Question

: Use P04637 as the query for PSI-BLAST search, select the nr database, exclude all primate organism(s), and run many iterations until obtaining the hit of Electrophorus electricus. (revise with more limitation of information) Report for P04637.......: Use P04637 as the query for PSI-BLAST search, select the nr database, exclude all primate organism(s), and run many iterations until obtaining the hit of Electrophorus electricus. (revise with more limitation of information) Report for P04637 a. Locus name & gene name b. Type of molecule & its length c. Scientific name & common name of organism Report for Electrophorus electricus alignment d. Number of iteration until obtaining the hit of Electrophorus electricus e. Bit score, raw score, E-value f. Identity, positive/similarity, gap g. The range length

Answer 1

Question

P04637 is cellular tumor antigen p53 is present in human. When this protein is used as a query against Electrophorus electricus. The result of the PSI blast is:

Figure: PSI BLAST Result

select all 14 sequences selected PSI-BLAST iteration 2 Max Total Query Evalue Select for PSI Per. Ident Used to Newly build added Description Accession score score cover blast PSSM > > ✓ > > > > ✓ > > > > ✓ > cellular tumor antigen p53 isoform X 578 cellular tumor antigen p53 isoform X 572 cellular tumor antigen p53 isoform X 567 cellular tumor antigen p53 isoform X 549 cellular tumor antigen p53-like (Elect 508 tumor protein 63-like isoform XZ (Ele 480 tumor protein p73-like [Electrophoru: 469 tumor protein 63-like isoform X5 (Ele 465 tumor protein 63-like isoform X2 [Ele 468 tumor protein 63-like isoform X1 (Ele 468 tumor protein 63-like isoform X6. [Ele 459 tumor protein 63-like isoform X4 (Ele 461 tumor protein 63-like isoform X3 (Ele 461 cellular tumor antigen p53 isoform X 397 578 99% 572 99% 567 99% 549 97% 508 97% 83% 469 93% 465 80% 468 82% 468 82% 459 80% 461 80% 461 80% 397 63% 0.0 48.50% XP_0268542161 0.0 48.14% XP_0268542151 0.0 44.91% XP_0268542141 0.0 45.41% XP_0268542171 0.0 40.99% XP_0268657521 1e-168 42.26% XP_026863526.1. 1e-161 36.92% XP_0268670911 3e-161 43.03% XP_026863523.1 4e-161 41.92% XP_0268635201 4e-161 41.92% XP_026863519.1 7e-159 42.81% XP_026863525.1 1e-158 42.63% XP_0268635221 2e-158 42.63% XP_026863521.1 1e-138 48.26% XP_026854218.1 > OOOOOOOOOOOO > ✓ > > > > > > > >

Figure: Descriptive result

cellular tumor antigen p53 isoform X3 (Electrophorus electricus) Sequence ID:XP_026854216.1 Length: 409 Number of Matches: 1 Range 1:33 to 409 Genpept Graphics Next Match Previous Match Related Score Expect Method Identities Positives Information 578 bits(1490) 0.0 Composition-based stats. 194/400(49%) 249/400(62%) Gener ated gene details Query 3 EPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAM-DDLML Genome Data E + + +EP +F+DLW N++ PP + +D + +D+ Sbjct 33 ETEKEGLMEEPTESQEFADLWS-QNLMVPKPDDSSWGNDNEF Viewer - aligned genomic context Query 61 DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTY EPE V PP+ + PA S+VP Y G+YFLF S TAK Sbjet 83 -EQPLFSE--VQMEPPQPSTSPPA--------STVPVTTDYPGAYDFTL Query 121 SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAI SVTCTYSP LNK+FCQLAKTCPVQ+ V+S PP G +RA A+YK+S+H+ EV Sbict 130 SVTCTYSPDLNKLFCOLAKTCPVOMEVNSLPPLGAVL Query 181 RCSD-SDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPE + + + +GLAPP HL+RVEGNR Y +D NT RHSV+VPYEPP+VGS+CTT+ Sbjct 190 KTQETNNGLAPPGHLLRVEGNSRAIYQEDDNTLRHSVLVPYEPPI Query 240 SSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRR1 SSCMGGM+RRPILTIITLE GLLGR SFEVRVCACPGRDR+ EE N +K+ Sbjct 250 SSCMGGMSRRPILTIITLETQDGQLLGRRSFEVRVCACPGRDRKIE Query 299 LPPGSTKRALPNNTSSSPOPKKKPL-DGEYFTLQIRGRERFEMFR PG KR +P+ +S+ K + E +TLQ+RG+ER+EM +++N+LELD A Sbjct 310 KTPGPAKRNMPPHPEASKKAKTSSTSNEELYTLQVRGKERYEML Query 356 GKEPGGSRAHSSHLKSKKGQS--TSRHKKLMFKTEGPDSD 393 E + + KKG + R K+LM KE DSD Sbjct 370 DVEKYRQKLLTRSRKEKDGAAPEPKRGKRLMVKEEKSDSD 409

