Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_078427052.1 BK574_RS00635 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_002019605.1:WP_078427052.1 Length = 392 Score = 296 bits (759), Expect = 5e-85 Identities = 159/390 (40%), Positives = 244/390 (62%), Gaps = 3/390 (0%) Query: 14 NWKPATQAI-RGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 N++ T+ I RG ++S G + LF +S + + A RF+GD++G YSRL NPT Sbjct: 3 NYRLETEVIHRGYESKSFQGSLTPPLFQSSTFTMESAEQGERRFAGDEEGYIYSRLGNPT 62 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 V +LE+RIA LEG EA A +SGMAA++A L + +GDH++ +G L + Sbjct: 63 VTILEERIAELEGGEAGLAFSSGMAAVSATLFALVRSGDHILVSEGVYGCTYGLLELLKD 122 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 +F ++ ++ + IRP TKV + ETP NPTM +VDL+ + + +E G VVD Sbjct: 123 RFKVDYDLIAMDKEEHIRSYIRPETKVIYVETPINPTMKLVDLQLISKLGKETGAKVVVD 182 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTL 252 N FATP LQRP+ GADVV +SATK + G G V+AG + G+EEFIN + ++ G + Sbjct: 183 NTFATPYLQRPILLGADVVVHSATKYISGHGDVVAGLMVGSEEFINEVRMTTQKDIGGII 242 Query: 253 SPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQM 310 SPF+AW++++GL+TL +R+ R NA+++A ++ ++ + FPG S Q ++ QM Sbjct: 243 SPFDAWLLIRGLKTLPVRMDRHCSNAIQIANKMKNHPKIKEIIFPGDESFSQVDVIEKQM 302 Query: 311 AAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLM 370 AG + S ++GG+ A L++ L LI I+ ++GD+ +L+ HPA+ THS V E++R M Sbjct: 303 KQAGGMISFLVNGGKETAQRLMNELKLIKIAVSLGDAETLIQHPATMTHSVVPEEKRAQM 362 Query: 371 GVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 G+G +LRL+VGLE ED+ D++QAL + Sbjct: 363 GIGPELLRLSVGLEAWEDIWVDIEQALEKI 392 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: 340 Number of extensions: 10 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: 392 Length adjustment: 31 Effective length of query: 371 Effective length of database: 361 Effective search space: 133931 Effective search space used: 133931 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