Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate RR42_RS06465 RR42_RS06465 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__Cup4G11:RR42_RS06465 Length = 436 Score = 263 bits (673), Expect = 6e-75 Identities = 159/421 (37%), Positives = 234/421 (55%), Gaps = 18/421 (4%) Query: 9 FTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAA 68 F T LH+ G+ PIH + +F ++D+ A +F ++ G+ Y R NPTVA Sbjct: 6 FDTLALHAGAAPDPATGARATPIHLTTSFVFKDSEHAASLFNMERAGHVYSRISNPTVAV 65 Query: 69 LEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQG 127 LE++I +E+G I A+G AA+ V L+ G H+V+S+ L+G + N L T+ G Sbjct: 66 LEERIAALENGAGAIGVASGQAALHLAVATLMGAGSHIVASSALYGGSHNLLHYTLRRFG 125 Query: 128 AKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTM 187 + + V A D+ AAI T+L+F ET+ NP V D+ + +L ++ GI +VD+T Sbjct: 126 IETTFVQARDIDAWRAAIRPETKLLFGETLGNPGLDVLDIPTLAQLGQDNGIPLLVDSTF 185 Query: 188 TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHIAENY---- 240 T+PYL +P +GAGL+ +S TK +GGHG +GG L + G FD+ R+P ++E Y Sbjct: 186 TTPYLLKPFDLGAGLLYHSATKFLGGHGTTIGGVLAEGGTFDFEASGRFPELSEPYAGFH 245 Query: 241 ------KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALAL 294 + AP + + R + LRDFG L P AA + G ET+ LR R NA + Sbjct: 246 NMVFTEESTVAP--FLLRARREGLRDFGACLSPMAAWQLLQGIETLPLRMARHVDNARRV 303 Query: 295 AQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDCFD-YLNRLRLA 352 Q L + V +V YP LESHP +AL++ L R G++ SF LK ++ L L Sbjct: 304 VQFLVSHPMVESVAYPELESHPDYALARRLLPRGAGAVFSFNLKGNRAAGQRFIESLALF 363 Query: 353 IPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 +N+GD R+LVI A T + M A + GI+E IR+SVGLED DDL+ D ++ L Sbjct: 364 SHLANVGDARSLVIHPASTTHFRMDAAALQAAGISEGTIRLSVGLEDPDDLIDDLKRGLK 423 Query: 413 A 413 A Sbjct: 424 A 424 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: 431 Number of extensions: 22 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: 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