GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Burkholderia phytofirmans PsJN

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate BPHYT_RS15425 BPHYT_RS15425 serine/threonine dehydratase

Query= BRENDA::O59791
         (323 letters)



>FitnessBrowser__BFirm:BPHYT_RS15425
          Length = 321

 Score =  426 bits (1094), Expect = e-124
 Identities = 206/318 (64%), Positives = 255/318 (80%)

Query: 5   LVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNA 64
           L  PT+DDV  A+ R+   A++TPVLTSST N+   A VFFKCENFQ+MGAFKFRGA NA
Sbjct: 4   LPAPTFDDVLDAAARLNGVAHRTPVLTSSTFNERTGASVFFKCENFQRMGAFKFRGAYNA 63

Query: 65  LSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVI 124
           +S  +  QRKAGVLT+SSGNHAQAIALSA++ GI A I+MP DAP AKVAATKGYGG+VI
Sbjct: 64  ISHFDAEQRKAGVLTYSSGNHAQAIALSARLAGIHATIVMPQDAPAAKVAATKGYGGEVI 123

Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGG 184
            YDRY ++RE++ + ++E  G+T+IPPYDHPHV+AGQGTA KEL EE GPLD LFVCLGG
Sbjct: 124 TYDRYTENREEIGRRLAEERGMTLIPPYDHPHVIAGQGTAVKELIEETGPLDMLFVCLGG 183

Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGN 244
           GGL+SGSALAA   +P C V G+EPEAGNDGQQS  +G IVHIDTP+TIADGA + HLG+
Sbjct: 184 GGLISGSALAAAALSPACTVIGIEPEAGNDGQQSLARGEIVHIDTPRTIADGAASTHLGD 243

Query: 245 YTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIG 304
           YTF+II++ V  I TVSD +LI+ ++F+A RMKIVVEPTGCL+ AA       +  KR+G
Sbjct: 244 YTFAIIRKLVAQIETVSDAQLIETMRFFAQRMKIVVEPTGCLAAAAVLNGIVPVTGKRVG 303

Query: 305 IIISGGNVDIERYAHFLS 322
           +++SGGNVD+E+ A +L+
Sbjct: 304 VVVSGGNVDLEKLAQYLA 321


Lambda     K      H
   0.318    0.135    0.384 

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: 330
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 323
Length of database: 321
Length adjustment: 28
Effective length of query: 295
Effective length of database: 293
Effective search space:    86435
Effective search space used:    86435
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 (21.7 bits)
S2: 48 (23.1 bits)

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

Links

Downloads

Related tools

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