Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_086509774.1 BZY95_RS09910 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_002151265.1:WP_086509774.1 Length = 424 Score = 450 bits (1158), Expect = e-131 Identities = 235/422 (55%), Positives = 308/422 (72%), Gaps = 6/422 (1%) Query: 10 TRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVL 69 T ALH GY P +Q + AVPI+QTTS+ F + HAA LF L+ G IY+RI NPT +VL Sbjct: 5 TIALHHGYAPDDQH--AVAVPIHQTTSFSFDSAQHAADLFDLKVEGNIYSRIMNPTCAVL 62 Query: 70 EERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSG 129 E+R+AALE G+ LAVASG AAITYAI IA GD IVS S LYGGTYNLF HTL + G Sbjct: 63 EQRVAALEGGIAGLAVASGMAAITYAIQTIAEAGDNIVSISELYGGTYNLFAHTL-PRQG 121 Query: 130 IIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTV 189 I V+F D+ D IE I +TKAV+ E++GNP +V D +AE+AHRHGVP+IVDNTV Sbjct: 122 IEVRFADKDDIDGIESLIDARTKAVFCESVGNPSGSVVDMARLAEVAHRHGVPVIVDNTV 181 Query: 190 -APYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNG--KFPELVEPDPSY 246 P+++RP EHGADIV++SATK+IGGHGT++GG+IVDSG+F W + +FP L EPD SY Sbjct: 182 PTPFLWRPIEHGADIVIHSATKYIGGHGTTVGGVIVDSGRFPWADHPQRFPLLNEPDVSY 241 Query: 247 HGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIV 306 HGV Y EAA+IA+ R LR++G+ +S A+ + GLETL+LR+++ C+NALK+ Sbjct: 242 HGVCYTRDIGEAAFIARARVVPLRNMGAALSAQAAWNLLQGLETLALRIERICDNALKVA 301 Query: 307 EFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLIS 366 E+L++H AV+WV Y G+K + A +Y+ I++FG++GG+EAG +F D+L +I Sbjct: 302 EYLEAHDAVTWVQYAGLPGHKDHQLAQRYMGGRASGILSFGIQGGREAGARFYDALGMIL 361 Query: 367 HLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQALRK 426 L NIGDA+T + PASTTH+QL++EE VTPDM+RLS+GIE V+DIIADL+QAL Sbjct: 362 RLVNIGDAKTCSSIPASTTHRQLSDEELAAASVTPDMVRLSIGIEHVDDIIADLEQALAA 421 Query: 427 SQ 428 SQ Sbjct: 422 SQ 423 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: 556 Number of extensions: 20 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: 424 Length adjustment: 32 Effective length of query: 398 Effective length of database: 392 Effective search space: 156016 Effective search space used: 156016 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