Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011384943.1 AMB_RS12895 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000009985.1:WP_011384943.1 Length = 430 Score = 231 bits (590), Expect = 2e-65 Identities = 139/421 (33%), Positives = 220/421 (52%), Gaps = 19/421 (4%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T +LH+ + GS+ P++ + ++ + D+ A +F K+ G Y R NPT LE Sbjct: 10 TIVLHAGYRADPATGSVAVPVYQTTSYQFRDSEHAANLFALKELGNIYTRLMNPTTDVLE 69 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWMTVGAQ-GAK 129 ++ +E G + + A+G AA + L + GD+ V+S L+G T +L+ Q G + Sbjct: 70 QRLAALEGGVAALAVASGQAASTFAILNLAQAGDNFVTSTDLYGGTWNLFANTFKQLGIE 129 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 VD D + A TR + ET+ NP+ QV + + +L + G+ +VDNT S Sbjct: 130 ARFVDPADPEAFVRATDDKTRAWYAETLPNPKLQVFPIAEVAKLANQVGVPLIVDNT-AS 188 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW----TRYPHIAENYKKNPA 245 P + +P ++GA +VV S TK IGGHG ++GGA+ D G FDW R+P + E Sbjct: 189 PVIAKPLSLGAHIVVYSCTKYIGGHGTSIGGAIVDGGTFDWEKHAKRFPLLNEPDPSYHG 248 Query: 246 PQWGMA-----------QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALAL 294 W A + R LRD G ++ P A + G ET+ LR C+NA A+ Sbjct: 249 AVWTQAVKPLGPIAYIIRARVTLLRDIGAAISPFNAFQVLQGMETLPLRMREHCRNASAV 308 Query: 295 AQMLQADERVAAVYYPGL-ESHPQHALSKALFRSFGSLMSFELKDGIDC-FDYLNRLRLA 352 AQ L +VA V +P L + + AL +G L+ FELK G + +++ L+L Sbjct: 309 AQFLAGHHKVAHVIHPSLQDGEYRRRADAALKGGYGGLLGFELKGGAEAGRRFIDALKLL 368 Query: 353 IPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 +N+GD R+L I A T ++ A+ + + G+ +R+S+G+E DD++AD +QALD Sbjct: 369 YHVANIGDARSLAIHPASTTHSQLSADDQLASGVTPGYVRLSIGIEHIDDILADLKQALD 428 Query: 413 A 413 A Sbjct: 429 A 429 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: 431 Number of extensions: 12 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: 430 Length adjustment: 32 Effective length of query: 381 Effective length of database: 398 Effective search space: 151638 Effective search space used: 151638 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 09 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