Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate HSERO_RS18310 HSERO_RS18310 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__HerbieS:HSERO_RS18310 Length = 429 Score = 233 bits (594), Expect = 8e-66 Identities = 135/428 (31%), Positives = 221/428 (51%), Gaps = 15/428 (3%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M D + F T +H ++ PI+ +V F ++D + A++F K G Y R Sbjct: 1 MPDNPQWKFETISVHGGYDPDPTTRAVAVPIYQTVAFAFDDTQHGADLFDLKVQGNIYSR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120 NPT LE ++ +E G + A+G AA+ +Q + GD++VS++ L+G T +L+ Sbjct: 61 IMNPTQDVLEKRLAALEGGIGALALASGQAAVTYAIQTIAEAGDNIVSASTLYGGTYNLF 120 Query: 121 M-TVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G + D + E I T+ +++E+I NP + D+ + ++ G+ Sbjct: 121 AHTLPQYGVQTRFADPRQPASFEPLIDDRTKAIYIESIGNPLGNITDIAAVADIAHRHGV 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAEN 239 +VDNT+ +PYL RP GA +VV+SLTK +GGHG LGGA+ D+G+F W ++ + Sbjct: 181 PLIVDNTVATPYLLRPFEHGADIVVHSLTKYLGGHGTTLGGAIVDSGKFPWAKHKQRFKR 240 Query: 240 YKKNPAPQWG------------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERE 287 + G + + R LR+ G +L P A I G ET+ LR +R Sbjct: 241 LNEPDVSYHGVVYTEALGEAAYIGRARVVPLRNMGAALSPFNAFQILQGIETLGLRLDRI 300 Query: 288 CKNALALAQMLQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGID-CFDY 345 N LA+AQ L+ +V V Y GLE HP HAL++ F+ S +++F + +G + + Sbjct: 301 TANTLAVAQYLKRHPKVRWVNYAGLEDHPDHALAQTYFKGRASGVLTFGVANGREGGARF 360 Query: 346 LNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVA 405 + L+L N+GD ++L A T ++ G+ E +R+S+G+E DDL+A Sbjct: 361 QDALQLFTRLVNIGDAKSLATHPASTTHRQLSPTELEKAGVTEDTVRLSIGIEHIDDLLA 420 Query: 406 DFRQALDA 413 D QAL + Sbjct: 421 DLEQALQS 428 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: 487 Number of extensions: 25 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: 429 Length adjustment: 32 Effective length of query: 381 Effective length of database: 397 Effective search space: 151257 Effective search space used: 151257 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