GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Algiphilus aromaticivorans DG1253

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_043772607.1 U743_RS16760 long-chain-fatty-acid--CoA ligase

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



>NCBI__GCF_000733765.1:WP_043772607.1
          Length = 540

 Score =  249 bits (636), Expect = 2e-70
 Identities = 163/511 (31%), Positives = 275/511 (53%), Gaps = 23/511 (4%)

Query: 36  DAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVN 95
           D   YT+ +   R   +A+++ + G++ G   + LA N  + +EL++A+   G++++ +N
Sbjct: 36  DIHRYTYGEAAARARQMANALTAAGLKPGERAATLAWNGYRHFELYYAISGIGSVMHTIN 95

Query: 96  LRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSE 155
            RL    ++ +++H+E +++F D     ++ +AIA   K   V   V M+D  +     E
Sbjct: 96  PRLHPEQVAWIVNHAEDRILFFDATFAPIV-DAIA--DKCPTVQHWVAMSDPDKM---PE 149

Query: 156 LGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVD 215
           L      SY+D +     +++W +   E     L YTSGTT +PKG+++ HR + + T  
Sbjct: 150 LKNVSATSYEDFMAGQPTEYEWPV-LDENTAACLCYTSGTTGNPKGILYSHRSLVLHTYG 208

Query: 216 SLID--WGVPKQPVYLWTLPMFHANGWSYPWGMAAVGGTNICLR--KFDSEIIYDMIKRH 271
           + +   +GV    V L  +PMFH N WS P+ + A+GG  +     K D E +Y++ +  
Sbjct: 209 ACLPDAFGVTAMDVVLPVVPMFHVNAWSLPY-VGALGGVKLVFPGPKLDGESLYELFESE 267

Query: 272 GVTHMCGAPVVLNMLSNAPGSEPLK-TTVQIMTAG--APPPSAVLFRTESLGFAVSHGYG 328
           GVT   G P V  ++        L+ +T++ MT G  A PP+ +    +  G  + H +G
Sbjct: 268 GVTISAGVPTVWQLVLQHLQKNKLQLSTLKRMTVGGSACPPALMETFEKEFGVRLEHAWG 327

Query: 329 LTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTL 388
           +TE + L      K +   L   E+ +++ +QG   V   ++ +VD   G    +DG + 
Sbjct: 328 MTEMSPLGTYNHLKAKHQKLSEDEQFQVRIKQG-RAVFGVEMKIVDE-NGKRQPQDGKST 385

Query: 389 GEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGE 448
           G++ +RG  ++  Y K  E    S   DGWF TGDVG + PDGYL I DR+KDVI SGGE
Sbjct: 386 GDLHVRGPWIIKQYFKKDE----SPLIDGWFPTGDVGHIDPDGYLTITDRTKDVIKSGGE 441

Query: 449 NLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSK 508
            + S+++E+I  SHP +  AA +A   E W E P   V LK+G  +  T+++++++   K
Sbjct: 442 WIGSIDLENIAMSHPAVATAACIAAKHEKWDERPLLLVQLKEG--QSATKEDLLKHYEGK 499

Query: 509 LPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539
           + ++  P  ++F + LP  +TGKVQK  LRD
Sbjct: 500 IAKWWTPDDILFVDGLPLGATGKVQKNKLRD 530


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: 769
Number of extensions: 52
Number of successful extensions: 8
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 Sep 24 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