Alignments for a candidate for glyA in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Hydrogenovibrio halophilus DSM 15072

Align Glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_019894223.1 A377_RS0101085 serine hydroxymethyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2685
         (418 letters)



>NCBI__GCF_000384235.1:WP_019894223.1
          Length = 425

 Score =  629 bits (1623), Expect = 0.0
 Identities = 313/423 (73%), Positives = 355/423 (83%), Gaps = 6/423 (1%)

Query: 1   MFSKHDQIKGYDDELLAAMNAEDARQEHHIELIASENYTSQRVMQAQGSGLTNKYAEGYP 60
           MF     I GYDDEL  AM AE  RQE HIELIASENYTS RVM+AQGS LTNKYAEGYP
Sbjct: 1   MFEPTMTIAGYDDELATAMQAEATRQEDHIELIASENYTSPRVMEAQGSVLTNKYAEGYP 60

Query: 61  GKRYYGGCEHVDVVEQLAIDRARQLFGADYANVQPHSGSQANAAVYLALLQAGDTVLGMS 120
            KRYYGGCEHVDVVEQLAIDRA++LFGADYANVQPHSGSQANA VY+AL++ G+TVLGMS
Sbjct: 61  FKRYYGGCEHVDVVEQLAIDRAKELFGADYANVQPHSGSQANAPVYMALMKPGETVLGMS 120

Query: 121 LAHGGHLTHGAKVSFSGKLYNAVQYGIDTTTGLIDYDEVERLAVEHKPKMIIAGFSAYSK 180
           LAHGGHLTHGA V+FSGK+Y AVQYG++  TG IDYDEV RLA EH+PKMI+AGFSAYS+
Sbjct: 121 LAHGGHLTHGAHVNFSGKIYKAVQYGLNPETGEIDYDEVARLAREHQPKMIVAGFSAYSQ 180

Query: 181 TLDFPRFRQIADKVGAYFFVDMAHVAGLVATGLYPNPLPYADVVTTTTHKTLRGPRGGLI 240
            +D+ RFR+IAD+VGAY  VDMAHVAGLVA G+YPNP+PYADVVTTTTHKTLRGPR GLI
Sbjct: 181 VVDWGRFREIADEVGAYLLVDMAHVAGLVAAGIYPNPVPYADVVTTTTHKTLRGPRSGLI 240

Query: 241 LAKANPELEKKLNAAVFPGGQGGPLMHVIAAKAVCFKEALEPAFKTYQSQVIRNAQAMAQ 300
           LAK+NPELEKKLN+A+FPG QGGPLMHVIAAKAV FKEA+EP FKTY   V++NA+AMA+
Sbjct: 241 LAKSNPELEKKLNSAIFPGQQGGPLMHVIAAKAVAFKEAMEPEFKTYAENVVKNAKAMAK 300

Query: 301 VFIERGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGRAGITVNKNAVPNDPQSPFVTS 360
           VF+ERGYDVVS GT+NHLFLVSLI QGLTGK  DAALG A IT+NKN+VPNDP+SPFVTS
Sbjct: 301 VFMERGYDVVSKGTENHLFLVSLIEQGLTGKLVDAALGAAHITINKNSVPNDPKSPFVTS 360

Query: 361 GLRIGTPAITSRGFKEAQSIALAGWICDIL------DHLGDADIEANVARQAAALCADFP 414
           G+R+GT A T+RGF EA S  LA W+CD++      +   D  + A V  +  ALCA  P
Sbjct: 361 GIRVGTAASTTRGFTEADSTDLAHWMCDVIAACDQENETWDEAVVAQVREKVTALCAQRP 420

Query: 415 VYR 417
           VYR
Sbjct: 421 VYR 423


Lambda     K      H
   0.319    0.135    0.395 

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: 649
Number of extensions: 22
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: 418
Length of database: 425
Length adjustment: 32
Effective length of query: 386
Effective length of database: 393
Effective search space:   151698
Effective search space used:   151698
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Protein sequences (fasta format)
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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