2.)
inparanoid.o1481440:
BBH:1408
prozentual :
1408/4451 = 0.32 file CP000393.faa
1408/2892 = 0.49 file CP000435.faa
paralog:
1527 -1408 in-paralogs from CP000393.faa = 119
1445 - 1408 in-paralogs from CP000435.faa = 37
inparanoid.o1481441
BBH: 1338
1338/4451 = 0.3 file CP000393.faa
1338/2997 = 0.45file CP000554.faa
paralog :
1468 - 1338 = 130 in-paralogs from CP000393.faa
1381 - 1338 = 43 in-paralogs from CP000554.faa
inparanoid.o1481442:
BBH : 1792
1792/ 2892 sequences in file CP000435.faa = 0.62
1792 /2997 sequences in file CP000554.faa = 0.6
paralog:
1818 in-paralogs from CP000435.faa -1792 = 26
1832 in-paralogs from CP000554.faa-1792 = 40
Aufgabenteil 2:
1.) 1.Protein :
hypothetical protein Tery_0047 [Trichodesmium eryth
raeum IMS101]
show homologes -> viele homologe, E-value ca.: E-10
homologe zB
- GUN4-like PriAC=Q10Z72 [Trichodesmium erythraeum (strain IMS101)] OrderedLocusNames=Tery_3350; e-value: 9.52E-128 identity: 47.7%
- COG0457: FOG: TPR repeat [Nostoc punctiforme PCC 73102] ||Version: ZP_00106722.1 GI:2312475 ||DBSource: REFSEQ: accession NZ_AAAY02000091.1
e-value : 1.9E-117 identity : 45.2%
- hypothetical protein Npun02004668 [Nostoc punctiforme PCC 73102] ||Version: ZP_00108944.1 GI:2312706 ||DBSource: REFSEQ: accession NZ_AAAY02000041.1 e-value : 2.99E-109 identity: 42.4%
-> uniprot/swissprot:
nicht mehr so gute homologe, bester e-value : 1.22E-05 identity: 23.5%
protein ID: CNKR2_MOUSE : Connector enhancer of kinase suppressor of ras 2 (Connector enhancer of KSR2) (CNK2) PriAC=Q80YA9 SecAC=Q80TP2 [Mus musculus (Mouse)] Name=Cnksr2; Synonyms=Kiaa0902;
2.Protein :
hypothetical protein Tery_0056 [Trichodesmium eryth
raeum IMS101]
für dieses protein sehr viele homologe :
e-value : 1.59E-145 identity: 99.1%
Hypothetical protein PriAC=Q10YL2 [Trichodesmium erythraeum (strain IMS101)] OrderedLocusNames=Tery_3580;
oder COG5659: FOG: Transposase [Nostoc punctiforme PCC 73102] ||Version: ZP_00107548.1 GI:2312562 ||DBSource: REFSEQ: accession NZ_AAAY02000097.1
e-value : 2.22E-103 identity: 68.4%
mit swissprot:
wieder keine homologe, bestes "homologes protein" : e-value : 1.04E-04 identity: 23.7% Transposase for insertion sequence element IS231C PriAC=P12250 [Bacillus thuringiensis subsp. berliner]
3.Protein : hypothetical protein sync_0018 [Synechococcus sp. C
C9311] query length : 1111aa
auch viele homologe, gute e-values aber schlechte identity
zB e-value: 8.97E-51 identity: 25.5% für hypothetical protein WH7805_09564 [Synechococcus sp. WH 7805] ||Version: ZP_01124897.1 GI:8880938 ||DBSource: REFSEQ: accession NZ_AAOK01000005.1
e-value : 4.61E-34 identity: 23.4%
für Putative hemagglutinin/hemolysin-related protein PriAC=Q1R1I9 [Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768)] OrderedLocusNames=Csal_0055;
mit swissprot: viele homologe, e-values alle besser als E-10 !!
