GapMind for catabolism of small carbon sources

 

Alignments 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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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