Align Methionine synthase; Homocysteine methyltransferase; Methylcobalamin:homocysteine methyltransferase; EC 2.1.1.- (characterized)
to candidate WP_011973643.1 MAEO_RS04680 methionine synthase
Query= SwissProt::P55299 (309 letters) >NCBI__GCF_000017185.1:WP_011973643.1 Length = 324 Score = 236 bits (602), Expect = 5e-67 Identities = 141/327 (43%), Positives = 194/327 (59%), Gaps = 27/327 (8%) Query: 1 MITTVVGSYPATPREPETLRERISSFIGSYDACRPAIETAVRDQVRAGVDIISDGQVRGD 60 MI TVVGSYP P+ + ++I +G +D + AIE ++ QV AG+DI+SDGQ RGD Sbjct: 1 MIKTVVGSYPVVKGAPQNIMDKIKDKLGMFDEFKYAIEQSIYGQVEAGIDILSDGQTRGD 60 Query: 61 MVGHFAEAMGGMMVKDGVSIIFSRITPPAGSIGSDDLIYAIKILRKLTDDESKGVKGIIT 120 MV F + G K V I T P I +D+ Y+ KIL+ L + ++K +KG++T Sbjct: 61 MVEIFVSNLYGFEGKRVVGKI--EHTKP---ITLNDIKYSNKILKSLPNTQNKSIKGLLT 115 Query: 121 GPSTMAHASKIEG--FYSPQKRERAIMDMADALRVEAEHLQDAGALMIQIDEPFLSTGMV 178 GP T+A + +IE YS K E I D+A AL+ EA +Q+ + IQIDEP LSTGM Sbjct: 116 GPCTIASSIRIENNNHYSDNKDENLIYDLAVALKKEALDIQNEVST-IQIDEPILSTGMY 174 Query: 179 DMGTARRAVKRISGALDVDVSLHVCGDISGVIGELLTFPVDMLDLEFAGRPSNLEVLAEK 238 D+ A++A+ I+ L++ +S+HVCG +SG+ EL F VDMLD EFA NLEVL + Sbjct: 175 DLDMAKKAINLITEDLNIPISMHVCGGVSGIYSELHNFNVDMLDFEFASNKKNLEVLEDI 234 Query: 239 WRGDKKLGFGCVDTSTEVVESTDTIKNLIERGADIAGEDNLY----------------ID 282 +KK+GFGC++T + VES D IK+LI G +I ++ + ID Sbjct: 235 ---NKKIGFGCINTKLKTVESVDDIKSLIGEGVEILKNNSKFNGINGNMVDKLNNFVVID 291 Query: 283 PDCGMRKLPREAAFSKLRNMVKAASEF 309 PDCGMR LP A KL+NM A EF Sbjct: 292 PDCGMRLLPLGVAQQKLKNMCMACDEF 318 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: 253 Number of extensions: 11 Number of successful extensions: 5 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: 324 Length adjustment: 27 Effective length of query: 282 Effective length of database: 297 Effective search space: 83754 Effective search space used: 83754 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