GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Xenophilus azovorans DSM 13620

Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_038211125.1 Q392_RS19260 D-2-hydroxyacid dehydrogenase family protein

Query= uniprot:Q5JGC4
         (304 letters)



>NCBI__GCF_000745855.1:WP_038211125.1
          Length = 322

 Score =  186 bits (472), Expect = 6e-52
 Identities = 107/262 (40%), Positives = 156/262 (59%), Gaps = 5/262 (1%)

Query: 26  YEEYPDEDRLVELVKDVDAIIV-RSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAAEE 84
           Y ++ + + + E +   DA+++ R +  + R +IE  PKL+ +   GV    IDL+AA E
Sbjct: 39  YGDHVEGEAVAERLASYDAVVLMRERTALGRALIERLPKLRAVFTTGVRNLAIDLEAARE 98

Query: 85  RGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELEGKTIGV 144
           RGI V  +  ASS   AELA+GL+ A++R+I   DR +R G W  +  +G  L+GKT+G+
Sbjct: 99  RGIVVCGTDSASS--TAELALGLMIALSRQIVAEDRAVRAGRW--QTVVGSSLQGKTLGI 154

Query: 145 VGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVTLHVPLV 204
           VG G++G QVA     LGM  + +     +ERA  +  +  D   L   +DVV+LH+ L 
Sbjct: 155 VGLGKLGAQVAGYGRMLGMHTIAWSENLTQERAVGLHCERVDKRALFTRADVVSLHLVLS 214

Query: 205 DATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFEEEPLPAD 264
           + T  ++    L  MK  A+LIN AR  +VD DALV AL +G I GA +DVFE EPLP D
Sbjct: 215 ERTRGVVGARELSWMKRDALLINTARAGLVDMDALVSALHDGRIGGAAIDVFEREPLPPD 274

Query: 265 HPLTKLDNVVLTPHIGASTVEA 286
            P+ K    +LTPH+G +T +A
Sbjct: 275 APILKAPRTILTPHLGYATRDA 296


Lambda     K      H
   0.317    0.136    0.378 

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: 252
Number of extensions: 15
Number of successful extensions: 3
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: 304
Length of database: 322
Length adjustment: 27
Effective length of query: 277
Effective length of database: 295
Effective search space:    81715
Effective search space used:    81715
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: 48 (23.1 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