Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_028584498.1 G494_RS0110400 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000429965.1:WP_028584498.1 Length = 404 Score = 193 bits (490), Expect = 9e-54 Identities = 127/366 (34%), Positives = 197/366 (53%), Gaps = 17/366 (4%) Query: 34 GEHG---EALFTTSSYVFRTAADAAARFAGE-VPGNVYSRYTNPTVRTFEERIAALEGAE 89 GEHG ++ +S++V AA F+GE G +YSR NPTV +AALE E Sbjct: 18 GEHGGVAPSISRSSTFVVDDPESMAALFSGEREDGFLYSRSFNPTVNVLCRSLAALEATE 77 Query: 90 QAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLA 149 A+ TASGM+AI ++ LC GDH++ S +++G + +L + + I + SD A Sbjct: 78 AAMGTASGMAAIATTLLQLCRHGDHIVASDTIYGGSHALLETLLPQLNITTTFVDSSDPA 137 Query: 150 AWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLG 209 A EAA P+T++ + E+ NP + DI ALA +AH G L VDN F +P + P LG Sbjct: 138 AVEAAITPHTRVIYSETMGNPTLRIADIRALATVAHDHGLQLVVDNTF-SPVVVTPALLG 196 Query: 210 ADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVV----GFLRTAGPTLSPFNAWLFLKGL 265 ADVV++S TK+I+G + G + G ++E++ G + GPT+ P A+ + L Sbjct: 197 ADVVVYSLTKFINGASDLIAGAICGSEAFIRELMDLHSGRIMLTGPTMDPRVAFDIHQRL 256 Query: 266 ETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELAR---RQQSGFGAVVSF 322 L +RM+ H A+A+AE LE G+ V Y GL SHPQH+L Q G+G +++ Sbjct: 257 PHLPLRMREHGRRAMAMAELLE-DLGL-TVRYPGLASHPQHQLFAGMVNQGYGYGGMLTL 314 Query: 323 DV--KGGRDAAWRFIDATRMVS-ITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSL 379 D +G + R + + +LG T I+ + ++ + D+ + G+ L Sbjct: 315 DCGSRGQAEELMRVLQNEEQFGLLAVSLGYFDTLISCSSASTSSEIGELDQQKMGLAPGL 374 Query: 380 IRVAVG 385 +R+AVG Sbjct: 375 LRLAVG 380 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: 355 Number of extensions: 15 Number of successful extensions: 5 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: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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 10 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