Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate HSERO_RS15115 HSERO_RS15115 aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__HerbieS:HSERO_RS15115 Length = 385 Score = 172 bits (436), Expect = 1e-47 Identities = 109/362 (30%), Positives = 190/362 (52%), Gaps = 13/362 (3%) Query: 24 VAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKAD 83 +A + ++L G PDF + AA +A+ E + Y P AG LR+A+ ++K Sbjct: 24 LASEKGAVNLGQGFPDFHCDPALVAAVTQAMQEGLNQYPPMAGVPVLREAIAEKVEKLYG 83 Query: 84 FNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV--D 141 YD SEI +T GA+Q I + + PGDEVI+ P+Y Y P I L G PV V + Sbjct: 84 HRYDPVSEITVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCYVPAIELAGGVPVFVQME 143 Query: 142 TTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDE 201 + G+ + ++ A+TP T+ +++ P NPTG + ++ ++A +++G ++ +LSDE Sbjct: 144 VGAQGYSIPWDKVKAAVTPKTRMIMVNTPHNPTGSVMRAADVAALADIVRGTDILILSDE 203 Query: 202 IYSELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQ 258 +Y + YD +PH S+A + L +++ + + K++ +TGW++G++ AP + KVHQ Sbjct: 204 VYEHMVYDGQPHESLARHPELAERSFINSSFGKTYHVTGWKVGYVAAPAALTAEFRKVHQ 263 Query: 259 YNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIF 318 +NV ++ Q L A L + Y+ + D L + +++ G + F Sbjct: 264 FNVFTVNTPVQ-YGLAAYMKDPAPYLDLPAFYQHKRDLFRTGLANTRFELLPSQGTY--F 320 Query: 319 PSIKSFGMTSF---DFSMALLEDAGVALVPGSSF--STYGEGYVRLSFACSMDTLREGLD 373 +K +++ +F L + GVA +P S+F + G VR FA +TL+ L+ Sbjct: 321 QCVKYGAISALPEAEFCKWLTSEIGVAAIPVSAFYNTPRESGIVRFCFAKKDETLQLALE 380 Query: 374 RL 375 RL Sbjct: 381 RL 382 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: 321 Number of extensions: 21 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: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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 09 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