Query 046428
Match_columns 94
No_of_seqs 100 out of 114
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 12:00:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046428.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046428hhsearch_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 1.5E-42 3.3E-47 257.9 7.6 76 12-87 95-170 (170)
2 PF10894 DUF2689: Protein of u 63.1 3.5 7.5E-05 26.7 0.7 9 22-30 21-29 (61)
3 PRK13724 conjugal transfer pro 57.9 4.8 0.0001 26.3 0.7 9 22-30 21-29 (65)
4 PF11395 DUF2873: Protein of u 50.4 16 0.00034 22.1 2.0 23 18-40 3-25 (43)
5 PF15601 Imm42: Immunity prote 49.0 11 0.00025 27.3 1.6 24 12-35 5-28 (134)
6 KOG4833 Uncharacterized conser 46.5 6.5 0.00014 34.3 -0.0 26 20-54 499-524 (573)
7 PF03770 IPK: Inositol polypho 46.4 7.3 0.00016 28.7 0.2 18 12-29 158-175 (197)
8 PRK04989 psbM photosystem II r 41.2 4.4 9.5E-05 23.8 -1.3 14 67-80 6-19 (35)
9 CHL00080 psbM photosystem II p 39.9 4.8 0.0001 23.4 -1.2 15 67-81 6-20 (34)
10 PF15623 CT47: Cancer/testis g 39.4 13 0.00029 30.3 0.7 21 14-34 113-133 (279)
11 PLN02667 inositol polyphosphat 33.0 24 0.00052 28.2 1.2 15 14-28 235-249 (286)
12 TIGR03038 PS_II_psbM photosyst 32.9 7.1 0.00015 22.6 -1.3 14 67-80 6-19 (33)
13 PF05237 MoeZ_MoeB: MoeZ/MoeB 32.6 5.5 0.00012 25.6 -2.0 29 45-73 6-36 (84)
14 PRK14094 psbM photosystem II r 29.3 10 0.00022 23.7 -1.1 15 67-81 6-20 (50)
15 PF05403 Plasmodium_HRP: Plasm 27.7 40 0.00087 26.3 1.6 19 28-46 9-27 (218)
16 PF09904 HTH_43: Winged helix- 26.9 22 0.00047 24.5 0.1 33 51-87 33-65 (90)
17 KOG3030 Lipid phosphate phosph 26.3 74 0.0016 26.0 3.0 46 26-73 185-230 (317)
18 PF10961 DUF2763: Protein of u 23.6 62 0.0013 21.8 1.8 34 9-42 6-42 (91)
19 PF10582 Connexin_CCC: Gap jun 22.6 77 0.0017 20.5 2.0 30 42-73 29-58 (67)
20 PF10660 MitoNEET_N: Iron-cont 22.4 34 0.00073 22.1 0.3 34 17-53 29-62 (64)
21 COG5416 Uncharacterized integr 21.4 2.3E+02 0.005 19.9 4.3 55 13-74 16-70 (98)
22 PRK04439 S-adenosylmethionine 20.6 36 0.00079 29.0 0.2 10 81-90 23-32 (399)
23 PF05151 PsbM: Photosystem II 20.3 13 0.00029 21.2 -1.7 14 67-80 6-19 (31)
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=1.5e-42 Score=257.88 Aligned_cols=76 Identities=66% Similarity=1.184 Sum_probs=74.6
Q ss_pred cccccceeeecchhhHHHHHHHHHHhHhccCCccceeCCCCCccHHHHHHhhhhHHHHhhhheeeecCCCCccccc
Q 046428 12 LDLRKYRIRFIDGVHAVLSVIVFAAAALRDKNVLSCFFPTPKHETQEVLDIVPVGIGLICSLLFVIFPTRRHGIGY 87 (94)
Q Consensus 12 ~~~s~YrLr~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~vF~iFPt~RhGIGy 87 (94)
++++|||||++|||||++|++||+++|++|+|||+||||++++|+||+|+++|+++|++||++||+|||+||||||
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 3689999999999999999999999999999999999999999999999999999999999999999999999998
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=63.06 E-value=3.5 Score=26.71 Aligned_cols=9 Identities=67% Similarity=0.567 Sum_probs=7.9
Q ss_pred cchhhHHHH
Q 046428 22 IDGVHAVLS 30 (94)
Q Consensus 22 ~DfvHA~lS 30 (94)
-||+||++|
T Consensus 21 DDFmhaVlS 29 (61)
T PF10894_consen 21 DDFMHAVLS 29 (61)
T ss_pred HHHHHHHHh
Confidence 499999997
No 3
>PRK13724 conjugal transfer protein TrbD; Provisional
Probab=57.91 E-value=4.8 Score=26.31 Aligned_cols=9 Identities=67% Similarity=0.567 Sum_probs=8.0
Q ss_pred cchhhHHHH
Q 046428 22 IDGVHAVLS 30 (94)
Q Consensus 22 ~DfvHA~lS 30 (94)
-||+||++|
T Consensus 21 DDF~h~VlS 29 (65)
T PRK13724 21 DDFMHAVLS 29 (65)
T ss_pred HHHHHHHHh
Confidence 499999987
No 4
>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=50.39 E-value=16 Score=22.13 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=20.1
Q ss_pred eeeecchhhHHHHHHHHHHhHhc
Q 046428 18 RIRFIDGVHAVLSVIVFAAAALR 40 (94)
Q Consensus 18 rLr~~DfvHA~lS~~VF~avAl~ 40 (94)
.|+.+||--.++|++.|+++.+.
T Consensus 3 ~ltl~dfylc~l~~llflv~iml 25 (43)
T PF11395_consen 3 HLTLFDFYLCFLSFLLFLVIIML 25 (43)
T ss_pred ceehhHHHHHHHHHHHHHHHHHH
Confidence 47789999999999999998764
No 5
>PF15601 Imm42: Immunity protein 42
Probab=48.98 E-value=11 Score=27.32 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=19.7
Q ss_pred cccccceeeecchhhHHHHHHHHH
Q 046428 12 LDLRKYRIRFIDGVHAVLSVIVFA 35 (94)
Q Consensus 12 ~~~s~YrLr~~DfvHA~lS~~VF~ 35 (94)
.+..-|.+.-.||+|+|+|.+..-
T Consensus 5 ~~~~~~eiG~~dfl~sFFsti~~~ 28 (134)
T PF15601_consen 5 VGFSWYEIGPPDFLHSFFSTISYR 28 (134)
T ss_pred cCceEEEeCCHHHHHHHHHHHHHH
Confidence 355679999999999999987653
No 6
>KOG4833 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.50 E-value=6.5 Score=34.28 Aligned_cols=26 Identities=38% Similarity=0.641 Sum_probs=21.4
Q ss_pred eecchhhHHHHHHHHHHhHhccCCccceeCCCCCc
Q 046428 20 RFIDGVHAVLSVIVFAAAALRDKNVLSCFFPTPKH 54 (94)
Q Consensus 20 r~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~~ 54 (94)
+.+||+||+- ++|-|...||||..+.
T Consensus 499 piidfnhaVc---------fsdLnIadcflpieSr 524 (573)
T KOG4833|consen 499 PIIDFNHAVC---------FSDLNIADCFLPIESR 524 (573)
T ss_pred HHHHHHHHHH---------HhcccHhHheehhHhh
Confidence 4689999864 5789999999998764
No 7
>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=46.43 E-value=7.3 Score=28.71 Aligned_cols=18 Identities=22% Similarity=0.194 Sum_probs=10.8
Q ss_pred cccccceeeecchhhHHH
Q 046428 12 LDLRKYRIRFIDGVHAVL 29 (94)
Q Consensus 12 ~~~s~YrLr~~DfvHA~l 29 (94)
....++++|.+||.|+..
