GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_2 in Thioalkalivibrio halophilus HL17

Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_077243567.1 B1A74_RS01430 methionine synthase

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



>NCBI__GCF_001995255.1:WP_077243567.1
          Length = 1263

 Score =  112 bits (279), Expect = 7e-29
 Identities = 94/285 (32%), Positives = 138/285 (48%), Gaps = 33/285 (11%)

Query: 37  ELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAARLKLHDAHRR--VRELNVAGAELG 94
           +L ++  P  I  ++   ++AG+D+   NTF GT  R+ + D H    V ELN   A+L 
Sbjct: 54  DLLSLTRPDIIEQIHNDYLEAGADIIEANTFNGT--RIAMADYHMEDLVPELNRESAKLA 111

Query: 95  RNVADRSERKIA-----VAGSVGPTGEIMQPVGELSHALA--------VEMFHEQAEALK 141
           R  AD    K       VAG +GPT        +++   A        V  + E AEAL 
Sbjct: 112 RKAADAWTAKTPDKPRFVAGILGPTNRTASISPDVNDPGARNVDFDTLVAAYKEAAEALI 171

Query: 142 EGGVDVLWLETISAPEEYRAAAEAFKLA------DMPWC--GTMSFDTAGRTMMGVTSAD 193
           EGGVD+L +ET+      +AA  A K        D+P    GT++ D +GRT+ G T+  
Sbjct: 172 EGGVDLLLIETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTIT-DASGRTLSGQTTEA 230

Query: 194 MAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHY 253
               V   +P  ++ G NC  GA ++ + V   +    T  + +  NAG+P        Y
Sbjct: 231 FWNSVRHANP--VSIGLNCALGAKEMRQYVEELSRIADTH-VSAHPNAGLPNEFGD---Y 284

Query: 254 DGTPTLMG-EYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRP 297
           D +P  M  +    A      IIGGCCGT+P+H+RAMREA++  P
Sbjct: 285 DESPEQMAADVGPWAEQGMLNIIGGCCGTLPEHIRAMREAVEKFP 329


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: 974
Number of extensions: 57
Number of successful extensions: 3
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: 1263
Length adjustment: 38
Effective length of query: 300
Effective length of database: 1225
Effective search space:   367500
Effective search space used:   367500
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: 54 (25.4 bits)

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