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_004312943.1 C665_RS12780 bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000310185.1:WP_004312943.1 Length = 423 Score = 414 bits (1063), Expect = e-120 Identities = 207/433 (47%), Positives = 288/433 (66%), Gaps = 13/433 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ +H G D ++ AVPIY TTSY F++++HG+ LF L+V G +Y+R NPT+ Sbjct: 4 ETIAVHGGYSP--DPTTKAVAVPIYQTTSYAFDDTQHGADLFDLKVQGNIYTRIMNPTTA 61 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+A LEGG ALAV+SG +A T AIQ +A GDNIVS S LYGGTYN F +F +F Sbjct: 62 VLEQRVAQLEGGIGALAVASGMSAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTFPQF 121 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIE RF + +P+ F + D RTKA+Y E++GNP NV D ++ IAHK G+P++VDNT Sbjct: 122 GIEVRFADYRDPDSFAALIDARTKAIYCESVGNPLGNVTDIGRLAEIAHKAGVPLIVDNT 181 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 Y C+P ++GADIV H+ TK++GGHG +IGG+IVDSGKFPW ++ +F + ++P Sbjct: 182 V-PSPYLCRPFEHGADIVVHALTKYLGGHGNSIGGVIVDSGKFPWAEHKARFKRLNEPDV 240 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG Y EA G A+I R LR+ G ++PF SFL+LQG+ETL+LR +R N +K Sbjct: 241 SYHGVCYTEALGAAAFIGRARVVPLRNTGAAISPFNSFLILQGIETLALRMDRICTNTIK 300 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A++L++ V WV+Y GL H+ H +KY+ G+LSFGVK A Sbjct: 301 VAEYLKKHAKVEWVNYAGLPDHADHALVQKYMGGRASGILSFGVKGGFEA---------- 350 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G + D LKL + L N+GDAK+L P TTH+QL+ E +GV+ D++R+S+GIE ID Sbjct: 351 GGRFQDALKLITRLVNIGDAKSLACHPASTTHRQLSPAELAKAGVSPDMVRLSIGIEHID 410 Query: 426 DIIADFQQSFETV 438 DI+AD +Q+ V Sbjct: 411 DIVADLEQALAAV 423 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: 557 Number of extensions: 30 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: 423 Length adjustment: 32 Effective length of query: 412 Effective length of database: 391 Effective search space: 161092 Effective search space used: 161092 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 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