GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Thioalkalivibrio paradoxus ARh 1

Align Phosphoserine phosphatase; PSP; EC 3.1.3.3 (characterized)
to candidate WP_025367425.1 THITH_RS09165 HAD-IA family hydrolase

Query= SwissProt::Q72H00
         (249 letters)



>NCBI__GCF_000227685.2:WP_025367425.1
          Length = 254

 Score = 73.2 bits (178), Expect = 5e-18
 Identities = 46/122 (37%), Positives = 61/122 (50%), Gaps = 1/122 (0%)

Query: 113 FRERRRYPLYPEAEAFLAEARRRGLALALLTNGVPDLQREKLVGAGLAHHFSLVLISGEV 172
           F E   +  YPE +A L   RR GL LA+++N    L      G GL      V+ + EV
Sbjct: 109 FAEPSAWQKYPEIDALLQGLRRSGLRLAIVSNFDARLV-PVCRGLGLEPRVDTVVFAAEV 167

Query: 173 GIGKPDPRLFRMALCAFGVAPEEAAMVGDNPQKDVRGARLAGVRAVWVDRGLRPEDPEAS 232
           G  KP   +F  A+   GVAP     VGD+  +DV GAR AG+RAV++ R      P   
Sbjct: 168 GAAKPRAGIFHEAVARLGVAPANTLHVGDSFAEDVAGARAAGLRAVYLQRDQADHRPMGD 227

Query: 233 PD 234
           P+
Sbjct: 228 PE 229


Lambda     K      H
   0.322    0.140    0.417 

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: 159
Number of extensions: 8
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: 249
Length of database: 254
Length adjustment: 24
Effective length of query: 225
Effective length of database: 230
Effective search space:    51750
Effective search space used:    51750
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 (21.9 bits)
S2: 46 (22.3 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