1.Genes não
Corinebacterineae
•Específicos de C. pseudotuberculosis
•Transferidos de outros clados
txid85007[Orgn] AND chromosome[Replicon Type] AND complete[PROP] AND reference[PROP]
110,052 seqs
RGMG
CpCDS
tBLASTn
26 genomes:
Corynebacterium (7)
Mycobacterium (17)
Rhodococcus (1)
Nocardia (1)
317 NH-CpCDS
Other txid85007
tBLASTn
C. pseudotuberculosis:
SMase D
Serine protease precursor
310 NH-CpCDS
UniprotKB + nr
tBLASTn
280 “no hit”
30 CpCDS
26 distinct
putative CAAX amino terminal protease family protein
hypothetical protein ABC0212
regulatory protein (padR family)
similar to superfamily I DNA and RNA helicases and helicase subunits
conserved phage-associated protein
conserved phage-associated protein
hypothetical phage-associated protein
PTS system, fructose-specific IIBC component
protein of unknown function DUF181
hypothetical protein Strop_2434
Lantibiotic dehydratase domain protein
hypothetical protein Strop_2432
Secreted subtilisin-like peptidase
CAAX amino terminal protease family protein
nitrite reductase periplasmic cytochrome c552
putative cytochrome c nitrite reductase, small subunit NrfH
viral A-type inclusion protein, putative
serine proteinase precursor**
hypothetical protein MUL_3536
transcriptional antiterminator, BglG
nucleoside transporter
similar to superfamily I DNA and RNA helicases and helicase subunits
transcriptional antiterminator, BglG
hypothetical protein ACTODO_01808
hypothetical protein ACTODO_01815
hypothetical protein ACTODO_01815
hypothetical protein ACTODO_01815
Secreted subtilisin-like peptidase
hypothetical protein XfasaDRAFT_1247
hypothetical protein SpneT_02001734
De onde eles vieram?
YP_946759.1
YP_173716.1
NP_781294.1
YP_001107303.1
YP_056299.1
YP_056299.1
YP_056300.1
YP_001813295.1
YP_001159253.1
YP_001159259.1
YP_001537420.1
YP_001159257.1
ZP_01042386.1
YP_084726.1
NP_969614.1
YP_630432.1
XP_001319569.1
gb|AAA67924.1
YP_907156.1
ZP_01665177.1
ZP_01170419.1
YP_001107303.1
ZP_01665177.1
ZP_02044925.1
ZP_02044932.1
ZP_02044932.1
ZP_02044932.1
ZP_01042386.1
ZP_00651843.1
ZP_01407840.1
Hit
Actinobacteria
Proteobacteria
Proteobacteria
Actinobacteria
Actinobacteria Firmicutes
Actinobacteria Firmicutes
Actinobacteria
Firmicutes
Actinobacteria Firmicutes
Actinobacteria
Actinobacteria
Actinobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria Planctomycetes
Eukaryotes/Protozoa
Firmicutes
Actinobacteria
Firmicutes
Firmicutes
Actinobacteria
Firmicutes
Actinobacteria Cyanobacteria
Actinobacteria
Actinobacteria Firmicutes
Actinobacteria Firmicutes
Proteobacteria
Proteobacteria
ProteobacteriaProteobacteria
Firmicutes
Occurence in other clades
Chloroflexi
Proteo
Eukaryotes/Insecta
Proteo
Proteo
Archaea
Bacterioidetes
Cyanobacteria
Spirochaetes
Bacterioides/Chlorobi
Chloroflexi
Firmicutes
Deinococcus/Thermus
Planctomycetes
Chlamidiae/Verrucomicrobia group
Firmicutes
Chlamidiae/Verrucomicrobia group
Bacterioides/Chlorobi
Firmicutes
Bacterioides/Chlorobi
Synergistetes
Actinobacteria
Proteobacteria
Proteobacteria
Firmicutes
Firmicutes
Actinobacteria
Proteobacteria
Proteobacteria
Bacterioides/Chlorobi
Spirochaetes
Chloroflexi
Bacterioides/Chlorobi
Proteobacteria
Actinobacteria
Actinobacteria
Actinobacteria
Fusobacteria
Chlamidiae/Verrucomicrobia gr
Spirochaetes
Bacterioides/Chlorobi
Spirochaetes
Eukaryotes/general
Bacterioides/Chlorobi Eukaryotes/general
Deinococcus/ThermusActinobacteria
Eukaryotes/Embryophyta
Firmicutes
2.Homologia com baixa
similaridade
•Caso da SMase
•Matrizes PSSM para COG
•Matrizes para novos clusters Seed Linkage
COG
COG
(psi)tblastn
PSSM
86 hits
114,320
PSSM not BLOSUM
nr
Tx85007
Clusters
tBLASTn
48 hits
PSSM not “nr”
4 hits:
Not Corinebacterineae
COG annotated
common
No hit
Ex:
Cp-V1.6830 COG0419
Cp-V1.2590 COG1178
From 280 putative exclusive Cp-CDS, four are found by search using the PSSM matrices, but
are no-hits to nr, uniprot and cog:
Cp-DraftV1.0010
COG0697-Permeases of the
drug/metabolite transporter
(DMT) superfamily
Nostoc sp.
