GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Pseudovibrio axinellae Ad2

Align Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 (characterized)
to candidate WP_068008417.1 PsAD2_RS16680 threonine ammonia-lyase

Query= SwissProt::Q7XSN8
         (339 letters)



>NCBI__GCF_001623255.1:WP_068008417.1
          Length = 413

 Score =  205 bits (521), Expect = 2e-57
 Identities = 116/309 (37%), Positives = 181/309 (58%), Gaps = 8/309 (2%)

Query: 21  IHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALD 80
           + +I EA   I   V KTP L +  +DA  G  +F K E  Q   AFK RGA N +  L 
Sbjct: 11  LSNIEEAANNIKGAVLKTPFLPAIQLDAATGASVFVKYENMQVTNAFKERGALNKLLHLS 70

Query: 81  DDEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVS 140
           D E S+GV+  S+GNHA AVAL A+  GIPA IV+P   P  KV+  K +G  +I +  +
Sbjct: 71  DTEKSRGVIAMSAGNHAQAVALHAQRLGIPALIVMPNGTPYVKVEATKAFGAKVILAGET 130

Query: 141 IESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLIS 200
           ++  ++ A R+ +E     VHPF++   I+GQGT++LE+L E P++DT++VP+ GGG+IS
Sbjct: 131 VDDAKNEADRLAQEHNYTWVHPFDDLEVIAGQGTIALEMLREQPDLDTLVVPVGGGGMIS 190

Query: 201 GVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRAFL-GDLTWPV 259
           G+A+AAKAI P I I+  E      S  +   G+ +     N++A+G+   + G LT  +
Sbjct: 191 GMAVAAKAIKPDIEIIGVE-SDLYPSMYAALRGRSMEC-GGNSLAEGIAVKVPGTLTQQL 248

Query: 260 VRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIG 319
            +  V+D+++V ++ I +A+ +    LK   E +GA GLAA  +   +         K+G
Sbjct: 249 CKQFVNDVLLVSESQIEEAINVFLTRLKTVAEGAGAAGLAAICAHPER-----FAGKKVG 303

Query: 320 IIVSGGNVD 328
           +++ GGN++
Sbjct: 304 LVLCGGNIN 312


Lambda     K      H
   0.316    0.133    0.381 

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: 285
Number of extensions: 14
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: 339
Length of database: 413
Length adjustment: 30
Effective length of query: 309
Effective length of database: 383
Effective search space:   118347
Effective search space used:   118347
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: 50 (23.9 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