Query 022002
Match_columns 304
No_of_seqs 35 out of 37
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 07:16:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022002hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3966 p53-mediated apoptosis 40.1 21 0.00045 35.5 2.3 24 186-209 131-154 (360)
2 KOG4686 Predicted sugar transp 36.3 31 0.00068 35.2 2.9 42 201-246 349-396 (459)
3 PF11137 DUF2909: Protein of u 33.3 57 0.0012 25.3 3.3 53 125-192 6-60 (63)
4 PF12794 MscS_TM: Mechanosensi 30.3 66 0.0014 31.1 4.0 78 112-191 127-219 (340)
5 PF07123 PsbW: Photosystem II 29.4 45 0.00096 29.7 2.4 29 247-277 95-123 (138)
6 PF11014 DUF2852: Protein of u 27.6 72 0.0016 27.6 3.3 28 252-279 3-30 (115)
7 PLN00082 photosystem II reacti 24.7 65 0.0014 25.7 2.3 28 247-276 23-50 (67)
8 PF15348 GEMIN8: Gemini of Caj 21.4 55 0.0012 30.4 1.6 24 212-235 184-207 (209)
9 PLN00077 photosystem II reacti 20.5 82 0.0018 27.8 2.3 28 247-276 84-111 (128)
10 PF01788 PsbJ: PsbJ; InterPro 18.7 66 0.0014 23.4 1.2 22 115-136 7-31 (40)
No 1
>KOG3966 consensus p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms; Defense mechanisms]
Probab=40.12 E-value=21 Score=35.53 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=14.7
Q ss_pred hcccCccCCCCCchhHHHHHHHHH
Q 022002 186 GSQKGFLQPQLPFIPFAVLLGPYL 209 (304)
Q Consensus 186 gv~~g~~gP~l~f~~~~v~L~PYL 209 (304)
++.|||++|++..+-..+-..|.+
T Consensus 131 ~~vw~wl~~~ls~lfg~iwVlPiF 154 (360)
T KOG3966|consen 131 NVVWGWLHPILSLLFGYIWVLPIF 154 (360)
T ss_pred cchHhhhhHHHHHHHHHHHHHHHH
Confidence 478899998554444444444444
No 2
>KOG4686 consensus Predicted sugar transporter [Carbohydrate transport and metabolism]
Probab=36.34 E-value=31 Score=35.15 Aligned_cols=42 Identities=19% Similarity=0.461 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCceeeeeeeeh------hhHHHHHHH
Q 022002 201 FAVLLGPYLLLLSIQILTEMLTWHWQSPVWLVTPVVY------ESYRVLQLM 246 (304)
Q Consensus 201 ~~v~L~PYLvgL~VQia~E~lt~~~kSPVWpvVPvIY------evYRl~QL~ 246 (304)
+...+-||..++..-..+-+++ -.-||+||.+- +.|-+-|=.
T Consensus 349 ~Ft~lsPy~~m~~lGLsysllA----cslWP~va~~vpE~qLGTaygf~qsI 396 (459)
T KOG4686|consen 349 FFTFLSPYTSMTFLGLSYSLLA----CSLWPCVASLVPEEQLGTAYGFIQSI 396 (459)
T ss_pred HhhhccHHHHHHHHhhhHHHHH----HHHhhhhhhhCCHHHhcchHHHHHHH
Confidence 4667789998888888888887 55699999875 356666653
No 3
>PF11137 DUF2909: Protein of unknown function (DUF2909); InterPro: IPR021313 This is a family of proteins conserved in Proteobacteria of unknown function.
