Query 025184
Match_columns 256
No_of_seqs 164 out of 273
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:25:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025184.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025184hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00066 PsbP domain-containin 100.0 3.8E-67 8.1E-72 472.0 22.3 225 30-256 34-259 (262)
2 PLN00067 PsbP domain-containin 100.0 1.7E-46 3.6E-51 335.7 20.7 202 40-255 42-263 (263)
3 PLN00042 photosystem II oxygen 100.0 1.9E-44 4.2E-49 323.1 19.8 203 20-256 30-260 (260)
4 PLN00059 PsbP domain-containin 100.0 5.5E-41 1.2E-45 300.4 18.3 196 16-256 53-285 (286)
5 PLN03152 hypothetical protein; 100.0 5.8E-36 1.3E-40 262.0 15.8 223 1-256 1-241 (241)
6 PF01789 PsbP: PsbP; InterPro 100.0 3.8E-35 8.1E-40 251.0 13.0 143 86-255 20-174 (175)
7 PF08786 DUF1795: Domain of un 97.7 0.00074 1.6E-08 54.6 12.2 119 112-253 2-130 (130)
8 PRK11615 hypothetical protein; 94.6 1.4 3.1E-05 38.4 13.5 127 111-255 49-184 (185)
9 COG5435 Uncharacterized conser 92.5 2.2 4.8E-05 36.1 10.7 121 112-255 9-141 (147)
10 PF10738 Lpp-LpqN: Probable li 82.9 27 0.0006 30.2 11.5 127 112-255 33-173 (175)
11 PF10518 TAT_signal: TAT (twin 79.3 2.2 4.8E-05 25.6 2.5 16 41-56 2-17 (26)
12 COG3212 Predicted membrane pro 72.9 12 0.00026 31.5 6.2 52 172-237 84-135 (144)
13 PF12712 DUF3805: Domain of un 68.1 74 0.0016 26.9 10.3 112 112-254 11-129 (153)
14 TIGR02811 formate_TAT formate 65.4 5.8 0.00013 29.1 2.4 15 38-52 6-20 (66)
15 PF07009 DUF1312: Protein of u 58.1 30 0.00066 27.4 5.6 40 199-238 31-81 (113)
16 PF03991 Prion_octapep: Copper 57.1 5 0.00011 17.9 0.5 6 102-107 2-7 (8)
17 PLN00058 photosystem II reacti 54.6 14 0.00031 29.2 3.0 42 10-52 12-60 (103)
18 PF05757 PsbQ: Oxygen evolving 53.6 3.9 8.4E-05 36.4 -0.3 27 26-52 14-40 (202)
19 PF09211 DUF1958: Domain of un 50.2 43 0.00093 24.6 4.7 38 192-229 3-45 (65)
20 TIGR01409 TAT_signal_seq Tat ( 44.2 23 0.00049 21.5 2.2 13 41-53 1-13 (29)
21 PF14030 DUF4245: Protein of u 43.9 2E+02 0.0044 24.5 10.7 100 116-243 63-165 (169)
22 smart00564 PQQ beta-propeller 38.2 36 0.00078 20.1 2.5 22 220-241 11-32 (33)
23 PF10399 UCR_Fe-S_N: Ubiquitin 36.1 33 0.00071 22.9 2.1 13 38-50 6-18 (41)
24 PRK07459 single-stranded DNA-b 28.8 2.4E+02 0.0053 22.6 6.6 47 164-212 45-94 (121)
25 TIGR03512 GldD_lipo gliding mo 27.6 4.3E+02 0.0094 23.3 11.1 149 85-255 24-185 (186)
26 PF15495 Fimbrillin_C: Major f 25.4 1.5E+02 0.0032 22.5 4.4 33 201-233 5-44 (85)
27 KOG4649 PQQ (pyrrolo-quinoline 24.5 76 0.0016 30.0 3.1 42 201-242 41-90 (354)
28 PF07174 FAP: Fibronectin-atta 23.8 51 0.0011 30.8 1.9 14 112-125 119-132 (297)
29 PLN00064 photosystem II protei 23.2 1.1E+02 0.0024 26.4 3.7 16 37-52 30-45 (166)
30 PF13964 Kelch_6: Kelch motif 20.8 96 0.0021 20.2 2.3 19 218-236 5-23 (50)
31 PF08006 DUF1700: Protein of u 20.3 50 0.0011 28.0 1.0 22 162-183 42-63 (181)
No 1
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=100.00 E-value=3.8e-67 Score=472.01 Aligned_cols=225 Identities=76% Similarity=1.253 Sum_probs=210.2
Q ss_pred ecCCCCCccccchhHHHHHHHHHHHhhhhccCCCCchhhhhhhcccCCCCCCCCCCCCCceeeeccCCCCCCCCCCCccc
Q 025184 30 CSTGSDSVDGVMKRRSVLVSGASLISSAVLGFPADGLAVVKQGLLAGRVPGLSEPDEQGWRTYRRPDDKSGGHGVGWSPI 109 (256)
Q Consensus 30 ~~~~~~~~~~~~sRR~aL~~~~~~~a~~~~~~p~~a~a~~~~g~~A~~~pg~s~~~~~gf~~y~~p~d~~gg~g~~~~~~ 109 (256)
|..+.++..+.++||++|+++++++...++++|+++.|+ .||++||++||||+|++.||++|+||++++|||||||++|
T Consensus 34 ~~~~~~~~~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~-~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i 112 (262)
T PLN00066 34 ADEETEDVATAVSRRSALASGAAAASSAVLAFPGEGLAV-KQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEI 112 (262)
T ss_pred cchhhhhhcchhhHHHHHHHHHHHHhhhhhcCCcchhhh-hhcccccCCCCCCCccccceEEEecCccccCcCCCCcccc
Confidence 445556667789999999988876566667899988773 7999999999999999999999999999999999999999
Q ss_pred cceEEecCCCCeecccccccCCCCceeEEEeCCCCCeEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccCCCc
Q 025184 110 IPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKKGRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGENV 189 (256)
Q Consensus 110 ~~Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~~ 189 (256)
+||+|+||+||+|++|+++|++++++|+||.|+.++||+|+|+|++||+++++++++|+|||+||+|++.|+++++|.+.
