Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_028486937.1 B076_RS0108550 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000483485.1:WP_028486937.1 Length = 425 Score = 468 bits (1204), Expect = e-136 Identities = 241/416 (57%), Positives = 303/416 (72%), Gaps = 5/416 (1%) Query: 12 ALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVLEE 71 ALH GYE E T S AVPIYQTTSY F D+ H A LF L+ PG IYTRI NPT +VLE Sbjct: 7 ALHHGYES-EPTTKSAAVPIYQTTSYTFDDTQHGADLFDLKVPGNIYTRIMNPTTAVLES 65 Query: 72 RIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSGII 131 R+A +E GV ALAVASG +AITYAI IA GD IVS S LYGGTYNLF HT + + GI Sbjct: 66 RVAEMEGGVAALAVASGMSAITYAIQAIAQAGDNIVSTSQLYGGTYNLFAHT-FPRQGIE 124 Query: 132 VKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTVA- 190 V+ + D + E+AI E T+A++ E+IGNP V D +AEIA++HGVPL+VDNTVA Sbjct: 125 VRMIQADDFEGFEKAIDENTRAIFCESIGNPAGNVVDIAKLAEIANKHGVPLMVDNTVAT 184 Query: 191 PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNG--KFPELVEPDPSYHG 248 PY+ +PFE GADIV++S TKFIGGHGT++GG IVDSGKFDW +FP L EPDPSYHG Sbjct: 185 PYLCKPFEFGADIVIHSLTKFIGGHGTTLGGAIVDSGKFDWVANAKRFPMLNEPDPSYHG 244 Query: 249 VSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIVEF 308 V Y AA+IA+CR LR+ G+ ++P +AFL + GLETL LRM++HCENALK E+ Sbjct: 245 VIYTRDIGAAAFIARCRVVPLRNTGAALAPHSAFLIMQGLETLGLRMERHCENALKAAEY 304 Query: 309 LKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLISHL 368 L++HP VSWVNY +K K K I++FG+KGG+EAG +FID+L +I L Sbjct: 305 LQNHPKVSWVNYAALPNDKYHAICQKITKGQASGILSFGIKGGREAGGQFIDALKMILRL 364 Query: 369 ANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQAL 424 NIGDA++LA HPA+TTH+QL+ E + GV+ D++RLS+GIE ++DIIAD++QAL Sbjct: 365 VNIGDAKSLACHPATTTHRQLSPAELQQAGVSEDLVRLSIGIEHIDDIIADIEQAL 420 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: 555 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 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