Query 032127
Match_columns 147
No_of_seqs 137 out of 187
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:57:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00042 photosystem II oxygen 100.0 4.6E-34 1E-38 238.5 7.1 116 28-146 27-154 (260)
2 PLN00059 PsbP domain-containin 99.9 7.8E-26 1.7E-30 190.0 7.9 104 40-147 65-174 (286)
3 PF01789 PsbP: PsbP; InterPro 99.8 8E-22 1.7E-26 154.1 3.4 80 68-147 6-86 (175)
4 PLN00067 PsbP domain-containin 99.7 2.8E-18 6.2E-23 143.8 6.7 95 51-147 40-178 (263)
5 PLN00066 PsbP domain-containin 99.6 2.8E-15 6.1E-20 126.1 7.2 97 51-147 42-180 (262)
6 PLN03152 hypothetical protein; 98.5 9.7E-08 2.1E-12 79.4 4.1 59 88-147 79-162 (241)
7 PF12712 DUF3805: Domain of un 88.3 0.58 1.3E-05 37.0 3.4 45 86-131 2-47 (153)
8 PF10518 TAT_signal: TAT (twin 72.4 3 6.6E-05 23.5 1.7 13 54-66 2-14 (26)
9 PLN02729 PSII-Q subunit 66.4 4 8.7E-05 34.2 1.9 29 52-80 48-76 (220)
10 TIGR02811 formate_TAT formate 65.3 9.3 0.0002 26.1 3.2 13 51-63 6-18 (66)
11 PF07174 FAP: Fibronectin-atta 52.7 8.3 0.00018 33.6 1.6 21 87-107 111-131 (297)
12 PF05757 PsbQ: Oxygen evolving 49.5 5.8 0.00013 32.7 0.1 21 40-61 16-36 (202)
13 PRK10882 hydrogenase 2 protein 39.9 34 0.00073 29.9 3.4 9 55-63 2-10 (328)
14 PF10399 UCR_Fe-S_N: Ubiquitin 37.3 32 0.0007 21.4 2.1 12 50-61 5-16 (41)
15 PF12318 FAD-SLDH: Membrane bo 35.2 25 0.00053 27.8 1.6 7 54-60 2-8 (168)
16 PRK05363 TMAO/DMSO reductase; 33.3 71 0.0015 28.1 4.3 10 53-62 20-29 (319)
17 PF12559 Inhibitor_I10: Serine 28.7 22 0.00047 23.9 0.3 12 94-105 44-55 (56)
18 COG4784 Putative Zn-dependent 27.9 43 0.00092 30.6 2.1 30 75-104 274-306 (479)
19 PF08786 DUF1795: Domain of un 25.3 61 0.0013 23.5 2.2 43 96-140 3-46 (130)
20 TIGR01409 TAT_signal_seq Tat ( 24.5 53 0.0011 18.5 1.4 12 54-65 1-12 (29)
21 PF08006 DUF1700: Protein of u 24.1 15 0.00032 28.6 -1.3 14 134-147 44-57 (181)
22 PF10633 NPCBM_assoc: NPCBM-as 23.7 85 0.0018 20.8 2.5 36 93-132 24-61 (78)
23 PRK10123 wcaM putative colanic 23.7 1.4E+02 0.003 26.9 4.5 25 121-145 111-139 (464)
24 PRK07474 sulfur oxidation prot 22.6 67 0.0015 25.4 2.1 9 53-61 7-15 (154)
25 PF05984 Cytomega_UL20A: Cytom 21.8 59 0.0013 23.9 1.5 16 55-70 2-17 (100)
26 TIGR02543 List_Bact_rpt Lister 21.5 96 0.0021 19.2 2.3 34 91-127 2-36 (44)
27 PLN00058 photosystem II reacti 20.6 84 0.0018 23.5 2.1 15 51-65 46-60 (103)
No 1
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=100.00 E-value=4.6e-34 Score=238.47 Aligned_cols=116 Identities=33% Similarity=0.549 Sum_probs=99.3
Q ss_pred ccccccCCccceeeccCccccccchhhhHHHHHH---HHHHHhhhhCCCccccccc-----ccCCcccceeC-CCCeEEe
Q 032127 28 TRSATAFSCQNFFTCPEDISSDEENKSKRRLLLM---GAGLLTANLLPANSLFAQE-----IPKNYDAFVDR-IDGYSYV 98 (147)
Q Consensus 28 ~r~~~~~~~~~~~~c~~~~~~~~~~~~~RR~aL~---g~aa~~a~~~pa~aA~ae~-----~p~g~~~f~d~-~dGysfl 98 (147)
