GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Enterococcus termitis LMG 8895

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_069665193.1 BCR25_RS19025 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P39912
         (358 letters)



>NCBI__GCF_001730305.1:WP_069665193.1
          Length = 341

 Score =  285 bits (728), Expect = 2e-81
 Identities = 139/261 (53%), Positives = 186/261 (71%)

Query: 95  LVSRKKKPEDTIVDIKGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAF 154
           L SR+  PE+TIVD+ G KIGDG    + GPC++E  +Q+ E A  AK  G  ILRGGAF
Sbjct: 71  LTSREFHPENTIVDVDGVKIGDGSMTMMAGPCSIEGLDQIRECARIAKAGGATILRGGAF 130

Query: 155 KPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQN 214
           KPRTSPY FQGL  EGL+ +++ ADEFD+ VI+E++   HI+   +Y D++QIGARNMQN
Sbjct: 131 KPRTSPYAFQGLEEEGLKYIRQAADEFDMKVITEVMDEGHIDMIAEYSDILQIGARNMQN 190

Query: 215 FELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTL 274
           F+LL+A G   KP+ LKRG++ TI E++NAAEYI +QGN  +I  ERGIRTYETATRNTL
Sbjct: 191 FKLLQAVGKTGKPIGLKRGISGTIDEWLNAAEYIAAQGNFNVIFIERGIRTYETATRNTL 250

Query: 275 DISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDS 334
           D+SAVP++K+ +H P+ VD +H  G  DL+   A+A +A GADG++ E+HPDP  A SD 
Sbjct: 251 DLSAVPLIKKLSHFPIIVDPSHGVGIWDLVPSMARAGVAAGADGLIVEIHPDPVNAWSDG 310

Query: 335 AQQMAIPEFEKWLNELKPMVK 355
            Q +    + + + E+  M K
Sbjct: 311 PQSLNEKTYMRMMQEVHIMEK 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: 324
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 341
Length adjustment: 29
Effective length of query: 329
Effective length of database: 312
Effective search space:   102648
Effective search space used:   102648
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 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