Query 035725
Match_columns 86
No_of_seqs 100 out of 113
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:50:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05078 DUF679: Protein of un 100.0 5.1E-42 1.1E-46 251.0 6.9 76 4-79 95-170 (170)
2 PF10894 DUF2689: Protein of u 64.5 3.6 7.7E-05 26.2 1.0 9 14-22 21-29 (61)
3 PF15623 CT47: Cancer/testis g 62.4 4.1 9E-05 32.6 1.2 24 2-26 110-133 (279)
4 PRK13724 conjugal transfer pro 59.7 4.9 0.00011 25.8 1.0 9 14-22 21-29 (65)
5 PF11395 DUF2873: Protein of u 54.9 14 0.0003 21.9 2.3 23 10-32 3-25 (43)
6 KOG4833 Uncharacterized conser 52.0 5.8 0.00013 34.0 0.5 26 12-46 499-524 (573)
7 PF15601 Imm42: Immunity prote 51.5 11 0.00023 27.0 1.7 23 5-27 6-28 (134)
8 PRK04989 psbM photosystem II r 48.8 3 6.6E-05 24.0 -1.2 14 59-72 6-19 (35)
9 CHL00080 psbM photosystem II p 47.8 3.3 7.2E-05 23.7 -1.1 15 59-73 6-20 (34)
10 TIGR03038 PS_II_psbM photosyst 40.2 4.9 0.00011 22.9 -1.2 14 59-72 6-19 (33)
11 PF05237 MoeZ_MoeB: MoeZ/MoeB 39.9 4 8.6E-05 25.9 -1.8 29 37-65 6-36 (84)
12 PF03770 IPK: Inositol polypho 39.3 8.1 0.00018 28.0 -0.5 16 6-21 160-175 (197)
13 PRK14094 psbM photosystem II r 36.6 7 0.00015 24.1 -1.0 15 59-73 6-20 (50)
14 PF05403 Plasmodium_HRP: Plasm 32.2 31 0.00067 26.5 1.7 19 20-38 9-27 (218)
15 PF09904 HTH_43: Winged helix- 31.5 15 0.00033 24.9 -0.1 33 43-79 33-65 (90)
16 PF12949 HeH: HeH/LEM domain; 30.6 19 0.0004 20.3 0.2 12 74-85 15-26 (35)
17 KOG3030 Lipid phosphate phosph 29.5 63 0.0014 25.9 3.1 46 18-65 185-230 (317)
18 PLN02667 inositol polyphosphat 29.1 17 0.00037 28.5 -0.2 15 6-20 235-249 (286)
19 PF08134 cIII: cIII protein fa 26.2 44 0.00096 20.0 1.3 34 29-62 4-40 (44)
20 PRK14386 hypothetical protein; 26.2 62 0.0013 22.5 2.2 46 37-82 22-69 (106)
21 PF05151 PsbM: Photosystem II 25.9 9.5 0.00021 21.4 -1.5 14 59-72 6-19 (31)
22 COG4818 Predicted membrane pro 25.4 49 0.0011 23.1 1.6 17 17-33 33-49 (105)
23 PRK13735 conjugal transfer mat 23.6 49 0.0011 30.4 1.6 17 50-66 89-105 (942)
24 PF10660 MitoNEET_N: Iron-cont 22.1 34 0.00074 21.7 0.3 33 9-44 29-61 (64)
25 PRK04439 S-adenosylmethionine 21.2 35 0.00076 28.6 0.2 10 73-82 23-32 (399)
26 PF10582 Connexin_CCC: Gap jun 21.1 71 0.0015 20.3 1.6 31 34-66 29-59 (67)
No 1
>PF05078 DUF679: Protein of unknown function (DUF679); InterPro: IPR007770 This family contains uncharacterised plant proteins of unknown function.
