Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_012101348.1 CKL_RS04800 homocysteine methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000016505.1:WP_012101348.1 Length = 801 Score = 185 bits (469), Expect = 4e-51 Identities = 102/253 (40%), Positives = 149/253 (58%), Gaps = 9/253 (3%) Query: 4 TVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANIL 63 T V S T T I+G E +IGERINPTGR EL+ G + ++K+A+ Q GANIL Sbjct: 299 TAVCSATDTVIVG--EKIKIIGERINPTGRSIYKKELKEGSINYIQKEAIMQKEEGANIL 356 Query: 64 DINAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLL 123 +N G+ P NE E +M K + VQ + PL IDS P LE G++ G+P++ Sbjct: 357 GVNVGL-----PEINEVE--IMKKAIRAVQKVVQLPLSIDSPDPQVLETGIRMYNGKPVI 409 Query: 124 NSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAH 183 NSV G ++ +E V P+VKKY V+A++ D+ GI + R +A+KI++ A+ +GI Sbjct: 410 NSVNGSKKSMEEVFPIVKKYGGCVIALTIDEKGIPHTAEGRVKIAEKIIKTASIYGINKK 469 Query: 184 DIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPM 243 +I++D L + + A + ++ + E+ GV T G SN+SFGLPNR +N FL M Sbjct: 470 NIIIDCLTLTVSAQQKEVLETIKAIKMVTEKFGVKTVLGVSNISFGLPNRSILNRTFLAM 529 Query: 244 AMGAGMTSAIMNP 256 A+ AG+ IMNP Sbjct: 530 ALQAGLNLPIMNP 542 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: 548 Number of extensions: 16 Number of successful extensions: 2 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: 801 Length adjustment: 35 Effective length of query: 318 Effective length of database: 766 Effective search space: 243588 Effective search space used: 243588 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.
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:
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