Query 000495
Match_columns 1462
No_of_seqs 203 out of 216
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:38:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000495.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000495hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0196 Tyrosine kinase, EPH ( 96.5 0.002 4.3E-08 81.1 4.4 55 796-863 261-319 (996)
2 PF07699 GCC2_GCC3: GCC2 and G 96.1 0.003 6.4E-08 54.3 2.0 26 805-832 9-34 (48)
3 PF10256 Erf4: Golgin subfamil 91.7 0.24 5.2E-06 49.7 4.8 67 966-1032 21-91 (118)
4 PF07562 NCD3G: Nine Cysteines 90.8 0.067 1.5E-06 47.6 -0.1 36 795-832 6-51 (54)
5 PHA02637 TNF-alpha-receptor-li 87.3 0.7 1.5E-05 48.2 4.2 57 797-858 31-92 (127)
6 cd00185 TNFR Tumor necrosis fa 85.4 0.62 1.3E-05 45.7 2.6 65 793-864 12-87 (98)
7 PHA02637 TNF-alpha-receptor-li 85.2 0.61 1.3E-05 48.6 2.6 41 789-830 38-87 (127)
8 KOG0921 Dosage compensation co 83.2 2.7 5.8E-05 55.0 7.4 31 539-573 1121-1151(1282)
9 PF07699 GCC2_GCC3: GCC2 and G 77.1 1.8 4E-05 37.4 2.3 32 791-822 7-43 (48)
10 KOG0921 Dosage compensation co 74.0 7.3 0.00016 51.3 7.2 8 172-179 1190-1197(1282)
11 PTZ00382 Variant-specific surf 61.1 5.8 0.00013 39.6 2.2 24 805-831 4-27 (96)
12 KOG4069 Uncharacterized conser 60.2 17 0.00037 38.5 5.4 78 965-1046 45-135 (154)
13 cd04299 GT1_Glycogen_Phosphory 53.9 9.3 0.0002 50.2 2.9 110 1018-1139 435-556 (778)
14 cd00185 TNFR Tumor necrosis fa 53.1 12 0.00026 36.9 2.9 31 804-834 11-43 (98)
15 KOG4289 Cadherin EGF LAG seven 52.5 11 0.00025 51.5 3.3 85 1305-1401 2171-2257(2531)
16 cd00055 EGF_Lam Laminin-type e 52.1 7.7 0.00017 33.9 1.3 27 789-818 17-43 (50)
17 smart00180 EGF_Lam Laminin-typ 52.0 7.9 0.00017 33.5 1.3 20 797-816 21-40 (46)
18 PF05268 GP38: Phage tail fibr 51.4 63 0.0014 37.1 8.3 36 211-247 115-152 (260)
19 PF14946 DUF4501: Domain of un 49.4 63 0.0014 35.6 7.7 32 876-907 83-115 (180)
20 PF12273 RCR: Chitin synthesis 46.8 16 0.00035 37.7 2.9 22 881-902 2-24 (130)
21 KOG3973 Uncharacterized conser 42.9 89 0.0019 38.0 8.2 7 289-295 453-459 (465)
22 KOG1836 Extracellular matrix g 40.5 18 0.0004 51.0 2.7 43 790-832 794-838 (1705)
23 TIGR02094 more_P_ylases alpha- 39.9 22 0.00048 45.5 3.2 104 1025-1139 354-467 (601)
24 KOG1836 Extracellular matrix g 38.4 25 0.00054 49.8 3.5 65 796-864 697-769 (1705)
25 PF07354 Sp38: Zona-pellucida- 38.1 19 0.00042 41.9 2.0 35 794-831 218-261 (271)
26 PF00053 Laminin_EGF: Laminin 37.1 13 0.00029 32.1 0.4 22 797-818 21-42 (49)
27 PF15496 DUF4646: Domain of un 36.5 56 0.0012 34.0 4.9 70 971-1041 43-120 (123)
28 KOG2675 Adenylate cyclase-asso 34.8 23 0.0005 43.7 2.0 27 340-366 444-470 (480)
29 PRK09677 putative lipopolysacc 33.5 1E+02 0.0022 33.8 6.5 61 87-150 35-95 (192)
30 KOG4611 Uncharacterized conser 30.7 45 0.00096 40.3 3.4 63 807-873 52-125 (747)
31 PF10256 Erf4: Golgin subfamil 30.5 49 0.0011 33.5 3.2 53 1147-1199 29-106 (118)
32 cd00064 FU Furin-like repeats. 29.5 40 0.00087 29.0 2.1 22 796-817 18-42 (49)
33 PF15496 DUF4646: Domain of un 27.4 49 0.0011 34.5 2.7 25 1146-1170 45-69 (123)
34 PF02166 Androgen_recep: Andro 27.2 21 0.00045 42.8 0.0 26 21-57 335-360 (423)
35 KOG0994 Extracellular matrix g 26.7 63 0.0014 44.1 4.0 65 797-866 785-856 (1758)
36 PF04519 Bactofilin: Polymer-f 26.5 2.5E+02 0.0054 27.5 7.3 57 71-150 5-61 (101)
37 KOG4258 Insulin/growth factor 26.4 42 0.00091 44.5 2.4 46 805-873 304-350 (1025)
38 PF05281 Secretogranin_V: Neur 25.7 1E+02 0.0022 35.2 4.9 91 761-867 49-144 (208)
39 PRK06958 single-stranded DNA-b 23.8 4.6E+02 0.01 29.5 9.4 36 108-145 71-109 (182)
40 PF15195 TMEM210: TMEM210 fami 23.5 49 0.0011 33.6 1.8 10 41-50 101-110 (116)
41 KOG4180 Predicted kinase [Gene 22.4 1.5E+02 0.0033 36.0 5.7 21 1083-1103 103-123 (395)
42 PF00020 TNFR_c6: TNFR/NGFR cy 21.6 42 0.00091 27.9 0.8 19 810-830 1-19 (39)
43 PF12661 hEGF: Human growth fa 21.5 28 0.00061 23.7 -0.2 11 797-807 3-13 (13)
44 PF05268 GP38: Phage tail fibr 21.5 1.6E+02 0.0035 34.1 5.4 40 245-284 113-157 (260)
45 KOG4260 Uncharacterized conser 21.4 57 0.0012 38.5 2.0 28 798-827 132-159 (350)
No 1
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=96.54 E-value=0.002 Score=81.07 Aligned_cols=55 Identities=31% Similarity=0.726 Sum_probs=41.8
Q ss_pred cCCCCCcc----cccceeCCCCceecccCCCCCCcccCCCCCCCCCcceecccCcccCCCCCccccCCCccC
Q 000495 796 KACPRGLY----GVFCEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVSERYHM 863 (1462)
Q Consensus 796 ~~CP~G~~----G~fC~eCP~GtYKn~~Gs~~~~C~pC~~~~lp~ra~yiyv~~G~~~~~CpY~C~sdk~~~ 863 (1462)
=-|.+||. |.-|+.||.||||...| ...|.+||.++..+ -...+.|. |..++|+.
