GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lat in Magnetospirillum magneticum AMB-1

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein

Query= BRENDA::P9WQ77
         (449 letters)



>lcl|NCBI__GCF_000009985.1:WP_083763404.1 AMB_RS01605 aspartate
           aminotransferase family protein
          Length = 384

 Score =  156 bits (395), Expect = 1e-42
 Identities = 135/418 (32%), Positives = 193/418 (46%), Gaps = 49/418 (11%)

Query: 37  LDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNS 96
           L   R  G+YL  A  GRRYLD    VA +ALG   P LV        L   A      S
Sbjct: 9   LAFERGEGAYLFTA-DGRRYLDFAAGVAVNALGHCHPRLVK------ALTAQAAKVWHTS 61

Query: 97  DVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPAL 156
           ++Y VA    V   A+++       +FF   GA A+E ++K A     RH+ A G     
Sbjct: 62  NLYRVAGQESVA--AKLVERSFADTVFFCNSGAEALECSIKMA----RRHHFAAGNPQRY 115

Query: 157 GTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAE 216
             +++   GAFHGR+  T++    K  +    P  D           G D      L A 
Sbjct: 116 --RIICAEGAFHGRTLATVAAGGQKKHLEGFAPAVD-----------GFDHVPYGNLNA- 161

Query: 217 ALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTG 276
                RA+      + A  + EP+QGEGG     P++   +R   DEF  LLIFDEVQTG
Sbjct: 162 ----LRASIT---EETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTG 214

Query: 277 CGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFA----VPSRLNSTWG 332
            G TGT +A++Q  +APDI+   K     G+  G  V        A    VP    ST+G
Sbjct: 215 MGRTGTLFAHEQAGIAPDIMGVAK-----GLGGGFPVGACLATTKAASGMVPGTHGSTFG 269

Query: 333 GNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFS 392
           GN   M  A  +L+++   G  E        LR+++++ AA FP VV + RG GLM    
Sbjct: 270 GNPLAMAVAGEVLDIMAEPGFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGIK 329

Query: 393 --LPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVV 448
             +P T    E++ +L +  ++ + AG + VR  PPL ++ A++D A+  +  A   V
Sbjct: 330 PRMPNT----EMVARLAEGGLLTVGAGDNIVRLLPPLIINDAQVDEAVGILARAFDEV 383


Lambda     K      H
   0.323    0.137    0.412 

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: 24
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: 449
Length of database: 384
Length adjustment: 31
Effective length of query: 418
Effective length of database: 353
Effective search space:   147554
Effective search space used:   147554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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