+|.....++++ ++|++|++ ..+.++||.+|+ |++++++.+.|+++||||+ +|++.++|+++ +|||+|+
T Consensus 27 ~~~~~~~~~~~-~~~~~~~~--~~~~~srr~~l~~~~ga~a~~~~~~pa~aay~~~anvfg~~k~~~gF~~y~~dgY~Fl 103 (260)
T PLN00042 27 ARAVSASRPSQ-VVCRAQEE--DNSAVSRRAALALLAGAAAAGAKVSPANAAYGESANVFGKPKTNTGFLPYNGDGFKLL 103 (260)
T ss_pred ccccCCCCCcc-eeeecccc--ccccccHHHHHHHHHHHHHhhcccCchhhhhcchhhccCCCCCCCCCeEeeCCCeEEe
Confidence 34444555555 69999876 446689998877 4455678999999999999 88888888888 5999999
Q ss_pred ccCCce---EeeecCCcceecCcccCccceEEEEecCCCCCcccCCCcccc
Q 032127 99 YPSDWT---EFEFTGHDSGFKDRYLQLQNVRVRFIPTDKKDVHDLGPMEEF 146 (147)
Q Consensus 99 yPs~W~---ev~~~G~d~~f~D~~~~~eNVsV~Vsp~~~~sI~dfGsPeev 146 (147)
||++|+ |++++|+|++|||+|+++|||+|+|+|++|++|+|||+||||
T Consensus 104 yP~~W~~~ke~~~~G~dv~f~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~ 154 (260)
T PLN00042 104 VPSKWNPSKEREFPGQVLRFEDNFDATSNLSVMVTPTDKKSITDYGSPEEF 154 (260)
T ss_pred cCCCCccccccccCCceEEeeccccccccEEEEEecCCcCCHhhcCCHHHH
Confidence 999995 778899999999999999999999999999999999999996
No 2
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.92 E-value=7.8e-26 Score=190.01 Aligned_cols=104 Identities=28% Similarity=0.462 Sum_probs=82.2
Q ss_pred eeccCccccccchhhhHHHHHH-HH--HHHhhhhCCCcccccccccCCcccceeCCCCeEEeccCCceEeeecCCcceec
Q 032127 40 FTCPEDISSDEENKSKRRLLLM-GA--GLLTANLLPANSLFAQEIPKNYDAFVDRIDGYSYVYPSDWTEFEFTGHDSGFK 116 (147)
Q Consensus 40 ~~c~~~~~~~~~~~~~RR~aL~-g~--aa~~a~~~pa~aA~ae~~p~g~~~f~d~~dGysflyPs~W~ev~~~G~d~~f~ 116 (147)
+.|..+.+ ..-+++||++|+ +. +.+.....-...|+|+ |+||+.|+|..|||+|+||.||++|...|+|++||
T Consensus 65 ~~~~~~~~--~~~~~~rr~~~~~~l~~~~~~~s~~~~~~a~a~--~~~l~~y~D~~DGY~FlYP~GWi~V~~~G~DVvFr 140 (286)
T PLN00059 65 INCLTDAK--QVCAVGRRKSMMMGLLMSGLIVSEANLPTAFAS--IPVFREYIDTFDGYSFKYPQNWIQVRGAGADIFFR 140 (286)
T ss_pred eecccchh--hhhhhhhhhhhHHHHHHHHHHHHhhcCchhhcC--CcccceeEcCCCCeEEeCCCCCeEeccCCCceEEe
Confidence 35664442 344789999975 22 1122222223356764 66899999999999999999999999999999999
Q ss_pred CcccCccceEEEEecCC---CCCcccCCCccccC
Q 032127 117 DRYLQLQNVRVRFIPTD---KKDVHDLGPMEEFL 147 (147)
Q Consensus 117 D~~~~~eNVsV~Vsp~~---~~sI~dfGsPeeva 147 (147)
|+++.+|||||+|+|++ +++|+|||+|+||+
T Consensus 141 D~Ie~~ENVSV~ISs~sss~~~sLeDLGsP~eVg 174 (286)
T PLN00059 141 DPVVLDENLSVEFSSPSSSKYTSLEDLGSPEEVG 174 (286)
T ss_pred ccCccccceEEEEecCCcccCCChHHcCCHHHHH
Confidence 99999999999999764 89999999999984
No 3
>PF01789 PsbP: PsbP; InterPro: IPR002683 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbP. Both PsbP and PsbQ (IPR008797 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [, ]. The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity []. PsbP is encoded in the nuclear genome in plants.; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 2VU4_A 1V2B_A 2LNJ_A 2XB3_A.
