Query 017401
Match_columns 372
No_of_seqs 29 out of 31
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 08:15:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4275 Predicted E3 ubiquitin 95.2 0.0059 1.3E-07 60.9 0.3 59 188-250 147-205 (350)
2 PF01105 EMP24_GP25L: emp24/gp 80.0 0.55 1.2E-05 39.6 0.0 92 182-285 3-101 (183)
3 PF10342 GPI-anchored: Ser-Thr 73.1 19 0.00042 27.8 6.9 68 197-272 9-82 (93)
4 cd04971 Ig_TrKABC_d5 Fifth dom 49.8 47 0.001 26.0 5.3 67 235-310 9-81 (81)
5 PF04151 PPC: Bacterial pre-pe 34.4 2E+02 0.0044 21.6 7.8 64 192-267 4-69 (70)
6 cd05737 Ig_Myomesin_like_C C-t 33.5 2.3E+02 0.005 22.0 7.2 16 196-211 12-27 (92)
7 cd05898 Ig5_KIRREL3 Fifth immu 33.2 1.1E+02 0.0023 25.5 5.2 18 194-211 10-27 (98)
8 KOG1692 Putative cargo transpo 30.2 4.2E+02 0.009 25.8 9.1 93 180-284 20-114 (201)
9 PF12124 Nsp3_PL2pro: Coronavi 29.7 25 0.00054 28.1 0.8 20 187-208 12-41 (66)
10 cd05870 Ig5_NCAM-2 Fifth immun 29.3 2.6E+02 0.0056 22.0 6.6 15 197-211 13-27 (98)
11 PF07679 I-set: Immunoglobulin 28.0 2.6E+02 0.0055 20.8 8.6 17 195-211 10-26 (90)
12 PRK09774 fec operon regulator 23.8 5.2E+02 0.011 25.4 8.9 66 174-253 112-178 (319)
13 PLN02899 alpha-galactosidase 23.1 79 0.0017 35.0 3.4 54 259-318 559-613 (633)
14 PF03351 DOMON: DOMON domain; 21.8 1.4E+02 0.003 24.2 3.8 30 238-267 4-35 (124)
15 TIGR02229 caa3_sub_IV caa(3)-t 21.3 22 0.00047 30.1 -1.0 32 330-362 55-86 (92)
No 1
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.20 E-value=0.0059 Score=60.95 Aligned_cols=59 Identities=3% Similarity=-0.362 Sum_probs=53.5
Q ss_pred CCcceEEEEeeccceEEEEEEEecCCCcEEEEEEecCccccccccCCCCCCCcceeeEEeccc
Q 017401 188 DSHQEWIIYLNKGSQINISYSVKSPGSSVFLIIAQGNEGLRQWLFDPTFPNTTLSWNVIQGSG 250 (372)
Q Consensus 188 ~ShKeW~y~LNKGS~I~IsYsv~s~~SsL~LvIaqG~~~~~~Wl~dPt~PnttlSWnvI~G~G 250 (372)
.|.|.|..++|+|++.+.+|+ .+++.+.|++|-.++++|.+||+.+.++.+|+.+.|+-
T Consensus 147 ~S~ks~~~~~~~~f~r~~~ss----~vap~~~~~s~~~~~~~~~~~~~~~~~sq~qse~sq~~ 205 (350)
T KOG4275|consen 147 RSKKSTRRRSDGYFNRRYHSS----PVAPGGPGLSLGLSTLSEHPEHGLHPHSQRQSENSQMS 205 (350)
T ss_pred hhhhcchhhcccceeeeeccC----CCCCCCccccccccccccCCCCCCCchhhhhhhhcccc
Confidence 789999999999999998888 67888899999999999999999999999999665543
No 2
>PF01105 EMP24_GP25L: emp24/gp25L/p24 family/GOLD; InterPro: IPR009038 The GOLD (for Golgi dynamics) domain is a protein module found in several eukaryotic Golgi and lipid-traffic proteins. It is typically between 90 and 150 amino acids long. Most of the size difference observed in the GOLD-domain superfamily is traceable to a single large low-complexity insert that is seen in some versions of the domain. With the exception of the p24 proteins, which have a simple architecture with the GOLD domain as their only globular domain, all other GOLD-domain proteins contain additional conserved globular domains. In these proteins, the GOLD domain co-occurs with lipid-, sterol- or fatty acid-binding domains such as PH, CRAL-TRIO, FYVE oxysterol binding- and acyl CoA-binding domains, suggesting that these proteins may interact with membranes. The GOLD domain can also be found associated with a RUN domain, which may have a role in the interaction of various proteins with cytoskeletal filaments. The GOLD domain is predicted to mediate diverse protein-protein interactions []. A secondary structure prediction for the GOLD domain reveals that it is likely to adopt a compact all-beta-fold structure with six to seven strands. Most of the sequence conservation is centred on the hydrophobic cores that support these predicted strands. The predicted secondary-structure elements and the size of the conserved core of the domain suggests that it may form a beta- sandwich fold with the strands arranged in two beta sheets stacked on each other []. Some proteins known to contain a GOLD domain are listed below: Eukaryotic proteins of the p24 family. Animal Sec14-like proteins. They are involved in secretion. Human Golgi resident protein GCP60. It interacts with the Golgi integral membrane protein Giantin. Yeast oxysterol-binding protein homologue 3 (OSH3). ; GO: 0006810 transport, 0016021 integral to membrane; PDB: 1P23_A 1M23_A.
Probab=80.05 E-value=0.55 Score=39.60 Aligned_cols=92 Identities=18% Similarity=0.165 Sum_probs=0.0
Q ss_pred EEEecCCCcceEEEEeeccceEEEEEEEecCC--CcEEEEEEecCccccccccCCCC--CCCcceeeEEecccEEEEEEe
Q 017401 182 IVSVPADSHQEWIIYLNKGSQINISYSVKSPG--SSVFLIIAQGNEGLRQWLFDPTF--PNTTLSWNVIQGSGVIHQHIF 257 (372)
Q Consensus 182 ~~~V~s~ShKeW~y~LNKGS~I~IsYsv~s~~--SsL~LvIaqG~~~~~~Wl~dPt~--PnttlSWnvI~G~G~ieq~I~ 257 (372)
.+.|+++..+=....+.+|+.|.++|.|.+.+ ..+.+.|. ||.. ..-...+... ..|..+++..
T Consensus 3 ~f~l~~g~~~Cf~e~v~~~~~i~~~y~v~~~~~~~~v~~~i~-----------~~~~~~~~i~~~~~~~-~~~~f~f~~~ 70 (183)
T PF01105_consen 3 TFELEPGETECFYEEVPKGTTIRGSYRVTDGGGAYDVDFTIR-----------DPDPNGEVIYSKSDKE-SEGSFSFTAK 70 (183)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred EEEECCCCcEEEEEEcCCCcEEEEEEEEeeccccceEEEEEE-----------ecccCCceeeeecccc-cCCcEEEEec
Confidence 35678888888999999999999999999875 45555544 2211 1111112222 2378899999
Q ss_pred cccceEEEEeccCCce---eEEEEEEEEEEE
Q 017401 258 TSSSYYVGLGNLNSEE---VEVQLNLRLRAF 285 (372)
Q Consensus 258 ~ss~YYVavgNlN~~d---Vev~Lni~V~a~ 285 (372)
+.-.|.+-+.|..+.. ..|.+++.+...
T Consensus 71 ~~G~y~iCf~n~~~~~~~~~~v~~~~~~~~~ 101 (183)
T PF01105_consen 71 ESGEYQICFDNSSSSFSPSKRVSFDIDVGNE 101 (183)
T ss_dssp -------------------------------
T ss_pred cCCCEEEEEEcCCCCccccEEEEEEEEEeec
Confidence 9999999999998764 777777777543
No 3
>PF10342 GPI-anchored: Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; InterPro: IPR018466 This entry represents glycoproteins involved in cell wall (1-->6)-beta-glucan assembly. In yeast a null mutation leads to severe growth defects, aberrant multi-budded morphology, and mating defects [, ]. The entry includes DRMIP and Hesp-379, which are involved in both fruiting body formation and in host attack respectively. Hesp-379 is a haustorially expressed secreted protein; the haustorium being the small sucker that penetrates host tissue [].
