GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysJ in Desulfovibrio vulgaris Miyazaki F

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)

Query= curated2:Q5SHH5
         (395 letters)



>lcl|FitnessBrowser__Miya:8502443 DvMF_3149 acetylornithine
           aminotransferase (RefSeq)
          Length = 402

 Score =  241 bits (616), Expect = 2e-68
 Identities = 141/398 (35%), Positives = 218/398 (54%), Gaps = 12/398 (3%)

Query: 7   EDWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEV 66
           E + AL   E++L    Y ++ + + RGQG+R+WD +G EY+D + G  V +LGH + E+
Sbjct: 3   ERFEALKAREESLLCRTYGRYPISVARGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEEL 62

Query: 67  VEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA 126
            E    QA  L+ +        + +    L +       + F  NSG EANEAA+K AR 
Sbjct: 63  AEVAAAQARKLVHVSNLFYQEEQLDLAERLLST--SHCTKAFFCNSGAEANEAAIKLARR 120

Query: 127 HT----GRKKF--VAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKR 180
           +     GR+ +  +     F GRT+ +++ T + K+++ F P+ E    +P  D+EAL+ 
Sbjct: 121 YMQRVQGREAYEIITLTGAFHGRTLATVAATGQAKFQDGFYPMPEGFRQVPSGDIEALRA 180

Query: 181 AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAF 240
           A+  +TA V++E VQGEGGV P  P++ RA + + +EKG L + DEIQ GM RTG+ ++F
Sbjct: 181 AIGPQTAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSF 240

Query: 241 EHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRY 300
           +++G+ PDI++ AKAL  G+P+GA +  +EVAR    G H TTFG   L  A     +  
Sbjct: 241 QNYGLEPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEI 300

Query: 301 LERTRLWERAAELGPWFMEKLRAIPSP---KIREVRGMGLMVGLELKEKAAPYIARLEKE 357
           + R  L  RAA  G   M++ RA+       I  VRG+GLM+G+ L          L   
Sbjct: 301 MLRDDLAGRAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVVLAFPGKEVWQALIDR 360

Query: 358 HRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395
             +  L     V+R LP L I + DL+   +A+  +L+
Sbjct: 361 GFICNL-TQDCVLRLLPALTIPRADLDAFADALEDILS 397


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: 340
Number of extensions: 16
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: 402
Length adjustment: 31
Effective length of query: 364
Effective length of database: 371
Effective search space:   135044
Effective search space used:   135044
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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