Query 033813
Match_columns 111
No_of_seqs 27 out of 29
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:35:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033813.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033813hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00058 photosystem II reacti 100.0 2.4E-55 5.2E-60 316.0 6.9 103 1-111 1-103 (103)
2 TIGR02811 formate_TAT formate 82.1 1.8 3.9E-05 28.7 3.0 15 53-67 5-19 (66)
3 PF11054 Surface_antigen: Spor 77.0 0.76 1.7E-05 38.2 -0.0 15 92-106 195-209 (254)
4 PF10399 UCR_Fe-S_N: Ubiquitin 71.5 6.7 0.00015 24.1 3.2 16 52-67 4-19 (41)
5 PF02315 MDH: Methanol dehydro 66.2 2.1 4.5E-05 31.1 0.2 38 61-98 3-52 (93)
6 PF10518 TAT_signal: TAT (twin 59.5 13 0.00027 20.7 2.5 18 57-74 2-19 (26)
7 PLN00042 photosystem II oxygen 34.8 75 0.0016 26.5 4.4 27 58-84 51-78 (260)
8 COG5572 Predicted integral mem 33.9 39 0.00084 25.0 2.4 33 57-89 11-43 (104)
9 PF05757 PsbQ: Oxygen evolving 27.6 20 0.00044 28.5 0.0 46 22-80 7-54 (202)
10 PF12276 DUF3617: Protein of u 24.7 71 0.0015 22.5 2.3 7 83-89 25-31 (162)
11 PF10814 DUF2562: Protein of u 22.4 39 0.00085 26.0 0.7 26 55-80 85-110 (133)
12 PF02630 SCO1-SenC: SCO1/SenC; 21.1 42 0.00092 24.5 0.6 17 82-98 95-111 (174)
No 1
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=100.00 E-value=2.4e-55 Score=315.98 Aligned_cols=103 Identities=56% Similarity=0.793 Sum_probs=97.8
Q ss_pred CccchhhhhhhccccccCCCcccccCCcceEEeeehhhhcccccccccccccccccchhHHHHHHHHHHHHHhhhhhhhh
Q 033813 1 MASMTMAAASLLPTSMAKNPAATRAKRGGLIVVAKAASSKAENVSMEFKNKDESSSNGRRELVFAAAAAAACSIAKVAMA 80 (111)
Q Consensus 1 MAS~TMta~Sfl~~~a~~~~~~~~a~rR~lvVv~~Aa~~~~~~~~~~~~~~~~~~~~gRR~lmFAAAAAAvcsva~~AmA 80 (111)
|||||||+ ||| +++++ |+++++||+|+|| ||+ +++++|++++++ + |++||||||||++||++||||+|+|||
T Consensus 1 MAS~TMta-Sfl--~~~~~-~~~~~~rr~l~Vv-~Aa-k~~~~e~v~~~~-~-e~~~gRR~~mfaaaAaav~s~a~~A~a 72 (103)
T PLN00058 1 MASMTMTA-TFL--PAVAK-LPSATGGRRLSVV-RAS-TSDNTPSLEVKE-Q-QSTTMRRDLMFTAAAAAVCSLAKVAMA 72 (103)
T ss_pred CccchhHH-HHH--HHHhc-cCCcccCceEEEE-Ecc-ccccccceeecc-c-cchhhHHHHHHHHHHHHHHhhhHHHhh
Confidence 99999999 999 47777 8899999999998 999 999999999997 4 899999999999999999999999999
Q ss_pred hcCCCCCCChhhhhhcCCceeeccccccccC
Q 033813 81 ESEEPKRGTPDAKKKYAPVCVTMPTARICRK 111 (111)
Q Consensus 81 e~~ePKrGTpeAKKkYApVCVTmPTArICr~ 111 (111)
|++||||||||||||||||||||||||||||
T Consensus 73 ~~~epk~Gt~eAKKkYa~iCVtmPTA~iC~~ 103 (103)
T PLN00058 73 EEEEPKRGTEAAKKKYAQVCVTMPTAKICRY 103 (103)
T ss_pred cccCCCCCCHHHHhcccceeecCchhhhhcC
Confidence 7789999999999999999999999999998
No 2
>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=82.15 E-value=1.8 Score=28.74 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=11.0
Q ss_pred ccccchhHHHHHHHH
Q 033813 53 ESSSNGRRELVFAAA 67 (111)
Q Consensus 53 ~~~~~gRR~lmFAAA 67 (111)
.+.+.+|||+|-.++
T Consensus 5 ~~~~~sRR~Flk~lg 19 (66)
T TIGR02811 5 QKADPSRRDLLKGLG 19 (66)
T ss_pred ccCCccHHHHHHHHH
Confidence 456789999887544
No 3
>PF11054 Surface_antigen: Sporozoite TA4 surface antigen; InterPro: IPR021288 This family of proteins is a Eukaryotic family of surface antigens. One of the better characterised members of the family is the sporulated TA4 antigen. The TA4 gene encodes a single polypeptide of 25 kDa which contains a 17 and a 8kDa polypeptide [].
