 ~~~~qdr~~~~~w~RH~LA~v~V~n-G---kLYTL~~qtpE~RW~kvk~~f~~V~dSF~V~ 285 (286)
T PLN00059 229 AVMPQDRVARLEWNRRYLAVLGVEN-D---RLYSIRLQTPEKVFLEEEKDLRRVMDSFRVE 285 (286)
T ss_pred cccccccccccccceeeEEEEEEeC-C---EEEEEEcCCcHHHHHHHHHHHHHHHhheeec
Confidence 256999999999985 3 9999999999999999999999999999985
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=3.6e-45 Score=332.97 Aligned_cols=190 Identities=24% Similarity=0.316 Sum_probs=152.6
Q ss_pred cccccccccccccccchhHHHHHHHHHHhhhcccchhhhhh-------------ccCCceeeeeCCCceEEEccCCCccC
Q 024710 60 TLNRFRIEEQDDDSRTKRREVMFQLAFTACSFPAIVSYALA-------------ANEDLRVYTDELNKFEISIPQDWQLG 126 (264)
Q Consensus 60 ~~~~~~~~~~~~~~~~~RR~aLl~i~~a~~a~~~~~s~A~A-------------~~~gf~~y~D~~dGYsf~yPs~W~~~ 126 (264)
++||++.++. ..++||.+|+++++++ ++++.+.+|.| ..+||.+|+ +|||+|+||++|+++
T Consensus 38 ~~~~~~~~~~---~~~srr~~l~~~~ga~-a~~~~~~pa~aay~~~anvfg~~k~~~gF~~y~--~dgY~FlyP~~W~~~ 111 (260)
T PLN00042 38 VVCRAQEEDN---SAVSRRAALALLAGAA-AAGAKVSPANAAYGESANVFGKPKTNTGFLPYN--GDGFKLLVPSKWNPS 111 (260)
T ss_pred eeeecccccc---ccccHHHHHHHHHHHH-HhhcccCchhhhhcchhhccCCCCCCCCCeEee--CCCeEEecCCCCccc
Confidence 6788875544 6799999999888875 44555555422 136999998 699999999999955
Q ss_pred -CCCCCCcceEEEeccCCCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcccccCCCC---------C--CCeeeE
Q 024710 127 -AGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRP---------P--GVAAKL 194 (264)
Q Consensus 127 -~G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~---------~--~~~A~L 194 (264)
+.+.+|. +++|+|+++.++||||+|+|+ ++++|+|||+|+||++++.+.|.+....+ | .++|+|
T Consensus 112 ke~~~~G~--dv~f~D~~~~~eNVSV~Ispt--~k~sI~dlGsPee~l~~vgylL~kq~~a~~t~s~~Gf~p~~vata~L 187 (260)
T PLN00042 112 KEREFPGQ--VLRFEDNFDATSNLSVMVTPT--DKKSITDYGSPEEFLSKVSYLLGKQAYSGETASEGGFDANAVATAAV 187 (260)
T ss_pred cccccCCc--eEEeeccccccccEEEEEecC--CcCCHhhcCCHHHHHHHHHHHHHhhhccCccccccCcCcccccceeE
Confidence 3344565 588999999999999999998 67899999999997777665554321121 2 347899
Q ss_pred EEeeec----CceEEEEEEEECCC--CCceeEEEEEEEecCCccceeEEEEcccCchhhHHH-HHHHHHhhcceee
Q 024710 195 IDCKAS----KGFYYIEYTLQNPG--ESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKY-GSNIEKAVASFRF 263 (264)
Q Consensus 195 ldA~sr----~gyY~~EY~v~~p~--e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~-~~~l~~vvdSF~v 263 (264)
|++++| +.||+|||.++.++ ++.||+|++++|. || |||||++|+||+||.|+ ++.|+.|++||+|
T Consensus 188 leas~re~dGk~YY~lE~~~~~ad~d~~~RH~LatatV~-~G---kLYtl~aqa~EkRW~K~~~k~l~~v~~SFsV 259 (260)
T PLN00042 188 LESSTQEVGGKPYYYLSVLTRTADGDEGGKHQLITATVS-DG---KLYICKAQAGDKRWFKGARKFVEGAASSFSV 259 (260)
T ss_pred EEeeeEEeCCeEEEEEEEEEecCCCCCCCceEEEEEEEE-CC---EEEEEEecCchhhhhHHHHHHHHHHHhceec
Confidence 999998 34999999999875 5789999999997 44 99999999999999998 6789999999997
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=100.00 E-value=1.2e-39 Score=279.40 Aligned_cols=152 Identities=32% Similarity=0.503 Sum_probs=130.4
Q ss_pred ccCCceeeeeCCCceEEEccCCCccCCCCCCCcceEEEeccCCCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcc
Q 024710 101 ANEDLRVYTDELNKFEISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGL 180 (264)
Q Consensus 101 ~~~gf~~y~D~~dGYsf~yPs~W~~~~G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l 180 (264)
..+||++|.|+.+||+|+||++|+..++ +|. .++|+|+.+.++||+|+|+|++.++ +|+|||+|++||++|+...
