Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011800504.1 PNAP_RS05450 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015505.1:WP_011800504.1 Length = 404 Score = 347 bits (891), Expect = e-100 Identities = 182/400 (45%), Positives = 258/400 (64%), Gaps = 8/400 (2%) Query: 9 RSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRL 68 +++ N P T A+R G RS++GE SEAL+LTSG+ A +A RF+G ++G TY+R Sbjct: 4 QALPGNLHPDTLAVRVGIERSQYGENSEALYLTSGFVQPDAETSARRFAGTEEGFTYART 63 Query: 69 QNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTD 128 NPTV EQR+A LEG EA A +SGM A+ + L AGDH++ ++ FGS L Sbjct: 64 SNPTVAAFEQRLAALEGTEAAIAASSGMGAILMMGMGLLRAGDHVVCSQSVFGSTLNLFG 123 Query: 129 TQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIV 188 + KFG+ET+ V D Q+ A+RPNTK+ F ETP NP +V D++A+ +A G + Sbjct: 124 KEFAKFGVETSFVSQTDIAQWQAAMRPNTKLLFAETPTNPLTEVCDIRALADVAHAGGAL 183 Query: 189 TVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT 248 VDN F +PALQRP + GAD+V +S TK +DGQGRV+AGA+CG + I + P R Sbjct: 184 LAVDNCFCSPALQRPTELGADLVIHSGTKYLDGQGRVMAGAICGPSKLIVDVFGPIVRTA 243 Query: 249 GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLA 306 G L+PFNAWVVLKG+ETL +R+Q QS AL +A++LE V RV +PGLPSHPQH LA Sbjct: 244 GMVLAPFNAWVVLKGMETLRIRMQAQSATALAIAQWLETHPAVTRVYYPGLPSHPQHELA 303 Query: 307 MSQMAA-AGPIFSIELDGG-----RTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHS 360 M Q + G + S ++ GG R A ++++ ++ I+ N+GD++S++THP +T+H Sbjct: 304 MRQQSGLGGAVVSFDVRGGDPETARANAFHVINSTQVVSIATNLGDTKSIITHPGTTSHG 363 Query: 361 GVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 + E QR G+ +G++R GLE +DL ADL + L S+ Sbjct: 364 RLTEAQRQAAGIKQGLIRFATGLEHIDDLKADLARGLDSL 403 Lambda K H 0.319 0.134 0.396 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: 453 Number of extensions: 21 Number of successful extensions: 3 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: 402 Length of database: 404 Length adjustment: 31 Effective length of query: 371 Effective length of database: 373 Effective search space: 138383 Effective search space used: 138383 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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