GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens GW456-L13

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971
          Length = 406

 Score =  265 bits (677), Expect = 2e-75
 Identities = 152/364 (41%), Positives = 209/364 (57%), Gaps = 13/364 (3%)

Query: 32  VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGE 91
           VRG G+RVWD  G E ID  GG  V  LGH +P +V A+  QA  L  +           
Sbjct: 29  VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANKLWHVSNVFTNEPALR 88

Query: 92  FYRTLTAILPPELNRVFPVNSGTEANEAALKFARA----HTGRKKF--VAAMRGFSGRTM 145
               L      E  R F  NSG EANEAA K AR       G +K+  +AA+  F GRT+
Sbjct: 89  LAHKLVDATFAE--RAFFCNSGAEANEAAFKLARRVAFDRYGSEKYEIIAALNSFHGRTL 146

Query: 146 GSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPATP 205
            +++V  + KY + F P +  +  +PYND+ ALK AV ++T AV+LEP+QGEGGV PA  
Sbjct: 147 FTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAEL 206

Query: 206 EFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGAA 265
            +L+ ARE+  E  ALL+ DE+QTGMGRTG  FA++H+G++PDILT AK+LGGG P+ A 
Sbjct: 207 AYLQGARELCNEHNALLVFDEVQTGMGRTGHLFAYQHYGVIPDILTSAKSLGGGFPIAAM 266

Query: 266 VMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIP 325
           +  E++A+ +  G HGTT+GGNPLA A   A I  +    +          F  +L  I 
Sbjct: 267 LTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVIDVINTPEVLAGVNAKHDKFKARLEQIG 326

Query: 326 SP--KIREVRGMGLMVGLELKEK---AAPYIARLEKEHRVLALQAGPTVIRFLPPLVIEK 380
                  +VRG+GL++G  L +     A  I    ++  ++ LQAGP V+RF P LV+E 
Sbjct: 327 EKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNAAEQEGLMILQAGPDVVRFAPSLVVED 386

Query: 381 EDLE 384
            D++
Sbjct: 387 ADID 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: 402
Number of extensions: 20
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:

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