GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Lentibacillus jeotgali Grbi

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_010529812.1 ON01_RS04515 D-amino-acid transaminase

Query= BRENDA::E6TUA8
         (302 letters)



>NCBI__GCF_000224785.1:WP_010529812.1
          Length = 287

 Score =  142 bits (359), Expect = 7e-39
 Identities = 85/272 (31%), Positives = 147/272 (54%), Gaps = 7/272 (2%)

Query: 6   IFSNGKFVTKQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIMLEI 65
           I S   F  +        + G  +GDG++E IR+Y G  + +TEH+ RL+ SA++I +++
Sbjct: 7   ILSQADFTNRDSLTYPFEERGLQFGDGIYEVIRIYQGAYYLITEHVNRLFRSAEAIKIDL 66

Query: 66  PYSKEDFQQIIVDTVRKNQLES-GYIRVVVSRGPGNLGLDPSRCSAPHVIVIAEELALFP 124
           P+S+++   ++ D + +N++ S G + +  +RG           +  +V    +++   P
Sbjct: 67  PFSRQEITSLLHDLLSQNEMTSDGIVYLQATRGSAPRNHAFPVDTPANVYAYVQDM---P 123

Query: 125 KELYELGLTVASVASRRNRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQGYVT 184
           ++   L   V+++  R  R +  +  IKSLN L N+L K  A + G++EA++  D G VT
Sbjct: 124 RKTKNLTNGVSAITKRDTRWE--NCYIKSLNLLPNVLAKQAAQENGSYEAILERD-GKVT 180

Query: 185 EGSADNIFIVKNNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHDVYVADEV 244
           E S+ N+++VK+  I T P     L G  R  +   A        E  F+  D+  ADEV
Sbjct: 181 ECSSSNVYLVKDGKIYTHPATNRILHGCVRMRVEQFAAGLNIPFVEQAFSIEDIADADEV 240

Query: 245 FLTGTAAEVIAVVEVDKRMISDGKPGKVTNHL 276
           FL+ + +EV+ +VEVD + I++G PGK T  L
Sbjct: 241 FLSSSTSEVMPIVEVDGKKIAEGIPGKTTQML 272


Lambda     K      H
   0.318    0.136    0.385 

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: 236
Number of extensions: 10
Number of successful extensions: 3
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: 302
Length of database: 287
Length adjustment: 26
Effective length of query: 276
Effective length of database: 261
Effective search space:    72036
Effective search space used:    72036
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 (21.7 bits)
S2: 48 (23.1 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