Alignments for a candidate for glyA in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Archaeoglobus veneficus SNP6

Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.- (characterized)
to candidate WP_013683034.1 ARCVE_RS01615 serine hydroxymethyltransferase

Query= SwissProt::O27433
         (423 letters)



>NCBI__GCF_000194625.1:WP_013683034.1
          Length = 406

 Score =  420 bits (1080), Expect = e-122
 Identities = 223/412 (54%), Positives = 278/412 (67%), Gaps = 10/412 (2%)

Query: 9   EKIRQLMKDHNSWMESSINLIASENITSSRVKEALLSDLSHRYAEGLPGERLYEGCRYID 68
           E++  ++++H+  M SS+ LIASEN+TS  V+    SDL HRYA G  GER YEGC YID
Sbjct: 5   EQVFSIIEEHHRLMASSLPLIASENVTSMAVRRCYTSDLGHRYAMGEIGERAYEGCEYID 64

Query: 69  EIEELTIELSKRLFRAEHANVQPTSGVVANLACFFATAEVGDPIMAMEVPYGGHISHARV 128
           EIE   +EL+KRLF AEHANV+P SG VAN+A + A    GD I ++ V  GGH SH   
Sbjct: 65  EIERKAVELTKRLFNAEHANVRPISGTVANIAVYHALTSCGDSIFSLPVECGGHTSHD-- 122

Query: 129 SAAGVRGFQIYTHPFDFENMNIDADAMKKKILEVKPRIILFGGSLFLFPHPVEEALEAAE 188
             A +R   ++  PFD E  NID DA  + I EVKPR+I+ G S+FLFPHPV+E +E A 
Sbjct: 123 DTARIRCLNVHFLPFDSERFNIDIDAASRMIREVKPRLIVLGASVFLFPHPVKEIVEIAA 182

Query: 189 EVGARIMYDGAHVLGLIAGGYFQDPLREGADMLVGSTHKTFPGPQGGIILCREELAADID 248
           EVGA ++YD +HVLGLIAG  FQDP++EGAD++  STHKTF GPQ  IILC+ ELA  ID
Sbjct: 183 EVGANVIYDASHVLGLIAGKQFQDPVKEGADVVTASTHKTFFGPQRAIILCKSELAEKID 242

Query: 249 EAVFPGLVSNHHLHHVAGLGIATAEMLEFGAEYAAQTINNARKLAENLHELGFNVLCEHL 308
            AV P +VSNHHL+ +AG  IA  EMLEFG  YA QT+ NA++LAE L+ELG  V+ E  
Sbjct: 243 YAVMPCVVSNHHLNTLAGYVIACLEMLEFGESYAKQTVRNAKRLAERLYELGMKVVGEAE 302

Query: 309 DFTESHQVVMDVSDIGRAAEISKRLEANNIILNKNLLPWDDVNRSDDPSGIRIGTQEITR 368
            FTESHQVV+DV D  +AA   K LE   II N+ LLPW +       +GIRIG QE+TR
Sbjct: 303 GFTESHQVVIDVDDGEKAA---KTLEKAGIITNRCLLPWSE----GKSAGIRIGVQEVTR 355

Query: 369 RGMKESEMSEVAEYIKRVVMDGKDVRDEVAEFMSSYTRVHYAFEDSEAYKYM 420
            GMK  EM  +AE I +  +DG DVR EV E    +  V Y FE+S AY ++
Sbjct: 356 LGMKGGEMEYIAELISK-ALDGIDVRSEVVELSKQFNTVKYTFEESHAYSFI 406


Lambda     K      H
   0.318    0.135    0.389 

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: 492
Number of extensions: 22
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: 423
Length of database: 406
Length adjustment: 31
Effective length of query: 392
Effective length of database: 375
Effective search space:   147000
Effective search space used:   147000
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 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