Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_014026249.1 PYRFU_RS03465 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000223395.1:WP_014026249.1 Length = 402 Score = 245 bits (625), Expect = 2e-69 Identities = 146/367 (39%), Positives = 208/367 (56%), Gaps = 25/367 (6%) Query: 23 VSAPIYLSTAYRH----RGIGESTGFDYVRTKNPTRQLVEDAIANLENGARGLAFSSGMA 78 V PIY + + H + + Y R NPT +E I LE G L F++GMA Sbjct: 37 VVPPIYRTAMFHHPREDAPLIRGRPYKYSREDNPTLVALEKMITELEGGEDTLVFATGMA 96 Query: 79 AIQTIM-ALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDEDCLRSKITPNT 137 AI T++ AL K GD ++VS + YG T +LFE +K+GL +E+ + P T Sbjct: 97 AISTVLLALLKPGDRVVVSREAYGATLKLFEF-LRKWGLNVVLAGPDNEEIIYEASKPGT 155 Query: 138 KAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIVIHSATK 197 K VFVET TNPL++ A++ IA+ +E G +L+VDNTF TPV+ RPLE GA +VIHS TK Sbjct: 156 KMVFVETITNPLLRVANVPEIAKAARESGAILVVDNTFATPVIFRPLEHGATLVIHSLTK 215 Query: 198 YLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRMRQHQAN 257 Y+ GHND+L G V E + E+++ + +G + ++L+ RG+KTL +R+ +H N Sbjct: 216 YMAGHNDVLGGSVTGPAEIIANELWEWRRMLGTTMDVEQAFLVARGLKTLEIRVERHCRN 275 Query: 258 AQELAAFLEEQEEISDVLYPG------------------KGGMLSFRLQ-KEEWVNPFLK 298 A +A FL + ++ V YPG GG++SFR++ +E V K Sbjct: 276 AMYVAEFLADHPKVLQVYYPGLPNSPGYELARKLFPPGMYGGVVSFRVKGGKEAVMKLFK 335 Query: 299 ALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDL 358 LK I + SLGG ES I YP +H +PEE R G+ L+R SVG+E+ ED+ EDL Sbjct: 336 RLKYIRPSPSLGGPESLIAYPVMSSHSTMPEEERRKLGITEDLVRLSVGLENPEDIVEDL 395 Query: 359 KQALCQV 365 QAL + Sbjct: 396 DQALSAI 402 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: 340 Number of extensions: 13 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: 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