Probab=99.84 E-value=8e-22 Score=154.11 Aligned_cols=80 Identities=38% Similarity=0.596 Sum_probs=62.3
Q ss_pred hhhCCCcccccccccCCcccceeCCCCeEEeccCCceEeeecCCcceecCcccCccceEEEEecCCCC-CcccCCCcccc
Q 032127 68 ANLLPANSLFAQEIPKNYDAFVDRIDGYSYVYPSDWTEFEFTGHDSGFKDRYLQLQNVRVRFIPTDKK-DVHDLGPMEEF 146 (147)
Q Consensus 68 a~~~pa~aA~ae~~p~g~~~f~d~~dGysflyPs~W~ev~~~G~d~~f~D~~~~~eNVsV~Vsp~~~~-sI~dfGsPeev 146 (147)
+.+.++..+.++..++||+.|.|..+||+|+||++|+++++.|++++|+|+++.++||+|+|+|+.+. +|+|||+|+||
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~y~d~~~~y~f~~P~gW~~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~v 85 (175)
T PF01789_consen 6 ALLSSANVACAAEASTGFQPYTDSDDGYSFLYPSGWEEVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEEV 85 (175)
T ss_dssp ----------STT--SSEEEEEECTTTEEEEEETTEEEEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHHH
T ss_pred EeeccchhhhcccCCCCceEEEcCCCCEEEECCCCCeecCCCCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHHH
Confidence 33344555555667889999999999999999999999999999999999999999999999999755 99999999997
Q ss_pred C
Q 032127 147 L 147 (147)
Q Consensus 147 a 147 (147)
+
T Consensus 86 a 86 (175)
T PF01789_consen 86 A 86 (175)
T ss_dssp H
T ss_pred H
Confidence 4
No 4
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.74 E-value=2.8e-18 Score=143.82 Aligned_cols=95 Identities=23% Similarity=0.451 Sum_probs=67.2
Q ss_pred chhhhHHHHHHHHHHHhhh-hCCCccccccc---------ccC--CcccceeC-----------CCCeEEeccCCceEee
Q 032127 51 ENKSKRRLLLMGAGLLTAN-LLPANSLFAQE---------IPK--NYDAFVDR-----------IDGYSYVYPSDWTEFE 107 (147)
Q Consensus 51 ~~~~~RR~aL~g~aa~~a~-~~pa~aA~ae~---------~p~--g~~~f~d~-----------~dGysflyPs~W~ev~ 107 (147)
...+.||+.|.|+++.... .....++.|-+ .|. ||-.|... -.||+|+||.+|+++.
