Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_017597122.1 D471_RS0102240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000341125.1:WP_017597122.1 Length = 390 Score = 302 bits (773), Expect = 1e-86 Identities = 168/354 (47%), Positives = 220/354 (62%), Gaps = 4/354 (1%) Query: 42 TSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLD 100 T T A S G F Y+R NPT A E VA LEGG A A SGM A T+T+ LL Sbjct: 38 TETMAASFQGAGSPFVYARYGNPTVAALEDAVADLEGGAGAIASGSGMGAITATLWALLG 97 Query: 101 AGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTN 160 G HVVA + LYGGT L +R R G++ + VD DPAA AA+R DT+++ +ET N Sbjct: 98 TGGHVVAQERLYGGTQALLTTLRERW-GVEVTQVDAGDPAAVDAALRPDTRVLVLETIAN 156 Query: 161 PMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVG 220 P ++ D+ A+ +AR+HG +VDNTFA+P+L RP+ GAD+VVHSATKY+ GHSD +G Sbjct: 157 PTGQVADLPALTALARRHGTTVIVDNTFATPLLCRPIEHGADIVVHSATKYMGGHSDTIG 216 Query: 221 GIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLE 280 G+AV D L ++ N G V PF ++L RGL TL +RMR HC NA LA+ L+ Sbjct: 217 GVAVFADAGTLT-RVRERTNEFGAVMEPFAAWLINRGLSTLGVRMRRHCANAEELARRLD 275 Query: 281 THPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTLAES 339 HPA+ +V Y GL HP H A+ + GFGG+++ L GG +A + F E+ L LA S Sbjct: 276 RHPAVTRVHYAGLPDHPGHATARELLDGGFGGVLAFELAGGLEAGRSFAERVRLAVLAPS 335 Query: 340 LGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 LG V +LV HPA +H + + G+S+ L+RLS GIED+ DL DLERAL Sbjct: 336 LGDVRTLVMHPASTSHRMLDAEGLARAGVSEGLIRLSAGIEDVEDLWADLERAL 389 Lambda K H 0.320 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: 519 Number of extensions: 34 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: 397 Length of database: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 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 Jul 25 2024. The underlying query database was built on Jul 25 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