COG0697
Cyanobacteria
Cp-DraftV1.8610
COG0488- ATPase
components of ABC
transporters with duplicated
ATPase domains
Listeria
COG0488
Firmicutes
Cp-DraftV1.15550
COG1191- DNA-directed RNA
polymerase specialized sigma
subunit
Treponema pallidum
COG1191
Spirochaetes
Cp-DraftV1.17210
COG1994-Zn-dependent
proteases
Nostoc sp.
COG1994
Cyanobacteria
Proteobacteria
Arthrobacter sp.
Bacillus clausii KSM-K16
Clostridium tetani E88
Saccharopolyspora erythraea NRRL 2338
Propionibacterium acnes
Propionibacterium acnes
Propionibacterium acnes
Exiguobacterium sp.
Salinispora tropica CNB-440
Salinispora tropica CNB-441
Salinispora tropica CNB-442
Salinispora tropica CNB-443
Idiomarina baltica OS145
Bacillus cereus E33L
Bdellovibrio bacteriovorus HD100
Myxococcus xanthus DK 1622
Trichomonas vaginalis G3
Enterococcus faecalis V583
Mycobacterium ulcerans Agy99
Thermosinus carboxydivorans
Bacillus sp. NRRL B-14911
Saccharopolyspora erythraea NRRL 2338
Thermosinus carboxydivorans
Actinomyces odontolyticus ATCC
Actinomyces odontolyticus ATCC
Actinomyces odontolyticus ATCC
Actinomyces odontolyticus ATCC
Idiomarina baltica OS145
Xylella fastidiosa Dixon
Streptococcus pneumoniae
NC_002935
Corynebacterium diphtheriae NCTC 13129
NC_004369
Corynebacterium efficiens YS-314
NC_006958
Corynebacterium glutamicum ATCC 13032
NC_003450
Corynebacterium glutamicum ATCC 13032
NC_009342
Corynebacterium glutamicum R
NC_007164
Corynebacterium jeikeium K411
NC_010545
Corynebacterium urealyticum DSM 7109
NC_010397
Mycobacterium abscessus chromosome Chromosome, complete sequence
NC_008595
Mycobacterium avium 104
NC_002944
Mycobacterium avium subsp. paratuberculosis K-10
NC_002945
Mycobacterium bovis AF2122/97
NC_008769
Mycobacterium bovis BCG str. Pasteur 1173P2
NC_009338
Mycobacterium gilvum PYR-GCK
NC_002677
Mycobacterium leprae TN
NC_008596
Mycobacterium smegmatis str. MC2 155
NC_009077
Mycobacterium sp. JLS
NC_008705
Mycobacterium sp. KMS
NC_008146
Mycobacterium sp. MCS
NC_002755
Mycobacterium tuberculosis CDC1551
NC_009565
Mycobacterium tuberculosis F11
NC_009525
Mycobacterium tuberculosis H37Ra
NC_000962
Mycobacterium tuberculosis H37Rv
NC_008611
Mycobacterium ulcerans Agy99
NC_008726
Mycobacterium vanbaalenii PYR-1
NC_006361
Nocardia farcinica IFM 10152
NC_008268
Rhodococcus sp. RHA1