GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_3 in Desulfovibrio bastinii DSM 16055

Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_027178998.1 G496_RS0109010 methionine synthase

Query= reanno::Phaeo:GFF1582
         (353 letters)



>NCBI__GCF_000429985.1:WP_027178998.1
          Length = 804

 Score =  164 bits (414), Expect = 1e-44
 Identities = 102/313 (32%), Positives = 159/313 (50%), Gaps = 24/313 (7%)

Query: 5   VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64
           V+ S+ ++  +GF+    +IGERINPTG+K L+AEL+ G F+   K A  Q+ AGA ILD
Sbjct: 302 VITSRAESVCIGFNHTGVIIGERINPTGKKVLSAELQEGRFTEALKFAGQQIEAGAPILD 361

Query: 65  INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124
           +N G        P   E  ++  + + +      PL IDS+ P A+EA L    G PL+N
Sbjct: 362 VNVGA-------PMVDETMILPALCKEIIAQHQVPLSIDSTNPDAVEAALWNYPGTPLVN 414

Query: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184
           S++GE  R+E + PL KK+  P + +    + +  +   +  V +K++  A   GIP   
Sbjct: 415 SISGEPGRMERLGPLCKKFGAPFILLPIIGSKLPFECKDKIEVTEKLLREAEALGIPRRL 474

Query: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244
           I+VD L + + +   A +     +R  +EE  + T  G SNVSFGLP R  +N+ FL + 
Sbjct: 475 IMVDALALTVSSRPMAARHCMDFIRHCKEEWNLPTVLGLSNVSFGLPARELLNSTFLTLC 534

Query: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMF---------GL 295
            G G+ + I NP          A  +  + +A ++L    + E F+ M+           
Sbjct: 535 QGQGLCAFISNP--------NSARLRESLYSAEVLLARDKQAENFIDMYSEWSPAAPSST 586

Query: 296 GSTKPRAGKEMEA 308
           G TK   GK+  A
Sbjct: 587 GGTKGGEGKKSGA 599


Lambda     K      H
   0.315    0.134    0.379 

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: 571
Number of extensions: 24
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: 353
Length of database: 804
Length adjustment: 35
Effective length of query: 318
Effective length of database: 769
Effective search space:   244542
Effective search space used:   244542
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: 42 (22.0 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