Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012589230.1 MSIL_RS00925 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000021745.1:WP_012589230.1 Length = 436 Score = 228 bits (580), Expect = 4e-64 Identities = 144/420 (34%), Positives = 217/420 (51%), Gaps = 18/420 (4%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH+ + G++ PI+ + ++ + D + A++F ++ G Y R GNPT+ LE Sbjct: 10 TLALHAGWRADPATGAVAVPIYQTTSYQFRDTQHAADLFALRELGNIYTRIGNPTLDVLE 69 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 ++ +E G + + A+G AA VQ L R GD++VS+ L+G T +L+ T+ QG + Sbjct: 70 QRVAAIEGGVAALALASGQAASAFAVQNLARAGDNIVSATDLYGGTWNLFANTLKDQGIE 129 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 V VD D + A A TR + ET+ NP+ V + I + R GI +VDNT + Sbjct: 130 VRFVDPDDPEAFRRATDARTRAYYAETLPNPKLTVLPIAEIAAIGRALGIPLIVDNT-AA 188 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW----TRYPHIAENYKKNPA 245 P L RP GA +VV S TK +GGHGN++GG + D G FDW R P + Sbjct: 189 PILCRPLDHGAAIVVYSATKYLGGHGNSIGGLIVDGGNFDWEGHKERQPALNTPDPSYHG 248 Query: 246 PQWGMA-----------QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALAL 294 W A ++R LRD G +L P A + G E++ LR ER NA A+ Sbjct: 249 AVWTEAVKPIGPVAYIIKVRTTLLRDIGAALSPFNAFLLLQGIESLPLRIERHVSNAEAV 308 Query: 295 AQMLQADERVAAVYYPGLES-HPQHALSKALFRSFGSLMSFELKDGIDCFDYLNRLRLAI 353 A+ L V V YP L+S + + L +G L+ FEL + +++ L L Sbjct: 309 ARYLSRHAGVKTVIYPSLQSGATRERADRYLKGGYGGLVGFELSSAEEGRKFIDSLELFY 368 Query: 354 PTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 +N+GD+R+L I A T ++ E + S G+ +R+SVG+E DD++AD QAL A Sbjct: 369 HVANIGDSRSLAIHPATTTHSQLSGEDQLSTGVTPGYVRLSVGVEHIDDIIADLDQALAA 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: 456 Number of extensions: 19 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: 436 Length adjustment: 32 Effective length of query: 381 Effective length of database: 404 Effective search space: 153924 Effective search space used: 153924 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