Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__WCS417:GFF2301 Length = 411 Score = 305 bits (780), Expect = 2e-87 Identities = 175/387 (45%), Positives = 231/387 (59%), Gaps = 12/387 (3%) Query: 13 GPATRAIHAGYRPDPATGAVNVPIYASSTFAQDGV-------GGLRGGFEYARTGNPTRA 65 G +TRAIH GY P GA+ PIY S+TFA G G Y R NPT A Sbjct: 9 GFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNPTLA 68 Query: 66 ALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRW 125 LE+ +A +E G A AFSSGM A +LRPGD V++ YG TF L+ + Sbjct: 69 LLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGIGEF 128 Query: 126 DVQYTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDR-SAKVLVDN 184 ++ V L DL A+ AA+TP TR+I+ ETP NP L + DI A+A L + + ++VDN Sbjct: 129 GIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLVVDN 188 Query: 185 TFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDE-EFAFLQNGAGAVP 243 T+ +P LQ+PL LGADVV+HS TKY+ GH D+ G V+N L++ GAV Sbjct: 189 TYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAVSNQALAQRIRLQGLKDLTGAVM 248 Query: 244 GPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQM 303 P DA L MRGLKTL LRM RH NA AVAE L HP+V SV YPGL S P +E+A +QM Sbjct: 249 SPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYELATQQM 308 Query: 304 RGFGGMVSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLE-- 361 + GGM++ ++ G + ++F A SLG ESL +HP++MTH++ + Sbjct: 309 KMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQERAAH 368 Query: 362 -VPDDLVRLSVGIEDIADLLGDLEQAL 387 + + LVRLSVG+ED+ADLL D++QAL Sbjct: 369 GISEGLVRLSVGLEDVADLLADVQQAL 395 Lambda K H 0.319 0.135 0.393 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: 454 Number of extensions: 20 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: 388 Length of database: 411 Length adjustment: 31 Effective length of query: 357 Effective length of database: 380 Effective search space: 135660 Effective search space used: 135660 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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