Query 002049
Match_columns 975
No_of_seqs 177 out of 190
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 15:21:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07699 GCC2_GCC3: GCC2 and G 96.9 0.0005 1.1E-08 56.5 2.2 26 805-832 9-34 (48)
2 KOG0196 Tyrosine kinase, EPH ( 96.3 0.0036 7.7E-08 76.4 4.5 55 796-863 261-319 (996)
3 PF07562 NCD3G: Nine Cysteines 94.0 0.012 2.5E-07 50.0 -0.6 36 795-832 6-51 (54)
4 PHA02637 TNF-alpha-receptor-li 93.4 0.093 2E-06 52.2 4.3 58 797-859 31-93 (127)
5 cd00185 TNFR Tumor necrosis fa 89.1 0.67 1.5E-05 43.4 5.0 66 793-864 12-87 (98)
6 PHA02637 TNF-alpha-receptor-li 82.7 1 2.2E-05 45.0 2.9 41 789-830 38-87 (127)
7 PF07699 GCC2_GCC3: GCC2 and G 74.9 2.7 5.8E-05 34.7 2.6 33 790-822 6-43 (48)
8 cd00185 TNFR Tumor necrosis fa 71.8 5.1 0.00011 37.6 4.1 32 804-835 11-44 (98)
9 PF12273 RCR: Chitin synthesis 71.2 3.3 7.1E-05 40.8 2.7 21 881-901 2-23 (130)
10 PF14946 DUF4501: Domain of un 64.5 7.2 0.00016 40.8 3.7 85 810-907 28-115 (180)
11 PTZ00382 Variant-specific surf 63.1 5.6 0.00012 37.9 2.5 24 805-831 4-27 (96)
12 PHA02691 hypothetical protein; 62.3 4.4 9.6E-05 39.7 1.6 47 880-926 2-51 (110)
13 KOG1836 Extracellular matrix g 60.9 7.9 0.00017 52.5 4.1 42 790-831 794-837 (1705)
14 smart00180 EGF_Lam Laminin-typ 55.3 7.2 0.00016 32.1 1.5 19 798-816 22-40 (46)
15 KOG4289 Cadherin EGF LAG seven 55.1 9 0.0002 50.7 3.0 80 786-873 1733-1846(2531)
16 cd00055 EGF_Lam Laminin-type e 54.6 7.3 0.00016 32.4 1.5 27 789-818 17-43 (50)
17 KOG0921 Dosage compensation co 54.4 26 0.00057 45.0 6.6 9 172-180 1190-1198(1282)
18 PF07354 Sp38: Zona-pellucida- 51.2 12 0.00026 41.8 2.9 23 806-831 239-261 (271)
19 PF00053 Laminin_EGF: Laminin 46.6 9 0.0002 31.5 0.8 22 798-819 22-43 (49)
20 cd00064 FU Furin-like repeats. 42.5 21 0.00045 29.3 2.3 9 807-815 17-25 (49)
21 KOG2675 Adenylate cyclase-asso 42.1 15 0.00033 43.5 2.0 24 342-365 446-469 (480)
22 PF05268 GP38: Phage tail fibr 41.0 77 0.0017 35.0 6.8 37 210-247 114-152 (260)
23 PF04519 Bactofilin: Polymer-f 37.7 3.1E+02 0.0066 25.6 9.6 15 136-150 82-96 (101)
24 PF02166 Androgen_recep: Andro 37.1 11 0.00024 43.2 0.0 26 21-57 335-360 (423)
25 KOG1056 Glutamate-gated metabo 36.4 39 0.00084 43.4 4.4 39 793-835 493-540 (878)
26 PF15195 TMEM210: TMEM210 fami 32.2 28 0.00061 33.8 1.8 11 40-50 100-110 (116)
27 PHA03066 Hypothetical protein; 28.8 40 0.00087 33.3 2.2 44 883-926 5-51 (110)
28 PF00020 TNFR_c6: TNFR/NGFR cy 26.3 26 0.00057 27.7 0.4 20 810-831 1-20 (39)
29 PF05281 Secretogranin_V: Neur 25.4 1E+02 0.0022 33.7 4.6 90 762-867 50-144 (208)
30 COG4736 CcoQ Cbb3-type cytochr 25.1 96 0.0021 27.8 3.7 35 867-908 3-37 (60)
31 PF05545 FixQ: Cbb3-type cytoc 24.5 1E+02 0.0023 25.7 3.7 33 867-906 3-35 (49)
32 PRK09677 putative lipopolysacc 23.7 1.9E+02 0.004 30.3 6.2 60 88-150 36-95 (192)
33 PF12661 hEGF: Human growth fa 23.5 25 0.00054 22.6 -0.1 11 797-807 3-13 (13)
34 KOG2906 RNA polymerase III sub 22.5 51 0.0011 32.2 1.6 31 805-836 2-33 (105)
35 PF15048 OSTbeta: Organic solu 22.5 1.2E+02 0.0025 30.9 4.1 30 869-898 19-53 (125)
36 KOG4260 Uncharacterized conser 21.1 64 0.0014 36.6 2.3 28 798-827 132-159 (350)
No 1
>PF07699 GCC2_GCC3: GCC2 and GCC3; InterPro: IPR011641 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups []: Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis []. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases []. This entry represents various ephrin type A and B receptors, which have tyrosine kinase activity.
