Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_011842012.1 RSPH17029_RS15120 methionine synthase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000015985.1:WP_011842012.1 Length = 908 Score = 86.7 bits (213), Expect = 2e-21 Identities = 86/285 (30%), Positives = 127/285 (44%), Gaps = 40/285 (14%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MTR + S + +L D PF +GER N TG + + D++ + A QV GA Sbjct: 1 MTRYLRLSGLEPFVLTPDIPFVNVGERTNVTGSARFRKLITNRDYAAALEVARDQVQNGA 60 Query: 61 NILDIN--AGVVYNSNPNPNETEPPLMTKIVELVQGLTD---TPLCIDSSVPGALEAGLQ 115 ILD+N G++ M + + L+ D PL IDSS +EAGLQ Sbjct: 61 QILDVNMDEGLI---------DSKAAMVEFLNLIASEPDIARVPLMIDSSKWEVIEAGLQ 111 Query: 116 AAEGRPLLNSVTGE--EERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 173 +G+P++NS++ + EE L Y VV ++ D+ G ++ FA I Sbjct: 112 CVQGKPVVNSISLKEGEESFRRQAGLCLAYGAAVVVMAFDEEGQADS----FARKTTICA 167 Query: 174 RA-----ADFGIPAHDIVVDPLVMPIGAMATA-------GQQVFALVRRLREEL-GVNTT 220 RA + G P DI+ DP V A+AT G R +R +L + + Sbjct: 168 RAYRILVEEVGFPPEDIIFDPNVF---AVATGIEEHDNYGVDFIEAARWIRAKLPHAHVS 224 Query: 221 CGASNVSFGL----PNRHGINNAFLPMAMGAGMTSAIMNPVALPI 261 G SN+SF P R ++ FL A+ AGM I+N L + Sbjct: 225 GGVSNLSFSFRGNEPVREAMHAVFLYHAIRAGMDMGIVNAGQLAV 269 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: 539 Number of extensions: 27 Number of successful extensions: 3 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: 908 Length adjustment: 36 Effective length of query: 317 Effective length of database: 872 Effective search space: 276424 Effective search space used: 276424 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: 53 (25.0 bits)
This GapMind analysis is from Apr 16 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