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_006748629.1 THITH_RS06230 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000227685.2:WP_006748629.1 Length = 427 Score = 423 bits (1087), Expect = e-123 Identities = 208/430 (48%), Positives = 296/430 (68%), Gaps = 10/430 (2%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T +HAG D R+ AVPIY TTSY F++++HG+ LF L+VPG +Y+R NPT+ Sbjct: 3 FETQAIHAGFSP--DPTTRAVAVPIYQTTSYAFDDTQHGADLFDLKVPGNIYTRIMNPTT 60 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +VLE+R+AALEGG ALA +SG AA T ++ LA G N+V+TS LYGGTYN F + R Sbjct: 61 DVLEQRVAALEGGVGALAFASGMAAITASLMTLAEAGHNVVTTSTLYGGTYNLFAHTLPR 120 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 +GIE RF + + + D+ T+AV+ E+IGNP NV D + +AH HGIP++VDN Sbjct: 121 YGIEVRFAPPGDIDAMRGLIDQDTRAVFCESIGNPAGNVADLAALADLAHGHGIPLIVDN 180 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T + Y C+P ++GAD+V HS TK++GGHGTTIGG++VDSG+FPW D+ E+FP +QP Sbjct: 181 TVPSP-YLCRPFEHGADVVVHSLTKYMGGHGTTIGGVLVDSGRFPWADHAERFPGLTQPD 239 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 YHG Y EA+G AYI R LR++G ++PF SF +LQG+ETL+LR +RH ENAL Sbjct: 240 PSYHGVTYTEAFGPAAYIGRARVVPLRNMGAAISPFNSFQVLQGIETLALRMDRHCENAL 299 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +A++L++ VSWV+Y GL H H A++Y+ G+LSFG++ P+ + Sbjct: 300 AVAQFLDRHAAVSWVAYAGLPDHPDHPLARRYMGGRAAGILSFGIRS-PHGG------RA 352 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 +GA+ +D L+L + L N+GDAK+L P TTH+QL+ +E +GV +D++R+SVGIE + Sbjct: 353 AGAKFIDALQLVTRLVNIGDAKSLACHPATTTHRQLSAQELERAGVREDMVRLSVGIEHV 412 Query: 425 DDIIADFQQS 434 DDI+ D +Q+ Sbjct: 413 DDILGDLEQA 422 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: 18 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: 427 Length adjustment: 32 Effective length of query: 412 Effective length of database: 395 Effective search space: 162740 Effective search space used: 162740 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