Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_078427052.1 BK574_RS00635 methionine gamma-lyase
Query= BRENDA::H7C6A2 (386 letters) >NCBI__GCF_002019605.1:WP_078427052.1 Length = 392 Score = 326 bits (836), Expect = 6e-94 Identities = 167/391 (42%), Positives = 249/391 (63%), Gaps = 10/391 (2%) Query: 6 NTQGFSTASIHAGYEPDDYYGSINTPIYASTTFAQNAPNELRK-------GYEYTRVGNP 58 N T IH GYE + GS+ P++ S+TF + + + GY Y+R+GNP Sbjct: 2 NNYRLETEVIHRGYESKSFQGSLTPPLFQSSTFTMESAEQGERRFAGDEEGYIYSRLGNP 61 Query: 59 TIVALEQTVAALEGAKYGRAFSSGMAATDILFRIILKPGDHIVLGNDAYGGTYRLIDTVF 118 T+ LE+ +A LEG + G AFSSGMAA +++ GDHI++ YG TY L++ + Sbjct: 62 TVTILEERIAELEGGEAGLAFSSGMAAVSATLFALVRSGDHILVSEGVYGCTYGLLELLK 121 Query: 119 TAWGVEYTVVDTSVVEEVKAAIKDNTKLIWVETPTNPALGITDIEAVAKLTEGTNAKLVV 178 + V+Y ++ E +++ I+ TK+I+VETP NP + + D++ ++KL + T AK+VV Sbjct: 122 DRFKVDYDLIAMDKEEHIRSYIRPETKVIYVETPINPTMKLVDLQLISKLGKETGAKVVV 181 Query: 179 DNTFASPYLQQPLKLGAHAVLHSTTKYIGGHSDVVGGLVVTNDQEMDEELLFMQGGIGPI 238 DNTFA+PYLQ+P+ LGA V+HS TKYI GH DVV GL+V +++ ++E + Q IG I Sbjct: 182 DNTFATPYLQRPILLGADVVVHSATKYISGHGDVVAGLMVGSEEFINEVRMTTQKDIGGI 241 Query: 239 PSVFDAYLTARGLKTLAVRMDRHCDNAEKIAEFLDSRPEVSTVLYPGLKNHPGHEVAAKQ 298 S FDA+L RGLKTL VRMDRHC NA +IA + + P++ +++PG ++ +V KQ Sbjct: 242 ISPFDAWLLIRGLKTLPVRMDRHCSNAIQIANKMKNHPKIKEIIFPGDESFSQVDVIEKQ 301 Query: 299 MKRFGGMISVRFAGGEEAAKKFCTSTKLICLAESLGGVESLLEHPATMTHQ---SAAGSQ 355 MK+ GGMIS GG+E A++ KLI +A SLG E+L++HPATMTH +Q Sbjct: 302 MKQAGGMISFLVNGGKETAQRLMNELKLIKIAVSLGDAETLIQHPATMTHSVVPEEKRAQ 361 Query: 356 LEVPRDLVRISIGIEDIEDLLADVEQALNNL 386 + + +L+R+S+G+E ED+ D+EQAL + Sbjct: 362 MGIGPELLRLSVGLEAWEDIWVDIEQALEKI 392 Lambda K H 0.316 0.134 0.385 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: 387 Number of extensions: 17 Number of successful extensions: 3 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: 386 Length of database: 392 Length adjustment: 30 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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