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:

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