Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_029933346.1 N746_RS0100205 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000711195.1:WP_029933346.1 Length = 425 Score = 238 bits (608), Expect = 2e-67 Identities = 148/418 (35%), Positives = 227/418 (54%), Gaps = 18/418 (4%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH+ + ++ PI+ + +F +++A+ A++F K PG Y R NPT LE Sbjct: 5 TLALHAGYEPEATTKAVAVPIYQTSSFAFDNAQHAADLFDLKVPGNIYSRMMNPTNTVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 ++T ME G + + ATGMAAI VQ L GD+++S++ L+G T +L+ T+ QG + Sbjct: 65 ARLTAMEGGLAALAVATGMAAITYTVQTLAEAGDNILSTSELYGGTYNLFAHTLPRQGLE 124 Query: 130 VSMVDATDVKNVEAA--ITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTM 187 V D D + E A I T++++ ETI NP + D++R+ +L GI VVD+T+ Sbjct: 125 VRFFDK-DASDEELAGLIDEKTKMLYCETIGNPSGSIVDIERLAKLAHAHGIPLVVDSTV 183 Query: 188 TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT----RYP--------H 235 SP L+RP GA +V++S TK IGGHG LGG + D G F W R+P + Sbjct: 184 PSPALWRPIEYGADIVIHSATKYIGGHGTTLGGVIVDAGTFPWAENAGRFPLLNTPDISY 243 Query: 236 IAENYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALA 295 Y ++ +A+ R LR+ G +L +A + G ET+ LR ER C+NA A+A Sbjct: 244 HGVTYTQDFGQAAFIARCRVVPLRNMGAALSANSAFQLLQGLETLTLRMERICQNAQAVA 303 Query: 296 QMLQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGID-CFDYLNRLRLAI 353 + L A V+ V Y GL SH HAL++ S ++SF L G + + + L+L I Sbjct: 304 EFLDAHPAVSWVNYAGLPSHKDHALAQKYMNGQASGILSFGLASGREGTRRFYDALKLII 363 Query: 354 PTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 N+GD ++ A T ++ S G+ ++R+S+G+E DDL+AD QAL Sbjct: 364 RLVNIGDAKSCASIPAETTHRQLNDAELKSAGVPPEMVRLSIGIEHIDDLIADIDQAL 421 Lambda K H 0.319 0.134 0.391 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: 410 Number of extensions: 16 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: 413 Length of database: 425 Length adjustment: 32 Effective length of query: 381 Effective length of database: 393 Effective search space: 149733 Effective search space used: 149733 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