Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate SMc01809 SMc01809 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__Smeli:SMc01809 Length = 426 Score = 254 bits (649), Expect = 3e-72 Identities = 151/423 (35%), Positives = 234/423 (55%), Gaps = 24/423 (5%) Query: 8 GFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVA 67 GF+T +H+ Q G+ PI+ + +F + D A +F +Q G Y R NPT A Sbjct: 6 GFSTLAIHAGAQPDPTTGARATPIYQTTSFVFNDTDHAAALFGLQQFGNIYTRIMNPTQA 65 Query: 68 ALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQ 126 LE++I +E G + + ++G AA + ++R GD+ VS+ L+G + N A Sbjct: 66 VLEERIAALEGGTAGLAVSSGHAAQLLVFHTIMRPGDNFVSARQLYGGSANQFGHAFKAF 125 Query: 127 GAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNT 186 +V D+ + ++ +A I T+ +F+E++ANP D+ I ++ R G+ +VDNT Sbjct: 126 DWQVRWADSAEPESFDAQIDERTKAIFIESLANPGGTFVDIAAIADVARRHGLPLIVDNT 185 Query: 187 MTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHIAENYKKN 243 M +PYL RP GA +VV+SLTK IGGHGN++GG + D G FDW+ +YP ++E Sbjct: 186 MATPYLMRPLEHGADIVVHSLTKFIGGHGNSMGGIIVDGGTFDWSKSGKYPLLSE----- 240 Query: 244 PAPQWGMAQI-------------RAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKN 290 P P++G + R LRDFG ++ P A I G ET+ LR +R C N Sbjct: 241 PRPEYGGVVLHQAFGNFAFAIAARVLGLRDFGPAISPFNAFLIQTGVETLPLRMQRHCDN 300 Query: 291 ALALAQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDCFD-YLNR 348 AL +A+ L+ E+V+ V Y GLE P HAL K + G++ +F L G + ++ Sbjct: 301 ALEVAKWLKGHEKVSWVRYSGLEDDPNHALQKRYSPKGAGAVFTFGLAGGYEAGKRFVEA 360 Query: 349 LRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFR 408 L + +N+GDTR+LVI A T ++ E++ + G +IR+SVG+ED D++AD Sbjct: 361 LEMFSHLANIGDTRSLVIHPASTTHRQLTPEQQVAAGAGPDVIRLSVGIEDVADIIADLE 420 Query: 409 QAL 411 QAL Sbjct: 421 QAL 423 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: 499 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: 426 Length adjustment: 32 Effective length of query: 381 Effective length of database: 394 Effective search space: 150114 Effective search space used: 150114 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