Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_073041003.1 BUB04_RS15165 methyltetrahydrofolate cobalamin methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_900129305.1:WP_073041003.1 Length = 269 Score = 155 bits (391), Expect = 1e-42 Identities = 91/236 (38%), Positives = 138/236 (58%), Gaps = 10/236 (4%) Query: 23 VIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILDINAGVVYNSNPNPNETEP 82 +IGE+IN T R+++A + D ++ A Q GA+ LD+NAG ++P + EP Sbjct: 3 IIGEKINGT-RRRVAQAIVERDHEFIKDLARKQAEGGAHYLDVNAG----TSP---DREP 54 Query: 83 PLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLNSVTGEEERLEHVLPLVKK 142 M ++E +Q + D PLC+DS+ P ALE+GLQ + L+NS++GE+ R+E VLPL K Sbjct: 55 EDMVWLIENIQEVVDLPLCLDSANPAALESGLQVVKRPALINSLSGEKARIEGVLPLAGK 114 Query: 143 YNVPVVAISNDD-TGISEDPDVRFAVAKKIVERAADFGIPAHDIVVDPLVMPIGAMATAG 201 Y +V ++ DD TGI + + R + K+V A + G+ + +DPLV I +G Sbjct: 115 YQTGLVVLALDDLTGIPKRSEERLEIVSKLVGLAEEQGLSHEQLFIDPLVTAISTGVDSG 174 Query: 202 QQVFALVRRLREEL-GVNTTCGASNVSFGLPNRHGINNAFLPMAMGAGMTSAIMNP 256 F ++ +R+ + TCG SN+SFGLP R IN FL M M G+ SAI++P Sbjct: 175 MVTFETIKGIRQRYPAAHITCGLSNISFGLPLRSLINRTFLAMCMMCGLDSAIIDP 230 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: 205 Number of extensions: 11 Number of successful extensions: 4 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: 269 Length adjustment: 27 Effective length of query: 326 Effective length of database: 242 Effective search space: 78892 Effective search space used: 78892 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: 48 (23.1 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