Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012412634.1 NPUN_RS32660 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000020025.1:WP_012412634.1 Length = 434 Score = 249 bits (635), Expect = 1e-70 Identities = 148/424 (34%), Positives = 232/424 (54%), Gaps = 20/424 (4%) Query: 7 YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 Y F T +H+ ++ + + PI+ + ++ ++D A +F ++ G Y R NPT Sbjct: 5 YRFETLQVHAGQEPAPGNNARAVPIYQTTSYVFDDTEHGARLFALQEFGNIYTRIMNPTT 64 Query: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGA 125 E +I +E G + + A+G AA + + + GD++VS++FL+G T N +++ Sbjct: 65 DVFEKRIAALEGGVAALATASGQAAQFLAISTIAQAGDNIVSTSFLYGGTYNQFKVSLPR 124 Query: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185 G V V+ D ++ AI A T+ ++VETI NP+ + D + + E GI +VDN Sbjct: 125 LGINVKFVEGDDPESFRQAIDARTKALYVETIGNPQYNIPDFAALAHIAHENGIPLIVDN 184 Query: 186 TM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAE---- 238 T YL RP GA +VV S TK IGGHG ++GG + D+G+FDW ++P E Sbjct: 185 TFGAGGYLARPIEHGADIVVESATKWIGGHGTSIGGVIVDSGKFDWGNGKFPLFTEPAPG 244 Query: 239 ----NYKKNPAPQWGMAQI------RAKALRDFGGSLGPEAAHHIAVGAETIALRQEREC 288 N+++ P I R + LRDFG SL P A + G ET++LR +R Sbjct: 245 YHGLNFQEVFGPSGSFGNIAFIIRARVEGLRDFGPSLSPFNAFLLLQGLETLSLRVDRHV 304 Query: 289 KNALALAQMLQADERVAAVYYPGLESHPQHALSKALFR-SFGSLMSFELKDGIDCFD-YL 346 NAL LA+ L+ E+V V YPGL +H H +K R FG +++F +K G++ ++ Sbjct: 305 SNALELARWLEQQEQVLWVNYPGLPNHSYHERAKKYLRHGFGGVLNFGIKGGLEAGKAFI 364 Query: 347 NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVAD 406 N ++LA +N+GD +TLVI A T ++ E + S G+ L+RVSVG+E DD+ D Sbjct: 365 NHVKLASHLANVGDAKTLVIHPASTTHQQLSDEEQLSAGVTPDLVRVSVGIEHIDDIKED 424 Query: 407 FRQA 410 F+QA Sbjct: 425 FQQA 428 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: 475 Number of extensions: 24 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 381 Effective length of database: 402 Effective search space: 153162 Effective search space used: 153162 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: 51 (24.3 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