GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Magnetospirillum magneticum AMB-1

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

Query= uniprot:Q5JFW3
         (362 letters)



>NCBI__GCF_000009985.1:WP_083763404.1
          Length = 384

 Score =  263 bits (671), Expect = 8e-75
 Identities = 156/373 (41%), Positives = 211/373 (56%), Gaps = 24/373 (6%)

Query: 1   MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59
           MP Y R  L   RGEG Y++   GRRYLD  AG+ VN LGH HP  V  ++ Q  K+   
Sbjct: 1   MPTYARADLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHT 60

Query: 60  GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR---LATG---RSEIVAM 113
             ++    +E +  +L      + V+  NSG EA+E +IK AR    A G   R  I+  
Sbjct: 61  SNLYRVAGQESVAAKLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICA 120

Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173
             AFHGRTL +++A  +KK+ EGF P V GF H+P+ N+ A + +IT+ETAA++ EP+QG
Sbjct: 121 EGAFHGRTLATVAAGGQKKHLEGFAPAVDGFDHVPYGNLNALRASITEETAAILVEPVQG 180

Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232
           EGGIVP D ++++ LR   ++ G LLI DEVQ+G+ RTG   A E  G+ PDI+ + KG+
Sbjct: 181 EGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQAGIAPDIMGVAKGL 240

Query: 233 GNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVE-------- 280
           G GFPV   L   +    +  G HGSTFGGNPLA       L I+     +E        
Sbjct: 241 GGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAEPGFLEHVQAMAAL 300

Query: 281 ---KAGEKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLL 337
              K  +    F G  V + RG GLM+GI  R P    V  L E G+L   AG+ ++RLL
Sbjct: 301 LRSKVEDTAARFPGV-VEEVRGLGLMLGIKPRMPNTEMVARLAEGGLLTVGAGDNIVRLL 359

Query: 338 PPLIIEGDTLEEA 350
           PPLII    ++EA
Sbjct: 360 PPLIINDAQVDEA 372


Lambda     K      H
   0.320    0.140    0.410 

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: 373
Number of extensions: 18
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: 362
Length of database: 384
Length adjustment: 30
Effective length of query: 332
Effective length of database: 354
Effective search space:   117528
Effective search space used:   117528
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 (21.8 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