GapMind for Amino acid biosynthesis

 

Alignments for a candidate for IGPS in Enterococcus termitis LMG 8895

Align Indole-3-glycerol phosphate synthase; IGPS; EC 4.1.1.48 (uncharacterized)
to candidate WP_069663042.1 BCR25_RS07715 indole-3-glycerol phosphate synthase TrpC

Query= curated2:Q8Y6Q4
         (252 letters)



>NCBI__GCF_001730305.1:WP_069663042.1
          Length = 252

 Score =  290 bits (743), Expect = 1e-83
 Identities = 151/252 (59%), Positives = 188/252 (74%)

Query: 1   MTFLEEILAQKEVEVAKMPLEQVAEKRKTYSFYEFLKANTNTMQLIAEVKRASPSKGEIN 60
           M FLE+I+ +K+ E+ KMPLE++   R+T SFYE +K N   + +I EVKRASPSKG IN
Sbjct: 1   MDFLEKIITEKKQEIQKMPLEKLQPLRQTTSFYERVKKNPEKIHIIGEVKRASPSKGAIN 60

Query: 61  MGVNPVLQAKSYQAAGAGMISVLTDPVFFKGSIEDLREVAKNVGIPVLCKDFIISEKQLI 120
           + VN + QAK+Y+ AG   ISVLTDP FFKGSIEDLR+VA  V IPVLCKDFII EKQLI
Sbjct: 61  LSVNVIEQAKAYEKAGVTAISVLTDPTFFKGSIEDLRQVAAEVSIPVLCKDFIIDEKQLI 120

Query: 121 RARNAGATVVLLIISALTEEKLITLFEQALALDLEVLVEVHDQEELAVAQKIGAQLIGVN 180
           RARNAGAT+VLLI+SAL+  +L  L+EQA  L LEVLVEVHD++E  +A+++GA LIGVN
Sbjct: 121 RARNAGATIVLLIVSALSRSRLKKLYEQARTLGLEVLVEVHDEQEQTIAEELGASLIGVN 180

Query: 181 NRNLHTFEVDIAVSERLASDFSSDACFISESGFRTAEDVARVSQKYDAVLVGEALMREAT 240
           NRNL TF+V + VS+ L     +DA +ISESGF  A  V +V  KY A+LVGE LMR+  
Sbjct: 181 NRNLKTFDVSLNVSQLLGEKQRTDAVYISESGFSDATQVEQVKDKYQAILVGEGLMRQTE 240

Query: 241 PEVAAKSLKVTR 252
           P    K L+V+R
Sbjct: 241 PMDKVKELQVSR 252


Lambda     K      H
   0.317    0.131    0.344 

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: 204
Number of extensions: 7
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: 252
Length of database: 252
Length adjustment: 24
Effective length of query: 228
Effective length of database: 228
Effective search space:    51984
Effective search space used:    51984
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: 46 (22.3 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