GapMind for Amino acid biosynthesis

 

Alignments for a candidate for SST in Burkholderia phytofirmans PsJN

Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate BPHYT_RS01595 BPHYT_RS01595 homoserine O-acetyltransferase

Query= SwissProt::S2KHP1
         (367 letters)



>FitnessBrowser__BFirm:BPHYT_RS01595
          Length = 381

 Score =  267 bits (682), Expect = 4e-76
 Identities = 149/349 (42%), Positives = 207/349 (59%), Gaps = 7/349 (2%)

Query: 13  PVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADPSP--GWWEYM 70
           P+++  G  L    +  ET+G L     NA+L+   L+ S H A   AD     GWW+ M
Sbjct: 17  PLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYADNPKDIGWWDNM 76

Query: 71  IGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGAC 130
           +GPGKP+DT++FFVI +N+LGSCFGSTGP SI+PATG PY   FP ++VED V A     
Sbjct: 77  VGPGKPLDTDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPVVTVEDWVNAQARVA 136

Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190
              GI     V G SLGGM ALA+++MYP      I +++    +   IA   + R A+ 
Sbjct: 137 DQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKLSAQNIAFNEVARSAIL 196

Query: 191 ADPAWAGGN-YAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDR--ERLEGSDDSAN-PF 246
           +DP + GGN YA    PK G+RVAR +G +TY S ++  ++F R   R EG+ D+ N  F
Sbjct: 197 SDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGRSLRRAEGAVDAYNFNF 256

Query: 247 AMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALV 306
            + F+V+SY+     KFAD FDAN YL +++A+D FD A+  DG L AAV    AK  L+
Sbjct: 257 DVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFDGDLTAAVAHTTAK-YLI 315

Query: 307 AGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERF 355
           A  +TDW F   + R++ + L      V+Y E+ +  GHDAFL+D  R+
Sbjct: 316 ASFSTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLDDARY 364


Lambda     K      H
   0.320    0.135    0.414 

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: 389
Number of extensions: 18
Number of successful extensions: 5
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: 367
Length of database: 381
Length adjustment: 30
Effective length of query: 337
Effective length of database: 351
Effective search space:   118287
Effective search space used:   118287
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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