Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011765155.1 AZO_RS07195 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000061505.1:WP_011765155.1 Length = 434 Score = 259 bits (663), Expect = 8e-74 Identities = 159/428 (37%), Positives = 230/428 (53%), Gaps = 16/428 (3%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M +G T LH+ + HGS PIH + ++ + DA Q A +F ++PG+ Y R Sbjct: 1 MTQSDLFGRETLALHAGQSPDPVHGSRATPIHFTTSYVFSDADQAAALFNLERPGHVYSR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSL 119 NPT A LE+++ +E G I A+G AA+ + L+ G H+V+S L+G + N L Sbjct: 61 ISNPTTAVLEERVAALEGGVGAIAVASGQAALHLAITTLMGAGGHIVASRALYGGSHNLL 120 Query: 120 WMTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G + VD D+ AAI TRL F E++ NP V D+ + L + + Sbjct: 121 GYTLPRFGIHTTFVDPHDLDAWRAAIRPETRLFFGESVGNPGLDVLDIPAVSALAHQHRL 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTR---YPHI 236 +VD T+ SP L RP +GA LV++S TK +GGHG A+GG + D G FDW +P + Sbjct: 181 PLLVDATLVSPLLQRPLDLGADLVMHSATKYLGGHGVAVGGVIVDGGRFDWEASGLFPTL 240 Query: 237 AENY---------KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERE 287 E Y +++P + + + R + LRDFG L P A I G ET+ LR Sbjct: 241 TEPYDGFHGMDFAEESPVAAF-LLRARREGLRDFGACLSPMNAFQILQGLETLPLRMRAH 299 Query: 288 CKNALALAQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGID-CFDY 345 NA A+A+ L A V V YPGL H HAL+ L G++MSF+LK G + + Sbjct: 300 VANARAVAEHLAAHPLVEKVAYPGLPGHRDHALAARLLPHGCGAVMSFDLKGGREGGRAF 359 Query: 346 LNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVA 405 + LRL +N+GD ++LVI A T + M A A+ GI E +R+SVG+E+T DL+A Sbjct: 360 IGALRLFSHLANVGDAKSLVIHPASTTHFRMSAADLAAAGIGEGTVRLSVGIENTADLIA 419 Query: 406 DFRQALDA 413 D + L A Sbjct: 420 DLDRGLAA 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: 477 Number of extensions: 27 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: 434 Length adjustment: 32 Effective length of query: 381 Effective length of database: 402 Effective search space: 153162 Effective search space used: 153162 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: 51 (24.3 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