Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_036260103.1 DL86_RS08255 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000746085.1:WP_036260103.1 Length = 437 Score = 255 bits (651), Expect = 2e-72 Identities = 161/421 (38%), Positives = 225/421 (53%), Gaps = 49/421 (11%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQ---------GFEYSRTHNPTRFAY 69 TLA+H G DP+TGAV PIY T++Y Q +H G Y+R NPT Sbjct: 10 TLALHAGWRADPATGAVAVPIYQTTSY-QFRDTQHAADLFALKELGNIYTRIGNPTVDVL 68 Query: 70 ERCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ VAALEGG A A ASG AA++ +V L G ++V+ DLYGGT+ LF + G Sbjct: 69 EQRVAALEGGVAALALASGQAASAFSVQNLARVGDNIVSSTDLYGGTWNLFANTLK-DQG 127 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 ++ FVD +DP F+ A A T+ + ET NP L + IA +A I R G+ +VDNT Sbjct: 128 IEVRFVDPSDPENFRRATDARTRAYYAETLPNPKLAVFPIAEVAAIGRAFGIPLIVDNT- 186 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN-------------------- 228 A+P+L RP++ GA +VV+SATKYL GH + +GG+ V G N Sbjct: 187 AAPILCRPIAHGAAIVVYSATKYLGGHGNSIGGLIVDGGNFDWEQFKERQPALNTPDPSY 246 Query: 229 ---------------AELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENAL 273 A + + L +G PF++FL L+G+++L LR+ H NA Sbjct: 247 HGAVWTEAVKPLGPIAYIIKARTTLLRDLGAPLAPFNAFLILQGIESLALRIERHARNAE 306 Query: 274 ALAQWLETHPAIEKVIYPGLASHPQHVLA-KRQMSGFGGIVSIVLKGGFDAAKRFCEKTE 332 A+A L P I KVIYP L + A K + G+GG+V LKGG +A +RF + E Sbjct: 307 AVANHLTKKPEITKVIYPSLQTGATRERADKYLVGGYGGLVGFELKGGAEAGRRFIDHLE 366 Query: 333 LFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERA 392 LF ++G SL HPA TH+ + + G++ VRLS+GIE + D+ DL++A Sbjct: 367 LFYHVANIGDSRSLAIHPATTTHSQLSAEEQSATGVTPGYVRLSIGIEHIDDIIADLDQA 426 Query: 393 L 393 L Sbjct: 427 L 427 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: 514 Number of extensions: 29 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: 437 Length adjustment: 31 Effective length of query: 366 Effective length of database: 406 Effective search space: 148596 Effective search space used: 148596 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