Probab=96.93 E-value=0.0005 Score=56.54 Aligned_cols=26 Identities=31% Similarity=0.887 Sum_probs=22.8
Q ss_pred ccceeCCCCceeccCCCCCCCcccCCCC
Q 002049 805 VFCEECPVGTFKNVSGSDRALCRNCSSN 832 (975)
Q Consensus 805 ~fC~eCP~GtYKn~~gs~~~~C~pCp~~ 832 (975)
.-|++||+||||+..|+ ..|++||.+
T Consensus 9 ~~C~~Cp~GtYq~~~g~--~~C~~Cp~g 34 (48)
T PF07699_consen 9 NKCQPCPKGTYQDEEGQ--TSCTPCPPG 34 (48)
T ss_pred CccCCCCCCccCCccCC--ccCccCcCC
Confidence 36999999999999975 599999974
No 2
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=96.31 E-value=0.0036 Score=76.41 Aligned_cols=55 Identities=33% Similarity=0.776 Sum_probs=39.0
Q ss_pred CCCCCCCc----cccceeCCCCceeccCCCCCCCcccCCCCCCCCCcceeeccCCccCCCCCccccCCcccC
Q 002049 796 KACPRGLY----GVFCEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVSERYHM 863 (975)
Q Consensus 796 ~~CP~G~y----G~fC~eCP~GtYKn~~gs~~~~C~pCp~~~~p~ra~~i~~rggv~~~~Cpy~C~s~~y~~ 863 (975)
=-|-+||. +.-|+.||.||||...+ ..+|.+||.++..+ ..| .+.| +|.++.|+-
T Consensus 261 C~C~aGye~~~~~~~C~aCp~G~yK~~~~--~~~C~~CP~~S~s~-------~eg--a~~C--~C~~gyyRA 319 (996)
T KOG0196|consen 261 CVCKAGYEEAENGKACQACPPGTYKASQG--DSLCLPCPPNSHSS-------SEG--ATSC--TCENGYYRA 319 (996)
T ss_pred eeecCCCCcccCCCcceeCCCCcccCCCC--CCCCCCCCCCCCCC-------CCC--CCcc--cccCCcccC
Confidence 46888883 45799999999999874 69999999865532 122 3455 467666643
No 3
>PF07562 NCD3G: Nine Cysteines Domain of family 3 GPCR; InterPro: IPR011500 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). GPCR family 3 receptors (also known as family C) are structurally similar to other GPCRs, but do not show any significant sequence similarity and thus represent a distinct group. Structurally they are composed of four elements; an N-terminal signal sequence; a large hydrophilic extracellular agonist-binding region containing several conserved cysteine residues which could be involved in disulphide bonds; a shorter region containing seven transmembrane domains; and a C-terminal cytoplasmic domain of variable length []. Family 3 members include the metabotropic glutamate receptors, the extracellular calcium-sensing receptors, the gamma-amino-butyric acid (GABA) type B receptors, and the vomeronasal type-2 receptors [, , , ]. As these receptors regulate many important physiological processes they are potentially promising targets for drug development. This entry represents a conserved sequence, found in the extracellular region, that contains several highly-conserved Cys residues that are predicted to form disulphide bridges.; GO: 0004930 G-protein coupled receptor activity, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 2E4X_B 2E4Y_A 2E4U_B 2E4V_B 2E4W_A.
Probab=94.01 E-value=0.012 Score=50.02 Aligned_cols=36 Identities=33% Similarity=0.826 Sum_probs=20.9
Q ss_pred cCCCCCCCc-----cc-----cceeCCCCceeccCCCCCCCcccCCCC
Q 002049 795 GKACPRGLY-----GV-----FCEECPVGTFKNVSGSDRALCRNCSSN 832 (975)
Q Consensus 795 g~~CP~G~y-----G~-----fC~eCP~GtYKn~~gs~~~~C~pCp~~ 832 (975)
.++|++|++ +. -|++||.|+|.|.+ |...|++||.+
T Consensus 6 S~~C~pG~~k~~~~~~~~CCw~C~~C~~~~is~~~--~~~~C~~C~~~ 51 (54)
T PF07562_consen 6 SEPCPPGQRKKIQKGQPSCCWDCVPCPEGEISNQT--DSTSCTKCPEG 51 (54)
T ss_dssp S----TTTEEEE--SSS-S--EEEE--TTEEEE----ETTEEEE--TT
T ss_pred CCCCCCCCEECccCCCcceEEEeecCCCCcEECCC--CccccccCCCc
Confidence 478999984 32 39999999999987 67999999964
No 4
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=93.40 E-value=0.093 Score=52.16 Aligned_cols=58 Identities=22% Similarity=0.543 Sum_probs=40.9
Q ss_pred CCCCCCc--c-ccceeCCCCceeccCCC--CCCCcccCCCCCCCCCcceeeccCCccCCCCCccccCC
Q 002049 797 ACPRGLY--G-VFCEECPVGTFKNVSGS--DRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVSE 859 (975)
Q Consensus 797 ~CP~G~y--G-~fC~eCP~GtYKn~~gs--~~~~C~pCp~~~~p~ra~~i~~rggv~~~~Cpy~C~s~ 859 (975)
.|..+-| + .-|.+||.|||+...=+ ....|.|||..++-...++.. ....|.-.|+++
T Consensus 31 ~C~e~EY~~~~~CC~kCPPGt~v~~~Ct~~t~T~C~PCp~GTYTe~~N~~~-----~C~~C~~~Cd~~ 93 (127)
T PHA02637 31 KCKDNEYKRHNLCCLSCPPGTYASRLCDIKTNTQCTPCGSGTFTSHNNHLP-----ACLSCNGRCDRV 93 (127)
T ss_pred CCCCCcCcCCCeEcCCCCCCCEEeCcCCCCCCcccccCCCCCeeccCCCCC-----cccccCCccCcc
Confidence 6888865 3 35999999999873221 246899999877765555443 367888888864
No 5
>cd00185 TNFR Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
Probab=89.11 E-value=0.67 Score=43.45 Aligned_cols=66 Identities=24% Similarity=0.543 Sum_probs=41.1
Q ss_pred EecCCCCCCCcc---------ccceeCCCCceeccCCCCCCCcccCCCCCCCCCcceeeccCCc-cCCCCCccccCCccc
Q 002049 793 VTGKACPRGLYG---------VFCEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGV-TECPCPYKCVSERYH 862 (975)
Q Consensus 793 i~g~~CP~G~yG---------~fC~eCP~GtYKn~~gs~~~~C~pCp~~~~p~ra~~i~~rggv-~~~~Cpy~C~s~~y~ 862 (975)
.-=+.||+|++- .-|++||.|||++... ....|++|.. -+ ...++....-. ..+.|- |.++.|-
T Consensus 12 ~cC~~C~pG~~~~~~C~~~~~t~C~~C~~g~ys~~~~-~~~~C~~c~~--C~-~g~~~~~~ct~t~dt~C~--C~~G~y~ 85 (98)
T cd00185 12 LCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTYTDSWN-HLPKCLSCRT--CD-SGLVEKAPCTATRNTVCG--CKPGFYC 85 (98)
T ss_pred CCCCCCCCCccCCCcCCCCCCCeecCCCCCCcccCCC-CCCcCCcCcc--CC-CCCEEEccCCCCCCCeEe--CCCCCEe
Confidence 455889999852 3599999999998653 2368999975 43 23344333322 223564 7777664
Q ss_pred CC
Q 002049 863 MP 864 (975)
Q Consensus 863 ~p 864 (975)
.+
T Consensus 86 ~~ 87 (98)
T cd00185 86 LT 87 (98)
T ss_pred cC
Confidence 43
No 6
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=82.74 E-value=1 Score=45.01 Aligned_cols=41 Identities=27% Similarity=0.665 Sum_probs=30.3
Q ss_pred CCceEecCCCCCCCc---------cccceeCCCCceeccCCCCCCCcccCC
Q 002049 789 GNGTVTGKACPRGLY---------GVFCEECPVGTFKNVSGSDRALCRNCS 830 (975)
Q Consensus 789 ~nGti~g~~CP~G~y---------G~fC~eCP~GtYKn~~gs~~~~C~pCp 830 (975)
..+.+-=+.||||+| ..-|.+||.|||-...- ....|.+|.
