Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate GFF1835 HP15_1792 B12-dependent methionine synthase
Query= reanno::Phaeo:GFF1321 (338 letters) >FitnessBrowser__Marino:GFF1835 Length = 1232 Score = 117 bits (294), Expect = 1e-30 Identities = 109/363 (30%), Positives = 162/363 (44%), Gaps = 51/363 (14%) Query: 1 MTNTFTTLLETKDAL-----LADGATGTNLFNMGLQS----GDA-----------PELWN 40 MT+ T L + AL + DG GT + N+ L GD +L N Sbjct: 1 MTDRTTRLDQLHKALQERIVILDGGMGTMIQNLKLDEKAFRGDRFADYEREVQGNNDLLN 60 Query: 41 VDEPKKITALYQGAVDAGSDLFLTNTFGGTAARLKLHDAHRRVRELNVAGAELGRNVAD- 99 + +P + ++ +DAG+D+ TNTF T + RELNVA AEL R +AD Sbjct: 61 LTQPALLRNIHADYLDAGADIIETNTFNSTQLSQADYGLEAIARELNVAAAELARQIADE 120 Query: 100 ----RSERKIAVAGSVGPTG-------EIMQP-VGELSHALAVEMFHEQAEALKEGGVDV 147 E+ VAG+VGPT ++ P + V+ ++E L EGG D+ Sbjct: 121 YTAKNPEKPRFVAGAVGPTSRTASISPDVNNPGYRNVDFQTLVDNYYEAVGGLVEGGCDL 180 Query: 148 LWLETISAPEEYRAAAEAFK--------LADMPWCGTMSFDTAGRTMMGVTSADMAQLVE 199 + +ETI +AA A + + GT++ D +GRT+ G T+ V Sbjct: 181 ILIETIFDTLNAKAAIYATQQYFEDSGITLPIMISGTIT-DASGRTLSGQTTEAFWNSVA 239 Query: 200 EFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHYDGTPTL 259 P++ G NC GA + V +A+ T + + NAG+P YD TP Sbjct: 240 H--AKPISVGLNCALGADALRPYVEELSAKAETY-VSAHPNAGLPNEFG---EYDQTPEE 293 Query: 260 MGE-YAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRGEQLTLERIVEVLG--PFTS 316 M E ARD IIGGCCG+ PDH+ A+ +A+ P + + + + G PFT Sbjct: 294 MAEIIEGFARDGFLNIIGGCCGSRPDHIEAIAQAVSKYPPRKIPERPKALRLSGLEPFTG 353 Query: 317 DSD 319 D + Sbjct: 354 DDN 356 Lambda K H 0.317 0.134 0.397 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: 891 Number of extensions: 49 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: 338 Length of database: 1232 Length adjustment: 38 Effective length of query: 300 Effective length of database: 1194 Effective search space: 358200 Effective search space used: 358200 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: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 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