Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__psRCH2:GFF1235 Length = 382 Score = 166 bits (419), Expect = 1e-45 Identities = 106/360 (29%), Positives = 178/360 (49%), Gaps = 8/360 (2%) Query: 24 VAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKAD 83 +A ++L+ G PDF P ++ A + Y P G LR+ V + Sbjct: 20 LAADTGALNLSQGFPDFDGPEALREAVAGHVMAGHNQYAPMTGLPALREQVAAKVAGLYG 79 Query: 84 FNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTT 143 + DA +E+ IT GA+QAI A + ++ PGDEVI+ P Y YEP + L G + + Sbjct: 80 RDVDAAAEVTITPGATQAIFCAIQAVIRPGDEVIVFDPCYDSYEPSVQLAGGVCIHQQLS 139 Query: 144 SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIY 203 F++ + + DA+TP T+ +VL P NP+G + ++L +AAL++ R++++LSDE+Y Sbjct: 140 LPDFRIDWQRLADAITPRTRMIVLNTPHNPSGALIDADDLDRLAALIRERDIYLLSDEVY 199 Query: 204 SELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYN 260 L +D R H S+ + L + VI+ K++ +TGW+ G++ AP ++ + KVHQY Sbjct: 200 EHLVFDGREHASVLRHDELYQRAFVISSFGKTYHVTGWKTGYVVAPPMLSVELRKVHQYV 259 Query: 261 VSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPS 320 + Q A + + + + Y+ + D D L + +G ++ Sbjct: 260 SFTGVTPLQWALADFMAAHPEHLAELPAFYQAKRDLFCDLLAGSRFSFTRAAGTYFQLAD 319 Query: 321 IKSFGMTSFDFSMA--LLEDAGVALVPGSSFSTYGEG---YVRLSFACSMDTLREGLDRL 375 + D +MA L + GVA +P S F + VR FA +TLR+ +RL Sbjct: 320 YSAIRPDLDDVAMAEWLTREHGVACIPISVFYQHPPANLRLVRFCFAKREETLRQAAERL 379 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: 349 Number of extensions: 19 Number of successful extensions: 2 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 Aug 03 2021. The underlying query database was built on Aug 03 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