Probab=33.33 E-value=57 Score=25.32 Aligned_cols=53 Identities=23% Similarity=0.355 Sum_probs=32.6
Q ss_pred hHhhcchhhhhhHHHHHhhhcccccccCCCccCCCCCCCCcchhhhhhhhh--hhHHhHHhhhhcccCcc
Q 022002 125 ILLGTDCIFNIGATLFLLMADSCARSKNTTRACNSKPPFSYKFWNMVANTT--GFIIPLLMLFGSQKGFL 192 (304)
Q Consensus 125 vLlgtealFyiGatlFLlmaD~~~Rp~~~~~~~~~~~P~syk~W~~~~~il--G~viPlv~m~gv~~g~~ 192 (304)
+++..=.+|++|.++|+++-|+. + +.|.....+.=+ +.++=++.+++.+.||+
T Consensus 6 v~lll~ii~sL~saL~~l~kd~~-~--------------~~rm~~~L~~RV~lS~~l~~lil~~~~~G~i 60 (63)
T PF11137_consen 6 VLLLLAIIASLFSALFFLVKDKG-S--------------SKRMVKALGRRVGLSALLFLLILIALYTGWI 60 (63)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCC-C--------------CchHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 34466789999999999999943 1 112222222222 23444555668999998
No 4
>PF12794 MscS_TM: Mechanosensitive ion channel inner membrane domain 1
Probab=30.28 E-value=66 Score=31.10 Aligned_cols=78 Identities=19% Similarity=0.254 Sum_probs=51.1
Q ss_pred cccchhhhhhhhHhHh-----------hcc----hhhhhhHHHHHhhhcccccccCCCccCCCCCCCCcchhhhhhhhhh
Q 022002 112 QFLKWPMWLLGPCILL-----------GTD----CIFNIGATLFLLMADSCARSKNTTRACNSKPPFSYKFWNMVANTTG 176 (304)
Q Consensus 112 ~~~k~plWLlGPsvLl-----------gte----alFyiGatlFLlmaD~~~Rp~~~~~~~~~~~P~syk~W~~~~~ilG 176 (304)
+.+||-.|.+-|.+.+ ..| ..|-++.....++.-+..|+..+...- ++..+.+....+.....
T Consensus 127 ~~l~~~~~~~~pl~~~~~~~~~~~~~~~~d~LGrl~~ii~~~~l~~~~~~l~~~~~~~~~~--~~~~~~~~~~~l~~~~l 204 (340)
T PF12794_consen 127 RQLRWLIWVLVPLLFISIFAENLPDGLARDVLGRLAFIILLLLLAVFLWRLLRPGWGLYQP--KPDSWIHRLRYLWWPLL 204 (340)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCchhhhhhhHHHHHHHHHHHHHHHHHHHHHccccccccC--CCcchhHHHHHHHHHHH
Confidence 5688999999999888 111 223333333334444566666555222 44456666777777778
Q ss_pred hHHhHHhhhhcccCc
Q 022002 177 FIIPLLMLFGSQKGF 191 (304)
Q Consensus 177 ~viPlv~m~gv~~g~ 191 (304)
.++|++..+.+..||
T Consensus 205 i~~Pl~li~la~~GY 219 (340)
T PF12794_consen 205 ILAPLALIVLALLGY 219 (340)
T ss_pred HHHHHHHHHHHHHhH
Confidence 899999999888898
No 5
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 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 []. This family represents the low molecular weight transmembrane protein PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=29.40 E-value=45 Score=29.72 Aligned_cols=29 Identities=38% Similarity=0.685 Sum_probs=24.6
Q ss_pred hhcccccccccchHHHHHhhhHHHHHHHHHH
Q 022002 247 RGLKLGAELSAPAWIVHTVRGLVCWWILILG 277 (304)
Q Consensus 247 RglqLv~~l~al~wv~~~i~GLvc~W~L~lg 277 (304)
-|+.|+-+++.+.|++..+-||+ |.||+-
T Consensus 95 TGL~lGlsn~~LgwIL~gVf~lI--WslY~~ 123 (138)
T PF07123_consen 95 TGLPLGLSNNLLGWILLGVFGLI--WSLYFV 123 (138)
T ss_pred ccccccccCchhHHHHHHHHHHH--HHHHHh
Confidence 48899999999999999988875 888753
No 6
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=27.60 E-value=72 Score=27.56 Aligned_cols=28 Identities=32% Similarity=0.573 Sum_probs=23.5
Q ss_pred ccccccchHHHHHhhhHHHHHHHHHHHH
Q 022002 252 GAELSAPAWIVHTVRGLVCWWILILGVQ 279 (304)
Q Consensus 252 v~~l~al~wv~~~i~GLvc~W~L~lg~q 279 (304)
+++-+-|+|+.-||.|.+.+|-+-|+|-
T Consensus 3 l~~~~~~a~Ia~mVlGFi~fWPlGla~L 30 (115)
T PF11014_consen 3 LDPRWKPAWIAAMVLGFIVFWPLGLALL 30 (115)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4566789999999999999999876653
No 7
>PLN00082 photosystem II reaction centre W protein (PsbW); Provisional
Probab=24.66 E-value=65 Score=25.67 Aligned_cols=28 Identities=36% Similarity=0.737 Sum_probs=23.1
Q ss_pred hhcccccccccchHHHHHhhhHHHHHHHHH
Q 022002 247 RGLKLGAELSAPAWIVHTVRGLVCWWILIL 276 (304)
Q Consensus 247 RglqLv~~l~al~wv~~~i~GLvc~W~L~l 276 (304)
-|+.|+-+++.+.|++..+-+++ |.+|.
