GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_0337
          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.

Links

Downloads

Related tools

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