Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Cola:Echvi_4510 Length = 403 Score = 266 bits (680), Expect = 8e-76 Identities = 152/399 (38%), Positives = 223/399 (55%), Gaps = 13/399 (3%) Query: 13 DLEGAAFDTLAVRAGQRRTP-EGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYT 71 D + T A+ AG+ P G L +++Y+ + E +Y+R+ Sbjct: 5 DFKNLGEQTRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIYTRWG 64 Query: 72 NPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDK 131 NPTV EE++A LE AE AVA ASGM AI L L +GDH +VS + + + ++ Sbjct: 65 NPTVHQLEEKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAALSEMTNE 124 Query: 132 YFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALL 191 IQ+ SDL+A +AA K NT+L ++E+P NP+ L DI A+A IA GA L Sbjct: 125 MVPSLNIQITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGAGARL 184 Query: 192 AVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-- 249 AVD+ F TPA +PL+LGAD ++HS TKY+ G G +GG + GR + + +TA Sbjct: 185 AVDSTFATPAATKPLQLGADFIVHSLTKYLGGHGDALGGAILGRKADLAPL--RKKTAIR 242 Query: 250 -GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHEL 308 G +SPFNAWL L+GL T IRM+AH +AL +A +LE+ P ++RV Y GLPSHPQHEL Sbjct: 243 MGAVISPFNAWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQHEL 302 Query: 309 ARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAH-------PATTS 361 A++Q F +++F V+ G+ + F D R+V +LG ++ I + ++ Sbjct: 303 AKKQMKNFSGMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLIFYLDSADLKESSFK 362 Query: 362 HGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 ++ GD + R++VGLED D+ D+ R L Sbjct: 363 FATGKQDESWEIYAGDGIFRLSVGLEDSKDIIDDLNRAL 401 Lambda K H 0.319 0.133 0.392 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: 371 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: 403 Length of database: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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