GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Azorhizobium caulinodans ORS 571

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_012172161.1 AZC_RS18745 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P00901
         (198 letters)



>NCBI__GCF_000010525.1:WP_012172161.1
          Length = 401

 Score = 68.2 bits (165), Expect = 2e-16
 Identities = 52/183 (28%), Positives = 82/183 (44%), Gaps = 18/183 (9%)

Query: 15  NVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAGVSIEAILH--FAG 72
           N+++ L   G +V V+     + A + AL P+ + +S GP  P+  G     ++    A 
Sbjct: 223 NILRLLATAGCKVTVVPATT-SAADVLALQPDGVFLSNGPGDPAATGEYAVPVIRELIAK 281

Query: 73  KLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLG--VFTGLNNPLTVTRYHS 130
           ++P  G+CLGHQ IG A GG  ++  Q  HG   PV     G    T +N        H 
Sbjct: 282 EIPTFGICLGHQMIGLAVGGRTLKMHQGHHGANHPVKDLTTGKVEITSMN--------HG 333

Query: 131 LVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPE-SILTEQGHELFAN 189
             V R++LP   + T  +  +  +     G+      +  VQ+HPE S      H LF  
Sbjct: 334 FAVDRDSLPANAQETHVSLFDGSNA----GIALADKPVFSVQYHPEASPGPRDSHYLFTR 389

Query: 190 FLK 192
           F++
Sbjct: 390 FVE 392


Lambda     K      H
   0.320    0.138    0.411 

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: 193
Number of extensions: 12
Number of successful extensions: 2
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: 198
Length of database: 401
Length adjustment: 26
Effective length of query: 172
Effective length of database: 375
Effective search space:    64500
Effective search space used:    64500
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: 47 (22.7 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