Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate Dsui_2241 Dsui_2241 OAH/OAS sulfhydrylase
Query= BRENDA::P94890 (442 letters) >FitnessBrowser__PS:Dsui_2241 Length = 424 Score = 468 bits (1205), Expect = e-136 Identities = 240/428 (56%), Positives = 305/428 (71%), Gaps = 11/428 (2%) Query: 14 KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73 K ET+A+H G PDPTT + AVP+YQTTSY F +T H A LF L+ GNIYTR+MNPT D Sbjct: 3 KLETLAVHAGYSPDPTTKAAAVPIYQTTSYAFDNTQHGADLFDLKVAGNIYTRIMNPTQD 62 Query: 74 VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133 VLEKRVAALEGG+A LA ASGQ+A A+ I EAG IV++++LYGGTYNL +TFP+L Sbjct: 63 VLEKRVAALEGGIAGLALASGQAAITYAIQTIAEAGDNIVSTATLYGGTYNLFAHTFPQL 122 Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193 GI+V F D DP +F K + KT+A YAET+GNP + DI ++++A G+PL++DNT Sbjct: 123 GIQVRFADYRDPASFEKLIDGKTKAIYAETIGNPLGNITDIEKLAEIAHRNGIPLIVDNT 182 Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKNFTEPDPS 251 + SP+L+ P++ GADIVVHSLTK+LGGHG SIGGII+D G F W K FK EPD S Sbjct: 183 VASPFLLRPIEFGADIVVHSLTKYLGGHGNSIGGIIVDSGKFPWAEHKTRFKRLNEPDVS 242 Query: 252 YHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMER 311 YHG+ + E G A+I +ARV LR+ G AISPFNA+ ILQG+ET LRMER Sbjct: 243 YHGVVYTEALGP--------AAYIGRARVVPLRNTGAAISPFNAFLILQGIETAALRMER 294 Query: 312 HSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAK 371 + N + VA++LQ H K++WVNY GL ++A AKKY G I+ F ++GG+E Sbjct: 295 ITDNTIAVAKYLQSHKKVKWVNYAGLENHPDHALAKKY-LGGKPSGILTFGVEGGIEGGT 353 Query: 372 KFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDI 431 +F D L+LF+ L NIGDAKSLA HPASTTH+QL E AGVT VRLS+G+E+IDD+ Sbjct: 354 RFQDALQLFTRLVNIGDAKSLACHPASTTHRQLNPEELAKAGVTVDTVRLSIGIEHIDDL 413 Query: 432 LVDLEEAL 439 + DLE+AL Sbjct: 414 IADLEQAL 421 Lambda K H 0.317 0.137 0.402 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: 557 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: 442 Length of database: 424 Length adjustment: 32 Effective length of query: 410 Effective length of database: 392 Effective search space: 160720 Effective search space used: 160720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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