T Consensus 40 ~~~~~rr~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~v~ 119 (263)
T PLN00067 40 AVVIHRRELLLGLALAPLILIAPEPPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQTR 119 (263)
T ss_pred cchhHHHHHHhhhhhhhhhhccCCchhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcCcc
Confidence 3457899999877654221 12222333322 222 45555432 3699999999999888
Q ss_pred ec----C-----------CcceecCcccCccceEEEEecC------CCCCcccCCCccccC
Q 032127 108 FT----G-----------HDSGFKDRYLQLQNVRVRFIPT------DKKDVHDLGPMEEFL 147 (147)
Q Consensus 108 ~~----G-----------~d~~f~D~~~~~eNVsV~Vsp~------~~~sI~dfGsPeeva 147 (147)
+. | +|++|+|++ ++||+|+|+|+ ++++|+|||+||||+
T Consensus 120 Vs~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl 178 (263)
T PLN00067 120 VANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKLI 178 (263)
T ss_pred ccccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHHH
Confidence 75 4 899999955 77999999997 568999999999984
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.58 E-value=2.8e-15 Score=126.06 Aligned_cols=97 Identities=18% Similarity=0.350 Sum_probs=67.6
Q ss_pred chhhhHHHHHHHHHHH---hhhhCCCc--cc-cccc----------ccCCcccceeC-------------CCCeEEeccC
Q 032127 51 ENKSKRRLLLMGAGLL---TANLLPAN--SL-FAQE----------IPKNYDAFVDR-------------IDGYSYVYPS 101 (147)
Q Consensus 51 ~~~~~RR~aL~g~aa~---~a~~~pa~--aA-~ae~----------~p~g~~~f~d~-------------~dGysflyPs 101 (147)
...++||.+|+..+++ ++...|+. |+ +|-. --.|++.|.-+ ...|+|+||.
T Consensus 42 ~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~ 121 (262)
T PLN00066 42 ATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQ 121 (262)
T ss_pred cchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCC
Confidence 3467999999844333 11223322 22 3311 12356666543 2569999999
Q ss_pred CceEeeec-----CCcceecCcccCccceEEEEecC--------CCCCcccCCCccccC
Q 032127 102 DWTEFEFT-----GHDSGFKDRYLQLQNVRVRFIPT--------DKKDVHDLGPMEEFL 147 (147)
Q Consensus 102 ~W~ev~~~-----G~d~~f~D~~~~~eNVsV~Vsp~--------~~~sI~dfGsPeeva 147 (147)
+|+|+.+. |.++.|++..+.++||+|+|+|+ ++++|+|||+||||+
T Consensus 122 GW~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi 180 (262)
T PLN00066 122 GWEEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVI 180 (262)
T ss_pred CCeEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHH
Confidence 99999886 65566666668999999999997 689999999999974
No 6
>PLN03152 hypothetical protein; Provisional
Probab=98.51 E-value=9.7e-08 Score=79.43 Aligned_cols=59 Identities=25% Similarity=0.437 Sum_probs=43.5
Q ss_pred ceeCCCCeEEeccCCceEe----eec-CC------------cceecCcccCccceEEEEecC--------CCCCcccCCC
Q 032127 88 FVDRIDGYSYVYPSDWTEF----EFT-GH------------DSGFKDRYLQLQNVRVRFIPT--------DKKDVHDLGP 142 (147)
Q Consensus 88 f~d~~dGysflyPs~W~ev----~~~-G~------------d~~f~D~~~~~eNVsV~Vsp~--------~~~sI~dfGs 142 (147)
|.=++|||+.-||-++..+ ++. |- ..||- --|.+|||||+|+|+ +.++|+|||+
T Consensus 79 ~~~~g~gf~~~~pp~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~-s~D~sEnVSVVIspv~~LK~tfle~kDLtDLGs 157 (241)
T PLN03152 79 FQFYGDGFSIRVPPSFEDIMEPEDYNAGLSLYGDKAKPRTFAARFA-SPDGSEVLSVVIRPSNQLKITFLEAKDITDLGS 157 (241)
T ss_pred hhhhCCceEEeCCCChhhhcChhhcccccceecCCCCCcceeeeec-CCCCCceEEEEEecCccccccccccCChhHcCC
Confidence 3445899999999999433 222 21 12332 346899999999996 6899999999
Q ss_pred ccccC
Q 032127 143 MEEFL 147 (147)
Q Consensus 143 Peeva 147 (147)
|+||+
T Consensus 158 p~EVg 162 (241)
T PLN03152 158 LKEAA 162 (241)
T ss_pred HHHHH
Confidence 99985
No 7
>PF12712 DUF3805: Domain of unknown function (DUF3805); InterPro: IPR024315 This entry represents an N-terminal domain found in a family of bacterial proteins, whose function is unknown. In two related Bacteroides species, the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.; PDB: 3HLZ_A.
