GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Corynebacterium deserti GIMN1.010

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_053544053.1 CDES_RS02115 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_001277995.1:WP_053544053.1
          Length = 568

 Score =  157 bits (398), Expect = 8e-43
 Identities = 143/521 (27%), Positives = 239/521 (45%), Gaps = 41/521 (7%)

Query: 39  SYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRL 98
           S T+++  +     A+ + +LG+  G  V+++ PN PQ     +AV   GA +   N   
Sbjct: 51  SQTYAELDKEVRRTAAGLRALGVRPGDRVAIILPNCPQHIAAFYAVLKLGATVIEHNPLY 110

Query: 99  DARTI--SILLHHSESKLIF------VDHLSRDLILEAIA---LFPKQAPVPRLVF---- 143
            A  +      H +   +++      V+ L  +  LE I    +      V RL      
Sbjct: 111 TAHELLEPFKDHGARVAIVWDKASPVVEKLRGETNLETIVSVNMINAMPTVQRLALKLPI 170

Query: 144 --MADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPM-ILNYTSGTTSSPK 200
             +    E+ + S      F +       G+ +     P    D + ++ YTSGTT +PK
Sbjct: 171 PALRKSREALSGSAPNTVPFETLASAAMGGEGEDIVSEPSVTKDTVALILYTSGTTGTPK 230

Query: 201 GVVHCHRGIFIMTVDSLIDW--GVPKQPV-YLWTLPMFHANGWSYPWGMAA-VGGTNICL 256
           G    H  +F   +     W  G+  +P   L  LPMFHA G +    ++  +GG  + L
Sbjct: 231 GAQLTHGNLFSNLLQGK-HWVPGLGDKPERMLAALPMFHAYGLTMVGTLSVFIGGEMVLL 289

Query: 257 RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSE--PLKTTVQIMTAGAPPPSAVLF 314
                ++I +++K+H  T + G P +   + +A   E  P+K      +  +   +  + 
Sbjct: 290 PTPRIDLIMNIMKKHTPTWLPGVPTLYEKIVDASDKEGIPIKGVRNAFSGASTLSTRTVE 349

Query: 315 RTES-LGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVV 373
           R E+  G  +  GYGLTET+ ++V           P ++  R +   G+     T + + 
Sbjct: 350 RWENHTGGRLVEGYGLTETSPIIVGN---------PMSDH-RKQGYVGI-PFPDTIVRIA 398

Query: 374 DPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYL 433
           +P        DG   GEV+++G  V  GYL   E T  S   + W+ TGDVGVM  DG++
Sbjct: 399 NPENLDETVPDGEE-GEVLVKGPQVFKGYLNQEEATKNSFHGE-WYRTGDVGVMEEDGFI 456

Query: 434 EIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLT 493
            +  R K+VII+GG N+   EVE ++ +HPD+ +AAVV  P E   E   A ++L +G  
Sbjct: 457 RLVARIKEVIITGGFNVYPAEVEDVITAHPDVEDAAVVGIPREDGSENVVAAITLVEGAA 516

Query: 494 KKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQK 534
             P  + + ++ R  L RY VP+T    EE+P+   GK+++
Sbjct: 517 LDP--EGLKDFARENLTRYKVPRTFYHFEEMPRDQMGKIRR 555


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: 779
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 568
Length adjustment: 36
Effective length of query: 520
Effective length of database: 532
Effective search space:   276640
Effective search space used:   276640
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