T Consensus 261 C~C~aGye~~~~~~~C~aCp~G~yK~~~~--~~~C~~CP~~S~s~---------~ega~~C~--C~~gyyRA 319 (996)
T KOG0196|consen 261 CVCKAGYEEAENGKACQACPPGTYKASQG--DSLCLPCPPNSHSS---------SEGATSCT--CENGYYRA 319 (996)
T ss_pred eeecCCCCcccCCCcceeCCCCcccCCCC--CCCCCCCCCCCCCC---------CCCCCccc--ccCCcccC
Confidence 47999984 67799999999999865 48999999875432 12346675 88888873
No 2
>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=96.13 E-value=0.003 Score=54.35 Aligned_cols=26 Identities=31% Similarity=0.887 Sum_probs=23.0
Q ss_pred ccceeCCCCceecccCCCCCCcccCCCC
Q 000495 805 VFCEECPVGTFKNVSGSDRALCRNCSSN 832 (1462)
Q Consensus 805 ~fC~eCP~GtYKn~~Gs~~~~C~pC~~~ 832 (1462)
.-|++||.||||+..|. ..|.+||.+
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 46999999999999886 589999975
No 3
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=91.75 E-value=0.24 Score=49.73 Aligned_cols=67 Identities=19% Similarity=0.347 Sum_probs=45.0
Q ss_pred CCcchhhhhhcHHHHHHHHHHHHHHHhhh--h--hhhhhhheeeeeecchhHHHHHHHHHHHHHHHHHHHH
Q 000495 966 SPPEQVIEIVYEDAFNRFADEINALAAYQ--W--WEGSVYSILSVLAYPLAWSWLQLCRKNKLQQLREFVR 1032 (1462)
Q Consensus 966 spP~~i~~iVyed~Fn~Fad~IN~laay~--~--We~~i~~iLsvl~YPlaw~~~q~rRrkk~~rL~efv~ 1032 (1462)
.-|.++...+.+++|++++++||+..+=. . |.-++-.+|.++..=+..++.+...||++++|.+|+.
T Consensus 21 ~~P~~L~~~is~~ef~~iI~~IN~~l~~a~~~~~~~~~~~~~l~~lt~~l~~~~~~~~~~~~~~~le~~l~ 91 (118)
T PF10256_consen 21 EYPGELSGYISPEEFEEIINTINQILKEAFEPISWRNIIENILGCLTLGLSSLCFKTHYKRKLRELEKYLE 91 (118)
T ss_pred cCCHhhcCCCCHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777899999999999999999987322 1 3344544555544222222234556677888999996
No 4
>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=90.85 E-value=0.067 Score=47.56 Aligned_cols=36 Identities=31% Similarity=0.744 Sum_probs=20.4
Q ss_pred ccCCCCCccc----------ccceeCCCCceecccCCCCCCcccCCCC
Q 000495 795 GKACPRGLYG----------VFCEECPVGTFKNVSGSDRALCRNCSSN 832 (1462)
Q Consensus 795 g~~CP~G~~G----------~fC~eCP~GtYKn~~Gs~~~~C~pC~~~ 832 (1462)
...|++|++- +-|++||.|+|.|.+ +...|.+||.+
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 4689999862 349999999999986 45899999965
No 5
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=87.27 E-value=0.7 Score=48.17 Aligned_cols=57 Identities=23% Similarity=0.571 Sum_probs=34.3
Q ss_pred CCCCCcc---cccceeCCCCceecccC--CCCCCcccCCCCCCCCCcceecccCcccCCCCCccccC
Q 000495 797 ACPRGLY---GVFCEECPVGTFKNVSG--SDRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVS 858 (1462)
Q Consensus 797 ~CP~G~~---G~fC~eCP~GtYKn~~G--s~~~~C~pC~~~~lp~ra~yiyv~~G~~~~~CpY~C~s 858 (1462)
.|..+-| +.-|.+||.|||+...= .....|.|||.++.....++.. .=..|.-.|++
T Consensus 31 ~C~e~EY~~~~~CC~kCPPGt~v~~~Ct~~t~T~C~PCp~GTYTe~~N~~~-----~C~~C~~~Cd~ 92 (127)
T PHA02637 31 KCKDNEYKRHNLCCLSCPPGTYASRLCDIKTNTQCTPCGSGTFTSHNNHLP-----ACLSCNGRCDR 92 (127)
T ss_pred CCCCCcCcCCCeEcCCCCCCCEEeCcCCCCCCcccccCCCCCeeccCCCCC-----cccccCCccCc
Confidence 6887755 34588999999887431 1245799998765444333321 11456555654
No 6
>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=85.43 E-value=0.62 Score=45.65 Aligned_cols=65 Identities=25% Similarity=0.568 Sum_probs=40.6
Q ss_pred EEccCCCCCcc---------cccceeCCCCceecccCCCCCCcccCCCCCCCCCcceecccCc--ccCCCCCccccCCCc
Q 000495 793 VTGKACPRGLY---------GVFCEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGG--VTECPCPYKCVSERY 861 (1462)
Q Consensus 793 i~g~~CP~G~~---------G~fC~eCP~GtYKn~~Gs~~~~C~pC~~~~lp~ra~yiyv~~G--~~~~~CpY~C~sdk~ 861 (1462)
.-=+.||+|++ ..-|++||.|+|.+... ....|++|..= + ...++ ++.+ ...+.|- |.+++|
T Consensus 12 ~cC~~C~pG~~~~~~C~~~~~t~C~~C~~g~ys~~~~-~~~~C~~c~~C--~-~g~~~-~~~ct~t~dt~C~--C~~G~y 84 (98)
T cd00185 12 LCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTYTDSWN-HLPKCLSCRTC--D-SGLVE-KAPCTATRNTVCG--CKPGFY 84 (98)
T ss_pred CCCCCCCCCccCCCcCCCCCCCeecCCCCCCcccCCC-CCCcCCcCccC--C-CCCEE-EccCCCCCCCeEe--CCCCCE
Confidence 44578999986 25699999999988753 23578888642 2 11222 2222 2235675 888887
Q ss_pred cCC
Q 000495 862 HMP 864 (1462)
Q Consensus 862 ~~p 864 (1462)
...
T Consensus 85 ~~~ 87 (98)
T cd00185 85 CLT 87 (98)
T ss_pred ecC
Confidence 544
No 7
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=85.18 E-value=0.61 Score=48.57 Aligned_cols=41 Identities=27% Similarity=0.665 Sum_probs=30.6
Q ss_pred CCceEEccCCCCCcc---------cccceeCCCCceecccCCCCCCcccCC
Q 000495 789 GNGTVTGKACPRGLY---------GVFCEECPVGTFKNVSGSDRALCRNCS 830 (1462)
Q Consensus 789 ~nGTi~g~~CP~G~~---------G~fC~eCP~GtYKn~~Gs~~~~C~pC~ 830 (1462)
..+..-=+.||||++ ..-|.+||.|||..... ....|.+|.