T Consensus 113 ~~Y~F~yP~GW~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~g~~~ 192 (262)
T PLN00066 113 TPYSFKVPQGWEEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELIGEPV 192 (262)
T ss_pred CCeEEECCCCCeEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhcCCCc
Confidence 99999999999999999999999999999999999999999999999998655899999999999999999999998887
Q ss_pred -ccceeEeeeEEEcCeeeEEEEEcCCceEEEEEEeCCEEEEEEEecCccchHhhhHHHHHHhhccccC
Q 025184 190 -EGKVLSMDVEELCGRKYYRYELEPPHVLITATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRVV 256 (256)
Q Consensus 190 -~a~ll~a~~r~~dG~~YY~yEl~~pH~L~satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrvv 256 (256)
+++|+++++++.||++||+||| .+|+|++|||++||||+|++++||+||+|++++|++|++||+|+
T Consensus 193 ~e~eLl~a~~re~dGktYY~~E~-~rH~LasaTV~~GrLYt~~asape~rW~k~~~~lr~v~dSF~V~ 259 (262)
T PLN00066 193 EEGKVLSMEVAEHSGRTYYQFEL-PPHTLVTATAAGNRVYIFSVTANGLQWKRHYKDLKRIAKSFRVV 259 (262)
T ss_pred cccceeEeeeeecCCcEEEEEEE-eCceEEEEEEECCEEEEEEeecchHhhHHHHHHHHHHhhceeee
Confidence 7999999999999999999999 68999999999999999999999999999999999999999985
No 2
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=1.7e-46 Score=335.73 Aligned_cols=202 Identities=32% Similarity=0.580 Sum_probs=169.1
Q ss_pred cchhHHHHHHHHHHHhhhhccCCCCchhhhhhhcccCCCCCCCCCCCCCceeee-----ccCCCCCCCCCCCccccceEE
Q 025184 40 VMKRRSVLVSGASLISSAVLGFPADGLAVVKQGLLAGRVPGLSEPDEQGWRTYR-----RPDDKSGGHGVGWSPIIPYLF 114 (256)
Q Consensus 40 ~~sRR~aL~~~~~~~a~~~~~~p~~a~a~~~~g~~A~~~pg~s~~~~~gf~~y~-----~p~d~~gg~g~~~~~~~~Ysf 114 (256)
...||+.|.|++.+...+++..|.....++..|.+.+..| +.+||..|+ +|.-+.| +|.+|+|
T Consensus 42 ~~~rr~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~lp~~~-----~~~~~~~f~~~~~~tpalra~-------~i~gY~F 109 (263)
T PLN00067 42 VIHRRELLLGLALAPLILIAPEPPAEAREVEVGSYLPPSP-----SDPSFVLFKASPKDTPALRAG-------NVQPYQF 109 (263)
T ss_pred hhHHHHHHhhhhhhhhhhccCCchhhhheehhhcccCCCC-----CCCceEEEecCCCCCcccccC-------CcccceE
Confidence 4689999998776322222223332334567788875554 448999994 6666666 5899999
Q ss_pred ecCCCCeecccccccCC--------CCceeEEEeCCCCCeEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccC
Q 025184 115 SVPQEWDEVPVSIADLG--------GTEIDLRFASPKKGRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIG 186 (256)
Q Consensus 115 ~~P~gW~e~~vs~~D~~--------~~g~d~rF~d~~~~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g 186 (256)
.||++|++++|+++-.| .+|+|++|+|+.++||+|+|+|+.|+++ .++++|+|||+||+|+++|++.++|
T Consensus 110 lyP~gW~~v~Vs~~~sGnycqp~c~~p~~dv~F~D~~dgnVSVIVSPV~r~t~--k~~~sIeDlGsPeeVl~~Lg~~v~g 187 (263)
T PLN00067 110 ILPPTWKQTRVANILSGNYCQPKCAEPWVEVKFEDEKQGKVQVVASPLIRLTN--KPNATIEEIGSPEKLIASLGPFVTG 187 (263)
T ss_pred eCCCCCcCccccccccCccccccccCCCceEEEeCCCCCCEEEEEeccccccc--CCCCChHHccCHHHHHHHhhHHhhc
Confidence 99999999999876333 2589999999999999999999999886 5789999999999999999999997
Q ss_pred CCc-ccceeEeeeEEEcCeeeEEEEEcCC------ceEEEEEEeCCEEEEEEEecCccchHhhhHHHHHHhhcccc
Q 025184 187 ENV-EGKVLSMDVEELCGRKYYRYELEPP------HVLITATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRV 255 (256)
Q Consensus 187 ~~~-~a~ll~a~~r~~dG~~YY~yEl~~p------H~L~satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrv 255 (256)
.+. +++||++++++.||++||+|||..| |+|+++||++||||||+++++|+||+|+++.|++|++||+|
T Consensus 188 ~~~~~~eLLeAs~re~dGktYY~~E~~tp~a~~gRHnLataTV~~GkLYtf~asanEkRW~K~k~~l~~V~dSFsV 263 (263)
T PLN00067 188 NSYDPDELLETSVEKIGDQTYYKYVLETPFALTGSHNLAKATAKGNTVVLFVVSASDKQWQSSEKTLKAILDSFQA 263 (263)
T ss_pred CCCCCcceEEeeeEeeCCeEEEEEEEEecCCCCCceEEEEEEEECCEEEEEEecCCHHHHHHHHHHHHHHHHhccC
Confidence 554 5899999999999999999999765 99999999999999999999999999999999999999986
No 3
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=1.9e-44 Score=323.07 Aligned_cols=203 Identities=27% Similarity=0.434 Sum_probs=162.0
Q ss_pred cCccceeeeeecCCCCCccccchhHHHHHHHHHHHhhhhccCCCCchhhhhhhcccCCCCCCCCCCCCCceeeeccCCCC
Q 025184 20 NGISRVKAVACSTGSDSVDGVMKRRSVLVSGASLISSAVLGFPADGLAVVKQGLLAGRVPGLSEPDEQGWRTYRRPDDKS 99 (256)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~sRR~aL~~~~~~~a~~~~~~p~~a~a~~~~g~~A~~~pg~s~~~~~gf~~y~~p~d~~ 99 (256)
...+++..+.|.++.++. ..++||.+|+.++++++...-..|+. ++||+.| +++|. ..+..||.+| . .
T Consensus 30 ~~~~~~~~~~~~~~~~~~-~~~srr~~l~~~~ga~a~~~~~~pa~----aay~~~a-nvfg~-~k~~~gF~~y---~--~ 97 (260)
T PLN00042 30 VSASRPSQVVCRAQEEDN-SAVSRRAALALLAGAAAAGAKVSPAN----AAYGESA-NVFGK-PKTNTGFLPY---N--G 97 (260)
T ss_pred cCCCCCcceeeecccccc-ccccHHHHHHHHHHHHHhhcccCchh----hhhcchh-hccCC-CCCCCCCeEe---e--C
Confidence 334478899999987654 55799999987777544444345654 5899998 58872 2344999999 3 4
Q ss_pred CCCCCCCccccceEEecCCCCeecccccccCCCCceeEEEeCCCC--CeEEEEEEecccccccCCCcccccccCCHHHHH
Q 025184 100 GGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK--GRLFVIVAPVLRFADDLGDDATIEKIGPPEKVI 177 (256)
Q Consensus 100 gg~g~~~~~~~~Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~--~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~ 177 (256)
|| |+|.||++|+++.+. +..|+|++|+|+++ +||+|+|+|+ ++++|+|||+|||++
T Consensus 98 dg----------Y~FlyP~~W~~~ke~----~~~G~dv~f~D~~~~~eNVSV~Ispt--------~k~sI~dlGsPee~l 155 (260)
T PLN00042 98 DG----------FKLLVPSKWNPSKER----EFPGQVLRFEDNFDATSNLSVMVTPT--------DKKSITDYGSPEEFL 155 (260)
T ss_pred CC----------eEEecCCCCcccccc----ccCCceEEeeccccccccEEEEEecC--------CcCCHhhcCCHHHHH
Confidence 77 999999999977653 33688999999987 5999999994 568999999999965
Q ss_pred HHh----Ccccc-CC---------C--cccceeEeeeEEEcCeeeEEEEEcC---------CceEEEEEEeCCEEEEEEE
Q 025184 178 NAF----GPEVI-GE---------N--VEGKVLSMDVEELCGRKYYRYELEP---------PHVLITATAAGNRLYLFSV 232 (256)
Q Consensus 178 ~~l----~~~~~-g~---------~--~~a~ll~a~~r~~dG~~YY~yEl~~---------pH~L~satv~~GrLYtl~~ 232 (256)
+.+ +++++ ++ + .+++|+++++++.||++||+|||.. +|+|+++||+|||||||++
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 554 44434 22 1 1468999999999999999999942 3999999999999999999
Q ss_pred ecCccchHhh-hHHHHHHhhccccC
Q 025184 233 TGNGLQWKRH-YTDLKKIADSFRVV 256 (256)
Q Consensus 233 ~a~e~rW~k~-~~~Lr~v~~SFrvv 256 (256)
++||+||+|+ ++.|++|++||+|.
T Consensus 236 qa~EkRW~K~~~k~l~~v~~SFsVa 260 (260)
T PLN00042 236 QAGDKRWFKGARKFVEGAASSFSVA 260 (260)
T ss_pred cCchhhhhHHHHHHHHHHHhceecC
Confidence 9999999998 66899999999973
No 4
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=5.5e-41 Score=300.41 Aligned_cols=196 Identities=26% Similarity=0.383 Sum_probs=156.5
Q ss_pred cccccCccceeeeeecCCCCCccccchhHHHHHHHHHHHhhhh---ccCCCCchhhhhhhcccCCCCCCCCCCCCCceee
Q 025184 16 SSVENGISRVKAVACSTGSDSVDGVMKRRSVLVSGASLISSAV---LGFPADGLAVVKQGLLAGRVPGLSEPDEQGWRTY 92 (256)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~sRR~aL~~~~~~~a~~~---~~~p~~a~a~~~~g~~A~~~pg~s~~~~~gf~~y 92 (256)
+.-..++-.|.++.|..+.+... .++||.+|+..+. ++.++ ..+|. ++| .| +||+.|
T Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~-~~~rr~~~~~~l~-~~~~~~s~~~~~~---------a~a--~~-------~~l~~y 112 (286)
T PLN00059 53 SAKSAKPDSPVAINCLTDAKQVC-AVGRRKSMMMGLL-MSGLIVSEANLPT---------AFA--SI-------PVFREY 112 (286)
T ss_pred cccccCCCCCeeeecccchhhhh-hhhhhhhhHHHHH-HHHHHHHhhcCch---------hhc--CC-------ccccee
Confidence 33334445689999999977654 4589998663221 12222 12331 122 13 689999
Q ss_pred eccCCCCCCCCCCCccccceEEecCCCCeecccccccCCCCceeEEEeCCCC--CeEEEEEEecccccccCCCccccccc
Q 025184 93 RRPDDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK--GRLFVIVAPVLRFADDLGDDATIEKI 170 (256)
Q Consensus 93 ~~p~d~~gg~g~~~~~~~~Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~--~~vsVvv~p~~rl~~~~~~~~sI~dl 170 (256)
.|+.|| |+|.||.||.++.+. |.|+.|+|+++ +||+|+|+|+.. +++++|+||
T Consensus 113 ---~D~~DG----------Y~FlYP~GWi~V~~~-------G~DVvFrD~Ie~~ENVSV~ISs~ss-----s~~~sLeDL 167 (286)
T PLN00059 113 ---IDTFDG----------YSFKYPQNWIQVRGA-------GADIFFRDPVVLDENLSVEFSSPSS-----SKYTSLEDL 167 (286)
T ss_pred ---EcCCCC----------eEEeCCCCCeEeccC-------CCceEEeccCccccceEEEEecCCc-----ccCCChHHc
Confidence 999999 999999999998864 56679999998 599999998611 257999999
Q ss_pred CCHHHHHHHhCccccCC--------CcccceeEeeeEEE-cCeeeEEEEEc--C---------------------CceEE
Q 025184 171 GPPEKVINAFGPEVIGE--------NVEGKVLSMDVEEL-CGRKYYRYELE--P---------------------PHVLI 218 (256)
Q Consensus 171 Gspeev~~~l~~~~~g~--------~~~a~ll~a~~r~~-dG~~YY~yEl~--~---------------------pH~L~ 218 (256)
|+|+||+++|+.+++++ .++++||++++|+. ||++||+|||. + +|+|+
T Consensus 168 GsP~eVgerLlkqvLa~f~str~GsgReaeLVsA~~Re~~DGktYY~lEY~Vks~~~~n~~~~~~qdr~~~~~w~RH~LA 247 (286)
T PLN00059 168 GSPEEVGKRVLRQYLTEFMSTRLGVKREANILSTSSRVADDGKLYYQVEVNIKSYANNNELAVMPQDRVARLEWNRRYLA 247 (286)
T ss_pred CCHHHHHHHHHHHHhcccccccCCCCcceEEEEeeeEEccCCcEEEEEEEEEEcCcccccccccccccccccccceeeEE
Confidence 99999999999888765 24799999999975 99999999984 2 39999
Q ss_pred EEEEeCCEEEEEEEecCccchHhhhHHHHHHhhccccC
Q 025184 219 TATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRVV 256 (256)
Q Consensus 219 satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrvv 256 (256)
+++|.|||||||++|+||+||.|+++.|++|++||+|+
T Consensus 248 ~v~V~nGkLYTL~~qtpE~RW~kvk~~f~~V~dSF~V~ 285 (286)
T PLN00059 248 VLGVENDRLYSIRLQTPEKVFLEEEKDLRRVMDSFRVE 285 (286)
T ss_pred EEEEeCCEEEEEEcCCcHHHHHHHHHHHHHHHhheeec
Confidence 99999999999999999999999999999999999985
No 5
>PLN03152 hypothetical protein; Provisional
Probab=100.00 E-value=5.8e-36 Score=261.98 Aligned_cols=223 Identities=22% Similarity=0.331 Sum_probs=164.1
Q ss_pred CCccccccccccccccccccCccceeeeeecCCCCCccccchhHHHHHHHHHHHhhhhccCCCCchhhhhhhccc---CC
Q 025184 1 MGTTLFSSCSFLAQISSVENGISRVKAVACSTGSDSVDGVMKRRSVLVSGASLISSAVLGFPADGLAVVKQGLLA---GR 77 (256)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sRR~aL~~~~~~~a~~~~~~p~~a~a~~~~g~~A---~~ 77 (256)
|-.+|.|+++-.-.++...+.++.+ ..+ ...+||++++..+.+++..+.+ +.+. .++..- ..
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~~~~~-~~~---------~~~~~r~~~~~t~~~~~~~~~~-~~~~----~~~~~~~~~~~ 65 (241)
T PLN03152 1 MAALLLSLSPHPPNPQNPNPRKPKP-LSR---------CGASRRDFILHTASLCASSLAA-QNPL----PPSLADPSKPS 65 (241)
T ss_pred CceeEeecCCCCCCCCCCCCCCCCc-ccc---------ccccccceeeehhHHHHhhhhc-CCCC----CccccCCCCCC
Confidence 5566777776644444444444333 222 2347999998777655443332 2211 111111 23
Q ss_pred CCCCCC-CCCCCceeeeccCCCCCCCCCCCccccceEEecCCCCeeccccc---------ccC-CCCceeEEEeCCCC-C
Q 025184 78 VPGLSE-PDEQGWRTYRRPDDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSI---------ADL-GGTEIDLRFASPKK-G 145 (256)
Q Consensus 78 ~pg~s~-~~~~gf~~y~~p~d~~gg~g~~~~~~~~Ysf~~P~gW~e~~vs~---------~D~-~~~g~d~rF~d~~~-~ 145 (256)
.|.++. +++..|..| .++| |++.||++|+++.... .|+ +-..+.+||.++++ +
T Consensus 66 ~~~~~~~~nt~~w~~~-----~g~g----------f~~~~pp~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~D~sE 130 (241)
T PLN03152 66 KPLLSGIANTKSWFQF-----YGDG----------FSIRVPPSFEDIMEPEDYNAGLSLYGDKAKPRTFAARFASPDGSE 130 (241)
T ss_pred Cchheeeecchhhhhh-----hCCc----------eEEeCCCChhhhcChhhcccccceecCCCCCcceeeeecCCCCCc
Confidence 455554 788888888 3677 9999999999766431 111 12567899999987 6
Q ss_pred eEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccCCCc-ccceeEeeeEEEcCeeeEEEEEcC--CceEEEEEE
Q 025184 146 RLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGENV-EGKVLSMDVEELCGRKYYRYELEP--PHVLITATA 222 (256)
Q Consensus 146 ~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~~-~a~ll~a~~r~~dG~~YY~yEl~~--pH~L~satv 222 (256)
||||+|+|+++|+.+|.++++|+|||+|+||++.|+|. |..+ .++.++. .++.+||+||+|||.. .|+|++|+|
T Consensus 131 nVSVVIspv~~LK~tfle~kDLtDLGsp~EVgkv~vP~--g~~~~saR~iel-~~E~dGKtYY~lEy~v~~RH~LaTVaV 207 (241)
T PLN03152 131 VLSVVIRPSNQLKITFLEAKDITDLGSLKEAAKIFVPG--GATLYSARTIKV-KEEEGIRTYYFYEFGRDEQHVALVATV 207 (241)
T ss_pred eEEEEEecCccccccccccCChhHcCCHHHHHHhhCCC--cccccccceeee-eeecCCceeEEEEEEeCCcEEEEEEEE
Confidence 99999999999999888999999999999999999765 3222 4555555 3489999999999865 499999999
Q ss_pred eCCEEEEEEEecCccchHhhhHHHHHHhhccccC
Q 025184 223 AGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRVV 256 (256)
Q Consensus 223 ~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrvv 256 (256)
++||||||.++++|+||+|++++|+++++||+|+
T Consensus 208 srGKLYTl~aSt~EkRW~Kvk~kfr~aa~SFsV~ 241 (241)
T PLN03152 208 NSGKAYIAGATAPESKWDDDGVKLRSAAISLTVL 241 (241)
T ss_pred cCCeEEEEecCCchhchHHHHHHHHHHHhheeeC
Confidence 9999999999999999999999999999999986
No 6
>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=3.8e-35 Score=250.97 Aligned_cols=143 Identities=32% Similarity=0.614 Sum_probs=124.4
Q ss_pred CCCceeeeccCCCCCCCCCCCccccceEEecCCCCeecccccccCCCCceeEEEeCCCC--CeEEEEEEecccccccCCC
Q 025184 86 EQGWRTYRRPDDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK--GRLFVIVAPVLRFADDLGD 163 (256)
Q Consensus 86 ~~gf~~y~~p~d~~gg~g~~~~~~~~Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~--~~vsVvv~p~~rl~~~~~~ 163 (256)
+.||++| .|..+| |+|.||++|+++.+ .|.+++|+|+.+ +||+|+|.|+ ..