Probab=88.28 E-value=0.58 Score=36.99 Aligned_cols=45 Identities=29% Similarity=0.452 Sum_probs=26.7
Q ss_pred ccceeCCCCeEEeccCCceEeeecCCc-ceecCcccCccceEEEEec
Q 032127 86 DAFVDRIDGYSYVYPSDWTEFEFTGHD-SGFKDRYLQLQNVRVRFIP 131 (147)
Q Consensus 86 ~~f~d~~dGysflyPs~W~ev~~~G~d-~~f~D~~~~~eNVsV~Vsp 131 (147)
+-|+.++.=|++.||.+|-|.+ +|.+ -.|.|+-.-+-|..+..-.
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfE-D~E~sflFYnp~~WTGNfRISayk 47 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFE-DGEGSFLFYNPDQWTGNFRISAYK 47 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE----TTEEEEE-SSS---EEEEEEEE
T ss_pred CcccCCCceEEEecCCCcchhc-cCCcceEEEChHHhcCceEEEEEe
Confidence 4578888889999999999888 5554 5788888888888876553
No 8
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=72.39 E-value=3 Score=23.49 Aligned_cols=13 Identities=31% Similarity=0.401 Sum_probs=9.7
Q ss_pred hhHHHHHHHHHHH
Q 032127 54 SKRRLLLMGAGLL 66 (147)
Q Consensus 54 ~~RR~aL~g~aa~ 66 (147)
.+||+.|.+.+++
T Consensus 2 ~sRR~fLk~~~a~ 14 (26)
T PF10518_consen 2 LSRRQFLKGGAAA 14 (26)
T ss_pred CcHHHHHHHHHHH
Confidence 5799999855544
No 9
>PLN02729 PSII-Q subunit
Probab=66.40 E-value=4 Score=34.18 Aligned_cols=29 Identities=21% Similarity=0.118 Sum_probs=16.3
Q ss_pred hhhhHHHHHHHHHHHhhhhCCCccccccc
Q 032127 52 NKSKRRLLLMGAGLLTANLLPANSLFAQE 80 (147)
Q Consensus 52 ~~~~RR~aL~g~aa~~a~~~pa~aA~ae~ 80 (147)
-..+||.+|.-+++..++-+.+.+++||.
T Consensus 48 ~~~~rr~~lgl~a~~l~~~s~~~~~~A~~ 76 (220)
T PLN02729 48 FQTTRRLALGLASIALIGNSGNGVSLAED 76 (220)
T ss_pred hhhhHHHHHHHHHHHHhcchhhhHHHhcc
Confidence 36789999853322222223356677765
No 10
>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=65.25 E-value=9.3 Score=26.07 Aligned_cols=13 Identities=38% Similarity=0.496 Sum_probs=9.4
Q ss_pred chhhhHHHHHHHH
Q 032127 51 ENKSKRRLLLMGA 63 (147)
Q Consensus 51 ~~~~~RR~aL~g~ 63 (147)
+..++||..|.++
T Consensus 6 ~~~~sRR~Flk~l 18 (66)
T TIGR02811 6 KADPSRRDLLKGL 18 (66)
T ss_pred cCCccHHHHHHHH
Confidence 4457899998843
No 11
>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=52.68 E-value=8.3 Score=33.57 Aligned_cols=21 Identities=33% Similarity=0.762 Sum_probs=16.8
Q ss_pred cceeCCCCeEEeccCCceEee
Q 032127 87 AFVDRIDGYSYVYPSDWTEFE 107 (147)
Q Consensus 87 ~f~d~~dGysflyPs~W~ev~ 107 (147)
++.+...||+|++|.+|++-+
T Consensus 111 rvdn~~gGFS~vvP~GW~~Sd 131 (297)
T PF07174_consen 111 RVDNAAGGFSYVVPAGWVESD 131 (297)
T ss_pred cccccccceEEeccCCccccc
Confidence 566667999999999996443
No 12
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=49.53 E-value=5.8 Score=32.67 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=0.0
Q ss_pred eeccCccccccchhhhHHHHHH
Q 032127 40 FTCPEDISSDEENKSKRRLLLM 61 (147)
Q Consensus 40 ~~c~~~~~~~~~~~~~RR~aL~ 61 (147)
+.|+++.+ ..+...+||.+|.