- Mesocentin precursor PriAC=Q09165 SecAC=Q8MTB9 [Caenorhabditis elegans] Name=dig-1; ORFNames=K07E12.1; e-value : 5.36E-20 identity: 25%
alignment anschaun : 13100aa
auf swissprotseite und dann abstracts durchgelesen nach function :
"Identification of the hydrophobic glycoproteins of Caenorhabditis elegans"
Hydrophobic proteins such as integral membrane proteins are difficult to separate, and therefore to study, at a proteomics level. However, the Asn-linked (N-linked) carbohydrates (N-glycans) contained in membrane glycoproteins are important in differentiation, embryogenesis, inflammation, cancer and metastasis, and other vital cellular processes. Thus, the identification of these proteins and their sites of glycosylation in a well-characterized model organism is the first step toward understanding the mechanisms by which N-glycans and their associated proteins function in vivo.
anderer abstract: "The C. elegans gene dig-1 encodes a novel adhesion molecule of the immunoglobulin superfamily that functions during sensory process development in the nervous system.";
Unpublished observations (APR-2006).
Funktion : Encodes an adhesion molecule involved in sensory map formation. Functions during sensory process development in the nervous system.
Subcellular location : Secreted protein; extracellular space; extracellular matrix.
# SIMILARITY: Contains 2 EGF-like domains.
# SIMILARITY: Contains 11 fibronectin type-III domains.
# SIMILARITY: Contains 7 Ig-like C2-type (immunoglobulin-like) domains.
# SIMILARITY: Contains 1 Sushi (CCP/SCR) domain.
# SIMILARITY: Contains 4 VWFA domains.
- Halomucin precursor PriAC=Q18DN4 [Haloquadratum walsbyi (strain DSM 16790)] Name=hmu; OrderedLocusNames=HQ1081A; e-value : 4.66E-15 identity: 21.9%
sequence length : 9159aa
references: nur nucleotide sequence artikel, nicht so gut.
bei comments:
* FUNCTION: May protect the organism from dessication stress. May also contribute to the rigidity and maintenance of the unique square cell morphology of H.walsbyi.
* SUBCELLULAR LOCATION: Secreted protein (Potential).
* PTM: Probably glycosylated with sugar containing sialic acid. This may further contribute to its overall negative charge, thereby creating an aqueous shield covering the cells.
* SIMILARITY: Contains 2 C-type lectin domains.
* SIMILARITY: Contains 1 cadherin domain.
- Hypothetical protein yeeJ PriAC=P76347 SecAC=P94750 [Escherichia coli] Name=yeeJ; OrderedLocusNames=b1978, JW5833; e-value : 2.54E-14 identity: 21.2%
sequence length : 2358 aa
ein hypothetical protein , viele references ( 4stück)
aber alle blöd, weil nur nucleotide sequence , keine information über die function : nur :
* SIMILARITY: Belongs to the intimin/invasin family.
* SIMILARITY: Contains 13 Big-1 (bacterial Ig-like domain 1) domains.
Summary:
hypothetical protein sync_0048 [Synechococcus sp. C
C9311]
Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. It catalyzes the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure.
LOX1_LENCU
1.7E-03
35.6%
2.2) STRING:
3.Protein : aus SIMAP fanden wir raus dass es an Rezoptoren codiert , aus STRING : der beste hit : SAV2654
Serine-threoinine rich antigen (2271 aa)
(Staphylococcus aureus Mu50) , ist auch ein Antigen, somit übereinstimmen die Funktionen
1.Protein:
bei String bester hit : selber hypothetical protein
predicted interaktionspartner: siehe bild database_Rro
insg: keine funktion gefunden
2.Protein: bester hit : Transposase -> identisch mit SIMAP, somit ist die Funktion von dem Protein eine Transposase, auch die Interaktionspartner sind Transpsasen
4.Protein : bei string kein homologe gefunden
5.Protein : Hypothetical protein P9303_02741 [Prochlorococcus m
arinus str. MIT 9303] bei SIMAP wurde nichts gefunden , bei string schon -> sehr viele homologe mit sehr guten e-values E-66, Funktion nicht eindeutig klassifizier bar, da sehr viele untershciedliche interaktionspartner vorhergesagt wurden . Der beste hit selber ist ein precursor.
6.Protein : Hypothetical protein P9303_02771 [Prochlorococcus m
arinus str. MIT 9303] einziges homologe : SYNW1273
Possible-TPR Domain containing protein (781 aa)
(Synechococcus sp. WH8102)
interaktionspartner sind rnpA
Ribonuclease P protein component (EC 3.1.26.5) (RNaseP protein) (RNase P protein) und SYNW2212
Hypothetical protein precursor (145 aa). -> funktion nicht eindeutig, bei SIMAP nichts gefunden