Alignments for a candidate for glyA in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Paraburkholderia phymatum STM815

Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate WP_012402632.1 BPHY_RS16750 serine hydroxymethyltransferase

Query= SwissProt::Q3JGP5
         (424 letters)



>NCBI__GCF_000020045.1:WP_012402632.1
          Length = 424

 Score =  779 bits (2012), Expect = 0.0
 Identities = 384/424 (90%), Positives = 410/424 (96%)

Query: 1   MSNANPFFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYA 60
           MSNANPFFSQSLAERDA+VR ++LKELERQQSQVELIASENIVSRAVL+AQGSVLTNKYA
Sbjct: 1   MSNANPFFSQSLAERDAAVRKSVLKELERQQSQVELIASENIVSRAVLEAQGSVLTNKYA 60

Query: 61  EGYPGKRYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTV 120
           EGYPGKRYYGGCEF DEVEALAIER+K+LFNAG ANVQPHSGAQANG+VMLALAKPGDT+
Sbjct: 61  EGYPGKRYYGGCEFVDEVEALAIERIKKLFNAGFANVQPHSGAQANGSVMLALAKPGDTI 120

Query: 121 LGMSLDAGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFS 180
           LGMSLDAGGHLTHGAKPALSGKWFNA+QYGV+R+TM +DYDQ+E LA +HKPS++IAGFS
Sbjct: 121 LGMSLDAGGHLTHGAKPALSGKWFNAVQYGVNRETMRVDYDQIEKLAHEHKPSMLIAGFS 180

Query: 181 AYPRKLDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR 240
           AYPR+LDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR
Sbjct: 181 AYPRELDFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPR 240

Query: 241 GGFVLTNDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQA 300
           GGFVLTNDEE+AKKINSAVFPGLQGGPLMHVIAGKAVAFGEAL D FKTYID VLANAQA
Sbjct: 241 GGFVLTNDEEVAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALEDSFKTYIDNVLANAQA 300

Query: 301 LGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPT 360
           LG+VLK GGVDLVTGGTDNHLLLVDLRPKGLKG QVEQALERAGITCNKNGIPFD EKPT
Sbjct: 301 LGEVLKEGGVDLVTGGTDNHLLLVDLRPKGLKGTQVEQALERAGITCNKNGIPFDTEKPT 360

Query: 361 ITSGIRLGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCER 420
           +TSGIRLGTPAGTTRGFG AEFR+VGR+ILEVF+ALR++P+GD ATEQRVRREIFALCER
Sbjct: 361 VTSGIRLGTPAGTTRGFGVAEFRDVGRMILEVFDALRSHPDGDAATEQRVRREIFALCER 420

Query: 421 FPIY 424
           FPIY
Sbjct: 421 FPIY 424


Lambda     K      H
   0.318    0.136    0.391 

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: 765
Number of extensions: 18
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: 424
Length of database: 424
Length adjustment: 32
Effective length of query: 392
Effective length of database: 392
Effective search space:   153664
Effective search space used:   153664
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis