GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alr in Halioglobus japonicus S1-36

Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_084197780.1 C0029_RS15255 N-acetyl-gamma-glutamyl-phosphate reductase

Query= BRENDA::C7ACH5
         (393 letters)



>NCBI__GCF_002869505.1:WP_084197780.1
          Length = 343

 Score =  144 bits (363), Expect = 4e-39
 Identities = 79/197 (40%), Positives = 115/197 (58%), Gaps = 6/197 (3%)

Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253
           VG +GY G EL+  +  HP   + A+T  A+S   G+ + DL+P L+G  DL      D+
Sbjct: 7   VGGTGYTGVELLRLLATHPQAEVVAITSRAES---GRRVDDLYPNLRGHYDLAFSE-PDV 62

Query: 254 SEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYPE 313
           +  +   DVVF AT H V+ ++ P+ L AG  + DLS  +R+ DA  + ++YG  H  P 
Sbjct: 63  ATLA-ACDVVFFATPHNVAMNMVPELLAAGARIVDLSADYRIRDAELWSQWYGEPHASPN 121

Query: 314 LLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATSGV 373
           +L QA YGL E     +  A L+A PGCYPT+ QL L PL+   L+D  +  + ++ SGV
Sbjct: 122 ILRQAVYGLPEVNRQAIAGAQLVACPGCYPTSVQLGLIPLLAKGLVDPARL-IASSASGV 180

Query: 374 SGAGRKAAISNSFCEVS 390
           SGAGR+  + N F EV+
Sbjct: 181 SGAGRQGKVDNIFPEVA 197


Lambda     K      H
   0.320    0.136    0.403 

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: 345
Number of extensions: 15
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: 393
Length of database: 343
Length adjustment: 30
Effective length of query: 363
Effective length of database: 313
Effective search space:   113619
Effective search space used:   113619
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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:

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