Probab=73.10 E-value=19 Score=27.83 Aligned_cols=68 Identities=16% Similarity=0.334 Sum_probs=45.3
Q ss_pred eeccceEEEEEEEecC-CCcEEEEEEecCccccccccCCCCCCCcceeeEEec-ccEEEEEEec----ccceEEEEeccC
Q 017401 197 LNKGSQINISYSVKSP-GSSVFLIIAQGNEGLRQWLFDPTFPNTTLSWNVIQG-SGVIHQHIFT----SSSYYVGLGNLN 270 (372)
Q Consensus 197 LNKGS~I~IsYsv~s~-~SsL~LvIaqG~~~~~~Wl~dPt~PnttlSWnvI~G-~G~ieq~I~~----ss~YYVavgNlN 270 (372)
+..|+.+.|+|+.... ...+.+.+.+|......=. .++ -.-+.+ .|..+.++.. ++.|+|.+.|..
T Consensus 9 ~~~g~~~~I~W~~~~~~~~~~~I~L~~g~~~~~~~~-------~~i-a~~v~~~~gs~~~~~p~~l~~~~~Y~i~~~~~~ 80 (93)
T PF10342_consen 9 WTAGQPITITWTSDGTDPGNVTIYLCNGNNTNLNFV-------QTI-ASNVSNSDGSYTWTIPSDLPSGGDYFIQIVNSS 80 (93)
T ss_pred EECCCcEEEEEeCCCCCCcEEEEEEEcCCCCCccee-------EEE-EecccCCCCEEEEEcCCCCCCCCcEEEEEEECC
Confidence 5678999999999864 7889999999988222100 111 111222 3777777643 678999999766
Q ss_pred Cc
Q 017401 271 SE 272 (372)
Q Consensus 271 ~~ 272 (372)
..
T Consensus 81 ~~ 82 (93)
T PF10342_consen 81 NN 82 (93)
T ss_pred CC
Confidence 55
No 4
>cd04971 Ig_TrKABC_d5 Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC. TrkABC_d5: the fifth domain of Trk receptors TrkA, TrkB and TrkC, this is an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share significant sequence homology and domain organization. The first three domains are leucine-rich domains. The fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrkA, Band C mediate the trophic effects of the neurotrophin Nerve growth factor (NGF) family. TrkA is recognized by NGF. TrkB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. TrkC is recognized by NT-3. NT-3 is promiscuous as in some cell systems it activates TrkA and TrkB receptors. TrkA is a receptor foun
Probab=49.79 E-value=47 Score=26.01 Aligned_cols=67 Identities=18% Similarity=0.186 Sum_probs=35.8
Q ss_pred CCCCCcceeeEEecccEEEEEEecccceEEEEecc--CCceeEEEEEEEEEEEEeeccCceeeeecCCC----ceEEEEe
Q 017401 235 TFPNTTLSWNVIQGSGVIHQHIFTSSSYYVGLGNL--NSEEVEVQLNLRLRAFLYNTSDAYYKCTFADG----LCSLSVL 308 (372)
Q Consensus 235 t~PnttlSWnvI~G~G~ieq~I~~ss~YYVavgNl--N~~dVev~Lni~V~a~lYdTt~A~y~CS~~ng----~Ctl~L~ 308 (372)
++|..+..|.- +|. .|..++...+-.... +.......|.| +..- ......|+|.-.|. .++++|.
