Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_089752071.1 BMZ06_RS10900 long-chain-fatty-acid--CoA ligase

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



>NCBI__GCF_900113125.1:WP_089752071.1
          Length = 526

 Score =  343 bits (880), Expect = 1e-98
 Identities = 205/530 (38%), Positives = 303/530 (57%), Gaps = 23/530 (4%)

Query: 13  PLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAP 72
           PL    FL+RA  +YGD  +++ D  + T+ Q + R   L+  ++ LG+     V+ LAP
Sbjct: 4   PLVLTDFLDRAVELYGDKPAIIDDERTLTYKQLNGRVNQLSRGLSDLGVTKEDKVAYLAP 63

Query: 73  NVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALF 132
           N  +M E  + V   GA++  +N RL       +L HSESK++FVD    DL      + 
Sbjct: 64  NTLEMLEGFYGVFQVGAVMTPLNTRLKPADYQFILEHSESKVLFVDS---DLYHLVETVL 120

Query: 133 PKQAPVPRLVFMADESESGNSSELGKEFFCSYKD-LIDRGDPDFKWVMPKSEWDPMILNY 191
           P+   +  ++   DE E   S E    +  S+ D L +R D +        E D   L Y
Sbjct: 121 PQLPQLEHVIVHGDEKEGATSYE---PWLASFADELFERADLE--------ETDIASLLY 169

Query: 192 TSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAAVGG 251
           TSGTT +PKGV+  HR  ++  + ++    V  Q   L  LPMFH NGW  P+   A G 
Sbjct: 170 TSGTTGNPKGVLLSHRANYLHAMSTMHHLRVSDQDTLLHVLPMFHVNGWGSPFYYTANGA 229

Query: 252 TNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGS--EPLKTTVQIMTAG-APP 308
           T + LRK D +++ + IK+HGV+ +  AP VLNML     +    ++  V+++ AG APP
Sbjct: 230 TQVMLRKTDPKLMLEKIKKHGVSVLHMAPTVLNMLMEEYDAVQPQIEQDVRVVIAGSAPP 289

Query: 309 PSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQT 368
           P+ V    E LG+     YG+TE + L+ +   +     LP+ E+ RLK++ G   +M +
Sbjct: 290 PAFVRKVEEDLGWKFIQVYGMTEISPLITTSELRSMDLDLPSEEQYRLKAKAGY-EMMGS 348

Query: 369 KIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMH 428
           K+ VVD   G  V  DG ++GE++ R   +M GY K+ E T  ++  DGW YTGD+ V+ 
Sbjct: 349 KVRVVDEF-GEEVAHDGKSIGEIITRTNGIMEGYFKNEEATNAAIR-DGWLYTGDMAVVD 406

Query: 429 PDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSL 488
               +EI DR KDVIISGGEN+SS+EVE++LY HP +LEAAVVA P + WGE P A V L
Sbjct: 407 EKHTIEIVDRKKDVIISGGENISSIEVEAVLYEHPSVLEAAVVATPHDKWGEVPKAVVVL 466

Query: 489 KKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILR 538
           ++G T   +E+E++ +CR KL  +  P ++ F +ELPKT++GK+QK I+R
Sbjct: 467 REGET--VSEEELIMFCREKLAHFKAPNSITFIDELPKTASGKIQKVIIR 514


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: 744
Number of extensions: 28
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: 526
Length adjustment: 35
Effective length of query: 521
Effective length of database: 491
Effective search space:   255811
Effective search space used:   255811
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: 52 (24.6 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)
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 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