T Consensus 20 ~~~~~~y---~d~~~~----------y~f~~P~gW~~~~~-------~G~~v~f~d~~~~~~nvsV~v~p~-------~~ 72 (175)
T PF01789_consen 20 STGFQPY---TDSDDG----------YSFLYPSGWEEVDV-------SGADVVFRDPIDADENVSVVVSPV-------PK 72 (175)
T ss_dssp -SSEEEE---EECTTT----------EEEEEETTEEEEES-------TTEEEEEEETTETTSEEEEEEEE--------ST
T ss_pred CCCceEE---EcCCCC----------EEEECCCCCeecCC-------CCeEEEEECcccccceEEEEEEec-------CC
Confidence 3899999 777787 99999999988776 367789999976 4999999997 34
Q ss_pred cccccccCCHHHHHHHhCccccCCC---cccceeEeeeEEEcCeeeEEEEEcC-------CceEEEEEEeCCEEEEEEEe
Q 025184 164 DATIEKIGPPEKVINAFGPEVIGEN---VEGKVLSMDVEELCGRKYYRYELEP-------PHVLITATAAGNRLYLFSVT 233 (256)
Q Consensus 164 ~~sI~dlGspeev~~~l~~~~~g~~---~~a~ll~a~~r~~dG~~YY~yEl~~-------pH~L~satv~~GrLYtl~~~ 233 (256)
..+|+|||+|+++++.+++.++++. ..++++++++++.+|++||+|||.. +|+|+++|+.+||||+|+++
T Consensus 73 ~~sl~~lGs~~~va~~l~~~~~~~~~~~~~a~li~a~~~~~~g~~yY~~Ey~~~~~~~~~rh~l~~~tv~~g~lY~l~~~ 152 (175)
T PF01789_consen 73 DFSLEDLGSPEEVAERLLNGELASPGSGREAELISASEREVDGKTYYEYEYTVQSPNEGRRHNLAVVTVKNGKLYTLTAQ 152 (175)
T ss_dssp S-SGGGG-SHHHHHHHHHHHCCCHCTSSEEEEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEE
T ss_pred cCchhhcCCHHHHHHHHhhhhcccccCCcceEEEEeeeeecCCccEEEEEEEeccCCCcccEEEEEEEEECCEEEEEEEE
Confidence 4599999999999999998887554 3689999999999999999999852 29999999999999999999
Q ss_pred cCccchHhhhHHHHHHhhcccc
Q 025184 234 GNGLQWKRHYTDLKKIADSFRV 255 (256)
Q Consensus 234 a~e~rW~k~~~~Lr~v~~SFrv 255 (256)
++|+||+++++.|++|++||+|
T Consensus 153 a~e~~w~k~~~~l~~iv~SF~v 174 (175)
T PF01789_consen 153 APESRWDKVEPKLRKIVDSFRV 174 (175)
T ss_dssp EEHHHHHTCHHHHHHHHHC-EE
T ss_pred cCHHHHHHHHHHHHHHHhcEEe
Confidence 9999999999999999999997
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=97.74 E-value=0.00074 Score=54.63 Aligned_cols=119 Identities=15% Similarity=0.218 Sum_probs=72.7
Q ss_pred eEEecCCCCeecccccccCCCCceeEEEeCCCCCeEEEEE--EecccccccCCCcccccccCCHHHHHHHhCccccCCCc
Q 025184 112 YLFSVPQEWDEVPVSIADLGGTEIDLRFASPKKGRLFVIV--APVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGENV 189 (256)
Q Consensus 112 Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~~~vsVvv--~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~~ 189 (256)
-+|.+|.+|++..++. +++.++.....+++| .++ .+.. ++++..++.+..+ ....
T Consensus 2 g~~~lP~~~~D~t~nv---------~~~~~~~~~~~slvIsR~~l-------~~g~------tl~~~~~~q~~~l-~~~l 58 (130)
T PF08786_consen 2 GSLTLPDGWQDRTMNV---------LVLPDSGGSGPSLVISRDPL-------PDGE------TLEDYLQRQLAQL-RKQL 58 (130)
T ss_dssp EEEEEETTSEE--BEE---------EEE--BTTB-EEEEEEEE----------TTS-------HHHHHHHHHHHH-HCCS
T ss_pred ceEeCCCcceeceEEE---------EEccCCCCCcceEEEEeccC-------CCCC------CHHHHHHHHHHHH-HhhC
Confidence 3789999999987652 244444443444554 343 2333 4455554443322 1111
Q ss_pred -ccceeEeeeEEEcCeeeEEEEE--cCC----ceEEEEEEeC-CEEEEEEEecCccchHhhhHHHHHHhhcc
Q 025184 190 -EGKVLSMDVEELCGRKYYRYEL--EPP----HVLITATAAG-NRLYLFSVTGNGLQWKRHYTDLKKIADSF 253 (256)
Q Consensus 190 -~a~ll~a~~r~~dG~~YY~yEl--~~p----H~L~satv~~-GrLYtl~~~a~e~rW~k~~~~Lr~v~~SF 253 (256)
.-++++.+..+.+|..-+.+++ ..+ |+...+...+ +++|+|+.+++....+..++.+..|++||
T Consensus 59 ~~~~~~~~~~~~l~~~~a~~l~~~~~~~g~~v~Q~q~~~~~~~~~~l~~T~t~~~~~~~~~~~~~~~i~~Sf 130 (130)
T PF08786_consen 59 PGFQLVERQPITLGGRPARELEYSFRSGGQPVYQRQAAVLLPGRRVLVFTYTAPGPFTEEQRAHWEAILKSF 130 (130)
T ss_dssp TT-EEEEEEEEEETTEEEEEEEEEEEETTCEEEEEEEEEEEC-CCEEEEEEEEECCCHHHHHHHHHHHHCT-
T ss_pred CCcEEEeeEEEEeCCCCeEEEEEEEeeCCEEEEEEEEEEEECCCEEEEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 2355665566678877655554 222 8887777777 99999999999999999999999999998
No 8
>PRK11615 hypothetical protein; Provisional
Probab=94.65 E-value=1.4 Score=38.42 Aligned_cols=127 Identities=13% Similarity=0.166 Sum_probs=78.7
Q ss_pred ceEEecCCCCeecccccccCCCCce-eEEEeCCCCCeEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccCCCc
Q 025184 111 PYLFSVPQEWDEVPVSIADLGGTEI-DLRFASPKKGRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGENV 189 (256)
Q Consensus 111 ~Ysf~~P~gW~e~~vs~~D~~~~g~-d~rF~d~~~~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~~ 189 (256)
+.+|.+|.|+.+.... .|+.+. --.|.|+....+-++|.+ + .+... .+.+..+|..+- ...
