Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate HSERO_RS18310 HSERO_RS18310 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::P94890 (442 letters) >FitnessBrowser__HerbieS:HSERO_RS18310 Length = 429 Score = 461 bits (1187), Expect = e-134 Identities = 233/437 (53%), Positives = 311/437 (71%), Gaps = 13/437 (2%) Query: 9 MPRN--FKPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTR 66 MP N +K ETI++HGG +PDPTT + AVP+YQT ++ F DT H A LF L+ GNIY+R Sbjct: 1 MPDNPQWKFETISVHGGYDPDPTTRAVAVPIYQTVAFAFDDTQHGADLFDLKVQGNIYSR 60 Query: 67 LMNPTTDVLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLL 126 +MNPT DVLEKR+AALEGG+ ALA ASGQ+A A+ I EAG IV++S+LYGGTYNL Sbjct: 61 IMNPTQDVLEKRLAALEGGIGALALASGQAAVTYAIQTIAEAGDNIVSASTLYGGTYNLF 120 Query: 127 HYTFPKLGIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGV 186 +T P+ G++ F D P +F +D+T+A Y E++GNP + DIAAV+ +A GV Sbjct: 121 AHTLPQYGVQTRFADPRQPASFEPLIDDRTKAIYIESIGNPLGNITDIAAVADIAHRHGV 180 Query: 187 PLVIDNTMPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKN 244 PL++DNT+ +PYL+ P +HGADIVVHSLTK+LGGHGT++GG I+D G F W K FK Sbjct: 181 PLIVDNTVATPYLLRPFEHGADIVVHSLTKYLGGHGTTLGGAIVDSGKFPWAKHKQRFKR 240 Query: 245 FTEPDPSYHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVET 304 EPD SYHG+ + E G+ A+I +ARV LR++G A+SPFNA+QILQG+ET Sbjct: 241 LNEPDVSYHGVVYTEALGE--------AAYIGRARVVPLRNMGAALSPFNAFQILQGIET 292 Query: 305 LPLRMERHSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIK 364 L LR++R + N L VA++L++HPK+ WVNY GL ++A A+ Y +G ++ F + Sbjct: 293 LGLRLDRITANTLAVAQYLKRHPKVRWVNYAGLEDHPDHALAQTYF-KGRASGVLTFGVA 351 Query: 365 GGVEKAKKFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVG 424 G E +F D L+LF+ L NIGDAKSLA HPASTTH+QL+ E AGVT VRLS+G Sbjct: 352 NGREGGARFQDALQLFTRLVNIGDAKSLATHPASTTHRQLSPTELEKAGVTEDTVRLSIG 411 Query: 425 LENIDDILVDLEEALKN 441 +E+IDD+L DLE+AL++ Sbjct: 412 IEHIDDLLADLEQALQS 428 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: 570 Number of extensions: 26 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: 429 Length adjustment: 32 Effective length of query: 410 Effective length of database: 397 Effective search space: 162770 Effective search space used: 162770 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