Query 022978
Match_columns 289
No_of_seqs 168 out of 230
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:33:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022978.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022978hhsearch_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 1E-49 2.2E-54 366.1 18.7 233 12-273 38-286 (286)
2 PLN00042 photosystem II oxygen 100.0 1.5E-48 3.3E-53 358.4 18.0 199 49-271 47-259 (260)
3 PLN00067 PsbP domain-containin 100.0 2.4E-36 5.2E-41 277.5 16.9 140 88-271 102-263 (263)
4 PF01789 PsbP: PsbP; InterPro 100.0 3.2E-36 7E-41 262.4 12.8 155 78-272 18-175 (175)
5 PLN00066 PsbP domain-containin 100.0 1.2E-31 2.5E-36 248.0 16.1 136 87-273 109-260 (262)
6 PLN03152 hypothetical protein; 99.9 6.5E-26 1.4E-30 204.4 13.6 180 38-272 26-241 (241)
7 PF08786 DUF1795: Domain of un 97.5 0.0033 7.1E-08 51.9 12.5 69 193-269 61-130 (130)
8 PRK11615 hypothetical protein; 89.4 16 0.00035 33.0 14.8 99 146-271 84-184 (185)
9 COG5435 Uncharacterized conser 87.5 7 0.00015 34.2 9.9 76 194-275 69-145 (147)
10 PF12712 DUF3805: Domain of un 81.2 22 0.00048 31.1 10.0 133 83-278 1-137 (153)
11 PF10738 Lpp-LpqN: Probable li 68.7 50 0.0011 29.5 9.4 70 195-272 101-174 (175)
12 PF07174 FAP: Fibronectin-atta 62.1 1.1E+02 0.0024 29.7 10.7 22 84-105 110-132 (297)
13 smart00564 PQQ beta-propeller 60.3 10 0.00022 23.3 2.5 23 234-256 9-31 (33)
14 PF10518 TAT_signal: TAT (twin 42.4 21 0.00046 22.1 1.9 20 52-71 2-21 (26)
15 PF07009 DUF1312: Protein of u 39.4 1E+02 0.0022 25.1 6.0 47 202-258 32-85 (113)
16 PF01011 PQQ: PQQ enzyme repea 38.0 18 0.00039 23.6 1.1 23 236-258 5-27 (38)
17 PF09211 DUF1958: Domain of un 35.8 29 0.00062 26.5 2.0 17 194-210 3-19 (65)
18 PF00031 Cystatin: Cystatin do 33.8 62 0.0013 24.6 3.7 47 169-217 14-60 (94)
19 PLN00059 PsbP domain-containin 31.5 41 0.00089 32.4 2.7 42 135-179 140-181 (286)
20 PLN00064 photosystem II protei 25.2 78 0.0017 28.3 3.2 36 48-83 30-66 (166)
21 TIGR02811 formate_TAT formate 24.5 52 0.0011 24.8 1.8 11 49-59 6-16 (66)
22 KOG4649 PQQ (pyrrolo-quinoline 22.6 63 0.0014 31.5 2.3 49 204-258 42-90 (354)
23 PF14326 DUF4384: Domain of un 20.8 93 0.002 23.7 2.5 57 228-288 6-63 (83)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=100.00 E-value=1e-49 Score=366.07 Aligned_cols=233 Identities=19% Similarity=0.250 Sum_probs=201.5
Q ss_pred CccccccCCCccccccccccCCCCceeeeccCCCccccccchhHHHHHHHHH--hhhhccCCCCCCCcccccCcceeeeC
Q 022978 12 RLHFIRNHRGSIVQGQKNCRLNNKAIVCSCASSKPIQQNGFCRRDLVLFGLS--SSLSLGFPTPGSVAGEDVKMASFVDE 89 (289)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~rR~~ll~gl~--~~~a~~~p~~~A~A~~a~~f~~~~D~ 89 (289)
++.+.||+++++.++.++++.+...+...|.. +.+..+++.||.+|+.++. ...+.......|+|. .++|+.|+|+
T Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~rr~~~~~~l~~~~~~~s~~~~~~a~a~-~~~l~~y~D~ 115 (286)
T PLN00059 38 HLLFSRPISSGPKHQSAKSAKPDSPVAINCLT-DAKQVCAVGRRKSMMMGLLMSGLIVSEANLPTAFAS-IPVFREYIDT 115 (286)
T ss_pred hhhccccccCCcccccccccCCCCCeeeeccc-chhhhhhhhhhhhhHHHHHHHHHHHHhhcCchhhcC-CcccceeEcC
Confidence 47789999999999999999999899888885 5667899999999887664 333333444477775 4569999999
Q ss_pred CCceEEeccCCCCCcceeccccccccccccCCCCCCCCCcceeeec----cccccccceeEEEEeCCchhhhhcccCccc
Q 022978 90 INAYTYLYPMELPSKKFLFKWVESRKPERYSSAAPLSPNARLRIVS----ERVDIIDNLIISVTIGPPNVQFLKSKDKST 165 (289)
Q Consensus 90 ~dGYsF~YP~~W~s~e~~~~g~~~r~~D~~~s~apLs~nvrv~iv~----e~~~i~dn~~Vsvs~GPp~~~~l~~~d~~~ 165 (289)
.|||+|+||.+| .+|...|+|++|+|.++. ++|++|.|.+ +.++|.| +|+|+++.
T Consensus 116 ~DGY~FlYP~GW--i~V~~~G~DVvFrD~Ie~----~ENVSV~ISs~sss~~~sLeD-------LGsP~eVg-------- 174 (286)
T PLN00059 116 FDGYSFKYPQNW--IQVRGAGADIFFRDPVVL----DENLSVEFSSPSSSKYTSLED-------LGSPEEVG-------- 174 (286)
T ss_pred CCCeEEeCCCCC--eEeccCCCceEEeccCcc----ccceEEEEecCCcccCCChHH-------cCCHHHHH--------
Confidence 999999999999 788889999999999984 3899999875 4799999 99999877
Q ss_pred cchHHHHHhhhccccccccccccccccccEEeeeecee-CCeeeEEEEEEEecC---------CCCCCCCCCCcceEEEE
Q 022978 166 WNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKV-DGEPYWFYEYLIRKS---------PTNLGQEPNLYRHYVAS 235 (289)
Q Consensus 166 ~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~-dGk~YY~~Ey~v~~~---------p~~~a~~~e~~RH~La~ 235 (289)
|.|.+++|+++++.|. |.+ ++++||+|++|+. ||++||+|||.+++. ++++.+.++|.||+|++
T Consensus 175 ---erLlkqvLa~f~str~--Gsg-ReaeLVsA~~Re~~DGktYY~lEY~Vks~~~~n~~~~~~qdr~~~~~w~RH~LA~ 248 (286)
T PLN00059 175 ---KRVLRQYLTEFMSTRL--GVK-REANILSTSSRVADDGKLYYQVEVNIKSYANNNELAVMPQDRVARLEWNRRYLAV 248 (286)
T ss_pred ---HHHHHHHhcccccccC--CCC-cceEEEEeeeEEccCCcEEEEEEEEEEcCcccccccccccccccccccceeeEEE
Confidence 8999999998766444 222 2599999999977 999999999999984 67788889999999999
Q ss_pred EEEECCEEEEEEeecCcchhhhhchhHHHhhcceeEcC
Q 022978 236 TAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHLLP 273 (289)
Q Consensus 236 ~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~~ 273 (289)
++|+|||||||++|+||+||.|+++.|++||+||+|.+
T Consensus 249 v~V~nGkLYTL~~qtpE~RW~kvk~~f~~V~dSF~V~~ 286 (286)
T PLN00059 249 LGVENDRLYSIRLQTPEKVFLEEEKDLRRVMDSFRVEK 286 (286)
T ss_pred EEEeCCEEEEEEcCCcHHHHHHHHHHHHHHHhheeecC
Confidence 99999999999999999999999999999999999974
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=1.5e-48 Score=358.37 Aligned_cols=199 Identities=20% Similarity=0.306 Sum_probs=168.0
Q ss_pred cccchhHHHHHHHHHh--hhhccCCCCCCCcccccCcceee-------eCCCceEEeccCCC-CCcceeccccccccccc
Q 022978 49 QNGFCRRDLVLFGLSS--SLSLGFPTPGSVAGEDVKMASFV-------DEINAYTYLYPMEL-PSKKFLFKWVESRKPER 118 (289)
Q Consensus 49 ~~~~~rR~~ll~gl~~--~~a~~~p~~~A~A~~a~~f~~~~-------D~~dGYsF~YP~~W-~s~e~~~~g~~~r~~D~ 118 (289)
...+.||++|+.++++ .++.+.|+++||||++++|++.. .++|||+|+||.+| +++++.++|+|++|+|+
T Consensus 47 ~~~~srr~~l~~~~ga~a~~~~~~pa~aay~~~anvfg~~k~~~gF~~y~~dgY~FlyP~~W~~~ke~~~~G~dv~f~D~ 126 (260)
T PLN00042 47 NSAVSRRAALALLAGAAAAGAKVSPANAAYGESANVFGKPKTNTGFLPYNGDGFKLLVPSKWNPSKEREFPGQVLRFEDN 126 (260)
T ss_pred cccccHHHHHHHHHHHHHhhcccCchhhhhcchhhccCCCCCCCCCeEeeCCCeEEecCCCCccccccccCCceEEeecc
Confidence 3556677666554444 34778999999999987766532 15699999999999 77888999999999999
Q ss_pred cCCCCCCCCCcceeeec-cccccccceeEEEEeCCchhhhhcccCccccchHHHHHhhhccc--cccccccccccccccE
Q 022978 119 YSSAAPLSPNARLRIVS-ERVDIIDNLIISVTIGPPNVQFLKSKDKSTWNAKDVADSVLSDK--SALRVTSSQRMAESSV 195 (289)
Q Consensus 119 ~~s~apLs~nvrv~iv~-e~~~i~dn~~Vsvs~GPp~~~~l~~~d~~~~~~~~la~~vLa~~--ssgr~~~g~rv~~a~l 195 (289)
|+.. +|++|+|.+ ++++|.| +|+|++ |++.++ +.|++++++++ +++++ .++.+++++|
T Consensus 127 ~~~~----eNVSV~Ispt~k~sI~d-------lGsPee-~l~~vg------ylL~kq~~a~~t~s~~Gf-~p~~vata~L 187 (260)
T PLN00042 127 FDAT----SNLSVMVTPTDKKSITD-------YGSPEE-FLSKVS------YLLGKQAYSGETASEGGF-DANAVATAAV 187 (260)
T ss_pred cccc----ccEEEEEecCCcCCHhh-------cCCHHH-HHHHHH------HHHHhhhccCccccccCc-CcccccceeE
Confidence 9943 888999988 8899999 999986 555544 67899999887 23334 3666778999
Q ss_pred EeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcceEEEEEEEECCEEEEEEeecCcchhhhh-chhHHHhhcceeE
Q 022978 196 LDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYRHYVASTAEREGYLYSISASTLGKQWDEM-GPFLEKSVASFHL 271 (289)
Q Consensus 196 l~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~-~~~l~~vv~SFrv 271 (289)
|+++++++||++||+|||.+++ +++++++||+|+++||+|||||||++|+||+||+|+ ++.|++|++||+|
T Consensus 188 leas~re~dGk~YY~lE~~~~~-----ad~d~~~RH~LatatV~~GkLYtl~aqa~EkRW~K~~~k~l~~v~~SFsV 259 (260)
T PLN00042 188 LESSTQEVGGKPYYYLSVLTRT-----ADGDEGGKHQLITATVSDGKLYICKAQAGDKRWFKGARKFVEGAASSFSV 259 (260)
T ss_pred EEeeeEEeCCeEEEEEEEEEec-----CCCCCCCceEEEEEEEECCEEEEEEecCchhhhhHHHHHHHHHHHhceec
Confidence 9999999999999999999998 778899999999999999999999999999999998 5679999999997
No 3
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=100.00 E-value=2.4e-36 Score=277.45 Aligned_cols=140 Identities=17% Similarity=0.299 Sum_probs=120.8
Q ss_pred eCCCceEEeccCCCCCcceecc---------------ccccccccccCCCCCCCCCcceeeec-------ccccccccee
Q 022978 88 DEINAYTYLYPMELPSKKFLFK---------------WVESRKPERYSSAAPLSPNARLRIVS-------ERVDIIDNLI 145 (289)