T Consensus 9 G~P~P~v~W~k---~g~---~i~~~~~~~~~~~~~~~~~~~~~~~L~I--~~~~-~~D~G~YtC~A~N~~G~~~~~~~~~ 79 (81)
T cd04971 9 GNPKPTLTWYH---NGA---VLNESDYIRTEIHYEVTTPTEYHGCLQF--DNPT-HVNNGNYTLVASNEYGQDSKSISAH 79 (81)
T ss_pred eeCCCcEEEEE---CCE---ECcCCCceeEEEEeecccccccEEEEEE--CCCC-cccCeEEEEEEEeCCCCeeeEEEee
Confidence 57888899976 553 233444333322221 11222223333 2111 12247899999876 6888888
Q ss_pred eC
Q 017401 309 FP 310 (372)
Q Consensus 309 fp 310 (372)
|+
T Consensus 80 ~~ 81 (81)
T cd04971 80 FM 81 (81)
T ss_pred eC
Confidence 75
No 5
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=34.36 E-value=2e+02 Score=21.62 Aligned_cols=64 Identities=14% Similarity=0.223 Sum_probs=37.7
Q ss_pred eEEEEeeccceEEEEEEEecCCCcEEEEEEecC-ccccccccCCCCCCCcceeeEEecc-cEEEEEEecccceEEEEe
Q 017401 192 EWIIYLNKGSQINISYSVKSPGSSVFLIIAQGN-EGLRQWLFDPTFPNTTLSWNVIQGS-GVIHQHIFTSSSYYVGLG 267 (372)
Q Consensus 192 eW~y~LNKGS~I~IsYsv~s~~SsL~LvIaqG~-~~~~~Wl~dPt~PnttlSWnvI~G~-G~ieq~I~~ss~YYVavg 267 (372)
-|.+-+++|.+++|+ +......+-|.+.... ..+.+.-..++ + .|+ -.|+++..+.-.|||.|.
T Consensus 4 ~y~f~v~ag~~l~i~--l~~~~~d~dl~l~~~~g~~~~~~d~~~~-~---------~~~~~~i~~~~~~~GtYyi~V~ 69 (70)
T PF04151_consen 4 YYSFTVPAGGTLTID--LSGGSGDADLYLYDSNGNSLASYDDSSQ-S---------GGNDESITFTAPAAGTYYIRVY 69 (70)
T ss_dssp EEEEEESTTEEEEEE--ECETTSSEEEEEEETTSSSCEECCCCTC-E---------TTSEEEEEEEESSSEEEEEEEE
T ss_pred EEEEEEcCCCEEEEE--EcCCCCCeEEEEEcCCCCchhhheecCC-C---------CCCccEEEEEcCCCEEEEEEEE
Confidence 477889999997776 4443334555555544 22222222221 0 112 348888899999999873
No 6
>cd05737 Ig_Myomesin_like_C C-temrinal immunoglobulin (Ig)-like domain of myomesin and M-protein. Ig_Myomesin_like_C: domain similar to the C-temrinal immunoglobulin (Ig)-like domain of myomesin and M-protein. Myomesin and M-protein are both structural proteins localized to the M-band, a transverse structure in the center of the sarcomere, and are candidates for M-band bridges. Both proteins are modular, consisting mainly of repetitive Ig-like and fibronectin type III (FnIII) domains. Myomesin is expressed in all types of vertebrate striated muscle; M-protein has a muscle-type specific expression pattern. Myomesin is present in both slow and fast fibers; M-protein is present only in fast fibers. It has been suggested that myomesin acts as a molecular spring with alternative splicing as a means of modifying its elasticity.
Probab=33.49 E-value=2.3e+02 Score=21.99 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=11.2
Q ss_pred EeeccceEEEEEEEec
Q 017401 196 YLNKGSQINISYSVKS 211 (372)
Q Consensus 196 ~LNKGS~I~IsYsv~s 211 (372)
-...|.++++.+.+..
T Consensus 12 ~v~~G~~v~L~C~v~G 27 (92)
T cd05737 12 TIMEGKTLNLTCTVFG 27 (92)
T ss_pred EEeCCCcEEEEEEEEe
Confidence 3567788888777664
No 7
>cd05898 Ig5_KIRREL3 Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2). Ig5_KIRREL3: the fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1). These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development. Neph1 and 2 may mediate axonal guidance and synapse formation in certain areas of the CNS. In the kidney, they participate in the formation of the slit diaphragm.
