GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Marinobacter adhaerens HP15

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 GFF1060 HP15_1039 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Marino:GFF1060
          Length = 542

 Score =  621 bits (1601), Expect = 0.0
 Identities = 300/550 (54%), Positives = 389/550 (70%), Gaps = 17/550 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L  + ANY   +P+ F++R A V+P   +VIHG+  Y W QTY+RCRRLASAL  R IG 
Sbjct: 9   LAPVDANYAVQSPVDFIERTATVYPEYPAVIHGAIRYNWAQTYERCRRLASALKGRGIGR 68

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA++ PNIPAM EAHFGVPM GAVLN +N+RL+A  +AF+L H ++ V++ D+EF  
Sbjct: 69  GDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVIADREFGE 128

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           +  D++  ++ K       PL+I + D    PE     +    ++YE FL  GDP + W 
Sbjct: 129 VIRDAVSRLDTK-------PLVIDVDD----PE-YGEGVQVSDLDYEAFLQEGDPTFQWS 176

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P +EW +I+L YTSGTT +PKGVV HHRGAYI A+ N  +W M    VYLWTLPMFHCN
Sbjct: 177 FPENEWDAISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVWSMDMHPVYLWTLPMFHCN 236

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311
           GWCFPW++  ++GT +CLR+V  +++  +I  ++VTH C AP+VLNA++N P E     +
Sbjct: 237 GWCFPWTITAMAGTHVCLRRVDPEKILQLIRDHQVTHMCGAPIVLNALLNVP-ESAKAGI 295

Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
            H V  MTAGAAPP  V+ ++ + G +V H YGL+E YGP TVCAWK EWD+LP   +A+
Sbjct: 296 DHDVKSMTAGAAPPAQVIGAIEEMGIQVTHVYGLTEVYGPVTVCAWKSEWDALPLHDRAR 355

Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431
             ARQGVRY  +    V D  T +PVP DGKT GEI  RGN VMKGYLKNP+A +E F G
Sbjct: 356 KKARQGVRYHTLAGTMVGDPNTMEPVPKDGKTIGEIFLRGNTVMKGYLKNPKATEEAFRG 415

Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491
           GWFH+GD+AV H D Y+EIKDR KD+IISGGENIS++EVE+ +Y HPAVLEA+VVARPDE
Sbjct: 416 GWFHTGDLAVWHEDGYMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDE 475

Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551
           +W E+PCAFVTLK   E  D ++  +DI+ FCRE L  + VPK++VF  LPKT+TGKIQK
Sbjct: 476 KWGETPCAFVTLKP--EAGDVSE--EDIINFCREHLARFKVPKTIVFSELPKTSTGKIQK 531

Query: 552 HILRTKAKEM 561
            +LR +AKE+
Sbjct: 532 FVLRDQAKEL 541


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: 938
Number of extensions: 29
Number of successful extensions: 4
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: 542
Length adjustment: 36
Effective length of query: 533
Effective length of database: 506
Effective search space:   269698
Effective search space used:   269698
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