T Consensus 158 ~~~~~~~vklIDFAH~~~ 175 (197)
T PF03770_consen 158 DPPNKVDVKLIDFAHVFP 175 (197)
T ss_dssp ---S-EEEEEE--TTEEE
T ss_pred CCCCcccEEEEECCCccc
Confidence 345789999999999876
No 8
>PRK04989 psbM photosystem II reaction center protein M; Provisional
Probab=41.21 E-value=4.4 Score=23.75 Aligned_cols=14 Identities=57% Similarity=1.156 Sum_probs=12.0
Q ss_pred HHHhhhheeeecCC
Q 046428 67 IGLICSLLFVIFPT 80 (94)
Q Consensus 67 vG~~~S~vF~iFPt 80 (94)
.|++++.+|+..||
T Consensus 6 lgfiAt~Lfi~iPt 19 (35)
T PRK04989 6 LGFVASLLFVLVPT 19 (35)
T ss_pred HHHHHHHHHHHHHH
Confidence 58899999998886
No 9
>CHL00080 psbM photosystem II protein M
Probab=39.88 E-value=4.8 Score=23.44 Aligned_cols=15 Identities=33% Similarity=0.813 Sum_probs=12.6
Q ss_pred HHHhhhheeeecCCC
Q 046428 67 IGLICSLLFVIFPTR 81 (94)
Q Consensus 67 vG~~~S~vF~iFPt~ 81 (94)
.|++++.+|+..||-
T Consensus 6 lgfiAt~LFi~iPt~ 20 (34)
T CHL00080 6 LAFIATALFILVPTA 20 (34)
T ss_pred HHHHHHHHHHHHHHH
Confidence 589999999998873
No 10
>PF15623 CT47: Cancer/testis gene family 47
Probab=39.42 E-value=13 Score=30.28 Aligned_cols=21 Identities=33% Similarity=0.691 Sum_probs=16.9
Q ss_pred cccceeeecchhhHHHHHHHH
Q 046428 14 LRKYRIRFIDGVHAVLSVIVF 34 (94)
Q Consensus 14 ~s~YrLr~~DfvHA~lS~~VF 34 (94)
...||+.|+|.||+.|-=+-.
T Consensus 113 maGfR~~fLDLVhslL~RiY~ 133 (279)
T PF15623_consen 113 MAGFRFMFLDLVHSLLNRIYY 133 (279)
T ss_pred cccceeeHHHHHHHHHHHHhh
Confidence 357999999999998876543
No 11
>PLN02667 inositol polyphosphate multikinase
Probab=33.04 E-value=24 Score=28.19 Aligned_cols=15 Identities=13% Similarity=0.361 Sum_probs=13.3
Q ss_pred cccceeeecchhhHH
Q 046428 14 LRKYRIRFIDGVHAV 28 (94)
Q Consensus 14 ~s~YrLr~~DfvHA~ 28 (94)
.++.++|.|||-|+.
T Consensus 235 ~~~v~VkmIDFAH~~ 249 (286)
T PLN02667 235 DSRVEVKLVDFAHVL 249 (286)
T ss_pred CCcceEEEEeCcccc
Confidence 568999999999985
No 12
>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=32.86 E-value=7.1 Score=22.60 Aligned_cols=14 Identities=50% Similarity=1.153 Sum_probs=11.5
Q ss_pred HHHhhhheeeecCC
Q 046428 67 IGLICSLLFVIFPT 80 (94)
Q Consensus 67 vG~~~S~vF~iFPt 80 (94)
.|++++.+|...||
T Consensus 6 l~fiAt~Lfi~iPt 19 (33)
T TIGR03038 6 LGFIATLLFILVPT 19 (33)
T ss_pred HHHHHHHHHHHHHH
Confidence 47888888888886
No 13
>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=32.61 E-value=5.5 Score=25.63 Aligned_cols=29 Identities=31% Similarity=0.591 Sum_probs=17.0
Q ss_pred cceeCCCCCcc--HHHHHHhhhhHHHHhhhh
Q 046428 45 LSCFFPTPKHE--TQEVLDIVPVGIGLICSL 73 (94)
Q Consensus 45 v~Cf~P~~~~~--~~~ll~~lPl~vG~~~S~ 73 (94)
.+|+||..... .-+-.-.++..+|+++|+
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 112336788888888875
No 14
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=29.30 E-value=10 Score=23.75 Aligned_cols=15 Identities=53% Similarity=0.824 Sum_probs=12.4
Q ss_pred HHHhhhheeeecCCC
Q 046428 67 IGLICSLLFVIFPTR 81 (94)
Q Consensus 67 vG~~~S~vF~iFPt~ 81 (94)
.|++++.+|+..||-
T Consensus 6 lgfiAtaLFi~iPT~ 20 (50)
T PRK14094 6 FGFVASLLFVGVPTI 20 (50)
T ss_pred HHHHHHHHHHHHHHH
Confidence 588999999988873
No 15
>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=27.67 E-value=40 Score=26.27 Aligned_cols=19 Identities=42% Similarity=0.499 Sum_probs=16.7
Q ss_pred HHHHHHHHHhHhccCCccc
Q 046428 28 VLSVIVFAAAALRDKNVLS 46 (94)
Q Consensus 28 ~lS~~VF~avAl~D~nvv~ 46 (94)
+||..||..|-|+|.|-..
