GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_2 in Desulfovibrio gracilis DSM 16080

Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_078718028.1 B5D49_RS12400 methionine synthase

Query= reanno::Phaeo:GFF1321
         (338 letters)



>NCBI__GCF_900167125.1:WP_078718028.1
          Length = 806

 Score =  125 bits (315), Expect = 3e-33
 Identities = 90/287 (31%), Positives = 139/287 (48%), Gaps = 12/287 (4%)

Query: 5   FTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLT 64
           F  LL+       DG  GT L   GL  G +PEL+ +  P  +  +++  + AG+ +  T
Sbjct: 4   FRKLLKDDQVRFFDGGYGTLLQQRGLPPGMSPELFGLKSPDAVLQVHRDYLAAGAQVLTT 63

Query: 65  NTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGEL 124
           NTFGG+  +L        V +LN A   L R  A  +     VA S+GPTG   +P+GEL
Sbjct: 64  NTFGGSRFKL---GPDADVYDLNKAMCTLARKAAGDN---AFVAASIGPTGHFCEPLGEL 117

Query: 125 SHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAG 183
           +    V+ + EQ +   +GG D++  ET     E RA   A + + D+P   +M+F+ A 
Sbjct: 118 TFRELVQAYKEQIQGCVDGGADLILGETHFDLAEARAVVIATREVCDLPVAVSMTFEGA- 176

Query: 184 RTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGI 243
            ++ G T       ++      +A   NC  G   I   V     + +T P+    NAG+
Sbjct: 177 NSLTGTTPLHFIDTMQNMGVDMVA--TNCSAGPEQIADVVRAMLPRLST-PLYVAANAGL 233

Query: 244 PKY-VDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAM 289
           P+   +G+  +   P    + +    D GAK +GGCCGT PDH+RA+
Sbjct: 234 PELDENGNTVFRLGPDDFAKQSTRFFDMGAKFVGGCCGTGPDHIRAL 280


Lambda     K      H
   0.317    0.134    0.397 

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: 728
Number of extensions: 43
Number of successful extensions: 4
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: 338
Length of database: 806
Length adjustment: 35
Effective length of query: 303
Effective length of database: 771
Effective search space:   233613
Effective search space used:   233613
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: 52 (24.6 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