GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Echinicola vietnamensis KMM 6221, DSM 17526

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase

Query= curated2:Q9V1I4
         (364 letters)



>FitnessBrowser__Cola:Echvi_0577
          Length = 413

 Score =  206 bits (524), Expect = 9e-58
 Identities = 126/377 (33%), Positives = 202/377 (53%), Gaps = 30/377 (7%)

Query: 12  RGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFEHEEKEEM 71
           RGEG+++WD EG++Y D ++       GH HP+ ++ + +Q   L +    F ++     
Sbjct: 32  RGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPF 91

Query: 72  LEELSRWVNFEYVYMGNSGTEAVEAALKFARLYTGRKE--------IIAMTNAFHGRTMG 123
            + L+ +  ++ V   N+G E VE A+K AR +   K+        II   N FHGRT  
Sbjct: 92  EKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNFHGRTTT 151

Query: 124 ALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAV--IFEPIQGESGIIPAK 181
            +S +     +K+F P  PGF  IP +D++A K+ ++++   +  + EPIQGE+G+   K
Sbjct: 152 VISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSKNIIGYLVEPIQGEAGVYVPK 211

Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNG-VPVS 239
           E ++K +  + +D G L +ADE+Q+G+ RTGK LA +H  V+PD++ LGK I  G  PVS
Sbjct: 212 EGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKAISGGFYPVS 271

Query: 240 LTLTNFD----VERGKHGSTFGGNPLACKAVAVTLRILRKERLVEKAS-------EKFIK 288
             L +      ++ G+HGSTFGGNPL  K     L +++ E+L E A        E+  +
Sbjct: 272 AVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLGKLFRERIQQ 331

Query: 289 VKGKD--VVTTRGRGLMIGIVL-----KKPVGRYVEELQNEGYLVHTSGQRVIRLLPPLI 341
           +  K   V   RG+GL+  IV+          R    L+  G L   +   +IR  PPL+
Sbjct: 332 LVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGNIIRFAPPLV 391

Query: 342 ISKEKMMEVKSAIEGVI 358
           I++E++ +    IE  I
Sbjct: 392 ITEEQLHDCCDIIEKTI 408


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: 380
Number of extensions: 26
Number of successful extensions: 6
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: 413
Length adjustment: 30
Effective length of query: 334
Effective length of database: 383
Effective search space:   127922
Effective search space used:   127922
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