Query 000976
Match_columns 1204
No_of_seqs 161 out of 187
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 12:17:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000976.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000976hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0196 Tyrosine kinase, EPH ( 96.3 0.0034 7.4E-08 77.8 4.5 54 553-619 261-318 (996)
2 PF07699 GCC2_GCC3: GCC2 and G 96.2 0.0022 4.8E-08 54.0 1.7 26 562-589 9-34 (48)
3 KOG0921 Dosage compensation co 95.1 0.041 8.8E-07 69.4 7.2 12 165-176 938-949 (1282)
4 cd00185 TNFR Tumor necrosis fa 92.8 0.16 3.4E-06 48.7 4.7 65 550-621 12-87 (98)
5 PF10256 Erf4: Golgin subfamil 92.7 0.34 7.3E-06 47.6 7.1 67 726-792 21-91 (118)
6 PF07562 NCD3G: Nine Cysteines 92.7 0.025 5.5E-07 49.1 -0.7 36 552-589 6-51 (54)
7 PHA02637 TNF-alpha-receptor-li 91.9 0.14 3.1E-06 52.1 3.3 57 554-615 31-92 (127)
8 PHA02637 TNF-alpha-receptor-li 88.2 0.35 7.5E-06 49.4 2.6 41 546-587 38-87 (127)
9 KOG0921 Dosage compensation co 84.2 1.9 4E-05 55.5 6.5 26 95-120 839-864 (1282)
10 PF07699 GCC2_GCC3: GCC2 and G 80.8 1.3 2.7E-05 37.5 2.4 30 550-579 9-43 (48)
11 KOG3973 Uncharacterized conser 71.7 13 0.00028 43.8 7.9 16 180-196 225-240 (465)
12 cd00185 TNFR Tumor necrosis fa 65.8 6.5 0.00014 37.8 3.4 31 561-591 11-43 (98)
13 PF15496 DUF4646: Domain of un 61.9 7.7 0.00017 39.3 3.3 22 877-898 46-67 (123)
14 KOG4289 Cadherin EGF LAG seven 58.4 7.2 0.00016 52.4 2.9 86 1043-1140 2169-2256(2531)
15 PF05268 GP38: Phage tail fibr 55.9 23 0.00051 39.6 5.9 27 412-440 126-152 (260)
16 smart00180 EGF_Lam Laminin-typ 54.2 7.6 0.00016 32.8 1.5 24 547-573 17-40 (46)
17 cd00055 EGF_Lam Laminin-type e 53.4 7.7 0.00017 33.1 1.5 27 546-575 17-43 (50)
18 PTZ00146 fibrillarin; Provisio 53.1 30 0.00066 40.1 6.5 10 435-444 64-73 (293)
19 KOG4069 Uncharacterized conser 52.6 44 0.00095 34.9 6.8 70 725-798 45-125 (154)
20 KOG3973 Uncharacterized conser 51.9 53 0.0011 39.1 8.1 8 106-113 152-159 (465)
21 PF10256 Erf4: Golgin subfamil 50.8 23 0.0005 34.9 4.5 65 874-942 26-115 (118)
22 PF07354 Sp38: Zona-pellucida- 45.4 13 0.00029 42.4 2.1 36 550-588 217-261 (271)
23 PF00053 Laminin_EGF: Laminin 39.7 13 0.00027 31.4 0.7 21 555-575 22-42 (49)
24 KOG1836 Extracellular matrix g 39.4 23 0.0005 49.3 3.3 34 553-587 697-732 (1705)
25 KOG1836 Extracellular matrix g 36.9 24 0.00052 49.1 2.9 43 547-589 794-838 (1705)
26 PF12273 RCR: Chitin synthesis 35.5 31 0.00067 34.9 2.8 20 638-657 2-22 (130)
27 PF11145 DUF2921: Protein of u 32.4 1.1E+02 0.0024 40.6 7.6 116 1016-1131 593-723 (909)
28 cd00064 FU Furin-like repeats. 31.2 29 0.00063 29.2 1.5 22 553-574 18-42 (49)
29 KOG0994 Extracellular matrix g 30.4 50 0.0011 44.3 4.0 40 554-597 785-824 (1758)
30 PF05268 GP38: Phage tail fibr 29.5 87 0.0019 35.4 5.1 14 480-493 143-156 (260)
31 KOG4260 Uncharacterized conser 29.0 36 0.00077 39.3 2.2 21 554-574 131-151 (350)
32 PTZ00382 Variant-specific surf 27.7 43 0.00093 32.9 2.2 25 562-589 4-28 (96)
33 COG4907 Predicted membrane pro 27.2 40 0.00087 41.3 2.3 13 105-117 173-185 (595)
34 COG1512 Beta-propeller domains 24.7 72 0.0016 36.7 3.7 12 368-379 257-268 (271)
35 PF14946 DUF4501: Domain of un 24.6 2.2E+02 0.0048 31.0 6.8 29 633-661 83-112 (180)
36 KOG4260 Uncharacterized conser 24.6 42 0.00091 38.8 1.7 36 553-588 170-205 (350)
37 KOG3915 Transcription regulato 24.5 1E+02 0.0022 37.9 4.9 9 400-408 101-109 (641)
38 KOG4180 Predicted kinase [Gene 23.3 1.3E+02 0.0028 35.9 5.3 28 835-863 96-123 (395)
39 KOG4289 Cadherin EGF LAG seven 22.7 82 0.0018 43.4 3.9 36 544-587 1734-1774(2531)
40 PTZ00146 fibrillarin; Provisio 22.6 1.2E+02 0.0026 35.3 4.9 6 704-709 275-280 (293)
41 PF04790 Sarcoglycan_1: Sarcog 22.5 8.4E+02 0.018 28.2 11.4 59 292-352 162-222 (264)
42 PF15496 DUF4646: Domain of un 20.7 1.2E+02 0.0026 31.0 3.9 70 731-801 43-120 (123)
43 PF00020 TNFR_c6: TNFR/NGFR cy 20.3 40 0.00086 27.4 0.4 20 567-588 1-20 (39)
No 1
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=96.31 E-value=0.0034 Score=77.83 Aligned_cols=54 Identities=39% Similarity=0.883 Sum_probs=39.9
Q ss_pred cCCCCCCC----cccceeCCCCccccccCCCCCCcccCCCCCCCCCceEEeeeCCccCCCCCccccCCccc
Q 000976 553 KACPKGLY----GIFCEECPVGTYKNVTGSDKSLCHQCPPQEFPHRAVYISVRGGIAETPCPYRCISERYH 619 (1204)
Q Consensus 553 k~CP~Gly----G~fC~eCP~GtYK~~tGs~~~~C~pCp~~~~P~ra~yiyvr~G~~~~~CpY~C~sdk~~ 619 (1204)
=-|.+||. |.-|+.||.||||...| ...|.+||.+...+ .. ..++|. |..++|+
T Consensus 261 C~C~aGye~~~~~~~C~aCp~G~yK~~~~--~~~C~~CP~~S~s~-------~e--ga~~C~--C~~gyyR 318 (996)
T KOG0196|consen 261 CVCKAGYEEAENGKACQACPPGTYKASQG--DSLCLPCPPNSHSS-------SE--GATSCT--CENGYYR 318 (996)
T ss_pred eeecCCCCcccCCCcceeCCCCcccCCCC--CCCCCCCCCCCCCC-------CC--CCCccc--ccCCccc
Confidence 46899984 77799999999999764 57899999854221 11 246775 8888775
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=96.25 E-value=0.0022 Score=53.98 Aligned_cols=26 Identities=42% Similarity=1.095 Sum_probs=22.6
Q ss_pred ccceeCCCCccccccCCCCCCcccCCCC
Q 000976 562 IFCEECPVGTYKNVTGSDKSLCHQCPPQ 589 (1204)
Q Consensus 562 ~fC~eCP~GtYK~~tGs~~~~C~pCp~~ 589 (1204)
.-|++||.||||+..|. ..|.+||..
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 45999999999999876 479999975
No 3
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.14 E-value=0.041 Score=69.38 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=7.9
Q ss_pred hhhccccceeee
Q 000976 165 EELLMSDSVIKV 176 (1204)
Q Consensus 165 ~~~lm~~s~ikv 176 (1204)
|..-.++++.|+
T Consensus 938 ~r~~l~~~~~~~ 949 (1282)
T KOG0921|consen 938 ERYSLSNPVLKM 949 (1282)
T ss_pred Hhhhhcchhhhh
Confidence 455667777666
No 4
>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=92.77 E-value=0.16 Score=48.67 Aligned_cols=65 Identities=28% Similarity=0.568 Sum_probs=42.1
Q ss_pred EEccCCCCCCC---------cccceeCCCCccccccCCCCCCcccCCCCCCCCCceEEeeeCCcc--CCCCCccccCCcc
Q 000976 550 TTGKACPKGLY---------GIFCEECPVGTYKNVTGSDKSLCHQCPPQEFPHRAVYISVRGGIA--ETPCPYRCISERY 618 (1204)
Q Consensus 550 I~gk~CP~Gly---------G~fC~eCP~GtYK~~tGs~~~~C~pCp~~~~P~ra~yiyvr~G~~--~~~CpY~C~sdk~ 618 (1204)
.-=+.||+|++ ..-|++||.|+|...... ...|++|.. -+ ...++ ++.+.. .+.|- |.+++|
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 LCCDQCPPGTYLSKDCTPGSDTVCEPCPPGTYTDSWNH-LPKCLSCRT--CD-SGLVE-KAPCTATRNTVCG--CKPGFY 84 (98)
T ss_pred CCCCCCCCCccCCCcCCCCCCCeecCCCCCCcccCCCC-CCcCCcCcc--CC-CCCEE-EccCCCCCCCeEe--CCCCCE
Confidence 44578999985 356999999999986532 257999975 44 22233 323322 46685 888777
Q ss_pred cCC
Q 000976 619 HMP 621 (1204)
Q Consensus 619 ~~p 621 (1204)
...
T Consensus 85 ~~~ 87 (98)
T cd00185 85 CLT 87 (98)
T ss_pred ecC
Confidence 544
No 5
>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=92.73 E-value=0.34 Score=47.64 Aligned_cols=67 Identities=22% Similarity=0.341 Sum_probs=45.7
Q ss_pred CCcchhhhhhchHHHHHHHHHHHhhhhhh--h--hhhHHHHHhHHhhcchhHHHHHHHHHHHHHHHHHHHH
Q 000976 726 TPPEQIKEIVYEGAFNSFVDEINAIATYH--W--WEGAIYSILAILAYPLAWSWQQWRRRMKLQRLREYVR 792 (1204)
Q Consensus 726 spP~~i~~IVyed~Fn~Fad~IN~laay~--~--We~~iy~iLsvl~YPlaw~wlq~rRrkkl~rL~efv~ 792 (1204)
.-|.++...+.+++|++++++||+..+=. . |.-++-.+|.++..=+...+.....||++++|.+|+.
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 46778999999999999999999987322 2 4444555555554222222234556677888999996
No 6
>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=92.70 E-value=0.025 Score=49.13 Aligned_cols=36 Identities=36% Similarity=0.812 Sum_probs=19.8
Q ss_pred ccCCCCCCCc----------ccceeCCCCccccccCCCCCCcccCCCC
Q 000976 552 GKACPKGLYG----------IFCEECPVGTYKNVTGSDKSLCHQCPPQ 589 (1204)
Q Consensus 552 gk~CP~GlyG----------~fC~eCP~GtYK~~tGs~~~~C~pCp~~ 589 (1204)
..+|++|++. +-|++||.|+|.+.+ +...|.+||.+
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 4689999852 239999999999987 44689999974
No 7
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=91.90 E-value=0.14 Score=52.06 Aligned_cols=57 Identities=26% Similarity=0.596 Sum_probs=37.4
Q ss_pred CCCCCCC---cccceeCCCCccccccCC--CCCCcccCCCCCCCCCceEEeeeCCccCCCCCccccC
Q 000976 554 ACPKGLY---GIFCEECPVGTYKNVTGS--DKSLCHQCPPQEFPHRAVYISVRGGIAETPCPYRCIS 615 (1204)
Q Consensus 554 ~CP~Gly---G~fC~eCP~GtYK~~tGs--~~~~C~pCp~~~~P~ra~yiyvr~G~~~~~CpY~C~s 615 (1204)
.|..+-| +.-|.+||.|+|.....+ ....|.|||..+.....++.. ....|.-.|++
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 6888865 445999999999874433 235799999876444333321 25677777776
No 8
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=88.18 E-value=0.35 Score=49.36 Aligned_cols=41 Identities=24% Similarity=0.617 Sum_probs=31.0
Q ss_pred CCceEEccCCCCCCC---------cccceeCCCCccccccCCCCCCcccCC
Q 000976 546 ENGTTTGKACPKGLY---------GIFCEECPVGTYKNVTGSDKSLCHQCP 587 (1204)
Q Consensus 546 ~~GTI~gk~CP~Gly---------G~fC~eCP~GtYK~~tGs~~~~C~pCp 587 (1204)
..|..-=+.||||++ ..-|.+||.|||...... ...|.+|.
T Consensus 38 ~~~~~CC~kCPPGt~v~~~Ct~~t~T~C~PCp~GTYTe~~N~-~~~C~~C~ 87 (127)
T PHA02637 38 KRHNLCCLSCPPGTYASRLCDIKTNTQCTPCGSGTFTSHNNH-LPACLSCN 87 (127)
T ss_pred cCCCeEcCCCCCCCEEeCcCCCCCCcccccCCCCCeeccCCC-CCcccccC
Confidence 445667789999985 667999999999875432 34688887
No 9
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=84.23 E-value=1.9 Score=55.48 Aligned_cols=26 Identities=15% Similarity=0.218 Sum_probs=12.5
Q ss_pred CccccccceeeccCCCCCcceeEEEe
Q 000976 95 YNMSTDTETLLLEFPNQPLWTNVYVQ 120 (1204)
Q Consensus 95 ~n~~t~t~t~ll~fp~~plw~~v~~~ 120 (1204)
|-..|.-...|+.-|-.|+-..++|-
T Consensus 839 n~elt~lg~~la~l~iep~~~k~~~l 864 (1282)
T KOG0921|consen 839 NDELTPLGRMLARLPIEPRIGKMMIL 864 (1282)
T ss_pred cCcccchhhhhhhccCcccccceeee
Confidence 33334444445555555555544443
No 10
>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=80.79 E-value=1.3 Score=37.55 Aligned_cols=30 Identities=40% Similarity=0.912 Sum_probs=24.0
Q ss_pred EEccCCCCCCC----c-ccceeCCCCccccccCCC
Q 000976 550 TTGKACPKGLY----G-IFCEECPVGTYKNVTGSD 579 (1204)
Q Consensus 550 I~gk~CP~Gly----G-~fC~eCP~GtYK~~tGs~ 579 (1204)
-.=.+||.|+| | ..|.+||.|+|....|+.
T Consensus 9 ~~C~~Cp~GtYq~~~g~~~C~~Cp~g~~T~~~Gs~ 43 (48)
T PF07699_consen 9 NKCQPCPKGTYQDEEGQTSCTPCPPGSTTSSEGST 43 (48)
T ss_pred CccCCCCCCccCCccCCccCccCcCCCccCCcCCc
Confidence 44579999987 3 459999999998877764
No 11
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=71.73 E-value=13 Score=43.79 Aligned_cols=16 Identities=25% Similarity=0.771 Sum_probs=8.8
Q ss_pred hhhhhhhheeecceEEE
Q 000976 180 LRMTVKIFLMWNSEMLV 196 (1204)
Q Consensus 180 l~~~~~~~lm~~s~~~i 196 (1204)
|.+||.- ..||-+|.-
T Consensus 225 L~vTVqS-F~Wsdr~k~ 240 (465)
T KOG3973|consen 225 LKVTVQS-FLWSDRLKM 240 (465)
T ss_pred HHHHHHh-hcccHHHHH
Confidence 5556655 356665543
No 12
>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=65.77 E-value=6.5 Score=37.83 Aligned_cols=31 Identities=35% Similarity=1.096 Sum_probs=23.2
Q ss_pred cccceeCCCCccccccCC--CCCCcccCCCCCC
Q 000976 561 GIFCEECPVGTYKNVTGS--DKSLCHQCPPQEF 591 (1204)
Q Consensus 561 G~fC~eCP~GtYK~~tGs--~~~~C~pCp~~~~ 591 (1204)
+.-|..||.|+|-...+. ....|.+|+..++
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 555999999999876532 2357999998654
No 13
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=61.86 E-value=7.7 Score=39.34 Aligned_cols=22 Identities=18% Similarity=0.096 Sum_probs=18.2
Q ss_pred cCChHHHHHHHHHHHHHHHHhh
Q 000976 877 LVPPTICYRLVAGLNAQLRLVR 898 (1204)
Q Consensus 877 ~~~~~~w~~fVa~lN~qlR~v~ 898 (1204)
.|..+.|.+|+.+|+...++-.
