Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate YP_004142536.1 Mesci_3363 methionine synthase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000185905.1:YP_004142536.1 Length = 324 Score = 395 bits (1015), Expect = e-115 Identities = 217/367 (59%), Positives = 257/367 (70%), Gaps = 62/367 (16%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MTRT+V S T+ I+GFD+PFCVIGERINPTGRKKLAAE+ AG+F TV +DAL Q GA Sbjct: 1 MTRTIVASATREIIIGFDQPFCVIGERINPTGRKKLAAEMIAGNFETVIRDALEQAACGA 60 Query: 61 NILDINAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGR 120 +LD+NAGV ++ NPNETEP L+ + +E+VQGL D PL IDSSV A+EA L+ A+GR Sbjct: 61 TMLDVNAGV---TSVNPNETEPGLLVQTLEIVQGLVDLPLSIDSSVTAAIEAALKVAKGR 117 Query: 121 PLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGI 180 PL+NSVTGEEE+LE +LPLVKKYNVPVVAISND+TGIS DPDVRFAVAKKIVER ADFGI Sbjct: 118 PLVNSVTGEEEKLEAILPLVKKYNVPVVAISNDETGISMDPDVRFAVAKKIVERCADFGI 177 Query: 181 PAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAF 240 PAHD+VVDPLVMPIGA+ AG+QVFAL+RRLREEL VNTTCG SN+SFGLP+RHGIN AF Sbjct: 178 PAHDVVVDPLVMPIGALGDAGRQVFALLRRLREELKVNTTCGLSNISFGLPHRHGINAAF 237 Query: 241 LPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKP 300 +PM +GAGMTSAIMNPV +P Sbjct: 238 IPMVIGAGMTSAIMNPV-----------------------------------------RP 256 Query: 301 RAGKEMEAIRAANLLTNNDPHGGEWIKANKE--PAKEGE------------EGRGRGG-R 345 +EMEA+R AN+L D + WI+ K+ PA+ G+ +G G GG R Sbjct: 257 ---QEMEAVRGANVLNGTDENCTNWIRTYKDYKPAEGGQAVAAPTQVNAPGDGAGNGGRR 313 Query: 346 AGGRRRR 352 GGR R Sbjct: 314 RGGREAR 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: 368 Number of extensions: 10 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