Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_012281270.1 HM1_RS00425 homocysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000019165.1:WP_012281270.1 Length = 431 Score = 539 bits (1388), Expect = e-158 Identities = 267/430 (62%), Positives = 337/430 (78%), Gaps = 4/430 (0%) Query: 1 MDWKKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTR 60 M KK+ ++T ALH G+ P +Q T SRAVPIYQTTSYVFRD DHAA LFAL+EPG IYTR Sbjct: 1 MTEKKWRFDTIALHEGHVP-DQDTLSRAVPIYQTTSYVFRDVDHAANLFALKEPGHIYTR 59 Query: 61 IGNPTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLF 120 I NPT VLE+R+AAL+ GVGALA++SGQ+AIT +ILNI GDEIV+ ++LYGGTYNLF Sbjct: 60 IDNPTTDVLEKRLAALDGGVGALALSSGQSAITLSILNICAAGDEIVAATSLYGGTYNLF 119 Query: 121 RHTLYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHG 180 HTL + G+ ++FVD ++P N AI EKTKA+Y ETIGNP V D EA+A +AH G Sbjct: 120 THTL-PRLGVKIRFVDPSNPDNFRAAINEKTKAIYGETIGNPKCDVLDIEAVAAVAHEAG 178 Query: 181 VPLIVDNTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWT-NGKFPE 238 +PLIVDNT P + RP + GADIVVYSATKFIGGHG +IGG+IVDSGKFDWT N KFP Sbjct: 179 IPLIVDNTFGTPALCRPIDFGADIVVYSATKFIGGHGIAIGGVIVDSGKFDWTQNDKFPG 238 Query: 239 LVEPDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKH 298 + PDPSYHG+ Y + AA++ K R QLLRD+G+C+SPFNAFL +LG+ETLSLRM++H Sbjct: 239 FINPDPSYHGIVYAKDIGPAAFVVKARVQLLRDMGNCISPFNAFLLLLGVETLSLRMERH 298 Query: 299 CENALKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKF 358 N ++V+FL++HP VSWV+YP + + + A KYL +G GAI+TFG+KGG EAG++F Sbjct: 299 VSNTRRVVDFLRNHPLVSWVSYPECSDHASCDLAKKYLPKGAGAILTFGIKGGVEAGRRF 358 Query: 359 IDSLTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIA 418 IDSL + SHLAN+GDA++L IHPASTTH QL+EE GV+PD++RLS+G+ED +D+I Sbjct: 359 IDSLQIFSHLANVGDAKSLVIHPASTTHSQLSEEALRAAGVSPDLVRLSIGLEDPDDLIE 418 Query: 419 DLDQALRKSQ 428 DL QALR ++ Sbjct: 419 DLAQALRAAE 428 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: 590 Number of extensions: 18 Number of successful extensions: 5 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: 431 Length adjustment: 32 Effective length of query: 398 Effective length of database: 399 Effective search space: 158802 Effective search space used: 158802 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