GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Marinobacter adhaerens HP15

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate GFF3630 HP15_3572 aminotransferase, classes I and II

Query= BRENDA::P9WPZ5
         (397 letters)



>FitnessBrowser__Marino:GFF3630
          Length = 401

 Score =  101 bits (251), Expect = 4e-26
 Identities = 89/282 (31%), Positives = 124/282 (43%), Gaps = 13/282 (4%)

Query: 88  VLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVP------D 141
           +L+  G   +I AA +    PG  V++  P Y  +   V  +G   +  PLVP      D
Sbjct: 90  ILMAPGVVPSINAACMAYAGPGEGVIIQPPVYPPFFSSVRHSGRVVIENPLVPEDPDTGD 149

Query: 142 GRGFALDADALRR-AVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVVITDEV 200
              + +D D L   A  P  R L++ SPHNP G V S  EL A+ +IA    LVV++DE+
Sbjct: 150 PGHYRMDLDHLEECAARPDARVLLLCSPHNPVGRVWSEEELRAVLDIARRHQLVVVSDEI 209

Query: 201 YEHLVF-DHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGP-AELIAGVRAAK 258
           +  LVF D  RH  LA   G  +  +   + +K FN  G  +     P AE    ++A  
Sbjct: 210 HCDLVFPDKPRHTMLANLAGPDDALVMAVAPSKSFNMPGLGLSALVIPDAERRKAMKAVF 269

Query: 259 QYLSYVGGAPFQPA-VALALDTEDAWVAALRNSLRARRDRL--AAGLTEIGFAVHDSYGT 315
           + +      PF  A           W+  L   L+A RD +  A G    G  V    GT
Sbjct: 270 ESMHLPQCNPFSIAGFEAGYRHGGPWLDDLMAYLQANRDYVVEAVGQRLPGVRVSAPEGT 329

Query: 316 YFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAG 357
           Y +  D R LG DD+         K GV   P  +F DP +G
Sbjct: 330 YLMWLDCRELGLDDA-GLKRFFVRKAGVGMNPGLSFGDPGSG 370


Lambda     K      H
   0.321    0.135    0.405 

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: 435
Number of extensions: 24
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: 397
Length of database: 401
Length adjustment: 31
Effective length of query: 366
Effective length of database: 370
Effective search space:   135420
Effective search space used:   135420
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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