Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_028989181.1 G579_RS0104235 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000423825.1:WP_028989181.1 Length = 397 Score = 367 bits (943), Expect = e-106 Identities = 196/391 (50%), Positives = 255/391 (65%), Gaps = 4/391 (1%) Query: 13 QNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 ++W+P T A+R G + GE SE +F TS Y + A +AAARF+G Q G YSR NPT Sbjct: 8 EDWQPDTLAVRAGVHTTPEGEHSEPIFPTSSYVFQSAAEAAARFAG-QPGNVYSRYTNPT 66 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 V E+R+A LEGAE+C AT SGMAA A + L AGDH++ RA FG+ L L Sbjct: 67 VRAFEERLAALEGAESCVATGSGMAACLATFMALLKAGDHVVASRAIFGTTVQLLSNILG 126 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 +FG+ETT VD D + AIRPNT++ F ETP+NP ++ DL A+ AIA E G VVD Sbjct: 127 RFGLETTFVDLTDLGAWRAAIRPNTRMLFLETPSNPMTEIGDLAALAAIAHEAGARLVVD 186 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTL 252 N F TP LQRP+DFGADVV SATK +DG GR L GAV G+ E + F R GP++ Sbjct: 187 NTFCTPVLQRPLDFGADVVIQSATKYIDGHGRCLGGAVLGSRELMEGP-RGFLRTAGPSM 245 Query: 253 SPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQM 310 SPFNAWV LKGLETL LR+ R + +A +A +LE +V RV +PGL SHPQH LA Q Sbjct: 246 SPFNAWVFLKGLETLSLRMARHNASAQALAEWLEAQPQVNRVFYPGLASHPQHALAQRQQ 305 Query: 311 AAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLM 370 G I S +L GG+ A LDAL + ++ N+GD+++ +TH ASTTHS V+ + R Sbjct: 306 KGPGGILSFDLKGGQPAAWAFLDALRICSLTANLGDAKTTVTHAASTTHSRVSPEARAAA 365 Query: 371 GVGEGMLRLNVGLEDPEDLIADLDQALGSVG 401 G+ +G++R++VGLED EDL DL + L ++G Sbjct: 366 GITDGLVRISVGLEDVEDLRQDLARGLAAIG 396 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: 412 Number of extensions: 8 Number of successful extensions: 4 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: 397 Length adjustment: 31 Effective length of query: 371 Effective length of database: 366 Effective search space: 135786 Effective search space used: 135786 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