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 445667789999986 56799999999977543 345688776
No 8
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=83.25 E-value=2.7 Score=55.02 Aligned_cols=31 Identities=29% Similarity=0.322 Sum_probs=15.4
Q ss_pred ccCCCCccccccccceEEEEEEEEeeEEeeEEEee
Q 000495 539 LLHPLEDCNLNSSLSFTLQICRAEEINIEGIIKGS 573 (1462)
Q Consensus 539 ~l~p~~dc~~N~sl~ftLqicrVeditv~g~v~GS 573 (1462)
.|.|+..=-+|.- =||||-+-..|+..|.-|
T Consensus 1121 qLdpvnarllnmi----RdIs~pSAa~inLmig~~ 1151 (1282)
T KOG0921|consen 1121 QLDPVNARLLNMI----RDISRPSAADINLMIGDS 1151 (1282)
T ss_pred ccCchhHHHHHHH----HHhcccccccccceeccC
Confidence 3555544333322 245666666666555544
No 9
>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=77.15 E-value=1.8 Score=37.40 Aligned_cols=32 Identities=38% Similarity=0.902 Sum_probs=24.8
Q ss_pred ceEEccCCCCCcc----c-ccceeCCCCceecccCCC
Q 000495 791 GTVTGKACPRGLY----G-VFCEECPVGTFKNVSGSD 822 (1462)
Q Consensus 791 GTi~g~~CP~G~~----G-~fC~eCP~GtYKn~~Gs~ 822 (1462)
+.-.=.+||.|+| | ..|.+||.|+|-...|+.
T Consensus 7 ~~~~C~~Cp~GtYq~~~g~~~C~~Cp~g~~T~~~Gs~ 43 (48)
T PF07699_consen 7 GNNKCQPCPKGTYQDEEGQTSCTPCPPGSTTSSEGST 43 (48)
T ss_pred CCCccCCCCCCccCCccCCccCccCcCCCccCCcCCc
Confidence 3344579999987 3 559999999998877763
No 10
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=74.01 E-value=7.3 Score=51.31 Aligned_cols=8 Identities=63% Similarity=1.286 Sum_probs=3.1
Q ss_pred CCCCCCCC
Q 000495 172 AGGGHGGR 179 (1462)
Q Consensus 172 ~GGGHGGr 179 (1462)
+|||+||.
T Consensus 1190 sgGGYGgg 1197 (1282)
T KOG0921|consen 1190 SGGGYGGG 1197 (1282)
T ss_pred CCCCcCCC
Confidence 33444333
No 11
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=61.10 E-value=5.8 Score=39.57 Aligned_cols=24 Identities=25% Similarity=0.493 Sum_probs=18.2
Q ss_pred ccceeCCCCceecccCCCCCCcccCCC
Q 000495 805 VFCEECPVGTFKNVSGSDRALCRNCSS 831 (1462)
Q Consensus 805 ~fC~eCP~GtYKn~~Gs~~~~C~pC~~ 831 (1462)
..|.+|..|+|++.. ...|.+|+.
T Consensus 4 ~~Ct~C~~g~~~~~~---~~~C~~C~~ 27 (96)
T PTZ00382 4 AVCTSCDSDKKPNKD---GSGCVLCSV 27 (96)
T ss_pred cccCcCCCCCccCCC---CCcCCcCCC
Confidence 468999999988854 356888874
No 12
>KOG4069 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.22 E-value=17 Score=38.49 Aligned_cols=78 Identities=24% Similarity=0.338 Sum_probs=54.3
Q ss_pred CCCcchhhhhhcHHHHHHHHHHHHHHHhh-------hhhhhhhhheeeeeecchhHHHHHHHHHHHHHHHHHHHHhh---
Q 000495 965 HSPPEQVIEIVYEDAFNRFADEINALAAY-------QWWEGSVYSILSVLAYPLAWSWLQLCRKNKLQQLREFVRSE--- 1034 (1462)
Q Consensus 965 ~spP~~i~~iVyed~Fn~Fad~IN~laay-------~~We~~i~~iLsvl~YPlaw~~~q~rRrkk~~rL~efv~se--- 1034 (1462)
...|..+++.|..+.|+.=+..+|++-|= ..+|+.+ =++.+|-.|.--. --=+||+++|+||+.++
T Consensus 45 ~~~pa~le~~i~R~vfE~Ti~rlN~~yAeAE~~~~qty~Egcl---gC~TaY~iy~cte-thYek~L~klskfl~~qNe~ 120 (154)
T KOG4069|consen 45 AEYPARLEEKIPRDVFENTIVRLNRIYAEAEAITPQTYFEGCL---GCFTAYAIYACTE-THYEKKLDKLSKFLNRQNEE 120 (154)
T ss_pred ecCcHHHhccCcHHHHHHHHHHHHHHHHHHHhcCCcchHHHHH---HHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhhh
Confidence 35789999999999999999999998432 2466644 3555665544433 23357899999999854
Q ss_pred -cCc--cccccchhh
Q 000495 1035 -YDH--SCLRSCRSR 1046 (1462)
Q Consensus 1035 -ydh--~clRs~rsR 1046 (1462)
|.| .=+|++--|
T Consensus 121 IY~~~Gl~l~dP~eR 135 (154)
T KOG4069|consen 121 IYHHVGLHLRDPMER 135 (154)
T ss_pred hccccceeecCchhh
Confidence 777 345665555
No 13
>cd04299 GT1_Glycogen_Phosphorylase_like This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The members of this family are found in bacteria and Archaea.
Probab=53.88 E-value=9.3 Score=50.18 Aligned_cols=110 Identities=25% Similarity=0.337 Sum_probs=64.6
Q ss_pred HHHHHHHH-HHHHHHHhhcCccccccchhhhhhcceEEeecCC-ceEEEEEEecCCCCcCCCCCccccc---------CC
Q 000495 1018 LCRKNKLQ-QLREFVRSEYDHSCLRSCRSRALYEGLKVAATAD-LMLAYIDFFLGGDEKRADLPPRLNQ---------RL 1086 (1462)
Q Consensus 1018 ~rRrkk~~-rL~efv~seydh~clRs~rsRaly~~lKvs~S~D-ysLaYiD~f~~~d~kr~dl~~~i~q---------~~ 1086 (1462)
|..|++.| +|+++|+......+.|.-.+.+.-.....-..|| ++++++==|- .|||.+|-.+... .-
T Consensus 435 w~~K~~~K~~L~~~v~~~~~~~~~~~g~~~~~~~~~~~~ldpd~ltigfarRfa--~YKR~~Lil~dl~rl~~il~~~~~ 512 (778)
T cd04299 435 WEVRQQLRRRLIEFVRRRLRRQWLRRGASAEEIGEADDVLDPNVLTIGFARRFA--TYKRATLLLRDPERLKRLLNDPER 512 (778)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhcCCchhhhhhcCCccCCCccEEeeeecch--hhhhHHHHHHHHHHHHHHhhCCCC
Confidence 33444443 5888887655444443222221111122234566 6667766664 6899998443222 25
Q ss_pred ceEEEEecccccccCcccC-CchhhhhhcccccccccccCCCcccccccccccc
Q 000495 1087 PMSLCFGGDGSYMSPFSLH-NDNIVTSLMSQVNDFINLQGCPFVNYMVFLNDEN 1139 (1462)
Q Consensus 1087 Pm~Ilf~GdGSymsPf~L~-sD~lL~sl~~q~n~~~n~~~~~~~~~~v~~~d~~ 1139 (1462)
|+-+||+|.+ | .|.-=+.++.+++++.+.-..+ ..+||..|++
T Consensus 513 pvQ~IfaGKA--------hP~d~~gK~iIk~i~~~a~~p~~~--~kVvfle~Yd 556 (778)
T cd04299 513 PVQFIFAGKA--------HPADEPGKELIQEIVEFSRRPEFR--GRIVFLEDYD 556 (778)