T Consensus 49 Kl~FtLPag~sdqsgk---~Gtq~nn~~vYad~tg~kavIVi~g-----D--~~~~~------Ld~la~rl~~qQ--r~r 110 (185)
T PRK11615 49 KLSFTLPADMSDQSGK---LGTQANNMHVYADATGQKAVIVILG-----D--DTNED------LAVLAKRLEDQQ--RSR 110 (185)
T ss_pred EEEEEcCCcccccccc---ccccccceEEEEcCCCCEEEEEEeC-----C--CChhh------HHHHHHHHHHHH--Hhh
Confidence 7999999999975432 222211 237888766554444432 1 11111 344455553321 111
Q ss_pred cc--ceeEeeeEEEcCeeeEEEEEcC--C--ceEE--EEEEeCCEEEEEEEecCccchHhhhHHHHHHhhcccc
Q 025184 190 EG--KVLSMDVEELCGRKYYRYELEP--P--HVLI--TATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRV 255 (256)
Q Consensus 190 ~a--~ll~a~~r~~dG~~YY~yEl~~--p--H~L~--satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrv 255 (256)
.+ .+++-+.-+.+|+..+..+-.. . ..+. ..+..++||-++-+..|.+.=.+....-++|+++..+
T Consensus 111 dp~lqvvsnK~i~i~G~~~qQLDS~~t~~Gqk~~SSvvL~~v~~rl~tlQitlpA~nqqqaq~~ae~ii~tl~~ 184 (185)
T PRK11615 111 DPQLQVVTNKAIELKGHKLQQLDSIISAKGQTAYSSVVLGKVDNQLLTMQITLPADNQQQAQTTAENIINTLVI 184 (185)
T ss_pred CcCceeecceeEEECCeeeEEeeeeeecCCceEEEEEEEEeeCCeEEEEEEecCCCCHHHHHHHHHHHHhheec
Confidence 22 3344445568999999998532 1 3343 4446789999999999999888888888999887654
No 9
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=92.48 E-value=2.2 Score=36.12 Aligned_cols=121 Identities=15% Similarity=0.230 Sum_probs=73.9
Q ss_pred eEEecCCCCeecccccccCCCCceeEEEeCCCCC--eEEEEEEe-cccccccCCCcccccccCCHHHHHHHhCccccCCC
Q 025184 112 YLFSVPQEWDEVPVSIADLGGTEIDLRFASPKKG--RLFVIVAP-VLRFADDLGDDATIEKIGPPEKVINAFGPEVIGEN 188 (256)
Q Consensus 112 Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~~--~vsVvv~p-~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~ 188 (256)
-.|.+|..|++..+. .|....++ .++.+|+- .. .......+|= ++-+..+-+++-|
T Consensus 9 G~l~lP~~w~DrSvN-----------vf~~~~~gt~~~sfvIsRd~~------~~g~~~~~y~--~rql~~l~k~Lpg-- 67 (147)
T COG5435 9 GTLELPAAWQDRSVN-----------VFVSGDNGTSGFSFVISRDPL------EPGDTFPEYV--QRQLALLRKQLPG-- 67 (147)
T ss_pred eeEcCcchhccceEE-----------EEEecCCCcceeEEEEecCCC------CCCCcHHHHH--HHHHHHHHhhCCC--
Confidence 479999999998875 46665554 57777752 11 1222222221 1111122111111
Q ss_pred cccceeEeeeEEEcC----eeeEEEEEc---CC--ceEEEEEEeCCEEEEEEEecCccchHhhhHHHHHHhhcccc
Q 025184 189 VEGKVLSMDVEELCG----RKYYRYELE---PP--HVLITATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFRV 255 (256)
Q Consensus 189 ~~a~ll~a~~r~~dG----~~YY~yEl~---~p--H~L~satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFrv 255 (256)
-++..-.+-+.+| ..+|.|... .. |++.+..-.++++-+|+++++..-=++.++....++.||..
T Consensus 68 --y~~~~~~e~~v~~~aa~~~~y~w~~~~~~~r~v~q~~~~i~~g~~vLifT~Tt~~~ftp~q~~~~~~~I~Sf~p 141 (147)
T COG5435 68 --YELHHRREIEVGGAAAPLLDYQWTSPEGEQRRVQQRQVFIERGDTVLIFTLTTPGEFTPSQKKAWEQVIQSFVP 141 (147)
T ss_pred --eEEeeccccccCccccceeEEEeecCCCCCceEEEEEeecccCCeEEEEEecCCCCCCHHHHHHHHHHHHhcCC
Confidence 2333333344566 346777763 22 67777656778999999999988888889999999999974
No 10
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=82.92 E-value=27 Score=30.22 Aligned_cols=127 Identities=14% Similarity=0.179 Sum_probs=64.6
Q ss_pred eEEecCCCCeecccccccCCCCceeEEEeCCCC---CeEEEEEEecccccccCCCcccccccCCHHHHHHHhCcccc-CC
Q 025184 112 YLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK---GRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVI-GE 187 (256)
Q Consensus 112 Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~---~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~-g~ 187 (256)
-++-.|+||....-.+. ...-..+....... .|..|+|..+ .-+| +|+|+++.--..+- .+
T Consensus 33 v~lP~P~GW~~~~~~~~--~~a~~vi~~~~~~~~~~Pnavv~V~kL---~G~~----------Dp~e~l~~a~~d~~~l~ 97 (175)
T PF10738_consen 33 VSLPTPPGWEPAPDPNP--PWAYAVIVDPQADGGFPPNAVVTVSKL---TGDF----------DPAEALEHAPADAQNLP 97 (175)
T ss_pred EeccCCcCcccCCCCCC--CceEEEEEeccccCCCCCceEEEEEec---cCCC----------CHHHHHHhchhhHhhCc
Confidence 67888999998653221 00011122222111 3888888765 2233 56777653211110 11
Q ss_pred CcccceeEeeeEEEcCeeeEE----EEEcCC--c--eEEEEEEeCCEEEE--EEEecCccchHhhhHHHHHHhhcccc
Q 025184 188 NVEGKVLSMDVEELCGRKYYR----YELEPP--H--VLITATAAGNRLYL--FSVTGNGLQWKRHYTDLKKIADSFRV 255 (256)
Q Consensus 188 ~~~a~ll~a~~r~~dG~~YY~----yEl~~p--H--~L~satv~~GrLYt--l~~~a~e~rW~k~~~~Lr~v~~SFrv 255 (256)
.++ .++.+.-+-+|-.=+. |+.... | +-.+|.-.++..|. |++++.+.+=....+..+.|.+.|+|
T Consensus 98 g~~--~~~~s~~~~~GfpS~~i~GtY~~~g~~~~~~~r~VV~~~~~~~Ylvqltvt~~~~qa~~~~~a~~aI~~g~~I 173 (175)
T PF10738_consen 98 GFR--ELDGSPSDFSGFPSSQIEGTYDKDGMRLHTSQRTVVIPGDDQRYLVQLTVTTTADQAVALADATEAIDEGFTI 173 (175)
T ss_pred Ccc--cccCCccccCCCceeEEEEEEeeCCEEeEeEEEEEEEeCCCcEEEEEEEeeccccchhhhhhHHHHHHcCCEe
Confidence 111 2232333344533333 222211 2 33333333555555 56678888888889999999999987
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=79.30 E-value=2.2 Score=25.60 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=11.6
Q ss_pred chhHHHHHHHHHHHhh
Q 025184 41 MKRRSVLVSGASLISS 56 (256)
Q Consensus 41 ~sRR~aL~~~~~~~a~ 56 (256)
.+||++|-+.++++++
T Consensus 2 ~sRR~fLk~~~a~~a~ 17 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAA 17 (26)
T ss_pred CcHHHHHHHHHHHHHH
Confidence 5899999977664333
No 12
>COG3212 Predicted membrane protein [Function unknown]
Probab=72.92 E-value=12 Score=31.45 Aligned_cols=52 Identities=23% Similarity=0.242 Sum_probs=36.4
Q ss_pred CHHHHHHHhCccccCCCcccceeEeeeEEEcCeeeEEEEEcCCceEEEEEEeCCEEEEEEEecCcc
Q 025184 172 PPEKVINAFGPEVIGENVEGKVLSMDVEELCGRKYYRYELEPPHVLITATAAGNRLYLFSVTGNGL 237 (256)
Q Consensus 172 speev~~~l~~~~~g~~~~a~ll~a~~r~~dG~~YY~yEl~~pH~L~satv~~GrLYtl~~~a~e~ 237 (256)
+.+++.+..+.+. .+++.+.+-.+.+|+.+|+.|+. ..+|+-|.+.+.|..-
T Consensus 84 s~~ea~~iAl~~~-----~G~v~dieLe~~~g~~vYevei~---------~~d~~e~ev~iDA~TG 135 (144)
T COG3212 84 SLEEAKEIALKRV-----PGKVDDIELEEDNGRLVYEVEIV---------KDDGQEYEVEIDAKTG 135 (144)
T ss_pred CHHHHHHHHHHHC-----CCceeEEEEeccCCEEEEEEEEE---------eCCCcEEEEEEecCCC
Confidence 5566665543332 24666766677899999999996 4468888888877643
No 13
>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=68.14 E-value=74 Score=26.95 Aligned_cols=112 Identities=20% Similarity=0.291 Sum_probs=49.7
Q ss_pred eEEecCCCCeecccccccCCCCceeEEEeCCCC--CeEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccCC-C
Q 025184 112 YLFSVPQEWDEVPVSIADLGGTEIDLRFASPKK--GRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGE-N 188 (256)
Q Consensus 112 Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~--~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~-~ 188 (256)
|+..||.+|.|..-. -+ -.-|.||.. ||+.+..-- +. +-.-..++++.-+..-.+. .
T Consensus 11 FS~~YP~~W~EfED~-E~------sflFYnp~~WTGNfRISayk--------~~-----~~~ygk~~i~~EL~en~~a~~ 70 (153)
T PF12712_consen 11 FSMEYPADWNEFEDG-EG------SFLFYNPDQWTGNFRISAYK--------GG-----SAQYGKECIRQELKENPSAKL 70 (153)
T ss_dssp EEEEE-TT-EEE----TT------EEEEE-SSS---EEEEEEEE---------------STTHHHHHHHHHHHH-TT-EE
T ss_pred EEEecCCCcchhccC-Cc------ceEEEChHHhcCceEEEEEe--------cc-----cccchHHHHHHHHHhCCCcce
Confidence 999999999986621 11 136899988 677654432 01 0112333443332332221 1
Q ss_pred cc-cc---eeEeeeEEEcCeeeEEEEEcCCceEEEEEEeCCEEEEEEEecCccchHhhhHHHHHHhhccc
Q 025184 189 VE-GK---VLSMDVEELCGRKYYRYELEPPHVLITATAAGNRLYLFSVTGNGLQWKRHYTDLKKIADSFR 254 (256)
Q Consensus 189 ~~-a~---ll~a~~r~~dG~~YY~yEl~~pH~L~satv~~GrLYtl~~~a~e~rW~k~~~~Lr~v~~SFr 254 (256)
++ .+ ..+.+..+.+|. ||+= |.- +|-.++..|.|.-+.+-.. ....-+.|+.|..
T Consensus 71 vkvg~~~caYs~E~f~eeg~-~Yts-----H~W--vtg~~~~sfeCSFTv~kg~---~~~~aE~iiasL~ 129 (153)
T PF12712_consen 71 VKVGNWECAYSKEMFQEEGA-YYTS-----HLW--VTGEGDVSFECSFTVPKGE---SVKEAEEIIASLE 129 (153)
T ss_dssp EEETTEEEEEEEEEEEETTE-EEEE-----EEE--EEEETTEEEEEEEEEETT------HHHHHHHHH-E
T ss_pred EEeccEEEEEEhhhhhccCe-eEEE-----EEE--EEecCceEEEEEEEccCCC---CcchHHHHHhhhe
Confidence 11 11 123333344554 3332 322 4467788888888766442 2333445555544
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=65.37 E-value=5.8 Score=29.07 Aligned_cols=15 Identities=20% Similarity=0.120 Sum_probs=10.9
Q ss_pred cccchhHHHHHHHHH
Q 025184 38 DGVMKRRSVLVSGAS 52 (256)
Q Consensus 38 ~~~~sRR~aL~~~~~ 52 (256)
...++||.+|.++++
T Consensus 6 ~~~~sRR~Flk~lg~ 20 (66)
T TIGR02811 6 KADPSRRDLLKGLGV 20 (66)
T ss_pred cCCccHHHHHHHHHH
Confidence 346699999986543
No 15
>PF07009 DUF1312: Protein of unknown function (DUF1312); InterPro: IPR010739 This family consists of several bacterial proteins of around 120 residues in length. The function of this family is unknown.; PDB: 4ESN_B 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2KPP_A 3LD7_C.
Probab=58.12 E-value=30 Score=27.41 Aligned_cols=40 Identities=10% Similarity=0.008 Sum_probs=31.3
Q ss_pred EEEcCeeeEEEEEcC---C--------ceEEEEEEeCCEEEEEEEecCccc
Q 025184 199 EELCGRKYYRYELEP---P--------HVLITATAAGNRLYLFSVTGNGLQ 238 (256)
Q Consensus 199 r~~dG~~YY~yEl~~---p--------H~L~satv~~GrLYtl~~~a~e~r 238 (256)
...||+.|+.|.|.. + .....+-+.+|+.+.....||++-
T Consensus 31 I~~~g~~~~~i~L~~~~~~~~i~i~~~~g~~~i~i~~g~vrv~~s~Cpdki 81 (113)
T PF07009_consen 31 IYVDGKEVKRIPLDKVNEDKTIEIDGDGGYNTIEIKDGKVRVIESDCPDKI 81 (113)
T ss_dssp EEETTEEEEEEETTS-BSEEEEEEETTTCEEEEEEETTEEEEEEESTSS-H
T ss_pred EEECCEEEEEEECCCCCCCEEEEEecCCcEEEEEEECCEEEEEECCCCCcc
Confidence 357999998887754 2 456677899999999999999874
No 16
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=57.05 E-value=5 Score=17.88 Aligned_cols=6 Identities=67% Similarity=1.692 Sum_probs=4.4
Q ss_pred CCCCCc
Q 025184 102 HGVGWS 107 (256)
Q Consensus 102 ~g~~~~ 107 (256)
|||+|-
T Consensus 2 hgG~Wg 7 (8)
T PF03991_consen 2 HGGGWG 7 (8)
T ss_pred CCCcCC
Confidence 678883
No 17
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=54.57 E-value=14 Score=29.15 Aligned_cols=42 Identities=24% Similarity=0.379 Sum_probs=26.2
Q ss_pred cccccccccccCccceeeeeecCCCC-------CccccchhHHHHHHHHH
Q 025184 10 SFLAQISSVENGISRVKAVACSTGSD-------SVDGVMKRRSVLVSGAS 52 (256)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~sRR~aL~~~~~ 52 (256)
+-+++++.. .+|++..+++.+...+ ..++..+||.++..+++
T Consensus 12 ~~~~~~~~~-~~rr~l~Vv~Aak~~~~e~v~~~~~e~~~gRR~~mfaaaA 60 (103)
T PLN00058 12 PAVAKLPSA-TGGRRLSVVRASTSDNTPSLEVKEQQSTTMRRDLMFTAAA 60 (103)
T ss_pred HHHhccCCc-ccCceEEEEEccccccccceeeccccchhhHHHHHHHHHH
Confidence 356666644 4444777777665542 12466789999876555
No 18
>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=53.59 E-value=3.9 Score=36.38 Aligned_cols=27 Identities=22% Similarity=0.197 Sum_probs=0.0
Q ss_pred eeeeecCCCCCccccchhHHHHHHHHH
Q 025184 26 KAVACSTGSDSVDGVMKRRSVLVSGAS 52 (256)
Q Consensus 26 ~~~~~~~~~~~~~~~~sRR~aL~~~~~ 52 (256)
..+.|+++....+...+||.+|.++++
T Consensus 14 ~~~~vra~~~~~~~~~~RRa~l~~l~a 40 (202)
T PF05757_consen 14 AGVVVRASQSPAQQQTSRRAVLGSLLA 40 (202)
T ss_dssp ---------------------------
T ss_pred ccceeccccCcccccccHHHHHHHHHH
Confidence 334466665444456689988775544
No 19
>PF09211 DUF1958: Domain of unknown function (DUF1958); InterPro: IPR015294 Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. Penicillin-binding protein 4 (PBP4) functions as a transpeptidase, and belongs to MEROPS peptidase family S11 (clan SE). PBP4 acts co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents []. This entry represents the C-terminal domain PBP4.; PDB: 1TVF_A 3HUN_A 3HUM_B.