Probab=33.16 E-value=1.1e+02 Score=25.53 Aligned_cols=18 Identities=17% Similarity=0.316 Sum_probs=14.7
Q ss_pred EEEeeccceEEEEEEEec
Q 017401 194 IIYLNKGSQINISYSVKS 211 (372)
Q Consensus 194 ~y~LNKGS~I~IsYsv~s 211 (372)
+.+-++|.+.++.+.|.+
T Consensus 10 s~~~~~G~~~~L~C~~~s 27 (98)
T cd05898 10 VQYAVRGERGKVKCFIGS 27 (98)
T ss_pred eEEEeCCCcEEEEEEEcc
Confidence 456789999999999876
No 8
>KOG1692 consensus Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.17 E-value=4.2e+02 Score=25.79 Aligned_cols=93 Identities=16% Similarity=0.154 Sum_probs=64.4
Q ss_pred eEEEEecCCCcceEEEEeeccceEEEEEEEecCCCcEEEEEEecCccccccccCCCCCCCcceeeEEecccEEEEEEecc
Q 017401 180 KIIVSVPADSHQEWIIYLNKGSQINISYSVKSPGSSVFLIIAQGNEGLRQWLFDPTFPNTTLSWNVIQGSGVIHQHIFTS 259 (372)
Q Consensus 180 s~~~~V~s~ShKeW~y~LNKGS~I~IsYsv~s~~SsL~LvIaqG~~~~~~Wl~dPt~PnttlSWnvI~G~G~ieq~I~~s 259 (372)
.+.+++.++..+=+.-.|++|.++-++|.|...+-.-.=+.+-|-++=.=-. +.++ -+|+.+++..++
T Consensus 20 ~~~is~~ah~eeCf~e~~~~gd~~~vsF~v~~gg~~~vd~~I~gP~~~~i~~---~~~~---------ssgk~tF~a~~~ 87 (201)
T KOG1692|consen 20 GYGISLDAHEEECFFENLEEGDKLSVSFEVIDGGFLGVDVEITGPDGKIIHK---GKRE---------SSGKYTFTAPKK 87 (201)
T ss_pred heeEEEccchhhhHhhhhccCCEEEEEEEEecCCccceeEEEECCCCchhhh---cccc---------cCceEEEEecCC
Confidence 4567788888777888899999999999999864433334444544322111 2222 269999999999
Q ss_pred cceEEEEeccCC--ceeEEEEEEEEEE
Q 017401 260 SSYYVGLGNLNS--EEVEVQLNLRLRA 284 (372)
Q Consensus 260 s~YYVavgNlN~--~dVev~Lni~V~a 284 (372)
-.|-.-+.|=++ +.=+|+.+|.+--
T Consensus 88 G~Y~fCF~N~~s~mtpk~V~F~ihvg~ 114 (201)
T KOG1692|consen 88 GTYTFCFSNKMSTMTPKTVMFTIHVGH 114 (201)
T ss_pred ceEEEEecCCCCCCCceEEEEEEEEee
Confidence 999999999888 4445555555443
No 9
>PF12124 Nsp3_PL2pro: Coronavirus polyprotein cleavage domain; InterPro: IPR022733 This domain is found in SARS coronaviruses, and is about 70 amino acids in length. It is found associated with various other coronavirus proteins due to the polyprotein nature of most viral translation. PL2pro is a domain of the non-structural protein nsp3. The domain performs three of the cleavages required to separate the translated polyprotein into its distinct proteins. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity, 0016788 hydrolase activity, acting on ester bonds, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2KAF_A 2KQW_A.
Probab=29.75 E-value=25 Score=28.08 Aligned_cols=20 Identities=35% Similarity=0.836 Sum_probs=15.3
Q ss_pred CCCcceEEE----------EeeccceEEEEEE
Q 017401 187 ADSHQEWII----------YLNKGSQINISYS 208 (372)
Q Consensus 187 s~ShKeW~y----------~LNKGS~I~IsYs 208 (372)
++|+|.|+| ||.+|.+ |-|.
T Consensus 12 agsy~dwsysgqrtelgveflkrgdk--ivyh 41 (66)
T PF12124_consen 12 AGSYRDWSYSGQRTELGVEFLKRGDK--IVYH 41 (66)
T ss_dssp HTEETTEE----EETTEEEEEEETTE--EEEE
T ss_pred cccccccccccceehhhhHHHhcCCE--EEEE
Confidence 578999988 8999998 5554
No 10
>cd05870 Ig5_NCAM-2 Fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). Ig5_NCAM-2: the fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is organized similarly to NCAM , including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule.
