Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_085639258.1 MGEO_RS14540 methyltetrahydrofolate cobalamin methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_002115805.1:WP_085639258.1 Length = 360 Score = 563 bits (1450), Expect = e-165 Identities = 290/360 (80%), Positives = 310/360 (86%), Gaps = 7/360 (1%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MTRT+VESKTKTAI+GFD+PFCVIGERINPTGRK L ELE GDFS VE DALAQV AGA Sbjct: 1 MTRTIVESKTKTAIIGFDQPFCVIGERINPTGRKILNEELERGDFSRVEADALAQVAAGA 60 Query: 61 NILDINAGVVYNSN-------PNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAG 113 NILDIN+G V+++ + N EP LM ++VE VQ +TD PLCIDSSVPGALE G Sbjct: 61 NILDINSGAVFSNKMAEDPRYADNNFVEPTLMKELVERVQAVTDCPLCIDSSVPGALENG 120 Query: 114 LQAAEGRPLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 173 L AAEGRPLLNSVTGEEERLE VLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE Sbjct: 121 LAAAEGRPLLNSVTGEEERLELVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 180 Query: 174 RAADFGIPAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNR 233 RAADFGIPAHDIVVDPLVMPIGAM TAG QVF LVRRLREELGVNTTCGASN+SFGLPNR Sbjct: 181 RAADFGIPAHDIVVDPLVMPIGAMGTAGLQVFTLVRRLREELGVNTTCGASNISFGLPNR 240 Query: 234 HGINNAFLPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMF 293 HGINNAFLPMAMGAGMTSAIMNPVALP+ KIAEK+AEV AAGI+LPE M+DE F +F Sbjct: 241 HGINNAFLPMAMGAGMTSAIMNPVALPVGPTKIAEKRAEVAAAGIMLPEDMDDETFCTIF 300 Query: 294 GLGSTKPRAGKEMEAIRAANLLTNNDPHGGEWIKANKEPAKEGEEGRGRGGRAGGRRRRA 353 GLGSTKPR GKEMEAIRAAN LTNND GG WI N++P K G+EGRGR GR GGRRRRA Sbjct: 301 GLGSTKPRPGKEMEAIRAANFLTNNDEGGGAWIAFNRQPPKAGQEGRGREGRTGGRRRRA 360 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: 453 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: 360 Length adjustment: 29 Effective length of query: 324 Effective length of database: 331 Effective search space: 107244 Effective search space used: 107244 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: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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