T Consensus 46 DVs~eDW~~F~~dl~~aa~ls~ 67 (123)
T PF15496_consen 46 DVSEEDWTRFLNDLSEAASLSP 67 (123)
T ss_pred CCCHHHHHHHHHHHHHHHhcCc
Confidence 5899999999999999844433
No 14
>KOG4289 consensus Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms]
Probab=58.43 E-value=7.2 Score=52.37 Aligned_cols=86 Identities=24% Similarity=0.194 Sum_probs=50.5
Q ss_pred hhhhHHHHHHHHHHhhHHHHHHHHHHHHHhhhhhHHHH-HHhccccccccccchhhhhhccCCCCcc-cccchhhhhhhh
Q 000976 1043 HQDLVGLVISVLLLGDFSLVLLTLLQLYSISLVDVFLV-LFILPLGILLPFPAGINALFSHGPRRSV-GLARVYALWNVT 1120 (1204)
Q Consensus 1043 ~~~lv~l~is~lll~D~~ltll~llq~y~is~~~~~~v-l~~lPl~~~~p~~~Glnalfs~~~rrs~-~~ar~yalwN~~ 1120 (1204)
-+..+|+.+..|+|+=+.++++-+|---+.+|...+++ |++ +-| +|+||.-+.. -+.-+-+|--.+
T Consensus 2169 t~a~~gvslaal~lt~~llls~RsLksn~~~I~~~l~~Al~l----------~~L--~Fv~gi~~nq~~CtvvailLhf~ 2236 (2531)
T KOG4289|consen 2169 TYAAVGVSLAALLLTFLLLLSLRSLKSNSHGIHFNLAAALGL----------AQL--VFVLGINQNQFYCTVVAILLHFT 2236 (2531)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhHHHHHHhH----------HHH--HhhhhcccCchhhHHHHHHHHHH
Confidence 34566666666776666666666665556666533322 222 222 6666665542 233444566667
Q ss_pred hhhHHHHHhhhhcccccCCC
Q 000976 1121 SLINVGVAFLCGYVHYSSGS 1140 (1204)
Q Consensus 1121 Sl~n~~va~icg~~~~~~~~ 1140 (1204)
++.-..=+|+.|+--|-|-.
T Consensus 2237 ~~stFaWlfl~gLhlYRml~ 2256 (2531)
T KOG4289|consen 2237 YLSTFAWLFLEGLHLYRMLT 2256 (2531)
T ss_pred HhhhHHHHHHHHHHHHHHHh
Confidence 77777778888887776544
No 15
>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=55.85 E-value=23 Score=39.63 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=13.9
Q ss_pred CCCCCCccEEEEeeccCCcceeEeeeEEE
Q 000976 412 GNSTAGGGIIVMGSFEHPLSSLSVEGSVK 440 (1204)
Q Consensus 412 ~~GGaGGGiI~I~A~~~~L~~L~l~GsI~ 440 (1204)
..|++||=+|+=.... .| +|..+|.|-
T Consensus 126 ~~g~~GG~~I~N~iG~-rL-RI~N~GaIA 152 (260)
T PF05268_consen 126 SAGAAGGHAIQNDIGG-RL-RINNNGAIA 152 (260)
T ss_pred CCccccceeeecCCcc-eE-EEecCCEEe
Confidence 4466777777633221 22 455555553
No 16
>smart00180 EGF_Lam Laminin-type epidermal growth factor-like domai.
Probab=54.21 E-value=7.6 Score=32.85 Aligned_cols=24 Identities=29% Similarity=0.753 Sum_probs=20.0
Q ss_pred CceEEccCCCCCCCcccceeCCCCccc
Q 000976 547 NGTTTGKACPKGLYGIFCEECPVGTYK 573 (1204)
Q Consensus 547 ~GTI~gk~CP~GlyG~fC~eCP~GtYK 573 (1204)
.|.- .|++++.|..|++|+.|+|-
T Consensus 17 ~G~C---~C~~~~~G~~C~~C~~g~~g 40 (46)
T smart00180 17 TGQC---ECKPNVTGRRCDRCAPGYYG 40 (46)
T ss_pred CCEE---ECCCCCCCCCCCcCCCCcCC
Confidence 4544 39999999999999999995
No 17
>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=53.41 E-value=7.7 Score=33.11 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=22.0
Q ss_pred CCceEEccCCCCCCCcccceeCCCCccccc
Q 000976 546 ENGTTTGKACPKGLYGIFCEECPVGTYKNV 575 (1204)
Q Consensus 546 ~~GTI~gk~CP~GlyG~fC~eCP~GtYK~~ 575 (1204)
.+|+- .|++|+.|..|++|+.|+|...
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 45555 3999999999999999999653
No 18
>PTZ00146 fibrillarin; Provisional
Probab=53.07 E-value=30 Score=40.05 Aligned_cols=10 Identities=30% Similarity=0.474 Sum_probs=6.4
Q ss_pred eeeEEEeCCC
Q 000976 435 VEGSVKADGQ 444 (1204)
Q Consensus 435 l~GsI~AnGg 444 (1204)
..|...+.|.
T Consensus 64 ~~gv~~~~~~ 73 (293)
T PTZ00146 64 FPGVFIAKGK 73 (293)
T ss_pred ecCEEEeecC
Confidence 4677777654
No 19
>KOG4069 consensus Uncharacterized conserved protein [Function unknown]
Probab=52.64 E-value=44 Score=34.92 Aligned_cols=70 Identities=20% Similarity=0.381 Sum_probs=50.1
Q ss_pred CCCcchhhhhhchHHHHHHHHHHHhhhhh-------hhhhhHHHHHhHHhhcchhHHHHHHHHHHHHHHHHHHHHhh---
Q 000976 725 HTPPEQIKEIVYEGAFNSFVDEINAIATY-------HWWEGAIYSILAILAYPLAWSWQQWRRRMKLQRLREYVRSE--- 794 (1204)
Q Consensus 725 ~spP~~i~~IVyed~Fn~Fad~IN~laay-------~~We~~iy~iLsvl~YPlaw~wlq~rRrkkl~rL~efv~se--- 794 (1204)
...|..+++.|..+.|+.=+..+|++-|= ..+|+.+ =++.+|-.|.--. --=+||+++++||+.++
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 34789999999999999999999998432 2466664 5666666554333 23357899999999843
Q ss_pred -cCch
Q 000976 795 -YDHA 798 (1204)
Q Consensus 795 -ydh~ 798 (1204)
|.|.
