GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Klebsiella variicola At-22

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_012542544.1 KVAR_RS19155 amidohydrolase

Query= curated2:A8YUT2
         (384 letters)



>NCBI__GCF_000025465.1:WP_012542544.1
          Length = 392

 Score =  196 bits (498), Expect = 9e-55
 Identities = 124/352 (35%), Positives = 193/352 (54%), Gaps = 14/352 (3%)

Query: 5   TESELIQIRRHLHEIPELALQEKETHDYLLKIIKGFNSEFLTIKVPEELPTAILV--LIK 62
           TE E+I IR +LH  PEL+L+E  T +    ++ G  +E+   +V   L    +V  L K
Sbjct: 12  TEDEMISIRHYLHANPELSLEEFNTSE----LVAGKLAEW-GYQVTRGLGKTGVVGSLSK 66

Query: 63  GSNPQRTIGYRTDIDALPVEEKTNLPFSSTHPGIMHACGHDIHMSVALGLLSYFSENQPK 122
           G +P RTIG R D+DALP+ E T+LP++ST PG MHACGHD H ++ L    Y +    +
Sbjct: 67  GDSP-RTIGLRADMDALPIHETTDLPWASTVPGKMHACGHDGHTTILLAAAKYIASPACQ 125

Query: 123 DN--LLFFFQPAEESESGGKKAYEDGIFEGKFRPDEFYGLHDNPELPAGAIGCREGTLFA 180
            N  +   FQPAEE+  G     +DG+FE +F  +  +GLH+ P LP G +G   G   A
Sbjct: 126 FNGTVHLIFQPAEEAIGGADLMIKDGLFE-QFPCERIFGLHNMPGLPVGKLGFYAGNFMA 184

Query: 181 GTTEVNIDLIGKGGHAAFPQNANDTVVAAASLIMQIQTVISRSIDPIQSGVITLGKVRAG 240
               V I + G GGH A P+   D +VA A+L+M +Q++++R++ P ++ V+++G  +AG
Sbjct: 185 SADTVKITITGYGGHGAHPERTVDPIVAGAALVMALQSIVARNVPPGETAVVSVGTFQAG 244

Query: 241 TIRNVIAGQTRIEGTIRGLTQKMILQIDQRLQDLCEGIARSYNMKVNLELNQGGYWPVEN 300
              NVI     +E ++R +   +   + +R+ +L +  A+SY     +E+    Y  + N
Sbjct: 245 IASNVIPESVVMELSVRAMKPDIRDLLIKRIHELADFTAKSYGASSVVEV-YDSYPVLTN 303

Query: 301 NPELT--KNFISYMKNNPEVDFVETKPKMTGEDFGFLLAKFPGTMFWLGVGD 350
           +PE T     ++      E       P    EDF F+L + PG+ F LG G+
Sbjct: 304 SPEETDFARALALEVFGREGVLESVSPMNASEDFAFMLRERPGSYFLLGNGE 355


Lambda     K      H
   0.318    0.138    0.403 

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: 409
Number of extensions: 26
Number of successful extensions: 6
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: 384
Length of database: 392
Length adjustment: 30
Effective length of query: 354
Effective length of database: 362
Effective search space:   128148
Effective search space used:   128148
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: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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