Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_004511499.1 GMET_RS07870 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000012925.1:WP_004511499.1 Length = 414 Score = 345 bits (886), Expect = 1e-99 Identities = 185/422 (43%), Positives = 266/422 (63%), Gaps = 14/422 (3%) Query: 4 KKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGN 63 + + +T +H G EP G+ VPI Q++S+ ++ +F + G +YTRI N Sbjct: 3 RDFQLDTLLIHGGLEPGP--AGATTVPIVQSSSFAHETAEDLEDIFRGRKAGHVYTRINN 60 Query: 64 PTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHT 123 PT LE R+A LE G+ A+A +SG AAIT A+L+I GDEI+S ++L+GGT++LFR T Sbjct: 61 PTTESLERRLALLEGGISAIATSSGMAAITLAVLSIVRCGDEILSSASLFGGTFSLFRDT 120 Query: 124 LYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPL 183 L GI +FVD +D + A+TE+T+ +++ET+GNP L VPD A+A IA GVPL Sbjct: 121 L-SNYGIATRFVDPSDLAAMRAAVTERTRLIFVETMGNPRLDVPDLAALAAIAREAGVPL 179 Query: 184 IVDNTV-APYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEP 242 +VD TV P + R E GADI+V+S +K+I G G++IGG I+D G FDW +P Sbjct: 180 VVDATVTTPVLGRVKELGADIIVHSTSKYINGTGSAIGGAIIDCGTFDWRRESYP----- 234 Query: 243 DPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENA 302 H YV+ F++ A+ A+ R + +DLG+C +P N++L G+ET++LRM+++C NA Sbjct: 235 ----HFEPYVKKFRQFAFSARARKLIHKDLGACPAPMNSYLLSEGIETMALRMERNCANA 290 Query: 303 LKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSL 362 ++ EFL +HP V+WVNYP + E A YGA++TFG+ K A ID L Sbjct: 291 QRLAEFLAAHPKVAWVNYPGLTSSPWHETAKAQFGGRYGALLTFGL-ADKAAAFHCIDGL 349 Query: 363 TLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQ 422 L +LANIGD +TL IHPAST EE+ GV+ +MIR+SVGIE ++DII D + Sbjct: 350 RLAKNLANIGDTKTLVIHPASTICADFGPEEKALMGVSEEMIRVSVGIEAIDDIIEDFAE 409 Query: 423 AL 424 +L Sbjct: 410 SL 411 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: 463 Number of extensions: 16 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: 414 Length adjustment: 32 Effective length of query: 398 Effective length of database: 382 Effective search space: 152036 Effective search space used: 152036 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: 50 (23.9 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