GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Lentibacillus jeotgali Grbi

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_010530050.1 ON01_RS05690 dihydrodipicolinate synthase family protein

Query= BRENDA::A9CFV4
         (303 letters)



>NCBI__GCF_000224785.1:WP_010530050.1
          Length = 292

 Score =  139 bits (350), Expect = 8e-38
 Identities = 85/282 (30%), Positives = 141/282 (50%), Gaps = 3/282 (1%)

Query: 2   KFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLA 61
           KFEG+Y   +TP+  D ++D    + + E L+   V G+I  G  GEY   + +ER  + 
Sbjct: 3   KFEGVYISLVTPMTKDYKVDYKRLSEICEWLIGKGVDGLIPAGPLGEYATLSNEERRKVV 62

Query: 62  AYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHAL 121
               +    R+ ++VGTGA+ T D I++AK AK   AD IL   P    P E E   H  
Sbjct: 63  ETVIKASKRRVSVIVGTGASATRDVIDWAKHAKSNEADGILALPPVNYKPLENEVITHFE 122

Query: 122 AVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKFPQI 181
           A+     +PI+ +N P   GV +  +  +++ +S+N+V +KE SGD+  +  +  K   +
Sbjct: 123 AISE-VGIPIIAFNNPRDFGVDLSPDLLAKISESENIVGVKEFSGDIRRVQEILEK-TNL 180

Query: 182 ALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLM 241
            +  G DD A+E    GA  W    SN LP E + L++    E+ F++   +   ++ L 
Sbjct: 181 EVFVGVDDLAMEGALCGASGWTSGVSNALPEEGIKLFQ-LAKERRFEEASILYRDLVKLF 239

Query: 242 DFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQ 283
            +    + +QSIK+  E+ G   G  R P   L +   + ++
Sbjct: 240 HYDANPQLIQSIKYMMELAGQPVGPTRPPRLALTNKAYKEIE 281


Lambda     K      H
   0.320    0.135    0.397 

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: 176
Number of extensions: 11
Number of successful extensions: 4
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: 303
Length of database: 292
Length adjustment: 26
Effective length of query: 277
Effective length of database: 266
Effective search space:    73682
Effective search space used:    73682
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: 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