Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_052665963.1 NITAL_RS09145 methyltetrahydrofolate--corrinoid methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000969705.1:WP_052665963.1 Length = 303 Score = 342 bits (877), Expect = 7e-99 Identities = 193/350 (55%), Positives = 230/350 (65%), Gaps = 52/350 (14%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MT+TVV S T+ ++GF PF +IGE+INPTGRK LA EL+AGDFS V DALAQV AGA Sbjct: 1 MTQTVVSSGTREVVIGFGRPFVMIGEKINPTGRKILAEELKAGDFSRVAADALAQVEAGA 60 Query: 61 NILDINAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGR 120 +LD+NAGV P EP L+ V+LVQ LTD PL IDSSV ALEAG+ +G+ Sbjct: 61 QMLDVNAGV-------PLADEPALLAHAVQLVQSLTDAPLSIDSSVVEALEAGIAVYQGK 113 Query: 121 PLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGI 180 PL+NSVTGE+E +E VLPLV ++ VVAISND+TGISEDPDVRF VA++IV RAAD GI Sbjct: 114 PLINSVTGEDEVMERVLPLVARHGAAVVAISNDETGISEDPDVRFEVARRIVNRAADHGI 173 Query: 181 PAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAF 240 P D++VDPLVMPIGAM +AGQQVF L+RRLREEL VNT CGASNVSFGLPNRH I F Sbjct: 174 PREDVIVDPLVMPIGAMGSAGQQVFRLLRRLREELEVNTICGASNVSFGLPNRHAITGTF 233 Query: 241 LPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKP 300 L MA+GAGMTSAIMNP+ EV+ Sbjct: 234 LSMAIGAGMTSAIMNPM------------HPEVKT------------------------- 256 Query: 301 RAGKEMEAIRAANLLTNNDPHGGEWIKANKEPAKEGEEGRGRGGRAGGRR 350 A+ AA++L +D + WI+AN++P EG GR R GRR Sbjct: 257 -------AVTAADVLAGHDANCAAWIRANRQPDGEG-TGRESSRRRAGRR 298 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: 317 Number of extensions: 5 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: 2 Length of query: 353 Length of database: 303 Length adjustment: 28 Effective length of query: 325 Effective length of database: 275 Effective search space: 89375 Effective search space used: 89375 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