T Consensus 38 ~~~~~CC~kCPPGt~v~~~Ct~~t~T~C~PCp~GTYTe~~N-~~~~C~~C~ 87 (127)
T PHA02637 38 KRHNLCCLSCPPGTYASRLCDIKTNTQCTPCGSGTFTSHNN-HLPACLSCN 87 (127)
T ss_pred cCCCeEcCCCCCCCEEeCcCCCCCCcccccCCCCCeeccCC-CCCcccccC
Confidence 456667789999984 45799999999976432 245688886
No 7
>PF07699 GCC2_GCC3: GCC2 and GCC3; InterPro: IPR011641 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups []: Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis []. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases []. This entry represents various ephrin type A and B receptors, which have tyrosine kinase activity.
Probab=74.93 E-value=2.7 Score=34.72 Aligned_cols=33 Identities=36% Similarity=0.883 Sum_probs=24.5
Q ss_pred CceEecCCCCCCCc----c-ccceeCCCCceeccCCCC
Q 002049 790 NGTVTGKACPRGLY----G-VFCEECPVGTFKNVSGSD 822 (975)
Q Consensus 790 nGti~g~~CP~G~y----G-~fC~eCP~GtYKn~~gs~ 822 (975)
.+.-.=.+||+|+| | ..|+.||.++|-...|+.
T Consensus 6 ~~~~~C~~Cp~GtYq~~~g~~~C~~Cp~g~~T~~~Gs~ 43 (48)
T PF07699_consen 6 SGNNKCQPCPKGTYQDEEGQTSCTPCPPGSTTSSEGST 43 (48)
T ss_pred CCCCccCCCCCCccCCccCCccCccCcCCCccCCcCCc
Confidence 34445589999986 3 359999999887777763
No 8
>cd00185 TNFR Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
Probab=71.83 E-value=5.1 Score=37.62 Aligned_cols=32 Identities=25% Similarity=0.816 Sum_probs=24.0
Q ss_pred cccceeCCCCceeccCCC--CCCCcccCCCCCCC
Q 002049 804 GVFCEECPVGTFKNVSGS--DRALCRNCSSNELP 835 (975)
Q Consensus 804 G~fC~eCP~GtYKn~~gs--~~~~C~pCp~~~~p 835 (975)
+.-|..||.|+|...... ....|.|||.+++-
T Consensus 11 ~~cC~~C~pG~~~~~~C~~~~~t~C~~C~~g~ys 44 (98)
T cd00185 11 GLCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTYT 44 (98)
T ss_pred CCCCCCCCCCccCCCcCCCCCCCeecCCCCCCcc
Confidence 456999999999876532 34689999986663
No 9
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=71.16 E-value=3.3 Score=40.80 Aligned_cols=21 Identities=33% Similarity=0.838 Sum_probs=12.1
Q ss_pred e-ehhhHHHHHHHHHHHHHHhh
Q 002049 881 W-LFGLILLGLLILLALVLSVA 901 (975)
Q Consensus 881 ~-~F~L~l~~llilla~vls~~ 901 (975)
| +|++||+++||+|++++.+.
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~ 23 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHN 23 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHH
Confidence 6 56666666666655555444
No 10
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=64.49 E-value=7.2 Score=40.75 Aligned_cols=85 Identities=26% Similarity=0.438 Sum_probs=47.7
Q ss_pred CCCCceeccCCCCCCCcccCCCCCCCCCcceeeccCCccCCCCCccccCC-cccC-CcccchHHHHHHHhCCce-ehhhH
Q 002049 810 CPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVSE-RYHM-PHCYTTLEELVYTFGGPW-LFGLI 886 (975)
Q Consensus 810 CP~GtYKn~~gs~~~~C~pCp~~~~p~ra~~i~~rggv~~~~Cpy~C~s~-~y~~-p~C~t~le~li~~~GGp~-~F~L~ 886 (975)
|-.|-|.........-|..|-+.+++. | ..+.|.+-=... ...| .-=-||. .-.+|+|+ .-.||
T Consensus 28 CgPGcyr~~~edgs~sCv~c~n~t~~~---~-------n~s~c~~~~grg~~~pmNrStgtpg---~p~~g~P~vAASL~ 94 (180)
T PF14946_consen 28 CGPGCYRHWNEDGSVSCVQCGNGTFPA---Y-------NGSECRSLAGRGAQFPMNRSTGTPG---RPHTGGPQVAASLF 94 (180)
T ss_pred cCCcceeeecCCCCeEEEEcCCCcccc---c-------CccccccccccCCccccccccCCCC---CCcCCChhHHHHHH
Confidence 555655543333456778887655542 1 124454431110 1111 1111222 23689999 67788
Q ss_pred HHHHHHHHHHHHHhhheeccC
Q 002049 887 LLGLLILLALVLSVARMKYMG 907 (975)
Q Consensus 887 l~~llilla~vls~~R~K~~~ 907 (975)
|=.+||-++|+||++-+-|-|
T Consensus 95 LgTffIS~~LilSvA~FFYLK 115 (180)
T PF14946_consen 95 LGTFFISLGLILSVASFFYLK 115 (180)
T ss_pred HHHHHHHHHHHHHHhhheeec
Confidence 888999999999987665544
No 11
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=63.08 E-value=5.6 Score=37.91 Aligned_cols=24 Identities=25% Similarity=0.493 Sum_probs=19.1
Q ss_pred ccceeCCCCceeccCCCCCCCcccCCC
Q 002049 805 VFCEECPVGTFKNVSGSDRALCRNCSS 831 (975)
Q Consensus 805 ~fC~eCP~GtYKn~~gs~~~~C~pCp~ 831 (975)
..|.+|..|+|++.. ...|.+|+.
T Consensus 4 ~~Ct~C~~g~~~~~~---~~~C~~C~~ 27 (96)
T PTZ00382 4 AVCTSCDSDKKPNKD---GSGCVLCSV 27 (96)
T ss_pred cccCcCCCCCccCCC---CCcCCcCCC
Confidence 369999999998854 457999985
No 12
>PHA02691 hypothetical protein; Provisional
Probab=62.34 E-value=4.4 Score=39.67 Aligned_cols=47 Identities=21% Similarity=0.266 Sum_probs=32.6
Q ss_pred ceehhhHHHHHHHHHHHHHHhhheeccC--CCccCCCCcc-ccccccccc
Q 002049 880 PWLFGLILLGLLILLALVLSVARMKYMG--GDELPALVPA-RRIDHSFPF 926 (975)
Q Consensus 880 p~~F~L~l~~llilla~vls~~R~K~~~--~d~~~~~~~~-~~iD~sfp~ 926 (975)
.|++.+++++++++|+|.+.++|-.+-. .+++..+++. +|.|..||.