T Consensus 121 IY~~~ 125 (154)
T KOG4069|consen 121 IYHHV 125 (154)
T ss_pred hcccc
Confidence 6664
No 20
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=51.86 E-value=53 Score=39.06 Aligned_cols=8 Identities=63% Similarity=1.090 Sum_probs=4.3
Q ss_pred ccCCCCCc
Q 000976 106 LEFPNQPL 113 (1204)
Q Consensus 106 l~fp~~pl 113 (1204)
|.||.+|-
T Consensus 152 L~~~k~p~ 159 (465)
T KOG3973|consen 152 LNFPKQPG 159 (465)
T ss_pred cCCCCCCC
Confidence 45666553
No 21
>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=50.77 E-value=23 Score=34.95 Aligned_cols=65 Identities=15% Similarity=0.322 Sum_probs=44.9
Q ss_pred hcccCChHHHHHHHHHHHHHHHHh-hcc------------------------ccchhhHhHHHHHhhcCCCccccCCeEE
Q 000976 874 MSQLVPPTICYRLVAGLNAQLRLV-RRG------------------------RLRATFRPVLRWLETHANPTLQLHGLRV 928 (1204)
Q Consensus 874 ~~q~~~~~~w~~fVa~lN~qlR~v-~~~------------------------slr~tl~~vi~~lesh~n~~l~~~Gvrv 928 (1204)
++..+++++|+++|.++|..++.. ..- .-+..+..+=+||+..|++.++.+|+++
T Consensus 26 L~~~is~~ef~~iI~~IN~~l~~a~~~~~~~~~~~~~l~~lt~~l~~~~~~~~~~~~~~~le~~l~~~N~~~~~~~gi~i 105 (118)
T PF10256_consen 26 LSGYISPEEFEEIINTINQILKEAFEPISWRNIIENILGCLTLGLSSLCFKTHYKRKLRELEKYLEQLNEELFKPRGIKI 105 (118)
T ss_pred hcCCCCHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcEE
Confidence 455789999999999999998877 321 1122344466788888887899999854
Q ss_pred EEEEEEEeceeeEE
Q 000976 929 DLAWFQATACGYCQ 942 (1204)
Q Consensus 929 ~L~~fqata~g~~q 942 (1204)
- -.-.+||-.
T Consensus 106 i----~pr~~g~ls 115 (118)
T PF10256_consen 106 I----SPRRSGYLS 115 (118)
T ss_pred E----chhHceEEE
Confidence 3 233555543
No 22
>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=45.43 E-value=13 Score=42.40 Aligned_cols=36 Identities=28% Similarity=0.574 Sum_probs=27.3
Q ss_pred EEccCCCCCCC---------cccceeCCCCccccccCCCCCCcccCCC
Q 000976 550 TTGKACPKGLY---------GIFCEECPVGTYKNVTGSDKSLCHQCPP 588 (1204)
Q Consensus 550 I~gk~CP~Gly---------G~fC~eCP~GtYK~~tGs~~~~C~pCp~ 588 (1204)
+.=..|+|||+ -.=|+-|++|||....+ ..|+.|+.
T Consensus 217 v~idsC~PGfG~N~~~h~~C~~CCVvCsPgTysp~~~---~~C~~C~~ 261 (271)
T PF07354_consen 217 VRIDSCRPGFGKNDILHSDCPSCCVVCSPGTYSPDDD---VHCQQCNS 261 (271)
T ss_pred EEeeccCCCCCcCcccCCCCCCeeEECCCcccCCCCC---ceEEecCc
Confidence 34467888886 12499999999987654 58999996
No 23
>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=39.70 E-value=13 Score=31.45 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=17.4
Q ss_pred CCCCCCcccceeCCCCccccc
Q 000976 555 CPKGLYGIFCEECPVGTYKNV 575 (1204)
Q Consensus 555 CP~GlyG~fC~eCP~GtYK~~ 575 (1204)
|++++.|..|++|..|+|...
T Consensus 22 C~~~~~G~~C~~C~~g~~~~~ 42 (49)
T PF00053_consen 22 CKPGTTGPRCDQCKPGYFGLP 42 (49)
T ss_dssp BSTTEESTTS-EE-TTEECST
T ss_pred ccccccCCcCcCCCCcccccc
Confidence 999999999999999999764
No 24
>KOG1836 consensus Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures]
Probab=39.41 E-value=23 Score=49.27 Aligned_cols=34 Identities=32% Similarity=0.708 Sum_probs=25.5
Q ss_pred cCCCCCCCcccceeCCCCccccccCCCCC--CcccCC
Q 000976 553 KACPKGLYGIFCEECPVGTYKNVTGSDKS--LCHQCP 587 (1204)
Q Consensus 553 k~CP~GlyG~fC~eCP~GtYK~~tGs~~~--~C~pCp 587 (1204)
=.||+||-|-||+.|+.|+.+. ++.... .|.+|+
T Consensus 697 c~C~~g~tG~~Ce~C~~gfrr~-~~~~~~~~~c~~C~ 732 (1705)
T KOG1836|consen 697 CTCPVGYTGQFCESCAPGFRRL-SPQLGPFCPCIPCD 732 (1705)
T ss_pred ccCCCCcccchhhhcchhhhcc-cccCCCCCcccccc
Confidence 5799999999999999999665 344444 455555
No 25
>KOG1836 consensus Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures]
Probab=36.87 E-value=24 Score=49.14 Aligned_cols=43 Identities=35% Similarity=0.688 Sum_probs=34.7
Q ss_pred CceEEccCCCCCCCcccceeCCCCccccccCCC--CCCcccCCCC
Q 000976 547 NGTTTGKACPKGLYGIFCEECPVGTYKNVTGSD--KSLCHQCPPQ 589 (1204)
Q Consensus 547 ~GTI~gk~CP~GlyG~fC~eCP~GtYK~~tGs~--~~~C~pCp~~ 589 (1204)
..++.-|.||+||.|..|++|.-|+|=+..+-+ ...|++|+-+
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 456667899999999999999999998865432 2489999964
No 26
>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=35.54 E-value=31 Score=34.86 Aligned_cols=20 Identities=35% Similarity=0.891 Sum_probs=9.5
Q ss_pred h-hhHHHHHHHHHHHHHHHHH
Q 000976 638 W-LFCLLLVGLLILLALVLSV 657 (1204)
Q Consensus 638 ~-~F~lll~~llvLlalv~s~ 657 (1204)
| +|+||+++++++|+++..+
T Consensus 2 W~l~~iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCH 22 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHH
Confidence 5 4555554444444444433
No 27
>PF11145 DUF2921: Protein of unknown function (DUF2921); InterPro: IPR021319 This eukaryotic family of proteins has no known function.