T Consensus 19 ~~~~~~~y~d~~~~y~f~~P~gW~~~~~--~G~--~v~f~d~~~~~~nvsV~v~p~~~~~-sl~~lGs~~~va~~l~~~~ 93 (175)
T PF01789_consen 19 ASTGFQPYTDSDDGYSFLYPSGWEEVDV--SGA--DVVFRDPIDADENVSVVVSPVPKDF-SLEDLGSPEEVAERLLNGE 93 (175)
T ss_dssp --SSEEEEEECTTTEEEEEETTEEEEES--TTE--EEEEEETTETTSEEEEEEEE-STS--SGGGG-SHHHHHHHHHHHC
T ss_pred CCCCceEEEcCCCCEEEECCCCCeecCC--CCe--EEEEECcccccceEEEEEEecCCcC-chhhcCCHHHHHHHHhhhh
Confidence 3479999999999999999999986544 443 4789999999999999999998776 9999999999999999987
Q ss_pred cccCCCCCCCeeeEEEeeec--C--ceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHH
Q 024710 181 DRSWRRPPGVAAKLIDCKAS--K--GFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEK 256 (264)
Q Consensus 181 ~~s~~~~~~~~A~LldA~sr--~--gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~ 256 (264)
.++ ...++.++||++.++ + .||+|||.++.+++++||.|++++|. || |||||++|++|++|+|+++.|++
T Consensus 94 ~~~--~~~~~~a~li~a~~~~~~g~~yY~~Ey~~~~~~~~~rh~l~~~tv~-~g---~lY~l~~~a~e~~w~k~~~~l~~ 167 (175)
T PF01789_consen 94 LAS--PGSGREAELISASEREVDGKTYYEYEYTVQSPNEGRRHNLAVVTVK-NG---KLYTLTAQAPESRWDKVEPKLRK 167 (175)
T ss_dssp CCH--CTSSEEEEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEEEEEE-TT---EEEEEEEEEEHHHHHTCHHHHHH
T ss_pred ccc--ccCCcceEEEEeeeeecCCccEEEEEEEeccCCCcccEEEEEEEEE-CC---EEEEEEEEcCHHHHHHHHHHHHH
Confidence 632 222499999999998 3 49999999999987789999999997 44 99999999999999999999999
Q ss_pred hhcceee
Q 024710 257 AVASFRF 263 (264)
Q Consensus 257 vvdSF~v 263 (264)
|++||+|
T Consensus 168 iv~SF~v 174 (175)
T PF01789_consen 168 IVDSFRV 174 (175)
T ss_dssp HHHC-EE
T ss_pred HHhcEEe
Confidence 9999998
No 4
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=2.2e-34 Score=262.24 Aligned_cols=177 Identities=14% Similarity=0.194 Sum_probs=138.2
Q ss_pred ccchhHHHHHHHHHHhh-hcccchhhhhh-------------ccCCceeeee-----------CCCceEEEccCCCccCC
Q 024710 73 SRTKRREVMFQLAFTAC-SFPAIVSYALA-------------ANEDLRVYTD-----------ELNKFEISIPQDWQLGA 127 (264)
Q Consensus 73 ~~~~RR~aLl~i~~a~~-a~~~~~s~A~A-------------~~~gf~~y~D-----------~~dGYsf~yPs~W~~~~ 127 (264)
....||++|.+++++.+ .... ..++.| ...||--|.- .-.||+|+||.||+...