Figure: Locus, gene name

TIUVI. III.I .YUV LOCUS XP_026854216 409 aa linear VRT 08-NOV-2018 DEFINITION cellular tumor antigen p53 isoform X3 Electrophorus electricus). ACCESSION XP_026854216 VERSION XP_026854216.1 DBLINK BioProject: PRJNA504029 DESOURCE REFSEQ: accession XM 026998415.1 KEYWORDS RefSeq. SOURCE Electrophorus electricus (electric eel) ORGANISM Electrophorus electricus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Gymnotiformes: Gymnotoidei; Gymnotidae; Electrophorus. COMMENT MODEL REFSEO: This record is predicted by automated computational analysis. This record is derived from a genomic sequence (NW 020825969.1) annotated using gene prediction method: Gnomon. Also see: Documentation of NCBI's Annotation Process ##Genome-Annotation-Data-START## Annotation Provider : NCBI Annotation Status Full annotation Annotation Name Electrophorus electricus Annotation Release 100 Annotation Version : 100 Annotation Pipeline : NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 8.1 Annotation Method : Best-placed RefSeg; Gnomon Features Annotated Gene; mRNA; CDS; ncRNA ##Genome-Annotation-Data-END## COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..409 organism="Electrophorus electricus" isolate="MRS-EE1" /db_xref="taxon:8005" /chromosome="Unknown" /tissue_type="main electric organ" Protein 1..409 /product="cellular tumor antigen p53 isoform X3" /calculated_mol_wt=46009 Region 104..299 /region name="P53" /note="P53 DNA-binding domain; pfam00870" /db_xref="CDD:307150" Site order(185,188,248,252) /site_type="other" note="zinc binding site [ion binding)" /db_xref="CDD:176262" order(186..188,190) /site_type="other" /note="dimerization site (polypeptide binding" /db_xref="CDD:176262" Site order(249,251,258,283,285..287,290) /site_type="DNA binding" /note="DNA binding site (nucleotide binding)" /db_xref="CDD:176262" Region 332..367 /region_name="P53_tetramer" /note="P53 tetramerisation motif: pfam07710" /db_xref="CDD:311579" CDS 1..409 gene="tp53" coded_by="XM_026998415.1:167..1396" /db_xref="GeneID:113570174" ORIGIN 1 mngrvhhlge dhisvrksfl ellyplsctn eletekeglm eeptesqefa dlwsqnlmvp 61 kpddsswgnd neftledlhd mleqplfsev qmeppqpsts ppastvpvtt dypgaydfti 121 rfqqsstaks vtctyspdin klfcqlaktc pvqmevnslp plgavirata vykksehvae

a. The locus as given in the result is XP_026854216.

The gene name is cellular tumor antigen p53 isoform

b. The type of molecule is protein and its length is 409 amino acid.

c. Scientific name is

Electrophorus electricus

Common name is electric eel

d. Number of iteration 2

e.

Range 1:33 to 409 Genpept Graphics Next Match Previous Match Related Information Score Expect Method Identities Positives 578 bits(1490) 0.0 Composition-based stats. 194/400( 49%) 249/400(62%) Geng2, forgiated