Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_092057476.1 BQ4888_RS11910 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_900111775.1:WP_092057476.1 Length = 799 Score = 194 bits (494), Expect = 5e-54 Identities = 109/302 (36%), Positives = 165/302 (54%), Gaps = 15/302 (4%) Query: 3 RTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANI 62 R + S++ +G P +IGERINPTG+K +AEL G + + ++A Q GA + Sbjct: 299 RGFLSSRSAVVEIGGAAPCAIIGERINPTGKKAYSAELREGKTAYIRREAQEQTRVGAAL 358 Query: 63 LDINAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPL 122 LD+N G P EP + + V V G++ PL +DSS P ALE L+A +G+ L Sbjct: 359 LDVNCGT-------PGVDEPAALERAVYAVSGVSSAPLVLDSSDPAALERALKAVDGKVL 411 Query: 123 LNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPA 182 +NSV+GEE+ +LPL +KY V+ ++ D++GI E + R VA KI+E A G+P Sbjct: 412 INSVSGEEKSRRVILPLARKYGAAVIGLALDESGIPETAEGRTRVAGKILEAALAAGLPK 471 Query: 183 HDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLP 242 D+V+D L + + A + +R +R+ELG+ T G SN+SFGLPNR ++ F Sbjct: 472 EDVVIDCLTLTVSAEQKRAMETIRALRAVRDELGLATVLGVSNISFGLPNRPVLSATFFA 531 Query: 243 MAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKPRA 302 MA+ AG+ +AI+NP K AA ++L + E F+ ++G P Sbjct: 532 MALEAGLAAAIVNP--------KEERMMDAFRAAMVLLGKDERAEEFIAVYGGAQAVPTV 583 Query: 303 GK 304 K Sbjct: 584 PK 585 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: 586 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 353 Length of database: 799 Length adjustment: 35 Effective length of query: 318 Effective length of database: 764 Effective search space: 242952 Effective search space used: 242952 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