Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate GFF659 HP15_641 homocysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__Marino:GFF659 Length = 425 Score = 462 bits (1188), Expect = e-134 Identities = 239/422 (56%), Positives = 302/422 (71%), Gaps = 5/422 (1%) Query: 10 TRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVL 69 T ALHAG++ + T + PIYQTTSY F D+ H A LF L+ G IYTRI NPT +VL Sbjct: 5 TLALHAGFKS-DPTTRAATTPIYQTTSYTFDDTQHGADLFDLKVQGNIYTRIMNPTNAVL 63 Query: 70 EERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSG 129 EER+A LE GVGALAVASG AAITYA+ I G+ IVS S LYGGTYNLF H+L G Sbjct: 64 EERMAELEGGVGALAVASGMAAITYALQTICKVGNNIVSTSQLYGGTYNLFAHSL-PNQG 122 Query: 130 IIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTV 189 I K V D +E+AI E T+A++ E+IGNP V D + AEIAH+HG+PL+VDNTV Sbjct: 123 IECKMVRHDDFDAVEKAIDENTRALFCESIGNPAGNVVDIQRWAEIAHKHGIPLMVDNTV 182 Query: 190 A-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDW--TNGKFPELVEPDPSY 246 A P++ RP EHGADIV++S TK+IGGHGT++ G++VDSGKFDW + KFP L EPDPSY Sbjct: 183 ATPFLCRPIEHGADIVIHSLTKYIGGHGTTVAGVVVDSGKFDWKASADKFPMLNEPDPSY 242 Query: 247 HGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIV 306 HGV Y + AA+I +CR LR+ G+ ++PFNAFL + GLETL+LRM++HCENA K+ Sbjct: 243 HGVVYTDALGPAAFIGRCRVVPLRNTGAALAPFNAFLIMQGLETLALRMERHCENAEKVA 302 Query: 307 EFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLIS 366 FL+ HP+V WVNY + + K I++FG+KGG+EAG KFID+L LI Sbjct: 303 NFLQEHPSVEWVNYATLANSPYKATCEKISGGKASGILSFGIKGGREAGAKFIDALELIL 362 Query: 367 HLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQALRK 426 L NIGDA++LA HPA+TTH+QL EE GV+ D++RLS+GIE V+DIIAD+ QAL K Sbjct: 363 RLVNIGDAKSLACHPATTTHRQLNPEELKSAGVSEDLVRLSIGIEHVDDIIADITQALDK 422 Query: 427 SQ 428 +Q Sbjct: 423 AQ 424 Lambda K H 0.317 0.136 0.398 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: 567 Number of extensions: 22 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: 430 Length of database: 425 Length adjustment: 32 Effective length of query: 398 Effective length of database: 393 Effective search space: 156414 Effective search space used: 156414 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 (21.6 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