GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas baetica a390

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_100845302.1 C0J26_RS20655 long-chain-fatty-acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_003031005.1:WP_100845302.1
          Length = 562

 Score =  133 bits (334), Expect = 2e-35
 Identities = 117/367 (31%), Positives = 174/367 (47%), Gaps = 34/367 (9%)

Query: 192 LYYTSGTTGLPKGVMHHHRGAFLN------AMAEVLEHQMDL----NSVYLWTLPMFHAA 241
           L YT GTTGL KG M  H     N       +A++      L      V +  LP++H  
Sbjct: 212 LQYTGGTTGLAKGAMLTHGNLVANMQQVRACLAQLGPDGQPLLREGQEVMIAPLPLYHIY 271

Query: 242 SWGFSWATVAV-GATNVCLDKV-DYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLK 299
           ++  +   + V G  NV +    D     + ++  + + +    T++V L D+     L 
Sbjct: 272 AFTANCMCMMVSGNHNVLITNPRDIAGFIKELKNWKFSELLGLNTLFVALMDHPDFKTLD 331

Query: 300 FSNRVHMLVAGAAPAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLE 356
           FS        G A   AT +  ++I G  C +   YGLTET  P +           P  
Sbjct: 332 FSTLKLTNSGGTALVKATAERWEQITG--CRITEGYGLTET-SPVACTN--------PYG 380

Query: 357 EQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESF 416
           +Q++L    G+P     + V + +G   P   +  GE+ ++G  +  GY++ PE TAE  
Sbjct: 381 DQSRL-GTVGLPVPGTLLKVINDDGVEQPLGER--GELCIKGPQIMKGYWQKPEATAEVL 437

Query: 417 -RDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGT 475
             +GWF SGD AV+ PDG++ IVDR KD+I   G  V    +E  +M  P V   AV G 
Sbjct: 438 DAEGWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGV 497

Query: 476 PDEKWGEVVTARIELQE-GVKLTEEEVIKFCKERLAHFECPK-IVEFGPIPMTATGKMQK 533
           PDE+ GE V   +  +E GV L  EE+  +CKE    ++ PK IV    +PMT  GK+ +
Sbjct: 498 PDERSGEAVKLFVVARESGVSL--EELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILR 555

Query: 534 YVLRNEA 540
             LR+ A
Sbjct: 556 RELRDIA 562


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: 689
Number of extensions: 29
Number of successful extensions: 4
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: 562
Length adjustment: 36
Effective length of query: 513
Effective length of database: 526
Effective search space:   269838
Effective search space used:   269838
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