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_050461123.1 AKL27_RS02665 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_001189915.1:WP_050461123.1 Length = 423 Score = 426 bits (1094), Expect = e-124 Identities = 213/429 (49%), Positives = 291/429 (67%), Gaps = 13/429 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ +H G D ++ AVPIY T SY F++++HG+ LF L+V G +Y+R NPT + Sbjct: 4 ETIAVHGGYSP--DPTTKAAAVPIYQTVSYAFDDTQHGADLFDLKVAGNIYTRIMNPTQD 61 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+A LEGG AALA++SGQAA T AIQ +A GDNIVS S LYGGTYN F + +F Sbjct: 62 VLEKRVAELEGGIAALALASGQAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQF 121 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIE RF + +PE F K+ D++TKAV++E+IGNP N+ D EKI IAH+HG+P++VDNT Sbjct: 122 GIETRFADYRDPESFGKLIDDKTKAVFVESIGNPLGNITDIEKIAEIAHRHGVPLIVDNT 181 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 Y +PI +GADIV HS TK++GGHG ++GG IVDSGKFPW ++ +KF + ++P Sbjct: 182 V-PSPYLLRPIDFGADIVVHSLTKYLGGHGNSLGGAIVDSGKFPWAEHKQKFKRLNEPDV 240 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 YHG +Y EA G AYI R LR+ G ++PF +FL+LQG+ETL+LR ER N Sbjct: 241 SYHGVVYTEALGAAAYIGRARVVPLRNTGAAISPFNAFLILQGIETLALRMERITSNTAH 300 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A++L+Q V WV+Y GL H H A+KYL G+L+FGVK Sbjct: 301 IAQFLQQHAKVQWVNYAGLPDHPDHALAQKYLGGRPSGILTFGVKG----------GLAG 350 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G + D LKL + L N+GDAK+L P TTH+QLN +E + +GVT+D +R+S+GIE ID Sbjct: 351 GTRFQDALKLFTRLVNIGDAKSLACHPASTTHRQLNPEELVKAGVTEDTVRLSIGIEHID 410 Query: 426 DIIADFQQS 434 D++AD +Q+ Sbjct: 411 DLLADLEQA 419 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: 564 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