Query 021996
Match_columns 304
No_of_seqs 158 out of 1191
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 07:13:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13947 GUB_WAK_bind: Wall-as 99.9 4.5E-24 9.7E-29 168.7 10.4 102 26-132 1-106 (106)
2 PF14380 WAK_assoc: Wall-assoc 99.3 2E-12 4.3E-17 100.0 4.9 49 215-265 46-94 (94)
3 PF08488 WAK: Wall-associated 93.2 0.21 4.5E-06 39.1 5.2 12 222-233 65-76 (103)
4 PHA03099 epidermal growth fact 81.0 1.1 2.3E-05 36.3 1.9 33 240-274 52-84 (139)
5 PF08693 SKG6: Transmembrane a 75.6 1.4 3E-05 28.3 0.9 13 288-300 27-39 (40)
6 PF12191 stn_TNFRSF12A: Tumour 71.7 2.8 6E-05 33.8 1.9 13 228-242 41-53 (129)
7 PTZ00382 Variant-specific surf 62.5 7.5 0.00016 29.9 2.7 12 289-300 83-94 (96)
8 PF00008 EGF: EGF-like domain 59.7 6.3 0.00014 23.7 1.5 24 240-265 5-28 (32)
9 cd00053 EGF Epidermal growth f 47.3 27 0.00059 20.1 3.0 22 245-268 11-32 (36)
10 KOG1219 Uncharacterized conser 44.5 9.7 0.00021 44.6 0.9 53 240-295 3949-4009(4289)
11 PF12662 cEGF: Complement Clr- 43.5 25 0.00055 19.9 2.1 18 256-273 1-22 (24)
12 smart00179 EGF_CA Calcium-bind 42.5 33 0.00073 20.5 2.9 28 240-270 10-38 (39)
13 PF07645 EGF_CA: Calcium-bindi 36.5 28 0.0006 22.1 1.8 23 240-265 11-33 (42)
14 cd00054 EGF_CA Calcium-binding 36.4 46 0.00099 19.4 2.8 27 241-270 11-37 (38)
15 PHA02887 EGF-like protein; Pro 32.4 46 0.001 26.6 2.7 35 236-272 84-123 (126)
16 smart00181 EGF Epidermal growt 25.8 97 0.0021 18.0 2.9 27 240-270 7-34 (35)
17 PF01034 Syndecan: Syndecan do 25.7 21 0.00045 25.4 -0.2 9 294-302 31-39 (64)
18 PF01299 Lamp: Lysosome-associ 25.4 31 0.00067 32.1 0.8 25 268-293 262-286 (306)
19 PF10873 DUF2668: Protein of u 24.3 35 0.00076 28.3 0.8 17 288-304 77-93 (155)
20 PF07974 EGF_2: EGF-like domai 23.1 1E+02 0.0022 18.5 2.5 26 240-270 7-32 (32)
21 PF05337 CSF-1: Macrophage col 22.0 30 0.00065 31.8 0.0 20 283-302 234-253 (285)
22 PF04478 Mid2: Mid2 like cell 21.9 52 0.0011 27.6 1.4 9 288-296 63-71 (154)
No 1
>PF13947 GUB_WAK_bind: Wall-associated receptor kinase galacturonan-binding
Probab=99.91 E-value=4.5e-24 Score=168.69 Aligned_cols=102 Identities=35% Similarity=0.770 Sum_probs=86.4
Q ss_pred cCcccCCcCCccccCCCCCCCCCCc-cCCCCceEeecC--ceeeeeCCccEEEEEEEcCCCEEEEEeCCCCCccCCCCCC
Q 021996 26 INKCRSYCGNITIDYPFAIQQGCGH-PGFRDLLFCVND--FLMFHISSGSYRVLEIDYAYQSLTLHDAHMSTCDNMVLGG 102 (304)
Q Consensus 26 ~~~C~~~CG~i~I~YPFg~~~~Cg~-p~F~~~L~C~~~--~~~l~~~~~~~~V~~I~~~~~~i~v~~~~~~~C~~~~~~~ 102 (304)
+++|+.+|||++|+||||++++|++ |+|+ |+|+++ .++|.+..++|+|++|+|++++|+|.+++...|+......
T Consensus 1 ~~~C~~~CGnv~IpYPFgi~~~C~~~~~F~--L~C~~~~~~~~l~l~~~~~~V~~I~~~~~~i~v~~~~~~~~~~~~~~~ 78 (106)
T PF13947_consen 1 KPGCPSSCGNVSIPYPFGIGPGCGRDPGFE--LTCNNNTSPPKLLLSSGNYEVLSISYENGTIRVSDPISSNCYSSSSSN 78 (106)
T ss_pred CCCCCCccCCEeecCCCccCCCCCCCCCcE--EECCCCCCCceeEecCCcEEEEEEecCCCEEEEEeccccceecCCCCc
Confidence 4789999999999999999999999 9999 999987 4677778899999999999999999999888887654432
Q ss_pred C-CCceeecccCCcccccCCCceEEEEcCCC
Q 021996 103 K-GNGFAVEQWRAPYFNPTADNVFMLIGCSA 132 (304)
Q Consensus 103 ~-~~~~~l~~~~~pf~~~~~~N~~~~~gC~~ 132 (304)
. ...+++ ..||+.++..|.++++||++
T Consensus 79 ~~~~~~~~---~~~~~~s~~~N~~~~~GC~t 106 (106)
T PF13947_consen 79 SSNSNLSL---NGPFFFSSSSNKFTVVGCNT 106 (106)
T ss_pred ccccEEee---cCCceEccCCcEEEEECCCC
Confidence 2 223444 45788888999999999985
No 2
>PF14380 WAK_assoc: Wall-associated receptor kinase C-terminal
Probab=99.31 E-value=2e-12 Score=99.97 Aligned_cols=49 Identities=24% Similarity=0.636 Sum_probs=44.5
Q ss_pred CCCCCCcccceEEEeeecCCcccccccccCCceeccCCCCCceeEeeCCCC
Q 021996 215 IDGPSEWSYGIRVKYSVQGGDQFCRACEATGGTCGFGTDGVRQLCMCGSVN 265 (304)
Q Consensus 215 ~~~~~~~~~gf~L~W~i~~~~~~C~~C~~s~g~Cg~~~~~~g~~C~C~~~~ 265 (304)
.+|.++|++||+|+|.+. +.+|.+|+.|+|+|||+.+...|.|+|+||+
T Consensus 46 ~~~~~~L~~GF~L~w~~~--~~~C~~C~~SgG~Cgy~~~~~~f~C~C~dg~ 94 (94)
T PF14380_consen 46 GNYEEVLKKGFELEWNAD--SGDCRECEASGGRCGYDSNSEQFTCFCSDGP 94 (94)
T ss_pred hHHHHHHhcCcEEEEeCC--CCcCcChhcCCCEeCCCCCCceEEEECCCCC
Confidence 357889999999999984 4899999999999999999999999999974
No 3
>PF08488 WAK: Wall-associated kinase; InterPro: IPR013695 This domain is found together with the eukaryotic protein kinase domain IPR000719 from INTERPRO in plant wall-associated kinases (WAKs) and related proteins. WAKs are serine-threonine kinases which might be involved in signalling to the cytoplasm and are required for cell expansion []. ; GO: 0004674 protein serine/threonine kinase activity, 0016021 integral to membrane
Probab=93.18 E-value=0.21 Score=39.10 Aligned_cols=12 Identities=0% Similarity=0.086 Sum_probs=10.0
Q ss_pred ccceEEEeeecC
Q 021996 222 SYGIRVKYSVQG 233 (304)
Q Consensus 222 ~~gf~L~W~i~~ 233 (304)
..+++|+|.|..
