Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_018234022.1 THITHI_RS0115500 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000378965.1:WP_018234022.1 Length = 393 Score = 358 bits (920), Expect = e-103 Identities = 183/387 (47%), Positives = 256/387 (66%), Gaps = 2/387 (0%) Query: 13 QNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 +N+ T+A+R G R+ GE SEA+F TS + ++ A AAARF G + G YSR NPT Sbjct: 5 ENYAFETRAVRAGQHRTHEGEHSEAIFPTSSFVFENAAQAAARFGGTEPGNIYSRFTNPT 64 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 V ++R+A +EG EAC AT+SGM+A+ + + L AGDH++ R+ FG+ L L Sbjct: 65 VRTFQERLAAMEGGEACIATSSGMSAILSTCMALLKAGDHIVSSRSVFGTTTSLFTNYLT 124 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 +FG+ V D + + AIRP T++ + E+P+NP ++VD++A+ +AR RG + VVD Sbjct: 125 RFGVPVDFVPLPDLEAWEAAIRPETRMLYVESPSNPLTELVDIRALADLARSRGCLLVVD 184 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTL 252 N F TPALQ P+ GAD+V +SATK +DGQGR + GAV G E + + F R GPT+ Sbjct: 185 NCFCTPALQLPLALGADIVIHSATKYLDGQGRCVGGAVVGDAERVGKDVFGFLRTGGPTM 244 Query: 253 SPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQM 310 SPFNAWV LKGLETL LR++ SENAL +AR+L+ RV RV+FPGL HPQH LA +Q Sbjct: 245 SPFNAWVFLKGLETLSLRMRAHSENALHLARWLKAHPRVARVHFPGLEDHPQHELAKAQQ 304 Query: 311 AAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLM 370 + G I S E+ GGR A ++DA ++ I+ N+GD++S +THPA+TTH + +QR Sbjct: 305 SGFGGIVSFEVTGGRELAWRVIDATRMLSITANLGDTKSTITHPATTTHGRLTPEQREEQ 364 Query: 371 GVGEGMLRLNVGLEDPEDLIADLDQAL 397 GVGE ++R+ VGLE D+ ADL + L Sbjct: 365 GVGESLIRVAVGLEAITDIQADLARGL 391 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: 433 Number of extensions: 20 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: 402 Length of database: 393 Length adjustment: 31 Effective length of query: 371 Effective length of database: 362 Effective search space: 134302 Effective search space used: 134302 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