Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate GFF750 PGA1_c07640 O-acetylhomoserine / O-acetylserine sulfhydrylase
Query= CharProtDB::CH_124469 (429 letters) >FitnessBrowser__Phaeo:GFF750 Length = 430 Score = 417 bits (1072), Expect = e-121 Identities = 216/422 (51%), Positives = 284/422 (67%), Gaps = 2/422 (0%) Query: 8 FETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADV 67 F+TLQ+HAG +PD AT +R PIY TT+YVFRD DH LF LQE G+IYSR+ NPT V Sbjct: 9 FDTLQIHAGAKPDPATGARQTPIYQTTAYVFRDADHAAALFNLQEVGFIYSRLTNPTVAV 68 Query: 68 FEKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLG 127 ++RIA LE G A+ SSG +A MAL L G N+V+++ LYGGT F T+ R G Sbjct: 69 LQERIATLEGGVGAVCCSSGHAAQIMALFPLMGPGCNVVASTRLYGGTVTQFSQTIKRFG 128 Query: 128 ITTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTF 187 + KFV+ D+P +AA ID++T+AV+ ES+ NP V D IA+VA AAGVPL++DNT Sbjct: 129 WSAKFVDFDNPEAVAAAIDDDTRAVFGESVANPGGYVTDIRSIADVADAAGVPLIIDNT- 187 Query: 188 GGGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPG 247 YL PI HGA +V HS TK++ G+GT GGVIVDSGKFDW N K FP ++P P Sbjct: 188 SATPYLCSPIAHGATLVVHSTTKYLTGNGTVTGGVIVDSGKFDWSANDK-FPSLSQPEPA 246 Query: 248 YHGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFAL 307 YHG+ F ETFG LA+ F LRD+G NP L G+ETLSLRMERH +NA + Sbjct: 247 YHGLKFHETFGGLAFTFHGIAIGLRDLGMTMNPQAAHYTLMGVETLSLRMERHCENAKTV 306 Query: 308 AKYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSRKVVNALKLA 367 A +LE+ P+V++V+Y GL S H AK++ G G + +F KGG D K+VN+L++ Sbjct: 307 ASWLEQDPRVDYVTYAGLPSSPYHARAKEHYPKGTGGLFTFAVKGGYDACVKLVNSLEIF 366 Query: 368 SQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFAQALE 427 S +AN+GD ++L+I A TTH QLT E+Q +AG +++RV++GIE+ DD+IAD QAL Sbjct: 367 SHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAGANVVRVSIGIENADDLIADLDQALS 426 Query: 428 VA 429 A Sbjct: 427 KA 428 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: 523 Number of extensions: 18 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: 429 Length of database: 430 Length adjustment: 32 Effective length of query: 397 Effective length of database: 398 Effective search space: 158006 Effective search space used: 158006 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 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