Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Dsui_2039 Dsui_2039 OAH/OAS sulfhydrylase
Query= BRENDA::E9AFE7 (409 letters) >FitnessBrowser__PS:Dsui_2039 Length = 428 Score = 250 bits (639), Expect = 5e-71 Identities = 150/412 (36%), Positives = 219/412 (53%), Gaps = 39/412 (9%) Query: 24 GFDTLQVHAGVRPDPVTGAILTPIYQSTTFVQES------INSYQAKGYSYTRSANPTVA 77 GFDTL +HAG PD TG+ TPIYQ+ +V +S + + Q G Y+R +NPTVA Sbjct: 7 GFDTLSLHAGQVPDAATGSRATPIYQTAAYVFDSPEHAASLFNLQTFGNVYSRLSNPTVA 66 Query: 78 VLEQKLCALENGSYCTVYNTGMAATTTAISSFMNAGDHAILTNCCYGGTNRACRVFFSRL 137 VLE+++ ALE G +GMAA A+ + AGD + YGGT+ V F +L Sbjct: 67 VLEERIAALEGGKAAVAVASGMAAQMVALLNLCEAGDEIVAARTLYGGTHTQLDVNFRKL 126 Query: 138 GMEFTFVDMRDPQNVIDSIKPNTKLVISETPANPTLILIDVAAVSKICKERGIVHMCDNT 197 G+ FVD DP+N +I P TK++ +ET NP L ++D+ AV++I G+ DNT Sbjct: 127 GINTIFVDSDDPENFAKAITPRTKVIYAETMGNPGLNVLDIEAVARIANAAGLPLFVDNT 186 Query: 198 FATAYIMRPLDHGADVTLISTTKYVDGHDMTVGGALVTNSK------------------- 238 FA+ Y+ RP + GA + + S TK++ GH T+GG +V + K Sbjct: 187 FASPYLCRPFEWGAAIVVHSATKFIGGHGTTLGGIIVESGKFPWDNGKFATMTEPSPGYH 246 Query: 239 -----------ELDAKVRLT-QNILGNVMSPQVAFLQLQTVKTMSLRVTKQSHNAQKIAE 286 AK R+ G +SP AFL LQ V+T+SLR+ + NA IA Sbjct: 247 GVKFYETFGNFGFTAKCRMEGLRTFGPALSPFNAFLLLQGVETLSLRMDRHCSNALAIAR 306 Query: 287 FLETHRAVDRVVYPGLASHPQKELADRQHRNNLHGGMLWFEVKGGTAAGRRLMDTVPRPW 346 LE H V+ V YPGL S +LA + G +L F +KGG AAG+ +D+V Sbjct: 307 HLEAHPQVEWVNYPGLPSSKYHDLAQKYLPKGA-GAVLTFGIKGGAAAGQEFIDSV-EFL 364 Query: 347 SLCENLGASESIITCPSVMTHANMTSEDRMKVGITDGFVRVSCGIEDVDDLI 398 S N+G +++++ P+ TH MT E + G+ +R+S G+E +DD++ Sbjct: 365 SHLANIGDAKTLVIHPASTTHRQMTPEQQTAAGVPPDLIRLSVGLETLDDIL 416 Lambda K H 0.319 0.132 0.388 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: 425 Number of extensions: 22 Number of successful extensions: 5 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: 409 Length of database: 428 Length adjustment: 32 Effective length of query: 377 Effective length of database: 396 Effective search space: 149292 Effective search space used: 149292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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