T Consensus 16 ~~vra~~~-~~~~~~~RRa~l~ 36 (202)
T PF05757_consen 16 VVVRASQS-PAQQQTSRRAVLG 36 (202)
T ss_dssp ----------------------
T ss_pred ceeccccC-cccccccHHHHHH
Confidence 35777652 2345678999975
No 13
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=39.89 E-value=34 Score=29.94 Aligned_cols=9 Identities=44% Similarity=0.545 Sum_probs=6.8
Q ss_pred hHHHHHHHH
Q 032127 55 KRRLLLMGA 63 (147)
Q Consensus 55 ~RR~aL~g~ 63 (147)
+||..|.++
T Consensus 2 ~RR~fl~~~ 10 (328)
T PRK10882 2 NRRNFLKAA 10 (328)
T ss_pred CHHHHHHHH
Confidence 599999743
No 14
>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=37.31 E-value=32 Score=21.44 Aligned_cols=12 Identities=33% Similarity=0.354 Sum_probs=5.9
Q ss_pred cchhhhHHHHHH
Q 032127 50 EENKSKRRLLLM 61 (147)
Q Consensus 50 ~~~~~~RR~aL~ 61 (147)
+....+||..|.
T Consensus 5 ~~~~~~RRdFL~ 16 (41)
T PF10399_consen 5 EPVDPTRRDFLT 16 (41)
T ss_dssp -----HHHHHHH
T ss_pred CCCCchHHHHHH
Confidence 345678999885
No 15
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=35.23 E-value=25 Score=27.80 Aligned_cols=7 Identities=57% Similarity=0.629 Sum_probs=5.8
Q ss_pred hhHHHHH
Q 032127 54 SKRRLLL 60 (147)
Q Consensus 54 ~~RR~aL 60 (147)
.+||++|
T Consensus 2 ~sRR~~L 8 (168)
T PF12318_consen 2 LSRRRLL 8 (168)
T ss_pred CcHHHHH
Confidence 5799998
No 16
>PRK05363 TMAO/DMSO reductase; Reviewed
Probab=33.30 E-value=71 Score=28.15 Aligned_cols=10 Identities=30% Similarity=0.298 Sum_probs=7.4
Q ss_pred hhhHHHHHHH
Q 032127 53 KSKRRLLLMG 62 (147)
Q Consensus 53 ~~~RR~aL~g 62 (147)
=..||+.|.+
T Consensus 20 ~~~rr~~l~~ 29 (319)
T PRK05363 20 YLNRRRFLKA 29 (319)
T ss_pred HHHHHHHHHH
Confidence 3479999964
No 17
>PF12559 Inhibitor_I10: Serine endopeptidase inhibitors; InterPro: IPR022217 This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation. ; PDB: 1IXU_A.