Probab=100.00 E-value=5.1e-42 Score=251.00 Aligned_cols=76 Identities=67% Similarity=1.204 Sum_probs=75.0
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHhccCCcccccCCCCCccHHHHHHHhhhHHHHhhhheeeecCCCCccccC
Q 035725 4 PDLNKYRIRFIDGVHAVLSVLVFAAVALRDKNVLSCFFPTPKHETQEVLDIVPVGIGLICSLLFVIFPTRRHGIGY 79 (86)
Q Consensus 4 ~~~s~yrLr~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~vF~iFPt~RhGIGy 79 (86)
++++|||||++|||||++|++||+++|++|+|||+||||++++|+||+|+++|++||++||++||+|||+||||||
T Consensus 95 ~~~~~yrlr~~DfvHA~lS~~VF~aval~d~~v~~Cf~P~~~~~~~~~l~~lP~~vG~~~S~vF~~FPt~R~GIGy 170 (170)
T PF05078_consen 95 RDLSKYRLRFIDFVHAFLSVVVFLAVALSDQNVVSCFFPSPSSETKEVLMNLPLGVGVLCSMVFMIFPTTRHGIGY 170 (170)
T ss_pred cccccceEehhhhhHHHHHHHHHHHhheeCCCcceecCCCCchhHHHHHHHhHHHHHHhHeeEEEECCCCCCCCCC
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=64.47 E-value=3.6 Score=26.21 Aligned_cols=9 Identities=67% Similarity=0.567 Sum_probs=7.9
Q ss_pred chhhHHHHH
Q 035725 14 IDGVHAVLS 22 (86)
Q Consensus 14 ~DfvHA~lS 22 (86)
-||+||++|
T Consensus 21 DDFmhaVlS 29 (61)
T PF10894_consen 21 DDFMHAVLS 29 (61)
T ss_pred HHHHHHHHh
Confidence 499999987
No 3
>PF15623 CT47: Cancer/testis gene family 47
Probab=62.36 E-value=4.1 Score=32.56 Aligned_cols=24 Identities=29% Similarity=0.721 Sum_probs=18.4
Q ss_pred CCCCccccccccchhhHHHHHHHHH
Q 035725 2 DLPDLNKYRIRFIDGVHAVLSVLVF 26 (86)
Q Consensus 2 ~~~~~s~yrLr~~DfvHA~lS~~VF 26 (86)
.+| ...||+.|+|.||+.|-=+-.
T Consensus 110 ~fP-maGfR~~fLDLVhslL~RiY~ 133 (279)
T PF15623_consen 110 RFP-MAGFRFMFLDLVHSLLNRIYY 133 (279)
T ss_pred ccc-cccceeeHHHHHHHHHHHHhh
Confidence 445 467999999999998865543
No 4
>PRK13724 conjugal transfer protein TrbD; Provisional
Probab=59.66 E-value=4.9 Score=25.84 Aligned_cols=9 Identities=67% Similarity=0.567 Sum_probs=7.9
Q ss_pred chhhHHHHH
Q 035725 14 IDGVHAVLS 22 (86)
Q Consensus 14 ~DfvHA~lS 22 (86)
-||+||++|
T Consensus 21 DDF~h~VlS 29 (65)
T PRK13724 21 DDFMHAVLS 29 (65)
T ss_pred HHHHHHHHh
Confidence 499999987
No 5
>PF11395 DUF2873: Protein of unknown function (DUF2873); InterPro: IPR021532 This entry is represented by the human SARS coronavirus, Orf7b; it is a family of uncharacterised viral proteins.
Probab=54.95 E-value=14 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=20.1
Q ss_pred ccccchhhHHHHHHHHHHHHHhc
Q 035725 10 RIRFIDGVHAVLSVLVFAAVALR 32 (86)
Q Consensus 10 rLr~~DfvHA~lS~~VF~avAl~ 32 (86)
.|+.+||--.++|.+.|+++.+.
