Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_004514768.1 GMET_RS12040 homocysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000012925.1:WP_004514768.1 Length = 428 Score = 547 bits (1410), Expect = e-160 Identities = 275/425 (64%), Positives = 328/425 (77%), Gaps = 3/425 (0%) Query: 5 KYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNP 64 K ++T ALHAG EP + T SRAVPIYQT SY F+ S+HAA LF L+E G IYTR+ NP Sbjct: 5 KISFDTLALHAGQEP-DPTTLSRAVPIYQTASYAFKSSEHAANLFGLKEFGNIYTRLMNP 63 Query: 65 TVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTL 124 T VLE+R+A L+ GVGALAVASGQAAITYA+LNIA G IVS S LYGGTYNLF +TL Sbjct: 64 TSDVLEKRLAELDGGVGALAVASGQAAITYAVLNIAQAGQNIVSTSYLYGGTYNLFHYTL 123 Query: 125 YKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLI 184 K GI VKFVD +DP+N+ AI +KT+ VY E++GNP V DFEAIA IAH G+P + Sbjct: 124 -PKLGITVKFVDTSDPENVRRAIDDKTRLVYTESVGNPKNNVDDFEAIARIAHEAGIPFV 182 Query: 185 VDNTVAP-YIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPD 243 VDNTV Y+F+P EHGADIVVYS TKFIGGHGTSIGG +VD GKF W NG+FPE+ EPD Sbjct: 183 VDNTVTTSYLFKPLEHGADIVVYSLTKFIGGHGTSIGGAVVDGGKFPWNNGRFPEMTEPD 242 Query: 244 PSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENAL 303 PSYHG+ Y E +YI K R LLRD+G+C+SPFN+FLF+ GLETL +RM +H ENA Sbjct: 243 PSYHGLCYWEALGNLSYILKMRITLLRDMGACISPFNSFLFLQGLETLPVRMARHVENAR 302 Query: 304 KIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLT 363 + ++L+ HP VSWVNYP +K NA KYL +G GAI+ FG+ GG EAG++FIDS Sbjct: 303 AVAQWLEKHPLVSWVNYPGLASHKDHGNARKYLPKGEGAIIGFGINGGLEAGRRFIDSAK 362 Query: 364 LISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQA 423 L+SHLANIGDA++L IHPASTTHQQL+EEEQL +GVT D IRLS+GIE+V DIIAD+DQA Sbjct: 363 LLSHLANIGDAKSLVIHPASTTHQQLSEEEQLASGVTQDYIRLSIGIEEVADIIADIDQA 422 Query: 424 LRKSQ 428 L SQ Sbjct: 423 LAASQ 427 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: 610 Number of extensions: 26 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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 Jul 25 2024. The underlying query database was built on Jul 25 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