Probab=28.68 E-value=22 Score=23.85 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=3.9
Q ss_pred CeEEeccCCceE
Q 032127 94 GYSYVYPSDWTE 105 (147)
Q Consensus 94 GysflyPs~W~e 105 (147)
.+++-||++|.|
T Consensus 44 ~~TlKyPSD~ee 55 (56)
T PF12559_consen 44 IQTLKYPSDWEE 55 (56)
T ss_dssp -----SS-SS--
T ss_pred CcceeCCCcccc
Confidence 489999999975
No 18
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=27.90 E-value=43 Score=30.63 Aligned_cols=30 Identities=17% Similarity=0.385 Sum_probs=23.7
Q ss_pred ccccccccCCcc---cceeCCCCeEEeccCCce
Q 032127 75 SLFAQEIPKNYD---AFVDRIDGYSYVYPSDWT 104 (147)
Q Consensus 75 aA~ae~~p~g~~---~f~d~~dGysflyPs~W~ 104 (147)
..||+.+..||. .|.-.+=|++|.||.+|+
T Consensus 274 ~lyGDSp~eGyvRgq~FlH~~Lg~tf~~P~Gf~ 306 (479)
T COG4784 274 LLYGDSPQEGYVRGQTFLHPELGVTFDVPDGFK 306 (479)
T ss_pred cccCCCcccceecccceeccccceEEecCCceE
Confidence 347877767775 467778999999999995
No 19
>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=25.27 E-value=61 Score=23.50 Aligned_cols=43 Identities=16% Similarity=0.205 Sum_probs=19.0
Q ss_pred EEeccCCceEeeecCCcceecCcccCccceEEEEecC-CCCCcccC
Q 032127 96 SYVYPSDWTEFEFTGHDSGFKDRYLQLQNVRVRFIPT-DKKDVHDL 140 (147)
Q Consensus 96 sflyPs~W~ev~~~G~d~~f~D~~~~~eNVsV~Vsp~-~~~sI~df 140 (147)
+|..|.+|+.... +..++.|.-...-|+.|.-.+. +..++++|
T Consensus 3 ~~~lP~~~~D~t~--nv~~~~~~~~~~~slvIsR~~l~~g~tl~~~ 46 (130)
T PF08786_consen 3 SLTLPDGWQDRTM--NVLVLPDSGGSGPSLVISRDPLPDGETLEDY 46 (130)
T ss_dssp EEEEETTSEE--B--EEEEE--BTTB-EEEEEEEE---TTS-HHHH
T ss_pred eEeCCCcceeceE--EEEEccCCCCCcceEEEEeccCCCCCCHHHH
Confidence 5778999976432 2344555433344444444444 35555543
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=24.51 E-value=53 Score=18.52 Aligned_cols=12 Identities=42% Similarity=0.454 Sum_probs=8.2
Q ss_pred hhHHHHHHHHHH
Q 032127 54 SKRRLLLMGAGL 65 (147)
Q Consensus 54 ~~RR~aL~g~aa 65 (147)
++||+.|-..++
T Consensus 1 ~sRR~Flk~~~~ 12 (29)
T TIGR01409 1 LSRRDFLKGAAA 12 (29)
T ss_pred CchhhhHHHHHH
Confidence 379999984433
No 21
>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=24.09 E-value=15 Score=28.56 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=10.5
Q ss_pred CCCcccCCCccccC
Q 032127 134 KKDVHDLGPMEEFL 147 (147)
Q Consensus 134 ~~sI~dfGsPeeva 147 (147)
..=+++||+|+|+|
T Consensus 44 eeii~~LG~P~~iA 57 (181)
T PF08006_consen 44 EEIIAELGSPKEIA 57 (181)
T ss_pred HHHHHHcCCHHHHH
Confidence 45578899998865
No 22
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=23.72 E-value=85 Score=20.83 Aligned_cols=36 Identities=14% Similarity=0.126 Sum_probs=15.0
Q ss_pred CCeEEeccCCceEeeecCCcceecCcccC--ccceEEEEecC
Q 032127 93 DGYSYVYPSDWTEFEFTGHDSGFKDRYLQ--LQNVRVRFIPT 132 (147)
Q Consensus 93 dGysflyPs~W~ev~~~G~d~~f~D~~~~--~eNVsV~Vsp~ 132 (147)
-..++..|.+|. +...+..+. .+.+ ...+.+.|.+.
