Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 174 bits (440), Expect = 5e-48 Identities = 113/363 (31%), Positives = 183/363 (50%), Gaps = 8/363 (2%) Query: 21 SNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKK 80 S L A+H ++L G PDF P + A A+ + + Y P G LRQA+ Sbjct: 19 SQLAAEH-GAVNLGQGFPDFSAPQRLIDATTAAMADGLNQYPPMTGVAPLRQAIAQKSLD 77 Query: 81 KADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV 140 D ++EI +T+GA++AI A ++ G+EVI+ P Y YEP I+L GA+ V V Sbjct: 78 LYGAQVDPDTEITVTSGATEAIFNAIHAVVRAGEEVIVLDPAYDCYEPAIDLAGARAVHV 137 Query: 141 DTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSD 200 F + + A+TP T+ +++ P NP+G L+E +L+++A LL+G +++++SD Sbjct: 138 PLDPQTFAVDWDRVRAAITPRTRLLMVNTPHNPSGAMLAEADLQALADLLRGTDIYLISD 197 Query: 201 EIYSELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVH 257 E+Y + YD R H S + LR + VI+ K++ TGW+IG+ AP ++ KVH Sbjct: 198 EVYEHIIYDGRRHESALRHPELRARAFVISSFGKTYHCTGWKIGYAIAPPALSAEFRKVH 257 Query: 258 QYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGL-DVVKPSGAFY 316 QYN + +Q + + L + Y+ + D ++L L + P G F Sbjct: 258 QYNTFTSFGPAQYGFAAMIRDEPQHHLELGAFYQAKRDRFREQLAQTRLVPLAVPGGYFQ 317 Query: 317 IFPSIKSFGMTSFDFSMALLEDAGVALVPGSSF---STYGEGYVRLSFACSMDTLREGLD 373 + + +F L + GVA +P S F G+ VRL FA + TL ++ Sbjct: 318 LVDYSAISDLPDHEFVKWLTIEKGVAAIPLSPFYEAPPVGQRIVRLCFAKNEATLDAAIE 377 Query: 374 RLE 376 RL+ Sbjct: 378 RLQ 380 Lambda K H 0.319 0.135 0.388 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: 295 Number of extensions: 14 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: 393 Length of database: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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: 50 (23.9 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