T Consensus 9 ilsaavfasvllldnnns~ 27 (218)
T PF05403_consen 9 ILSAAVFASVLLLDNNNSE 27 (218)
T ss_pred HHHHHHHHHhheecCCcHH
Confidence 5899999999999998654
No 16
>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=26.93 E-value=22 Score=24.55 Aligned_cols=33 Identities=24% Similarity=0.677 Sum_probs=21.3
Q ss_pred CCCccHHHHHHhhhhHHHHhhhheeeecCCCCccccc
Q 046428 51 TPKHETQEVLDIVPVGIGLICSLLFVIFPTRRHGIGY 87 (94)
Q Consensus 51 ~~~~~~~~ll~~lPl~vG~~~S~vF~iFPt~RhGIGy 87 (94)
.|..+.+..+++|| .+|+-|.|+= ...||--||
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 34556789999999 9999998776 788888887
No 17
>KOG3030 consensus Lipid phosphate phosphatase and related enzymes of the PAP2 family [Lipid transport and metabolism]
Probab=26.29 E-value=74 Score=25.98 Aligned_cols=46 Identities=22% Similarity=0.260 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHhHhccCCccceeCCCCCccHHHHHHhhhhHHHHhhhh
Q 046428 26 HAVLSVIVFAAAALRDKNVLSCFFPTPKHETQEVLDIVPVGIGLICSL 73 (94)
Q Consensus 26 HA~lS~~VF~avAl~D~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~ 73 (94)
||.+|.-.+.-+|+-=++-..++- .++-.|-+|+-+|+++++++++
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 888888777777754445555544 4566899999999999988774
No 18
>PF10961 DUF2763: Protein of unknown function (DUF2763); InterPro: IPR024491 This entry represents an eukaryotic family of selenoproteins. It includes SelK, which seems to play an important role in protecting cells from endoplasmic reticulum stress-induced apoptosis [] and SelG, which may be involved in regulating the redox state of the cell [].
Probab=23.63 E-value=62 Score=21.85 Aligned_cols=34 Identities=21% Similarity=0.383 Sum_probs=22.9
Q ss_pred CCccc--cccceee-ecchhhHHHHHHHHHHhHhccC
Q 046428 9 GEILD--LRKYRIR-FIDGVHAVLSVIVFAAAALRDK 42 (94)
Q Consensus 9 ~~~~~--~s~YrLr-~~DfvHA~lS~~VF~avAl~D~ 42 (94)
|++.+ -+.+||+ +.||+++++-+++..-..|++.
T Consensus 6 G~V~e~~rspWrls~I~d~Fwgi~~fI~lFF~Tl~~p 42 (91)
T PF10961_consen 6 GQVLERKRSPWRLSRITDFFWGIINFIVLFFQTLFSP 42 (91)
T ss_pred CEEeecCCCCccHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 55544 5567776 8899999997777444455443
No 19
>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=22.64 E-value=77 Score=20.50 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=21.6
Q ss_pred CCccceeCCCCCccHHHHHHhhhhHHHHhhhh
Q 046428 42 KNVLSCFFPTPKHETQEVLDIVPVGIGLICSL 73 (94)
Q Consensus 42 ~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~ 73 (94)
.|++.||-+.|. +|.+....=.+++.+|=.
