Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_013537367.1 THEAM_RS03095 homocysteine S-methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000185805.1:WP_013537367.1 Length = 841 Score = 195 bits (496), Expect = 3e-54 Identities = 102/251 (40%), Positives = 153/251 (60%), Gaps = 7/251 (2%) Query: 6 VESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILDI 65 V S+TK ++G P +IGERINPTG+KKL L+A DFS V+++A QV GA++LD+ Sbjct: 302 VASRTKLVLIGTGHPTRIIGERINPTGKKKLQEALKAKDFSLVKQEAKKQVEEGADLLDV 361 Query: 66 NAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLNS 125 N GV P EP LM + V+ V D PL ID+ P A+E L+ +GRP++NS Sbjct: 362 NVGV-------PGADEPSLMREAVKTVMEAVDVPLVIDTKDPKAVEEALKMCDGRPVVNS 414 Query: 126 VTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHDI 185 V+GE++ +E +LP+ KY V+ ++ DD G+ E R + +++++ G+ Sbjct: 415 VSGEKKDVEQILPVAAKYGANVLLLAIDDEGLKEKAQERVEIIERLLKECEKVGVDRSST 474 Query: 186 VVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMAM 245 V D L + + AM + + +R ++E G+ TT G SNVSFGLP+R IN+AF+ MA+ Sbjct: 475 VADVLNLAVSAMPDSTVETLKAIRLVKERFGIATTLGVSNVSFGLPSRSLINSAFMAMAI 534 Query: 246 GAGMTSAIMNP 256 AG+ S I+NP Sbjct: 535 YAGLDSGIVNP 545 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: 610 Number of extensions: 28 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: 841 Length adjustment: 35 Effective length of query: 318 Effective length of database: 806 Effective search space: 256308 Effective search space used: 256308 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