Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 642684930 Cphamn1_2453 adenosylmethionine-8-amino-7-oxononanoate aminotransferase apoenzyme (EC 2.6.1.62)
Query= reanno::Marino:GFF3099 (404 letters) >IMG__ChlphaBS1_FD:642684930 Length = 434 Score = 154 bits (390), Expect = 4e-42 Identities = 111/327 (33%), Positives = 169/327 (51%), Gaps = 27/327 (8%) Query: 21 PGSIIPVRG-EGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NV 78 P + PV+G G RI ++GR ID G++HP L A+ Q EK+ H+ Sbjct: 25 PLPVYPVKGASGVRIELEDGRRLIDGMSSWWAAIHGYNHPVLNEAVRKQLEKMSHVMFGG 84 Query: 79 MTNEPALRLAKTLCDLTFA--ERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFK 136 T+EPA+RLA+ L DLT ++VFF++SG+ + E A K+A +Y +KN +++ + Sbjct: 85 FTHEPAVRLAEKLVDLTPGPLQKVFFSDSGSVSVEVAIKMALQYHHAAGRPKKNRLLTIR 144 Query: 137 NSFHGRTLFTVSVGGQPKYLEG----------FEPAPG-GIHHA----EFNDLESVKKLI 181 + +HG T +SV + G F AP G H D ++ Sbjct: 145 SGYHGDTFAAMSVCDPVTGMHGLFSGVLPQQLFAEAPACGFHDVWSDDSIGDFRRQVEMY 204 Query: 182 SKEKTCAIVVEPI-QGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240 +E A+++EP+ QG GG+ +L +R+LCD D LL+FDE+ +G GR+G +A Sbjct: 205 HRE-IAAVILEPVVQGAGGMRFYSPEYLVRVRELCDRYDLLLIFDEIATGFGRTGKMFAL 263 Query: 241 QMYGVVPDILSSAKGLGGGF-PVAAMLTTAKVA-----ASLGVGTHGSTYGGNALACAVA 294 + VVPDIL K L GG+ +AA LT V+ A GV HG T+ N LACAVA Sbjct: 264 EHADVVPDILCIGKALTGGYMTLAATLTNGDVSGVISNAEPGVFMHGPTFMANPLACAVA 323 Query: 295 QRVVDTVSQPEILKGVKARSDKLRKGM 321 +D +++ + V+ +L G+ Sbjct: 324 SASIDLLAESDWRNSVRVIEAQLASGL 350 Lambda K H 0.318 0.137 0.406 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: 460 Number of extensions: 15 Number of successful extensions: 5 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: 404 Length of database: 434 Length adjustment: 32 Effective length of query: 372 Effective length of database: 402 Effective search space: 149544 Effective search space used: 149544 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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