T Consensus 41 ~~~~rr~~~~~~~~~~~~~~~~-~~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~ 119 (263)
T PLN00067 41 VVIHRRELLLGLALAPLILIAP-EPPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTR 119 (263)
T ss_pred chhHHHHHHhhhhhhhhhhccC-CchhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCcc
Confidence 34789999999988631 2221 112222 1237766652 34699999999999331
Q ss_pred ------C-------CCCCcceEEEeccCCCCCceeEEEEecCC----CCccccccCCCHHHHHHHHHhcccccCCCCCCC
Q 024710 128 ------G-------EPNGFKSITAFYPQEASSSSVSVVITGLG----PDFTRMESFGKVEAFADTLVSGLDRSWRRPPGV 190 (264)
Q Consensus 128 ------G-------~~~g~k~Vv~F~p~~~~~eNVSVvITpv~----~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~~~~ 190 (264)
| +.|+. .++|+|+ .++||+|||+|+. .+.++|+|||+|++|+++|.+.+. .++++
T Consensus 120 Vs~~~sGnycqp~c~~p~~--dv~F~D~--~dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~v~----g~~~~ 191 (263)
T PLN00067 120 VANILSGNYCQPKCAEPWV--EVKFEDE--KQGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPFVT----GNSYD 191 (263)
T ss_pred ccccccCccccccccCCCc--eEEEeCC--CCCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHHhh----cCCCC
Confidence 2 12233 3789994 4779999999983 234799999999999999998876 56788
Q ss_pred eeeEEEeeec----CceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceee
Q 024710 191 AAKLIDCKAS----KGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 263 (264)
Q Consensus 191 ~A~LldA~sr----~gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v 263 (264)
.++||+++++ +.||+|||.+..++. .||+|++++|. + ||||||++|++|+||.|+++.|++|++||+|
T Consensus 192 ~~eLLeAs~re~dGktYY~~E~~tp~a~~-gRHnLataTV~-~---GkLYtf~asanEkRW~K~k~~l~~V~dSFsV 263 (263)
T PLN00067 192 PDELLETSVEKIGDQTYYKYVLETPFALT-GSHNLAKATAK-G---NTVVLFVVSASDKQWQSSEKTLKAILDSFQA 263 (263)
T ss_pred CcceEEeeeEeeCCeEEEEEEEEecCCCC-CceEEEEEEEE-C---CEEEEEEecCCHHHHHHHHHHHHHHHHhccC
Confidence 9999999999 349999999999984 79999999995 4 4999999999999999999999999999986
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=100.00 E-value=1.3e-32 Score=251.69 Aligned_cols=174 Identities=18% Similarity=0.262 Sum_probs=133.3
Q ss_pred ccchhHHHHHHHHHHh-hhcccchhhhhh----------------ccCCceeeeeCC-------------CceEEEccCC
Q 024710 73 SRTKRREVMFQLAFTA-CSFPAIVSYALA----------------ANEDLRVYTDEL-------------NKFEISIPQD 122 (264)
Q Consensus 73 ~~~~RR~aLl~i~~a~-~a~~~~~s~A~A----------------~~~gf~~y~D~~-------------dGYsf~yPs~ 122 (264)
..++||.+|+.+++++ +++.+.+..+.| ...||++|.-+. ..|+|+||.|
T Consensus 43 ~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~G 122 (262)
T PLN00066 43 TAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQG 122 (262)
T ss_pred chhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCCC
Confidence 4579999999776652 122222222222 124899998654 5799999999
Q ss_pred CccC---CCCCCCcceEEEeccCCCCCceeEEEEecCC------CCccccccCCCHHHHHHHHHhcccccCCCCCCCeee
Q 024710 123 WQLG---AGEPNGFKSITAFYPQEASSSSVSVVITGLG------PDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAK 193 (264)
Q Consensus 123 W~~~---~G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~------~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~~~~~A~ 193 (264)
|... ..+..|.. +.++.....++||+|+|+|+. .++++|+|||+|++|+++|.+.++ .++.++++
T Consensus 123 W~ev~VS~~d~gg~~--vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~----g~~~~e~e 196 (262)
T PLN00066 123 WEEVPVSIADLGGTE--IDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELI----GEPVEEGK 196 (262)
T ss_pred CeEeecccccCCCCc--eEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhc----CCCccccc
Confidence 9932 21112222 233444478999999999985 266899999999999999998865 55678899