Probab=32.38 E-value=1.1e+02 Score=40.58 Aligned_cols=116 Identities=18% Similarity=0.171 Sum_probs=65.5
Q ss_pred Ccccccccccceee--eeeeeeecCccc-chhhhHH---HHHHHHHHhhHHHHHHHHHHHHHhhhh------hHHHHHHh
Q 000976 1016 NNVQMLEERRDIFY--FLSFIVHNTKPV-GHQDLVG---LVISVLLLGDFSLVLLTLLQLYSISLV------DVFLVLFI 1083 (1204)
Q Consensus 1016 ~~l~~le~~r~~~~--p~s~~l~n~rp~-g~~~lv~---l~is~lll~D~~ltll~llq~y~is~~------~~~~vl~~ 1083 (1204)
.+++++.++=|++| |+.+-....-.- ...+.+. +=+.+.++.=......+.+|++-+.=. -=+.||.+
T Consensus 593 g~I~S~R~~~DpL~F~~~~l~~~~~~~~~q~~~~i~R~d~E~i~~~~s~tl~~~~~~~QL~~~k~~~~~~P~iSlvML~v 672 (909)
T PF11145_consen 593 GSISSTRDKSDPLYFEPLDLSTYPIYYRKQAEESIWRMDLEGIMRVISLTLSCVFIGLQLFHVKKHPDVLPYISLVMLGV 672 (909)
T ss_pred EEEEeccCCCCCccccceeeeeccceeccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhcCCCccchHhHHHHHH
Confidence 36677778888888 665544333111 2233332 111111111122334577898652210 12458888
Q ss_pred ccccccccccchhhhhhcc-CCCCcccccchhhhhhhhhhhH--HHHHhhh
Q 000976 1084 LPLGILLPFPAGINALFSH-GPRRSVGLARVYALWNVTSLIN--VGVAFLC 1131 (1204)
Q Consensus 1084 lPl~~~~p~~~Glnalfs~-~~rrs~~~ar~yalwN~~Sl~n--~~va~ic 1131 (1204)
+=|+-.+|..++.-|||.. ..++...+.+-=-+|..-.++- ++|||+.
T Consensus 673 ~aLGy~~pLv~n~EaLf~~~~~~~~~~~~~~~w~e~~e~~vr~ltmvAflL 723 (909)
T PF11145_consen 673 QALGYMIPLVLNFEALFKSSHNRQNIFLDSGGWLEVNEVMVRLLTMVAFLL 723 (909)
T ss_pred HHHhccchhhcCHHHHcCcCCCCceEEeecCchhHHHHHHHHHHHHHHHHH
Confidence 9999999999999999993 3344455544444555555555 4567765
No 28
>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=31.25 E-value=29 Score=29.15 Aligned_cols=22 Identities=45% Similarity=1.017 Sum_probs=10.1
Q ss_pred cCCCCCC--Ccccce-eCCCCcccc
Q 000976 553 KACPKGL--YGIFCE-ECPVGTYKN 574 (1204)
Q Consensus 553 k~CP~Gl--yG~fC~-eCP~GtYK~ 574 (1204)
+.|++|+ .+..|+ .||.++|.+
T Consensus 18 ~~C~~~~~~~~~~Cv~~C~~~~~~~ 42 (49)
T cd00064 18 TSCRHGFYLDGGTCVSECPEGTYAD 42 (49)
T ss_pred ccCcCccCCCCCcccccCCCCceec
Confidence 3444444 234454 455555443
No 29
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=30.35 E-value=50 Score=44.28 Aligned_cols=40 Identities=28% Similarity=0.598 Sum_probs=28.4
Q ss_pred CCCCCCCcccceeCCCCccccccCCCCCCcccCCCCCCCCCceE
Q 000976 554 ACPKGLYGIFCEECPVGTYKNVTGSDKSLCHQCPPQEFPHRAVY 597 (1204)
Q Consensus 554 ~CP~GlyG~fC~eCP~GtYK~~tGs~~~~C~pCp~~~~P~ra~y 597 (1204)
.|-|+--|-.|.+|.+|||- -..+=|++|.=+..-+-..|
T Consensus 785 qCkPnVVGR~CdqCApGtyG----FGPsGCk~CdC~~~Gs~~~~ 824 (1758)
T KOG0994|consen 785 QCKPNVVGRRCDQCAPGTYG----FGPSGCKACDCNSIGSLDKY 824 (1758)
T ss_pred cccCccccccccccCCcccC----cCCccCcccccccccccccc
Confidence 56677779999999999994 34466999986544333333
No 30
>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=29.45 E-value=87 Score=35.38 Aligned_cols=14 Identities=29% Similarity=0.620 Sum_probs=6.4
Q ss_pred eeeCCceeEEEecC
Q 000976 480 LDIGDSAVLSSVGG 493 (1204)
Q Consensus 480 l~l~g~G~LsA~GG 493 (1204)
|.+.++|.|...||
T Consensus 143 LRI~N~GaIAgGGG 156 (260)
T PF05268_consen 143 LRINNNGAIAGGGG 156 (260)
T ss_pred EEEecCCEEecCCC
Confidence 44445555544333
No 31
>KOG4260 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.02 E-value=36 Score=39.35 Aligned_cols=21 Identities=43% Similarity=1.048 Sum_probs=17.1
Q ss_pred CCCCCCCcccceeCCCCcccc
Q 000976 554 ACPKGLYGIFCEECPVGTYKN 574 (1204)
Q Consensus 554 ~CP~GlyG~fC~eCP~GtYK~ 574 (1204)
=||+|.||.-|.+||-|+=+.