T ss_pred CeEEEEEEec--------CccchHHHHHHHHHHHHHhCcCCC--CcEEEEcCCC
Confidence 9999999999 6 4666677777766665522222 2578888888
No 14
>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=53.09 E-value=12 Score=36.89 Aligned_cols=31 Identities=26% Similarity=0.842 Sum_probs=23.1
Q ss_pred cccceeCCCCceecccCC--CCCCcccCCCCCC
Q 000495 804 GVFCEECPVGTFKNVSGS--DRALCRNCSSNEL 834 (1462)
Q Consensus 804 G~fC~eCP~GtYKn~~Gs--~~~~C~pC~~~~l 834 (1462)
+.-|..||.|+|-..... ....|.|||.+.+
T Consensus 11 ~~cC~~C~pG~~~~~~C~~~~~t~C~~C~~g~y 43 (98)
T cd00185 11 GLCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTY 43 (98)
T ss_pred CCCCCCCCCCccCCCcCCCCCCCeecCCCCCCc
Confidence 456999999999876532 2457999998654
No 15
>KOG4289 consensus Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms]
Probab=52.54 E-value=11 Score=51.46 Aligned_cols=85 Identities=24% Similarity=0.203 Sum_probs=53.4
Q ss_pred hhHHHHHHHHhhhhhHHHHHHHHHHHHHhHHHHHHHH-HhhcccccCCCcccccccccCCCCCC-chhhhhhhhhhhhhH
Q 000495 1305 DLVGLLVSVLLLADFSLVLLTLLQMYSISLLNFFLVL-FILPLGLLFPFPAGISALFSHGPRRS-AGLARIYALWNITSL 1382 (1462)
Q Consensus 1305 ~~~~l~i~~~ll~d~s~~ll~llq~y~~s~~~~~~~l-~~lpl~~~~p~~ag~~alfs~~~rrs-~~~~r~~~lwn~~s~ 1382 (1462)
..|++....|||+=+.+++|-.|---+.++..-|++- .++-| +|-||--+. +-.+=+-+|--.+++
T Consensus 2171 a~~gvslaal~lt~~llls~RsLksn~~~I~~~l~~Al~l~~L------------~Fv~gi~~nq~~CtvvailLhf~~~ 2238 (2531)
T KOG4289|consen 2171 AAVGVSLAALLLTFLLLLSLRSLKSNSHGIHFNLAAALGLAQL------------VFVLGINQNQFYCTVVAILLHFTYL 2238 (2531)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhHHHHHHhHHHH------------HhhhhcccCchhhHHHHHHHHHHHh
Confidence 5677777777777777777777766666666544433 22222 344444333 334556677778888
Q ss_pred HHHHHHhhhceeeccccCC
Q 000495 1383 INVATAFICGYLHYRDHSS 1401 (1462)
Q Consensus 1383 ~n~~~a~~~g~~~~~~~~~ 1401 (1462)
.-.+-+|+.|+--|.|-..
T Consensus 2239 stFaWlfl~gLhlYRml~e 2257 (2531)
T KOG4289|consen 2239 STFAWLFLEGLHLYRMLTE 2257 (2531)
T ss_pred hhHHHHHHHHHHHHHHHhc
Confidence 8888888888777776543
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=52.08 E-value=7.7 Score=33.88 Aligned_cols=27 Identities=26% Similarity=0.628 Sum_probs=22.1
Q ss_pred CCceEEccCCCCCcccccceeCCCCceecc
Q 000495 789 GNGTVTGKACPRGLYGVFCEECPVGTFKNV 818 (1462)
Q Consensus 789 ~nGTi~g~~CP~G~~G~fC~eCP~GtYKn~ 818 (1462)
.+|.- .|++++.|..|++|+.|+|...
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 34554 4999999999999999999653
No 17
>smart00180 EGF_Lam Laminin-type epidermal growth factor-like domai.
Probab=52.03 E-value=7.9 Score=33.50 Aligned_cols=20 Identities=25% Similarity=0.750 Sum_probs=18.5
Q ss_pred CCCCCcccccceeCCCCcee
Q 000495 797 ACPRGLYGVFCEECPVGTFK 816 (1462)
Q Consensus 797 ~CP~G~~G~fC~eCP~GtYK 816 (1462)
.|++++.|..|++|+.|+|-
T Consensus 21 ~C~~~~~G~~C~~C~~g~~g 40 (46)
T smart00180 21 ECKPNVTGRRCDRCAPGYYG 40 (46)
T ss_pred ECCCCCCCCCCCcCCCCcCC
Confidence 49999999999999999996
No 18
>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=51.42 E-value=63 Score=37.15 Aligned_cols=36 Identities=25% Similarity=0.541 Sum_probs=20.6
Q ss_pred ccCCCCCCCCCCCCCCCcccEEEEEEceeEEE--ccEEE
Q 000495 211 YGSKGGTTFKGENFGGDGGGRIRLEVVNEIEV--NGSLL 247 (1462)
Q Consensus 211 ~GSGGG~~~~~~~~GG~GGG~I~i~a~~~l~l--~G~I~ 247 (1462)
+|-|| +++.....|.+||=+|+=....+|.| +|.|-
T Consensus 115 yGRGG-nGs~~~~~g~~GG~~I~N~iG~rLRI~N~GaIA 152 (260)
T PF05268_consen 115 YGRGG-NGSGSNSAGAAGGHAIQNDIGGRLRINNNGAIA 152 (260)
T ss_pred EecCC-CCCCCCCCccccceeeecCCcceEEEecCCEEe
Confidence 44443 44455567777787777555555554 44443
No 19
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=49.44 E-value=63 Score=35.62 Aligned_cols=32 Identities=41% Similarity=0.586 Sum_probs=22.0
Q ss_pred HcCCcchhH-HHHHHHHHHHHHHHHHhhheecC
Q 000495 876 TFGGPWLFG-LILLGLLILLALVLSVARMKYMG 907 (1462)
Q Consensus 876 tfGGp~~F~-lll~~llilLalvls~~R~k~~~ 907 (1462)
.+|||+..+ |||=.|+|-+++++|++-.-|-|
T Consensus 83 ~~g~P~vAASL~LgTffIS~~LilSvA~FFYLK 115 (180)
T PF14946_consen 83 HTGGPQVAASLFLGTFFISLGLILSVASFFYLK 115 (180)
T ss_pred cCCChhHHHHHHHHHHHHHHHHHHHHhhheeec
Confidence 489999544 44446677788889887665544
No 20
>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=46.81 E-value=16 Score=37.68 Aligned_cols=22 Identities=36% Similarity=0.871 Sum_probs=10.3
Q ss_pred c-hhHHHHHHHHHHHHHHHHHhh
Q 000495 881 W-LFGLILLGLLILLALVLSVAR 902 (1462)
Q Consensus 881 ~-~F~lll~~llilLalvls~~R 902 (1462)
| +|+||+++++++|+++..+.|
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~r 24 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNR 24 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHH
Confidence 5 444445455444444444433
No 21
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=42.91 E-value=89 Score=37.99 Aligned_cols=7 Identities=71% Similarity=1.341 Sum_probs=3.4
Q ss_pred CCCCeEE
Q 000495 289 GGGGRVS 295 (1462)
Q Consensus 289 GGGGRI~ 295 (1462)
|||||-.
