Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_078718028.1 B5D49_RS12400 methionine synthase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_900167125.1:WP_078718028.1 Length = 806 Score = 160 bits (405), Expect = 1e-43 Identities = 102/332 (30%), Positives = 162/332 (48%), Gaps = 17/332 (5%) Query: 5 VVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGANILD 64 V+ S+ + LG P +IGERINPTG+K+L EL+ G+ + + A QV GA +LD Sbjct: 300 VLTSRGEGVPLGKGHPAVLIGERINPTGKKQLIHELQQGEQTEALRLAGEQVDRGAPVLD 359 Query: 65 INAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGRPLLN 124 +N G P E + +V+ + G TPLC+DSS PGA+ L A G PL+N Sbjct: 360 VNVGA-------PMVDETVTLPALVKALTGRFTTPLCLDSSTPGAVAEALWAYPGSPLVN 412 Query: 125 SVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGIPAHD 184 S++G+ R+ + PL ++ P + + + R A+ +++++ A G+P Sbjct: 413 SISGDPGRMAELGPLCARFGAPFILLPIKGKKLPVTAPERIAIIEQLLDEAESLGVPRRL 472 Query: 185 IVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAFLPMA 244 VVD L + + + A + +R EELG+ TT G SNVSFGLP R +N+ FL M Sbjct: 473 AVVDGLALTVSSKPEAARATLETIRYCTEELGLATTLGLSNVSFGLPARDLLNSTFLSMC 532 Query: 245 MGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKPRAGK 304 + +G+ S I NP + A + + A+ ++L + F+ + KP G Sbjct: 533 LASGLASFIANPDS--------ARLREALAASEVLLNRDPQATYFINTY--SDWKPTGGT 582 Query: 305 EMEAIRAANLLTNNDPHGGEWIKANKEPAKEG 336 + T +P A + K+G Sbjct: 583 GQPGTNSPQQGTGGEPDSHPLFSAVVKGNKDG 614 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: 594 Number of extensions: 28 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: 806 Length adjustment: 35 Effective length of query: 318 Effective length of database: 771 Effective search space: 245178 Effective search space used: 245178 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