Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_085770126.1 B1812_RS02095 methionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_002117405.1:WP_085770126.1 Length = 425 Score = 221 bits (564), Expect = 2e-62 Identities = 151/414 (36%), Positives = 214/414 (51%), Gaps = 34/414 (8%) Query: 11 GDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQ---------------- 54 G+R L TL + G P S G+V PP++ TST+ + E + Sbjct: 12 GERELQPETLMLGYGYDPSLSEGSVKPPVFLTSTFVFKTAEEGRDFFDIMAGRRPPPNEG 71 Query: 55 --GFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDL 111 G YSR ++P E +A E FASGMAA +T M + G V+ L Sbjct: 72 PPGLIYSRFNHPNLEIVEDRLAIYEKAESGLVFASGMAAIATTMLAFVRPGETVLHSRPL 131 Query: 112 YGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAI-RADTK----MVWIETPTNPMLKLV 166 YGGT L + F D D A +AA RA+ + M++IETP+NPM LV Sbjct: 132 YGGTETLLLKTLAPFGVKAVGFTDGLDEANIRAAAARAEGEGRIAMIFIETPSNPMNSLV 191 Query: 167 DIAAIA----VIARKHGLLTVV--DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVG 220 DIA + IA++ G +V DNT P+ Q PL GADL +S TKY+ GHSD++G Sbjct: 192 DIALVRRIAEEIAQRQGSRPLVCCDNTLLGPVFQSPLRHGADLSCYSLTKYVGGHSDLIG 251 Query: 221 GIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLE 280 G A+ +AE + + ++++IG P ++ R L+TL LRM NA +A++L Sbjct: 252 GAAL--GSAENLKPLRAMRSAIGTQLDPHSCWMLARSLETLSLRMERAAANASIVARFLA 309 Query: 281 THPAIEKVIYPGL--ASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAE 338 THP + V YP L A HP L +RQ S G S +KGG + A F + +LF LA Sbjct: 310 THPKVALVHYPPLLPADHPARKLMERQSSSAGSTFSFDVKGGQEEAFAFLNRLQLFKLAV 369 Query: 339 SLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERA 392 SLGG ESL+ HP H+ + R ++GI+ +L+R+S+G+E DL D+ +A Sbjct: 370 SLGGTESLICHPTTTVHSGLTEEARREIGITPSLIRMSIGVEHPDDLLADIAQA 423 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: 461 Number of extensions: 26 Number of successful extensions: 6 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: 425 Length adjustment: 31 Effective length of query: 366 Effective length of database: 394 Effective search space: 144204 Effective search space used: 144204 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