Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_012412634.1 NPUN_RS32660 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000020025.1:WP_012412634.1 Length = 434 Score = 244 bits (622), Expect = 5e-69 Identities = 151/421 (35%), Positives = 224/421 (53%), Gaps = 48/421 (11%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYSRTHNPTRFAYE 70 TL +H GQ P P A PIY T++Y A+ + G Y+R NPT +E Sbjct: 9 TLQVHAGQEPAPGNNARAVPIYQTTSYVFDDTEHGARLFALQEFGNIYTRIMNPTTDVFE 68 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 + +AALEGG A A ASG AA + + AG ++V+ LYGGT+ F +V G+ Sbjct: 69 KRIAALEGGVAALATASGQAAQFLAISTIAQAGDNIVSTSFLYGGTYNQF-KVSLPRLGI 127 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF- 188 + FV+ DP +F+ AI A TK +++ET NP + D AA+A IA ++G+ +VDNTF Sbjct: 128 NVKFVEGDDPESFRQAIDARTKALYVETIGNPQYNIPDFAALAHIAHENGIPLIVDNTFG 187 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGI-------------------------- 222 A L RP+ GAD+VV SATK++ GH +GG+ Sbjct: 188 AGGYLARPIEHGADIVVESATKWIGGHGTSIGGVIVDSGKFDWGNGKFPLFTEPAPGYHG 247 Query: 223 ----AVVGDNAELAEQMAFLQNSIGGVQ------GPFDSFLALRGLKTLPLRMRAHCENA 272 V G + ++ + G++ PF++FL L+GL+TL LR+ H NA Sbjct: 248 LNFQEVFGPSGSFGNIAFIIRARVEGLRDFGPSLSPFNAFLLLQGLETLSLRVDRHVSNA 307 Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKT 331 L LA+WLE + V YPGL +H H AK+ + GFGG+++ +KGG +A K F Sbjct: 308 LELARWLEQQEQVLWVNYPGLPNHSYHERAKKYLRHGFGGVLNFGIKGGLEAGKAFINHV 367 Query: 332 ELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLER 391 +L + ++G ++LV HPA TH + + G++ LVR+SVGIE + D++ D ++ Sbjct: 368 KLASHLANVGDAKTLVIHPASTTHQQLSDEEQLSAGVTPDLVRVSVGIEHIDDIKEDFQQ 427 Query: 392 A 392 A Sbjct: 428 A 428 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: 500 Number of extensions: 25 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 397 Length of database: 434 Length adjustment: 31 Effective length of query: 366 Effective length of database: 403 Effective search space: 147498 Effective search space used: 147498 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