Aligments for a candidate for acs in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Magnetospirillum magneticum AMB-1

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 WP_043744440.1 AMB_RS12570 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000009985.1:WP_043744440.1
          Length = 544

 Score =  642 bits (1657), Expect = 0.0
 Identities = 307/550 (55%), Positives = 393/550 (71%), Gaps = 18/550 (3%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L K PANY  LTPL FL+R+A V+P R SV+HG   +TW+QTYDRCRRL SALA R +G 
Sbjct: 11  LDKNPANYVPLTPLGFLERSASVYPDRISVVHGDLRFTWKQTYDRCRRLGSALAARGVGV 70

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA++A N PA YEA FGVPM G VL  +NIRL+A  +AF+L H ++ V++ D+EF  
Sbjct: 71  GDTVAVMAANTPAAYEAAFGVPMTGGVLCALNIRLDAEAIAFMLQHGEAKVLLTDREFAP 130

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
             + +L L+E K       P++I I D       +      G +EYE F+A GDP Y W 
Sbjct: 131 TIKKALSLLEAK-------PIVIDIDDAAVTTGEM-----LGEMEYEAFIAGGDPEYAWV 178

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P+DEW +IAL YTSGTT +PKGVV HHRGAYI AL N + WGM    VYLWTLPMFHCN
Sbjct: 179 WPSDEWDAIALNYTSGTTGNPKGVVYHHRGAYINALGNVVNWGMTGHPVYLWTLPMFHCN 238

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311
           GWCFPW+LA L+GT++CLR+V    +++ I K+KVTH C AP+V+  ++NAP++D   PL
Sbjct: 239 GWCFPWTLAALAGTNVCLRRVDGGHMFAAIEKHKVTHMCGAPIVMGMLINAPEKDR-RPL 297

Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371
           PH V  MTA A PP +V+  +  +GF++ H YGL+E YGP+TVCAWK EWD LP + +AK
Sbjct: 298 PHPVEFMTAAAPPPAAVIGRLESQGFKITHVYGLTEVYGPATVCAWKEEWDELPLDERAK 357

Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431
           + +RQGVRY   E + V D  +  PVP DG T GE+ +RGN+VMKGYLKNP A  E F+G
Sbjct: 358 MKSRQGVRYVNEEAMMVADPVSLVPVPKDGATMGEVFYRGNVVMKGYLKNPSATNEAFSG 417

Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491
           GWFH+GD+ V H D YIE+KDRSKD+IISGGENIS++EVE V+Y HP+V EA+VVARPDE
Sbjct: 418 GWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVEGVLYQHPSVGEAAVVARPDE 477

Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551
           +W E+PCAF+ LK           A++IM FCRE+L  Y  P++VVF  LPKT+TGK+QK
Sbjct: 478 KWGETPCAFIGLKD-----GATATAEEIMAFCRERLAHYKCPRTVVFTNLPKTSTGKVQK 532

Query: 552 HILRTKAKEM 561
           ++LR  AK++
Sbjct: 533 YVLREMAKKL 542


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: 940
Number of extensions: 39
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: 544
Length adjustment: 36
Effective length of query: 533
Effective length of database: 508
Effective search space:   270764
Effective search space used:   270764
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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