Probab=76.95 E-value=0.76 Score=38.15 Aligned_cols=15 Identities=53% Similarity=0.922 Sum_probs=14.2
Q ss_pred hhhhcCCceeecccc
Q 033813 92 AKKKYAPVCVTMPTA 106 (111)
Q Consensus 92 AKKkYApVCVTmPTA 106 (111)
.|+-||=||-|||+|
T Consensus 195 ~~~gyAliCkT~P~A 209 (254)
T PF11054_consen 195 SKTGYALICKTMPAA 209 (254)
T ss_pred ccceEEEEEecCchh
Confidence 889999999999997
No 4
>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=71.47 E-value=6.7 Score=24.15 Aligned_cols=16 Identities=25% Similarity=0.410 Sum_probs=7.3
Q ss_pred cccccchhHHHHHHHH
Q 033813 52 DESSSNGRRELVFAAA 67 (111)
Q Consensus 52 ~~~~~~gRR~lmFAAA 67 (111)
+++...+|||.+..+.
T Consensus 4 ~~~~~~~RRdFL~~at 19 (41)
T PF10399_consen 4 NEPVDPTRRDFLTIAT 19 (41)
T ss_dssp ------HHHHHHHHHH
T ss_pred CCCCCchHHHHHHHHH
Confidence 3456789999885443
No 5
>PF02315 MDH: Methanol dehydrogenase beta subunit; InterPro: IPR003420 Methanol dehydrogenase (MDH) (1.1.99.8 from EC), found in Gram-negative bacteria, is a pyrroloquinoline quinone (PQQ)-containing enzyme which oxidises methanol to formaldehyde. It is located in the periplasmic space and passes electrons derived from the oxidation of methanol to the soluble cytochrome cL []. The enzyme is a tetramer composed of two large alpha subunits and two smaller beta subunits. The alpha subunit binds the PQQ cofactor and contains the active site, while the function of the beta subunit is currently unknown []. The alpha subunit forms an eight-bladed propeller structure, with several novel tryptophan-docking motifs linking the individual blades together. This entry represents the beta subunit of methanol dehydrogenase.; GO: 0004022 alcohol dehydrogenase (NAD) activity, 0015946 methanol oxidation, 0055114 oxidation-reduction process; PDB: 1LRW_B 2D0V_J 2AD6_B 1G72_B 4AAH_D 2AD8_D 2AD7_D 1H4J_D 1H4I_B 1W6S_B ....
Probab=66.21 E-value=2.1 Score=31.14 Aligned_cols=38 Identities=47% Similarity=0.645 Sum_probs=5.7
Q ss_pred HHHHHHHHHHHHhhhhhhhh-hc---------CCCCCCChhhh--hhcCC
Q 033813 61 ELVFAAAAAAACSIAKVAMA-ES---------EEPKRGTPDAK--KKYAP 98 (111)
Q Consensus 61 ~lmFAAAAAAvcsva~~AmA-e~---------~ePKrGTpeAK--KkYAp 98 (111)
.++++++++++.+.++.|+| |+ -|||+|=||-- -||-|
T Consensus 3 ~~~~~~~~~~~~~~a~~A~AYDGt~CkapG~CWEpkPGyPekiaGSKYDP 52 (93)
T PF02315_consen 3 TVLLAAAAAAALATAGAALAYDGTNCKAPGNCWEPKPGYPEKIAGSKYDP 52 (93)
T ss_dssp ----------------------S---SBTTB-----TTS-SS-TTSTT--
T ss_pred hhHHHHHHHHHHhcchhhhhccCcccCCCccccCCCCCCcccccccccCC
Confidence 35566677777778899998 52 38999999832 45533
No 6
>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=59.48 E-value=13 Score=20.65 Aligned_cols=18 Identities=39% Similarity=0.423 Sum_probs=13.6
Q ss_pred chhHHHHHHHHHHHHHhh
Q 033813 57 NGRRELVFAAAAAAACSI 74 (111)
Q Consensus 57 ~gRR~lmFAAAAAAvcsv 74 (111)
.-||+++-..+++++...
T Consensus 2 ~sRR~fLk~~~a~~a~~~ 19 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAAAA 19 (26)
T ss_pred CcHHHHHHHHHHHHHHHH
Confidence 359999998887766654
No 7
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=34.76 E-value=75 Score=26.53 Aligned_cols=27 Identities=37% Similarity=0.260 Sum_probs=12.0
Q ss_pred hhHHH-HHHHHHHHHHhhhhhhhhhcCC
Q 033813 58 GRREL-VFAAAAAAACSIAKVAMAESEE 84 (111)
Q Consensus 58 gRR~l-mFAAAAAAvcsva~~AmAe~~e 84 (111)
-||.. ...+.++++-+--..|.|.|.|
T Consensus 51 srr~~l~~~~ga~a~~~~~~pa~aay~~ 78 (260)
T PLN00042 51 SRRAALALLAGAAAAGAKVSPANAAYGE 78 (260)
T ss_pred cHHHHHHHHHHHHHhhcccCchhhhhcc
Confidence 45544 4444444554544444443333
No 8
>COG5572 Predicted integral membrane protein [Function unknown]
Probab=33.92 E-value=39 Score=25.02 Aligned_cols=33 Identities=36% Similarity=0.243 Sum_probs=22.2
Q ss_pred chhHHHHHHHHHHHHHhhhhhhhhhcCCCCCCC
Q 033813 57 NGRRELVFAAAAAAACSIAKVAMAESEEPKRGT 89 (111)
Q Consensus 57 ~gRR~lmFAAAAAAvcsva~~AmAe~~ePKrGT 89 (111)
..-|.+.-+|.++++.+.+++.-+...|||.|-
T Consensus 11 ~~~~am~aaAla~alal~A~~spa~aae~ka~A 43 (104)
T COG5572 11 LMTRAMTAAALAAALALSAGVSPAAAAEHKAGA 43 (104)
T ss_pred HHHHHHHHHHHHHHHHhhccCCchhhccccccc
Confidence 344566666667777777887777546898753
No 9
>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=27.65 E-value=20 Score=28.46 Aligned_cols=46 Identities=33% Similarity=0.320 Sum_probs=0.0
Q ss_pred ccccCCcceEEeeehhhhcccccccccccccccccchhHHHHH--HHHHHHHHhhhhhhhh
Q 033813 22 ATRAKRGGLIVVAKAASSKAENVSMEFKNKDESSSNGRRELVF--AAAAAAACSIAKVAMA 80 (111)
Q Consensus 22 ~~~a~rR~lvVv~~Aa~~~~~~~~~~~~~~~~~~~~gRR~lmF--AAAAAAvcsva~~AmA 80 (111)
+..+.+|+.++| ||. . . ..+....||.++- .+++++..+....+.+
T Consensus 7 ~~~~~~r~~~~v-ra~-~----------~-~~~~~~~RRa~l~~l~a~~~~~~~~~~~~~a 54 (202)
