GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Pontimonas salivibrio CL-TW6

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_104914239.1 C3B54_RS03160 aspartate ammonia-lyase

Query= BRENDA::Q9HTD7
         (474 letters)



>NCBI__GCF_002950575.1:WP_104914239.1
          Length = 476

 Score =  502 bits (1292), Expect = e-146
 Identities = 265/457 (57%), Positives = 327/457 (71%), Gaps = 1/457 (0%)

Query: 8   RIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAAADANRQL 67
           R+E+D LG +EVPADAY+G+ T RA++NF +S   +S+YP L+VALA VKQAAA ANR L
Sbjct: 2   RVERDSLGEMEVPADAYWGVHTARALHNFPISRRAISNYPDLLVALARVKQAAARANRDL 61

Query: 68  GHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIALEAMGHTK 127
           G L +DK  AI  AC  +I G  H+QFV+  IQGGAGTSTNM ANE+IAN ALE +GH K
Sbjct: 62  GVLEKDKADAIDAACQEIIDGYLHDQFVLGAIQGGAGTSTNMCANEIIANRALELLGHHK 121

Query: 128 GEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGVEFAGVLK 187
           GEY+YLHP +DVN +QSTND YPTAI+L ++ G   LL    +L +AF  K VEF  VLK
Sbjct: 122 GEYQYLHPIDDVNRSQSTNDVYPTAIKLAMVRGIQALLPEHRALAEAFGDKAVEFRDVLK 181

Query: 188 MGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTGINADPGY 247
           +GRTQLQDAVPMTLGQEF  F TT+ ED DRL  +    L EVN+G TAIGTGI AD  Y
Sbjct: 182 VGRTQLQDAVPMTLGQEFGGFKTTISEDFDRLGEVI-AFLCEVNMGATAIGTGITADSRY 240

Query: 248 QKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSGP 307
            +     LA ++G  ++ A DLIEATSD+G F+  SG+LKR+AVK+SKICNDLRLLSSGP
Sbjct: 241 AEAVRSHLAEVTGLDIRTAPDLIEATSDVGVFMTLSGVLKRSAVKISKICNDLRLLSSGP 300

Query: 308 RTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQLQLNVME 367
           + G+ EINLP  Q GSSIMPGKVNPVIPE VNQVAF VIG+D  +  AAE GQLQLN  E
Sbjct: 301 QAGLGEINLPAVQAGSSIMPGKVNPVIPEVVNQVAFSVIGSDATVCAAAEAGQLQLNAFE 360

Query: 368 PLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPYIGYENST 427
           P++A  I  S+  + +A   LR +C+ GITAN +R    V  S+G+VTAL P IGY  + 
Sbjct: 361 PVMAASILQSLMWMTKACRTLRVNCVVGITANEDRLAAQVASSVGVVTALTPAIGYRKAA 420

Query: 428 RIAKTALESGRGVLELVREEKLLDEATLADILLPENM 464
            +A  ALE  R + ELV +E L++E+ L   L P+ +
Sbjct: 421 ELAHKALEGHRSIRELVLQEGLMEESELDKALHPDRL 457


Lambda     K      H
   0.318    0.135    0.380 

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: 603
Number of extensions: 19
Number of successful extensions: 2
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: 474
Length of database: 476
Length adjustment: 33
Effective length of query: 441
Effective length of database: 443
Effective search space:   195363
Effective search space used:   195363
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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