T Consensus 3 ~ltl~dfylc~l~~llflv~iml 25 (43)
T PF11395_consen 3 HLTLFDFYLCFLSFLLFLVIIML 25 (43)
T ss_pred ceehhHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998764
No 6
>KOG4833 consensus Uncharacterized conserved protein [Function unknown]
Probab=52.03 E-value=5.8 Score=34.02 Aligned_cols=26 Identities=38% Similarity=0.641 Sum_probs=21.6
Q ss_pred ccchhhHHHHHHHHHHHHHhccCCcccccCCCCCc
Q 035725 12 RFIDGVHAVLSVLVFAAVALRDKNVLSCFFPTPKH 46 (86)
Q Consensus 12 r~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~~ 46 (86)
+.+||+||+- ++|-|+..||||..+.
T Consensus 499 piidfnhaVc---------fsdLnIadcflpieSr 524 (573)
T KOG4833|consen 499 PIIDFNHAVC---------FSDLNIADCFLPIESR 524 (573)
T ss_pred HHHHHHHHHH---------HhcccHhHheehhHhh
Confidence 5789999864 5789999999998763
No 7
>PF15601 Imm42: Immunity protein 42
Probab=51.52 E-value=11 Score=27.02 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=18.7
Q ss_pred CccccccccchhhHHHHHHHHHH
Q 035725 5 DLNKYRIRFIDGVHAVLSVLVFA 27 (86)
Q Consensus 5 ~~s~yrLr~~DfvHA~lS~~VF~ 27 (86)
+..-|.+.-.||+|+|+|.+..-
T Consensus 6 ~~~~~eiG~~dfl~sFFsti~~~ 28 (134)
T PF15601_consen 6 GFSWYEIGPPDFLHSFFSTISYR 28 (134)
T ss_pred CceEEEeCCHHHHHHHHHHHHHH
Confidence 34568999999999999987653
No 8
>PRK04989 psbM photosystem II reaction center protein M; Provisional
Probab=48.81 E-value=3 Score=24.00 Aligned_cols=14 Identities=57% Similarity=1.156 Sum_probs=12.1
Q ss_pred HHHhhhheeeecCC
Q 035725 59 IGLICSLLFVIFPT 72 (86)
Q Consensus 59 vG~~~S~vF~iFPt 72 (86)
.|++++.+|+..||
T Consensus 6 lgfiAt~Lfi~iPt 19 (35)
T PRK04989 6 LGFVASLLFVLVPT 19 (35)
T ss_pred HHHHHHHHHHHHHH
Confidence 58899999998887
No 9
>CHL00080 psbM photosystem II protein M
Probab=47.79 E-value=3.3 Score=23.73 Aligned_cols=15 Identities=33% Similarity=0.813 Sum_probs=12.7
Q ss_pred HHHhhhheeeecCCC
Q 035725 59 IGLICSLLFVIFPTR 73 (86)
Q Consensus 59 vG~~~S~vF~iFPt~ 73 (86)
.|++++.+|+..||-
T Consensus 6 lgfiAt~LFi~iPt~ 20 (34)
T CHL00080 6 LAFIATALFILVPTA 20 (34)
T ss_pred HHHHHHHHHHHHHHH
Confidence 589999999998873
No 10
>TIGR03038 PS_II_psbM photosystem II reaction center protein PsbM. Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles Pfam model pfam05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic.
Probab=40.18 E-value=4.9 Score=22.86 Aligned_cols=14 Identities=50% Similarity=1.153 Sum_probs=11.6
Q ss_pred HHHhhhheeeecCC
Q 035725 59 IGLICSLLFVIFPT 72 (86)
Q Consensus 59 vG~~~S~vF~iFPt 72 (86)
.|++++.+|...||
T Consensus 6 l~fiAt~Lfi~iPt 19 (33)
T TIGR03038 6 LGFIATLLFILVPT 19 (33)
T ss_pred HHHHHHHHHHHHHH
Confidence 47888888888886
No 11
>PF05237 MoeZ_MoeB: MoeZ/MoeB domain; InterPro: IPR007901 This putative domain is found in the MoeZ protein and the MoeB protein. The domain has two CXXC motifs that are only partly conserved. MoeZ is necessary for the synthesis of pyridine-2,6-bis(thiocarboxylic acid), a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to reduce both soluble and mineral forms of iron, and has antimicrobial activity towards several species of bacteria. MoeB is the molybdopterin synthase activating enzyme in the molybdopterin cofactor biosynthesis pathway. Both these enzymes are members of a superfamily consisting of related but structurally distinct proteins that are members of pathways involved in the transfer of sulphur-containing moieties to metabolites [] and both also contain the UBA/THIF-type NAD/FAD binding fold (IPR000594 from INTERPRO). ; PDB: 1JWA_B 1JW9_B 1JWB_B 1ZKM_D 1ZUD_3 1ZFN_D.