Probab=50.21 E-value=43 Score=24.63 Aligned_cols=38 Identities=26% Similarity=0.440 Sum_probs=23.6
Q ss_pred ceeEeeeEEEcCeeeE----EEEEcCCce-EEEEEEeCCEEEE
Q 025184 192 KVLSMDVEELCGRKYY----RYELEPPHV-LITATAAGNRLYL 229 (256)
Q Consensus 192 ~ll~a~~r~~dG~~YY----~yEl~~pH~-L~satv~~GrLYt 229 (256)
++|+..+.+.||++|| .|+...... --...+.+|+|++
T Consensus 3 KvLskG~h~IdGk~y~v~kDlYd~VpK~~~~~~~~v~dg~v~v 45 (65)
T PF09211_consen 3 KVLSKGEHTIDGKKYYVKKDLYDVVPKGKKPYKLKVKDGKVHV 45 (65)
T ss_dssp EEE-SEEEEETTEEEEESS-EEEEEETT--GSEEEEETTEEEE
T ss_pred ccccCccEEECCEEEEecCChhhhccCCCccceEEEeCCEEEE
Confidence 5788889999999997 355431111 1245567787765
No 20
>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=44.22 E-value=23 Score=21.49 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=9.6
Q ss_pred chhHHHHHHHHHH
Q 025184 41 MKRRSVLVSGASL 53 (256)
Q Consensus 41 ~sRR~aL~~~~~~ 53 (256)
++||++|-..++.
T Consensus 1 ~sRR~Flk~~~~~ 13 (29)
T TIGR01409 1 LSRRDFLKGAAAA 13 (29)
T ss_pred CchhhhHHHHHHH
Confidence 4899999866543
No 21
>PF14030 DUF4245: Protein of unknown function (DUF4245)
Probab=43.86 E-value=2e+02 Score=24.46 Aligned_cols=100 Identities=12% Similarity=0.252 Sum_probs=57.3
Q ss_pred cCCCCeecccccccCCC-CceeEEEeCCCCCeEEEEEEecccccccCCCcccccccCCHHHHHHHhCccccCCCccccee
Q 025184 116 VPQEWDEVPVSIADLGG-TEIDLRFASPKKGRLFVIVAPVLRFADDLGDDATIEKIGPPEKVINAFGPEVIGENVEGKVL 194 (256)
Q Consensus 116 ~P~gW~e~~vs~~D~~~-~g~d~rF~d~~~~~vsVvv~p~~rl~~~~~~~~sI~dlGspeev~~~l~~~~~g~~~~a~ll 194 (256)
+|.+|+....+-...++ ....+-|..+.+.=+++.-+.. +.+++...+.. ... +
T Consensus 63 lP~gW~~nSar~~~~~g~~~w~vG~vt~~~~yv~l~Qs~~-----------------~~~~~v~~~~~----~~~--~-- 117 (169)
T PF14030_consen 63 LPEGWKANSARRQGVGGVPAWHVGYVTPDGQYVQLTQSDA-----------------PEDTWVASVTG----NAR--E-- 117 (169)
T ss_pred CCCCceeeeEEecCCCCcceEEEEEEcCCCCEEEEEEcCC-----------------CHHHHHHHhhC----CCC--C--
Confidence 78899986654333333 4556677777776566655541 44555555422 221 1
Q ss_pred EeeeEEEcCeeeEEEEEc-CC-ceEEEEEEeCCEEEEEEEecCccchHhhh
Q 025184 195 SMDVEELCGRKYYRYELE-PP-HVLITATAAGNRLYLFSVTGNGLQWKRHY 243 (256)
Q Consensus 195 ~a~~r~~dG~~YY~yEl~-~p-H~L~satv~~GrLYtl~~~a~e~rW~k~~ 243 (256)
..+++.+|++.=.|+=. .. +.|+.- .++-=.++.-++++.+..+..
T Consensus 118 -~gt~~i~G~~W~~y~~~~~~~~a~v~~--~~~~t~vVtG~A~~~el~~lA 165 (169)
T PF14030_consen 118 -TGTRTIGGRTWQVYEGPDDGRDAWVRD--LGDVTVVVTGTASDEELETLA 165 (169)
T ss_pred -CccEEECCEEEEEEECCCCCcEEEEEe--cCCcEEEEEecCCHHHHHHHH
Confidence 45778999988777764 23 333332 355555556666665544443
No 22
>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=38.17 E-value=36 Score=20.06 Aligned_cols=22 Identities=14% Similarity=0.403 Sum_probs=18.0
Q ss_pred EEEeCCEEEEEEEecCccchHh
Q 025184 220 ATAAGNRLYLFSVTGNGLQWKR 241 (256)
Q Consensus 220 atv~~GrLYtl~~~a~e~rW~k 241 (256)
++-.+|+||.+.+...+.+|..
T Consensus 11 ~~~~~g~l~a~d~~~G~~~W~~ 32 (33)
T smart00564 11 VGSTDGTLYALDAKTGEILWTY 32 (33)
T ss_pred EEcCCCEEEEEEcccCcEEEEc
Confidence 3456799999999999999963
No 23
>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=36.06 E-value=33 Score=22.87 Aligned_cols=13 Identities=23% Similarity=0.092 Sum_probs=7.0
Q ss_pred cccchhHHHHHHH
Q 025184 38 DGVMKRRSVLVSG 50 (256)
Q Consensus 38 ~~~~sRR~aL~~~ 50 (256)
....+||.+|..+
T Consensus 6 ~~~~~RRdFL~~a 18 (41)
T PF10399_consen 6 PVDPTRRDFLTIA 18 (41)
T ss_dssp ----HHHHHHHHH
T ss_pred CCCchHHHHHHHH
Confidence 3456899999543
No 24
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=28.79 E-value=2.4e+02 Score=22.58 Aligned_cols=47 Identities=13% Similarity=0.111 Sum_probs=27.5
Q ss_pred cccccccCCHHHHHHHhCccccCCCc--ccceeEeeeEEEc-CeeeEEEEEc
Q 025184 164 DATIEKIGPPEKVINAFGPEVIGENV--EGKVLSMDVEELC-GRKYYRYELE 212 (256)
Q Consensus 164 ~~sI~dlGspeev~~~l~~~~~g~~~--~a~ll~a~~r~~d-G~~YY~yEl~ 212 (256)
--.|.-||..-|.+...+.+ |..+ +++|-.-+-.+.| |+.+|..|+.
T Consensus 45 w~~v~~wg~~Ae~~~~~l~K--G~~V~V~G~l~~~~~~d~d~G~~r~~~ei~ 94 (121)
T PRK07459 45 WFNLEIWGKTAQVAADYVKK--GSLIGITGSLKFDRWTDRNTGEDRSKPVIR 94 (121)
T ss_pred EEEEEEehHHHHHHHHHcCC--CCEEEEEEEEEecceEcCCCCeEEEEEEEE
Confidence 34678888654444433232 5543 4555433333445 9999999985
No 25
>TIGR03512 GldD_lipo gliding motility-associated lipoprotein GldD. Members of this protein family are found a number of Bacteriodetes lineage bacteria, including both species such as Flavobacterium johnsoniae, which possess a poorly understood form of rapid gliding motility, and other species which apparently do not. Mutation of GldD blocks both this motility and chitin utilization in the model species, Flavobacterium johnsoniae.
Probab=27.59 E-value=4.3e+02 Score=23.33 Aligned_cols=149 Identities=15% Similarity=0.197 Sum_probs=71.5
Q ss_pred CCCCceeeeccCCCCCCCCCCCccccceEEecCCCCeecccccccCCCCceeEEEeCCCCCeEEEEEEecccccccCCCc
Q 025184 85 DEQGWRTYRRPDDKSGGHGVGWSPIIPYLFSVPQEWDEVPVSIADLGGTEIDLRFASPKKGRLFVIVAPVLRFADDLGDD 164 (256)
Q Consensus 85 ~~~gf~~y~~p~d~~gg~g~~~~~~~~Ysf~~P~gW~e~~vs~~D~~~~g~d~rF~d~~~~~vsVvv~p~~rl~~~~~~~ 164 (256)
+..||....=|..++.-. ..--||+|+++.-=+..+. .+.+..|+.+-| +..+.+|.+.-.|++ .
