Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012042697.1 BBTA_RS11700 O-acetylhomoserine aminocarboxypropyltransferase
Query= metacyc::MONOMER-17873 (438 letters) >NCBI__GCF_000015165.1:WP_012042697.1 Length = 442 Score = 659 bits (1699), Expect = 0.0 Identities = 318/423 (75%), Positives = 362/423 (85%) Query: 14 HQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTRIGNPTQ 73 H +TLALHGGSYRADPTTGAVAVPIYQTTS+Q + HA+RL LEEIG YTRI NPTQ Sbjct: 7 HFETLALHGGSYRADPTTGAVAVPIYQTTSFQFQNADHASRLFALEEIGQVYTRIKNPTQ 66 Query: 74 DAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLFANTLRT 133 DAFE+RLAA+EGGV ALA++SGQ ASA A+ LAQAGDN+V+STDLYGGTW LF+ TL+ Sbjct: 67 DAFEERLAAIEGGVGALAVSSGQTASAFAIFNLAQAGDNVVSSTDLYGGTWTLFSQTLKQ 126 Query: 134 LGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGVPLIIDN 193 GIE RFVDP+DPE FRRATD +TR YY ETLPNPKL VFPI EVA IGRSLGVPLI+DN Sbjct: 127 FGIEVRFVDPSDPENFRRATDDKTRAYYAETLPNPKLNVFPIKEVADIGRSLGVPLILDN 186 Query: 194 TATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALLTGPEPS 253 TA+PLIARPF+HGAA+VVYSTTKYIGGHGT+IGGA+IDGG F W +A R LLT P+P+ Sbjct: 187 TASPLIARPFEHGAAIVVYSTTKYIGGHGTSIGGAVIDGGNFDWEKYAARFPLLTQPDPA 246 Query: 254 YHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLARHNANA 313 YH A WT+ A PFGP+AYILRAR +LRDLGAS+AP +AF IQGLETLPLRL +HN NA Sbjct: 247 YHGAVWTEAAKPFGPIAYILRARVKLLRDLGASLAPQNAFQFIQGLETLPLRLRQHNENA 306 Query: 314 IKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGRRFIEAL 373 IKVAD+L+ HP +S+V FPGLQ+GE RRRADAYLKGGYG L+GFEL GG E GRRFI+AL Sbjct: 307 IKVADFLSKHPAISNVIFPGLQTGENRRRADAYLKGGYGALVGFELKGGVEVGRRFIDAL 366 Query: 374 RLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDIIGDIAQ 433 +LFYHV NIGD RSLAIHPA+TTH QLSPE+Q A GVTPG+VRLS+GIEHPDDI+ D+ Q Sbjct: 367 QLFYHVANIGDVRSLAIHPASTTHQQLSPEEQLAAGVTPGYVRLSVGIEHPDDILADLTQ 426 Query: 434 ALD 436 ALD Sbjct: 427 ALD 429 Lambda K H 0.319 0.136 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: 660 Number of extensions: 13 Number of successful extensions: 1 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: 438 Length of database: 442 Length adjustment: 32 Effective length of query: 406 Effective length of database: 410 Effective search space: 166460 Effective search space used: 166460 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: 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