Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_066917961.1 ACG33_RS00985 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_001579945.1:WP_066917961.1 Length = 424 Score = 222 bits (565), Expect = 2e-62 Identities = 132/416 (31%), Positives = 216/416 (51%), Gaps = 15/416 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T +H + S+ PI+ +V + +++A+ A++F PG Y R NPT LE Sbjct: 5 TIAIHGGYETDPTTRSVAPPIYQTVAYEFDNAQHGADLFNLAVPGNIYTRIMNPTCDVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 ++ +E G ++ + GMAA+ + L GD++VS L+G T +L+ + G + Sbjct: 65 KRVAMLEGGVGSLALSAGMAAVHYAIINLAEAGDNIVSVPQLYGGTYTLFAHMLPKMGIE 124 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 +E I A T+ +F E+I NP + D++ + ++ R G+ +VDNT+ + Sbjct: 125 TRFAADDSAAAIEKLIDAKTKAIFFESIGNPAGNIVDVEAVAKMARGHGVATIVDNTVAT 184 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT----RYPHIAEN------ 239 P L +P G +VV++LTK +GGHG LGG + D+G F W RYP E Sbjct: 185 PSLLKPIDYGIDIVVHALTKYMGGHGTTLGGLIVDSGNFPWADHQQRYPMFNEPEEAYHG 244 Query: 240 --YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 Y P + + R LR+ G +L P A + G ET+ LR ER C+NA +A+ Sbjct: 245 VVYVDALGPAAYIGRARTVPLRNTGAALSPFNAFQLLQGIETLPLRMERHCENAQRVAEH 304 Query: 298 LQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGIDC-FDYLNRLRLAIPT 355 LQ V V Y GL++HP HAL++ + S +++F +K G D + + L+L Sbjct: 305 LQEHAMVEWVSYAGLKNHPHHALAQKYMKGRASGILTFGVKGGFDAGVKFYDALKLFKRL 364 Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 N+GD ++L A T ++ +++ +G+A IR+S+G+E +DL+ D QAL Sbjct: 365 VNIGDAKSLACHPASTTHRQLTEQQQREVGVAPEAIRLSIGIEAIEDLLEDLDQAL 420 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: 450 Number of extensions: 26 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: 424 Length adjustment: 32 Effective length of query: 381 Effective length of database: 392 Effective search space: 149352 Effective search space used: 149352 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