Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012102520.1 CKL_RS10680 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q187D4 (421 letters) >NCBI__GCF_000016505.1:WP_012102520.1 Length = 432 Score = 458 bits (1178), Expect = e-133 Identities = 218/423 (51%), Positives = 307/423 (72%), Gaps = 9/423 (2%) Query: 6 TICVQGNYKPGNGEPRVLPLYQSTTFKYSSIDQLAELFDLKVD--------GHIYSRISN 57 T VQG Y P +G+PRV + QST++KY + D++A + + D G++Y+R+ N Sbjct: 9 TRAVQGGYSPKSGDPRVASIVQSTSYKYDTFDEVANVAAVSADVTALNKQGGYLYTRVGN 68 Query: 58 PTIQAFEEKISLLEGGVSSVAVSSGQSANMLAVLNICKSGDSILCSSKVYGGTFNLLGPS 117 PT+ A E+K L+GGV ++A +SGQSA + +++NI SGD I+ +S +YGGT+NL Sbjct: 69 PTVTALEKKYVELQGGVEAIATASGQSAVVYSIINIANSGDQIIANSNLYGGTYNLFNTI 128 Query: 118 LKKFGIDLISFDLDSSEDEIVELAKENTKVVFAETLANPTLEVIDFEKIANVAKRINVPF 177 + K GI++ D +SE+EI+E A ENTK++F ET+ NP L V+DF+K ++VAK++++PF Sbjct: 129 IPKLGINVSFVDPTASEEEILEAATENTKLIFGETIGNPGLNVLDFDKFSSVAKKLDIPF 188 Query: 178 IVDNSLASPVLCNPLKYGANIVTHSTTKYLDGHASSVGGIIVDGGNFNWDNGKFPELVEP 237 IVDN++A+P L NP +YGANIV HSTTKY DGHA S+GGII+DGGNFNW NGKFP+ P Sbjct: 189 IVDNTIATPYLINPFEYGANIVVHSTTKYSDGHAVSLGGIIIDGGNFNWANGKFPDYTTP 248 Query: 238 DPTYHGISYTQKFGNAAYATKARVQLLRDYGNCLSPFNAYLTNLNVETLHLRMERHSENA 297 Y+ + + +FG A++ K R L+ ++G +PFNA+LTN+ +ETLHLRMERHS NA Sbjct: 249 TGPYN-VIFVNEFGKRAFSGKLRTNLVEEFGAAPAPFNAFLTNMGLETLHLRMERHSYNA 307 Query: 298 LKIARFLEKHENVDWINYPGLEDNKYYENAKKYLSRGCSGVLSFGVRGGLENAKKFVEKL 357 L +A++L H + W+ YP LE + YE A+KYL+ G SG+L+FGV+GG+E AK E L Sbjct: 308 LNLAKYLSNHPKIQWVRYPYLEWDPEYERAEKYLNGGASGILTFGVKGGIEAAKTLGENL 367 Query: 358 QIASLVTHVSDVRTCVIHPASTTHRQLTEEQLIASGVLPSLIRLSVGIENVEDLIADLNQ 417 ++AS+V ++ DVRT VIHPASTTH L+EEQ +GV P LIR+SVGIE++ED+IAD Q Sbjct: 368 KLASIVVNLGDVRTYVIHPASTTHLALSEEQQREAGVTPELIRVSVGIEDIEDIIADFQQ 427 Query: 418 ALN 420 AL+ Sbjct: 428 ALD 430 Lambda K H 0.316 0.135 0.387 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: 584 Number of extensions: 29 Number of successful extensions: 3 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: 421 Length of database: 432 Length adjustment: 32 Effective length of query: 389 Effective length of database: 400 Effective search space: 155600 Effective search space used: 155600 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 10 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