T Consensus 2 ~~l~~l~fFi~FL~l~Y~~ny~PTNKlqlaV~~l~~e~~~~k~~d~~~p~ 51 (110)
T PHA02691 2 SWALEVALFAAFLAAAYVLTFLPTNKMQLAVRELADARAWRQRTDAQLDG 51 (110)
T ss_pred chHHHHHHHHHHHHHHHHHhhccchhHHHhhhhhhhhhhHHhhccccCcc
Confidence 3778888999999999999887544222 3455555553 466777776
No 13
>KOG1836 consensus Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures]
Probab=60.88 E-value=7.9 Score=52.49 Aligned_cols=42 Identities=40% Similarity=0.755 Sum_probs=35.3
Q ss_pred CceEecCCCCCCCccccceeCCCCceeccCCCC--CCCcccCCC
Q 002049 790 NGTVTGKACPRGLYGVFCEECPVGTFKNVSGSD--RALCRNCSS 831 (975)
Q Consensus 790 nGti~g~~CP~G~yG~fC~eCP~GtYKn~~gs~--~~~C~pCp~ 831 (975)
.-++.-|.||+||.|.-|++|.-|+|=|..+-+ ...|++|+-
T Consensus 794 ~~~~iCk~Cp~gytG~rCe~c~dgyfg~p~~~~~~~~~c~~c~c 837 (1705)
T KOG1836|consen 794 ILEVVCKNCPPGYTGLRCEECADGYFGNPLGHDGDVRPCQSCQC 837 (1705)
T ss_pred ccceecCCCCCCCcccccccCCCccccCCCCCCCCcccCcccee
Confidence 667778999999999999999999998876421 259999996
No 14
>smart00180 EGF_Lam Laminin-type epidermal growth factor-like domai.
Probab=55.30 E-value=7.2 Score=32.15 Aligned_cols=19 Identities=26% Similarity=0.789 Sum_probs=18.0
Q ss_pred CCCCCccccceeCCCCcee
Q 002049 798 CPRGLYGVFCEECPVGTFK 816 (975)
Q Consensus 798 CP~G~yG~fC~eCP~GtYK 816 (975)
|++++.|..|++|+.|+|-
T Consensus 22 C~~~~~G~~C~~C~~g~~g 40 (46)
T smart00180 22 CKPNVTGRRCDRCAPGYYG 40 (46)
T ss_pred CCCCCCCCCCCcCCCCcCC
Confidence 9999999999999999996
No 15
>KOG4289 consensus Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms]
Probab=55.09 E-value=9 Score=50.66 Aligned_cols=80 Identities=28% Similarity=0.628 Sum_probs=50.2
Q ss_pred cccCCceEecCCCCCCCccccce-----eCCCCceeccCCCCCCCcccCCCCC----CCC-----------CcceeeccC
Q 002049 786 LAGGNGTVTGKACPRGLYGVFCE-----ECPVGTFKNVSGSDRALCRNCSSNE----LPH-----------RALYIPIRG 845 (975)
Q Consensus 786 ~~g~nGti~g~~CP~G~yG~fC~-----eCP~GtYKn~~gs~~~~C~pCp~~~----~p~-----------ra~~i~~rg 845 (975)
.++.+|-. -.||+||+|.+|+ +||-|+|- ...|.||.-.- -|. ..+|....+
T Consensus 1733 sp~a~GY~--C~C~~g~~G~~Ce~~~dq~CPrGWWG------~P~CgpC~CavsKgfdp~CnKt~G~CqCKe~hy~~~~~ 1804 (2531)
T KOG4289|consen 1733 SPGAHGYT--CECPPGYTGPYCELRADQPCPRGWWG------FPTCGPCNCAVSKGFDPDCNKTNGQCQCKENHYRPIGS 1804 (2531)
T ss_pred CCCCCcee--EECCCcccCcchhhhccCCCCCcccC------CCCccCccccccCCCCCCccccCcceeeccccccCCCc
Confidence 34445543 6899999999995 79999885 35788886310 000 123332211
Q ss_pred --------CccCCCCC----ccccCCcc--cCCcccchHHHH
Q 002049 846 --------GVTECPCP----YKCVSERY--HMPHCYTTLEEL 873 (975)
Q Consensus 846 --------gv~~~~Cp----y~C~s~~y--~~p~C~t~le~l 873 (975)
|...+.|. -+|.++.. +...|-.||.|.
T Consensus 1805 Cl~CdC~~Gs~Sr~C~adGqC~C~pgaiGRqCdrCd~pfaev 1846 (2531)
T KOG4289|consen 1805 CLPCDCYFGSDSRECDADGQCPCKPGAIGRQCDRCDNPFAEV 1846 (2531)
T ss_pred ceeeccccCCCcccccCCCcCCCCCccccccccccCChhhhc
Confidence 55666774 34777644 668899999874
No 16
>cd00055 EGF_Lam Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies
Probab=54.58 E-value=7.3 Score=32.42 Aligned_cols=27 Identities=26% Similarity=0.628 Sum_probs=22.2
Q ss_pred CCceEecCCCCCCCccccceeCCCCceecc
Q 002049 789 GNGTVTGKACPRGLYGVFCEECPVGTFKNV 818 (975)
Q Consensus 789 ~nGti~g~~CP~G~yG~fC~eCP~GtYKn~ 818 (975)
.+|.- .|++++.|..|++|+.|+|...
T Consensus 17 ~~G~C---~C~~~~~G~~C~~C~~g~~~~~ 43 (50)
T cd00055 17 GTGQC---ECKPNTTGRRCDRCAPGYYGLP 43 (50)
T ss_pred CCCEE---eCCCcCCCCCCCCCCCCCccCC
Confidence 45554 3999999999999999999754
No 17
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=54.39 E-value=26 Score=45.04 Aligned_cols=9 Identities=56% Similarity=0.996 Sum_probs=3.6
Q ss_pred CCCCCCCCC
Q 002049 172 AGGGHGGRG 180 (975)
Q Consensus 172 ~GGGhGG~G 180 (975)
+|||+||..
T Consensus 1190 sgGGYGggy 1198 (1282)
T KOG0921|consen 1190 SGGGYGGGY 1198 (1282)
T ss_pred CCCCcCCCC
Confidence 344444333
No 18
>PF07354 Sp38: Zona-pellucida-binding protein (Sp38); InterPro: IPR010857 This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90 kDa family of zona pellucida glycoproteins in a calcium-dependent manner []. These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur [].; GO: 0007339 binding of sperm to zona pellucida, 0005576 extracellular region
Probab=51.21 E-value=12 Score=41.81 Aligned_cols=23 Identities=30% Similarity=0.791 Sum_probs=20.0
Q ss_pred cceeCCCCceeccCCCCCCCcccCCC
Q 002049 806 FCEECPVGTFKNVSGSDRALCRNCSS 831 (975)
Q Consensus 806 fC~eCP~GtYKn~~gs~~~~C~pCp~ 831 (975)
=|+-|++|||....+ ..|+.|..
