GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS19480
          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:

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