Q ss_pred EEEeeec----CceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceeeC
Q 024710 194 LIDCKAS----KGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRFI 264 (264)
Q Consensus 194 LldA~sr----~gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v~ 264 (264)
||++.++ +.||.||| .||+|++|+|. +| |||||++|+||+||+|.++.|++|++||+|+
T Consensus 197 Ll~a~~re~dGktYY~~E~--------~rH~LasaTV~-~G---rLYt~~asape~rW~k~~~~lr~v~dSF~V~ 259 (262)
T PLN00066 197 VLSMEVAEHSGRTYYQFEL--------PPHTLVTATAA-GN---RVYIFSVTANGLQWKRHYKDLKRIAKSFRVV 259 (262)
T ss_pred eeEeeeeecCCcEEEEEEE--------eCceEEEEEEE-CC---EEEEEEeecchHhhHHHHHHHHHHhhceeee
Confidence 9999998 34999999 38999999997 43 9999999999999999999999999999985
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.95 E-value=1.5e-27 Score=213.44 Aligned_cols=143 Identities=18% Similarity=0.312 Sum_probs=110.5
Q ss_pred CceeeeeCCCceEEEccCCCccC-C-----------CCCCCcceEEEeccCCCCCceeEEEEecCC------CCcccccc
Q 024710 104 DLRVYTDELNKFEISIPQDWQLG-A-----------GEPNGFKSITAFYPQEASSSSVSVVITGLG------PDFTRMES 165 (264)
Q Consensus 104 gf~~y~D~~dGYsf~yPs~W~~~-~-----------G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~------~d~~sL~d 165 (264)
..-.|. ++||++-||-++... + |+.+--|.+.+-|.-.+.+|||||+|+|++ -+.++|+|
T Consensus 77 ~w~~~~--g~gf~~~~pp~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~D~sEnVSVVIspv~~LK~tfle~kDLtD 154 (241)
T PLN03152 77 SWFQFY--GDGFSIRVPPSFEDIMEPEDYNAGLSLYGDKAKPRTFAARFASPDGSEVLSVVIRPSNQLKITFLEAKDITD 154 (241)
T ss_pred hhhhhh--CCceEEeCCCChhhhcChhhcccccceecCCCCCcceeeeecCCCCCceEEEEEecCccccccccccCChhH
Confidence 444555 899999999999832 1 222233335677777889999999999986 25589999
Q ss_pred CCCHHHHHHHHHhcccccCCCCC-CCeeeEEEeeec---CceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcc
Q 024710 166 FGKVEAFADTLVSGLDRSWRRPP-GVAAKLIDCKAS---KGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQ 241 (264)
Q Consensus 166 fGsPeeva~~Lv~~l~~s~~~~~-~~~A~LldA~sr---~gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq 241 (264)
||+|+|||+.++.. +. .+.+++++.++. ++||+|||.++ .||+|++|+|. +| |||||+++
T Consensus 155 LGsp~EVgkv~vP~-------g~~~~saR~iel~~E~dGKtYY~lEy~v~-----~RH~LaTVaVs-rG---KLYTl~aS 218 (241)
T PLN03152 155 LGSLKEAAKIFVPG-------GATLYSARTIKVKEEEGIRTYYFYEFGRD-----EQHVALVATVN-SG---KAYIAGAT 218 (241)
T ss_pred cCCHHHHHHhhCCC-------cccccccceeeeeeecCCceeEEEEEEeC-----CcEEEEEEEEc-CC---eEEEEecC
Confidence 99999999666421 10 013444444332 66999999985 59999999996 44 99999999
Q ss_pred cCchhhHHHHHHHHHhhcceeeC
Q 024710 242 FVEEESEKYGSNIEKAVASFRFI 264 (264)
Q Consensus 242 ~~E~rw~k~~~~l~~vvdSF~v~ 264 (264)
++|+||.|++++|+.+++||+|+
T Consensus 219 t~EkRW~Kvk~kfr~aa~SFsV~ 241 (241)
T PLN03152 219 APESKWDDDGVKLRSAAISLTVL 241 (241)
T ss_pred CchhchHHHHHHHHHHHhheeeC
Confidence 99999999999999999999986
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=97.55 E-value=0.0031 Score=51.29 Aligned_cols=124 Identities=16% Similarity=0.207 Sum_probs=76.6
Q ss_pred EEEccCCCccCCCCCCCcceEEEeccCCCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcccccCCCCCCCeeeEE
Q 024710 116 EISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAKLI 195 (264)
Q Consensus 116 sf~yPs~W~~~~G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~~~~~A~Ll 195 (264)
+|..|.+|+...-. |.++.++.....|+.|...+++++ .+.+++.++.+..+-+ --..-+++
T Consensus 3 ~~~lP~~~~D~t~n------v~~~~~~~~~~~slvIsR~~l~~g-------~tl~~~~~~q~~~l~~-----~l~~~~~~ 64 (130)
T PF08786_consen 3 SLTLPDGWQDRTMN------VLVLPDSGGSGPSLVISRDPLPDG-------ETLEDYLQRQLAQLRK-----QLPGFQLV 64 (130)
T ss_dssp EEEEETTSEE--BE------EEEE--BTTB-EEEEEEEE---TT-------S-HHHHHHHHHHHHHC-----CSTT-EEE
T ss_pred eEeCCCcceeceEE------EEEccCCCCCcceEEEEeccCCCC-------CCHHHHHHHHHHHHHh-----hCCCcEEE
