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 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_089751845.1 BMZ06_RS09710 acyl--CoA ligase

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900113125.1:WP_089751845.1
          Length = 524

 Score =  353 bits (906), Expect = e-102
 Identities = 204/508 (40%), Positives = 297/508 (58%), Gaps = 13/508 (2%)

Query: 52  ERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWA 111
           E   + AL+W     G   +++Y +L   +N++ +    HGL+KGD + +M       + 
Sbjct: 23  EDPDRKALLWLS-EAGGRKEVTYEQLLHQANKMGNAFLDHGLQKGDKILVMIPRLIEAYQ 81

Query: 112 VFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLI 171
           V++A +K G V++PS+  L   +++YR +     A+IS       ++E   S ++ KF +
Sbjct: 82  VYIAALKAGLVIIPSSEMLRAKDLQYRITHGDVRAVISYHPFTEHLDEVKESDQLLKFSV 141

Query: 172 DGKRETW----NSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSIT 227
            G +E W      LED SS  E  DT  +D+    +TSGTTG PK V+HT   +    + 
Sbjct: 142 GGSKEGWFDFDGLLEDYSSTLETADTASDDMAFLSYTSGTTGNPKGVVHTH-GWGYAHLK 200

Query: 228 TASI--VGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVE 285
           TA+   + +++ D     +  GW K+ WS F S L  GA   G+ Y+GK + + YL  ++
Sbjct: 201 TAAYKWLAIQDGDTVWATAGPGWQKWVWSPFLSVLGTGAR--GLVYQGKFNPKTYLSLMD 258

Query: 286 NLGVTSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDF 344
              V   C  PT +R    +D LD ++   L S VSAGEPLN EVI  +K+ FN+T+RD 
Sbjct: 259 EHNVNVLCCTPTEYRLMAKVDNLDDYQLAGLHSAVSAGEPLNREVIDTFKNHFNVTVRDG 318

Query: 345 YGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPI 404
           YGQTE T +VG    ++V+PGSMG+P P   + ++D+  + + +  EVG I V L+  P 
Sbjct: 319 YGQTENTLLVGILKDMEVRPGSMGRPTPGNQVEIIDELAEPV-ETGEVGDIAVHLDT-PA 376

Query: 405 GLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESA 464
                Y D ++   S R  YY TGD+A  DE+GYF+F GR DD+I +S Y +GPFEVE A
Sbjct: 377 LFKEYYKDPERTKMSHRGHYYVTGDQARKDEDGYFWFEGRSDDIIISSGYTIGPFEVEDA 436

Query: 465 LLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRI 524
           L++H AV E AVV  PD VR  +VKA+IVL+  Y P+  L +E+++ +K   +PYK PR 
Sbjct: 437 LVKHKAVQECAVVSSPDEVRGNVVKAFIVLQNNYEPTDSLVKELQDHVKNTTAPYKYPRK 496

Query: 525 IEFVDELPKTISGKIRRVELRKREEEKR 552
           IEF +ELPKT SGKIRRVELRK+E   R
Sbjct: 497 IEFTEELPKTTSGKIRRVELRKKENASR 524


Lambda     K      H
   0.318    0.137    0.402 

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: 741
Number of extensions: 44
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: 564
Length of database: 524
Length adjustment: 35
Effective length of query: 529
Effective length of database: 489
Effective search space:   258681
Effective search space used:   258681
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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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