Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= curated2:Q30ZX9 (388 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 173 bits (438), Expect = 9e-48 Identities = 120/360 (33%), Positives = 179/360 (49%), Gaps = 9/360 (2%) Query: 31 RGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQYPSYTGMLAFRQEVANWYKRRYAV 90 RG D+I L +GDPD TP V +A A H Y G R +A RR + Sbjct: 30 RGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTH-YTPIPGRPELRAALARDVARRTGL 88 Query: 91 ELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCPPCYPVYAIASRFMGGVVQELPLLE 150 ++P+ V+ G++ G+ + V GD VLV P Y Y R G + +P+ Sbjct: 89 PVEPEN-VIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATL--VPVAP 145 Query: 151 ENDFLP-DLDAVDEATWEKARCIFVNYPNNPTAAMAPRSFFEKLIGIARKHNVIVVHDAA 209 + L D A+ A + R IF+ P NPT + E + +AR+H++ VV D Sbjct: 146 DAATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADEV 205 Query: 210 YTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNMTGWRIAMAVGNASLVAGLGKVKE 269 Y + ++ + + I +PG + + NSLSK + MTGWR V A LVA +G + Sbjct: 206 YASLTFDRPH--IGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263 Query: 270 NMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRDTVIAALNKI-GITCRVPEASLYV 328 M G VQ+AA+VA+ GD +A +R+ YR+RRD + AL + G+ C PEA +++ Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFM 323 Query: 329 WARV-PEGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGYFRISLTVNDERLEEAVSRIAS 387 V G + +F R+ +ETGV + FG A G R+S V++ L EA RIA+ Sbjct: 324 LVDVRGTGLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAEACRRIAA 383 Lambda K H 0.320 0.136 0.403 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: 400 Number of extensions: 25 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: 388 Length of database: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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