Confidence 46779999854211 333333333355555555566544 4677888888887632 12223455
Q ss_pred Eeeec--C--ceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcce
Q 024710 196 DCKAS--K--GFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASF 261 (264)
Q Consensus 196 dA~sr--~--gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF 261 (264)
+...- + .-+.++|+-..++. .-|...++..-. | +++|++|..++..-.+..+..++.+++||
T Consensus 65 ~~~~~~l~~~~a~~l~~~~~~~g~-~v~Q~q~~~~~~-~--~~~l~~T~t~~~~~~~~~~~~~~~i~~Sf 130 (130)
T PF08786_consen 65 ERQPITLGGRPARELEYSFRSGGQ-PVYQRQAAVLLP-G--RRVLVFTYTAPGPFTEEQRAHWEAILKSF 130 (130)
T ss_dssp EEEEEEETTEEEEEEEEEEEETTC-EEEEEEEEEEEC----CCEEEEEEEEECCCHHHHHHHHHHHHCT-
T ss_pred eeEEEEeCCCCeEEEEEEEeeCCE-EEEEEEEEEEEC-C--CEEEEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 54433 3 36889999887764 567776655543 2 49999999999999999999999999998
No 8
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=94.65 E-value=1.2 Score=39.34 Aligned_cols=133 Identities=18% Similarity=0.232 Sum_probs=78.8
Q ss_pred eEEEccCCCccCC-CCCCCcceEEEeccC-CCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcccccCCCCCCCee
Q 024710 115 FEISIPQDWQLGA-GEPNGFKSITAFYPQ-EASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAA 192 (264)
Q Consensus 115 Ysf~yPs~W~~~~-G~~~g~k~Vv~F~p~-~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~~~~~A 192 (264)
-++-.|.||.... ...+..-.+++.... ..-..|+-|+|..+..++ +|+|+.+.=-..+ +.-++-+
T Consensus 33 v~lP~P~GW~~~~~~~~~~a~~vi~~~~~~~~~~Pnavv~V~kL~G~~-------Dp~e~l~~a~~d~----~~l~g~~- 100 (175)
T PF10738_consen 33 VSLPTPPGWEPAPDPNPPWAYAVIVDPQADGGFPPNAVVTVSKLTGDF-------DPAEALEHAPADA----QNLPGFR- 100 (175)
T ss_pred EeccCCcCcccCCCCCCCceEEEEEeccccCCCCCceEEEEEeccCCC-------CHHHHHHhchhhH----hhCcCcc-
Confidence 5678899999653 223333334555442 333789999998775454 4666655321111 1112322
Q ss_pred eEEEeeec--Cce--EEEEEEEECCCCCceeEEEE--EEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceee
Q 024710 193 KLIDCKAS--KGF--YYIEYTLQNPGESRKHLFSA--IGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 263 (264)
Q Consensus 193 ~LldA~sr--~gy--Y~~EY~v~~p~e~~RH~ls~--v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v 263 (264)
.++++.- +|+ +.+|-+-+.++. +||...- |.-+.+++| |..|++++.+..-....+.++.|++.|+|
T Consensus 101 -~~~~s~~~~~GfpS~~i~GtY~~~g~-~~~~~~r~VV~~~~~~~Y--lvqltvt~~~~qa~~~~~a~~aI~~g~~I 173 (175)
T PF10738_consen 101 -ELDGSPSDFSGFPSSQIEGTYDKDGM-RLHTSQRTVVIPGDDQRY--LVQLTVTTTADQAVALADATEAIDEGFTI 173 (175)
T ss_pred -cccCCccccCCCceeEEEEEEeeCCE-EeEeEEEEEEEeCCCcEE--EEEEEeeccccchhhhhhHHHHHHcCCEe
Confidence 3333222 664 777755444432 3443332 333345554 78899999998888899999999999997
No 9
>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=92.70 E-value=1.5 Score=38.02 Aligned_cols=128 Identities=16% Similarity=0.169 Sum_probs=65.1
Q ss_pred eeeeeCCCceEEEccCCCccC-CCCCCCcceEEEeccCCCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcccccC
Q 024710 106 RVYTDELNKFEISIPQDWQLG-AGEPNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDRSW 184 (264)
Q Consensus 106 ~~y~D~~dGYsf~yPs~W~~~-~G~~~g~k~Vv~F~p~~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l~~s~ 184 (264)
+-|+.++.=|++.||.+|... +|+.+ ..|+.+..=+-|..+..-. =++-+-+.++...-++.
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfED~E~s-----flFYnp~~WTGNfRISayk-------~~~~~ygk~~i~~EL~e----- 64 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFEDGEGS-----FLFYNPDQWTGNFRISAYK-------GGSAQYGKECIRQELKE----- 64 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE---TTE-----EEEE-SSS---EEEEEEEE---------STTHHHHHHHHHHHH-----
