Aligments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Sphingomonas koreensis DSMZ 15582

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate Ga0059261_0337 Ga0059261_0337 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0337 Ga0059261_0337 Acyl-CoA
           synthetases (AMP-forming)/AMP-acid ligases II
          Length = 539

 Score =  222 bits (566), Expect = 3e-62
 Identities = 164/506 (32%), Positives = 248/506 (49%), Gaps = 27/506 (5%)

Query: 58  RRLASALADRSIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSH 117
           R+LA AL    I  G  VA +A N      A  G    G V++ +N RL    +AF+ +H
Sbjct: 50  RKLAQALERMGIKKGDRVATMAMNHSRHLVAWHGTIGMGGVIHTINPRLFEDQLAFIGNH 109

Query: 118 SQSSVIMVDQEFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEY 177
           ++  V+M D+ F  + +        K    +K     ++ D    P S   A + G   +
Sbjct: 110 AEDRVLMYDRMFQPIVD--------KMKPQWKTIEHYIVFD----PGSEAGAGADGPDSF 157

Query: 178 EDFLATGDPNYPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSN--PLIWGM 235
           E  +   D NY W    DE +   L YTSGTT +PKGV+  HR + I A++   P ++ +
Sbjct: 158 EAVIGAEDGNYAWVE-GDEREPCMLCYTSGTTGNPKGVLYTHRSSVIHAMAEIQPAVFDL 216

Query: 236 QDGAVYLWTLPMFHCNGWCFPWSLAVLSGTSICLRQVT-AKEVYSMIAKYKVTHFCAAPV 294
              +V L  +PMFH  GW  P++ A + G  + +  +   K +  ++ + KVTH    P 
Sbjct: 217 STQSVVLPVVPMFHAVGWGMPFA-APMVGVKLVMSAINEGKVLCELMNREKVTHTAGVPT 275

Query: 295 VLNAIVNAPKEDTILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTV 354
           V  A+     E   +P    V V   G+A P +++  + + G RV H +G++ET    T+
Sbjct: 276 VWFAMFQHMDETGDVPAYLKV-VTIGGSAAPRAMIERIMKMGARVNHAWGMTETSPIGTM 334

Query: 355 CAWKPEWDSLPPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMV 414
            +   +WD L  E +      QG    G+E   V D   G  +P DG+++G +  RG  +
Sbjct: 335 GSPSADWDDLSFEAKVDKMVCQGRAPFGVELRTVDDA--GNLLPRDGESSGRLQVRGPWI 392

Query: 415 MKGYLKNPEANKETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVV 474
           +K Y K+ E+     A GWF +GD+AV HPD  ++I DR+KDVI SGGE ISSVE+EN  
Sbjct: 393 IKQYFKD-ESGPCLTADGWFDTGDVAVLHPDGIMQITDRAKDVIKSGGEWISSVELENAA 451

Query: 475 YHHPAVLEASVVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPK 534
              P V EA+ +     +W E P   V  K   E       A  I +   + +  +W+P 
Sbjct: 452 VGCPGVAEAAAIGIHHPKWDERPLLLVIRKPGSE-----VTADQIQQHLAKHVAKWWLPD 506

Query: 535 SVVF-GPLPKTATGKIQKHILRTKAK 559
            + F   LP TATGK+ K  +R + K
Sbjct: 507 EIHFVEALPHTATGKLLKTAIRDQYK 532


Lambda     K      H
   0.319    0.134    0.422 

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: 743
Number of extensions: 41
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: 569
Length of database: 539
Length adjustment: 36
Effective length of query: 533
Effective length of database: 503
Effective search space:   268099
Effective search space used:   268099
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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:

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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