Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate AZOBR_RS11340 AZOBR_RS11340 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__azobra:AZOBR_RS11340 Length = 436 Score = 253 bits (646), Expect = 8e-72 Identities = 153/432 (35%), Positives = 239/432 (55%), Gaps = 19/432 (4%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M D K F T LH+ ++ G+ PI+ S ++ ++D A +F ++PG+ Y R Sbjct: 1 MADAKFLKFDTLSLHAGQRPDPATGARAVPIYQSTSYVFDDTDHAASLFNLERPGHIYSR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSL 119 NPTVA LE+++ ++ G +C A+G AA+ + L+ G H+V+S+ ++G + N L Sbjct: 61 ISNPTVAVLEERLAALDGGVGAVCTASGQAALTLAIMTLMDAGGHIVASSSIYGGSRNLL 120 Query: 120 WMTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G + V+ D+ AAI TRL+F E + NP +V D+ + + E G+ Sbjct: 121 AYTLPRFGITTTFVNPRDLDGFRAAIRPETRLLFGEVLGNPGLEVLDIPSLSAIAHEAGL 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHI 236 +VD T +PYL +P +VGA LV++S TK + GHG A+GG + D G FDW ++P + Sbjct: 181 PLMVDATFVTPYLCKPLSVGADLVMHSCTKWLAGHGVAIGGVVIDGGTFDWEASGKFPTL 240 Query: 237 AENYKK----NPAPQWGMA----QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQEREC 288 E Y + A ++G A + RA+ LRDFG + P A I G ET+ LR + Sbjct: 241 TEPYAGYHGIDFAEEYGPAAFVMRARAEGLRDFGACMSPMNAFQILQGVETLPLRMKGHI 300 Query: 289 KNALALAQMLQADE-----RVAAVYYPGLESHPQHAL-SKALFRSFGSLMSFELKDGIDC 342 N + L+++ VA V +P L HP H L ++ L GS++SF +K G + Sbjct: 301 HNTRKVLGFLESEAYAENGSVAWVTHPELPDHPDHRLRAQLLPHGAGSIISFGIKGGREA 360 Query: 343 -FDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTD 401 ++ +L L +N+GD ++LVI A T ++ AE A+ G+ E +IR+S+GLED D Sbjct: 361 GRRFIEKLALFSHLANVGDAKSLVIHPASTTHAQLDAEALAAAGVGEDMIRLSIGLEDCD 420 Query: 402 DLVADFRQALDA 413 DL+ D RQAL A Sbjct: 421 DLIDDLRQALRA 432 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: 460 Number of extensions: 23 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: 413 Length of database: 436 Length adjustment: 32 Effective length of query: 381 Effective length of database: 404 Effective search space: 153924 Effective search space used: 153924 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 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