Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_078428512.1 BK574_RS10075 methionine biosynthesis PLP-dependent protein
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_002019605.1:WP_078428512.1 Length = 368 Score = 495 bits (1274), Expect = e-145 Identities = 236/363 (65%), Positives = 293/363 (80%) Query: 3 QHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIA 62 + +ETKL QIGNR DE TGT++ P+Y STAYRH GIGESTGFDY RT NPTR ++E+AIA Sbjct: 4 EQLETKLVQIGNRLDEHTGTINTPVYFSTAYRHSGIGESTGFDYSRTGNPTRLVLENAIA 63 Query: 63 NLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDD 122 LE G RG A SSGM+AIQT+ +LFK GDE++ SSDLYGGTYRLFEN WK +GL+F Y D Sbjct: 64 ELEAGDRGFACSSGMSAIQTLFSLFKQGDEILASSDLYGGTYRLFENGWKNWGLSFSYGD 123 Query: 123 FSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQR 182 D + +I NTKA+F+E+PTNPLMQEAD++ + + ++H LL IVDNTFYTP++Q+ Sbjct: 124 PRDIETFEQQINENTKALFIESPTNPLMQEADLKQLGHLARKHNLLFIVDNTFYTPLIQQ 183 Query: 183 PLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMR 242 PL+ GADIVIHSA+KYLGGHND++AGL+V K E L E + N +G +L PFDSWLL+R Sbjct: 184 PLKEGADIVIHSASKYLGGHNDVIAGLIVGKGEELCERIGYFHNGMGGILSPFDSWLLIR 243 Query: 243 GMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGKGGMLSFRLQKEEWVNPFLKALKT 302 GMKTL+LRM QHQ NA+E+AA+L+E ++DVLYPG+GGMLSFR+++ WVNPFL+ LK Sbjct: 244 GMKTLTLRMEQHQKNAREVAAYLKEHPSVTDVLYPGRGGMLSFRIKEANWVNPFLQQLKL 303 Query: 303 ICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDLKQAL 362 I FAESLGGVES +TYP TQTH D+PEE+R ANGVC+RLLRFSVGIE+++DL DL QA Sbjct: 304 ISFAESLGGVESLMTYPTTQTHADMPEEVRFANGVCDRLLRFSVGIENSQDLIADLDQAF 363 Query: 363 CQV 365 V Sbjct: 364 NHV 366 Lambda K H 0.319 0.135 0.392 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: 465 Number of extensions: 14 Number of successful extensions: 1 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: 373 Length of database: 368 Length adjustment: 30 Effective length of query: 343 Effective length of database: 338 Effective search space: 115934 Effective search space used: 115934 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: 49 (23.5 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