Alignments for a candidate for acs in Acidovorax caeni R-24608

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Acidovorax caeni R-24608

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 WP_054255743.1 BN2503_RS06015 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_001298675.1:WP_054255743.1
          Length = 548

 Score =  585 bits (1508), Expect = e-171
 Identities = 293/552 (53%), Positives = 377/552 (68%), Gaps = 25/552 (4%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           LP+  AN+  L+PL F++R A V+P R +++HG    TW +TY RCR+LAS+L    IG 
Sbjct: 9   LPRNEANHAPLSPLAFIERTAEVYPDRLAIVHGELRQTWGETYKRCRQLASSLRRAGIGK 68

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
             TVA++ PN P M EAHFGVPM GAVLN +N RL+  T+AF+L H ++  ++VD EF  
Sbjct: 69  NDTVAVMLPNTPPMVEAHFGVPMAGAVLNTLNTRLDPETIAFMLDHGEAKALIVDPEFSA 128

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTC--APESLNRALSKGAIEYEDFLATGDPNYP 189
           +   +L L +  A      PL ++  +     AP     A S G   YEDF+A GDP + 
Sbjct: 129 VVAKALPLRKNPA------PLALIEVEDALYGAP-----AQSLGGTRYEDFVAAGDPAFA 177

Query: 190 WQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFH 249
           W+ P DEW +IAL YTSGTT +PKGVV HHRGA I A+SN L W M   AVYLWTLPMFH
Sbjct: 178 WELPGDEWDAIALNYTSGTTGNPKGVVYHHRGAAINAISNVLEWDMPKHAVYLWTLPMFH 237

Query: 250 CNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAP---KED 306
           CNGWCFPW++A  +G ++CLR+V A+ ++  I  + VTH+C AP+V   +VNAP   KE 
Sbjct: 238 CNGWCFPWTVAARAGVNVCLRRVDAQAIFDAIRNHGVTHYCGAPIVQGLLVNAPAAMKEG 297

Query: 307 TILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPP 366
               +P  V  M AGAAPP S++  M Q GF + H YGL+E YGP+TVCA    W+SL  
Sbjct: 298 ----VPAGVKAMVAGAAPPASMIEGMEQMGFDLTHVYGLTEVYGPATVCAKHDAWNSLDI 353

Query: 367 ETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANK 426
             +A+LNARQGVRY       V D +T +PVP DG+T GEI+FRGN+ MKGYLKNP+A +
Sbjct: 354 GERARLNARQGVRYHLQRAAMVCDPETMQPVPHDGETMGEIMFRGNIAMKGYLKNPQATE 413

Query: 427 ETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVV 486
           E F GGWFHSGD+AV++PD YI+IKDRSKD+IISGGENISS+EVE+V+Y HP VL  +VV
Sbjct: 414 EAFRGGWFHSGDLAVQYPDGYIKIKDRSKDIIISGGENISSIEVEDVLYRHPDVLAVAVV 473

Query: 487 ARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTAT 546
           A+PD +W E+PCAFV LK+            DI++ C++ L  + VP++VVFG LPKT+T
Sbjct: 474 AKPDPKWGETPCAFVELKA-----GALTTVDDIVQHCKKHLAGFKVPRAVVFGELPKTST 528

Query: 547 GKIQKHILRTKA 558
           GKIQK  LR KA
Sbjct: 529 GKIQKFELRRKA 540


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: 935
Number of extensions: 40
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: 548
Length adjustment: 36
Effective length of query: 533
Effective length of database: 512
Effective search space:   272896
Effective search space used:   272896
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 24 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)
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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
the source code
instructions for running GapMind on your computer

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