Q Consensus 88 D~~dGYsF~YP~~W~s~e~~~~---------------g~~~r~~D~~~s~apLs~nvrv~iv~-------e~~~i~dn~~ 145 (289)
.++.||+|+||.+| +++.++ |+|.+|+|+++ .|++|.|.+ +.++|+|
T Consensus 102 ~~i~gY~FlyP~gW--~~v~Vs~~~sGnycqp~c~~p~~dv~F~D~~d------gnVSVIVSPV~r~t~k~~~sIeD--- 170 (263)
T PLN00067 102 GNVQPYQFILPPTW--KQTRVANILSGNYCQPKCAEPWVEVKFEDEKQ------GKVQVVASPLIRLTNKPNATIEE--- 170 (263)
T ss_pred CCcccceEeCCCCC--cCccccccccCccccccccCCCceEEEeCCCC------CCEEEEEecccccccCCCCChHH---
Confidence 37899999999999 554443 58999999775 788888765 3478999
Q ss_pred EEEEeCCchhhhhcccCccccchHHHHHhhhccccccccccccccccccEEeeeeceeCCeeeEEEEEEEecCCCCCCCC
Q 022978 146 ISVTIGPPNVQFLKSKDKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQE 225 (289)
Q Consensus 146 Vsvs~GPp~~~~l~~~d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~ 225 (289)
+|+|++.+ +.|++.+++. ..++++||+|++++.||++||+|||.+++
T Consensus 171 ----lGsPeeVl-----------~~Lg~~v~g~----------~~~~~eLLeAs~re~dGktYY~~E~~tp~-------- 217 (263)
T PLN00067 171 ----IGSPEKLI-----------ASLGPFVTGN----------SYDPDELLETSVEKIGDQTYYKYVLETPF-------- 217 (263)
T ss_pred ----ccCHHHHH-----------HHhhHHhhcC----------CCCCcceEEeeeEeeCCeEEEEEEEEecC--------
Confidence 99999755 6677777641 22448999999999999999999999988
Q ss_pred CCCcceEEEEEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeE
Q 022978 226 PNLYRHYVASTAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHL 271 (289)
Q Consensus 226 ~e~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv 271 (289)
.+++||+|+++||++||||||++|++|+||+|+++.|++|++||+|
T Consensus 218 a~~gRHnLataTV~~GkLYtf~asanEkRW~K~k~~l~~V~dSFsV 263 (263)
T PLN00067 218 ALTGSHNLAKATAKGNTVVLFVVSASDKQWQSSEKTLKAILDSFQA 263 (263)
T ss_pred CCCCceEEEEEEEECCEEEEEEecCCHHHHHHHHHHHHHHHHhccC
Confidence 7799999999999999999999999999999999999999999986
No 4
>PF01789 PsbP: PsbP; InterPro: IPR002683 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbP. Both PsbP and PsbQ (IPR008797 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [, ]. The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity []. PsbP is encoded in the nuclear genome in plants.; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 2VU4_A 1V2B_A 2LNJ_A 2XB3_A.
Probab=100.00 E-value=3.2e-36 Score=262.41 Aligned_cols=155 Identities=24% Similarity=0.456 Sum_probs=132.9
Q ss_pred ccccCcceeeeCCCceEEeccCCCCCcceeccccccccccccCCCCCCCCCcceeeec--cccccccceeEEEEeCCchh
Q 022978 78 GEDVKMASFVDEINAYTYLYPMELPSKKFLFKWVESRKPERYSSAAPLSPNARLRIVS--ERVDIIDNLIISVTIGPPNV 155 (289)
Q Consensus 78 ~~a~~f~~~~D~~dGYsF~YP~~W~s~e~~~~g~~~r~~D~~~s~apLs~nvrv~iv~--e~~~i~dn~~Vsvs~GPp~~ 155 (289)
+...+|..|.|+.+||+|+||.+| .++...|++.+|+|.++. . +|++|.|.+ ...+|.| +|+|++
T Consensus 18 ~~~~~~~~y~d~~~~y~f~~P~gW--~~~~~~G~~v~f~d~~~~---~-~nvsV~v~p~~~~~sl~~-------lGs~~~ 84 (175)
T PF01789_consen 18 EASTGFQPYTDSDDGYSFLYPSGW--EEVDVSGADVVFRDPIDA---D-ENVSVVVSPVPKDFSLED-------LGSPEE 84 (175)
T ss_dssp T--SSEEEEEECTTTEEEEEETTE--EEEESTTEEEEEEETTET---T-SEEEEEEEE-STS-SGGG-------G-SHHH
T ss_pred cCCCCceEEEcCCCCEEEECCCCC--eecCCCCeEEEEECcccc---c-ceEEEEEEecCCcCchhh-------cCCHHH
Confidence 335669999999999999999999 788889999999999983 2 788888877 3338999 999987
Q ss_pred hhhcccCccccchHHHHHhhhccccccccccccccccccEEeeeeceeCCeeeEEEEEEEecCCCCCCCCCC-CcceEEE
Q 022978 156 QFLKSKDKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPN-LYRHYVA 234 (289)
Q Consensus 156 ~~l~~~d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e-~~RH~La 234 (289)
.. +.+++..+..+.+++ .++||++++++.||++||+|||.+++ ++ ..||+|+
T Consensus 85 va-----------~~l~~~~~~~~~~~~--------~a~li~a~~~~~~g~~yY~~Ey~~~~--------~~~~~rh~l~ 137 (175)
T PF01789_consen 85 VA-----------ERLLNGELASPGSGR--------EAELISASEREVDGKTYYEYEYTVQS--------PNEGRRHNLA 137 (175)
T ss_dssp HH-----------HHHHHHCCCHCTSSE--------EEEEEEEEEEEETTEEEEEEEEEEEE--------TTEEEEEEEE
T ss_pred HH-----------HHHhhhhcccccCCc--------ceEEEEeeeeecCCccEEEEEEEecc--------CCCcccEEEE
Confidence 55 778888777666543 39999999999999999999999988 54 8999999
Q ss_pred EEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeEc
Q 022978 235 STAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHLL 272 (289)
Q Consensus 235 ~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~ 272 (289)
+++++|||||+|++|++|+||+|+++.|++|++||+|+
T Consensus 138 ~~tv~~g~lY~l~~~a~e~~w~k~~~~l~~iv~SF~v~ 175 (175)
T PF01789_consen 138 VVTVKNGKLYTLTAQAPESRWDKVEPKLRKIVDSFRVY 175 (175)
T ss_dssp EEEEETTEEEEEEEEEEHHHHHTCHHHHHHHHHC-EE-
T ss_pred EEEEECCEEEEEEEEcCHHHHHHHHHHHHHHHhcEEeC
Confidence 99999999999999999999999999999999999985
