Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_092483634.1 BM299_RS10160 homocysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_900115975.1:WP_092483634.1 Length = 432 Score = 273 bits (699), Expect = 6e-78 Identities = 157/425 (36%), Positives = 239/425 (56%), Gaps = 14/425 (3%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M +K +GF T LH+ Q E S P++ + ++ + D+ A +F K+ G Y R Sbjct: 1 MMTEKKWGFETVALHAGYQPDCETLSRAVPVYQTTSYVFRDSEHAANLFALKETGNIYSR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120 GNPTV LE ++ +E G + ++G AAI + + GD +VSS+ L+G T +L+ Sbjct: 61 IGNPTVEVLEKRLAALEGGVGALALSSGHAAIYTTILNIASAGDEIVSSSSLYGGTFNLF 120 Query: 121 M-TVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G KV VD +N A++ T+ VF E I NPR V D++ E+ E GI Sbjct: 121 THTLPRLGIKVHFVDPGRPENFRKAVSDKTKAVFGEIIGNPRCDVLDIQGASEVAHEAGI 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHI 236 +VD+T T+P+L RP GA +VV+S+TK IGGHG ++GG + D+G+FDW ++P + Sbjct: 181 PLIVDSTFTTPFLCRPFEFGADIVVHSMTKFIGGHGTSMGGIIIDSGKFDWAQNDKFPGL 240 Query: 237 AE--------NYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQEREC 288 +Y K+ P + + RA+ LRD G L P A I G ET++LR ER Sbjct: 241 TNPDPSYHGISYTKDLGPAAFVGKARAQLLRDIGACLSPFNAFLILQGTETLSLRMERHV 300 Query: 289 KNALALAQMLQADERVAAVYYPGLESHPQHALSKA-LFRSFGSLMSFELKDGIDCFD-YL 346 NA +A L+ +V V YPGL SHP HAL+K L R G++M+F +K G++ ++ Sbjct: 301 SNAQQVANFLENHPQVNWVSYPGLSSHPSHALTKKYLSRGAGAIMTFGIKGGLEAGKRFI 360 Query: 347 NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVAD 406 LR+ +N+GD ++LVI A T ++ E G++ ++R+S+GLE +DL+ D Sbjct: 361 ENLRIFSHLANVGDAKSLVIHPASTTHSQLSEEELLKAGVSPDMVRLSIGLESIEDLLED 420 Query: 407 FRQAL 411 QAL Sbjct: 421 LDQAL 425 Lambda K H 0.319 0.134 0.391 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: 452 Number of extensions: 20 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: 413 Length of database: 432 Length adjustment: 32 Effective length of query: 381 Effective length of database: 400 Effective search space: 152400 Effective search space used: 152400 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