GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapA in Sinorhizobium meliloti 1021

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b21508 SM_b21508 dihydrodipicolinate synthetase

Query= BRENDA::Q7D0E8
         (302 letters)



>lcl|FitnessBrowser__Smeli:SM_b21508 SM_b21508 dihydrodipicolinate
           synthetase
          Length = 304

 Score =  371 bits (952), Expect = e-107
 Identities = 185/294 (62%), Positives = 224/294 (76%)

Query: 2   ATRFKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYMYLTREERRR 61
           A  F+GLSAFP TPAD  G+V  +A S L+ R+  A  DS+G+LGSTG Y +L+R ERRR
Sbjct: 4   AVLFEGLSAFPPTPADMDGKVSEDALSRLLERIRVARADSIGLLGSTGAYAFLSRGERRR 63

Query: 62  AIEAAATILRGRRTLMAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYHH 121
           A+E A   + GR  L+ G+GALRTDEA ALA+DA+ AGAD LLLAPVSYTPLT+EE Y H
Sbjct: 64  AVETAVECVGGRVPLIVGVGALRTDEAQALARDAKEAGADGLLLAPVSYTPLTEEEVYQH 123

Query: 122 FAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKMPLPADADYAGELARLR 181
           F AVAGA+ LPL IYNNP TT+F FS+EL+VRL+ +PNI A+KMPLPAD D+ GE+ARLR
Sbjct: 124 FVAVAGASDLPLCIYNNPGTTKFVFSEELIVRLSQVPNIAAVKMPLPADGDFEGEIARLR 183

Query: 182 PKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLMRAAQAGNAEEAKRLDA 241
            K S  FAIGYSGDWG  DA L+G D W+SVV GLLP PA +L RAA+AG+  EA R+D 
Sbjct: 184 AKTSAAFAIGYSGDWGAADALLSGADAWFSVVGGLLPAPASKLARAAKAGDRAEAHRIDM 243

Query: 242 TFQPLWALFKEFGSIRVIYAAANILSLTVSEPPRPILPLTSAERQRVEEALEAL 295
            FQPLWALFKEFGS RV+YA  +IL L  + PPRPILPL   +  RV++A++ L
Sbjct: 244 AFQPLWALFKEFGSFRVMYAIGSILGLFQALPPRPILPLGPGDSVRVKQAVQEL 297


Lambda     K      H
   0.319    0.133    0.381 

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: 255
Number of extensions: 6
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: 302
Length of database: 304
Length adjustment: 27
Effective length of query: 275
Effective length of database: 277
Effective search space:    76175
Effective search space used:    76175
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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