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.97 E-value=1.2e-31 Score=248.03 Aligned_cols=136 Identities=18% Similarity=0.369 Sum_probs=112.6
Q ss_pred eeCCCceEEeccCCCCCcceecc-----c--cccccccccCCCCCCCCCcceeeec---------cccccccceeEEEEe
Q 022978 87 VDEINAYTYLYPMELPSKKFLFK-----W--VESRKPERYSSAAPLSPNARLRIVS---------ERVDIIDNLIISVTI 150 (289)
Q Consensus 87 ~D~~dGYsF~YP~~W~s~e~~~~-----g--~~~r~~D~~~s~apLs~nvrv~iv~---------e~~~i~dn~~Vsvs~ 150 (289)
+.++..|+|+||.+| +|+.++ | +|.||.+.- +.|++|.|.+ ++++|.| |
T Consensus 109 ~~~i~~Y~F~yP~GW--~ev~VS~~d~gg~~vd~Rf~~~~------~~nvsVvVspv~rla~~~~~~~sI~d-------L 173 (262)
T PLN00066 109 WSEITPYSFKVPQGW--EEVPVSIADLGGTEIDLRFASDK------EGRLKVVVAPVLRFADNLGDNATIEE-------I 173 (262)
T ss_pred ccccCCeEEECCCCC--eEeecccccCCCCceEEEeccCC------CccEEEEEeccccccccccCCCChHH-------c
Confidence 347799999999999 666665 3 556666522 2788887765 5678888 9
Q ss_pred CCchhhhhcccCccccchHHHHHhhhccccccccccccccccccEEeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcc
Q 022978 151 GPPNVQFLKSKDKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYR 230 (289)
Q Consensus 151 GPp~~~~l~~~d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~R 230 (289)
|||++++ +.+++.++... .++++||++++++.||++||+||| . |
T Consensus 174 GspeeVi-----------~~l~~~v~g~~----------~~e~eLl~a~~re~dGktYY~~E~---~------------r 217 (262)
T PLN00066 174 GPPEKVI-----------SGFGPELIGEP----------VEEGKVLSMEVAEHSGRTYYQFEL---P------------P 217 (262)
T ss_pred CCHHHHH-----------HHHHHHhcCCC----------ccccceeEeeeeecCCcEEEEEEE---e------------C
Confidence 9999765 66777776332 345899999999999999999998 1 6
Q ss_pred eEEEEEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeEcC
Q 022978 231 HYVASTAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHLLP 273 (289)
Q Consensus 231 H~La~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~~ 273 (289)
|+|+++||.+||||||++|+||+||+|++++|++|++||+|+.
T Consensus 218 H~LasaTV~~GrLYt~~asape~rW~k~~~~lr~v~dSF~V~~ 260 (262)
T PLN00066 218 HTLVTATAAGNRVYIFSVTANGLQWKRHYKDLKRIAKSFRVVT 260 (262)
T ss_pred ceEEEEEEECCEEEEEEeecchHhhHHHHHHHHHHhhceeeec
Confidence 9999999999999999999999999999999999999999963
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.93 E-value=6.5e-26 Score=204.38 Aligned_cols=180 Identities=23% Similarity=0.325 Sum_probs=113.5
Q ss_pred eeeccCCCccccccchhHHHHHHHHH--h-hhhccCCCCCCCcccccC----cce-------eeeCCCceEEeccCCCCC
Q 022978 38 VCSCASSKPIQQNGFCRRDLVLFGLS--S-SLSLGFPTPGSVAGEDVK----MAS-------FVDEINAYTYLYPMELPS 103 (289)
Q Consensus 38 ~c~~~~~~~~~~~~~~rR~~ll~gl~--~-~~a~~~p~~~A~A~~a~~----f~~-------~~D~~dGYsF~YP~~W~s 103 (289)
.|+|.. .||++++-.++ + +++.--|...++|+..+. ..- |.--++||+.-||-++
T Consensus 26 ~~~~~~---------~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~~g~gf~~~~pp~f-- 94 (241)
T PLN03152 26 LSRCGA---------SRRDFILHTASLCASSLAAQNPLPPSLADPSKPSKPLLSGIANTKSWFQFYGDGFSIRVPPSF-- 94 (241)
T ss_pred cccccc---------cccceeeehhHHHHhhhhcCCCCCccccCCCCCCCchheeeecchhhhhhhCCceEEeCCCCh--
Confidence 466765 36887763332 1 122233455666655322 111 2236899999999998
Q ss_pred cce----ecccccccccc---------ccCCCCCCCCCcceeeec---------cccccccceeEEEEeCCchhhhhccc
Q 022978 104 KKF----LFKWVESRKPE---------RYSSAAPLSPNARLRIVS---------ERVDIIDNLIISVTIGPPNVQFLKSK 161 (289)
Q Consensus 104 ~e~----~~~g~~~r~~D---------~~~s~apLs~nvrv~iv~---------e~~~i~dn~~Vsvs~GPp~~~~l~~~ 161 (289)
+.+ ++..--+-|-| ||.|.- -++|++|.|.+ +.+||.| +|+|
T Consensus 95 ~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~D-~sEnVSVVIspv~~LK~tfle~kDLtD-------LGsp-------- 158 (241)
T PLN03152 95 EDIMEPEDYNAGLSLYGDKAKPRTFAARFASPD-GSEVLSVVIRPSNQLKITFLEAKDITD-------LGSL-------- 158 (241)
T ss_pred hhhcChhhcccccceecCCCCCcceeeeecCCC-CCceEEEEEecCccccccccccCChhH-------cCCH--------
Confidence 221 12111112222 444331 22455555543 4455555 5555
Q ss_pred CccccchHHHHHhhhccccccccccccccccccEEeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcceEEEEEEEECC
Q 022978 162 DKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYRHYVASTAEREG 241 (289)
Q Consensus 162 d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~La~~tv~~G 241 (289)
++++ .+|.+.+..+. .+.+++. +++.|||+||+|||.+ .+||+|++++|++|
T Consensus 159 -------~EVg-kv~vP~g~~~~-------saR~iel-~~E~dGKtYY~lEy~v------------~~RH~LaTVaVsrG 210 (241)
T PLN03152 159 -------KEAA-KIFVPGGATLY-------SARTIKV-KEEEGIRTYYFYEFGR------------DEQHVALVATVNSG 210 (241)
T ss_pred -------HHHH-HhhCCCccccc-------ccceeee-eeecCCceeEEEEEEe------------CCcEEEEEEEEcCC
Confidence 4566 44444432111 1334444 4588999999999998 27999999999999
