GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Shewanella loihica PV-4

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 5208066 Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__PV4:5208066
          Length = 405

 Score =  242 bits (617), Expect = 2e-68
 Identities = 149/388 (38%), Positives = 213/388 (54%), Gaps = 19/388 (4%)

Query: 24  YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83
           Y    ++ VRG+G+RVWD EGNE++D  GG  V  LGH +P +V A+K Q E +  +   
Sbjct: 20  YAPSAVIPVRGEGSRVWDQEGNEFVDFAGGIAVNCLGHCHPALVGALKEQGEKIWHLANV 79

Query: 84  LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAAM 137
           +           L      E  +V+  NSG EANEAALK AR +   K      + +A  
Sbjct: 80  MTNEPALALATKLVEATFAE--KVYFANSGAEANEAALKLARRYALDKFGAEKDQIIAFD 137

Query: 138 RGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGE 197
           + F GRT  ++SV  +  Y + F P  + +  +P+ND+ AL+  V ++T A++LEP+QGE
Sbjct: 138 KAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPFNDIAALEAEVSDKTCAIMLEPLQGE 197

Query: 198 GGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALG 257
           GG+  A PEFLRA R +  +  AL+I DE+QTG+GR G+ +A+    + PDILT AKALG
Sbjct: 198 GGIIDADPEFLRAVRALADKHNALVIFDEVQTGVGRLGELYAYMRTEVTPDILTTAKALG 257

Query: 258 GGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWF 317
           GG P+ A +   E+A  +  G HG+T+GGNPLA A G A +  +    + +         
Sbjct: 258 GGFPIAAMLTTTEIASHLKIGTHGSTYGGNPLACAIGNAVLDVVNTPEVLDGVKRREQLL 317

Query: 318 MEKLRAIPSP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIR 371
            + L  I        EVRG GL++G  L E    ++  ++     E  ++ L AGP VIR
Sbjct: 318 RDGLNQINEKYHVFTEVRGQGLLLGAVLNEQYQGRSKDFLVAGTSE-GLMCLIAGPNVIR 376

Query: 372 FLPPLVIEKED----LERVVEAVRAVLA 395
           F P LVI + D    L R   AV  V+A
Sbjct: 377 FTPSLVIPEADIAEGLARFERAVAKVVA 404


Lambda     K      H
   0.319    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: 390
Number of extensions: 25
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: 395
Length of database: 405
Length adjustment: 31
Effective length of query: 364
Effective length of database: 374
Effective search space:   136136
Effective search space used:   136136
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 (21.7 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