T Consensus 65 y~pv~L~W~i~t 76 (103)
T PF08488_consen 65 YVPVVLDWFIDT 76 (103)
T ss_pred eeEEEEEEEEec
Confidence 468999999964
No 4
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=80.97 E-value=1.1 Score=36.27 Aligned_cols=33 Identities=24% Similarity=0.427 Sum_probs=27.7
Q ss_pred ccccCCceeccCCCCCceeEeeCCCCCCCCCCCCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVNSTSNCDSVG 274 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~~~~~C~~~~ 274 (304)
-|. ||.|.+-..-+.+.|.|..|.....|+..-
T Consensus 52 YCl--HG~C~yI~dl~~~~CrC~~GYtGeRCEh~d 84 (139)
T PHA03099 52 YCL--HGDCIHARDIDGMYCRCSHGYTGIRCQHVV 84 (139)
T ss_pred EeE--CCEEEeeccCCCceeECCCCccccccccee
Confidence 576 579999888889999999998888998543
No 5
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=75.62 E-value=1.4 Score=28.34 Aligned_cols=13 Identities=15% Similarity=0.199 Sum_probs=7.9
Q ss_pred hhhhheeeeEEEe
Q 021996 288 SAGFFVLLSIWMT 300 (304)
Q Consensus 288 ~~g~~~~~~~~~~ 300 (304)
++|++.++||||+
T Consensus 27 vl~~~l~~~~rR~ 39 (40)
T PF08693_consen 27 VLGAFLFFWYRRK 39 (40)
T ss_pred HHHHHhheEEecc
Confidence 3556666666665
No 6
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=71.70 E-value=2.8 Score=33.82 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=7.1
Q ss_pred EeeecCCcccccccc
Q 021996 228 KYSVQGGDQFCRACE 242 (304)
Q Consensus 228 ~W~i~~~~~~C~~C~ 242 (304)
.|+.+. .+|-+|.
T Consensus 41 sWs~dL--dkCm~Cs 53 (129)
T PF12191_consen 41 SWSADL--DKCMSCS 53 (129)
T ss_dssp EEETTT--TEEEECC
T ss_pred cCcccc--cccccCc
Confidence 355443 4666664
No 7
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=62.47 E-value=7.5 Score=29.94 Aligned_cols=12 Identities=17% Similarity=0.301 Sum_probs=4.9
Q ss_pred hhhheeeeEEEe
Q 021996 289 AGFFVLLSIWMT 300 (304)
Q Consensus 289 ~g~~~~~~~~~~ 300 (304)
+||+.|++++||
T Consensus 83 v~~l~w~f~~r~ 94 (96)
T PTZ00382 83 VGFLCWWFVCRG 94 (96)
T ss_pred HHHHhheeEEee
Confidence 344444433343
No 8
>PF00008 EGF: EGF-like domain This is a sub-family of the Pfam entry This is a sub-family of the Pfam entry; InterPro: IPR006209 A sequence of about thirty to forty amino-acid residues long found in the sequence of epidermal growth factor (EGF) has been shown [, , , , ] to be present, in a more or less conserved form, in a large number of other, mostly animal proteins. The list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied. The functional significance of EGF domains in what appear to be unrelated proteins is not yet clear. However, a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase). The EGF domain includes six cysteine residues which have been shown (in EGF) to be involved in disulphide bonds. The main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet. Subdomains between the conserved cysteines vary in length.; GO: 0005515 protein binding; PDB: 1WHE_A 1CCF_A 1APO_A 1WHF_A 2VJ3_A 1TOZ_A 4D90_B 3CFW_A 1EDM_B 1IXA_A ....
Probab=59.69 E-value=6.3 Score=23.68 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=18.5
Q ss_pred ccccCCceeccCCCCCceeEeeCCCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVN 265 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~ 265 (304)
.|.. +|+|.... ..+|.|.|+.+.
T Consensus 5 ~C~n-~g~C~~~~-~~~y~C~C~~G~ 28 (32)
T PF00008_consen 5 PCQN-GGTCIDLP-GGGYTCECPPGY 28 (32)
T ss_dssp SSTT-TEEEEEES-TSEEEEEEBTTE
T ss_pred cCCC-CeEEEeCC-CCCEEeECCCCC
Confidence 4653 79998866 569999999863
No 9
>cd00053 EGF Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium.
Probab=47.31 E-value=27 Score=20.07 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=16.5
Q ss_pred CceeccCCCCCceeEeeCCCCCCC
Q 021996 245 GGTCGFGTDGVRQLCMCGSVNSTS 268 (304)
Q Consensus 245 ~g~Cg~~~~~~g~~C~C~~~~~~~ 268 (304)
++.|.... .+|.|.|+.+....
