Align Methionine synthase; Homocysteine methyltransferase; Methylcobalamin:homocysteine methyltransferase; EC 2.1.1.- (characterized)
to candidate WP_010876413.1 MTH_RS03635 methionine synthase
Query= SwissProt::P55299 (309 letters) >NCBI__GCF_000008645.1:WP_010876413.1 Length = 308 Score = 474 bits (1220), Expect = e-138 Identities = 235/306 (76%), Positives = 266/306 (86%) Query: 1 MITTVVGSYPATPREPETLRERISSFIGSYDACRPAIETAVRDQVRAGVDIISDGQVRGD 60 MITTVVGSYP PR PETL ER+ +F GSYD RPAIE AVRDQ RAGVDIISDGQVRGD Sbjct: 1 MITTVVGSYPTEPRGPETLGERLLNFFGSYDRYRPAIEAAVRDQFRAGVDIISDGQVRGD 60 Query: 61 MVGHFAEAMGGMMVKDGVSIIFSRITPPAGSIGSDDLIYAIKILRKLTDDESKGVKGIIT 120 MVGHFA A+GGM ++DG SII+SRITPPAGSIG+ DL YA +ILR LTDDES+GVKGIIT Sbjct: 61 MVGHFAAAIGGMKIEDGTSIIYSRITPPAGSIGAADLRYAYRILRGLTDDESRGVKGIIT 120 Query: 121 GPSTMAHASKIEGFYSPQKRERAIMDMADALRVEAEHLQDAGALMIQIDEPFLSTGMVDM 180 GPSTM +AS+IEGFY PQKR+RA+MDMA L++EA+HLQDAGA MIQIDEPFLSTG+VDM Sbjct: 121 GPSTMIYASRIEGFYDPQKRDRAVMDMAGVLKIEAKHLQDAGAAMIQIDEPFLSTGIVDM 180 Query: 181 GTARRAVKRISGALDVDVSLHVCGDISGVIGELLTFPVDMLDLEFAGRPSNLEVLAEKWR 240 TA RA+ I+ LD++VSLHVCGDI V+ +LL F VD+LDLEFAGRPSNLEVL EKWR Sbjct: 181 KTAGRAIDHIAAGLDIEVSLHVCGDIRNVLSDLLRFKVDVLDLEFAGRPSNLEVLEEKWR 240 Query: 241 GDKKLGFGCVDTSTEVVESTDTIKNLIERGADIAGEDNLYIDPDCGMRKLPREAAFSKLR 300 GDK +GFGCVDT+TE VES + I+NLI+RGADI GE+NLYIDPDCGMRKLPR+AAFSKLR Sbjct: 241 GDKGVGFGCVDTTTERVESMEEIRNLIKRGADIVGEENLYIDPDCGMRKLPRKAAFSKLR 300 Query: 301 NMVKAA 306 NMV AA Sbjct: 301 NMVMAA 306 Lambda K H 0.319 0.136 0.389 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: 383 Number of extensions: 5 Number of successful extensions: 1 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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