GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Magnetospirillum magneticum AMB-1

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383284.1 AMB_RS04295 acetyl-CoA
           C-acetyltransferase
          Length = 390

 Score =  297 bits (761), Expect = 3e-85
 Identities = 171/399 (42%), Positives = 244/399 (61%), Gaps = 9/399 (2%)

Query: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60
           M D  I  A RTP+G + G+L  ++A  LG + I+  ++R  GV+  AVD+V+ G    A
Sbjct: 1   MTDIVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKR-AGVEAEAVDEVLLGHILTA 59

Query: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120
           G   +N AR +A+ AG+P  A    IN+LCGSG+ AV    +AIK G+A +++AGG ESM
Sbjct: 60  G-CGQNTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESM 118

Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180
           + A   +          A + DT I     +       G+     TAEN+AE+F I+R +
Sbjct: 119 SNAQHAIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGI-----TAENLAEKFQITREE 173

Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240
           QDAFAL SQ KA  A + G    +IV V I  K+ + +  T +      +L+ +A+ K  
Sbjct: 174 QDAFALGSQNKAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPA 233

Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
            + DGTVTA NASG+NDG  AL++ + + A++ G++  AR+ G ATAG +P  MG GP P
Sbjct: 234 FKKDGTVTAANASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPVP 293

Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360
           ATQKLL +LG   + LD+IE NEAFA+Q +AV + +G   D  +VN NGGAIA+GHP+GA
Sbjct: 294 ATQKLLAKLGWKHEDLDLIEANEAFAAQAIAVNKGMGW--DTSKVNVNGGAIAIGHPIGA 351

Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399
           SGAR++   L+++ R + +  L T+CIG G GIAL +ER
Sbjct: 352 SGARILVDLLYEMGRRDAKKGLATLCIGGGMGIALCVER 390


Lambda     K      H
   0.319    0.134    0.386 

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: 398
Number of extensions: 13
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: 400
Length of database: 390
Length adjustment: 31
Effective length of query: 369
Effective length of database: 359
Effective search space:   132471
Effective search space used:   132471
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: 50 (23.9 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, the preprint 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