T Consensus 11 ~~~C~~~~--~~~~C~C~~g~~g~ 32 (36)
T cd00053 11 GGTCVNTP--GSYRCVCPPGYTGD 32 (36)
T ss_pred CCEEecCC--CCeEeECCCCCccc
Confidence 68888765 47999999865443
No 10
>KOG1219 consensus Uncharacterized conserved protein, contains laminin, cadherin and EGF domains [Signal transduction mechanisms]
Probab=44.49 E-value=9.7 Score=44.56 Aligned_cols=53 Identities=19% Similarity=0.237 Sum_probs=29.2
Q ss_pred ccccCCceeccCCCCCceeEeeCCCCCCCCCCCCCC------CC--Ccccccchhhhhhhheee
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVNSTSNCDSVGS------SS--SRISWPLSQISAGFFVLL 295 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~~~~~C~~~~~------~~--~~~~~~~~~~~~g~~~~~ 295 (304)
.|.. +|.|.+-.. .|.|+|..+--...|...+. .| +.-..+|+..|++|++++
T Consensus 3949 ~C~~-gg~C~n~~g--sf~CncT~g~~gr~c~~~~pni~~~~~~~gkaEli~I~V~l~~ifilv 4009 (4289)
T KOG1219|consen 3949 VCGT-GGQCINIPG--SFHCNCTPGILGRTCCAEKPNILSTVLWLGKAELIIIIVLLALIFILV 4009 (4289)
T ss_pred cccC-CceeeccCC--ceEeccChhHhcccCccccCccccccchhcccceeehhHHHHHHHHHH
Confidence 4653 788877443 48899998654444544331 12 112223444467777665
No 11
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=43.51 E-value=25 Score=19.90 Aligned_cols=18 Identities=17% Similarity=0.558 Sum_probs=12.7
Q ss_pred ceeEeeCCCCC----CCCCCCC
Q 021996 256 RQLCMCGSVNS----TSNCDSV 273 (304)
Q Consensus 256 g~~C~C~~~~~----~~~C~~~ 273 (304)
+|.|.|+.|.. ...|.++
T Consensus 1 sy~C~C~~Gy~l~~d~~~C~DI 22 (24)
T PF12662_consen 1 SYTCSCPPGYQLSPDGRSCEDI 22 (24)
T ss_pred CEEeeCCCCCcCCCCCCccccC
Confidence 48999999643 4467764
No 12
>smart00179 EGF_CA Calcium-binding EGF-like domain.
Probab=42.46 E-value=33 Score=20.47 Aligned_cols=28 Identities=32% Similarity=0.668 Sum_probs=18.9
Q ss_pred ccccCCceeccCCCCCceeEeeCCCCC-CCCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVNS-TSNC 270 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~~-~~~C 270 (304)
.|.. ++.|.+.. .+|.|.|+.+.. ...|
T Consensus 10 ~C~~-~~~C~~~~--g~~~C~C~~g~~~g~~C 38 (39)
T smart00179 10 PCQN-GGTCVNTV--GSYRCECPPGYTDGRNC 38 (39)
T ss_pred CcCC-CCEeECCC--CCeEeECCCCCccCCcC
Confidence 3653 67898643 479999999765 4444
No 13
>PF07645 EGF_CA: Calcium-binding EGF domain; InterPro: IPR001881 A sequence of about forty amino-acid residues found in epidermal growth factor (EGF) has been shown [, , , , , ] to be present in a large number of membrane-bound and extracellular, mostly animal, proteins. Many of these proteins require calcium for their biological function and a calcium-binding site has been found at the N terminus of some EGF-like domains []. Calcium-binding may be crucial for numerous protein-protein interactions. For human coagulation factor IX it has been shown [] that the calcium-ligands form a pentagonal bipyramid. The first, third and fourth conserved negatively charged or polar residues are side chain ligands. The latter is possibly hydroxylated (see aspartic acid and asparagine hydroxylation site) []. A conserved aromatic residue, as well as the second conserved negative residue, are thought to be involved in stabilising the calcium-binding site. As in non-calcium binding EGF-like domains, there are six conserved cysteines and the structure of both types is very similar as calcium-binding induces only strictly local structural changes []. +------------------+ +---------+ | | | | nxnnC-x(3,14)-C-x(3,7)-CxxbxxxxaxC-x(1,6)-C-x(8,13)-Cx | | +------------------+ 'n': negatively charged or polar residue [DEQN] 'b': possibly beta-hydroxylated residue [DN] 'a': aromatic amino acid 'C': cysteine, involved in disulphide bond 'x': any amino acid. ; GO: 0005509 calcium ion binding; PDB: 2VJ3_A 1TOZ_A 1LMJ_A 1UZQ_A 1UZK_A 1UZJ_B 1UZP_A 1EMO_A 1EMN_A 2RR0_A ....
