Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate RR42_RS32610 RR42_RS32610 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::P94890 (442 letters) >FitnessBrowser__Cup4G11:RR42_RS32610 Length = 424 Score = 436 bits (1122), Expect = e-127 Identities = 228/429 (53%), Positives = 295/429 (68%), Gaps = 12/429 (2%) Query: 14 KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73 K ETIA+HGG PDPTT + AVP+YQT +Y F + H A LF L+ GNIY+R+MNPT D Sbjct: 2 KIETIAVHGGYSPDPTTRAVAVPIYQTVAYAFDNAQHGADLFDLKVPGNIYSRIMNPTND 61 Query: 74 VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133 VLE+R+AALEGGV ALA ASG +A A+ I EAG I+++S LYGGTYNL +T P Sbjct: 62 VLEQRLAALEGGVGALALASGMAAITYAIQTIAEAGDNIISASQLYGGTYNLFAHTLPLS 121 Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193 GI+ F D +P F + +T+A + E++GNP + +DI A++KVA G+PL++DNT Sbjct: 122 GIETRFADGRNPAAFGDLVDARTKAIFVESVGNPLGNIVDIEAIAKVAHSHGIPLIVDNT 181 Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKNFTEPDPS 251 +PSPYL P +HGADIVVHSLTK+LGGHG S+GG I+D G F W K FK EPD S Sbjct: 182 VPSPYLCRPFEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFKRLNEPDVS 241 Query: 252 YHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMER 311 YHG+ + E G A+I +ARV LR+ G A+SPFNA+ ILQG+ETL LR++R Sbjct: 242 YHGVVYTEALGA--------AAYIGRARVVPLRNTGAALSPFNAFLILQGIETLALRLDR 293 Query: 312 HSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIK-GGVEKA 370 + NAL VA L+ PK+EWVN+ GL ++A ++Y G I+ F +K GG E Sbjct: 294 ITENALAVARHLKASPKVEWVNFAGLPEHPDHALVQRY-LGGRGPGILSFGLKSGGREAG 352 Query: 371 KKFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDD 430 +F+D L+LF+ L NIGDAKSLA HPASTTH+QL E +AGV+ VRLS+G+E+IDD Sbjct: 353 ARFLDALQLFTRLVNIGDAKSLATHPASTTHRQLDAAELKAAGVSEDMVRLSIGIEHIDD 412 Query: 431 ILVDLEEAL 439 +L DLE AL Sbjct: 413 LLEDLERAL 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: 535 Number of extensions: 17 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