Probab=29.27 E-value=2.6e+02 Score=21.97 Aligned_cols=15 Identities=7% Similarity=0.098 Sum_probs=10.3
Q ss_pred eeccceEEEEEEEec
Q 017401 197 LNKGSQINISYSVKS 211 (372)
Q Consensus 197 LNKGS~I~IsYsv~s 211 (372)
..+|+++.+.+.|..
T Consensus 13 ~~~G~~v~l~C~~~G 27 (98)
T cd05870 13 TVENGAATLSCKAEG 27 (98)
T ss_pred EcCCCcEEEEEeccc
Confidence 456778778776654
No 11
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=27.97 E-value=2.6e+02 Score=20.82 Aligned_cols=17 Identities=12% Similarity=0.436 Sum_probs=13.0
Q ss_pred EEeeccceEEEEEEEec
Q 017401 195 IYLNKGSQINISYSVKS 211 (372)
Q Consensus 195 y~LNKGS~I~IsYsv~s 211 (372)
.....|.++.+.+.+..
T Consensus 10 ~~v~~G~~~~l~c~~~~ 26 (90)
T PF07679_consen 10 VTVKEGESVTLECEVSG 26 (90)
T ss_dssp EEEETTSEEEEEEEEEE
T ss_pred EEEeCCCEEEEEEEEEe
Confidence 45677888888888876
No 12
>PRK09774 fec operon regulator FecR; Reviewed
Probab=23.77 E-value=5.2e+02 Score=25.38 Aligned_cols=66 Identities=15% Similarity=0.234 Sum_probs=43.8
Q ss_pred ccceeeeEEEEecCCCcceEEEEeeccceEEEEEEEecCCCcEEEEEEecCccccccccCC-CCCCCcceeeEEecccEE
Q 017401 174 VSTWSEKIIVSVPADSHQEWIIYLNKGSQINISYSVKSPGSSVFLIIAQGNEGLRQWLFDP-TFPNTTLSWNVIQGSGVI 252 (372)
Q Consensus 174 ~t~Wses~~~~V~s~ShKeW~y~LNKGS~I~IsYsv~s~~SsL~LvIaqG~~~~~~Wl~dP-t~PnttlSWnvI~G~G~i 252 (372)
.|.=.|.+.+.+|-+| .-+||.+|.|++.|+-+ .=.+-+.+|+--|.- ..|| ..| .-|-.|.|.+
T Consensus 112 ~T~~Ge~r~v~L~DGS----~v~Ln~~S~l~~~~~~~----~R~v~L~~Gea~F~V-a~d~~~rP-----F~V~t~~~~v 177 (319)
T PRK09774 112 RTAKGEVSRQRLEDGS----LLTLNTQSAVDVRFDAH----QRTVRLWYGEIAITT-AKDALQRP-----FRVLTRQGQL 177 (319)
T ss_pred ecCCCceEEEEcCCCC----EEEEcCCCeEEEeecCC----eeEEEEeccEEEEEE-cCCCCCCC-----EEEEeCCcEE
Confidence 3555688899999988 57899999999877632 223444688777664 3455 344 3333477776
Q ss_pred E
Q 017401 253 H 253 (372)
Q Consensus 253 e 253 (372)
+
T Consensus 178 ~ 178 (319)
T PRK09774 178 T 178 (319)
T ss_pred E
Confidence 5
No 13
>PLN02899 alpha-galactosidase
Probab=23.10 E-value=79 Score=35.03 Aligned_cols=54 Identities=17% Similarity=0.258 Sum_probs=39.2
Q ss_pred ccceEEEEeccCCceeEEEEEEEEEEEEeeccCceee-eecCCCceEEEEeeCCCcEEEEe
Q 017401 259 SSSYYVGLGNLNSEEVEVQLNLRLRAFLYNTSDAYYK-CTFADGLCSLSVLFPNGNAIVLT 318 (372)
Q Consensus 259 ss~YYVavgNlN~~dVev~Lni~V~a~lYdTt~A~y~-CS~~ng~Ctl~L~fp~tn~vVLT 318 (372)
+-+||||+=|||++..+++.. +=|..|+.-. =.....+|+..=.+.++++++++
T Consensus 559 ~g~~y~~~fnl~~~~~~~~~~------~~~~~~~~~~~~~~~~~~c~~~e~w~~~~~~~~~ 613 (633)
T PLN02899 559 KGEIYVAFFNLNQEKTKISAK------ISDLAKALPGSKNLRTSSCTGHEVWSGKDFGVIK 613 (633)
T ss_pred CccEEEEEEecCccceeEEEE------hhHhHhhccccccccccccceEEeccCCCccccc
Confidence 458999999999998876544 4455555444 22334489999999999988764