T Consensus 29 p~~VdCfVSRPt--EKtIfl~fM~~~s~vsi~ 58 (67)
T PF10582_consen 29 PNTVDCFVSRPT--EKTIFLIFMFAVSCVSIL 58 (67)
T ss_dssp SSSEEEE-SSHH--HHHHHHHHHHHHHHHHHH
T ss_pred CCcceEeCCCCc--hhhhHHHHHHHHHHHHHH
Confidence 478999997654 678887777778777644
No 20
>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=22.38 E-value=34 Score=22.14 Aligned_cols=34 Identities=24% Similarity=0.167 Sum_probs=2.1
Q ss_pred ceeeecchhhHHHHHHHHHHhHhccCCccceeCCCCC
Q 046428 17 YRIRFIDGVHAVLSVIVFAAAALRDKNVLSCFFPTPK 53 (94)
Q Consensus 17 YrLr~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~ 53 (94)
+||...||+|++- .+++++..---..++|+|..+
T Consensus 29 f~Ls~kdWl~Lvp---~~~~va~igYlayk~f~pk~~ 62 (64)
T PF10660_consen 29 FKLSVKDWLALVP---FAAAVAGIGYLAYKPFCPKKK 62 (64)
T ss_dssp ------------------------------CC---ST
T ss_pred ccccHHHHHHHHh---HHHHHHHHHHHhheeeccccc
Confidence 6888888888762 233334334445566666543
No 21
>COG5416 Uncharacterized integral membrane protein [Function unknown]
Probab=21.43 E-value=2.3e+02 Score=19.90 Aligned_cols=55 Identities=5% Similarity=0.086 Sum_probs=40.5
Q ss_pred ccccceeeecchhhHHHHHHHHHHhHhccCCccceeCCCCCccHHHHHHhhhhHHHHhhhhe
Q 046428 13 DLRKYRIRFIDGVHAVLSVIVFAAAALRDKNVLSCFFPTPKHETQEVLDIVPVGIGLICSLL 74 (94)
Q Consensus 13 ~~s~YrLr~~DfvHA~lS~~VF~avAl~D~nvv~Cf~P~~~~~~~~ll~~lPl~vG~~~S~v 74 (94)
.-++-|..|.=.+-.++-++.++.+|+-+++.+.--|+-.. -.+|++++++.|++
T Consensus 16 ~~~r~~~~w~vi~~gilillLllifav~Nt~~V~~~~lfg~-------~~~PLilvil~s~v 70 (98)
T COG5416 16 VRKRMKGQWTVIIVGILILLLLLIFAVINTDSVEFNYLFGQ-------WELPLILVILGAAV 70 (98)
T ss_pred hhhhccceeeHHHHHHHHHHHHHHHHHhccCceEEEeecch-------hhhhHHHHHHHHHH
Confidence 45667888888887788888888888888877777665533 35788888777754
No 22
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=20.59 E-value=36 Score=28.96 Aligned_cols=10 Identities=50% Similarity=0.571 Sum_probs=9.0
Q ss_pred CCcccccCCC
Q 046428 81 RRHGIGYLIT 90 (94)
Q Consensus 81 ~RhGIGyp~~ 90 (94)
.|+|||.|++
T Consensus 23 ERKGiGHPDt 32 (399)
T PRK04439 23 ERKGIGHPDT 32 (399)
T ss_pred eecCCCCChH
Confidence 5999999986
No 23
>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=20.35 E-value=13 Score=21.15 Aligned_cols=14 Identities=36% Similarity=0.906 Sum_probs=10.4
Q ss_pred HHHhhhheeeecCC
Q 046428 67 IGLICSLLFVIFPT 80 (94)
Q Consensus 67 vG~~~S~vF~iFPt 80 (94)
.|++++.+|...|+
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
Done!