Probab=39.92 E-value=4 Score=25.86 Aligned_cols=29 Identities=31% Similarity=0.591 Sum_probs=16.9
Q ss_pred ccccCCCCCcc--HHHHHHHhhhHHHHhhhh
Q 035725 37 LSCFFPTPKHE--TQEVLDIVPVGIGLICSL 65 (86)
Q Consensus 37 v~Cf~P~~~~~--~~~ll~~lPl~vG~~~S~ 65 (86)
-+|+||..... +-+-.-.++..+|+++|+
T Consensus 6 ~rCl~p~~~~~~~~C~~~GVlg~~~giigsl 36 (84)
T PF05237_consen 6 YRCLFPEPPESAPTCAEAGVLGPVVGIIGSL 36 (84)
T ss_dssp HHHHHTTSS--TTSSSTS-B-HHHHHHHHHH
T ss_pred ehhcCCCCCccCCCccccccccchHHHHHHH
Confidence 47999988211 112336788888888876
No 12
>PF03770 IPK: Inositol polyphosphate kinase ; InterPro: IPR005522 ArgRIII has been demonstrated to be an inositol polyphosphate kinase [] which catalyses the reaction ATP + 1D-myo-inositol 1,4,5-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate .; GO: 0008440 inositol trisphosphate 3-kinase activity; PDB: 2IF8_B 2IEW_B 1W2C_A 1W2F_A 1W2D_A 2A98_A 2AQX_A 1TZD_A.
Probab=39.32 E-value=8.1 Score=27.97 Aligned_cols=16 Identities=31% Similarity=0.389 Sum_probs=10.7
Q ss_pred ccccccccchhhHHHH
Q 035725 6 LNKYRIRFIDGVHAVL 21 (86)
Q Consensus 6 ~s~yrLr~~DfvHA~l 21 (86)
..++++|.|||.|+..
T Consensus 160 ~~~~~vklIDFAH~~~ 175 (197)
T PF03770_consen 160 PNKVDVKLIDFAHVFP 175 (197)
T ss_dssp -S-EEEEEE--TTEEE
T ss_pred CCcccEEEEECCCccc
Confidence 4679999999999876
No 13
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=36.56 E-value=7 Score=24.06 Aligned_cols=15 Identities=53% Similarity=0.824 Sum_probs=12.5
Q ss_pred HHHhhhheeeecCCC
Q 035725 59 IGLICSLLFVIFPTR 73 (86)
Q Consensus 59 vG~~~S~vF~iFPt~ 73 (86)
.|++++.+|+..||-
T Consensus 6 lgfiAtaLFi~iPT~ 20 (50)
T PRK14094 6 FGFVASLLFVGVPTI 20 (50)
T ss_pred HHHHHHHHHHHHHHH
Confidence 588999999988874
No 14
>PF05403 Plasmodium_HRP: Plasmodium histidine-rich protein (HRPII/III); InterPro: IPR008779 This family consists of several histidine-rich protein II and III sequence from Plasmodium falciparum [, ].
Probab=32.15 E-value=31 Score=26.46 Aligned_cols=19 Identities=47% Similarity=0.550 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHhccCCccc
Q 035725 20 VLSVLVFAAVALRDKNVLS 38 (86)
Q Consensus 20 ~lS~~VF~avAl~D~nvv~ 38 (86)
+||..||..|.|+|.|-..