T Consensus 239 CCVvCsPgTysp~~~---~~C~~C~~ 261 (271)
T PF07354_consen 239 CCVVCSPGTYSPDDD---VHCQQCNS 261 (271)
T ss_pred eeEECCCcccCCCCC---ceEEecCc
Confidence 599999999998764 69999995
No 19
>PF00053 Laminin_EGF: Laminin EGF-like (Domains III and V); InterPro: IPR002049 Laminins [] are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation. They are composed of distinct but related alpha, beta and gamma chains. The three chains form a cross-shaped molecule that consist of a long arm and three short globular arms. The long arm consist of a coiled coil structure contributed by all three chains and cross-linked by interchain disulphide bonds. Beside different types of globular domains each subunit contains, in its first half, consecutive repeats of about 60 amino acids in length that include eight conserved cysteines []. The tertiary structure [, ] of this domain is remotely similar in its N-terminal to that of the EGF-like module (see PDOC00021 from PROSITEDOC). It is known as a 'LE' or 'laminin-type EGF-like' domain. The number of copies of the LE domain in the different forms of laminins is highly variable; from 3 up to 22 copies have been found. A schematic representation of the topology of the four disulphide bonds in the LE domain is shown below. +-------------------+ +-|-----------+ | +--------+ +-----------------+ | | | | | | | | xxCxCxxxxxxxxxxxCxxxxxxxCxxCxxxxxGxxCxxCxxgaagxxxxxxxxxxxCxx sssssssssssssssssssssssssssssssssss 'C': conserved cysteine involved in a disulphide bond 'a': conserved aromatic residue 'G': conserved glycine (lower case = less conserved) 's': region similar to the EGF-like domain In mouse laminin gamma-1 chain, the seventh LE domain has been shown to be the only one that binds with a high affinity to nidogen []. The binding-sites are located on the surface within the loops C1-C3 and C5-C6 [, ]. Long consecutive arrays of LE domains in laminins form rod-like elements of limited flexibility [], which determine the spacing in the formation of laminin networks of basement membranes [].; PDB: 3TBD_A 3ZYG_B 3ZYI_B 2Y38_A 1KLO_A 1NPE_B 3ZYJ_B 1TLE_A.
Probab=46.63 E-value=9 Score=31.49 Aligned_cols=22 Identities=36% Similarity=0.727 Sum_probs=18.0
Q ss_pred CCCCCccccceeCCCCceeccC
Q 002049 798 CPRGLYGVFCEECPVGTFKNVS 819 (975)
Q Consensus 798 CP~G~yG~fC~eCP~GtYKn~~ 819 (975)
|++++.|..|++|..++|....
T Consensus 22 C~~~~~G~~C~~C~~g~~~~~~ 43 (49)
T PF00053_consen 22 CKPGTTGPRCDQCKPGYFGLPS 43 (49)
T ss_dssp BSTTEESTTS-EE-TTEECSTT
T ss_pred ccccccCCcCcCCCCccccccC
Confidence 9999999999999999997643
No 20
>cd00064 FU Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors.
Probab=42.50 E-value=21 Score=29.27 Aligned_cols=9 Identities=33% Similarity=1.099 Sum_probs=4.8
Q ss_pred ceeCCCCce
Q 002049 807 CEECPVGTF 815 (975)
Q Consensus 807 C~eCP~GtY 815 (975)
|..|+.++|
T Consensus 17 C~~C~~~~~ 25 (49)
T cd00064 17 CTSCRHGFY 25 (49)
T ss_pred CccCcCccC
Confidence 555555554
No 21
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=42.13 E-value=15 Score=43.48 Aligned_cols=24 Identities=29% Similarity=0.517 Sum_probs=11.5
Q ss_pred CCCccccccccCCCcceeeEEEEe
Q 002049 342 LPTNTDTLLLEFPKQQLWTNVYIR 365 (975)
Q Consensus 342 ~~t~t~T~ll~fp~~~l~~nv~v~ 365 (975)
.++.-|--..|||...-|.|.++.
T Consensus 446 vp~~~dgDy~EfpvPEQfkt~~~~ 469 (480)
T KOG2675|consen 446 VPTNEDGDYVEFPVPEQFKTKFNG 469 (480)
T ss_pred cccCCCCCcccccChHHHhhhccC
Confidence 333334444666655555554443
No 22
>PF05268 GP38: Phage tail fibre adhesin Gp38; InterPro: IPR007932 This entry is represented by Bacteriophage T2, Gp38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, Gp57, catalyses the organisation of Gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition [].
Probab=41.03 E-value=77 Score=35.00 Aligned_cols=37 Identities=24% Similarity=0.514 Sum_probs=21.2
Q ss_pred cccCCCCCCCCCCCCCcCcccEEEEEEceeeee--ecEEE
Q 002049 210 SYGSKGGTTFKGENFGGDGGGRIRLEVVNEIEV--NGSLL 247 (975)
Q Consensus 210 ~~GSGGG~~~~~~~~GG~GGG~I~I~a~~~L~l--~G~I~ 247 (975)
++|-|| +++.....+.+||=+|+=....+|+| +|.|.
T Consensus 114 ~yGRGG-nGs~~~~~g~~GG~~I~N~iG~rLRI~N~GaIA 152 (260)
T PF05268_consen 114 MYGRGG-NGSGSNSAGAAGGHAIQNDIGGRLRINNNGAIA 152 (260)
T ss_pred EEecCC-CCCCCCCCccccceeeecCCcceEEEecCCEEe
Confidence 444444 43445566777787887555455554 45554
No 23
>PF04519 Bactofilin: Polymer-forming cytoskeletal; InterPro: IPR007607 This family contains several uncharacterised hypothetical proteins.