T PF05757_consen 7 SRVASRRAGVVV-RAS-Q----------S-PAQQQTSRRAVLGSLLAAALAGGSFAQAAAA 54 (202)
T ss_dssp -------------------------------------------------------------
T ss_pred Ccccccccccee-ccc-c----------C-cccccccHHHHHHHHHHHHHHhhhccccccc
Confidence 344556666666 777 2 1 3345667888843 4444444444444444
No 10
>PF12276 DUF3617: Protein of unknown function (DUF3617); InterPro: IPR022061 This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Probab=24.67 E-value=71 Score=22.51 Aligned_cols=7 Identities=29% Similarity=0.344 Sum_probs=5.1
Q ss_pred CCCCCCC
Q 033813 83 EEPKRGT 89 (111)
Q Consensus 83 ~ePKrGT 89 (111)
..+|+|=
T Consensus 25 ~~~kpGl 31 (162)
T PF12276_consen 25 PDIKPGL 31 (162)
T ss_pred CCCCCcc
Confidence 5788884
No 11
>PF10814 DUF2562: Protein of unknown function (DUF2562); InterPro: IPR024245 This protein of unknown function appears to be found predominantly in Mycobacterium spp.
Probab=22.37 E-value=39 Score=25.98 Aligned_cols=26 Identities=31% Similarity=0.339 Sum_probs=20.8
Q ss_pred ccchhHHHHHHHHHHHHHhhhhhhhh
Q 033813 55 SSNGRRELVFAAAAAAACSIAKVAMA 80 (111)
Q Consensus 55 ~~~gRR~lmFAAAAAAvcsva~~AmA 80 (111)
..-+||.|+|++.+++|...+++|+.
T Consensus 85 ~rr~rRplliagv~~~vLagGavAfs 110 (133)
T PF10814_consen 85 RRRRRRPLLIAGVAVAVLAGGAVAFS 110 (133)
T ss_pred ccccccchHHHHHHHHHHhccceEEE
Confidence 44557999999999999777777775
No 12
>PF02630 SCO1-SenC: SCO1/SenC; InterPro: IPR003782 This family is involved in biogenesis of respiratory and photosynthetic systems. In yeast the SCO1 protein is specifically required for a post-translational step in the accumulation of subunits 1 and 2 of cytochrome c oxidase (COXI and COX-II) []. It is a mitochondrion-associated cytochrome c oxidase assembly factor. The purple nonsulphur photosynthetic eubacterium Rhodobacter capsulatus is a versatile organism that can obtain cellular energy by several means, including the capture of light energy for photosynthesis as well as the use of light-independent respiration, in which molecular oxygen serves as a terminal electron acceptor. The SenC protein is required for optimal cytochrome c oxidase activity in aerobically grown R. capsulatus cells and is involved in the induction of structural polypeptides of the light-harvesting and reaction centre complexes [].; PDB: 2K6V_A 3ME8_A 3ME7_A 2GT6_A 2GQL_A 2GQK_A 2GGT_B 1WP0_C 2HRN_A 2GQM_A ....
Probab=21.08 E-value=42 Score=24.52 Aligned_cols=17 Identities=53% Similarity=0.851 Sum_probs=13.7
Q ss_pred cCCCCCCChhhhhhcCC
Q 033813 82 SEEPKRGTPDAKKKYAP 98 (111)
Q Consensus 82 ~~ePKrGTpeAKKkYAp 98 (111)
+-+|+|-|||.-|+|+.
T Consensus 95 SvDP~~DTp~~L~~Y~~ 111 (174)
T PF02630_consen 95 SVDPERDTPEVLKKYAK 111 (174)
T ss_dssp ESSTTTC-HHHHHHHHH
T ss_pred EeCCCCCCHHHHHHHHH
Confidence 45899999999999974
Done!