No 14
>PF03351 DOMON: DOMON domain; InterPro: IPR005018 The DOMON domain is an 110-125 residue long domain which has been identified in the physiologically important enzyme dopamine beta-monooxygenase and in several other secreted and transmembrane proteins from both plants and animals. It has been named after DOpamine beta-MOnooxygenase N-terminal domain. The DOMON domain can be found in one to four copies and in association with other domains, such as the Cu-ascorbate dependent monooxygenase domain, the epidermal growth factor domain, the trypsin inhibitor-like domain (TIL), the SEA domain and the Reelin domain. The architectures of the DOMON domain proteins strongly suggest a function in extracellular adhesion []. The sequence conservation is predominantly centred around patches of hydrophobic residues. The secondary structure prediction of the DOMON domain points to an all-beta-strand fold with seven or eight core strands supported by a buried core of conserved hydrophobic residues. There is a chraracteristic motif with two small positions (Gly or Ser) corresponding to a conserved turn immediately C-terminal to strand three. It has been proposed that the DOMON domain might form a beta-sandwich structure, with the strands distributed into two beta sheets as is seen in many extracellular adhesion domains such as the immunoglobulin, fibronectin type III, cadherin and PKD domains [].
Probab=21.85 E-value=1.4e+02 Score=24.18 Aligned_cols=30 Identities=27% Similarity=0.491 Sum_probs=19.6
Q ss_pred CCcceeeEEecccEEEEEEe--cccceEEEEe
Q 017401 238 NTTLSWNVIQGSGVIHQHIF--TSSSYYVGLG 267 (372)
Q Consensus 238 nttlSWnvI~G~G~ieq~I~--~ss~YYVavg 267 (372)
+-.++|.+...+..|++++. .+..-|+|+|
T Consensus 4 ~~~l~w~~~~~~~~i~~~l~~~~~~~~w~aiG 35 (124)
T PF03351_consen 4 NFSLSWTVDGDNNTIEFELTGPANTNGWVAIG 35 (124)
T ss_pred eEEEEEEEECCCCEEEEEEEeccCCCCEEEEE
Confidence 34567777777777777777 4436666665
No 15
>TIGR02229 caa3_sub_IV caa(3)-type oxidase, subunit IV. This model represents a small set of proteins with weak similarity to the sequences in Pfam family pfam03626, which describes the cytochrome C oxidase subunit IV.
Probab=21.30 E-value=22 Score=30.10 Aligned_cols=32 Identities=9% Similarity=0.103 Sum_probs=27.6
Q ss_pred ceEEEEEecceeEeeehhHHHHHHHHHHHHHHH
Q 017401 330 NWQVRVSYEPRWLSYVVGICIFIPHFLLVAYHS 362 (372)
Q Consensus 330 ~WyVklSY~PRWitYIig~G~~~~illLl~~~~ 362 (372)
.+++++.|.||...+++..|+++ +.+|+.+-+
T Consensus 55 ~~FMHLk~e~~l~r~~~~~~~~~-l~i~~~~t~ 86 (92)
T TIGR02229 55 LYFMHLKRAHALLRLASAVAFAI-LAILFVITH 86 (92)
T ss_pred HHHHhhccccchHHHHHHHHHHH-HHHHHHHHH
Confidence 45788999999999999999999 888887654
Done!