Q ss_pred EEEEEEeecCcchhhhhchhHHHhhcceeEc
Q 022978 242 YLYSISASTLGKQWDEMGPFLEKSVASFHLL 272 (289)
Q Consensus 242 kLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~ 272 (289)
|||||+++++|+||+|++++|+++++||+|+
T Consensus 211 KLYTl~aSt~EkRW~Kvk~kfr~aa~SFsV~ 241 (241)
T PLN03152 211 KAYIAGATAPESKWDDDGVKLRSAAISLTVL 241 (241)
T ss_pred eEEEEecCCchhchHHHHHHHHHHHhheeeC
Confidence 9999999999999999999999999999985
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=97.46 E-value=0.0033 Score=51.93 Aligned_cols=69 Identities=14% Similarity=0.112 Sum_probs=59.9
Q ss_pred ccEEeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcceEEEEEEEEC-CEEEEEEeecCcchhhhhchhHHHhhcce
Q 022978 193 SSVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYRHYVASTAERE-GYLYSISASTLGKQWDEMGPFLEKSVASF 269 (289)
Q Consensus 193 a~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~La~~tv~~-GkLYtl~~qa~EkrW~k~~~~l~~vv~SF 269 (289)
-.+++...-+.+|.+-+.++|.-+. ....-|+..++...+ +++|+|+..++....++.++.++++++||
T Consensus 61 ~~~~~~~~~~l~~~~a~~l~~~~~~--------~g~~v~Q~q~~~~~~~~~~l~~T~t~~~~~~~~~~~~~~~i~~Sf 130 (130)
T PF08786_consen 61 FQLVERQPITLGGRPARELEYSFRS--------GGQPVYQRQAAVLLPGRRVLVFTYTAPGPFTEEQRAHWEAILKSF 130 (130)
T ss_dssp -EEEEEEEEEETTEEEEEEEEEEEE--------TTCEEEEEEEEEEEC-CCEEEEEEEEECCCHHHHHHHHHHHHCT-
T ss_pred cEEEeeEEEEeCCCCeEEEEEEEee--------CCEEEEEEEEEEEECCCEEEEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 5667766667799999999999977 667788988888888 99999999999999999999999999998
No 8
>PRK11615 hypothetical protein; Provisional
Probab=89.37 E-value=16 Score=33.02 Aligned_cols=99 Identities=8% Similarity=0.092 Sum_probs=67.2
Q ss_pred EEEEeCCchhhhhcccCccccchHHHHHhhhccccccccccccccccccEEeeee--ceeCCeeeEEEEEEEecCCCCCC
Q 022978 146 ISVTIGPPNVQFLKSKDKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHT--SKVDGEPYWFYEYLIRKSPTNLG 223 (289)
Q Consensus 146 Vsvs~GPp~~~~l~~~d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~--r~~dGk~YY~~Ey~v~~~p~~~a 223 (289)
|.|++|+....+| +.++.++..+... +..++--..+ -+++|++..+++-.+..
T Consensus 84 vIVi~gD~~~~~L----------d~la~rl~~qQr~---------rdp~lqvvsnK~i~i~G~~~qQLDS~~t~------ 138 (185)
T PRK11615 84 VIVILGDDTNEDL----------AVLAKRLEDQQRS---------RDPQLQVVTNKAIELKGHKLQQLDSIISA------ 138 (185)
T ss_pred EEEEeCCCChhhH----------HHHHHHHHHHHHh---------hCcCceeecceeEEECCeeeEEeeeeeec------
Confidence 3344677666564 4577777643322 2244433444 35699999999988865
Q ss_pred CCCCCcceEEEEEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeE
Q 022978 224 QEPNLYRHYVASTAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHL 271 (289)
Q Consensus 224 ~~~e~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv 271 (289)
....--+-++++.-+++|-||.+..|-+-=.+.+..-+.|+++..+
T Consensus 139 --~Gqk~~SSvvL~~v~~rl~tlQitlpA~nqqqaq~~ae~ii~tl~~ 184 (185)
T PRK11615 139 --KGQTAYSSVVLGKVDNQLLTMQITLPADNQQQAQTTAENIINTLVI 184 (185)
T ss_pred --CCceEEEEEEEEeeCCeEEEEEEecCCCCHHHHHHHHHHHHhheec
Confidence 3233334456677899999999999988888888888888887654
No 9
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=87.48 E-value=7 Score=34.19 Aligned_cols=76 Identities=18% Similarity=0.166 Sum_probs=57.2
Q ss_pred cEEeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcc-eEEEEEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeEc
Q 022978 194 SVLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYR-HYVASTAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHLL 272 (289)
Q Consensus 194 ~ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~R-H~La~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~ 272 (289)
++..-.+-+++|..-...+|.-.. .+.+++| |++.++..+++++-+|++.++-.-=++.++...+++.||...
T Consensus 69 ~~~~~~e~~v~~~aa~~~~y~w~~------~~~~~r~v~q~~~~i~~g~~vLifT~Tt~~~ftp~q~~~~~~~I~Sf~p~ 142 (147)
T COG5435 69 ELHHRREIEVGGAAAPLLDYQWTS------PEGEQRRVQQRQVFIERGDTVLIFTLTTPGEFTPSQKKAWEQVIQSFVPN 142 (147)
T ss_pred EEeeccccccCccccceeEEEeec------CCCCCceEEEEEeecccCCeEEEEEecCCCCCCHHHHHHHHHHHHhcCCC
Confidence 444445567789888888887765 1234444 556666667789999999999888888889999999999987
Q ss_pred CCC
Q 022978 273 PPT 275 (289)
Q Consensus 273 ~~~ 275 (289)
++-
T Consensus 143 ~~~ 145 (147)
T COG5435 143 PPE 145 (147)
T ss_pred CCC
Confidence 764
No 10
>PF12712 DUF3805: Domain of unknown function (DUF3805); InterPro: IPR024315 This entry represents an N-terminal domain found in a family of bacterial proteins, whose function is unknown. In two related Bacteroides species, the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.; PDB: 3HLZ_A.