T Consensus 9 ilsaavfasvllldnnns~ 27 (218)
T PF05403_consen 9 ILSAAVFASVLLLDNNNSE 27 (218)
T ss_pred HHHHHHHHHhheecCCcHH
Confidence 5899999999999988653
No 15
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=31.49 E-value=15 Score=24.92 Aligned_cols=33 Identities=24% Similarity=0.677 Sum_probs=21.5
Q ss_pred CCCccHHHHHHHhhhHHHHhhhheeeecCCCCccccC
Q 035725 43 TPKHETQEVLDIVPVGIGLICSLLFVIFPTRRHGIGY 79 (86)
Q Consensus 43 ~~~~~~~~ll~~lPl~vG~~~S~vF~iFPt~RhGIGy 79 (86)
.|..+.+..|++|| .+|+-|.++= ...||-.||
T Consensus 33 mPrRT~Qd~i~aL~-~~~I~~~Fvq---~G~R~~~Gy 65 (90)
T PF09904_consen 33 MPRRTIQDTIKALP-ELGIECEFVQ---DGERNNAGY 65 (90)
T ss_dssp --HHHHHHHHHGGG-GGT-EEEEE-----TTS-S--E
T ss_pred CCHhHHHHHHHHhh-cCCeEEEEEe---cCccCCCCc
Confidence 45566799999999 9999998776 788888887
No 16
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=30.63 E-value=19 Score=20.33 Aligned_cols=12 Identities=42% Similarity=0.833 Sum_probs=5.3
Q ss_pred CccccCCCCCCC
Q 035725 74 RHGIGYPITPGK 85 (86)
Q Consensus 74 RhGIGyp~~~~~ 85 (86)
.|||.||.+..|
T Consensus 15 ~~~I~~ps~AkK 26 (35)
T PF12949_consen 15 EHGIEFPSNAKK 26 (35)
T ss_dssp HHT---SSS--S
T ss_pred HcCCCCCCCCCH
Confidence 589999987655
No 17
>KOG3030 consensus Lipid phosphate phosphatase and related enzymes of the PAP2 family [Lipid transport and metabolism]
Probab=29.48 E-value=63 Score=25.94 Aligned_cols=46 Identities=22% Similarity=0.286 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhccCCcccccCCCCCccHHHHHHHhhhHHHHhhhh
Q 035725 18 HAVLSVLVFAAVALRDKNVLSCFFPTPKHETQEVLDIVPVGIGLICSL 65 (86)
Q Consensus 18 HA~lS~~VF~avAl~D~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~ 65 (86)
||.+|.-.++-+|+-=++-..++- .++-.|-+|+-+|++++++++.
T Consensus 185 HsS~s~y~~~flalyl~~~~~~~~--~~rllr~~l~f~~l~~A~~v~l 230 (317)
T KOG3030|consen 185 HSSFSFYAMGFLALYLQARLFWFG--RGRLLRPLLQFLPLMLALLVGL 230 (317)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCC--CchhHHHHHHHHHHHHHHHHee
Confidence 888887766666654444444444 4566899999999999888764
No 18
>PLN02667 inositol polyphosphate multikinase
Probab=29.08 E-value=17 Score=28.52 Aligned_cols=15 Identities=13% Similarity=0.386 Sum_probs=13.1
Q ss_pred ccccccccchhhHHH
Q 035725 6 LNKYRIRFIDGVHAV 20 (86)
Q Consensus 6 ~s~yrLr~~DfvHA~ 20 (86)
.++.++|.|||.|+.
