Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate WP_046010273.1 OLEAN_RS17345 O-acetylhomoserine aminocarboxypropyltransferase
Query= CharProtDB::CH_124469 (429 letters) >NCBI__GCF_000967895.1:WP_046010273.1 Length = 423 Score = 456 bits (1172), Expect = e-133 Identities = 229/421 (54%), Positives = 291/421 (69%), Gaps = 2/421 (0%) Query: 9 ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68 ET +HAG E D T + AVPIY TTSY FRD HG LF L+EPG IY+R+MNPT DV Sbjct: 4 ETQSIHAGFEDDPTTRAVAVPIYQTTSYSFRDTQHGADLFDLKEPGNIYTRIMNPTNDVL 63 Query: 69 EKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLGI 128 EKR+A +E G +A +SG +A+ A+ T+A+ GDNI+S S LYGGTYN F TLP GI Sbjct: 64 EKRVAEMEGGIGGVAFASGMAAITAAIQTVARTGDNIISVSQLYGGTYNFFAHTLPNQGI 123 Query: 129 TTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTFG 188 + GDD L A ID+NTKA++ ESIGNP N+ D + ++++AH G+P+MVDNT Sbjct: 124 EVRMAKGDDLAGLEALIDDNTKALFCESIGNPAGNIVDIQALSDMAHKHGIPVMVDNTVA 183 Query: 189 GGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPGY 248 L RPI+ GADIV HS TK+IGGHGT++GG+IVDSGKF WK + RFP FN+P P Y Sbjct: 184 TP-ILCRPIEQGADIVIHSLTKYIGGHGTSVGGIIVDSGKFPWKDHP-RFPAFNQPDPSY 241 Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308 HG+V+ + FG A+ R LR++G +PF FL+LQGLETLSLRMERH +NA +A Sbjct: 242 HGVVYADAFGPAAFIGRARVVPLRNMGAAISPFNSFLILQGLETLSLRMERHTENALKVA 301 Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSRKVVNALKLAS 368 KYL H V WV+Y GLE ++LAKK + A+LSFG KGG K ++AL L Sbjct: 302 KYLSAHDMVEWVNYAGLEGDKFYELAKKVVDGKPSAILSFGIKGGEANGAKFIDALLLVK 361 Query: 369 QLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFAQALEV 428 +L N+GDAK+L PA TTH QL DEE +AGV+++++R++VGIEHIDDII D QAL Sbjct: 362 RLVNIGDAKSLACHPASTTHRQLNDEELKNAGVSREMVRISVGIEHIDDIIEDIEQALVA 421 Query: 429 A 429 A Sbjct: 422 A 422 Lambda K H 0.318 0.135 0.399 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: 555 Number of extensions: 18 Number of successful extensions: 4 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: 429 Length of database: 423 Length adjustment: 32 Effective length of query: 397 Effective length of database: 391 Effective search space: 155227 Effective search space used: 155227 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: 51 (24.3 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