Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_086510355.1 BZY95_RS13035 methionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_002151265.1:WP_086510355.1 Length = 415 Score = 321 bits (823), Expect = 2e-92 Identities = 179/396 (45%), Positives = 237/396 (59%), Gaps = 13/396 (3%) Query: 7 HSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEY 58 HS G AT AIH GA+ PP++ TST+ A+ GE G Y Sbjct: 20 HSQQGQ---GFATRAIHAAYDSRDEQGALTPPMHLTSTFTFESVEQGAERFAGEAPGHFY 76 Query: 59 SRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGGTFR 117 SR NPT E+ +A LEG A ASGM A + +M LL G ++ LYG T Sbjct: 77 SRISNPTVATLEQRMANLEGAEAGLATASGMGAITALMWSLLRPGDELITDSHLYGCTHA 136 Query: 118 LFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARK 177 F G+ VDL+ PAA + AI TK+V+ ETP NP ++LVDI A++ IA + Sbjct: 137 FFHHGLTEF-GIRVKHVDLSQPAALEVAIGERTKLVYFETPANPTMRLVDIEAVSRIAHR 195 Query: 178 HGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAF 237 HG VVDNT+A+P++ RP+ GAD VVHSATKYL GH D++ G+ V + ++ Sbjct: 196 HGARVVVDNTYATPVITRPIEQGADFVVHSATKYLGGHGDLIAGVLVGSVDDIHRVRLTG 255 Query: 238 LQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHP 297 L++ G V PF +FL +RGLKTL +RM+ +AL +A+WLE HPA+E+V YPGL S P Sbjct: 256 LKDFTGAVMSPFTAFLIMRGLKTLEIRMQRQSASALEVARWLERHPAVERVHYPGLTSFP 315 Query: 298 QHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHAS 357 QH LA+RQMS +GGI++ L GG +A +RF + EL A SLG ESL+ HPA MTH+ Sbjct: 316 QHELARRQMSDYGGIIAFELAGGLEAGRRFMNRLELIQRAVSLGDAESLIQHPASMTHSV 375 Query: 358 IPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 + R + GIS+ L+RLSVG+E DLR DL +AL Sbjct: 376 LSPEERAEHGISETLIRLSVGLETPSDLRADLAQAL 411 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: 467 Number of extensions: 25 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: 397 Length of database: 415 Length adjustment: 31 Effective length of query: 366 Effective length of database: 384 Effective search space: 140544 Effective search space used: 140544 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