Alignments for a candidate for acs in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF3780 PGA1_262p01840 ATP-dependent AMP binding enzyme

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__Phaeo:GFF3780
          Length = 543

 Score =  468 bits (1205), Expect = e-136
 Identities = 237/542 (43%), Positives = 342/542 (63%), Gaps = 15/542 (2%)

Query: 9   ASSSPLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVS 68
           A+  PL+P+ FL RA T++ D  +V+Y  +  TW +   R   +A+ + SLGI  G  VS
Sbjct: 13  ANYVPLSPVSFLNRAETLHSDRPAVIYGDLRRTWGEVATRIRGVAAGLVSLGIGRGDTVS 72

Query: 69  VLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEA 128
           VL PN+P+++EL FA+P+ GA++N +N RL+  TI+ +L H+++K + VD     L+  A
Sbjct: 73  VLCPNIPELFELQFALPLTGAVINTLNTRLEPETIAYILDHADTKAVIVDRELIPLLSMA 132

Query: 129 IALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI 188
            A   +   V   + + D + +   + +GK     Y++L+  G       +P+ EWD + 
Sbjct: 133 FAAMGRSVSV---IEIDDRNVAAPHTLVGKP----YEELLTDGAGGAPLDLPQDEWDAIA 185

Query: 189 LNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAA 248
           LNYTSGT+  PKGVV+ HRG ++M + +   W  P  P+YL  +PMFH NGW + W MA 
Sbjct: 186 LNYTSGTSGRPKGVVYHHRGAYLMALGTAAAWQTPHYPIYLSVVPMFHCNGWGHSWVMAM 245

Query: 249 VGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP----GSEPLKTTVQIMTA 304
           +GGT +  R    ++I D I+ HGVTH   AP+VL ML+ A      + P    ++++TA
Sbjct: 246 LGGTMVFTRTPSPDLILDAIRSHGVTHFGAAPIVLQMLAEAEAETGSTTPFDPAIKVLTA 305

Query: 305 GAPPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364
           GAPPP +VL +T+++G  V   YGLTET G +  C W+  W      E+A+L+++QG+  
Sbjct: 306 GAPPPPSVLQKTKAMGLDVMQVYGLTETYGHISKCLWQDSWADKIEAEQAQLQAQQGIAM 365

Query: 365 VMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDV 424
            M   + V+D  TG  V RDG T GE+ +RG +VM GY KD + T K+   +GWF++GD 
Sbjct: 366 PMVEAVSVIDTDTGIPVARDGQTQGEIAVRGNTVMKGYYKDADATDKAF-ENGWFWSGDG 424

Query: 425 GVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCA 484
            V+H DGY++I+DR KDVIISGGEN+SSVEVE++LY HP +  AAVVA+PD  WGE PCA
Sbjct: 425 AVVHADGYMQIRDRLKDVIISGGENISSVEVEAVLYRHPAVQAAAVVAKPDPKWGEVPCA 484

Query: 485 FVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDMARGM 544
           F+ L+ G     T +EI+ +CR+ L  +  PKTVVF   LPKTSTGK+QKF LRD A+ M
Sbjct: 485 FIELRTG--SDLTSEEIIAFCRTHLAGFKAPKTVVF-TSLPKTSTGKIQKFQLRDAAKTM 541

Query: 545 GS 546
            +
Sbjct: 542 ST 543


Lambda     K      H
   0.319    0.135    0.412 

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: 837
Number of extensions: 39
Number of successful extensions: 6
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: 556
Length of database: 543
Length adjustment: 36
Effective length of query: 520
Effective length of database: 507
Effective search space:   263640
Effective search space used:   263640
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 (21.7 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
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