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_011840397.1 RSPH17029_RS02535 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000015985.1:WP_011840397.1 Length = 393 Score = 205 bits (521), Expect = 2e-57 Identities = 135/434 (31%), Positives = 216/434 (49%), Gaps = 51/434 (11%) Query: 7 TVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPG--YVYSRFQNPTS 64 T +H G + + A I+ T +V+++++ F +E ++Y+R+ NPT+ Sbjct: 9 TQLVHGGSRR---SQYGEMAEAIFLTQGFVYDSAEQAEARF-IETGADEFIYARYGNPTT 64 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 + EERIAA+EG A A +SG AA + + GD++V+ L+G + R Sbjct: 65 RMFEERIAAVEGTEDAFATASGMAAIHGVLTSIVRAGDHLVAARALFGSCIYILEEVLGR 124 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 FG+E FV+G + +++ TKAV+ E++ NP V D I IAH G V+VDN Sbjct: 125 FGVEVTFVDGTDLDQWRAAVRPGTKAVFFESVSNPTLEVADIGAIAEIAHAVGALVIVDN 184 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 F A F ++ GAD+V +SATK I G G +GG++ S Sbjct: 185 VF-ATPVFSTAVRQGADVVIYSATKHIDGQGRALGGVVCAS------------------- 224 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 A+I V ++ G M+PF ++L+L G+ TL LR + A Sbjct: 225 --------------QAFIRKVLEPFMKHTGGSMSPFNAWLMLNGMATLDLRCRAMADTAE 270 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 K+A+ LE P + V +P L SH H+ AK + G +++ DL K Sbjct: 271 KIARALEGHPQLGRVIHPALESHPQHDMAKAQMERP-GTMIAL---DLAGG-------KE 319 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 + + +D LK+ N+GDA+++ P TTH++L+D +K G+T L+R+SVG+E Sbjct: 320 AAFRFLDALKIVKISNNLGDARSIATHPATTTHQRLSDAQKAHLGITPGLVRLSVGLEDA 379 Query: 425 DDIIADFQQSFETV 438 DD+IAD +Q+ + Sbjct: 380 DDLIADLKQALAVI 393 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: 405 Number of extensions: 16 Number of successful extensions: 4 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: 393 Length adjustment: 32 Effective length of query: 412 Effective length of database: 361 Effective search space: 148732 Effective search space used: 148732 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 16 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