Probab=37.75 E-value=3.1e+02 Score=25.61 Aligned_cols=15 Identities=20% Similarity=0.372 Sum_probs=9.4
Q ss_pred EEEeeEEEccCcEEE
Q 002049 136 VSALNASFSSGSVVN 150 (975)
Q Consensus 136 l~A~niti~~~s~I~ 150 (975)
+.+..+.|..++.|+
T Consensus 82 i~~~~l~v~~ga~i~ 96 (101)
T PF04519_consen 82 ITAGKLEVEGGASIN 96 (101)
T ss_pred EEECEEEEeCCCEEE
Confidence 455666676666665
No 24
>PF02166 Androgen_recep: Androgen receptor; InterPro: IPR001103 Steroid or nuclear hormone receptors (NRs) constitute an important super-family of transcription regulators that are involved in diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members include the steroid hormone receptors and receptors for thyroid hormone, retinoids and 1,25-dihydroxy-vitamin D3. The proteins function as dimeric molecules in the nucleus to regulate the transcription of target genes in a ligand-responsive manner [, ]. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes and hormone resistance syndromes. Many do not yet have a defined ligand and are accordingly termed "orphan" receptors. More than 300 NRs have been described to date and a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The androgen receptor (AR) consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain (IPR001628 from INTERPRO) that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain (NTD) is unique to the androgen receptors and spans approximately the first 530 residues; the highly-conserved DNA-binding domain is smaller (around 65 residues) and occupies the central portion of the protein; and the hormone ligand binding domain (LBD) lies at the receptor C terminus. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. The LBDs of steroid hormone receptors fold into 12 helices that form a ligand-binding pocket. When an agonist is bound, helix 12 folds over the pocket to enclose the ligand []. When an antagonist is unbound, helix 12 is positioned away from the pocket in a way that interferes with the binding of coactivators to a groove in the hormone-binding domain formed after ligand binding. In AR, ligand binding that induces folding of helix 12 to overlie the pocket discloses a groove that binds a region of the NTD. Coactivator molecules can also bind to this groove, but the predominant site for coactivator binding to AR is in the NTD. AR ligand resides in a pocket and primarily contacts helices 4, 5, and 10. The DNA-binding region includes eight cysteine residues that form two coordination complexes, each composed of four cysteines and a Zn2+ ion. These two zinc fingers form the structure that binds to the major groove of DNA. The second zinc finger stabilises the binding complex by hydrophobic interactions with the first finger and contributes to specificity of receptor DNA binding. It is also necessary for receptor dimerisation that occurs during DNA binding Defects in the androgen receptor cause testicular feminisation syndrome, androgen insensibility syndrome (AIS) [, ]. AIS may be complete (CAIS), where external genitalia are phenotypically female; partial (PAIS), where genitalia are substantively ambiguous; or mild (MAIS), where external genitalia are normal male, or nearly so. Defects in the receptor also cause X-linked spinal and bulbar muscular atrophy (also known as Kennedy's disease).; GO: 0003677 DNA binding, 0004882 androgen receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0030521 androgen receptor signaling pathway, 0005634 nucleus; PDB: 1XOW_B 2Q7K_B 2Q7I_B.
Probab=37.11 E-value=11 Score=43.24 Aligned_cols=26 Identities=50% Similarity=0.989 Sum_probs=0.0
Q ss_pred cccccccceeeeCCCCCcccCCCCCCCCCCCCCCCCC
Q 002049 21 SLDQYNFPVIGFGADSLFHGDYTPPSPPPPIAPPHPP 57 (975)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 57 (975)
+-|-||||+- ..-|+|||||+|||+.
T Consensus 335 sRDyYnF~la-----------Lag~~~p~~~~hph~R 360 (423)
T PF02166_consen 335 SRDYYNFPLA-----------LAGPPPPPPPPHPHAR 360 (423)
T ss_dssp -------------------------------------
T ss_pred cccccccccc-----------cccccccccccccccc
Confidence 4567777752 2335555666677554
No 25
>KOG1056 consensus Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=36.45 E-value=39 Score=43.45 Aligned_cols=39 Identities=26% Similarity=0.583 Sum_probs=29.1
Q ss_pred EecCCCCCCCc-c--------ccceeCCCCceeccCCCCCCCcccCCCCCCC
Q 002049 793 VTGKACPRGLY-G--------VFCEECPVGTFKNVSGSDRALCRNCSSNELP 835 (975)
Q Consensus 793 i~g~~CP~G~y-G--------~fC~eCP~GtYKn~~gs~~~~C~pCp~~~~p 835 (975)
+=..+|-+|.. . .-|++|+...|++ |...|.+|+...-|
T Consensus 493 ~CS~pC~~g~~k~~~~~~~ccw~c~~c~~~eY~~----d~~tc~~C~~~~wp 540 (878)
T KOG1056|consen 493 VCSEPCLPGQRKKVTKGVTCCWHCTPCMSYEYVN----DEFTCSDCQLGQWP 540 (878)
T ss_pred cccCcCCcchhcccccCceeEEEcccCCCcceec----CcceeccCCcCcCC
Confidence 33578888872 1 2499999999999 45799999965444
No 26
>PF15195 TMEM210: TMEM210 family
Probab=32.24 E-value=28 Score=33.77 Aligned_cols=11 Identities=45% Similarity=1.096 Sum_probs=4.8
Q ss_pred cCCCCCCCCCC
Q 002049 40 GDYTPPSPPPP 50 (975)
Q Consensus 40 ~~~~~~~~~p~ 50 (975)
-+-+|++||||
T Consensus 100 m~~~p~~pppp 110 (116)
T PF15195_consen 100 MEASPEEPPPP 110 (116)
T ss_pred cCCCCCCCCcC
Confidence 34444444443
No 27
>PHA03066 Hypothetical protein; Provisional
Probab=28.77 E-value=40 Score=33.35 Aligned_cols=44 Identities=11% Similarity=0.203 Sum_probs=28.0
Q ss_pred hhhHHHHHHHHHHHHHHhhheeccC--CCccCCCCc-cccccccccc
Q 002049 883 FGLILLGLLILLALVLSVARMKYMG--GDELPALVP-ARRIDHSFPF 926 (975)
Q Consensus 883 F~L~l~~llilla~vls~~R~K~~~--~d~~~~~~~-~~~iD~sfp~ 926 (975)
+.|++++++++++|++.+++-.+.. .+++..+++ .||.|.+||+
T Consensus 5 ~~l~fFi~Fl~~~Y~~n~~PTNKlqlaV~~l~~e~~~ik~~d~~~P~ 51 (110)
T PHA03066 5 LYLLFFIIFLCISYYFNYYPTNKLQMAVKELNRENAIIKQRNDEFPT 51 (110)
T ss_pred HHHHHHHHHHHHHHHHhhccChhHHhhhhhhhHHHHHHHhhhccCCc
Confidence 4466677888899999776443221 245554443 4577888885
No 28
>PF00020 TNFR_c6: TNFR/NGFR cysteine-rich region; InterPro: IPR001368 A number of proteins, some of which are known to be receptors for growth factors have been found to contain a cysteine-rich domain at the N-terminal region that can be subdivided into four (or in some cases, three) repeats containing six conserved cysteines all of which are involved in intrachain disulphide bonds []. CD27 (also called S152 or T14) mediates a co-stimulatory signal for T and B cell activation and is involved in murine T cell development. Tyrosine-phosphorylation of ZAP-70 following CD27 ligation of T cells has been reported [], but not confirmed independently. CD30 was originally identified as Ki-1, an antigen expressed on Reed-Sternberg cells in Hodgkin's lymphomas and other non-Hodgkin's lymphomas, particularly diffuse large-cell lymphoma and immunoblastic lymphoma. CD30 has pleiotropic effects on CD30-positive lymphoma cell lines ranging from cell proliferation to cell death. It is thought to be involved in negative selection of T-cells in the thymus and is involved in TCR-mediated cell death. CD30 is a member of the TNFR family of molecules, activate NFkB through interaction with TRAF2 and TRAF5. CD40 (Bp50) plays a central role in the regulation of cell-mediated immunity as well as antibody mediated immunity. It is central to T cell dependent (TD)-responses and may influence survival of B cell lymphomas. CD95 (also called APO-1, fas antigen, Fas tumour necrosis factor receptor superfamily, member 6, TNFRSF6 or apoptosis antigen 1, APT1) is expressed, typically at high levels, on activated T and B cells. It is involved in the mediation of apoptosis-inducing signals. Other proteins known to belong to this family [, , , ] are, tumour Necrosis Factor type I and type II receptors (TNFR), Rabbit fibroma virus soluble TNF receptor (protein T2), lymphotoxin alpha/beta receptor, low-affinity nerve growth factor receptor (LA-NGFR) (p75), T-cell antigen OX40, Wsl-1, a receptor (for a yet undefined ligand) that mediates apoptosis and Vaccinia virus protein A53 (SalF19R). CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/).; GO: 0005488 binding; PDB: 3TJE_F 3QD6_S 3ALQ_U 3IJ2_Y 3BUK_D 1SG1_X 1NCF_B 1EXT_A 1FT4_B 1TNR_R ....