T ss_pred CcccCCCceEEEecCCCcchhccCCcc-----eEEEChHHhcCceEEEEEe-------cccccchHHHHHHHHHh-----
Confidence 468888889999999999843 45432 5688876677787765431 11222344555444443
Q ss_pred CCCCCCeeeEEEeeecCceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceee
Q 024710 185 RRPPGVAAKLIDCKASKGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 263 (264)
Q Consensus 185 ~~~~~~~A~LldA~sr~gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v 263 (264)
+..|+++....-+.-|.-|---..+.+-.-|+-.+ +.+ +..|.|.-..+- ..-.+..+.|+.|..|
T Consensus 65 ----n~~a~~vkvg~~~caYs~E~f~eeg~~YtsH~Wvt-g~~-----~~sfeCSFTv~k---g~~~~~aE~iiasL~v 130 (153)
T PF12712_consen 65 ----NPSAKLVKVGNWECAYSKEMFQEEGAYYTSHLWVT-GEG-----DVSFECSFTVPK---GESVKEAEEIIASLEV 130 (153)
T ss_dssp -----TT-EEEEETTEEEEEEEEEEEETTEEEEEEEEEE-EET-----TEEEEEEEEEET---T---HHHHHHHHH-EE
T ss_pred ----CCCcceEEeccEEEEEEhhhhhccCeeEEEEEEEE-ecC-----ceEEEEEEEccC---CCCcchHHHHHhhhee
Confidence 23356776665566676665444443334666655 553 277766555444 2234466777777654
No 10
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=91.96 E-value=2.4 Score=36.81 Aligned_cols=125 Identities=20% Similarity=0.325 Sum_probs=74.0
Q ss_pred EEEccCCCccCCCCCCCcceEEEeccCCCCCceeEEEEe--cCCCCccccccCCCHHHHHHHHHhcccccCCCCCCCeee
Q 024710 116 EISIPQDWQLGAGEPNGFKSITAFYPQEASSSSVSVVIT--GLGPDFTRMESFGKVEAFADTLVSGLDRSWRRPPGVAAK 193 (264)
Q Consensus 116 sf~yPs~W~~~~G~~~g~k~Vv~F~p~~~~~eNVSVvIT--pv~~d~~sL~dfGsPeeva~~Lv~~l~~s~~~~~~~~A~ 193 (264)
.|..|..|+.-. |-+|--....++-+|.+|+ |+.++ . +-.++.++.+..+-+ .=|+=+
T Consensus 10 ~l~lP~~w~DrS--------vNvf~~~~~gt~~~sfvIsRd~~~~g-~------~~~~y~~rql~~l~k---~Lpgy~-- 69 (147)
T COG5435 10 TLELPAAWQDRS--------VNVFVSGDNGTSGFSFVISRDPLEPG-D------TFPEYVQRQLALLRK---QLPGYE-- 69 (147)
T ss_pred eEcCcchhccce--------EEEEEecCCCcceeEEEEecCCCCCC-C------cHHHHHHHHHHHHHh---hCCCeE--
Confidence 578999998432 3333333333667778887 55443 1 234556666655532 112211
Q ss_pred EEEeeec--Cc--eEEEEEEEECC-CCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhhcceee
Q 024710 194 LIDCKAS--KG--FYYIEYTLQNP-GESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAVASFRF 263 (264)
Q Consensus 194 LldA~sr--~g--yY~~EY~v~~p-~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vvdSF~v 263 (264)
|..-.+- +| .-..+|.-+.+ .+++|=..-.+.+.++ .++-++|+.++-.--++-++...++|.||..
T Consensus 70 ~~~~~e~~v~~~aa~~~~y~w~~~~~~~r~v~q~~~~i~~g---~~vLifT~Tt~~~ftp~q~~~~~~~I~Sf~p 141 (147)
T COG5435 70 LHHRREIEVGGAAAPLLDYQWTSPEGEQRRVQQRQVFIERG---DTVLIFTLTTPGEFTPSQKKAWEQVIQSFVP 141 (147)
T ss_pred EeeccccccCccccceeEEEeecCCCCCceEEEEEeecccC---CeEEEEEecCCCCCCHHHHHHHHHHHHhcCC
Confidence 1111111 22 46667776664 3433333333466554 4999999999999899999999999999974
No 11
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=72.53 E-value=13 Score=36.94 Aligned_cols=23 Identities=4% Similarity=0.286 Sum_probs=19.7
Q ss_pred eeeeeCCCceEEEccCCCccCCC
Q 024710 106 RVYTDELNKFEISIPQDWQLGAG 128 (264)
Q Consensus 106 ~~y~D~~dGYsf~yPs~W~~~~G 128 (264)
+.|.-++-|++|.||.||..++.
T Consensus 288 q~FlH~~Lg~tf~~P~Gf~IdN~ 310 (479)
T COG4784 288 QTFLHPELGVTFDVPDGFKIDNS 310 (479)
T ss_pred cceeccccceEEecCCceEecCc
Confidence 46888999999999999996653
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=70.83 E-value=89 Score=30.01 Aligned_cols=136 Identities=18% Similarity=0.272 Sum_probs=73.2
Q ss_pred ceeeeeCCCceEEEccCCCccCC-CCCCCcceEEEe--ccCC------CCCce-eEEEEecCCCCccccccCC----CHH
Q 024710 105 LRVYTDELNKFEISIPQDWQLGA-GEPNGFKSITAF--YPQE------ASSSS-VSVVITGLGPDFTRMESFG----KVE 170 (264)
Q Consensus 105 f~~y~D~~dGYsf~yPs~W~~~~-G~~~g~k~Vv~F--~p~~------~~~eN-VSVvITpv~~d~~sL~dfG----sPe 170 (264)
--++.|...||+|++|.||.+++ ++.. +-.++.- -++. ....| -+|+.-.+ | ++=|- +-.
