Aligments for a candidate for lysJ in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Aligments for a candidate for lysJ in Pseudomonas fluorescens FW300-N2E3

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03025
          Length = 406

 Score =  267 bits (682), Expect = 5e-76
 Identities = 158/377 (41%), Positives = 222/377 (58%), Gaps = 17/377 (4%)

Query: 32  VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPT-PMRG 90
           VRG G+RVWD  G E ID  GG  V  LGH +P +V A+  QA  L  +       P   
Sbjct: 29  VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANKLWHVSNVFTNEPALR 88

Query: 91  EFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR--AHT--GRKKF--VAAMRGFSGRT 144
             ++ + A      +RVF  NSG EANEAA K AR  AH   G +K+  +AA+  F GRT
Sbjct: 89  LAHKLIDATFA---DRVFFCNSGAEANEAAFKLARRVAHDRFGSEKYEIIAALNSFHGRT 145

Query: 145 MGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPAT 204
           + +++V  + KY + F P +  +  + +ND++ALK A+ ++T AV+LEP+QGEGGV PA 
Sbjct: 146 LFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALKAAISDKTCAVVLEPIQGEGGVLPAD 205

Query: 205 PEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGA 264
             +L+ ARE+  +  ALLI DE+QTGMGR+G+ FA++H+G+ PDILT AK+LGGG P+ A
Sbjct: 206 LAYLQGARELCTQHNALLIFDEVQTGMGRSGELFAYQHYGVTPDILTSAKSLGGGFPIAA 265

Query: 265 AVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAI 324
            +  E++A+ +  G HGTT+GGNPLA A   A I  +    +          F  +L  I
Sbjct: 266 MLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLNGVKAKHDLFKTRLEQI 325

Query: 325 PSP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIRFLPPLVI 378
            +      +VRG+GL++G  L E    KA       E+E  ++ LQAGP VIRF P LV+
Sbjct: 326 GAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNAAERE-GLMILQAGPDVIRFAPSLVV 384

Query: 379 EKEDLERVVEAVRAVLA 395
           E  D+E  +E     +A
Sbjct: 385 EDADIEEGLERFERAVA 401


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: 385
Number of extensions: 19
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: 406
Length adjustment: 31
Effective length of query: 364
Effective length of database: 375
Effective search space:   136500
Effective search space used:   136500
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis