Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012384038.1 BIND_RS05265 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000019845.1:WP_012384038.1 Length = 408 Score = 416 bits (1070), Expect = e-121 Identities = 207/391 (52%), Positives = 270/391 (69%), Gaps = 2/391 (0%) Query: 13 QNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 + W+ AT+ + GGT RS +GET+EA+FLT GY Y A ARF G++ G YSR NPT Sbjct: 11 EGWRTATRLVHGGTTRSPFGETAEAIFLTQGYVYPTMEAAEARFKGEEPGFVYSRYNNPT 70 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 M E+R+ALLEGAEA RATASGMAA+TAALL L AGDH++ RA FGSC ++ + LP Sbjct: 71 NAMFEERMALLEGAEAARATASGMAAVTAALLAPLKAGDHVVASRALFGSCLYIVEELLP 130 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 ++GI +T+VD +D + + DA+RP T+ F E+P NP+++V D+ AV AIA G VVD Sbjct: 131 RYGIASTLVDGKDFKAWKDALRPQTQTLFLESPTNPSLEVYDIAAVAAIAHAHGARLVVD 190 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTL 252 NAFA+P LQ+P+ GAD V YSATK +DGQGR L G V +++FI L + R TGP L Sbjct: 191 NAFASPMLQKPLQLGADCVVYSATKHIDGQGRCLGGVVLSSKDFIETHLQTYLRQTGPAL 250 Query: 253 SPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQM 310 SPFNAW++LK LETL LR+Q+Q NA KVA FL + R +PG HPQ + QM Sbjct: 251 SPFNAWILLKSLETLPLRVQQQMANAAKVADFLADHPLIARCFYPGRADHPQAEIVKRQM 310 Query: 311 AAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLM 370 G + + E+ GG+ A +AL +I ISNN+GD++SL+THPA+TTH + + R M Sbjct: 311 LGGGTMVAFEVTGGKPAAFAFANALSIIKISNNLGDAKSLITHPATTTHQRLTPEARATM 370 Query: 371 GVGEGMLRLNVGLEDPEDLIADLDQALGSVG 401 G+GEG+LRL+VGLED EDLIADL AL +G Sbjct: 371 GIGEGLLRLSVGLEDAEDLIADLQAALAVLG 401 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: 407 Number of extensions: 15 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: 408 Length adjustment: 31 Effective length of query: 371 Effective length of database: 377 Effective search space: 139867 Effective search space used: 139867 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