Probab=36.51 E-value=28 Score=22.09 Aligned_cols=23 Identities=26% Similarity=0.482 Sum_probs=17.4
Q ss_pred ccccCCceeccCCCCCceeEeeCCCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVN 265 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~ 265 (304)
.| ..++.|.+.. .+|.|.|+.|.
T Consensus 11 ~C-~~~~~C~N~~--Gsy~C~C~~Gy 33 (42)
T PF07645_consen 11 NC-PENGTCVNTE--GSYSCSCPPGY 33 (42)
T ss_dssp SS-STTSEEEEET--TEEEEEESTTE
T ss_pred cC-CCCCEEEcCC--CCEEeeCCCCc
Confidence 46 4478898844 48999999964
No 14
>cd00054 EGF_CA Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements.
Probab=36.35 E-value=46 Score=19.43 Aligned_cols=27 Identities=33% Similarity=0.706 Sum_probs=18.6
Q ss_pred cccCCceeccCCCCCceeEeeCCCCCCCCC
Q 021996 241 CEATGGTCGFGTDGVRQLCMCGSVNSTSNC 270 (304)
Q Consensus 241 C~~s~g~Cg~~~~~~g~~C~C~~~~~~~~C 270 (304)
|. .++.|.+.. .+|.|.|..+.....|
T Consensus 11 C~-~~~~C~~~~--~~~~C~C~~g~~g~~C 37 (38)
T cd00054 11 CQ-NGGTCVNTV--GSYRCSCPPGYTGRNC 37 (38)
T ss_pred cC-CCCEeECCC--CCeEeECCCCCcCCcC
Confidence 64 367898644 3699999987554445
No 15
>PHA02887 EGF-like protein; Provisional
Probab=32.38 E-value=46 Score=26.62 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=29.3
Q ss_pred cccc-----ccccCCceeccCCCCCceeEeeCCCCCCCCCCC
Q 021996 236 QFCR-----ACEATGGTCGFGTDGVRQLCMCGSVNSTSNCDS 272 (304)
Q Consensus 236 ~~C~-----~C~~s~g~Cg~~~~~~g~~C~C~~~~~~~~C~~ 272 (304)
..|. -|. +|+|.+-..-+...|.|..|.....|..
T Consensus 84 ~pC~~eyk~YCi--HG~C~yI~dL~epsCrC~~GYtG~RCE~ 123 (126)
T PHA02887 84 EKCKNDFNDFCI--NGECMNIIDLDEKFCICNKGYTGIRCDE 123 (126)
T ss_pred cccChHhhCEee--CCEEEccccCCCceeECCCCcccCCCCc
Confidence 4675 587 7999999888999999999887777864
No 16
>smart00181 EGF Epidermal growth factor-like domain.
