Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate AO356_04305 AO356_04305 cysteine synthase
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04305 Length = 324 Score = 231 bits (590), Expect = 2e-65 Identities = 140/316 (44%), Positives = 185/316 (58%), Gaps = 12/316 (3%) Query: 2 RIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQL 61 RI + IG TPLV++N + P G T+ AK+E NPG S K RI MI AE+SG+L Sbjct: 3 RIFADNAHSIGNTPLVQINRIAPRGV-TILAKIEGRNPGYSVKCRIGANMIWDAESSGKL 61 Query: 62 KPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVP 121 KPG TIVEPTSGNTG+GLA VA RGYK + P +S ++R VL A GAE+V+ T Sbjct: 62 KPGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSIERRKVLKALGAELVL--TEPA 119 Query: 122 PHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIG 181 + ++ L D + P Q+ NP PA H TTGPEIW DT+G V VAG+G Sbjct: 120 KGMKGAIEKAAEILASDPSKYFMPQQFDNPANPAIHEKTTGPEIWNDTDGAVDVLVAGVG 179 Query: 182 TGGTITGAGRYLKEVSGGRVRIVGADPEGS--VYSGGAGR-----PYLVEGVGEDFWPAA 234 TGGTITG RY+K G + V +PE S + AG P+ ++G+G F P Sbjct: 180 TGGTITGVSRYIKNTCGKPILSVAVEPEVSPVITQAMAGHEIKPSPHKIQGIGAGFVPKN 239 Query: 235 YDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDA-LIVVL 293 D S+ D + V+D +S M RL +EE +L G SCG A+ A+++AE+ IVV+ Sbjct: 240 LDLSIVDLVERVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEMQGKTIVVI 299 Query: 294 LPDGGRGYMSK-IFND 308 LPD G Y+S +F+D Sbjct: 300 LPDSGERYLSSMLFSD 315 Lambda K H 0.316 0.135 0.398 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: 399 Number of extensions: 18 Number of successful extensions: 6 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: 464 Length of database: 324 Length adjustment: 30 Effective length of query: 434 Effective length of database: 294 Effective search space: 127596 Effective search space used: 127596 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 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