Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Dsui_3018 Dsui_3018 OAH/OAS sulfhydrylase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__PS:Dsui_3018 Length = 433 Score = 277 bits (708), Expect = 5e-79 Identities = 167/427 (39%), Positives = 235/427 (55%), Gaps = 14/427 (3%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M K Y T LH+ + ++G+ PI+ S +F ++D+ Q A +F ++ G+ Y R Sbjct: 1 MAGKDGYTLDTLALHAGQVPDPQYGARATPIYLSTSFVFKDSDQAAALFNMERAGHVYSR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120 NPTV+ LE++I +E G I A+G AA+ V L+ G H+V+S L+G +++L Sbjct: 61 ISNPTVSVLEERIAALEGGVGAIATASGQAAMHLAVATLMGAGSHIVASGALYGGSHNLL 120 Query: 121 -MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G + + V DV AAI NTRL+F ET+ NP V D+ RI L E G+ Sbjct: 121 DYTLRRFGIETTFVPTRDVDAWRAAIRPNTRLLFGETLGNPGLDVLDIPRIAALAHEHGL 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHI 236 +VD+T TSPYL +P GA LV +S TK + GHG A+GG L D+G FDW ++P + Sbjct: 181 PLLVDSTFTSPYLLKPFEHGADLVFHSATKFLCGHGTAVGGVLVDSGNFDWEASGKFPTL 240 Query: 237 AENYKKNPAPQWG--------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQEREC 288 E Y + + + R + LRDFG + P A I G ET+ LR +R Sbjct: 241 TEPYDGFHGMDFAEESTVAAFLLRARREGLRDFGACMSPMNAFQILQGVETLPLRMQRHV 300 Query: 289 KNALALAQMLQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDGIDC-FDYL 346 +NA L L A E V +V YPGLESHP HAL+ K L R GS+ SF +K G ++ Sbjct: 301 ENARKLVDFLAAHEAVESVAYPGLESHPDHALAQKLLPRGCGSVFSFSVKGGRPAGKKFI 360 Query: 347 NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVAD 406 L+L +N+GD ++LVI A T + M E + GI IR+SVGLED DDL+ D Sbjct: 361 ETLKLFSHLANVGDAKSLVIHPASTTHFRMSDEALLAAGIGAGTIRLSVGLEDADDLIED 420 Query: 407 FRQALDA 413 + L A Sbjct: 421 LSRGLAA 427 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: 459 Number of extensions: 21 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: 433 Length adjustment: 32 Effective length of query: 381 Effective length of database: 401 Effective search space: 152781 Effective search space used: 152781 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