Probab=25.80 E-value=97 Score=18.03 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=18.3
Q ss_pred ccccCCceeccCCCCCceeEeeCCCCCC-CCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVNST-SNC 270 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~~~-~~C 270 (304)
.|.. + .|... ..+|.|.|+.+... ..|
T Consensus 7 ~C~~-~-~C~~~--~~~~~C~C~~g~~g~~~C 34 (35)
T smart00181 7 PCSN-G-TCINT--PGSYTCSCPPGYTGDKRC 34 (35)
T ss_pred CCCC-C-EEECC--CCCeEeECCCCCccCCcc
Confidence 4654 3 88865 45899999997544 444
No 17
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=25.68 E-value=21 Score=25.37 Aligned_cols=9 Identities=22% Similarity=0.176 Sum_probs=0.5
Q ss_pred eeeEEEeec
Q 021996 294 LLSIWMTIN 302 (304)
Q Consensus 294 ~~~~~~~~~ 302 (304)
+++||||++
T Consensus 31 f~iyR~rkk 39 (64)
T PF01034_consen 31 FLIYRMRKK 39 (64)
T ss_dssp ------S--
T ss_pred HHHHHHHhc
Confidence 347775544
No 18
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=25.40 E-value=31 Score=32.10 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCcccccchhhhhhhhe
Q 021996 268 SNCDSVGSSSSRISWPLSQISAGFFV 293 (304)
Q Consensus 268 ~~C~~~~~~~~~~~~~~~~~~~g~~~ 293 (304)
.+|..... ...+.++|+++|+|+++
T Consensus 262 ~~C~~D~~-~~~vPIaVG~~La~lvl 286 (306)
T PF01299_consen 262 EECSSDDT-SDLVPIAVGAALAGLVL 286 (306)
T ss_pred hcCCcCCc-cchHHHHHHHHHHHHHH
Confidence 34554332 33455566666555443
No 19
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=24.31 E-value=35 Score=28.30 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=12.7
Q ss_pred hhhhheeeeEEEeecCC
Q 021996 288 SAGFFVLLSIWMTINHG 304 (304)
Q Consensus 288 ~~g~~~~~~~~~~~~~~ 304 (304)
++||++++..-||.+.|
T Consensus 77 va~i~icvCmc~kn~rg 93 (155)
T PF10873_consen 77 VAGIAICVCMCMKNSRG 93 (155)
T ss_pred HHHHHHHHhhhhhcCCC
Confidence 57888888777777654
No 20
>PF07974 EGF_2: EGF-like domain; InterPro: IPR013111 A sequence of about thirty to forty amino-acid residues long found in the sequence of epidermal growth factor (EGF) has been shown [, , , , ] to be present, in a more or less conserved form, in a large number of other, mostly animal proteins. The list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied. The functional significance of EGF domains in what appear to be unrelated proteins is not yet clear. However, a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase). The EGF domain includes six cysteine residues which have been shown (in EGF) to be involved in disulphide bonds. The main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet. Subdomains between the conserved cysteines vary in length. This entry contains EGF domains found in a variety of extracellular and membrane proteins
Probab=23.07 E-value=1e+02 Score=18.53 Aligned_cols=26 Identities=31% Similarity=0.695 Sum_probs=18.3
Q ss_pred ccccCCceeccCCCCCceeEeeCCCCCCCCC
Q 021996 240 ACEATGGTCGFGTDGVRQLCMCGSVNSTSNC 270 (304)
Q Consensus 240 ~C~~s~g~Cg~~~~~~g~~C~C~~~~~~~~C 270 (304)
.|.. +|+|... ..+|.|.++.....|
T Consensus 7 ~C~~-~G~C~~~----~g~C~C~~g~~G~~C 32 (32)
T PF07974_consen 7 ICSG-HGTCVSP----CGRCVCDSGYTGPDC 32 (32)
T ss_pred ccCC-CCEEeCC----CCEEECCCCCcCCCC
Confidence 4654 8999875 358999998665544
No 21
>PF05337 CSF-1: Macrophage colony stimulating factor-1 (CSF-1); InterPro: IPR008001 Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [].; GO: 0005125 cytokine activity, 0008083 growth factor activity, 0016021 integral to membrane; PDB: 3EJJ_A.
Probab=22.04 E-value=30 Score=31.82 Aligned_cols=20 Identities=10% Similarity=-0.154 Sum_probs=0.0
Q ss_pred cchhhhhhhheeeeEEEeec
Q 021996 283 PLSQISAGFFVLLSIWMTIN 302 (304)
Q Consensus 283 ~~~~~~~g~~~~~~~~~~~~ 302 (304)
-|..+++-+++|||||||-|
T Consensus 234 SiILVLLaVGGLLfYr~rrR 253 (285)
T PF05337_consen 234 SIILVLLAVGGLLFYRRRRR 253 (285)
T ss_dssp --------------------
T ss_pred chhhhhhhccceeeeccccc
Confidence 34556788899999996654
No 22
>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].
Probab=21.85 E-value=52 Score=27.59 Aligned_cols=9 Identities=22% Similarity=0.349 Sum_probs=5.4
Q ss_pred hhhhheeee
Q 021996 288 SAGFFVLLS 296 (304)
Q Consensus 288 ~~g~~~~~~ 296 (304)
++|++++++
T Consensus 63 ll~il~lvf 71 (154)
T PF04478_consen 63 LLGILALVF 71 (154)
T ss_pred HHHHHHhhe
Confidence 566666663
Done!