T Consensus 453 ggggrg~ 459 (465)
T KOG3973|consen 453 GGGGRGG 459 (465)
T ss_pred CCCCCcc
Confidence 3456643
No 22
>KOG1836 consensus Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures]
Probab=40.46 E-value=18 Score=51.03 Aligned_cols=43 Identities=42% Similarity=0.767 Sum_probs=35.7
Q ss_pred CceEEccCCCCCcccccceeCCCCceecccCC--CCCCcccCCCC
Q 000495 790 NGTVTGKACPRGLYGVFCEECPVGTFKNVSGS--DRALCRNCSSN 832 (1462)
Q Consensus 790 nGTi~g~~CP~G~~G~fC~eCP~GtYKn~~Gs--~~~~C~pC~~~ 832 (1462)
.-++.-|.||+||.|..|++|.-|+|=+..+- +...|++|+-+
T Consensus 794 ~~~~iCk~Cp~gytG~rCe~c~dgyfg~p~~~~~~~~~c~~c~c~ 838 (1705)
T KOG1836|consen 794 ILEVVCKNCPPGYTGLRCEECADGYFGNPLGHDGDVRPCQSCQCN 838 (1705)
T ss_pred ccceecCCCCCCCcccccccCCCccccCCCCCCCCcccCccceec
Confidence 66777799999999999999999999886643 23579999974
No 23
>TIGR02094 more_P_ylases alpha-glucan phosphorylases. This family consists of known phosphorylases, and homologs believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related family modeled by TIGR02093/PF00343.
Probab=39.93 E-value=22 Score=45.51 Aligned_cols=104 Identities=22% Similarity=0.337 Sum_probs=61.4
Q ss_pred HHHHHHHHhhcCccccccchhhhhhcceEEeecCC-ceEEEEEEecCCCCcCCCCCccccc---------CCceEEEEec
Q 000495 1025 QQLREFVRSEYDHSCLRSCRSRALYEGLKVAATAD-LMLAYIDFFLGGDEKRADLPPRLNQ---------RLPMSLCFGG 1094 (1462)
Q Consensus 1025 ~rL~efv~seydh~clRs~rsRaly~~lKvs~S~D-ysLaYiD~f~~~d~kr~dl~~~i~q---------~~Pm~Ilf~G 1094 (1462)
++|+++|+++....+.|.-.+.+....+..-..|| ++++.+==|- .+||.||-..+.. ..|+-+||+|
T Consensus 354 ~~L~~~v~~~~~~~~~~~g~~~~~~~~~gl~~dpd~~~ig~v~Rl~--~yKr~dLil~~i~~l~~i~~~~~~pvq~V~~G 431 (601)
T TIGR02094 354 ARLIDYIRRRLRERWLRRGADAAILMATDRFLDPDVLTIGFARRFA--TYKRADLIFRDLERLARILNNPERPVQIVFAG 431 (601)
T ss_pred HHHHHHHHHHhhhhhhhccCcchhhhhhccccCCCCcEEEEEEcch--hhhhHHHHHHHHHHHHHHhhCCCCCeEEEEEE
Confidence 45999999777766555333332222233334555 4555554443 6899998443211 2699999999
Q ss_pred ccccccCcccCCchhhhhhcccccccccccCCCcccccccccccc
Q 000495 1095 DGSYMSPFSLHNDNIVTSLMSQVNDFINLQGCPFVNYMVFLNDEN 1139 (1462)
Q Consensus 1095 dGSymsPf~L~sD~lL~sl~~q~n~~~n~~~~~~~~~~v~~~d~~ 1139 (1462)
.| .| .|.-=+.++.+++++.++-..|. .+||..|++
T Consensus 432 ka---~p----~d~~gk~~i~~i~~la~~~~~~~--kv~f~~~Yd 467 (601)
T TIGR02094 432 KA---HP----ADGEGKEIIQRIVEFSKRPEFRG--RIVFLENYD 467 (601)
T ss_pred ec---Cc----ccchHHHHHHHHHHHHhcccCCC--CEEEEcCCC
Confidence 99 22 35566666666655554322232 478887777
No 24
>KOG1836 consensus Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures]
Probab=38.38 E-value=25 Score=49.82 Aligned_cols=65 Identities=31% Similarity=0.594 Sum_probs=40.8
Q ss_pred cCCCCCcccccceeCCCCceeccc-CCCCCCcccCCCCCCCCCcceecccCccc-------CCCCCccccCCCccCC
Q 000495 796 KACPRGLYGVFCEECPVGTFKNVS-GSDRALCRNCSSNELPHRALYIPIRGGVT-------ECPCPYKCVSERYHMP 864 (1462)
Q Consensus 796 ~~CP~G~~G~fC~eCP~GtYKn~~-Gs~~~~C~pC~~~~lp~ra~yiyv~~G~~-------~~~CpY~C~sdk~~~p 864 (1462)
=.||+||.|-||+.|+.|+.+-.. +.....|.||+-+ -+ ..--..+.|+- .+.|. +|..++|.++
T Consensus 697 c~C~~g~tG~~Ce~C~~gfrr~~~~~~~~~~c~~C~cn--gh-~~~Cd~~tG~C~C~~~t~G~~C~-~C~~GfYg~~ 769 (1705)
T KOG1836|consen 697 CTCPVGYTGQFCESCAPGFRRLSPQLGPFCPCIPCDCN--GH-SNICDPRTGQCKCKHNTFGGQCA-QCVDGFYGLP 769 (1705)
T ss_pred ccCCCCcccchhhhcchhhhcccccCCCCCcccccccC--Cc-cccccCCCCceecccCCCCCchh-hhcCCCCCcc
Confidence 479999999999999999976643 3333457777643 11 33334444422 23443 6777777764
No 25
>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=38.10 E-value=19 Score=41.95 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=26.7
Q ss_pred EccCCCCCccc---------ccceeCCCCceecccCCCCCCcccCCC
Q 000495 794 TGKACPRGLYG---------VFCEECPVGTFKNVSGSDRALCRNCSS 831 (1462)
Q Consensus 794 ~g~~CP~G~~G---------~fC~eCP~GtYKn~~Gs~~~~C~pC~~ 831 (1462)
+=..|+|||+- -=|+-|++|||....+ ..|+.|..
T Consensus 218 ~idsC~PGfG~N~~~h~~C~~CCVvCsPgTysp~~~---~~C~~C~~ 261 (271)
T PF07354_consen 218 RIDSCRPGFGKNDILHSDCPSCCVVCSPGTYSPDDD---VHCQQCNS 261 (271)
T ss_pred EeeccCCCCCcCcccCCCCCCeeEECCCcccCCCCC---ceEEecCc
Confidence 33578888751 3599999999988754 58999984
No 26
>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=37.11 E-value=13 Score=32.06 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=18.1
Q ss_pred CCCCCcccccceeCCCCceecc
Q 000495 797 ACPRGLYGVFCEECPVGTFKNV 818 (1462)
Q Consensus 797 ~CP~G~~G~fC~eCP~GtYKn~ 818 (1462)
.|++++.|..|++|..|+|...
