Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate 5210267 Shew_2710 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= CharProtDB::CH_124469 (429 letters) >FitnessBrowser__PV4:5210267 Length = 429 Score = 437 bits (1124), Expect = e-127 Identities = 225/426 (52%), Positives = 287/426 (67%), Gaps = 6/426 (1%) Query: 9 ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68 E+L LH G +A T + AVPIY TTSY F D HG LF L+ G IY+R+MNPT DV Sbjct: 4 ESLALHHGYTSEATTKAAAVPIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTTDVL 63 Query: 69 EKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLGI 128 E+R+AA+E G A+A +SG +A+ A+ L + GDNIVSTS LYGGTYNLF TLPR G+ Sbjct: 64 EQRLAAIEGGIGALALASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQGV 123 Query: 129 TTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTFG 188 + DD + L A ID+ TKA++ ESIGNP N+ D R+AE+AH GVPL+VDNT Sbjct: 124 EVRMAAFDDFDGLEAHIDDKTKALFCESIGNPAGNIVDIARLAEIAHRHGVPLIVDNTV- 182 Query: 189 GGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPGY 248 L RP +HGADIV HS TK+IGGHGTTIGGVI+DSGKFDW +RF NEP P Y Sbjct: 183 ATPVLCRPFEHGADIVIHSLTKYIGGHGTTIGGVIIDSGKFDWAAQPQRFALLNEPDPSY 242 Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308 HG+V+T+ FG A+ CR LR+ G +P FLLLQGLETL+LRMERH NA ALA Sbjct: 243 HGVVYTQAFGPAAFIGRCRVVPLRNTGAALSPQSAFLLLQGLETLALRMERHCDNALALA 302 Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSRKV-----VNA 363 +LE+ P+V+WV+Y L++ +K ++SFG K ++ K ++A Sbjct: 303 NFLEQDPRVSWVNYGALDNSPYRDNCEKITSGKASGIISFGIKAEDSEAAKAAGGRFIDA 362 Query: 364 LKLASQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFA 423 L++ +L N+GDAK+L PA TTH QL EE AGV++DLIR++VGIEHI+DIIAD + Sbjct: 363 LQMILRLVNIGDAKSLACHPATTTHRQLNGEELAKAGVSEDLIRISVGIEHIEDIIADVS 422 Query: 424 QALEVA 429 QAL+ A Sbjct: 423 QALDKA 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: 544 Number of extensions: 21 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: 429 Length adjustment: 32 Effective length of query: 397 Effective length of database: 397 Effective search space: 157609 Effective search space used: 157609 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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