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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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:

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:

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:

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:

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