Alignments for a candidate for acs in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfacinum hydrothermale DSM 13146

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_084056164.1 B9A12_RS03050 fatty acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_900176285.1:WP_084056164.1
          Length = 548

 Score =  250 bits (638), Expect = 1e-70
 Identities = 167/549 (30%), Positives = 276/549 (50%), Gaps = 29/549 (5%)

Query: 12  VDPTGSWYSVLTPLLF---LERAGKYFKDKTAVVYRD-SRYTYSTFYDNVMVQASALMRR 67
           +D T S Y    PLL    L R  +Y  ++  +VYRD  RYTY   Y  +   A+AL   
Sbjct: 6   IDKTPSAYDY--PLLIKQLLHRPIRYAPEQE-IVYRDLCRYTYRDLYKRIGQAANALKAL 62

Query: 68  GFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE 127
           G      +  +  +   +LE F+ VP  G +L  +N RLSP+++ Y +NH++   ++V E
Sbjct: 63  GVEPGSTVGVMDWDSHRYLELFYAVPMMGAILHTVNIRLSPEQILYTVNHAEDDVLLVHE 122

Query: 128 PYLNSLLEVKDQIKA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKE 185
            +L  +  +KDQ +   +I+LL+D +  +A +TA   +   Y EL+ G   D    P  +
Sbjct: 123 DFLPIVEAIKDQFQTVKKIVLLKDSE--TAPQTA-VPLDGEYEELLAGADAD-YDFPDFD 178

Query: 186 EYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEH-------QMDLNSVYLWTLPMF 238
           E +  T +YT+GTTGLPKGV   HR   ++ +  +              N VY+   PMF
Sbjct: 179 ENTKATTFYTTGTTGLPKGVFFSHRQLVMHTITVMAAAGSLHTTATFRSNDVYMPLTPMF 238

Query: 239 HAASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNL 298
           H  +WG  +    +G   +   + +  +I +L+  E+VT     PT+   +        +
Sbjct: 239 HVHAWGLPYVATQLGVKQIYPGRYEPAMIMKLLVTEKVTFSHCVPTILHMILTSPAAKEV 298

Query: 299 KFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQ 358
             SN   +++ G+A      KA  + G  +   YG++ET    ++ + +        E+Q
Sbjct: 299 DLSNW-KVIIGGSALTKGLCKAAMDRGIDLITGYGMSETCPVLTLSQLQPHMLDWSKEDQ 357

Query: 359 AKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRD 418
             ++ R G P     + +   +G  +P DGK+ GEVV+R   +  GY+K+PE+  E ++ 
Sbjct: 358 IPVRCRTGQPIPLVNLQIMSPDGTFLPHDGKSTGEVVVRSPWLTQGYFKDPERAEELWQG 417

Query: 419 GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDE 478
           GW H+GD   +   GY++I DR KD+I TGGE +S++ +E  LM+   V   A    PDE
Sbjct: 418 GWLHTGDVGYIDETGYLQITDRIKDVIKTGGEWISTLELEDILMQHEAVSEAAAIAVPDE 477

Query: 479 KWGEVVTARIELQEGV--KLTEEEV----IKFCKE-RLAHFECPKIVEF-GPIPMTATGK 530
           KWGE     + L++    K++EE++    + F +E  +  +  P  V F   +P T+ GK
Sbjct: 478 KWGERPMVLVVLKDDYKGKVSEEDIKAHFMGFVEEGAITKWAVPDRVAFLDALPKTSVGK 537

Query: 531 MQKYVLRNE 539
           + K V+R +
Sbjct: 538 LDKKVMRQQ 546


Lambda     K      H
   0.319    0.136    0.411 

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: 787
Number of extensions: 43
Number of successful extensions: 5
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: 549
Length of database: 548
Length adjustment: 36
Effective length of query: 513
Effective length of database: 512
Effective search space:   262656
Effective search space used:   262656
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.

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Protein sequences (fasta format)
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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