T Consensus 131 CCp~gtyGpdCl~Cpggser~ 151 (350)
T KOG4260|consen 131 CCPDGTYGPDCLQCPGGSERP 151 (350)
T ss_pred ccCCCCcCCccccCCCCCcCC
Confidence 488888888899998887554
No 32
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=27.67 E-value=43 Score=32.86 Aligned_cols=25 Identities=28% Similarity=0.557 Sum_probs=18.3
Q ss_pred ccceeCCCCccccccCCCCCCcccCCCC
Q 000976 562 IFCEECPVGTYKNVTGSDKSLCHQCPPQ 589 (1204)
Q Consensus 562 ~fC~eCP~GtYK~~tGs~~~~C~pCp~~ 589 (1204)
..|.+|..|+|++..+ ..|.+|+.+
T Consensus 4 ~~Ct~C~~g~~~~~~~---~~C~~C~~~ 28 (96)
T PTZ00382 4 AVCTSCDSDKKPNKDG---SGCVLCSVG 28 (96)
T ss_pred cccCcCCCCCccCCCC---CcCCcCCCC
Confidence 3688999999887533 468888853
No 33
>COG4907 Predicted membrane protein [Function unknown]
Probab=27.24 E-value=40 Score=41.28 Aligned_cols=13 Identities=38% Similarity=0.555 Sum_probs=6.5
Q ss_pred eccCCCCCcceeE
Q 000976 105 LLEFPNQPLWTNV 117 (1204)
Q Consensus 105 ll~fp~~plw~~v 117 (1204)
+++|-..|+-+.|
T Consensus 173 v~~~~hp~~~~ev 185 (595)
T COG4907 173 VLVFGHPPLTGEV 185 (595)
T ss_pred eeEeecCCcccee
Confidence 4455555555444
No 34
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=24.72 E-value=72 Score=36.73 Aligned_cols=12 Identities=50% Similarity=1.041 Sum_probs=5.1
Q ss_pred CCCCCCCCCCCC
Q 000976 368 GSGGGHGGKGGL 379 (1204)
Q Consensus 368 GgGGGHGG~GG~ 379 (1204)
||||+.||.|+.
T Consensus 257 gGGgS~GGGGas 268 (271)
T COG1512 257 GGGGSSGGGGAS 268 (271)
T ss_pred CCCCCCCCCCCC
Confidence 344444444433
No 35
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=24.60 E-value=2.2e+02 Score=31.04 Aligned_cols=29 Identities=41% Similarity=0.522 Sum_probs=21.2
Q ss_pred HhCCch-hhHHHHHHHHHHHHHHHHHhhhe
Q 000976 633 TFGGPW-LFCLLLVGLLILLALVLSVARMK 661 (1204)
Q Consensus 633 tfGGp~-~F~lll~~llvLlalv~s~~R~k 661 (1204)
.+|||+ .-.|||=.|+|-++++++++-.-
T Consensus 83 ~~g~P~vAASL~LgTffIS~~LilSvA~FF 112 (180)
T PF14946_consen 83 HTGGPQVAASLFLGTFFISLGLILSVASFF 112 (180)
T ss_pred cCCChhHHHHHHHHHHHHHHHHHHHHhhhe
Confidence 579998 55566557777789999877654
No 36
>KOG4260 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.60 E-value=42 Score=38.82 Aligned_cols=36 Identities=19% Similarity=0.619 Sum_probs=27.6
Q ss_pred cCCCCCCCcccceeCCCCccccccCCCCCCcccCCC
Q 000976 553 KACPKGLYGIFCEECPVGTYKNVTGSDKSLCHQCPP 588 (1204)
Q Consensus 553 k~CP~GlyG~fC~eCP~GtYK~~tGs~~~~C~pCp~ 588 (1204)
=.|.+||.|..|.+|..++|...---....|++|..
T Consensus 170 CkC~~GY~Gp~C~~Cg~eyfes~Rne~~lvCt~Ch~ 205 (350)
T KOG4260|consen 170 CKCETGYTGPLCRYCGIEYFESSRNEQHLVCTACHE 205 (350)
T ss_pred ccccCCCCCccccccchHHHHhhcccccchhhhhhh
Confidence 489999999999999999997643223345777764
No 37
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=24.53 E-value=1e+02 Score=37.93 Aligned_cols=9 Identities=44% Similarity=0.759 Sum_probs=4.8
Q ss_pred CccCCCCCC
Q 000976 400 CELGSGSGN 408 (1204)
Q Consensus 400 ~~~GSGGG~ 408 (1204)
.+-|||||+
T Consensus 101 ~S~~S~~~~ 109 (641)
T KOG3915|consen 101 ASNGSGGGG 109 (641)
T ss_pred cCCCCCCCC
Confidence 444666544
No 38
>KOG4180 consensus Predicted kinase [General function prediction only]
Probab=23.28 E-value=1.3e+02 Score=35.87 Aligned_cols=28 Identities=32% Similarity=0.502 Sum_probs=19.6
Q ss_pred CCCCCCcccccccEEEEecCCCCcccCcc
Q 000976 835 RTDLPPCLHHRFPMSLIFGGDGSYMAPFS 863 (1204)
Q Consensus 835 r~dl~~~i~~~lPm~IlfsGdGSf~~Pf~ 863 (1204)
|.++... ..--.|+|-.||||+|+--=+
T Consensus 96 R~~lsq~-i~waD~VisvGGDGTfL~Aas 123 (395)
T KOG4180|consen 96 RNDLSQP-IRWADMVISVGGDGTFLLAAS 123 (395)
T ss_pred hhhccCc-CchhhEEEEecCccceeehhh
Confidence 4444333 444578999999999987666
No 39
>KOG4289 consensus Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms]
Probab=22.65 E-value=82 Score=43.39 Aligned_cols=36 Identities=36% Similarity=0.866 Sum_probs=28.1
Q ss_pred CCCCceEEccCCCCCCCcccce-----eCCCCccccccCCCCCCcccCC
Q 000976 544 GGENGTTTGKACPKGLYGIFCE-----ECPVGTYKNVTGSDKSLCHQCP 587 (1204)
Q Consensus 544 ~G~~GTI~gk~CP~GlyG~fC~-----eCP~GtYK~~tGs~~~~C~pCp 587 (1204)
+|.+| |.-.||+||+|.+|+ +||.||+-. ..|.||.
T Consensus 1734 p~a~G--Y~C~C~~g~~G~~Ce~~~dq~CPrGWWG~------P~CgpC~ 1774 (2531)
T KOG4289|consen 1734 PGAHG--YTCECPPGYTGPYCELRADQPCPRGWWGF------PTCGPCN 1774 (2531)
T ss_pred CCCCc--eeEECCCcccCcchhhhccCCCCCcccCC------CCccCcc
Confidence 34455 457999999999995 899999843 4588885
No 40
>PTZ00146 fibrillarin; Provisional
Probab=22.63 E-value=1.2e+02 Score=35.33 Aligned_cols=6 Identities=0% Similarity=-0.224 Sum_probs=2.3
Q ss_pred cceEeE
Q 000976 704 SHVHRM 709 (1204)
Q Consensus 704 ~Hv~Rm 709 (1204)
||....
T Consensus 275 y~~~h~ 280 (293)
T PTZ00146 275 FERDHA 280 (293)
T ss_pred ccCCcE
Confidence 443333
No 41
>PF04790 Sarcoglycan_1: Sarcoglycan complex subunit protein; InterPro: IPR006875 The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma and delta members [, ].; GO: 0007010 cytoskeleton organization, 0016012 sarcoglycan complex, 0016021 integral to membrane
Probab=22.46 E-value=8.4e+02 Score=28.25 Aligned_cols=59 Identities=17% Similarity=0.274 Sum_probs=41.7
Q ss_pred ceecCCCCCcccccCCcEE-EEEEEEEEEEeeeEEeccEEEEEecceEEEcc-CceEeecCCC
Q 000976 292 VELLHPPEDCNVNSSLSFT-LQICRVEDIVVDGLVEGSVVHFHRARTISVQS-SGAISASGMG 352 (1204)
Q Consensus 292 ~e~~~ppe~c~vN~s~~fT-LqI~rVEditv~G~i~GSvV~~~~a~tItI~~-~G~IsASGlG 352 (1204)
+..|.+|.+=++..+++-. |.+-.-|.+.+++. +| -|.+.+-..|.+++ +|.|.-+|.+
T Consensus 162 T~~Irs~~~~~L~leS~trsL~~~a~egV~i~a~-ag-~I~~~a~~di~L~S~~G~i~Lda~~ 222 (264)
T PF04790_consen 162 TPRIRSPPNEDLRLESPTRSLSMRAPEGVHIEAK-AG-DIEASARQDISLNSTDGSIVLDAEG 222 (264)
T ss_pred eccccCCCCcccccccCCcEEEEECCCCeEEEec-cC-cEEEEecCCEEEEecCCeEEEecCe
Confidence 3447777777777777776 77777888888885 33 34555667788877 6888777744
No 42
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=20.71 E-value=1.2e+02 Score=31.00 Aligned_cols=70 Identities=14% Similarity=0.246 Sum_probs=46.8
Q ss_pred hhhhhchHHHHHHHHHHHhhhhhhhhhhHHHHH------hH--HhhcchhHHHHHHHHHHHHHHHHHHHHhhcCchhhc
Q 000976 731 IKEIVYEGAFNSFVDEINAIATYHWWEGAIYSI------LA--ILAYPLAWSWQQWRRRMKLQRLREYVRSEYDHACLR 801 (1204)
Q Consensus 731 i~~IVyed~Fn~Fad~IN~laay~~We~~iy~i------Ls--vl~YPlaw~wlq~rRrkkl~rL~efv~seydh~clR 801 (1204)
...=|.++++.+|.++++.-++..-+|.++-.. +. +..|=.++.....+.+||-..+.++|. ..|+.|++
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 444568999999999999988887666432221 11 233444555666777777778888886 56666654
No 43
>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=20.25 E-value=40 Score=27.41 Aligned_cols=20 Identities=35% Similarity=0.913 Sum_probs=14.8
Q ss_pred CCCCccccccCCCCCCcccCCC
Q 000976 567 CPVGTYKNVTGSDKSLCHQCPP 588 (1204)
Q Consensus 567 CP~GtYK~~tGs~~~~C~pCp~ 588 (1204)
||.|+|.+..+. ..|.+|..
T Consensus 1 C~~g~y~~~~~~--~~C~~C~~ 20 (39)
T PF00020_consen 1 CPPGTYSDSENH--PQCLPCSR 20 (39)
T ss_dssp ECTTEEEESSCS--SSEEEEES
T ss_pred CccCcccCCCCC--CcCCccCC
Confidence 899999987543 67877654
Done!