Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate CCNA_01491 CCNA_01491 cystathionine beta-lyase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__Caulo:CCNA_01491 Length = 386 Score = 188 bits (478), Expect = 2e-52 Identities = 130/375 (34%), Positives = 187/375 (49%), Gaps = 8/375 (2%) Query: 16 TRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFE--YARTGNPTRAALEASLAA 73 TR IH G P VN PI ST L + Y TG T AL+ +LA Sbjct: 5 TRLIHTGSEPARLGRTVNPPIQRGSTVLLPDAASLYDDDQLTYGITGLSTPVALQNALAE 64 Query: 74 VEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDV--QYTP 131 +E + SG+AA A+ A+L+ GD V++ D AY T R D+V R+ V +Y Sbjct: 65 LEGATNVTLYPSGLAAITGAMLAVLKAGDEVLVVDSAYKPTRRFCDRVLGRFGVTTRYYD 124 Query: 132 VRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPAL 191 +L+ +A+ +T TRLI +E P + + DI AIA R L+DNT+A+ L Sbjct: 125 PKLSP-EALMGLVTSSTRLIVLEAPGSLTFEMQDIPAIAAAANARGVLTLIDNTWAAGLL 183 Query: 192 QQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAGAVPGPFDAYLT 251 +PL G + + + TKY+GGHSD G++ T D+ + + G DAY Sbjct: 184 FKPLAHGVTMSVQALTKYVGGHSDCFMGSVATCDDAVAKLLGDAMWDIGWSVSSDDAYTM 243 Query: 252 MRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMRGFGGMVS 311 +RGL+TL R+ RH+EN A+A +L + P V+ VL+P LP GH I R G G+ Sbjct: 244 LRGLRTLATRLPRHAENGLAIARWLQERPEVARVLHPALPGDAGHAIWKRDFTGACGLFG 303 Query: 312 VRMR-AGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVPDDLVRLS 370 V ++ ++A ++F L S GG ESL + A + LE P L+R Sbjct: 304 VVLKPCSQKAVHAFLDSLKLFGLGFSWGGYESLALNCDPQLGARSIPVDLEGP--LLRFH 361 Query: 371 VGIEDIADLLGDLEQ 385 +G+E I DL DL + Sbjct: 362 IGLEGIEDLKADLRR 376 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: 372 Number of extensions: 17 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: 388 Length of database: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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 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