Probab=81.15 E-value=22 Score=31.07 Aligned_cols=133 Identities=16% Similarity=0.136 Sum_probs=58.1
Q ss_pred cceeeeCCCceEEeccCCCCCccee-ccccccccccccCCCCCCCCCcceeeeccccccccceeEEEEeCCchhhhhccc
Q 022978 83 MASFVDEINAYTYLYPMELPSKKFL-FKWVESRKPERYSSAAPLSPNARLRIVSERVDIIDNLIISVTIGPPNVQFLKSK 161 (289)
Q Consensus 83 f~~~~D~~dGYsF~YP~~W~s~e~~-~~g~~~r~~D~~~s~apLs~nvrv~iv~e~~~i~dn~~Vsvs~GPp~~~~l~~~ 161 (289)
|++|+.++-=|+..||++| -|++ ..|--++|. +..-++|+-||.- -+-+..+
T Consensus 1 mkKfiSpg~WFS~~YP~~W--~EfED~E~sflFYn--------------------p~~WTGNfRISay-k~~~~~y---- 53 (153)
T PF12712_consen 1 MKKFISPGAWFSMEYPADW--NEFEDGEGSFLFYN--------------------PDQWTGNFRISAY-KGGSAQY---- 53 (153)
T ss_dssp -EEEE-GGG-EEEEE-TT---EEE---TTEEEEE---------------------SSS---EEEEEEE-E--STTH----
T ss_pred CCcccCCCceEEEecCCCc--chhccCCcceEEEC--------------------hHHhcCceEEEEE-ecccccc----
Confidence 5789999999999999999 4533 112222322 1124557666652 1111112
Q ss_pred CccccchHHHHHhhhccccccccccccccccccEEeeeec---eeCCeeeEEEEEEEecCCCCCCCCCCCcceEEEEEEE
Q 022978 162 DKSTWNAKDVADSVLSDKSALRVTSSQRMAESSVLDAHTS---KVDGEPYWFYEYLIRKSPTNLGQEPNLYRHYVASTAE 238 (289)
Q Consensus 162 d~~~~~~~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r---~~dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~La~~tv 238 (289)
+++..++-|....+. +.|...++--|.+. +.+| .||+= |.. ++-
T Consensus 54 ------gk~~i~~EL~en~~a-----~~vkvg~~~caYs~E~f~eeg-~~Yts-------------------H~W--vtg 100 (153)
T PF12712_consen 54 ------GKECIRQELKENPSA-----KLVKVGNWECAYSKEMFQEEG-AYYTS-------------------HLW--VTG 100 (153)
T ss_dssp ------HHHHHHHHHHH-TT------EEEEETTEEEEEEEEEEEETT-EEEEE-------------------EEE--EEE
T ss_pred ------hHHHHHHHHHhCCCc-----ceEEeccEEEEEEhhhhhccC-eeEEE-------------------EEE--EEe
Confidence 366666666533220 11122222222222 2344 34432 333 334
Q ss_pred ECCEEEEEEeecCcchhhhhchhHHHhhcceeEcCCCCCC
Q 022978 239 REGYLYSISASTLGKQWDEMGPFLEKSVASFHLLPPTDDY 278 (289)
Q Consensus 239 ~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~~~~~~~ 278 (289)
.++..|.|....+-. ......+.|+.|..|.+....|
T Consensus 101 ~~~~sfeCSFTv~kg---~~~~~aE~iiasL~vR~~~~ky 137 (153)
T PF12712_consen 101 EGDVSFECSFTVPKG---ESVKEAEEIIASLEVRKEGQKY 137 (153)
T ss_dssp ETTEEEEEEEEEETT------HHHHHHHHH-EE--TT---
T ss_pred cCceEEEEEEEccCC---CCcchHHHHHhhheehhccCCC
Confidence 566777766655421 1234578899999999988887
No 11
>PF10738 Lpp-LpqN: Probable lipoprotein LpqN; InterPro: IPR019674 This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein [].
Probab=68.70 E-value=50 Score=29.45 Aligned_cols=70 Identities=20% Similarity=0.172 Sum_probs=48.9
Q ss_pred EEeeeeceeCCeeeEEEEEEEecCCCCCCCCCCCcceEE--EEEEEECC--EEEEEEeecCcchhhhhchhHHHhhccee
Q 022978 195 VLDAHTSKVDGEPYWFYEYLIRKSPTNLGQEPNLYRHYV--ASTAEREG--YLYSISASTLGKQWDEMGPFLEKSVASFH 270 (289)
Q Consensus 195 ll~a~~r~~dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~L--a~~tv~~G--kLYtl~~qa~EkrW~k~~~~l~~vv~SFr 270 (289)
-++++.-+.+|-+=+.+|-.-+. +...+|.. .|+...++ +|-.|++++.+.+=....+..+.|++.|+
T Consensus 101 ~~~~s~~~~~GfpS~~i~GtY~~--------~g~~~~~~~r~VV~~~~~~~Ylvqltvt~~~~qa~~~~~a~~aI~~g~~ 172 (175)
T PF10738_consen 101 ELDGSPSDFSGFPSSQIEGTYDK--------DGMRLHTSQRTVVIPGDDQRYLVQLTVTTTADQAVALADATEAIDEGFT 172 (175)
T ss_pred cccCCccccCCCceeEEEEEEee--------CCEEeEeEEEEEEEeCCCcEEEEEEEeeccccchhhhhhHHHHHHcCCE
Confidence 55666667788888888744433 22233333 33333344 77788899999999999999999999999
Q ss_pred Ec
Q 022978 271 LL 272 (289)
Q Consensus 271 v~ 272 (289)
|.
T Consensus 173 It 174 (175)
T PF10738_consen 173 IT 174 (175)
T ss_pred ec
Confidence 84
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=62.12 E-value=1.1e+02 Score=29.65 Aligned_cols=22 Identities=14% Similarity=0.336 Sum_probs=18.5
Q ss_pred ceeeeCCCceEEeccCCC-CCcc
Q 022978 84 ASFVDEINAYTYLYPMEL-PSKK 105 (289)
Q Consensus 84 ~~~~D~~dGYsF~YP~~W-~s~e 105 (289)
+++.|..-||+|++|.+| .|+.
T Consensus 110 grvdn~~gGFS~vvP~GW~~Sda 132 (297)
T PF07174_consen 110 GRVDNAAGGFSYVVPAGWVESDA 132 (297)
T ss_pred ccccccccceEEeccCCcccccc
Confidence 678899999999999999 3443
No 13
>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=60.33 E-value=10 Score=23.33 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=19.2
Q ss_pred EEEEEECCEEEEEEeecCcchhh
Q 022978 234 ASTAEREGYLYSISASTLGKQWD 256 (289)
Q Consensus 234 a~~tv~~GkLYtl~~qa~EkrW~ 256 (289)
..++-.+|+||.+.+.+.+.+|.
T Consensus 9 v~~~~~~g~l~a~d~~~G~~~W~ 31 (33)
T smart00564 9 VYVGSTDGTLYALDAKTGEILWT 31 (33)
T ss_pred EEEEcCCCEEEEEEcccCcEEEE
Confidence 34455789999999999999996
No 14
>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=42.39 E-value=21 Score=22.10 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=12.3
Q ss_pred chhHHHHHHHHHhhhhccCC
Q 022978 52 FCRRDLVLFGLSSSLSLGFP 71 (289)
Q Consensus 52 ~~rR~~ll~gl~~~~a~~~p 71 (289)
+.||++|-.++++.++.+++
T Consensus 2 ~sRR~fLk~~~a~~a~~~~~ 21 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAAAALG 21 (26)
T ss_pred CcHHHHHHHHHHHHHHHHhc
Confidence 46888887766644443333
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=39.36 E-value=1e+02 Score=25.08 Aligned_cols=47 Identities=15% Similarity=-0.009 Sum_probs=31.9
Q ss_pred eeCCeeeEEEEE-------EEecCCCCCCCCCCCcceEEEEEEEECCEEEEEEeecCcchhhhh
Q 022978 202 KVDGEPYWFYEY-------LIRKSPTNLGQEPNLYRHYVASTAEREGYLYSISASTLGKQWDEM 258 (289)
Q Consensus 202 ~~dGk~YY~~Ey-------~v~~~p~~~a~~~e~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~ 258 (289)
..||+.|+.|.+ ...- .+.....++-++||+.+-..+.||++.=-++
T Consensus 32 ~~~g~~~~~i~L~~~~~~~~i~i----------~~~~g~~~i~i~~g~vrv~~s~CpdkiCv~~ 85 (113)
T PF07009_consen 32 YVDGKEVKRIPLDKVNEDKTIEI----------DGDGGYNTIEIKDGKVRVIESDCPDKICVKT 85 (113)
T ss_dssp EETTEEEEEEETTS-BSEEEEEE----------ETTTCEEEEEEETTEEEEEEESTSS-HHHHS
T ss_pred EECCEEEEEEECCCCCCCEEEEE----------ecCCcEEEEEEECCEEEEEECCCCCcchhhC
Confidence 458999987732 2211 2234456788999999999999999865544
No 16
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=38.04 E-value=18 Score=23.61 Aligned_cols=23 Identities=30% Similarity=0.563 Sum_probs=19.7
Q ss_pred EEEECCEEEEEEeecCcchhhhh
Q 022978 236 TAEREGYLYSISASTLGKQWDEM 258 (289)
Q Consensus 236 ~tv~~GkLYtl~~qa~EkrW~k~ 258 (289)
++-.+|+||.|++.+++..|...
T Consensus 5 ~~~~~g~l~AlD~~TG~~~W~~~ 27 (38)
T PF01011_consen 5 VGTPDGYLYALDAKTGKVLWKFQ 27 (38)
T ss_dssp EETTTSEEEEEETTTTSEEEEEE
T ss_pred EeCCCCEEEEEECCCCCEEEeee
Confidence 44578999999999999999864
No 17
>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=35.82 E-value=29 Score=26.46 Aligned_cols=17 Identities=29% Similarity=0.647 Sum_probs=14.3
Q ss_pred cEEeeeeceeCCeeeEE
Q 022978 194 SVLDAHTSKVDGEPYWF 210 (289)
Q Consensus 194 ~ll~a~~r~~dGk~YY~ 210 (289)
.||++.+.++||+.|+.
T Consensus 3 KvLskG~h~IdGk~y~v 19 (65)
T PF09211_consen 3 KVLSKGEHTIDGKKYYV 19 (65)
T ss_dssp EEE-SEEEEETTEEEEE
T ss_pred ccccCccEEECCEEEEe
Confidence 58999999999999983
No 18
>PF00031 Cystatin: Cystatin domain; InterPro: IPR000010 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The cystatins are cysteine proteinase inhibitors belonging to MEROPS inhibitor family I25, clan IH [, , ]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and C13 (legumain family). The cystatin family includes: The Type 1 cystatins, which are intracellular cystatins that are present in the cytosol of many cell types, but can also appear in body fluids at significant concentrations. They are single-chain polypeptides of about 100 residues, which have neither disulphide bonds nor carbohydrate side chains. The Type 2 cystatins, which are mainly extracellular secreted polypeptides synthesised with a 19-28 residue signal peptide. They are broadly distributed and found in most body fluids. The Type 3 cystatins, which are multidomain proteins. The mammalian representatives of this group are the kininogens. There are three different kininogens in mammals: H- (high molecular mass, IPR002395 from INTERPRO) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat. Unclassified cystatins. These are cystatin-like proteins found in a range of organisms: plant phytocystatins, fetuin in mammals, insect cystatins and a puff adder venom cystatin which inhibits metalloproteases of the MEROPS peptidase family M12 (astacin/adamalysin). Also a number of the cystatins-like proteins have been shown to be devoid of inhibitory activity. All true cystatins inhibit cysteine peptidases of the papain family (MEROPS peptidase family C1), and some also inhibit legumain family enzymes (MEROPS peptidase family C13). These peptidases play key roles in physiological processes, such as intracellular protein degradation (cathepsins B, H and L), are pivotal in the remodelling of bone (cathepsin K), and may be important in the control of antigen presentation (cathepsin S, mammalian legumain). Moreover, the activities of such peptidases are increased in pathophysiological conditions, such as cancer metastasis and inflammation. Additionally, such peptidases are essential for several pathogenic parasites and bacteria. Thus in animals cystatins not only have capacity to regulate normal body processes and perhaps cause disease when down-regulated, but in other organisms may also participate in defence against biotic and abiotic stress. ; GO: 0004869 cysteine-type endopeptidase inhibitor activity; PDB: 3L0R_B 2W9P_K 2W9Q_A 3S67_A 3QRD_D 1R4C_G 3GAX_A 1TIJ_B 1G96_A 3NX0_A ....