T Consensus 21 ~C~~~~~G~~C~~C~~g~~~~~ 42 (49)
T PF00053_consen 21 VCKPGTTGPRCDQCKPGYFGLP 42 (49)
T ss_dssp SBSTTEESTTS-EE-TTEECST
T ss_pred eccccccCCcCcCCCCcccccc
Confidence 3999999999999999999774
No 27
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=36.53 E-value=56 Score=34.02 Aligned_cols=70 Identities=16% Similarity=0.244 Sum_probs=45.8
Q ss_pred hhhhhcHHHHHHHHHHHHHHHhhhhhhhhhhheeee--------eecchhHHHHHHHHHHHHHHHHHHHHhhcCccccc
Q 000495 971 VIEIVYEDAFNRFADEINALAAYQWWEGSVYSILSV--------LAYPLAWSWLQLCRKNKLQQLREFVRSEYDHSCLR 1041 (1462)
Q Consensus 971 i~~iVyed~Fn~Fad~IN~laay~~We~~i~~iLsv--------l~YPlaw~~~q~rRrkk~~rL~efv~seydh~clR 1041 (1462)
...=|.++++.+|.++++.-++..-+|.++-...-+ ..|=.++...+.+.+||-..+.++|. ..++.++|
T Consensus 43 ~~~DVs~eDW~~F~~dl~~aa~ls~~~~~~~~~~~~~~~v~~Gi~~~~v~~~~~~~~~~~k~~~v~~~i~-~WN~~FF~ 120 (123)
T PF15496_consen 43 ASHDVSEEDWTRFLNDLSEAASLSPSQSIVAGVGPIVMGVGFGIPAYLVAKAIRKAMKEKKRGEVESTID-QWNEGFFR 120 (123)
T ss_pred hhcCCCHHHHHHHHHHHHHHHhcCcccceeeeeccccccccccchhhhhhHhhhhcccccchHHHHHHHH-HHHHHhcc
Confidence 334467899999999999998887776543322222 22333444666667777778888886 56665554
No 28
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=34.78 E-value=23 Score=43.74 Aligned_cols=27 Identities=30% Similarity=0.462 Sum_probs=16.5
Q ss_pred CCCCCccccccccCCCcceeeEEEEee
Q 000495 340 DNLPTNTDTLLLEFPKQQLWTNVYIRD 366 (1462)
Q Consensus 340 ~n~~t~t~T~ll~fp~~~lw~nv~V~~ 366 (1462)
-+.++..|--+.|||--.=|.|.++..
T Consensus 444 i~vp~~~dgDy~EfpvPEQfkt~~~~~ 470 (480)
T KOG2675|consen 444 INVPTNEDGDYVEFPVPEQFKTKFNGG 470 (480)
T ss_pred EecccCCCCCcccccChHHHhhhccCc
Confidence 345555666778887655565655544
No 29
>PRK09677 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional
Probab=33.52 E-value=1e+02 Score=33.84 Aligned_cols=61 Identities=15% Similarity=0.245 Sum_probs=40.4
Q ss_pred ceEEEccceeEEcCCceeeecccCcEEEEEeeeeEEecccceEEeeeEEEEEeeEEEcCCcEEE
Q 000495 87 DIYVEGSGNLHILPGVTLCCPIKGCLLTINVTGEFLLGRNSEIVAGTVYVSALNASFSSGSVVN 150 (1462)
Q Consensus 87 Dv~i~G~g~L~I~~gV~l~c~~~G~~I~v~~sG~~~lg~ns~i~agsv~L~A~niti~~~g~I~ 150 (1462)
..++++.+++++-++|.+ ..+|.+.+...+.+.+|+++.|-.........+++|.++..|.
T Consensus 35 pf~~~~~~~I~iG~~v~i---~~~~ri~~~~~~~i~IG~~v~Ig~~v~I~~~~~v~IG~~v~Ig 95 (192)
T PRK09677 35 PFYIRNDGSINFGEGFTS---GVGLRLDAFGRGKLFFGDNVQVNDYVHIACIESITIGRDTLIA 95 (192)
T ss_pred CEEEcCCCeEEECCceEE---CCCeEEEecCCCeEEECCCCEECCCcEEccCceEEECCCCEEC
Confidence 346666677777777766 6677777666777888888777655544444566666555553
No 30
>KOG4611 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.70 E-value=45 Score=40.29 Aligned_cols=63 Identities=30% Similarity=0.583 Sum_probs=0.0
Q ss_pred ceeCCCCceecccCCCCCCcccCCCCCCCCCcceecccCcccC------CCCCccccCCCccC-----CcccchHHHH
Q 000495 807 CEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGVTE------CPCPYKCVSERYHM-----PHCYTTLEEL 873 (1462)
Q Consensus 807 C~eCP~GtYKn~~Gs~~~~C~pC~~~~lp~ra~yiyv~~G~~~------~~CpY~C~sdk~~~-----p~C~T~lEel 873 (1462)
|+|||.||... .+.--|..|-++..--...-.-...-+.. ..|- .|-+++|++ ..|-|...|.
T Consensus 52 ceecpegtlss---pdqtgclncnngtchcpsqstlifrdasgnlltndafcg-ncasgfyrndngyctkcetscsem 125 (747)
T KOG4611|consen 52 CEECPEGTLSS---PDQTGCLNCNNGTCHCPSQSTLIFRDASGNLLTNDAFCG-NCASGFYRNDNGYCTKCETSCSEM 125 (747)
T ss_pred cccCCCcccCC---CccCCceecCCCccCCCCcceEEEEcCCCCeeccccccc-cccccceECCCcccccccccHhhh
No 31
>PF10256 Erf4: Golgin subfamily A member 7/ERF4 family; InterPro: IPR019383 Proteins in this entry include Golgin subfamily A member 7 and the Ras modification protein ERF4.
Probab=30.46 E-value=49 Score=33.49 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=39.3
Q ss_pred ccChhHHHHHHHHHhhhhhee-eccc------------------------cchhhhhHHHHHhhccCccccccCeEEE
Q 000495 1147 SVPPTVWYRLVAGVNAQLRLV-HCGH------------------------LKTTFGHLISWLDTHANPSLCQYGIRVD 1199 (1462)
Q Consensus 1147 ~~~~~~w~r~va~lN~qlr~v-~~g~------------------------lr~tl~~v~~~le~h~n~~l~~~gvrv~ 1199 (1462)
.++++.|.++|..+|..|+.- ..-. -++.+..+-+||++.|++.++.+|+++-
T Consensus 29 ~is~~ef~~iI~~IN~~l~~a~~~~~~~~~~~~~l~~lt~~l~~~~~~~~~~~~~~~le~~l~~~N~~~~~~~gi~ii 106 (118)
T PF10256_consen 29 YISPEEFEEIINTINQILKEAFEPISWRNIIENILGCLTLGLSSLCFKTHYKRKLRELEKYLEQLNEELFKPRGIKII 106 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcEEE
Confidence 689999999999999988765 2221 2223445778888887779999998653
No 32
>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=29.46 E-value=40 Score=29.01 Aligned_cols=22 Identities=41% Similarity=0.995 Sum_probs=13.5
Q ss_pred cCCCCCc--ccccce-eCCCCceec
Q 000495 796 KACPRGL--YGVFCE-ECPVGTFKN 817 (1462)
Q Consensus 796 ~~CP~G~--~G~fC~-eCP~GtYKn 817 (1462)
..|++|+ .+..|+ +||.++|.+
T Consensus 18 ~~C~~~~~~~~~~Cv~~C~~~~~~~ 42 (49)
T cd00064 18 TSCRHGFYLDGGTCVSECPEGTYAD 42 (49)
T ss_pred ccCcCccCCCCCcccccCCCCceec
Confidence 4566666 345566 666666665
No 33
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=27.35 E-value=49 Score=34.48 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=19.5
Q ss_pred cccChhHHHHHHHHHhhhhheeecc
Q 000495 1146 QSVPPTVWYRLVAGVNAQLRLVHCG 1170 (1462)
Q Consensus 1146 ~~~~~~~w~r~va~lN~qlr~v~~g 1170 (1462)
|.|.++.|.||+.+|+...++-...
