GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Burkholderia phytofirmans PsJN

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase

Query= curated2:Q9V1I4
         (364 letters)



>FitnessBrowser__BFirm:BPHYT_RS15580
          Length = 394

 Score =  215 bits (547), Expect = 2e-60
 Identities = 128/376 (34%), Positives = 204/376 (54%), Gaps = 21/376 (5%)

Query: 5   RKRLKIVRGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFE 64
           R  +    G+G +++D+ GKRYLD I G  V  LGH +   +E +  Q   L+   P F 
Sbjct: 17  RPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEALNKQSQLLINPSPAFY 76

Query: 65  HEEKEEMLEELSRWVNFEYVYMGNSGTEAVEAALKFARLY-----TGRKEIIAMTNAFHG 119
           ++   ++   L++   F+ V+  NSG EA E A+K AR +      G  EII   ++FHG
Sbjct: 77  NQPMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFKDGAFEIITFDHSFHG 136

Query: 120 RTMGALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAVIFEPIQGESGIIP 179
           RT+  +SA+ K  +   + P VPGF     ND+ + ++ I   T AV+ EPIQGE G+IP
Sbjct: 137 RTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVIP 196

Query: 180 AKEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNGVPV 238
           A  EF++ LR+LT+    LLI DEVQSG  R G   A E   +EPDI+TLGKGIG GVP+
Sbjct: 197 ATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEPDIMTLGKGIGGGVPL 256

Query: 239 SLTLTNFDV---ERGKHGSTFGGNPLACKAVAVTLRILRKERLVE--KASEKFIKVK--- 290
           +  L   ++   E G  G T+ GNPL        +  L     +E  +A  ++++ K   
Sbjct: 257 AALLAKAEIAVFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGLRARGEYLRAKLLE 316

Query: 291 ---GKDVVTTRGRGLMIGIVLKKPVGRYVEE----LQNEGYLVHTSGQRVIRLLPPLIIS 343
               +     RG GL+  ++L K +G  + E    +Q +G L++ +   ++R +P L ++
Sbjct: 317 LSEERGFEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPALNVT 376

Query: 344 KEKMMEVKSAIEGVIN 359
            E++ ++ + +  +++
Sbjct: 377 NEEIDQMMTMLRSILD 392


Lambda     K      H
   0.318    0.137    0.393 

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: 335
Number of extensions: 21
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: 364
Length of database: 394
Length adjustment: 30
Effective length of query: 334
Effective length of database: 364
Effective search space:   121576
Effective search space used:   121576
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 (21.6 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