Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate PP_1308 PP_1308 methionine gamma-lyase
Query= BRENDA::H7C6A2 (386 letters) >FitnessBrowser__Putida:PP_1308 Length = 398 Score = 306 bits (784), Expect = 7e-88 Identities = 164/386 (42%), Positives = 237/386 (61%), Gaps = 11/386 (2%) Query: 9 GFSTASIHAGYEPDDYYGSINTPIYASTTFAQNAPNE-------LRKGYEYTRVGNPTIV 61 GFST +IH GY+P + G++ P+Y + T+A G+ Y+R+ NPT+ Sbjct: 9 GFSTRAIHHGYDPLSHGGALVPPVYQTATYAFPTVEYGAACFAGEEPGHFYSRISNPTLA 68 Query: 62 ALEQTVAALEGAKYGRAFSSGMAATDILFRIILKPGDHIVLGNDAYGGTYRLIDTVFTAW 121 LEQ +A+LEG + G A +SGM A +L+PGD +++G YG T+ + + Sbjct: 69 LLEQRMASLEGGEAGLALASGMGAITSTLWTLLRPGDELIVGRTLYGCTFAFLHHGIGEF 128 Query: 122 GVEYTVVDTSVVEEVKAAIKDNTKLIWVETPTNPALGITDIEAVAKLTEGTNAKLVVDNT 181 GV+ VD + + +KAAI T++I+ ETP NP + + DI AV + G + +VVDNT Sbjct: 129 GVKVRHVDLNDAKALKAAISSKTRMIYFETPANPNMQLVDIAAVVEAVRGHDVHVVVDNT 188 Query: 182 FASPYLQQPLKLGAHAVLHSTTKYIGGHSDVVGGLVVTNDQEMDE-ELLFMQGGIGPIPS 240 + +PYLQ+PL+LGA V+HS TKY+ GH D+ GLVV +D L ++ G + S Sbjct: 189 YCTPYLQRPLELGADLVVHSATKYLSGHGDITAGLVVGRKVLVDRIRLEGLKDMTGAVLS 248 Query: 241 VFDAYLTARGLKTLAVRMDRHCDNAEKIAEFLDSRPEVSTVLYPGLKNHPGHEVAAKQMK 300 DA L RG+KTLA+RMDRHC NA+++AEFL +P+V + YPGL + + +A +QM+ Sbjct: 249 PHDAALLMRGIKTLALRMDRHCANAQQVAEFLVRQPQVELIHYPGLPSFAQYALAQRQMR 308 Query: 301 RFGGMISVRFAGGEEAAKKFCTSTKLICLAESLGGVESLLEHPATMTHQSAAGSQLE--- 357 GGMI+ GG EA ++F + +L A SLG ESL +HPA+MTH S + Sbjct: 309 LPGGMIAFELKGGIEAGRRFMNALQLFARAVSLGDAESLAQHPASMTHSSYTPQERAHHG 368 Query: 358 VPRDLVRISIGIEDIEDLLADVEQAL 383 + LVR+S+G+ED+EDLLADVEQAL Sbjct: 369 ISEGLVRLSVGLEDVEDLLADVEQAL 394 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: 417 Number of extensions: 20 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: 386 Length of database: 398 Length adjustment: 31 Effective length of query: 355 Effective length of database: 367 Effective search space: 130285 Effective search space used: 130285 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 09 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