Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011188941.1 DP_RS08645 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000025945.1:WP_011188941.1 Length = 423 Score = 234 bits (596), Expect = 5e-66 Identities = 142/395 (35%), Positives = 217/395 (54%), Gaps = 13/395 (3%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI S TF Y+ A +A++F K G+ Y R NPTVA EDKI ME G + ++G Sbjct: 26 PIAQSTTFKYDTAGAIADLFDLKAAGHMYSRISNPTVAVFEDKIAAMEGGVGALAVSSGQ 85 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVD-ATDVKNVEAAITA 147 AA V + + GDH ++ A L+G T +L+ ++ G +V+ VD A + ++AA Sbjct: 86 AASTISVINICQAGDHFIALATLYGGTFNLFKHSMKKWGIEVTFVDPAASPEEIKAAFKD 145 Query: 148 NTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSL 207 NT+L+F E+++NP T V D ++ + E G+ +VDNT +P L RP +GA +V +S Sbjct: 146 NTKLIFGESLSNPGTDVLDFEKFVAIKNEMGVPLIVDNTFPTPILCRPIELGADIVTHST 205 Query: 208 TKSIGGHGNALGGALTDTGEFDWT--RYPHIAE--------NYKKNPAPQWGMAQIRAKA 257 TK I GH ++GG + D+G FDWT ++P + E +Y + + + R + Sbjct: 206 TKYIDGHATSVGGIIIDSGNFDWTNGKFPGLTEPDDSYHGLSYTETFGKAAYIVKARVQW 265 Query: 258 LRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHPQ 317 +RD G P+ A +G ET+ LR ER +NAL LA+ L ++V V YP L + Sbjct: 266 IRDIGCYQTPQNAFLSNLGLETLHLRMERHSENALRLAEFLDGHDKVEWVKYPMLPADSN 325 Query: 318 HALSKALFRSFGSLMSFELKDGI-DCFDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEM 376 +AL K + +++F +K D +N L+LA ++ D RT V+ A ++ Sbjct: 326 YALCKKYLSAGSGVLTFGVKGSAQDAEKIMNSLQLAAIVVHVADVRTGVLHPASMTHRQL 385 Query: 377 GAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 +E GI LIRVSVG+E DD++ADF+QAL Sbjct: 386 SSEDLEKAGITPQLIRVSVGIEKIDDIIADFKQAL 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: 446 Number of extensions: 27 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: 423 Length adjustment: 32 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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