Alignments for a candidate for glyA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Paraburkholderia bryophila 376MFSha3.1

Align Serine hydroxymethyltransferase 2; SHMT 2; Serine methylase 2; EC 2.1.2.1 (characterized)
to candidate H281DRAFT_00990 H281DRAFT_00990 serine hydroxymethyltransferase (EC 2.1.2.1)

Query= SwissProt::Q3JGP5
         (424 letters)



>FitnessBrowser__Burk376:H281DRAFT_00990
          Length = 431

 Score =  631 bits (1628), Expect = 0.0
 Identities = 312/418 (74%), Positives = 351/418 (83%)

Query: 7   FFSQSLAERDASVRGAILKELERQQSQVELIASENIVSRAVLDAQGSVLTNKYAEGYPGK 66
           FF++ L  RD  +   I  EL RQQ+Q+ELIASENIVS AV++AQG+VLTNKYAEGYP K
Sbjct: 7   FFAEPLQSRDPVIASEIALELRRQQTQIELIASENIVSAAVMEAQGTVLTNKYAEGYPSK 66

Query: 67  RYYGGCEFADEVEALAIERVKRLFNAGHANVQPHSGAQANGAVMLALAKPGDTVLGMSLD 126
           RYYGGCE  D VEALAI+RVK LF A  ANVQPHSGAQANGAVMLAL KPG+TV+GMSLD
Sbjct: 67  RYYGGCEHVDRVEALAIDRVKALFEAEFANVQPHSGAQANGAVMLALVKPGETVMGMSLD 126

Query: 127 AGGHLTHGAKPALSGKWFNALQYGVSRDTMLIDYDQVEALAQQHKPSLIIAGFSAYPRKL 186
           AGGHLTHGA+PALSGKWFNA+QYGV+  T  +DY+QV +LAQ+H+P LIIAG+SAYPR L
Sbjct: 127 AGGHLTHGARPALSGKWFNAVQYGVNPQTYRVDYEQVRSLAQEHRPKLIIAGYSAYPRAL 186

Query: 187 DFARFRAIADSVGAKLMVDMAHIAGVIAAGRHANPVEHAHVVTSTTHKTLRGPRGGFVLT 246
           DFA FR IADSVGA LMVDMAHIAG++AAGRH NPV  A VVTSTTHKTLRGPRGGF+LT
Sbjct: 187 DFAAFRDIADSVGALLMVDMAHIAGIVAAGRHENPVRFADVVTSTTHKTLRGPRGGFILT 246

Query: 247 NDEEIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALTDDFKTYIDRVLANAQALGDVLK 306
           N+ +IAKKINSAVFPGLQGGPLMHVIAGKAVAFGEAL  +F  YID+VL NAQALGDVLK
Sbjct: 247 NNGDIAKKINSAVFPGLQGGPLMHVIAGKAVAFGEALRPEFTAYIDQVLRNAQALGDVLK 306

Query: 307 AGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITCNKNGIPFDPEKPTITSGIR 366
           +GG+ LVT GTDNHLLLVDLR K L G Q E+ALERAGITCNKNGIPFD E PT+TSGIR
Sbjct: 307 SGGLSLVTDGTDNHLLLVDLRSKRLTGTQAEKALERAGITCNKNGIPFDTESPTVTSGIR 366

Query: 367 LGTPAGTTRGFGAAEFREVGRLILEVFEALRTNPEGDHATEQRVRREIFALCERFPIY 424
           LGTPAGTTRGFG A+F ++G++ILEV  AL   P GD   E+ VR  +  LC +FPIY
Sbjct: 367 LGTPAGTTRGFGTAQFEQIGQMILEVLSALEQEPAGDEQVERAVRSRVRDLCSQFPIY 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: 660
Number of extensions: 24
Number of successful extensions: 1
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: 431
Length adjustment: 32
Effective length of query: 392
Effective length of database: 399
Effective search space:   156408
Effective search space used:   156408
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