Probab=26.27 E-value=26 Score=27.67 Aligned_cols=20 Identities=35% Similarity=0.909 Sum_probs=15.0
Q ss_pred CCCCceeccCCCCCCCcccCCC
Q 002049 810 CPVGTFKNVSGSDRALCRNCSS 831 (975)
Q Consensus 810 CP~GtYKn~~gs~~~~C~pCp~ 831 (975)
||.|+|.+..+ ...|.+|..
T Consensus 1 C~~g~y~~~~~--~~~C~~C~~ 20 (39)
T PF00020_consen 1 CPPGTYSDSEN--HPQCLPCSR 20 (39)
T ss_dssp ECTTEEEESSC--SSSEEEEES
T ss_pred CccCcccCCCC--CCcCCccCC
Confidence 89999998754 378877753
No 29
>PF05281 Secretogranin_V: Neuroendocrine protein 7B2 precursor (Secretogranin V); InterPro: IPR007945 Mature peptide hormones and neuropeptides are typically synthesised from much larger precursors and require several post-translational processing steps--including proteolytic cleavage--for the formation of the bioactive species. The subtilisin-related proteolytic enzymes that accomplish neuroendocrine-specific cleavages are known as prohormone convertases 1 and 2 (PC1 and PC2), which belong to MEROPS peptidase family S8B. The cell biology of these proteases within the regulated secretory pathway of neuroendocrine cells is complex, and they are themselves initially synthesised as inactive precursor molecules. ProPC1 propeptide cleavage occurs rapidly in the endoplasmic reticulum, yet its major site of action on prohormones takes place later in the secretory pathway. PC1 undergoes an interesting carboxyl terminal processing event whose function appears to be to activate the enzyme. ProPC2, on the other hand, exhibits comparatively long initial folding times and exits the endoplasmic reticulum without propeptide cleavage, in association with the neuroendocrine-specific protein 7B2. Once the proPC2/7B2 complex arrives at the trans-Golgi network, 7B2 is internally cleaved into two domains, the 21kDa fragment and a carboxy-terminal 31 residue peptide. PC2 propeptide removal occurs in the maturing secretory granule, most likely through autocatalysis, and 7B2 association does not appear to be directly required for this cleavage event. However, if proPC2 has not encountered 7B2 intracellularly, it cannot generate a catalytically active mature species. The molecular mechanism behind the intriguing intracellular association of 7B2 and proPC2 is still unknown, but may involve conformational rearrangement or stabilisation of a proPC2 conformer mediated by a 36-residue internal segment of 21kDa 7B2. This family represents, 7B2 (secretogranin V), which is the molecular escort protein for PC2. 7B2 is a bifunctional protein with an N-terminal activation domain and a C-terminal inhibitory domain (MEROPS inhibitor family I21, clan I-) separated by a furin cleavage site []. Although 7B2 represents a potent inhibitor of PC2, there is an absolute requirement of 7B2 for the activation of PC2, which is synthesised as a zymogen. Both the full length, 27 kDa, and the C-terminal peptide (CT domain) derived from intramolecular cleavage of 7B2 are potent inhibitors of PC2. Studies have shown that the active peptide in the CT domain to be LLRVHK, active in the nanomolar range not only against PC2 but also PC1 [, ]. Knock-out studies have shown that the PC2 nulls are not phenotypically equivalent to the 7B2 nulls, which suggests that 7B2 may have other activities in addition to being the activator of PC2 []. 7B2 exhibits both structural and functional homology to proSAAS (IPR010832 from INTERPRO), which is the PC1 binding protein. The CT domain of proSAAS contains the same inhibitor hexapeptide as 7B2, consequently both 7B2 and proSAAS are two members of a homologous family of prohormone convertase inhibitor proteins. ; GO: 0007218 neuropeptide signaling pathway, 0030141 stored secretory granule
Probab=25.38 E-value=1e+02 Score=33.66 Aligned_cols=90 Identities=24% Similarity=0.428 Sum_probs=52.6
Q ss_pred CccccccccceEEEecCCcCCCCCcccCCceEecCCCCCCC--ccccce---eCCCCceeccCCCCCCCcccCCCCCCCC
Q 002049 762 DEYLPLASVNGSIDARGGLGRGQGLAGGNGTVTGKACPRGL--YGVFCE---ECPVGTFKNVSGSDRALCRNCSSNELPH 836 (975)
Q Consensus 762 d~y~pia~~~G~I~~~GG~~~~~g~~g~nGti~g~~CP~G~--yG~fC~---eCP~GtYKn~~gs~~~~C~pCp~~~~p~ 836 (975)
+||.+=.+.-|.-.++||++.+....+..|.|-...=.+-- ---+|. +||+|+=. . ..| - ++++.
T Consensus 50 ~E~l~hssLwG~q~isGGagEG~q~L~~~~~i~n~~~~ktd~~lPaYCnPPNPCPvGyt~-~-----dgC---l-e~fEn 119 (208)
T PF05281_consen 50 QEYLQHSSLWGHQYISGGAGEGPQHLGPEGNIPNIKIVKTDNNLPAYCNPPNPCPVGYTA-E-----DGC---L-ENFEN 119 (208)
T ss_pred cccccccccCCceeeeCCCCccchhcCccCCcCcccccccccCCCCCCCCCCCCCCCccc-c-----cCc---c-cCCcc
Confidence 36776667788888999998876666666665332211110 113675 69998652 2 234 4 35656
Q ss_pred CcceeeccCCccCCCCCccccCCcccCCccc
Q 002049 837 RALYIPIRGGVTECPCPYKCVSERYHMPHCY 867 (975)
Q Consensus 837 ra~~i~~rggv~~~~Cpy~C~s~~y~~p~C~ 867 (975)
-|.|.-. -... ..|.=|..||-+|-
T Consensus 120 TAeFSRe--yQa~----QdC~CD~EHMf~C~ 144 (208)
T PF05281_consen 120 TAEFSRE--YQAA----QDCMCDTEHMFDCP 144 (208)
T ss_pred HHHhhHH--HHhc----CccCCCcccccCCc
Confidence 5655431 1111 23555788998886
No 30
>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=25.13 E-value=96 Score=27.84 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=23.8
Q ss_pred cchHHHHHHHhCCceehhhHHHHHHHHHHHHHHhhheeccCC
Q 002049 867 YTTLEELVYTFGGPWLFGLILLGLLILLALVLSVARMKYMGG 908 (975)
Q Consensus 867 ~t~le~li~~~GGp~~F~L~l~~llilla~vls~~R~K~~~~ 908 (975)
|+.+.++++.+| ++.+.+++++++++++|-+.++.
