GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Burkholderia phytofirmans PsJN

Align Uncharacterized aminotransferase MJ0959; EC 2.6.1.- (characterized, see rationale)
to candidate BPHYT_RS03855 BPHYT_RS03855 alanine--glyoxylate aminotransferase

Query= uniprot:Y959_METJA
         (385 letters)



>FitnessBrowser__BFirm:BPHYT_RS03855
          Length = 412

 Score =  148 bits (373), Expect = 3e-40
 Identities = 114/366 (31%), Positives = 181/366 (49%), Gaps = 10/366 (2%)

Query: 9   LLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFL-ITGSGT 67
           L+M  GP  +P  V  A  + VI H       ++       + VF T++   L + G G+
Sbjct: 31  LMMGAGPVPIPAAVAKANTI-VINHLGATMVKVIGQVKTMARYVFQTKSKWVLGVAGPGS 89

Query: 68  AAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEIL 127
           AAM+MAISN+   G +VL+I  G F ER A + +        LDV  G +A  + V E +
Sbjct: 90  AAMEMAISNLAWEGTRVLSIKNGFFSERMAEMGRRVGAHVSVLDVADGAVASLDEVAEAI 149

Query: 128 DKYDDIKAVTVVHNETSTGARN-PIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186
            + +  + VTVV  ETS    N  +K+I  + K   AL +VD V +L    + +D + ID
Sbjct: 150 -RRERPEVVTVVQGETSNTVWNYHLKDIAALAKAAGALVVVDAVCTLSTMPLEMDAWGID 208

Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIK-KNDDKVGFYLDLLAYKKYYEEKKQTPYTP 245
             +TG QK L++ PG++ I  S+ AW  +K +      + LD    + ++       YT 
Sbjct: 209 AVITGGQKGLSSIPGVSLIAFSDAAWTRVKTRTAPNAHWCLDASLAENFWHNAGY-HYTA 267

Query: 246 SVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSAK 305
            V+   AL+ AL LV  E +E R  RH + ++A + G+ A+G++L+A +  R  +V   +
Sbjct: 268 PVSGVLALHEALRLVCAETLEKRFARHLKCSQALQEGISALGLKLYAPQACRLNSVVGIE 327

Query: 306 YPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMG-ICGEKEVLATLACVELALK 364
            P G+      G +S  + + ++G        I RIG MG  C E  +  TL  +   + 
Sbjct: 328 VPAGLSPGDICGHISRHHQVEISGS---FGLPIVRIGQMGEQCREHNLFRTLHALGRTMV 384

Query: 365 ELGFEV 370
           +LG  V
Sbjct: 385 DLGSAV 390


Lambda     K      H
   0.316    0.135    0.379 

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: 339
Number of extensions: 21
Number of successful extensions: 2
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: 385
Length of database: 412
Length adjustment: 31
Effective length of query: 354
Effective length of database: 381
Effective search space:   134874
Effective search space used:   134874
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 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