Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_011307392.1 MBAR_RS12885 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000195895.1:WP_011307392.1 Length = 457 Score = 546 bits (1407), Expect = e-160 Identities = 267/418 (63%), Positives = 328/418 (78%), Gaps = 2/418 (0%) Query: 7 GYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTV 66 G +T A+HAG +P + ATG+R+VPIYQT +YVF+D++ AA LF L + G IYTR+ NPT Sbjct: 39 GVSTLAVHAGAKP-DPATGARSVPIYQTAAYVFKDAEEAADLFGLRKEGNIYTRLMNPTT 97 Query: 67 SVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYK 126 V E+RIAALE G+GALAVASG AAIT A+L PGDEI+SG LYGGTY LF +T + Sbjct: 98 DVFEKRIAALEGGIGALAVASGMAAITTALLTFTRPGDEIISGDKLYGGTYELFNYT-FP 156 Query: 127 KSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVD 186 K G VKFVD P+ + AI+EKTKA+Y+E+IGNPGL +PDFE +AEIAH G+P +VD Sbjct: 157 KLGRTVKFVDVGKPEEFKNAISEKTKAIYVESIGNPGLDIPDFEKLAEIAHGAGIPFVVD 216 Query: 187 NTVAPYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPDPSY 246 NTV+P I RP +HG DIVVYSATKFIGGHGTSIGG+IVDSG F W KFPE+ EPDP Y Sbjct: 217 NTVSPLILRPIDHGVDIVVYSATKFIGGHGTSIGGVIVDSGNFYWKPEKFPEICEPDPGY 276 Query: 247 HGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIV 306 HG+ Y E F +AA+IAK R Q +RD G+C+SPFN+FLF LGLETL LRMKKHC+NAL+I Sbjct: 277 HGLKYKEAFGKAAFIAKARVQFIRDTGACISPFNSFLFTLGLETLPLRMKKHCDNALEIA 336 Query: 307 EFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLIS 366 +FL+ HP VSWV+YP E + + E A KYLK GYGA++ FG+KGG KKFI+ L + S Sbjct: 337 KFLEKHPKVSWVSYPGLESHCSYELAKKYLKSGYGALIGFGIKGGARECKKFIEGLEIFS 396 Query: 367 HLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQAL 424 HLANIGDA++L IHPASTTH+QL++EEQL GVT D IRLS+GIED +D+I+D+ QAL Sbjct: 397 HLANIGDAKSLVIHPASTTHEQLSKEEQLACGVTEDFIRLSIGIEDAKDLISDIKQAL 454 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: 631 Number of extensions: 22 Number of successful extensions: 2 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: 457 Length adjustment: 32 Effective length of query: 398 Effective length of database: 425 Effective search space: 169150 Effective search space used: 169150 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