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_011307957.1 MBAR_RS16035 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000195895.1:WP_011307957.1 Length = 394 Score = 256 bits (655), Expect = 7e-73 Identities = 160/437 (36%), Positives = 235/437 (53%), Gaps = 52/437 (11%) Query: 5 FDTVQLHAGQE-NPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRF--QN 61 F T +HA ++ +P AH + PI+ T++++FEN++ G+ F E GYVY+R Sbjct: 7 FATKCVHAAEKPDPIFGAHTT---PIFQTSTFIFENARQGAARFAGEESGYVYARIPPNT 63 Query: 62 PTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKIS 121 PT VL E+ AALEGG A +SG AA T GD+++ST +YG TY+ F Sbjct: 64 PTHAVLAEKFAALEGGEAGQTFASGMAAVTAIALTALKQGDHLISTDVVYGCTYSLFSQV 123 Query: 122 FKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVV 181 GIE FV+ E ++ F TK V+LE+ NP NV D +I IA ++ V Sbjct: 124 LPGLGIEVSFVDTSKTENVKRAFKPETKMVFLESPANPTLNVCDIPEIARIARENEALCV 183 Query: 182 VDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFS 241 VDNTF A YF +P++ GAD+ S TK+IGGH +GGI+ + F Sbjct: 184 VDNTF-ATPYFQRPLELGADLSLSSCTKYIGGHADLLGGIVAGNNDF------------- 229 Query: 242 QPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGE 301 + +E++ G +M P ++L ++G++TL +R ERH E Sbjct: 230 ---------------------IDRMSEVVGYTGGIMGPHEAWLCIRGLKTLHIRMERHAE 268 Query: 302 NALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDP 361 NA+K+A++LE P V WV YPGL H +E A+K +S GF G+LSF VK A Sbjct: 269 NAMKVAEFLESRPEVEWVRYPGLPGHPQYELARKQMS-GFSGMLSFEVKGGIEA------ 321 Query: 362 FKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGI 421 G +++DN+KL S ++G TL+ P TH + + + + G+T L+R+SVGI Sbjct: 322 ----GRKLMDNVKLCSLAVSLGATDTLIQHPASMTHACVPHEVRKSVGITDGLVRLSVGI 377 Query: 422 EFIDDIIADFQQSFETV 438 E +DIIAD +Q+ E + Sbjct: 378 EDPEDIIADLKQALEVI 394 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: 463 Number of extensions: 22 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 394 Length adjustment: 32 Effective length of query: 412 Effective length of database: 362 Effective search space: 149144 Effective search space used: 149144 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: 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