Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_015819756.1 TERTU_RS11015 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000023025.1:WP_015819756.1 Length = 402 Score = 290 bits (741), Expect = 7e-83 Identities = 170/403 (42%), Positives = 245/403 (60%), Gaps = 14/403 (3%) Query: 1 MSNRTTHSHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGE-------- 52 M++ + S D L TLA+ GQ P G PIY TS++ +S G+ Sbjct: 1 MTDHHSDSFDFLAGAELDTLAVRAGQVRGPE-GEHSEPIYTTSSFVFASAGQAAARFRGD 59 Query: 53 HQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDL 111 G YSR NPT +E +AALEGG A ASGMAA ST M LL AG HVV + Sbjct: 60 DPGNVYSRYTNPTVRTFEDRIAALEGGEAGVATASGMAAILSTCMALLSAGDHVVCSRSV 119 Query: 112 YGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAI 171 +G T LF + ++ G+ V LTD AA++ +++ +T+++++ETP+NP+ + D+ + Sbjct: 120 FGTTTVLFTKYLQKF-GVQVDLVGLTDLAAWEQSLKPNTRLLFLETPSNPICDVADVRKL 178 Query: 172 AVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAEL 231 A +A +G L VVDN F +P LQ+PL+LGAD+VVHSATK+L+G +GG AVVG ++ Sbjct: 179 ADLAHSNGCLLVVDNCFCTPALQKPLALGADIVVHSATKFLDGQGRCMGG-AVVGRADQM 237 Query: 232 AEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYP 291 AE AFL+ + G PF++++ ++GL+TL LRM AH +ALALAQWL+ HP + KV Y Sbjct: 238 AEVTAFLR-TCGPTMSPFNAWVFVKGLETLRLRMEAHSASALALAQWLDEHPKVGKVNYA 296 Query: 292 GLASHPQHVLAKRQMSGFGGIVSI-VLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHP 350 GL HP H LA +Q S FGG++S VL +AA + + +L +LG ++ + HP Sbjct: 297 GLPEHPGHSLAVQQQSAFGGVLSFEVLPNTREAAWTVVDAARIMSLTANLGDAKTTIVHP 356 Query: 351 AVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 A TH + R GIS+ L+R++VG+E + DL+ DL+R L Sbjct: 357 ATTTHGRLSDEERSAAGISEGLIRVAVGLESINDLKKDLDRGL 399 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: 438 Number of extensions: 24 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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