Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate WP_086509774.1 BZY95_RS09910 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_002151265.1:WP_086509774.1 Length = 424 Score = 408 bits (1049), Expect = e-118 Identities = 209/429 (48%), Positives = 289/429 (67%), Gaps = 14/429 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ LH G D+ H + AVPI+ TTS+ F++++H + LF L+V G +YSR NPT Sbjct: 4 ETIALHHGYAP--DDQH-AVAVPIHQTTSFSFDSAQHAADLFDLKVEGNIYSRIMNPTCA 60 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+AALEGG A LAV+SG AA T AIQ +A GDNIVS S LYGGTYN F + R Sbjct: 61 VLEQRVAALEGGIAGLAVASGMAAITYAIQTIAEAGDNIVSISELYGGTYNLFAHTLPRQ 120 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIE RF + D+ + E + D RTKAV+ E++GNP +V D ++ +AH+HG+PV+VDNT Sbjct: 121 GIEVRFADKDDIDGIESLIDARTKAVFCESVGNPSGSVVDMARLAEVAHRHGVPVIVDNT 180 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 + +PI++GADIV HSATK+IGGHGTT+GG+IVDSG+FPW D+P++FP ++P Sbjct: 181 VPT-PFLWRPIEHGADIVIHSATKYIGGHGTTVGGVIVDSGRFPWADHPQRFPLLNEPDV 239 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG Y G A+I R LR++G ++ A++ LLQG+ETL+LR ER +NALK Sbjct: 240 SYHGVCYTRDIGEAAFIARARVVPLRNMGAALSAQAAWNLLQGLETLALRIERICDNALK 299 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A++LE V+WV Y GL H H+ A++Y+ G+LSFG++ A Sbjct: 300 VAEYLEAHDAVTWVQYAGLPGHKDHQLAQRYMGGRASGILSFGIQGGREA---------- 349 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 GA+ D L + L N+GDAKT P TTH+QL+D+E A+ VT D++R+S+GIE +D Sbjct: 350 GARFYDALGMILRLVNIGDAKTCSSIPASTTHRQLSDEELAAASVTPDMVRLSIGIEHVD 409 Query: 426 DIIADFQQS 434 DIIAD +Q+ Sbjct: 410 DIIADLEQA 418 Lambda K H 0.317 0.136 0.402 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: 528 Number of extensions: 20 Number of successful extensions: 3 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: 444 Length of database: 424 Length adjustment: 32 Effective length of query: 412 Effective length of database: 392 Effective search space: 161504 Effective search space used: 161504 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: 51 (24.3 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