T Consensus 109 ~grvdn~~gGFS~vvP~GW~~Sda~~L~-yG~alls~~~~~~~~~~~~~p~andt~v~lgrl--d---~kl~a~ae~dn~ 182 (297)
T PF07174_consen 109 PGRVDNAAGGFSYVVPAGWVESDASHLD-YGSALLSKQTGEPPMPGQPPPVANDTSVVLGRL--D---LKLFASAEPDNT 182 (297)
T ss_pred cccccccccceEEeccCCccccccceee-cceeeeccCCCCCCCCCCCCCcCCCceEEeccc--c---ccccccccCChH
Confidence 35778899999999999999764 3211 1112111 1111 11123 34444444 3 33343 344
Q ss_pred HHHHHHHhcccccCCCC-----CCCeeeEEEeeecCc---eEEEEEE-EECCCCCceeEEEEEEE-----ecCCccceeE
Q 024710 171 AFADTLVSGLDRSWRRP-----PGVAAKLIDCKASKG---FYYIEYT-LQNPGESRKHLFSAIGM-----ASNGWYNRLY 236 (264)
Q Consensus 171 eva~~Lv~~l~~s~~~~-----~~~~A~LldA~sr~g---yY~~EY~-v~~p~e~~RH~ls~v~V-----~~nG~y~kLY 236 (264)
..|.+|...++ +|.-+ -+|+...|++.--.| ||.+.|+ ..+|+.+ -.-.+|+. .+.|.-.|-|
T Consensus 183 kaa~rl~sdmg-effmp~pg~rinq~~~~l~~~g~~g~asyyevkf~d~~kp~gq--iw~~vvg~p~~~~~~~~~~~rwf 259 (297)
T PF07174_consen 183 KAAVRLASDMG-EFFMPYPGTRINQETTPLDANGMPGSASYYEVKFTDANKPNGQ--IWAGVVGSPVAPGTPRGTPQRWF 259 (297)
T ss_pred HHHHHHhcccc-ceeccCCCccccccccccccCCcccceeEEEEEeccCCCCCCc--eEEEeecCcCCCCCCCCCCceEE
Confidence 67888888775 33222 367888888665544 7877777 4556643 22233443 1122223667
Q ss_pred EEEcccCchhhHH
Q 024710 237 TVTGQFVEEESEK 249 (264)
Q Consensus 237 Tltaq~~E~rw~k 249 (264)
.+=+++....-+|
T Consensus 260 vvwlgt~~~pvd~ 272 (297)
T PF07174_consen 260 VVWLGTANNPVDK 272 (297)
T ss_pred EEEecCCCCCCCH
Confidence 7766665544443
No 13
>PRK11615 hypothetical protein; Provisional
Probab=60.23 E-value=1.3e+02 Score=27.13 Aligned_cols=137 Identities=15% Similarity=0.235 Sum_probs=76.3
Q ss_pred eeeeeCCCceEEEccCCCccCCCC---CCCcceEEEeccCCCCCceeEEEEecCCCCccccccCCCHHHHHHHHHhcccc
Q 024710 106 RVYTDELNKFEISIPQDWQLGAGE---PNGFKSITAFYPQEASSSSVSVVITGLGPDFTRMESFGKVEAFADTLVSGLDR 182 (264)
Q Consensus 106 ~~y~D~~dGYsf~yPs~W~~~~G~---~~g~k~Vv~F~p~~~~~eNVSVvITpv~~d~~sL~dfGsPeeva~~Lv~~l~~ 182 (264)
+...=-+.+++|..|.|+....|. .... ..+|-+. ...-+ |||.+- |. +=++ -+..+.+|+.+. |
T Consensus 41 q~VSLLdGKl~FtLPag~sdqsgk~Gtq~nn--~~vYad~--tg~ka-vIVi~g--D~-~~~~---Ld~la~rl~~qQ-r 108 (185)
T PRK11615 41 QPVSLLDGKLSFTLPADMSDQSGKLGTQANN--MHVYADA--TGQKA-VIVILG--DD-TNED---LAVLAKRLEDQQ-R 108 (185)
T ss_pred ceeEEeccEEEEEcCCccccccccccccccc--eEEEEcC--CCCEE-EEEEeC--CC-Chhh---HHHHHHHHHHHH-H
Confidence 444445788999999999943322 1111 2345552 22222 223221 21 1111 244555555543 1
Q ss_pred cCCCCCCCeeeEEEeeec----CceEEEEEEEECCCCCceeEEEEEEEecCCccceeEEEEcccCchhhHHHHHHHHHhh
Q 024710 183 SWRRPPGVAAKLIDCKAS----KGFYYIEYTLQNPGESRKHLFSAIGMASNGWYNRLYTVTGQFVEEESEKYGSNIEKAV 258 (264)
Q Consensus 183 s~~~~~~~~A~LldA~sr----~gyY~~EY~v~~p~e~~RH~ls~v~V~~nG~y~kLYTltaq~~E~rw~k~~~~l~~vv 258 (264)
+ +.| .=+++.-+.- .+.+.++=+++..+. ..++++-++.=| +||-||..--|-..-.+-+...+.|+
T Consensus 109 ~--rdp--~lqvvsnK~i~i~G~~~qQLDS~~t~~Gq---k~~SSvvL~~v~--~rl~tlQitlpA~nqqqaq~~ae~ii 179 (185)
T PRK11615 109 S--RDP--QLQVVTNKAIELKGHKLQQLDSIISAKGQ---TAYSSVVLGKVD--NQLLTMQITLPADNQQQAQTTAENII 179 (185)
T ss_pred h--hCc--CceeecceeEEECCeeeEEeeeeeecCCc---eEEEEEEEEeeC--CeEEEEEEecCCCCHHHHHHHHHHHH
Confidence 1 111 1112222211 457888888877653 355565554433 69999999999888888889999999
Q ss_pred cceee
Q 024710 259 ASFRF 263 (264)
Q Consensus 259 dSF~v 263 (264)
++.++
T Consensus 180 ~tl~~ 184 (185)
T PRK11615 180 NTLVI 184 (185)
T ss_pred hheec
Confidence 88765
No 14
>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=40.01 E-value=23 Score=26.58 Aligned_cols=15 Identities=20% Similarity=0.377 Sum_probs=11.6
Q ss_pred ccchhHHHHHHHHHH
Q 024710 73 SRTKRREVMFQLAFT 87 (264)
Q Consensus 73 ~~~~RR~aLl~i~~a 87 (264)
..++||++|.+++++
T Consensus 7 ~~~sRR~Flk~lg~~ 21 (66)
T TIGR02811 7 ADPSRRDLLKGLGVG 21 (66)
T ss_pred CCccHHHHHHHHHHH
Confidence 457999999876654
No 15
>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=36.57 E-value=25 Score=21.70 Aligned_cols=14 Identities=29% Similarity=0.173 Sum_probs=10.9
Q ss_pred chhHHHHHHHHHHh
Q 024710 75 TKRREVMFQLAFTA 88 (264)
Q Consensus 75 ~~RR~aLl~i~~a~ 88 (264)
++||++|-..+++.
