GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Lentibacillus jeotgali Grbi

Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_010530795.1 ON01_RS09455 pyridoxal phosphate-dependent aminotransferase

Query= CharProtDB::CH_004890
         (393 letters)



>NCBI__GCF_000224785.1:WP_010530795.1
          Length = 394

 Score =  557 bits (1436), Expect = e-163
 Identities = 273/392 (69%), Positives = 321/392 (81%)

Query: 1   MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60
           M+LA RV  LTPS+TLAITAKAKELK+ G+DVIGLGAGEPDFNTP++I+ AA  +M  G 
Sbjct: 1   MELANRVKTLTPSSTLAITAKAKELKSQGYDVIGLGAGEPDFNTPEYILKAAGEAMQNGF 60

Query: 61  TKYTPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIP 120
           TKYTP+GG+ ELK +IA KF+RD  + Y   +IIV TGAKHALYTLFQV+L++ DEVI+P
Sbjct: 61  TKYTPAGGITELKQAIANKFRRDNGLTYTTEEIIVTTGAKHALYTLFQVLLNKTDEVIVP 120

Query: 121 TPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMY 180
            PYWVSYPEQ+KLA GKPV++   E+N FKI+PEQL+ AIT KTKA++INSPSNPTG+MY
Sbjct: 121 APYWVSYPEQIKLAEGKPVFINAEEKNAFKITPEQLEAAITPKTKAVIINSPSNPTGMMY 180

Query: 181 TEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHS 240
            +EEL  LGE+CL+H+ILIVSDEIYEKL Y    HVS+A++S +LK+ TVIINGVSKSHS
Sbjct: 181 NQEELQQLGEICLKHNILIVSDEIYEKLIYTSDNHVSMAEISSQLKDHTVIINGVSKSHS 240

Query: 241 MTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300
           MTGWRIGYAAG  DIIK MTNLASHSTSNPTSIAQY A+AAYN   +P  EMRE F  RL
Sbjct: 241 MTGWRIGYAAGPADIIKPMTNLASHSTSNPTSIAQYAALAAYNTDEDPNAEMREIFSERL 300

Query: 301 NTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSG 360
             +Y  L +IPG SCVKP+GAFY+FPN +EA    GF  VD++VKALLEEEKVA+VPGSG
Sbjct: 301 ELLYDLLTDIPGISCVKPKGAFYVFPNVREAVSQNGFDTVDDWVKALLEEEKVALVPGSG 360

Query: 361 FGSPENVRLSYATSLDLLEEAIERIKRFVEKH 392
           FGSPENVRLSYA S D L+EA  RIKRF+  H
Sbjct: 361 FGSPENVRLSYAVSADSLKEAATRIKRFILNH 392


Lambda     K      H
   0.313    0.131    0.370 

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: 578
Number of extensions: 22
Number of successful extensions: 1
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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