T Consensus 24 v~~~l~~P~GW~-~~~~~~~~~---~l~pG~s~~~~~~V~vp 61 (78)
T PF10633_consen 24 VSLSLSLPEGWT-VSASPASVP---SLPPGESVTVTFTVTVP 61 (78)
T ss_dssp -EEEEE--TTSE----EEEEE-----B-TTSEEEEEEEEEE-
T ss_pred EEEEEeCCCCcc-ccCCccccc---cCCCCCEEEEEEEEECC
Confidence 356678899998 444443333 3333 44455555544
No 23
>PRK10123 wcaM putative colanic acid biosynthesis protein; Provisional
Probab=23.67 E-value=1.4e+02 Score=26.91 Aligned_cols=25 Identities=16% Similarity=0.429 Sum_probs=18.2
Q ss_pred CccceEEEEecCC----CCCcccCCCccc
Q 032127 121 QLQNVRVRFIPTD----KKDVHDLGPMEE 145 (147)
Q Consensus 121 ~~eNVsV~Vsp~~----~~sI~dfGsPee 145 (147)
.+.|+.+.|...| .-.+.-||+..+
T Consensus 111 ~~hnitldvrgsdc~ikgiamsgfgpvtq 139 (464)
T PRK10123 111 SMHNITLDVRGSDCTIKGLAMSGFGPVTQ 139 (464)
T ss_pred eeeeEEEeeccCceEEeeeeecccCceeE
Confidence 6789998888765 345677887654
No 24
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=22.57 E-value=67 Score=25.39 Aligned_cols=9 Identities=33% Similarity=0.279 Sum_probs=7.5
Q ss_pred hhhHHHHHH
Q 032127 53 KSKRRLLLM 61 (147)
Q Consensus 53 ~~~RR~aL~ 61 (147)
..+||++|.
T Consensus 7 ~~~rr~~l~ 15 (154)
T PRK07474 7 ALSRRQALA 15 (154)
T ss_pred CcCHHHHHH
Confidence 478999998
No 25
>PF05984 Cytomega_UL20A: Cytomegalovirus UL20A protein; InterPro: IPR009245 This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein [].
Probab=21.80 E-value=59 Score=23.92 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=11.9
Q ss_pred hHHHHHHHHHHHhhhh
Q 032127 55 KRRLLLMGAGLLTANL 70 (147)
Q Consensus 55 ~RR~aL~g~aa~~a~~ 70 (147)
.||..|++.+|+...+
T Consensus 2 aRRlwiLslLAVtLtV 17 (100)
T PF05984_consen 2 ARRLWILSLLAVTLTV 17 (100)
T ss_pred chhhHHHHHHHHHHHH
Confidence 5899998888765444
No 26
>TIGR02543 List_Bact_rpt Listeria/Bacterioides repeat. This model describes a conserved core region, about 43 residues in length, of at least two families of tandem repeats. These include 78-residue repeats from 2 to 15 in number, in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few bacteria.
Probab=21.55 E-value=96 Score=19.23 Aligned_cols=34 Identities=18% Similarity=0.403 Sum_probs=17.9
Q ss_pred CCCCeEEeccCCc-eEeeecCCcceecCcccCccceEE
Q 032127 91 RIDGYSYVYPSDW-TEFEFTGHDSGFKDRYLQLQNVRV 127 (147)
Q Consensus 91 ~~dGysflyPs~W-~ev~~~G~d~~f~D~~~~~eNVsV 127 (147)
.++||.|. || ..-++.++.--|-......+|+.|
T Consensus 2 ~k~GY~F~---GWY~d~~~~~~~~~~~~~~~~~~d~tl 36 (44)
T TIGR02543 2 TKPGYVFD---GWYGDSAFTTTVWNFTPDDMPTKDITL 36 (44)
T ss_pred CcCCcEee---eeEEcCCCCeeeEEecCCcccCCCEEE
Confidence 46899995 78 433333343334443334555544
No 27
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=20.60 E-value=84 Score=23.45 Aligned_cols=15 Identities=27% Similarity=0.383 Sum_probs=10.3
Q ss_pred chhhhHHHHHHHHHH
Q 032127 51 ENKSKRRLLLMGAGL 65 (147)
Q Consensus 51 ~~~~~RR~aL~g~aa 65 (147)
+...+||.++..++|
T Consensus 46 e~~~gRR~~mfaaaA 60 (103)
T PLN00058 46 QSTTMRRDLMFTAAA 60 (103)
T ss_pred cchhhHHHHHHHHHH
Confidence 456789999874444
Done!