Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_013076055.1 BTUS_RS10490 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000092905.1:WP_013076055.1 Length = 393 Score = 397 bits (1020), Expect = e-115 Identities = 202/374 (54%), Positives = 254/374 (67%), Gaps = 16/374 (4%) Query: 5 VETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANL 64 ++T+ +Q GNR D TG +S PI+ +T Y H G+G STGFDY RT NPTR +E+ IA L Sbjct: 3 IDTRCSQAGNRRDPTTGAISLPIHHATTYAHPGLGSSTGFDYTRTSNPTRLALEETIAAL 62 Query: 65 ENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFS 124 G RG AF+SGMAAI I LF+ GD L++S DLYGGTYRLFE ++ GL Y D S Sbjct: 63 HGGCRGFAFASGMAAIDAIARLFRPGDHLVLSDDLYGGTYRLFERFFRPLGLETTYVDTS 122 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D + +I P T+A+FVETPTNP ++ AD++ ++++ E GL LIVDNTF TP LQRPL Sbjct: 123 DLQAVAKQIRPRTRALFVETPTNPTLKIADLKGLSQVAHERGLWLIVDNTFMTPYLQRPL 182 Query: 185 ELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGM 244 ELGADIV+ SATKYLGGHND+LAG VVVK E L + QN+IGAVL P D+WLL+RG+ Sbjct: 183 ELGADIVVESATKYLGGHNDVLAGTVVVKSEALANSLAFIQNSIGAVLGPQDAWLLLRGI 242 Query: 245 KTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQ 288 KTL +RM +H+ NA+ LA +L +S V YPG GGM++F + Sbjct: 243 KTLHVRMDRHEGNARTLAEWLRAHPRVSRVYYPGLPDHPGHAVHRAQASGWGGMIAFEVP 302 Query: 289 KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 WV P L L+ I FAESLGG ES ITYPA QTH D+P ++R GV + LLR SVG+ Sbjct: 303 NNRWVPPILAHLRVITFAESLGGTESLITYPAVQTHADVPPDVRQRLGVTDSLLRLSVGL 362 Query: 349 EHAEDLKEDLKQAL 362 EH +DL +DL QAL Sbjct: 363 EHVDDLIQDLDQAL 376 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: 426 Number of extensions: 15 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: 393 Length adjustment: 30 Effective length of query: 343 Effective length of database: 363 Effective search space: 124509 Effective search space used: 124509 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 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