GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Lentibacillus jeotgali Grbi

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_010532310.1 ON01_RS17455 isochorismate synthase

Query= curated2:Q9YGB3
         (433 letters)



>NCBI__GCF_000224785.1:WP_010532310.1
          Length = 461

 Score =  149 bits (376), Expect = 2e-40
 Identities = 104/297 (35%), Positives = 152/297 (51%), Gaps = 12/297 (4%)

Query: 144 LVERARREESRLED------GGSEVIST-DAGMEEFVEIVRAGKEYIYSGDVFQVVLSRE 196
           L  R +R E+ L D      GG+ V ST D   EE+ + V+   +YI   DV ++VL+RE
Sbjct: 166 LASRIKRMENTLCDDSVYIPGGTGVESTEDIAPEEWKQTVKFATDYIKQSDVDKIVLARE 225

Query: 197 YRVRTDLDA--LEIYKRLVELNPSPYTFILEFE-KTVVGASPETMGSVEGRTFKINPIAG 253
             V+   +A    +   L+E   + Y F  E +    VG+SPE +   +        +AG
Sbjct: 226 LLVKLSDNAQITPVLGNLIETQTNSYVFAFERDGDCFVGSSPERLVRQDKNEVLSTCLAG 285

Query: 254 TAPRGRTGEEDRELEKALLSDEKERAEHVMLVDLARNDVRRVSKPGSVRLTRFFDVLKYS 313
           TAPRG+T +ED ++  +LL DEK R+EH  +V + R  + R  +   V        LK  
Sbjct: 286 TAPRGKTQKEDAKIGNSLLHDEKNRSEHDFVVKMIRQSMERYCRAVDVPDKPVIYPLK-- 343

Query: 314 HVQHIESEVVGELDEGKNAFDAMEAAFPAGTLTGAPKIRAMEIIDELERSRRKVYGGAVG 373
           ++QH+ + V   L EG + FD +    P   L G P+ +++E I   ER  R  YG  VG
Sbjct: 344 NLQHLYTPVKATLKEGYSIFDIIGKLHPTPALGGVPREKSLEFIRNQERLDRGWYGAPVG 403

Query: 374 YFSLTGDADMAIAIRMAEIEGRKASVRAGAGIVADSVPEKEFFETENKMRAVLKALG 430
           +       + A+AIR   I+G +AS+ AG GIV DS PE E+ ET  K   +L  LG
Sbjct: 404 WLDSNASGEFAVAIRSGLIQGDQASLFAGCGIVRDSDPEAEYEETNIKFTPMLSVLG 460


Lambda     K      H
   0.318    0.137    0.384 

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: 397
Number of extensions: 14
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: 433
Length of database: 461
Length adjustment: 33
Effective length of query: 400
Effective length of database: 428
Effective search space:   171200
Effective search space used:   171200
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: 51 (24.3 bits)

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

Links

Downloads

Related tools

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