T Consensus 235 ~~~v~VkmIDFAH~~ 249 (286)
T PLN02667 235 DSRVEVKLVDFAHVL 249 (286)
T ss_pred CCcceEEEEeCcccc
Confidence 468999999999985
No 19
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=26.21 E-value=44 Score=19.99 Aligned_cols=34 Identities=15% Similarity=0.363 Sum_probs=22.2
Q ss_pred HHhccCCcccccCCCCCcc---HHHHHHHhhhHHHHh
Q 035725 29 VALRDKNVLSCFFPTPKHE---TQEVLDIVPVGIGLI 62 (86)
Q Consensus 29 vAl~D~nvv~Cf~P~~~~~---~~~ll~~lPl~vG~~ 62 (86)
+++.-.+|.+-|||..++- .++++.+.-.-.-.+
T Consensus 4 ~~laG~gvmSAyYP~ESELskr~rrLIRaa~k~leal 40 (44)
T PF08134_consen 4 LQLAGSGVMSAYYPTESELSKRIRRLIRAARKQLEAL 40 (44)
T ss_pred EEecCceeeeeecCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566788999999988744 466666544333333
No 20
>PRK14386 hypothetical protein; Provisional
Probab=26.15 E-value=62 Score=22.53 Aligned_cols=46 Identities=24% Similarity=0.254 Sum_probs=31.8
Q ss_pred ccccC-CCCCccHHHHHHHhhhHHHHhhhheeeecCCCCccccC-CCC
Q 035725 37 LSCFF-PTPKHETQEVLDIVPVGIGLICSLLFVIFPTRRHGIGY-PIT 82 (86)
Q Consensus 37 v~Cf~-P~~~~~~~~ll~~lPl~vG~~~S~vF~iFPt~RhGIGy-p~~ 82 (86)
-+|.| |+.|+=+.|-++.-.+.-|..-++-=++==..=++.|| |+.
T Consensus 22 ~~CRf~PTCS~Ya~~Ai~~~G~~kG~~L~~~RIlRCnP~~~gGyDPVP 69 (106)
T PRK14386 22 PRCRYIPTCSQYALEALQTHGAIKGVWLSSKRICRCHPWGGSGYDPVP 69 (106)
T ss_pred CCCCcCcCHHHHHHHHHHHhCcHHHHHHHHHHHhcCCCCCCCCcCCCC
Confidence 57866 99999999999998888887766543322222367777 443
No 21
>PF05151 PsbM: Photosystem II reaction centre M protein (PsbM); InterPro: IPR007826 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 PsbM found in PSII. PsbM is one of the most hydrophobic proteins in the thylakoid membrane. The function of this protein is unknown.; GO: 0015979 photosynthesis, 0019684 photosynthesis, light reaction, 0009523 photosystem II, 0016021 integral to membrane; PDB: 3A0H_m 3ARC_m 3A0B_M 3PRR_M 3PRQ_M 1S5L_M 4FBY_e 3BZ2_M 3BZ1_M 2AXT_M ....
Probab=25.94 E-value=9.5 Score=21.39 Aligned_cols=14 Identities=36% Similarity=0.906 Sum_probs=10.5
Q ss_pred HHHhhhheeeecCC
Q 035725 59 IGLICSLLFVIFPT 72 (86)
Q Consensus 59 vG~~~S~vF~iFPt 72 (86)
.|++++.+|...||
T Consensus 6 l~fiAtaLfi~iPt 19 (31)
T PF05151_consen 6 LAFIATALFILIPT 19 (31)
T ss_dssp THHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHH
Confidence 47788888877775
No 22
>COG4818 Predicted membrane protein [Function unknown]
Probab=25.45 E-value=49 Score=23.10 Aligned_cols=17 Identities=35% Similarity=0.341 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHhcc
Q 035725 17 VHAVLSVLVFAAVALRD 33 (86)
Q Consensus 17 vHA~lS~~VF~avAl~D 33 (86)
.||.=|.+.|+.+++.+
T Consensus 33 FHAmQS~ltF~~l~~l~ 49 (105)
T COG4818 33 FHAMQSFLTFLGLWLLI 49 (105)
T ss_pred ehhHHHHHHHHHHHHHH
Confidence 39999999999999887
No 23
>PRK13735 conjugal transfer mating pair stabilization protein TraG; Provisional
Probab=23.61 E-value=49 Score=30.40 Aligned_cols=17 Identities=41% Similarity=0.567 Sum_probs=14.9
Q ss_pred HHHHHhhhHHHHhhhhe
Q 035725 50 EVLDIVPVGIGLICSLL 66 (86)
Q Consensus 50 ~ll~~lPl~vG~~~S~v 66 (86)
..+.|+|+|+|+.+|+.
