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

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_011385011.1 AMB_RS13240 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000009985.1:WP_011385011.1
          Length = 541

 Score =  583 bits (1504), Expect = e-171
 Identities = 291/553 (52%), Positives = 376/553 (67%), Gaps = 24/553 (4%)

Query: 12  LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71
           L +  AN+ ALTPL FL+RAA V P R +VIHG    TW +T+ RCR+LA+AL  R IG 
Sbjct: 10  LDRNAANFVALTPLTFLERAAAVWPDRLAVIHGPVRRTWAETFVRCRKLAAALTARGIGL 69

Query: 72  GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131
           G TVA++  N P  +EAHFGVP+ GAVLN +N RL+A  + F+L+H+++ +++ D+EF  
Sbjct: 70  GDTVALMGANTPETFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKILITDREFSP 129

Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191
           + + +L  +          P++ +        E L      G   YE  L       PW 
Sbjct: 130 VVKKALAALGRTI------PVIDIDDPQFKGGELL------GEKNYEQLLDEAASEAPWT 177

Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251
            P DEWQ+IAL YTSGTT +PKGVV HHRGA++ A+SN L W M D  VYLWTLPMFHCN
Sbjct: 178 LPTDEWQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCN 237

Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAP---KEDTI 308
           GWCFPW++AV++GTS+CLR V    +   I   KVT+FC AP+VLN I NAP   KE   
Sbjct: 238 GWCFPWTMAVVAGTSVCLRHVRVDAIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEG-- 295

Query: 309 LPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPET 368
             + H V VMTAGAAPP  V+  M + G+ V H YGL+E YGP+  C W  +W+ L  + 
Sbjct: 296 --ISHAVKVMTAGAAPPAPVIAGMERMGWEVTHVYGLTECYGPTVQCVWHDKWNGLSIDE 353

Query: 369 QAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKET 428
           +A++ ARQGVR   +E L + D  + +P P DGKT GEI  RGN VMKGYLKN +A +E 
Sbjct: 354 KAQIKARQGVRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEA 413

Query: 429 FAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVAR 488
           FAGGWFH+GD+AV HPD YIEIKDRSKD+IISGGENISS+EVE+++Y H AVLEA+VVAR
Sbjct: 414 FAGGWFHTGDLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVAR 473

Query: 489 PDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGK 548
           PDE+W E+PCAF+ LK   E  +      DI+ FCRE++  + VP+++VFG LPKT+TGK
Sbjct: 474 PDEKWGETPCAFIALKDGAEATE-----ADIITFCRERMAHFKVPRTIVFGGLPKTSTGK 528

Query: 549 IQKHILRTKAKEM 561
           +QK +LR KAKE+
Sbjct: 529 VQKFMLRQKAKEL 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: 872
Number of extensions: 31
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: 541
Length adjustment: 36
Effective length of query: 533
Effective length of database: 505
Effective search space:   269165
Effective search space used:   269165
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
the source code
instructions for running GapMind on your computer

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