GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens FW300-N2C3

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AO356_18725 AO356_18725 acetylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18725
          Length = 406

 Score =  259 bits (661), Expect = 1e-73
 Identities = 151/365 (41%), Positives = 209/365 (57%), Gaps = 15/365 (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  EFYRTLTAILPPELNRVFPVNSGTEANEAALKFARA----HTGRKKF--VAAMRGFSGRT 144
             ++ + A       R F  NSG EANEAA K AR       G +K+  +AA+  F GRT
Sbjct: 89  LAHKLVNATFA---ERAFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRT 145

Query: 145 MGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPAT 204
           + +++V  + KY + F P +  +  +PYND+ ALK AV ++T AV+LEP+QGEGGV PA 
Sbjct: 146 LFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAE 205

Query: 205 PEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGA 264
             +L+ AR++     ALL+ DE+QTGMGR+G  FA+ H+G+VPDILT AK+LGGG P+ A
Sbjct: 206 QAYLQGARDLCDAHDALLVFDEVQTGMGRSGHLFAYMHYGVVPDILTSAKSLGGGFPIAA 265

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

Query: 325 PSP--KIREVRGMGLMVGLELKEK---AAPYIARLEKEHRVLALQAGPTVIRFLPPLVIE 379
                   +VRG+GL++G  L +     A  I    ++  ++ LQAGP VIRF P LV+E
Sbjct: 326 GEKYGLFTQVRGLGLLIGCVLNDAWKGKAKDIFNAAEQEGLMILQAGPDVIRFAPSLVVE 385

Query: 380 KEDLE 384
             D++
Sbjct: 386 DADID 390


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: 394
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.

Links

Downloads

Related tools

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