T Consensus 24 KPkgylrleyP~~~Y~~~----~~~cPytFe~n~~A~v~~~--~~~~~cw~~i~Y-P~~ka~i~lTYkpV~-------~- 88 (186)
T TIGR03512 24 KPKGFLKLDYPEAKYDTL----TGDCPYTFEYNSIAKIVPT--KTAEPCWIDIYY-PEMKANIQITYKPVN-------N- 88 (186)
T ss_pred CCCceeeeeCChHHhhcc----cCCCCceEeccccceeeec--ccCCCceEEEEc-cccceEEEEEEEech-------h-
Confidence 336777664444333310 0112799999875553332 223334555533 334457777778862 1
Q ss_pred ccccccCCHHHHHHHhCccccCCCcccceeEeeeEE-EcCeee-EEEEEcCC----c-eEEEEEEe---CCEEEEEEEec
Q 025184 165 ATIEKIGPPEKVINAFGPEVIGENVEGKVLSMDVEE-LCGRKY-YRYELEPP----H-VLITATAA---GNRLYLFSVTG 234 (256)
Q Consensus 165 ~sI~dlGspeev~~~l~~~~~g~~~~a~ll~a~~r~-~dG~~Y-Y~yEl~~p----H-~L~satv~---~GrLYtl~~~a 234 (256)
..+++++---+-...-.+.|+.|+.+... .+.+.| -.||+... . ..+|=.++ .|-||==..--
T Consensus 89 -------nl~~ll~Da~kl~~kH~iKA~~I~e~~~~n~~~~vyG~~yev~GnaASq~QFy~TDSt~HFl~GaLYF~~~Pn 161 (186)
T TIGR03512 89 -------NLEELLKDAQKLANKHNIKADAIDEDVYINDTKNGYGMFYEVDGDAASQIQFYVTDSTKHFLRGSVYFRTSPN 161 (186)
T ss_pred -------hHHHHHHHHHHHhHhceecccccccceeecCCCceEEEEEEEecCCCccceEEEeccccceeeeeEEEccCCC
Confidence 12333321100011122345555544333 333444 35666432 1 11221122 26677544444
Q ss_pred CccchHhh---hHHHHHHhhcccc
Q 025184 235 NGLQWKRH---YTDLKKIADSFRV 255 (256)
Q Consensus 235 ~e~rW~k~---~~~Lr~v~~SFrv 255 (256)
.++--.-. +++++++++||+.
T Consensus 162 ~DSi~Pa~~Yik~Di~~lmeTl~W 185 (186)
T TIGR03512 162 FDSIAPAASYMKEDVMHLMETLKW 185 (186)
T ss_pred ccchhHHHHHHHHHHHHHHHhccc
Confidence 45544443 7899999999974
No 26
>PF15495 Fimbrillin_C: Major fimbrial subunit protein type IV, Fimbrillin, C-terminal
Probab=25.35 E-value=1.5e+02 Score=22.50 Aligned_cols=33 Identities=24% Similarity=0.301 Sum_probs=25.8
Q ss_pred EcCeeeEEEEEcC-----C--ceEEEEEEeCCEEEEEEEe
Q 025184 201 LCGRKYYRYELEP-----P--HVLITATAAGNRLYLFSVT 233 (256)
Q Consensus 201 ~dG~~YY~yEl~~-----p--H~L~satv~~GrLYtl~~~ 233 (256)
.+|..||.+.+.- + ..++-.+|-+|..|.|+++
T Consensus 5 ~~G~~YY~~~I~h~d~~~~~~~~~~~y~IvRNn~Y~l~I~ 44 (85)
T PF15495_consen 5 ENGVCYYYYWINHNDNNNPATMGQGEYGIVRNNVYKLTIT 44 (85)
T ss_pred eCCEEEEEEEecCCCCCcccccccceeceEeccEEEEEEE
Confidence 6899999999853 1 3455567888999999986
No 27
>KOG4649 consensus PQQ (pyrrolo-quinoline quinone) repeat protein [Secondary metabolites biosynthesis, transport and catabolism]
Probab=24.54 E-value=76 Score=29.99 Aligned_cols=42 Identities=14% Similarity=0.198 Sum_probs=34.8
Q ss_pred EcCeeeEEEEEcCC--------ceEEEEEEeCCEEEEEEEecCccchHhh
Q 025184 201 LCGRKYYRYELEPP--------HVLITATAAGNRLYLFSVTGNGLQWKRH 242 (256)
Q Consensus 201 ~dG~~YY~yEl~~p--------H~L~satv~~GrLYtl~~~a~e~rW~k~ 242 (256)
..|..|++=++..+ .+++++...+|+||-+...+.++-|.-.
T Consensus 41 ~sG~~~We~ilg~RiE~sa~vvgdfVV~GCy~g~lYfl~~~tGs~~w~f~ 90 (354)
T KOG4649|consen 41 QSGNLIWEAILGVRIECSAIVVGDFVVLGCYSGGLYFLCVKTGSQIWNFV 90 (354)
T ss_pred CCCcEEeehhhCceeeeeeEEECCEEEEEEccCcEEEEEecchhheeeee
Confidence 57888888777543 5778999999999999999999999743
No 28
>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=23.85 E-value=51 Score=30.83 Aligned_cols=14 Identities=29% Similarity=0.724 Sum_probs=12.4
Q ss_pred eEEecCCCCeeccc
Q 025184 112 YLFSVPQEWDEVPV 125 (256)
Q Consensus 112 Ysf~~P~gW~e~~v 125 (256)
|+|.||.||++..-
T Consensus 119 FS~vvP~GW~~Sda 132 (297)
T PF07174_consen 119 FSYVVPAGWVESDA 132 (297)
T ss_pred eEEeccCCcccccc
Confidence 99999999997664
No 29
>PLN00064 photosystem II protein Psb27; Provisional
Probab=23.21 E-value=1.1e+02 Score=26.43 Aligned_cols=16 Identities=19% Similarity=0.210 Sum_probs=10.7
Q ss_pred ccccchhHHHHHHHHH
Q 025184 37 VDGVMKRRSVLVSGAS 52 (256)
Q Consensus 37 ~~~~~sRR~aL~~~~~ 52 (256)
.....+||++|..+.+
T Consensus 30 ~~~~~~rr~~~~~~~~ 45 (166)
T PLN00064 30 RRNHLLRREFLSLATT 45 (166)
T ss_pred hhhhhHHHHHHHHHHH
Confidence 3456689999885433
No 30
>PF13964 Kelch_6: Kelch motif
Probab=20.84 E-value=96 Score=20.17 Aligned_cols=19 Identities=26% Similarity=0.536 Sum_probs=14.4
Q ss_pred EEEEEeCCEEEEEEEecCc
Q 025184 218 ITATAAGNRLYLFSVTGNG 236 (256)
Q Consensus 218 ~satv~~GrLYtl~~~a~e 236 (256)
.++++.+|+||++.-..+.
T Consensus 5 ~s~v~~~~~iyv~GG~~~~ 23 (50)
T PF13964_consen 5 HSAVVVGGKIYVFGGYDNS 23 (50)
T ss_pred CEEEEECCEEEEECCCCCC
Confidence 4556788999999877663
No 31
>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=20.33 E-value=50 Score=28.00 Aligned_cols=22 Identities=18% Similarity=0.505 Sum_probs=17.5
Q ss_pred CCcccccccCCHHHHHHHhCcc
Q 025184 162 GDDATIEKIGPPEKVINAFGPE 183 (256)
Q Consensus 162 ~~~~sI~dlGspeev~~~l~~~ 183 (256)
++..-+++||+|+++++.+..+
T Consensus 42 sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 42 SEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred CHHHHHHHcCCHHHHHHHHHHh
Confidence 3456789999999999988543
Done!