T Consensus 2 ~sRR~fLk~~~a~~ 15 (26)
T PF10518_consen 2 LSRRQFLKGGAAAA 15 (26)
T ss_pred CcHHHHHHHHHHHH
Confidence 68999998776653
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=36.50 E-value=19 Score=30.95 Aligned_cols=20 Identities=10% Similarity=0.272 Sum_probs=17.4
Q ss_pred cccccCCCHHHHHHHHHhcc
Q 024710 161 TRMESFGKVEAFADTLVSGL 180 (264)
Q Consensus 161 ~sL~dfGsPeeva~~Lv~~l 180 (264)
.=+++||+|+++|.+++...
T Consensus 45 eii~~LG~P~~iA~~i~~~~ 64 (181)
T PF08006_consen 45 EIIAELGSPKEIAREILAEY 64 (181)
T ss_pred HHHHHcCCHHHHHHHHHHhh
Confidence 45899999999999998764
No 17
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=23.29 E-value=76 Score=30.63 Aligned_cols=14 Identities=21% Similarity=0.211 Sum_probs=10.1
Q ss_pred chhHHHHHHHHHHh
Q 024710 75 TKRREVMFQLAFTA 88 (264)
Q Consensus 75 ~~RR~aLl~i~~a~ 88 (264)
++||.+|.++++++
T Consensus 1 ~~RR~fl~~~~~~~ 14 (328)
T PRK10882 1 MNRRNFLKAASAGA 14 (328)
T ss_pred CCHHHHHHHHHHHH
Confidence 46999998766554
No 18
>COG3540 PhoD Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]
Probab=21.83 E-value=1.6e+02 Score=30.55 Aligned_cols=40 Identities=13% Similarity=0.113 Sum_probs=24.0
Q ss_pred CCCcceEEEeccCC-CC-----CceeEEEEecCCCCccccccCCCHH
Q 024710 130 PNGFKSITAFYPQE-AS-----SSSVSVVITGLGPDFTRMESFGKVE 170 (264)
Q Consensus 130 ~~g~k~Vv~F~p~~-~~-----~eNVSVvITpv~~d~~sL~dfGsPe 170 (264)
||...+|++|.... ++ ..-|.+.|++. ++|++|...|++.
T Consensus 47 Dp~~~svviWTRl~P~p~~~g~~v~V~wEvs~~-~~f~~ivr~gt~~ 92 (522)
T COG3540 47 DPTATSVVIWTRLDPEPLNGGRPVPVIWEVSTD-ENFSNIVRKGTVI 92 (522)
T ss_pred CCCCCeEEEEEccCCccccCCCCcceEEEecCC-ccHHHHHhcCCcc
Confidence 55666677776541 11 34455555544 5888888777764
No 19
>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=20.28 E-value=34 Score=31.04 Aligned_cols=27 Identities=22% Similarity=0.187 Sum_probs=0.0
Q ss_pred ccccccccccccccccchhHHHHHHHHHH
Q 024710 59 RTLNRFRIEEQDDDSRTKRREVMFQLAFT 87 (264)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~RR~aLl~i~~a 87 (264)
.++||++. .......+||.+|.+++++
T Consensus 15 ~~~vra~~--~~~~~~~~RRa~l~~l~a~ 41 (202)
T PF05757_consen 15 GVVVRASQ--SPAQQQTSRRAVLGSLLAA 41 (202)
T ss_dssp -----------------------------
T ss_pred cceecccc--CcccccccHHHHHHHHHHH
Confidence 45677765 2223457788887644443
Done!