Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514089.1 GMET_RS03505 PLP-dependent aspartate aminotransferase family protein
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000012925.1:WP_004514089.1 Length = 391 Score = 361 bits (926), Expect = e-104 Identities = 189/377 (50%), Positives = 250/377 (66%), Gaps = 19/377 (5%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIAN 63 ++ T+ AQIG D TG V+ PIY + +RH G+G+STG+DY R+ NPTRQ +E+ IA Sbjct: 2 NIATQTAQIGLEWDTRTGAVTVPIYQTATFRHPGLGQSTGYDYTRSGNPTRQALEEGIAR 61 Query: 64 LENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDF 123 LE GARG A++SGMAAI ++ LFK GD L+V+ DLYGGT RLF+ + +Y L+F Y D Sbjct: 62 LEGGARGFAYASGMAAIANLLLLFKKGDHLVVTEDLYGGTCRLFDQIFTQYELSFTYVDT 121 Query: 124 SDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRP 183 SD +R+ I P TKA+FVE+ TNPL++ ADI ++ + +E GLL IVDNTF TP L RP Sbjct: 122 SDIKAVRAAIRPETKALFVESLTNPLLKVADIAALSALCRERGLLHIVDNTFLTPYLLRP 181 Query: 184 LELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243 + GADI ++SATKYL GHND ++GLV VKD +L E ++ QN++GAVL P DSWL +RG Sbjct: 182 FDHGADITVYSATKYLAGHNDTVSGLVAVKDPQLAERVYFLQNSVGAVLGPQDSWLTIRG 241 Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK-------------------GGMLS 284 MKTLS+R+ + Q NA +A +L + V YPG G M++ Sbjct: 242 MKTLSVRLDRQQENAGRVAQWLSNHPRVRKVYYPGLSGHPGHPGHELLARQARGFGAMIA 301 Query: 285 FRLQKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344 F + + V L + I FAESLGGVE+ IT+P QTH DIP E+R G+ + LLR Sbjct: 302 FEVDEHALVERLLLKTEVISFAESLGGVETLITFPQVQTHADIPPELRQRLGINDVLLRL 361 Query: 345 SVGIEHAEDLKEDLKQA 361 SVGIE A+DL +DL QA Sbjct: 362 SVGIEDADDLIDDLAQA 378 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: 431 Number of extensions: 14 Number of successful extensions: 2 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: 391 Length adjustment: 30 Effective length of query: 343 Effective length of database: 361 Effective search space: 123823 Effective search space used: 123823 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 Jul 25 2024. The underlying query database was built on Jul 25 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