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_011385011.1 AMB_RS13240 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385011.1 AMB_RS13240 acyl-CoA
           synthetase
          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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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