GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Desulfarculus baarsii DSM 2075

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_013258699.1 DEBA_RS09455 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P39912
         (358 letters)



>NCBI__GCF_000143965.1:WP_013258699.1
          Length = 343

 Score =  182 bits (463), Expect = 9e-51
 Identities = 113/264 (42%), Positives = 160/264 (60%), Gaps = 11/264 (4%)

Query: 96  VSRKKKPEDTIVDI-KGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAF 154
           ++R   P  +I+ +  G +IG      I GPCA+ES +Q+ + A      G  ILRGGAF
Sbjct: 75  LTRDFHPRPSIIRLGSGLRIGK-DLAVIAGPCAIESRDQLMKTAKLVVDAGANILRGGAF 133

Query: 155 KPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDY-IDVIQIGARNMQ 213
           KPRT    FQGL  +GL++L    ++F + VI+EI+    I   ++Y ID+ Q+GARN  
Sbjct: 134 KPRTIHRSFQGLREDGLKLLAEAREKFGIPVITEIMDARDIHLFVEYDIDIWQVGARNCL 193

Query: 214 NFELLKAAGAVK--KPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATR 271
           N+ LL A   +K  KPV+LKRG   +ISEF+ AA  +   GN ++ILCERG +T +   R
Sbjct: 194 NYTLLDALAEMKNPKPVVLKRGDHVSISEFLGAALRLYD-GNTKVILCERGDKTVDPVYR 252

Query: 272 NTLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVAL 331
           N L+++ V  LK+  HLPV VD +H TG R ++   A A +A GADG+M EVH  P  AL
Sbjct: 253 NVLNLNNVAWLKKRYHLPVLVDPSHGTGVRQIVPDMALAGIAAGADGLMVEVHHKPEEAL 312

Query: 332 SDSAQQMAIPEFEKWLNELKPMVK 355
            D AQ ++  +F+K    L P+V+
Sbjct: 313 CDGAQSLS-ADFKK----LTPLVR 331


Lambda     K      H
   0.316    0.134    0.369 

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: 330
Number of extensions: 18
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: 358
Length of database: 343
Length adjustment: 29
Effective length of query: 329
Effective length of database: 314
Effective search space:   103306
Effective search space used:   103306
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 25 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