GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Cupriavidus basilensis 4G11

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase

Query= curated2:Q9V1I4
         (364 letters)



>FitnessBrowser__Cup4G11:RR42_RS16955
          Length = 395

 Score =  212 bits (539), Expect = 2e-59
 Identities = 132/376 (35%), Positives = 205/376 (54%), Gaps = 23/376 (6%)

Query: 5   RKRLKIVRGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFE 64
           R  L    G+G ++ D  GKRYLD + G  V  LGH++   ++ + +Q  KL    P F 
Sbjct: 17  RPELVFTEGKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFY 76

Query: 65  HEEKEEMLEELSRWVNFEYVYMGNSGTEAVEAALKFARLYTGRK------EIIAMTNAFH 118
           +E    +  +L+    F+ V+  NSG EA E A+K AR + GRK      EII M ++FH
Sbjct: 77  NEPMLRLARQLTDASCFDKVFFANSGAEANEGAIKLARKW-GRKHKNGAFEIITMDHSFH 135

Query: 119 GRTMGALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAVIFEPIQGESGII 178
           GRT+  +SA+ K+ +   F P VPGF     ND+ + ++ I   T A++ EP+QGE G+I
Sbjct: 136 GRTLATMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLINDKTVAIMLEPVQGEGGVI 195

Query: 179 PAKEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNGVP 237
           PA  EF++ LR L +    L I DEVQ+G  R G   A E   VEPDI+TLGKGIG GVP
Sbjct: 196 PASREFMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGGVP 255

Query: 238 VSLTLTNFDV---ERGKHGSTFGGNPLACKAVAVTLRILRKERLVEKASEKFIKVKGKDV 294
           ++  L   +V   E G  G T+ GNP+     +  +  L     ++   +K   ++ + +
Sbjct: 256 LAALLCKAEVASFEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLREQLL 315

Query: 295 VTT--------RGRGLMIGIVLKKPVG-RYVEE---LQNEGYLVHTSGQRVIRLLPPLII 342
             T        RG GL+  +VL K +G + VEE   +Q +G L+++    ++R +P L +
Sbjct: 316 ALTSEFGLGGERGEGLLRALVLNKDIGPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNV 375

Query: 343 SKEKMMEVKSAIEGVI 358
           + E++ ++ S +  ++
Sbjct: 376 TIEEIDQMISMLRTLL 391


Lambda     K      H
   0.318    0.137    0.393 

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: 319
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: 364
Length of database: 395
Length adjustment: 30
Effective length of query: 334
Effective length of database: 365
Effective search space:   121910
Effective search space used:   121910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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