Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011307957.1 MBAR_RS16035 aminotransferase class V-fold PLP-dependent enzyme
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000195895.1:WP_011307957.1 Length = 394 Score = 310 bits (795), Expect = 4e-89 Identities = 167/391 (42%), Positives = 238/391 (60%), Gaps = 9/391 (2%) Query: 19 FDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY--TNPTV 75 F T V A ++ P G H +F TS+++F A AARFAGE G VY+R PT Sbjct: 7 FATKCVHAAEKPDPIFGAHTTPIFQTSTFIFENARQGAARFAGEESGYVYARIPPNTPTH 66 Query: 76 RTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKR 135 E+ AALEG E ASGM+A+ A+ ++ GDH++ + V+G T SLF + Sbjct: 67 AVLAEKFAALEGGEAGQTFASGMAAVTAIALTALKQGDHLISTDVVYGCTYSLFSQVLPG 126 Query: 136 FGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDN 195 GI+V + S + A KP TK+ F+ESP+NP + DI +A IA AL VDN Sbjct: 127 LGIEVSFVDTSKTENVKRAFKPETKMVFLESPANPTLNVCDIPEIARIARENEALCVVDN 186 Query: 196 CFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGE---QMKEVVGFLRTAGPT 252 F TP Q+PL+LGAD+ + S TKYI G +GG+VAG + +M EVVG+ G Sbjct: 187 TFATPYFQRPLELGADLSLSSCTKYIGGHADLLGGIVAGNNDFIDRMSEVVGY---TGGI 243 Query: 253 LSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQ 312 + P AWL ++GL+TL IRM+ H+ +A+ +AE+LE +P +E V Y GLP HPQ+ELAR+Q Sbjct: 244 MGPHEAWLCIRGLKTLHIRMERHAENAMKVAEFLESRPEVEWVRYPGLPGHPQYELARKQ 303 Query: 313 QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 SGF ++SF+VKGG +A + +D ++ S+ +LG T T I HPA+ +H + E R Sbjct: 304 MSGFSGMLSFEVKGGIEAGRKLMDNVKLCSLAVSLGATDTLIQHPASMTHACVPHEVRKS 363 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 GI D L+R++VG+ED +D+ AD+ + L + Sbjct: 364 VGITDGLVRLSVGIEDPEDIIADLKQALEVI 394 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: 385 Number of extensions: 9 Number of successful extensions: 2 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: 394 Length adjustment: 31 Effective length of query: 372 Effective length of database: 363 Effective search space: 135036 Effective search space used: 135036 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