GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Azospirillum brasilense Sp245

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 AZOBR_RS19480 AZOBR_RS19480 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS19480 AZOBR_RS19480 acyl-CoA
           synthetase
          Length = 556

 Score =  575 bits (1481), Expect = e-168
 Identities = 286/547 (52%), Positives = 373/547 (68%), Gaps = 18/547 (3%)

Query: 16  PANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTV 75
           PAN+  L+PL FL RAA V+P + ++ HG R  T+ Q +DR RR A AL    +  G TV
Sbjct: 20  PANHVPLSPLSFLKRAAKVYPDKPAIRHGRRTITYAQFHDRVRRFAGALLRAGVRRGDTV 79

Query: 76  AIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAED 135
           +++APN+PA+ EAH+ VP+ GAVLN +N RL+A  +AF+L HS++ +++VD+E   +A+ 
Sbjct: 80  SVLAPNVPALLEAHYAVPLAGAVLNALNTRLDAAAIAFILDHSETKLLIVDRELSPVAKA 139

Query: 136 SLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPAD 195
           +L   E        RP+ +V      A E    A S GA+EYEDFLA  DP  PW  P D
Sbjct: 140 ALARTE--------RPITLV----EIADEQAPDAPSLGAVEYEDFLAAADPA-PWHGPDD 186

Query: 196 EWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCF 255
           EWQ+IAL YTSGTT +PKGVV HHRGAY+ AL N     ++  +V+LWTLPMFHCNGW +
Sbjct: 187 EWQAIALNYTSGTTGNPKGVVYHHRGAYLNALGNAFTLNVRPESVFLWTLPMFHCNGWTY 246

Query: 256 PWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTV 315
            W++    GT +CLR+V    ++  IA+  VTH C AP+VLN +++AP      P P  V
Sbjct: 247 SWAVTAAGGTHVCLRRVEPAAIFDAIAELGVTHLCGAPIVLNMLIHAPAA-VRRPAPRRV 305

Query: 316 HVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNAR 375
            V T GAAPP +VL  M   GF V H YGL+E YGP+TVCA +  W+ L  +  A   AR
Sbjct: 306 IVGTGGAAPPSAVLAGMATLGFEVVHMYGLTECYGPATVCAPQDGWEDLDADGLALQFAR 365

Query: 376 QGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFH 435
           QGV +  +E   V+D +TG+PVPAD +T GEI  RGN VMKGYLKNP A KE    GWF 
Sbjct: 366 QGVNHVAVEDATVLDRETGRPVPADAQTIGEIALRGNTVMKGYLKNPAATKEALKDGWFR 425

Query: 436 SGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQE 495
           +GD+ V HPD YIE+KDRSKD+IISGGENISS+EVE  +Y HPAVLEA+VVARPD+RW E
Sbjct: 426 TGDLGVLHPDGYIEVKDRSKDIIISGGENISSLEVEEALYRHPAVLEAAVVARPDDRWGE 485

Query: 496 SPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILR 555
           SPCAFVT+K   E+  ++    DI+++CR+++  Y VP++VVF  LPKT+TGKIQK +LR
Sbjct: 486 SPCAFVTVKPGAERPSES----DIIQWCRDRIAHYKVPRTVVFSDLPKTSTGKIQKTVLR 541

Query: 556 TKAKEMG 562
             A+E+G
Sbjct: 542 DAARELG 548


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: 911
Number of extensions: 32
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: 569
Length of database: 556
Length adjustment: 36
Effective length of query: 533
Effective length of database: 520
Effective search space:   277160
Effective search space used:   277160
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:

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 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