T Consensus 89 ~~VDNVP~GlA~~asl~ 105 (942)
T PRK13735 89 YRVDNVPVGLAMPASLT 105 (942)
T ss_pred eEecccchHHHHHHHHH
Confidence 46899999999999874
No 24
>PF10660 MitoNEET_N: Iron-containing outer mitochondrial membrane protein N-terminus ; InterPro: IPR019610 The CDGSH iron sulphur domain are a group of iron-sulphur (Fe-S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H]. The CDGSH iron sulphur domain protein (also referred to as mitoNEET) is an integral membrane protein located in the outer mitochondrial membrane and whose function may be to transport iron into the mitochondria []. Iron in turn is essential for the function of several mitochondrial enzymes. This entry represents the N-terminal of the mitoNEET and Miner-type proteins that carry a CDGSH-type cluster-binding domain (IPR018967 from INTERPRO) that coordinate a redox-active 2Fe-2S cluster. In the outer mitochondrian membrane (OMM), the CDGSH 2Fe-2S-containing domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by the N-terminal domain found in higher vertebrates [, , ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 2R13_A 3REE_A 2QD0_B.
Probab=22.15 E-value=34 Score=21.72 Aligned_cols=33 Identities=24% Similarity=0.173 Sum_probs=1.5
Q ss_pred cccccchhhHHHHHHHHHHHHHhccCCcccccCCCC
Q 035725 9 YRIRFIDGVHAVLSVLVFAAVALRDKNVLSCFFPTP 44 (86)
Q Consensus 9 yrLr~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~ 44 (86)
+||...||+|++- .+++++..---..++|+|..
T Consensus 29 f~Ls~kdWl~Lvp---~~~~va~igYlayk~f~pk~ 61 (64)
T PF10660_consen 29 FKLSVKDWLALVP---FAAAVAGIGYLAYKPFCPKK 61 (64)
T ss_dssp ------------------------------CC---S
T ss_pred ccccHHHHHHHHh---HHHHHHHHHHHhheeecccc
Confidence 6777788887762 22333333333455555543
No 25
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=21.17 E-value=35 Score=28.56 Aligned_cols=10 Identities=60% Similarity=0.900 Sum_probs=8.9
Q ss_pred CCccccCCCC
Q 035725 73 RRHGIGYPIT 82 (86)
Q Consensus 73 ~RhGIGyp~~ 82 (86)
.|+|||.|++
T Consensus 23 ERKGiGHPDt 32 (399)
T PRK04439 23 ERKGIGHPDT 32 (399)
T ss_pred eecCCCCChH
Confidence 5999999986
No 26
>PF10582 Connexin_CCC: Gap junction channel protein cysteine-rich domain; InterPro: IPR019570 The connexins are a family of integral membrane proteins that oligomerise to form intercellular channels that are clustered at gap junctions. These channels are specialised sites of cell-cell contact that allow the passage of ions, intracellular metabolites and messenger molecules (with molecular weight less than 1-2kDa) from the cytoplasm of one cell to its opposing neighbours. They are found in almost all vertebrate cell types, and somewhat similar proteins have been cloned from plant species. Invertebrates utilise a different family of molecules, innexins, that share a similar predicted secondary structure to the vertebrate connexins, but have no sequence identity to them []. Vertebrate gap junction channels are thought to participate in diverse biological functions. For instance, in the heart they permit the rapid cell-cell transfer of action potentials, ensuring coordinated contraction of the cardiomyocytes. They are also responsible for neurotransmission at specialised 'electrical' synapses. In non-excitable tissues, such as the liver, they may allow metabolic cooperation between cells. In the brain, glial cells are extensively-coupled by gap junctions; this allows waves of intracellular Ca2+ to propagate through nervous tissue, and may contribute to their ability to spatially-buffer local changes in extracellular K+ concentration []. The connexin protein family is encoded by at least 13 genes in rodents, with many homologues cloned from other species. They show overlapping tissue expression patterns, most tissues expressing more than one connexin type. Their conductances, permeability to different molecules, phosphorylation and voltage-dependence of their gating, have been found to vary. Possible communication diversity is increased further by the fact that gap junctions may be formed by the association of different connexin isoforms from apposing cells. However, in vitro studies have shown that not all possible combinations of connexins produce active channels [, ]. Hydropathy analysis predicts that all cloned connexins share a common transmembrane (TM) topology. Each connexin is thought to contain 4 TM domains, with two extracellular and three cytoplasmic regions. This model has been validated for several of the family members by in vitro biochemical analysis. Both N- and C-termini are thought to face the cytoplasm, and the third TM domain has an amphipathic character, suggesting that it contributes to the lining of the formed-channel. Amino acid sequence identity between the isoforms is ~50-80%, with the TM domains being well conserved. Both extracellular loops contain characteristically conserved cysteine residues, which likely form intramolecular disulphide bonds. By contrast, the single putative intracellular loop (between TM domains 2 and 3) and the cytoplasmic C terminus are highly variable among the family members. Six connexins are thought to associate to form a hemi-channel, or connexon. Two connexons then interact (likely via the extracellular loops of their connexins) to form the complete gap junction channel. NH2-*** *** *************-COOH ** ** ** ** ** ** ** ** Cytoplasmic ---**----**-----**----**---------------- ** ** ** ** Membrane ** ** ** ** ---**----**-----**----**---------------- ** ** ** ** Extracellular ** ** ** ** ** ** Two sets of nomenclature have been used to identify the connexins. The first, and most commonly used, classifies the connexin molecules according to molecular weight, such as connexin43 (abbreviated to Cx43), indicating a connexin of molecular weight close to 43kDa. However, studies have revealed cases where clear functional homologues exist across species that have quite different molecular masses; therefore, an alternative nomenclature was proposed based on evolutionary considerations, which divides the family into two major subclasses, alpha and beta, each with a number of members []. Due to their ubiquity and overlapping tissue distributions, it has proved difficult to elucidate the functions of individual connexin isoforms. To circumvent this problem, particular connexin-encoding genes have been subjected to targeted-disruption in mice, and the phenotype of the resulting animals investigated. Around half the connexin isoforms have been investigated in this manner []. Further insight into the functional roles of connexins has come from the discovery that a number of human diseases are caused by mutations in connexin genes. For instance, mutations in Cx32 give rise to a form of inherited peripheral neuropathy called X-linked dominant Charcot-Marie-Tooth disease []. Similarly, mutations in Cx26 are responsible for both autosomal recessive and dominant forms of nonsyndromic deafness, a disorder characterised by hearing loss, with no apparent effects on other organ systems. This entry represents the cysteine rich domain of the connexins.; PDB: 2ZW3_F.
Probab=21.14 E-value=71 Score=20.31 Aligned_cols=31 Identities=23% Similarity=0.518 Sum_probs=22.0
Q ss_pred CCcccccCCCCCccHHHHHHHhhhHHHHhhhhe
Q 035725 34 KNVLSCFFPTPKHETQEVLDIVPVGIGLICSLL 66 (86)
Q Consensus 34 ~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~v 66 (86)
.+++.||-+.|. +|.+....=.+++.+|=.+
T Consensus 29 p~~VdCfVSRPt--EKtIfl~fM~~~s~vsi~L 59 (67)
T PF10582_consen 29 PNTVDCFVSRPT--EKTIFLIFMFAVSCVSILL 59 (67)
T ss_dssp SSSEEEE-SSHH--HHHHHHHHHHHHHHHHHHH
T ss_pred CCcceEeCCCCc--hhhhHHHHHHHHHHHHHHH
Confidence 468999997654 6788887777888776443
Done!