Alignments for a candidate for acs in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Nitriliruptor alkaliphilus DSM 45188

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_211262524.1 NITAL_RS19335 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_000969705.1:WP_211262524.1
          Length = 540

 Score =  219 bits (557), Expect = 3e-61
 Identities = 175/545 (32%), Positives = 271/545 (49%), Gaps = 46/545 (8%)

Query: 13  PLTPLGFLERAATVYGDCTSVVY---DAVSYTWSQTHRRCLCLASSIASLGIENGHVVSV 69
           PLT     E    V+G    V +    +   T+++T+ R   LA+ +ASLGI +G VV  
Sbjct: 10  PLTVTQLFEHGRKVHGHHEVVTWRGDHSRRVTFAETYDRAGRLAAGLASLGIGDGDVVGT 69

Query: 70  LAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAI 129
              N  +  E +FA+P  GA+L+ +N+RL    ++ ++     ++I VD    D ++  +
Sbjct: 70  FCWNHQEHVEAYFAIPCMGAVLHQLNIRLFPDQLTFVVADLGDRVIIVD----DSLIPLL 125

Query: 130 A-LFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI 188
           A +  +   V   V + D   S       +     Y DL+   DP F+W    +E     
Sbjct: 126 ARVLDELTTVEVFVVVGDGDASALDGHPAR--VVRYDDLLADADPGFRWP-ELAETAAAA 182

Query: 189 LNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW-GVPKQPVYLWTLPMFHANGWSYPWGMA 247
             YTSGTT +PKGVV+ HR I+  T+ +     GV      L  +P FHAN W    G+ 
Sbjct: 183 SCYTSGTTGNPKGVVYSHRSIWTHTLGAAAGGVGVGDGDKLLVIVPQFHANAW----GLI 238

Query: 248 AVG---GTNICL--RKFDSEIIYDMIKRHGVTHMCGAPVVLN-MLSNAPGSE-PLKTTVQ 300
            +G   G ++ L       E +   I+    T     P V N +L++  G +  L +   
Sbjct: 239 HIGWAYGADLLLPAEHLQPEPLVAFIEAERPTCSAAVPTVWNGVLAHGEGHDIDLSSLDW 298

Query: 301 IMTAGAPPPSAVLFRTES-LGFAVSHGYGLTETAGL-VVSCAWKKEWNHLPA--TERARL 356
           ++  G+  P +++ + E+  G  +  G+G+TE + L  VS          PA  T  A +
Sbjct: 299 VVVGGSAVPRSMISQFEARYGVTIIQGWGMTEMSPLGTVSTP--------PAGVTGEASI 350

Query: 357 KSRQGVGTVMQ-TKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGY--LKDPEGTAKSM 413
             R   G ++    + +VDP  GA    DG  +GE+ +RG  +  GY  +  PE      
Sbjct: 351 DYRAKTGRLVPGVDMRIVDP-DGAEQPWDGEAMGEIQVRGPWITAGYHGVDTPE-----K 404

Query: 414 TADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVAR 473
             DGW  TGDVGV+ P+G++++ DR+KDVI SGGE +SSV++E+ L  HPD+ E AV+A 
Sbjct: 405 FHDGWLRTGDVGVIEPNGFVQLVDRTKDVIKSGGEWISSVDLENALMGHPDVAECAVIAV 464

Query: 474 PDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQ 533
            DE W E P A V  ++G   + T +E+  Y   K+ R+ +P+   F  E+PKTS GK  
Sbjct: 465 ADERWDERPLACVVRREG--SEVTPEELNGYLEDKVARWWLPERYAFVAEVPKTSVGKFD 522

Query: 534 KFILR 538
           K +LR
Sbjct: 523 KKVLR 527


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: 811
Number of extensions: 54
Number of successful extensions: 7
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: 540
Length adjustment: 36
Effective length of query: 520
Effective length of database: 504
Effective search space:   262080
Effective search space used:   262080
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 2024 update 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