Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase
Query= BRENDA::H7C6A2 (386 letters) >FitnessBrowser__WCS417:GFF2301 Length = 411 Score = 312 bits (799), Expect = 1e-89 Identities = 170/390 (43%), Positives = 236/390 (60%), Gaps = 12/390 (3%) Query: 6 NTQGFSTASIHAGYEPDDYYGSINTPIYASTTFAQNAPNE-------LRKGYEYTRVGNP 58 N GFST +IH GY+P D++G++ PIY S TFA G+ YTR+ NP Sbjct: 6 NAFGFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNP 65 Query: 59 TIVALEQTVAALEGAKYGRAFSSGMAATDILFRIILKPGDHIVLGNDAYGGTYRLIDTVF 118 T+ LE +A LE AFSSGM A F +L+PGD +++ YG T+ L+ Sbjct: 66 TLALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGI 125 Query: 119 TAWGVEYTVVDTSVVEEVKAAIKDNTKLIWVETPTNPALGITDIEAVAKLT-EGTNAKLV 177 +G++ VD + + ++AA+ T++I+ ETP NP L + DI AVA L + N LV Sbjct: 126 GEFGIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLV 185 Query: 178 VDNTFASPYLQQPLKLGAHAVLHSTTKYIGGHSDVVGGLVVTNDQEMDE-ELLFMQGGIG 236 VDNT+ +PYLQ+PL+LGA V+HS TKY+ GH D+ G+ V+N L ++ G Sbjct: 186 VDNTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAVSNQALAQRIRLQGLKDLTG 245 Query: 237 PIPSVFDAYLTARGLKTLAVRMDRHCDNAEKIAEFLDSRPEVSTVLYPGLKNHPGHEVAA 296 + S DA L RGLKTLA+RMDRHC NA+ +AE L + P V +V YPGL++ P +E+A Sbjct: 246 AVMSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYELAT 305 Query: 297 KQMKRFGGMISVRFAGGEEAAKKFCTSTKLICLAESLGGVESLLEHPATMTHQSAAGSQL 356 +QMK GGMI+ GG E ++F + KL A SLG ESL +HPA+MTH + + Sbjct: 306 QQMKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQER 365 Query: 357 E---VPRDLVRISIGIEDIEDLLADVEQAL 383 + LVR+S+G+ED+ DLLADV+QAL Sbjct: 366 AAHGISEGLVRLSVGLEDVADLLADVQQAL 395 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: 409 Number of extensions: 17 Number of successful extensions: 5 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: 411 Length adjustment: 31 Effective length of query: 355 Effective length of database: 380 Effective search space: 134900 Effective search space used: 134900 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