Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate BPHYT_RS33490 BPHYT_RS33490 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__BFirm:BPHYT_RS33490
          Length = 543

 Score =  556 bits (1434), Expect = e-163
 Identities = 282/549 (51%), Positives = 363/549 (66%), Gaps = 20/549 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L +  ANY  LTP+ F+ RAA V+  R +V+HG     WR+TY+R RRLASAL    I  
Sbjct: 9   LERREANYVPLTPIDFIVRAAEVYGERPAVVHGEIRRNWRETYERARRLASALQQAGIQR 68

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA + PNIP M EAHFGVPM GAVLN +N RL+  ++ F+L H ++  ++VD E+  
Sbjct: 69  GDTVAALLPNIPPMIEAHFGVPMAGAVLNTLNTRLDVSSLLFMLRHGEAKALIVDTEYGE 128

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA-PESLNRALSKGAIEYEDFLATGDPNYPW 190
            A         +A   F    +I + D   A P    RA      +YE FL +GDP + W
Sbjct: 129 FAH--------RAALEFPDLRVISVADAMPADPSQFIRAT-----DYEAFLQSGDPEFAW 175

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
             PADEW +IAL YTSGTT  PKGVV HHRGAY+ ALSN L W M   A+YLWTLP+FHC
Sbjct: 176 AMPADEWDAIALNYTSGTTGDPKGVVYHHRGAYLNALSNILEWDMPKHAIYLWTLPLFHC 235

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCFPW++A  +G ++CLR+  AK V+ +I +  +TH+C AP+V +A+ NAP +     
Sbjct: 236 NGWCFPWTVAARAGVNVCLRKFDAKTVFDLIRREGITHYCGAPIVQSALANAPAQWRE-G 294

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
           + H V  M AGAAP P+V+  M + GF + H YGL+ETYGP+ VCA + EW++L    +A
Sbjct: 295 IEHRVSTMVAGAAPAPAVIAKMKEIGFDLTHVYGLTETYGPAAVCAKQEEWEALDDGARA 354

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
           ++NARQGVRY     + V+D  T  PVP DG+T GEI+FRGN+ MKGYLKN  A + TF 
Sbjct: 355 EMNARQGVRYHLQAAVTVLDPDTLTPVPDDGETIGEIMFRGNICMKGYLKNERATEATFQ 414

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGWFH+GD+ V+ PD YI I+DRSKD+IISGGENISS+EVE+ +Y HPAV  A+VVA  D
Sbjct: 415 GGWFHTGDLGVRMPDGYIRIRDRSKDIIISGGENISSIEVEDTLYRHPAVSVAAVVAMAD 474

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
            +W E PCAFV LK   +       A++I+  CR  L  Y +PK+V FG LPKT+TGKIQ
Sbjct: 475 PKWGEVPCAFVELKEGAQVS-----AEEIIAHCRLFLAGYKLPKAVRFGELPKTSTGKIQ 529

Query: 551 KHILRTKAK 559
           K  LR + K
Sbjct: 530 KFELRARIK 538


Lambda     K      H
   0.319    0.134    0.422 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 875
Number of extensions: 41
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 569
Length of database: 543
Length adjustment: 36
Effective length of query: 533
Effective length of database: 507
Effective search space:   270231
Effective search space used:   270231
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources