GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Marinobacter adhaerens HP15

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate GFF349 HP15_347 glutamate-1-semialdehyde 2,1-aminomutase

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__Marino:GFF349
          Length = 426

 Score =  136 bits (343), Expect = 1e-36
 Identities = 99/297 (33%), Positives = 152/297 (51%), Gaps = 15/297 (5%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           PI   H + A ++D D +RYID++G  G + LGH +  + +A+ AQ      Y    AP 
Sbjct: 33  PIFFKHAQGAYLYDEDDQRYIDYIGSWGPMILGHGDQRIKDALHAQVDLGVGYG---APT 89

Query: 75  GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTL 134
                + +++ + +P S  L  M+ NSG EA  + +++ARG TG+  I+ F+G +HG   
Sbjct: 90  ALETEMAKKVCELMP-SIELVRMV-NSGTEATMSTVRLARGYTGRDKIVKFEGCYHGHVD 147

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194
           + L   G  A     V   PG    +P   A+  +T         R    E+  + +AA 
Sbjct: 148 SLLVKAGSGA-LTLGVPNSPG----IPASLAEHTITLTYNDIDSVRECFREMG-DQIAAI 201

Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254
           I EPV G    +   P F + LR  CDE G ++I DE+ +GF R     A    G+ PDL
Sbjct: 202 IVEPVAGNMNCIPPVPGFLEGLREVCDEHGTVLIFDEVMTGF-RVSLGGAQGLYGVTPDL 260

Query: 255 LLLAKSIAGGMPLGAVVGRKELMAAL-PKGGL--GGTYSGNPISCAAALASLAQMTD 308
             L K I GG+P+GA  G++E+M  + P G +   GT SGNP++  A L +L  +++
Sbjct: 261 TALGKVIGGGLPVGAFGGKREIMEHISPLGPVYQAGTLSGNPLAMCAGLTTLNAISE 317


Lambda     K      H
   0.320    0.137    0.402 

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: 432
Number of extensions: 20
Number of successful extensions: 5
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: 416
Length of database: 426
Length adjustment: 32
Effective length of query: 384
Effective length of database: 394
Effective search space:   151296
Effective search space used:   151296
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 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