T Consensus 3 ~e~~~~~a~a~~-------t~~~~l~fiavi~~ayr~~~K~~ 37 (60)
T COG4736 3 YEMMRGFADAWG-------TIAFTLFFIAVIYFAYRPGKKGE 37 (60)
T ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHHHHhcccchhh
Confidence 566777777333 45555667888888888776653
No 31
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=24.50 E-value=1e+02 Score=25.71 Aligned_cols=33 Identities=21% Similarity=0.409 Sum_probs=18.8
Q ss_pred cchHHHHHHHhCCceehhhHHHHHHHHHHHHHHhhheecc
Q 002049 867 YTTLEELVYTFGGPWLFGLILLGLLILLALVLSVARMKYM 906 (975)
Q Consensus 867 ~t~le~li~~~GGp~~F~L~l~~llilla~vls~~R~K~~ 906 (975)
|+.+..+.+.++ +++++++++++++.+.|.|.+
T Consensus 3 ~~~~~~~~~~~~-------~v~~~~~F~gi~~w~~~~~~k 35 (49)
T PF05545_consen 3 YETLQGFARSIG-------TVLFFVFFIGIVIWAYRPRNK 35 (49)
T ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHcccch
Confidence 455666666322 444445556667767776654
No 32
>PRK09677 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional
Probab=23.66 E-value=1.9e+02 Score=30.33 Aligned_cols=60 Identities=15% Similarity=0.253 Sum_probs=32.5
Q ss_pred eEEEccceeEecCCceEEeeccCcEEEEEeeccEEecccceEEeeeEEEEEeeEEEccCcEEE
Q 002049 88 IYVEGSGNLHILPGVTLCCPIKGCLLTINVTGEFLLGRNSEIVAGTVYVSALNASFSSGSVVN 150 (975)
Q Consensus 88 v~i~G~g~l~i~~gv~l~c~~~G~~I~i~~sg~~~lg~~s~i~assi~l~A~niti~~~s~I~ 150 (975)
.++.+..++++-++|.+ ..+|.+.+...+.+.|++++.|-.........+++|.++..|.
T Consensus 36 f~~~~~~~I~iG~~v~i---~~~~ri~~~~~~~i~IG~~v~Ig~~v~I~~~~~v~IG~~v~Ig 95 (192)
T PRK09677 36 FYIRNDGSINFGEGFTS---GVGLRLDAFGRGKLFFGDNVQVNDYVHIACIESITIGRDTLIA 95 (192)
T ss_pred EEEcCCCeEEECCceEE---CCCeEEEecCCCeEEECCCCEECCCcEEccCceEEECCCCEEC
Confidence 34555556666666443 3456665555566666666666544443333455555554443
No 33
>PF12661 hEGF: Human growth factor-like EGF; PDB: 2YGQ_A 2E26_A 3A7Q_A 2YGP_A 2YGO_A 1HRE_A 1HAE_A 1HAF_A 1HRF_A.
Probab=23.54 E-value=25 Score=22.57 Aligned_cols=11 Identities=45% Similarity=1.066 Sum_probs=8.1
Q ss_pred CCCCCCccccc
Q 002049 797 ACPRGLYGVFC 807 (975)
Q Consensus 797 ~CP~G~yG~fC 807 (975)
.||+||.|..|
T Consensus 3 ~C~~G~~G~~C 13 (13)
T PF12661_consen 3 QCPPGWTGPNC 13 (13)
T ss_dssp EE-TTEETTTT
T ss_pred cCcCCCcCCCC
Confidence 48999988877
No 34
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=22.50 E-value=51 Score=32.22 Aligned_cols=31 Identities=26% Similarity=0.620 Sum_probs=16.1
Q ss_pred ccceeCCCC-ceeccCCCCCCCcccCCCCCCCC
Q 002049 805 VFCEECPVG-TFKNVSGSDRALCRNCSSNELPH 836 (975)
Q Consensus 805 ~fC~eCP~G-tYKn~~gs~~~~C~pCp~~~~p~ 836 (975)
.||..|.-. -++...--++--|+.||+ .+|.
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY-~~~I 33 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRTCPY-VFPI 33 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCCCCc-eeeE
Confidence 367777643 122111013457899996 5554
No 35
>PF15048 OSTbeta: Organic solute transporter subunit beta protein
Probab=22.46 E-value=1.2e+02 Score=30.92 Aligned_cols=30 Identities=30% Similarity=0.853 Sum_probs=19.1
Q ss_pred hHHHHHHHh----CCceehhhHHHHHHHH-HHHHH
Q 002049 869 TLEELVYTF----GGPWLFGLILLGLLIL-LALVL 898 (975)
Q Consensus 869 ~le~li~~~----GGp~~F~L~l~~llil-la~vl 898 (975)
-|||++--| .-||-|++|++..+++ |++||
T Consensus 19 ~LEemlW~fR~ED~tpWNysiL~Ls~vvlvi~~~L 53 (125)
T PF15048_consen 19 LLEEMLWFFRVEDATPWNYSILALSFVVLVISFFL 53 (125)
T ss_pred HHHHHHHheecCCCCCcchHHHHHHHHHHHHHHHH
Confidence 488877434 4689777776666444 55555
No 36
>KOG4260 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.07 E-value=64 Score=36.62 Aligned_cols=28 Identities=39% Similarity=0.940 Sum_probs=0.0
Q ss_pred CCCCCccccceeCCCCceeccCCCCCCCcc
Q 002049 798 CPRGLYGVFCEECPVGTFKNVSGSDRALCR 827 (975)
Q Consensus 798 CP~G~yG~fC~eCP~GtYKn~~gs~~~~C~ 827 (975)
||+|.||.-|..||-|+=|.=.| ...|+
T Consensus 132 Cp~gtyGpdCl~Cpggser~C~G--nG~C~ 159 (350)
T KOG4260|consen 132 CPDGTYGPDCLQCPGGSERPCFG--NGSCH 159 (350)
T ss_pred cCCCCcCCccccCCCCCcCCcCC--CCccc
Done!