T Consensus 45 ~DVs~eDW~~F~~dl~~aa~ls~~~ 69 (123)
T PF15496_consen 45 HDVSEEDWTRFLNDLSEAASLSPSQ 69 (123)
T ss_pred cCCCHHHHHHHHHHHHHHHhcCccc
Confidence 4699999999999999885444333
No 34
>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=27.21 E-value=21 Score=42.82 Aligned_cols=26 Identities=50% Similarity=0.989 Sum_probs=0.0
Q ss_pred cccccCcceeeeCCCCCcccCCCCCCCCCCCCCCCCC
Q 000495 21 SLDQYNFPVIGFGADSLFHGDYTPPSPPPPIAPPHPP 57 (1462)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 57 (1462)
+-|-||||.- ..-|+|||||+|||+.
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 2335556666777665
No 35
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=26.73 E-value=63 Score=44.13 Aligned_cols=65 Identities=26% Similarity=0.669 Sum_probs=43.4
Q ss_pred CCCCCcccccceeCCCCceecccCCCCCCcccCCCCCCCCCcceec-------ccCcccCCCCCccccCCCccCCcc
Q 000495 797 ACPRGLYGVFCEECPVGTFKNVSGSDRALCRNCSSNELPHRALYIP-------IRGGVTECPCPYKCVSERYHMPHC 866 (1462)
Q Consensus 797 ~CP~G~~G~fC~eCP~GtYKn~~Gs~~~~C~pC~~~~lp~ra~yiy-------v~~G~~~~~CpY~C~sdk~~~p~C 866 (1462)
.|-|+--|-.|.+|-+|||- +| .+=|++|.-+..-+-.+|-. -|.|+....|. +|.+++..-|-|
T Consensus 785 qCkPnVVGR~CdqCApGtyG--FG--PsGCk~CdC~~~Gs~~~~Cd~~tGQC~C~~g~ygrqCn-qCqpG~WgFPeC 856 (1758)
T KOG0994|consen 785 QCKPNVVGRRCDQCAPGTYG--FG--PSGCKACDCNSIGSLDKYCDKITGQCQCRPGTYGRQCN-QCQPGYWGFPEC 856 (1758)
T ss_pred cccCccccccccccCCcccC--cC--CccCccccccccccccccccccccceeeccccchhhcc-ccCCCccCCCcC
Confidence 67777889999999999993 33 47799998776655555544 23345555565 566665554444
No 36
>PF04519 Bactofilin: Polymer-forming cytoskeletal; InterPro: IPR007607 This family contains several uncharacterised hypothetical proteins.
Probab=26.45 E-value=2.5e+02 Score=27.54 Aligned_cols=57 Identities=18% Similarity=0.424 Sum_probs=0.0
Q ss_pred ccCeEEEeeceeeccCceEEEccceeEEcCCceeeecccCcEEEEEeeeeEEecccceEEeeeEEEEEeeEEEcCCcEEE
Q 000495 71 LETVCLLNSSLTFENDDIYVEGSGNLHILPGVTLCCPIKGCLLTINVTGEFLLGRNSEIVAGTVYVSALNASFSSGSVVN 150 (1462)
Q Consensus 71 ~~t~C~l~~s~~~~~qDv~i~G~g~L~I~~gV~l~c~~~G~~I~v~~sG~~~lg~ns~i~agsv~L~A~niti~~~g~I~ 150 (1462)
+...|.+.-++.+.. ++.|.|. +.| .+...+.++|+.++.+... +.|.++.| .|.++
T Consensus 5 I~~~~~i~G~i~~~~-~v~i~G~--------------v~G---~i~~~g~v~i~~~~~v~G~---i~~~~~~i--~G~v~ 61 (101)
T PF04519_consen 5 IGKGTKIEGDISSDG-DVRIDGR--------------VEG---NIKAEGKVKIGGNGEVKGD---IKADDVII--SGSVD 61 (101)
T ss_pred ECCCCEEEEEEEECc-EEEEEEE--------------EEE---EEEEceEEEEcCCCEEEEE---EEEeEEEE--cCEEe
No 37
>KOG4258 consensus Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms]
Probab=26.44 E-value=42 Score=44.52 Aligned_cols=46 Identities=26% Similarity=0.608 Sum_probs=30.5
Q ss_pred ccce-eCCCCceecccCCCCCCcccCCCCCCCCCcceecccCcccCCCCCccccCCCccCCcccchHHHH
Q 000495 805 VFCE-ECPVGTFKNVSGSDRALCRNCSSNELPHRALYIPIRGGVTECPCPYKCVSERYHMPHCYTTLEEL 873 (1462)
Q Consensus 805 ~fC~-eCP~GtYKn~~Gs~~~~C~pC~~~~lp~ra~yiyv~~G~~~~~CpY~C~sdk~~~p~C~T~lEel 873 (1462)
..|. +||.|+-.|. +..+|++|.. .||-.|.++ .+.-+=.+..|+|
T Consensus 304 ~~Cv~~CPsGy~~N~---~~~~C~~C~g-------------------~C~~vC~~~-~~tIds~~~Aq~L 350 (1025)
T KOG4258|consen 304 GQCVAKCPSGYKRNS---SSSECVKCEG-------------------PCPKVCEPG-TKTIDSVADAQNL 350 (1025)
T ss_pred ccchhhCCCcceecC---cccceeccCC-------------------CCcceeccC-ceEecchhhhHHh
Confidence 3566 8999987664 3589999962 799999863 2222334555554
No 38
>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=25.70 E-value=1e+02 Score=35.16 Aligned_cols=91 Identities=25% Similarity=0.454 Sum_probs=53.8
Q ss_pred CCcccccceeceEEEcCCCCCCCCCcccCCceEEccCCCCCc--ccccce---eCCCCceecccCCCCCCcccCCCCCCC
Q 000495 761 GDEYLPLASVNGSIDARGGLGRGQGLAGGNGTVTGKACPRGL--YGVFCE---ECPVGTFKNVSGSDRALCRNCSSNELP 835 (1462)
Q Consensus 761 gdey~~ia~~~G~I~~~GG~~~~~g~~G~nGTi~g~~CP~G~--~G~fC~---eCP~GtYKn~~Gs~~~~C~pC~~~~lp 835 (1462)
-+||.+=.+.-|.-.++||++.+....+..|.|-...=-+-- -=-+|. +||+|+- ... .|. .+++
T Consensus 49 d~E~l~hssLwG~q~isGGagEG~q~L~~~~~i~n~~~~ktd~~lPaYCnPPNPCPvGyt-~~d-----gCl----e~fE 118 (208)
T PF05281_consen 49 DQEYLQHSSLWGHQYISGGAGEGPQHLGPEGNIPNIKIVKTDNNLPAYCNPPNPCPVGYT-AED-----GCL----ENFE 118 (208)
