Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_012991515.1 THAL_RS02360 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000025605.1:WP_012991515.1 Length = 371 Score = 173 bits (438), Expect = 8e-48 Identities = 114/357 (31%), Positives = 183/357 (51%), Gaps = 13/357 (3%) Query: 28 EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87 EDV+ + IG+PD P V ++AI E YT + G ELRQ + + + Sbjct: 23 EDVVHMEIGEPDLDPPPGVWEHLERAIKERKYFYTASVGIEELRQKIAEHYWTYYGVDIS 82 Query: 88 AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHG- 146 E ++ITTG+S A + ILS GD + + P YP Y+ +L P+++ Sbjct: 83 PE-RVVITTGSSGAFLVVYSIILSAGDSIAIADPSYPCYKNFAHLLDINPILIPVGPETH 141 Query: 147 FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSEL 206 +++T ++E N K V + PSNPTG E+ L+S+ + + ++++SDEIY L Sbjct: 142 YQITPPMLEGL---NIKAVHISSPSNPTGTFYREDTLRSLCSYCDEKGIYLISDEIYHGL 198 Query: 207 TYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASS 266 Y+ +++ + ++ IV+NG SK M G+R+G++ P D+ + V Q A S Sbjct: 199 VYEGREHTVLEF-SERAIVVNGFSKFFCMPGFRLGWIILPPDLVRKAQIVLQNVFISAPS 257 Query: 267 ISQKAALEAVTNGFDDALI--MREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPSIKSF 324 +SQ AAL A FD + +RE Y++R D +Y L + P G FYI+ + + Sbjct: 258 LSQYAALGA----FDYKYLQKVREIYRERRDVLYRELKDVFNIPCPPEGGFYIWADVSRY 313 Query: 325 GMTSFDFSMALLEDAGVALVPGSSFS-TYGEGYVRLSFACSMDTLREGLDRLELFVL 380 S+ F M LLE A VA+ PG F Y+RL++ TL EG R++ +++ Sbjct: 314 TENSYQFCMDLLEKAKVAVTPGIDFGYNRTNTYIRLAYTKDKGTLLEGARRIKSYLM 370 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: 332 Number of extensions: 10 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: 393 Length of database: 371 Length adjustment: 30 Effective length of query: 363 Effective length of database: 341 Effective search space: 123783 Effective search space used: 123783 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 Jul 25 2024. The underlying query database was built on Jul 25 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