Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_064736010.1 H537_RS44490 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000430725.1:WP_064736010.1 Length = 421 Score = 236 bits (601), Expect = 1e-66 Identities = 147/385 (38%), Positives = 215/385 (55%), Gaps = 13/385 (3%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAY 69 AT A+H D S A PI TS Y A+ G +G YSR NPT ++ Sbjct: 7 ATRAVHEAHYQDLSD-AHCEPIATTSAYVFRSAADAARKFSGSAKGNVYSRFSNPTVSSF 65 Query: 70 ERCVAALEGGTRAFAFASGMAATSTVMEL-LDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ +AA+EG AFASGMAA + + L+AG +VV D++G T F + G Sbjct: 66 EKRLAAMEGAQDGVAFASGMAAIAALGHAWLEAGKNVVVSRDVFGTTLTAFRHYFGKL-G 124 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 + VDLT A++ AI DT++V++E+P+NP+ ++ +I +IA +A G L VDNT Sbjct: 125 VQVRTVDLTKLDAWRRAIDTDTRLVFLESPSNPVQQVGNIRSIAALAHACGALVAVDNTM 184 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGP 248 +P+ Q PL GAD+VVHSA KY++G V G AV+G +A+ L+ ++GG Sbjct: 185 LTPVFQNPLEHGADVVVHSAGKYIDGQGRCVAG-AVLGSERLMADLRGVLR-TLGGTLSA 242 Query: 249 FDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG 308 ++++ L+ L+TL LR+R ++ LA+WL H + +V Y +A HPQ L +Q +G Sbjct: 243 TNAWMLLKSLETLELRVRGASRSSEQLARWLGAHGRVGRVHYTAMAEHPQRPLILQQQTG 302 Query: 309 FGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGI 368 G + S + + A RF + +L +A ++G S+V HPA TH + R GI Sbjct: 303 HGAVFSFEVGQSQEDAWRFVDALKLVAIATNIGDTRSMVTHPASTTHCRLTAEERRLSGI 362 Query: 369 SDALVRLSVGIEDLGDLRGDLERAL 393 D LVRLSVG+ED DL DL+ AL Sbjct: 363 RDNLVRLSVGLEDPADLMADLDEAL 387 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: 384 Number of extensions: 14 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: 397 Length of database: 421 Length adjustment: 31 Effective length of query: 366 Effective length of database: 390 Effective search space: 142740 Effective search space used: 142740 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