Align Methionine synthase component, pterin-binding domain (EC:2.1.1.13) (characterized)
to candidate YP_001327454.1 Smed_1784 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase
Query= reanno::Phaeo:GFF1582 (353 letters) >NCBI__GCF_000017145.1:YP_001327454.1 Length = 319 Score = 393 bits (1009), Expect = e-114 Identities = 215/360 (59%), Positives = 252/360 (70%), Gaps = 54/360 (15%) Query: 1 MTRTVVESKTKTAILGFDEPFCVIGERINPTGRKKLAAELEAGDFSTVEKDALAQVMAGA 60 MTRT+V S T+ ++GFD+PFCVIGERINPTGRKKLAAE+ G+F TV KDAL QV AGA Sbjct: 1 MTRTIVASATREIVIGFDQPFCVIGERINPTGRKKLAAEMLEGNFDTVIKDALEQVAAGA 60 Query: 61 NILDINAGVVYNSNPNPNETEPPLMTKIVELVQGLTDTPLCIDSSVPGALEAGLQAAEGR 120 +LD+NAGV + NPNETEPPL+ K +E+VQGL D PL IDSSV A+EAGL+ A+GR Sbjct: 61 TMLDVNAGV---TAVNPNETEPPLLVKTLEIVQGLIDVPLSIDSSVTAAIEAGLRVAKGR 117 Query: 121 PLLNSVTGEEERLEHVLPLVKKYNVPVVAISNDDTGISEDPDVRFAVAKKIVERAADFGI 180 PL+NSVTGEEE+LE +LPL+KKY+VPVVAISND+TGIS DPDVRFAVAKKIVERA D GI Sbjct: 118 PLVNSVTGEEEKLEAILPLIKKYDVPVVAISNDETGISMDPDVRFAVAKKIVERAMDHGI 177 Query: 181 PAHDIVVDPLVMPIGAMATAGQQVFALVRRLREELGVNTTCGASNVSFGLPNRHGINNAF 240 HDIVVDPLVMPIGA+ AG+QVFAL+RRLREEL VNTTCG SN+SFGLP+RHGIN F Sbjct: 178 KPHDIVVDPLVMPIGALGDAGRQVFALLRRLREELKVNTTCGLSNISFGLPHRHGINAGF 237 Query: 241 LPMAMGAGMTSAIMNPVALPITQKKIAEKKAEVEAAGIILPEGMEDEAFVQMFGLGSTKP 300 +PM +GAGMTSAIMNP +P Sbjct: 238 IPMVIGAGMTSAIMNP-----------------------------------------CRP 256 Query: 301 RAGKEMEAIRAANLLTNNDPHGGEWIKANKE--PAKEGE-----EGRGRGGRAGGRRRRA 353 +EMEA+RAAN+L DP+ WI ++ PA+ G GGR GGR RA Sbjct: 257 ---QEMEAVRAANVLNGTDPNCTNWIMTYRDHKPAEGGHAVAAAAPSASGGRRGGRAARA 313 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: 384 Number of extensions: 11 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: 319 Length adjustment: 28 Effective length of query: 325 Effective length of database: 291 Effective search space: 94575 Effective search space used: 94575 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