T ss_pred ccccccccccCCceeeeCCCCccchhcCccCCcCcccccccccCCCCCCCCCCCCCCCcc-ccc-----Ccc----cCCc
Confidence 367776667888888999999776666666665332111000 015687 8999985 222 244 3466
Q ss_pred CCcceecccCcccCCCCCccccCCCccCCccc
Q 000495 836 HRALYIPIRGGVTECPCPYKCVSERYHMPHCY 867 (1462)
Q Consensus 836 ~ra~yiyv~~G~~~~~CpY~C~sdk~~~p~C~ 867 (1462)
.-|.|--.- .....|. | |-.||-.|-
T Consensus 119 nTAeFSRey--Qa~QdC~--C--D~EHMf~C~ 144 (208)
T PF05281_consen 119 NTAEFSREY--QAAQDCM--C--DTEHMFDCP 144 (208)
T ss_pred cHHHhhHHH--HhcCccC--C--CcccccCCc
Confidence 666554322 2233443 4 567888886
No 39
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=23.81 E-value=4.6e+02 Score=29.49 Aligned_cols=36 Identities=14% Similarity=0.016 Sum_probs=20.7
Q ss_pred ccCcEEEEEeeeeEEecccc---eEEeeeEEEEEeeEEEcC
Q 000495 108 IKGCLLTINVTGEFLLGRNS---EIVAGTVYVSALNASFSS 145 (1462)
Q Consensus 108 ~~G~~I~v~~sG~~~lg~ns---~i~agsv~L~A~niti~~ 145 (1462)
.+|+.|.| .|.+....-. -...-.+.|.|.+|.+..
T Consensus 71 kKGs~V~V--eGrL~~~~yeDkdG~kr~~~eVvA~~V~fL~ 109 (182)
T PRK06958 71 KKGSSVYI--EGRIRTRKWQGQDGQDRYSTEIVADQMQMLG 109 (182)
T ss_pred CCCCEEEE--EEEEEeCceECCCCcEEEEEEEEEeEEEECC
Confidence 56665543 4777665322 223346777888888743
No 40
>PF15195 TMEM210: TMEM210 family
Probab=23.49 E-value=49 Score=33.65 Aligned_cols=10 Identities=50% Similarity=1.321 Sum_probs=4.2
Q ss_pred CCCCCCCCCC
Q 000495 41 DYTPPSPPPP 50 (1462)
Q Consensus 41 ~~~~~~~~p~ 50 (1462)
+-+|++||||
T Consensus 101 ~~~p~~pppp 110 (116)
T PF15195_consen 101 EASPEEPPPP 110 (116)
T ss_pred CCCCCCCCcC
Confidence 3444444333
No 41
>KOG4180 consensus Predicted kinase [General function prediction only]
Probab=22.42 E-value=1.5e+02 Score=36.01 Aligned_cols=21 Identities=29% Similarity=0.533 Sum_probs=16.3
Q ss_pred ccCCceEEEEecccccccCcc
Q 000495 1083 NQRLPMSLCFGGDGSYMSPFS 1103 (1462)
Q Consensus 1083 ~q~~Pm~Ilf~GdGSymsPf~ 1103 (1462)
..--.|+|-.||||+|+--=+
T Consensus 103 i~waD~VisvGGDGTfL~Aas 123 (395)
T KOG4180|consen 103 IRWADMVISVGGDGTFLLAAS 123 (395)
T ss_pred CchhhEEEEecCccceeehhh
Confidence 334579999999999986655
No 42
>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=21.56 E-value=42 Score=27.94 Aligned_cols=19 Identities=37% Similarity=0.947 Sum_probs=13.9
Q ss_pred CCCCceecccCCCCCCcccCC
Q 000495 810 CPVGTFKNVSGSDRALCRNCS 830 (1462)
Q Consensus 810 CP~GtYKn~~Gs~~~~C~pC~ 830 (1462)
||.|+|.+..+. ..|.||.
T Consensus 1 C~~g~y~~~~~~--~~C~~C~ 19 (39)
T PF00020_consen 1 CPPGTYSDSENH--PQCLPCS 19 (39)
T ss_dssp ECTTEEEESSCS--SSEEEEE
T ss_pred CccCcccCCCCC--CcCCccC
Confidence 899999997543 6775554
No 43
>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=21.51 E-value=28 Score=23.65 Aligned_cols=11 Identities=45% Similarity=1.066 Sum_probs=8.3
Q ss_pred CCCCCcccccc
Q 000495 797 ACPRGLYGVFC 807 (1462)
Q Consensus 797 ~CP~G~~G~fC 807 (1462)
.||+||.|..|
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 48999999877
No 44
>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=21.49 E-value=1.6e+02 Score=34.07 Aligned_cols=40 Identities=30% Similarity=0.658 Sum_probs=18.5
Q ss_pred EEEecCCCC-CCCCcccCCccEEEEE--e--eeccceEEEEecCC
Q 000495 245 SLLADGGDV-GVKGGGGSGGSIYVKA--H--RMTGNGKISASGGN 284 (1462)
Q Consensus 245 ~I~AnGg~g-~~~gGGGSGGSI~L~a--~--~l~g~G~isA~GG~ 284 (1462)
.+.=-|+++ ....-|..||...=.. . ++.++|.|..-||.
T Consensus 113 t~yGRGGnGs~~~~~g~~GG~~I~N~iG~rLRI~N~GaIAgGGGG 157 (260)
T PF05268_consen 113 TMYGRGGNGSGSNSAGAAGGHAIQNDIGGRLRINNNGAIAGGGGG 157 (260)
T ss_pred EEEecCCCCCCCCCCccccceeeecCCcceEEEecCCEEecCCCC
Confidence 334445665 3445566666633211 1 23355666444333
No 45
>KOG4260 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.36 E-value=57 Score=38.48 Aligned_cols=28 Identities=39% Similarity=0.947 Sum_probs=0.0
Q ss_pred CCCCcccccceeCCCCceecccCCCCCCcc
Q 000495 798 CPRGLYGVFCEECPVGTFKNVSGSDRALCR 827 (1462)
Q Consensus 798 CP~G~~G~fC~eCP~GtYKn~~Gs~~~~C~ 827 (1462)
||+|.||.-|.+||-|+=+.-.|. ..|.
T Consensus 132 Cp~gtyGpdCl~Cpggser~C~Gn--G~C~ 159 (350)
T KOG4260|consen 132 CPDGTYGPDCLQCPGGSERPCFGN--GSCH 159 (350)
T ss_pred cCCCCcCCccccCCCCCcCCcCCC--Cccc
Done!