Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate YP_004143819.1 Mesci_4660 cystathionine beta-lyase
Query= BRENDA::H7C6A2 (386 letters) >NCBI__GCF_000185905.1:YP_004143819.1 Length = 393 Score = 197 bits (500), Expect = 6e-55 Identities = 125/382 (32%), Positives = 197/382 (51%), Gaps = 14/382 (3%) Query: 9 GFSTASIHAGYEPDDYYGSINTPI-YASTTFAQNAPNELRKGYEYT--RVGNPTIVALEQ 65 G +T H+G P DY+G +N P+ +AST ++A + + +YT G PT AL Sbjct: 13 GINTRLAHSGNNPHDYFGFVNPPVVHASTVLFRDAASMAARTQKYTYGTRGTPTTDALAH 72 Query: 66 TVAALEGAKYGRAFSSGMAATDILFRIILKPGDHIVLGNDAYGGTYRLIDTVFTAWGVEY 125 + ALEG+ SG+AA + + GDH+++ + Y T DT+ GVE Sbjct: 73 AIDALEGSAGTILVPSGLAAVTVPLLAFVSAGDHLLIVDTVYHPTRNFADTMLKRLGVEV 132 Query: 126 TVVDTSVVEEVKAAIKDNTKLIWVETPTNPALGITDIEAVAKLTEGTNAKLVVDNTFASP 185 V + A IK NTK+++ E+P + + DI A+AK A +++DNT+A+P Sbjct: 133 EYYAPHVGAGIAALIKPNTKVVFTESPASNTFEVQDIPAIAKAAHAAGAIVMMDNTWATP 192 Query: 186 YLQQPLKLGAHAVLHSTTKYIGGHSDVVGGLVVTNDQ---EMDEELLFMQGGIGPIPSVF 242 +PL G +H+ TKY GHSDV+ G V N+ + E + GP Sbjct: 193 LYFRPLDHGVDISIHAATKYPAGHSDVLLGTVSANESCWTHLYESFCTLGCCAGP----D 248 Query: 243 DAYLTARGLKTLAVRMDRHCDNAEKIAEFLDSRPEVSTVLYPGLKNHPGHEVAAKQMKRF 302 D Y RGL+++ VR++ H + IA +L+ + V+ VL+P L +HP HE+ + Sbjct: 249 DVYQVLRGLRSMGVRLEHHQRSTLAIASWLEGQKGVARVLHPALPSHPDHELWKRDFSGS 308 Query: 303 GGMISVRFA-GGEEAAKKFCTSTKLICLAESLGGVESLLEHPATMTHQSAAGSQLEVPRD 361 G+ S+ A GG++ F + ++ L S GG ESL P + + A + E P Sbjct: 309 SGIFSIVLAGGGQKQQHAFLDALQIFGLGYSWGGYESLAV-PVWLGDRVVAKAPYEGP-- 365 Query: 362 LVRISIGIEDIEDLLADVEQAL 383 L+R+ IG+ED++DL AD+ + L Sbjct: 366 LIRLQIGLEDVDDLKADISRGL 387 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: 432 Number of extensions: 29 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: 393 Length adjustment: 30 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 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