GOS 985020

From Metagenes
Warning: this metagenomic sequence has been carefully annotated by students during bioinformatics assignments. These quality annotations are therefore the result of a teaching exercise that you are most welcome to amend and extend if necessary!


Sequence
CAMERA AccNum : JCVI_READ_1091118859800
Annotathon code: GOS_985020
Sample :
  • GPS :9°9'52n; 79°50'10w
  • Panama Canal: Lake Gatun - Panama
  • Fresh Water (-2m, 28.6°C, 0.1-0.8 microns)
Authors
Team : BSB06CIIT
Username : aeman
Annotated on : 2009-06-06 13:57:12
  • zahra aeman

Synopsis

Genomic Sequence

>JCVI_READ_1091118859800 GOS_985020 Genomic DNA
AAAAGAAAATGGAAATGATGAGAAAGAGAGCCGCCGCGAAAAAGTAAGGCAAACAGTTAGAGACGCAAAGATTCAAAGAAGAATCCAAGCGGCAAAAGAT
AGAAAAAAGAATTAAGTTTCCATAATCCTAAGAAATCAGACAAAGCCCAGCCTAAAAACTGGGCTTTGTTCTTATTAAGAATCTAATTACTCCAGAGGTA
TTCTAATGAATCTTGAAGAACTAATTGAAAGCCATTTTGCTCCAAAGAAAGGAAACGATCTTATTATTCAACTGATAGAGCAAAGATTAGGCAATTCTTC
TTTGTTGTTTGAAGCAGAAGAACAAGGCGGCGGTAATCTTTTCTATGGCGATGAAAGAACATTAAAACTACCAGTCATTAGATTTAGCAAAAATATTGGT
AGAAAAAATACATATGATAGAAGCTTTTTAGATCTTGTTGTTCATAATCTAAAAAATATTTCTGGAAAAGACGGGGAACTATTACAAACAAGAATTGCAT
CTTTCCAAAAATTCTTTAATGGCAACTTTGAAGGCGAACTGGATATCTCAAATATTATTTCATATTGCATGATCTCTGAAGCTTTCTATCACTTGATTAA
TGATTATGATGCTTCAACGGCTGGAGACTTATTCGAGCCATTATTCGCAGCATTATTTGATGGAACAATTGTTGAAGCTCCAGAGGGAAAAAGAAACTAT
GCAGTAGAAGATGTTCAAATCGCATCAAAAGAAGGGCAGATACAAGATTTAAAGGATGTAAGCTTAAAACTTCTTTCTCCACGGGGAAATGTTTCTCAAA
ATTATAAAAATATATTAGAGAAATTAGTAAAGAGTGGAGGTATTTTATATGTTGTGGCGTATAAAGAAAAACAAAGCAACATTTCCTTTTATGCTCTTGA
TTTAACTCCAAATAATATTTTAGAAGTTGTTGCAATATTTCAAAATTAGTTGGTGGTGACAGAAATCTTCAAAT

Translation

[206 - 946/974]   direct strand


Annotator commentaries

THIS GENOMIC SEQUENCE IS NON CODING BECAUSE:

TRANSLATED PROTEIN OF LONGEST STRETCH OF ORF DOESNOT GIVE GOOD ALIGNMENT AND ITS EVALUE IS GREATER THAN ONE AND BITSCORE IS LESS THAN 100.


WHEN THIS PROTEIN WAS RUN ON INTERPROSCAN IT DOESNOT PREDICT ITS DOMAIN.




ORF finding

PROTOCOL

a) SMS ORFinder / forward strand / frames 2 / min 60 AA / 'any codon' initiation / 'universal' genetic code

b) SMS ORFinder / reverse strand / frames 1 / min 60 AA / 'any codon' initiation / 'universal' genetic code


RESULTS ANALYSIS


a)forward strand


only one ORF found out by sms orf finder on 2nd frame of the direct strand.


b)reverse strand


only one ORF found out by sms orf finder on first frame of the reverse strand.






RAW RESULTS


a) forward strand

ORF Number 1 on the direct strand extends from base 179 to base 949

gaatctaattactccagaggtattctaatgaatcttgaagaactaattgaaagccattttgctccaaagaaaggaaacg
atcttattattcaactgatagagcaaagattaggcaattcttctttgttgtttgaagcagaagaacaaggcggcggtaa
tcttttctatggcgatgaaagaacattaaaactaccagtcattagatttagcaaaaatattggtagaaaaaatacatat
gatagaagctttttagatcttgttgttcataatctaaaaaatatttctggaaaagacggggaactattacaaacaagaa
ttgcatctttccaaaaattctttaatggcaactttgaaggcgaactggatatctcaaatattatttcatattgcatgat
ctctgaagctttctatcacttgattaatgattatgatgcttcaacggctggagacttattcgagccattattcgcagca
ttatttgatggaacaattgttgaagctccagagggaaaaagaaactatgcagtagaagatgttcaaatcgcatcaaaag
aagggcagatacaagatttaaaggatgtaagcttaaaacttctttctccacggggaaatgtttctcaaaattataaaaat
atattagagaaattagtaaagagtggaggtattttatatgttgtggcgtataaagaaaaacaaagcaacatttcctttt
atgctcttgatttaactccaaataatattttagaagttgttgcaatatttcaaaattag


ORF Number 1 translates to give this protein:

ESNYSRGILMNLEELIESHFAPKKGNDLIIQLIEQRLGNSSLLFEAEEQGGGNLFYGDERTLKLPVIRFSKNIGRKNTYDRSFLDLVVHNLKNISGKDGELLQTRIASFQKFFNGNFEGELDISNIISYCMISEAFYHLINDYDASTAGDLFEPLFAALFDGTIVEAPEGKRNYAVEDVQIASKEGQI
QDLKDVSLKLLSPRGNVSQNYKNILEKLVKSGGILYVVAYKEKQSNISFYALDLTPNNILEVVAIFQN*

b) reverse strand

ORF Number 1 on the reverse strand extends from base 7 to base 378.

agatttctgtcaccaccaactaattttgaaatattgcaacaacttctaaaatattatttggagttaaatcaagagcataaa
aggaaatgttgctttgtttttctttatacgccacaacatataaaatacctccactctttactaatttctctaatatatttt
tataattttgagaaacatttccccgtggagaaagaagttttaagcttacatcctttaaatcttgtatctgcccttcttttg
atgcgatttgaacatcttctactgcatagtttctttttccctctggagcttcaacaattgttccatcaaataatgctgcga
ataatggctcgaataagtctccagccgttgaagcatcataatcattaa

ORF Number 1 translates to give this protein:

RFLSPPTNFEILQQLLKYYLELNQEHKRKCCFVFLYTPQHIKYLHSLLISLIYFYNFEKHFPVEKEVLSLHPLNLVSALLLMR
FEHLLLHSFFFPLELQQLFHQIMLRIMARISLQPLKHHNH*



Multiple Alignement

PROTOCOL



RESULTS ANALYSIS

RAW RESULTS

Protein Domains

PROTOCOL

INTERPROSCAN/ DEFAULT PARAMETERS


RESULTS ANALYSIS


InterProScan Results



SEQUENCE: Sequence_1 CRC64: 00E8203C90933252 LENGTH: 256 aa




No hits reported.





RAW RESULTS

Phylogeny

PROTOCOL



RESULTS ANALYSIS

RAW RESULTS

Taxonomy report

PROTOCOL



RESULTS ANALYSIS

RAW RESULTS

BLAST

PROTOCOL

BLASTp versus NR, NCBI default parameters apart from "Number of descriptions_500"


RESULTS ANALYSIS


alignment showed by the ncbiblast is black of that sequence that is worst alignment so protein function could not be predict accurately.

as shown below in the raw results bitscore is less than 100 and evalue is greater then 1 for example


ref|YP_947619.1| hypothetical protein AAur_1870 [Arthrobacter... 37.0 1.6].


SO THIS SEQUENCE IS NON CODING.



RAW RESULTS

ref|ZP_03672403.1|  glycoprotease family protein [Borrelia val...  37.7    0.96 
ref|YP_947619.1|  hypothetical protein AAur_1870 [Arthrobacter...  37.0    1.6   
ref|YP_831389.1|  AraC family transcriptional regulator [Arthr...  37.0    1.8   
ref|ZP_03539217.1|  glycoprotease family protein [Borrelia gar...  36.6    2.0  
ref|ZP_01902753.1|  putative PAS/PAC sensor protein [Roseobact...  36.6    2.1  
ref|YP_710218.1|  O-sialoglycoprotein endopeptidase [Borrelia ...  36.6    2.1   
ref|ZP_03435588.1|  glycoprotease family protein [Borrelia afz...  36.6    2.2  
ref|YP_073207.1|  O-sialoglycoprotein endopeptidase [Borrelia ...  36.6    2.2   
ref|ZP_01465408.1|  conserved hypothetical protein [Stigmatell...  36.2    2.7  
ref|YP_191875.1|  transposase [Gluconobacter oxydans 621H] >gb...  35.8    3.2   
ref|YP_192592.1|  transposase [Gluconobacter oxydans 621H] >gb...  35.8    3.2   
ref|YP_190438.1|  transposase (class II) [Gluconobacter oxydan...  35.8    3.2   
ref|YP_190858.1|  transposase [Gluconobacter oxydans 621H] >re...  35.8    3.3   
ref|ZP_03675065.1|  glycoprotease family protein [Borrelia spi...  35.8    3.9  
ref|XP_002069740.1|  GK11412 [Drosophila willistoni] >gb|EDW80...  35.4    4.1   
ref|YP_002375267.1|  glycoprotease family protein [Borrelia bu...  35.4    4.1   
ref|NP_212903.1|  O-sialoglycoprotein endopeptidase [Borrelia ...  35.4    4.2   
ref|ZP_03086971.1|  O-sialoglycoprotein endopeptidase [Borreli...  35.4    4.3  
ref|ZP_03772803.1|  glycoprotease family protein [Borrelia sp....  35.4    4.7  
ref|ZP_01890364.1|  hypothetical protein SCB49_14465 [unidenti...  35.4    5.1  
ref|ZP_01289775.1|  Periplasmic phosphate binding protein [del...  35.0    6.2  
ref|ZP_02868048.1|  hypothetical protein CLOSPI_01889 [Clostri...  34.7    7.2  
ref|ZP_03436833.1|  glycoprotease family protein [Borrelia bur...  34.7    7.4  
emb|CAG07121.1|  unnamed protein product [Tetraodon nigroviridis]  34.7    8.8