Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_041773934.1 LFE_RS02030 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000284315.1:WP_041773934.1 Length = 402 Score = 246 bits (627), Expect = 1e-69 Identities = 148/344 (43%), Positives = 189/344 (54%), Gaps = 20/344 (5%) Query: 39 GESTGFDYVRTKNPTRQLVEDAIANLENGARGLAFSSGMAAIQTIMA-LFKSGDELIVSS 97 GE GF Y R NPT + E ++ LE G + AF+SGM AI I+ L KS E+ Sbjct: 57 GEEEGFVYGRMGNPTTERFETLVSELEGGEKTRAFASGMGAISAILIHLTKSRPEMAFPK 116 Query: 98 DLYGGTYRLFENEWKKYGLTFHYDDFSDE---DCLRSKITPNTKAVFVETPTNPLMQEAD 154 LYGGT E G H+ D +E + L +++P T AVF ETP+NP+M D Sbjct: 117 VLYGGTRAFIEKYLIPQGCLIHWFDPREEGWGEELSRRLSPKTAAVFAETPSNPVMTVID 176 Query: 155 IEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKD 214 + ++ I K G+ L+VDNTF TP+LQ+PL LGADIV+HSATKYLGGH DLL G V Sbjct: 177 LGRLSGIAKSAGVPLVVDNTFATPILQKPLALGADIVVHSATKYLGGHGDLLGGTVTGNA 236 Query: 215 ERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDV 274 + F+ + +GA L PF SWLL+RGMKTL LRM H A +A FL + V Sbjct: 237 SLMERLSFEEGSYLGATLSPFHSWLLLRGMKTLPLRMEAHCRGAMNIAEFLSHHPMVKSV 296 Query: 275 LYPGK----------------GGMLSFRLQKEEWVNPFLKALKTICFAESLGGVESFITY 318 YPG GGMLSF L ++ L+ A SLG ES I + Sbjct: 297 HYPGLPGDPGHKVAALQMKGFGGMLSFSLGDDQKARKVASRLEFFKIAVSLGDPESLIEH 356 Query: 319 PATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDLKQAL 362 PA+ +H + E R+A G+ LR SVG+E EDL DLK+AL Sbjct: 357 PASLSHRQMSPEGRMALGIDPGFLRVSVGLEDPEDLILDLKRAL 400 Lambda K H 0.319 0.135 0.392 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: 388 Number of extensions: 17 Number of successful extensions: 3 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: 373 Length of database: 402 Length adjustment: 30 Effective length of query: 343 Effective length of database: 372 Effective search space: 127596 Effective search space used: 127596 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 (21.7 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