T Consensus 23 tGl~lGls~~~LgwIL~gvf~li--w~ly~ 50 (67)
T PLN00082 23 TGLGLGVSNGKLTWILVGVTALI--WALYF 50 (67)
T ss_pred ccccccccCchhhhHHHHHHHHH--HHHHh
Confidence 47888889999999999888774 88764
No 8
>PF15348 GEMIN8: Gemini of Cajal bodies-associated protein 8
Probab=21.42 E-value=55 Score=30.43 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhhcCCceeeeeee
Q 022002 212 LSIQILTEMLTWHWQSPVWLVTPV 235 (304)
Q Consensus 212 L~VQia~E~lt~~~kSPVWpvVPv 235 (304)
-.+|+.|++.-...+..-||+||.
T Consensus 184 aalql~fd~~~D~~~P~~WP~IPL 207 (209)
T PF15348_consen 184 AALQLSFDKHCDRKQPKYWPVIPL 207 (209)
T ss_pred HHHHHHHHhhhcccCCCCCCCCCC
Confidence 478999999999999999999996
No 9
>PLN00077 photosystem II reaction centre W protein; Provisional
Probab=20.55 E-value=82 Score=27.79 Aligned_cols=28 Identities=39% Similarity=0.718 Sum_probs=23.5
Q ss_pred hhcccccccccchHHHHHhhhHHHHHHHHH
Q 022002 247 RGLKLGAELSAPAWIVHTVRGLVCWWILIL 276 (304)
Q Consensus 247 RglqLv~~l~al~wv~~~i~GLvc~W~L~l 276 (304)
-|+.|+-.++.+.|++..+-||+ |.+|+
T Consensus 84 tGl~lGlsn~~LgwIL~gVf~li--w~ly~ 111 (128)
T PLN00077 84 TGLSLGLSNNLLGWILLGVFGLI--WSLYT 111 (128)
T ss_pred ccccccccCchhhHHHHhHHHHH--HHHHh
Confidence 47888999999999999888875 88865
No 10
>PF01788 PsbJ: PsbJ; InterPro: IPR002682 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 []. This family represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (IPR003372 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers []. In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_J 3ARC_J 3A0B_J 3KZI_J 2AXT_J 3PRQ_J 4FBY_b 3BZ2_J 1S5L_j 3PRR_J ....
Probab=18.70 E-value=66 Score=23.40 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=12.4
Q ss_pred chhhhhhhhHhHh---hcchhhhhh
Q 022002 115 KWPMWLLGPCILL---GTDCIFNIG 136 (304)
Q Consensus 115 k~plWLlGPsvLl---gtealFyiG 136 (304)
+-|+||+|-..=+ ++=.+||.|
T Consensus 7 RIPLWlVgtv~G~~vi~lvglFfYG 31 (40)
T PF01788_consen 7 RIPLWLVGTVAGIAVIGLVGLFFYG 31 (40)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHHHHC
T ss_pred cccchHHHHHHHHHHHHHHHHheec
Confidence 4599998865432 444455554
Done!