Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate WP_002719921.1 RSPH17029_RS07130 methyltetrahydrofolate cobalamin methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000015985.1:WP_002719921.1 Length = 324 Score = 452 bits (1162), Expect = e-132 Identities = 244/364 (67%), Positives = 270/364 (74%), Gaps = 56/364 (15%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MTRTV+ESKTKT ++GFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDAL QV GA Sbjct: 1 MTRTVLESKTKTVVIGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALEQVACGA 60 Query: 61 NILDINAGVVYNSN-------PNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAG 113 +LD+N+G V+ + + N EPPLM ++V +Q +TD PLCIDSSVPGALEAG Sbjct: 61 TVLDVNSGAVFTNKMAEDPRYADNNFVEPPLMKELVARIQAITDVPLCIDSSVPGALEAG 120 Query: 114 LQAAEGRPLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVE 173 L A EGRPLLNSVTGEEERLE VLPLVKKYNVPVVAISNDDTGIS+DPDVRFAVAKKIVE Sbjct: 121 LSACEGRPLLNSVTGEEERLELVLPLVKKYNVPVVAISNDDTGISQDPDVRFAVAKKIVE 180 Query: 174 RAADFGIPAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNR 233 RAADFGIPAHDIVVDPLVMP+GAMA+AGQQVFALVRRLR+ELGVNTTCGASNVSFGLPNR Sbjct: 181 RAADFGIPAHDIVVDPLVMPVGAMASAGQQVFALVRRLRDELGVNTTCGASNVSFGLPNR 240 Query: 234 HGINNAFLPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMF 293 HG+N AFLPMA+GAGMTSAIMNPV Sbjct: 241 HGVNAAFLPMAIGAGMTSAIMNPV------------------------------------ 264 Query: 294 GLGSTKPRAGKEMEAIRAANLLTNNDPHGGEWIKANK--EPAKEG---EEGRGRGGRAGG 348 EMEAIRAAN+L N+DP+G EWI+ ++ + KEG E AGG Sbjct: 265 --------RSVEMEAIRAANMLMNHDPNGSEWIRFSRILDAVKEGATFPEACAAQAAAGG 316 Query: 349 RRRR 352 R RR Sbjct: 317 RGRR 320 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: 405 Number of extensions: 16 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: 324 Length adjustment: 28 Effective length of query: 325 Effective length of database: 296 Effective search space: 96200 Effective search space used: 96200 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 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