Probab=33.80 E-value=62 Score=24.57 Aligned_cols=47 Identities=19% Similarity=0.301 Sum_probs=32.1
Q ss_pred HHHHHhhhccccccccccccccccccEEeeeeceeCCeeeEEEEEEEec
Q 022978 169 KDVADSVLSDKSALRVTSSQRMAESSVLDAHTSKVDGEPYWFYEYLIRK 217 (289)
Q Consensus 169 ~~la~~vLa~~ssgr~~~g~rv~~a~ll~a~~r~~dGk~YY~~Ey~v~~ 217 (289)
.++++..+...++.. ..+......+|+++.+..+.|. -|.+++.+.-
T Consensus 14 ~~~~~~al~~~N~~~-~~~~~~~~~~v~~a~~QvV~G~-~Y~i~~~~~~ 60 (94)
T PF00031_consen 14 QEAAEFALDKFNEQS-NSGYKFKLVKVISATTQVVAGI-NYYIEFEVGE 60 (94)
T ss_dssp HHHHHHHHHHHHHHS-TTSEEEEEEEEEEEEEEESSSE-EEEEEEEEEE
T ss_pred HHHHHHHHHHHHHhC-cccCcceeeeeeEEEEeecCCc-eEEEEEEEEc
Confidence 567777776654421 1244456689999999899997 6667888753
No 19
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=31.49 E-value=41 Score=32.35 Aligned_cols=42 Identities=19% Similarity=0.330 Sum_probs=26.5
Q ss_pred ccccccccceeEEEEeCCchhhhhcccCccccchHHHHHhhhccc
Q 022978 135 SERVDIIDNLIISVTIGPPNVQFLKSKDKSTWNAKDVADSVLSDK 179 (289)
Q Consensus 135 ~e~~~i~dn~~Vsvs~GPp~~~~l~~~d~~~~~~~~la~~vLa~~ 179 (289)
.+.....|||+|.|+ .|++....+..|+ ++|+++|+.++...
T Consensus 140 rD~Ie~~ENVSV~IS-s~sss~~~sLeDL--GsP~eVgerLlkqv 181 (286)
T PLN00059 140 RDPVVLDENLSVEFS-SPSSSKYTSLEDL--GSPEEVGKRVLRQY 181 (286)
T ss_pred eccCccccceEEEEe-cCCcccCCChHHc--CCHHHHHHHHHHHH
Confidence 366667777777765 3432233233443 58999999998544
No 20
>PLN00064 photosystem II protein Psb27; Provisional
Probab=25.22 E-value=78 Score=28.27 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=22.6
Q ss_pred ccccchhHHHHHHHHHhhh-hccCCCCCCCcccccCc
Q 022978 48 QQNGFCRRDLVLFGLSSSL-SLGFPTPGSVAGEDVKM 83 (289)
Q Consensus 48 ~~~~~~rR~~ll~gl~~~~-a~~~p~~~A~A~~a~~f 83 (289)
+++..+||+++..+.+++. +.++|..+|.|...+.|
T Consensus 30 ~~~~~~rr~~~~~~~~~~~~~~~~~~~~a~a~~~g~Y 66 (166)
T PLN00064 30 RRNHLLRREFLSLATTILTSAALLPVAPAFAASDEEY 66 (166)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhccCcchhhccCCCh
Confidence 3556688888776555443 34677778877554443
No 21
>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=24.52 E-value=52 Score=24.83 Aligned_cols=11 Identities=36% Similarity=0.468 Sum_probs=7.7
Q ss_pred cccchhHHHHH
Q 022978 49 QNGFCRRDLVL 59 (289)
Q Consensus 49 ~~~~~rR~~ll 59 (289)
...+.||++|.
T Consensus 6 ~~~~sRR~Flk 16 (66)
T TIGR02811 6 KADPSRRDLLK 16 (66)
T ss_pred cCCccHHHHHH
Confidence 34567898876
No 22
>KOG4649 consensus PQQ (pyrrolo-quinoline quinone) repeat protein [Secondary metabolites biosynthesis, transport and catabolism]
Probab=22.59 E-value=63 Score=31.50 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=33.7
Q ss_pred CCeeeEEEEEEEecCCCCCCCCCCCcceEEEEEEEECCEEEEEEeecCcchhhhh
Q 022978 204 DGEPYWFYEYLIRKSPTNLGQEPNLYRHYVASTAEREGYLYSISASTLGKQWDEM 258 (289)
Q Consensus 204 dGk~YY~~Ey~v~~~p~~~a~~~e~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~ 258 (289)
.|+.||.-+.-+|- +..-----++.|++..+|+||-|...++++-|.-.
T Consensus 42 sG~~~We~ilg~Ri------E~sa~vvgdfVV~GCy~g~lYfl~~~tGs~~w~f~ 90 (354)
T KOG4649|consen 42 SGNLIWEAILGVRI------ECSAIVVGDFVVLGCYSGGLYFLCVKTGSQIWNFV 90 (354)
T ss_pred CCcEEeehhhCcee------eeeeEEECCEEEEEEccCcEEEEEecchhheeeee
Confidence 47788865554442 11111122348899999999999999999999764
No 23
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=20.77 E-value=93 Score=23.69 Aligned_cols=57 Identities=23% Similarity=0.368 Sum_probs=30.4
Q ss_pred CcceEEEEEEEECCEEEEEEeecCcchhhhhchhHHHhhcceeEcCCCCCC-CCCCCCCCCC
Q 022978 228 LYRHYVASTAEREGYLYSISASTLGKQWDEMGPFLEKSVASFHLLPPTDDY-VPPYKDPWRF 288 (289)
Q Consensus 228 ~~RH~La~~tv~~GkLYtl~~qa~EkrW~k~~~~l~~vv~SFrv~~~~~~~-~~~~~~~~~~ 288 (289)
+.+=.+-+-+-++|+||.+...+..+ +.-++-.-.+.-+.....+.| +|+.+++|.|
T Consensus 6 Ge~v~~~~~~~~~~Yl~l~~~~~~G~----v~~L~Pn~~~~~~~v~ag~~~~iP~~~~~~~~ 63 (83)
T PF14326_consen 6 GERVRFRVTSNRDGYLYLFYIDADGK----VTLLFPNRYQPDNFVKAGQTYTIPDPGDRFSF 63 (83)
T ss_pred CCEEEEEEEeCCCeEEEEEEECCCCC----EEEEecCccccCceEcCCceEEcCCCCCceEE
Confidence 34445555556678888888765431 222222222222556666654 5656776654
Done!