Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P55218 (403 letters) >lcl|FitnessBrowser__Cola:Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases Length = 381 Score = 247 bits (631), Expect = 4e-70 Identities = 137/385 (35%), Positives = 219/385 (56%), Gaps = 12/385 (3%) Query: 19 FDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T + AG P G +F TS+YV ++ G+ G YSR NPT Sbjct: 3 FGTKVIHAGVAPDPTTGAIMTPIFQTSTYVQKSP--------GQHKGFEYSRTHNPTRDA 54 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 ++ IAALE + + +SGM AI AL+ L S GD V+ + ++G T +F K F ++G Sbjct: 55 LQKSIAALENGKHGLCFSSGMGAIDALI-KLLSPGDEVISTNDLYGGTYRIFTKVFAKYG 113 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 I+ + + D A+ E T+L + E+P+NP+ ++DI ALA IA LL VDN F Sbjct: 114 IKFHFVSMDDPASIEKYINDKTRLIWAETPTNPMMNIIDIKALAAIAGKHDLLLGVDNTF 173 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLR-TAGPTLSPF 256 TP LQ PL LGAD+V+HS TKY+ G + G + +++ E + F++ + G T P Sbjct: 174 ATPYLQNPLDLGADLVMHSVTKYLAGHSDVVMGALVVNDDRLAEDLAFIQNSCGATPGPQ 233 Query: 257 NAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF 316 + +L L+G++TL +RM+ H + +A +L P +++VY+ G HP H++A +Q F Sbjct: 234 DCFLVLRGIKTLHLRMERHCQNGKTIAGYLRHHPKVDKVYWPGFEDHPNHDIAAKQMRDF 293 Query: 317 GAVVSFDVKGGR-DAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGI 375 G ++SF + G + + A + ++ S+ +LG ++ HPA+ +H + +R + G+ Sbjct: 294 GGMISFSIVGDKQEDAKKVLENLHYFSLAESLGGVESLCGHPASMTHASIPKVEREKVGL 353 Query: 376 GDSLIRVAVGLEDLDDLKADMARGL 400 DSLIR++VG+ED +DLK D+A L Sbjct: 354 TDSLIRLSVGVEDAEDLKNDLAAAL 378 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: 357 Number of extensions: 13 Number of successful extensions: 4 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: 381 Length adjustment: 31 Effective length of query: 372 Effective length of database: 350 Effective search space: 130200 Effective search space used: 130200 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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