Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_052665669.1 NITAL_RS08275 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000969705.1:WP_052665669.1 Length = 416 Score = 233 bits (593), Expect = 1e-65 Identities = 152/410 (37%), Positives = 212/410 (51%), Gaps = 41/410 (10%) Query: 12 ADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTS-NLFR 70 +D++ G G L+ DGRR+LDF AG+ V GH +P +V A Q ++ H R Sbjct: 10 SDVIAVGGSGAELFGHDGRRYLDFTAGIGVLSTGHGHPRVVAAAQEQIGRIVHAQYTTVR 69 Query: 71 VAGQESLAKRLTEATFA--DTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQA 128 L++RLTE A D FF ++G EA E +L+R+ R +I F+ Sbjct: 70 HQPLLELSERLTEVMPAGIDAFFFASAGTEAVEAALRLVRQA------TGRPNVIAFDGG 123 Query: 129 FHGRTLAAVSAAQQEKLIK-GFGPLLDGFDLVPF--------GDLEAVRNAVT------- 172 FHGRT+ A+S + ++ G PL+ G PF + EA R A+ Sbjct: 124 FHGRTMGALSMTTSKTALRSGLAPLMGGVHTAPFPTAHRYGWSEAEATRFALAELDHLLA 183 Query: 173 -----DETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLF 227 DETA I +EP+ GEGG FLRGLRE CD HG+LL +DEIQ G+GRTG+ + Sbjct: 184 THTAPDETAAIFVEPVLGEGGYVPAPDAFLRGLRERCDRHGMLLVIDEIQTGIGRTGRFW 243 Query: 228 AHEWAGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVL 287 H+ AGI PD++ AKG+ GFPL A + G+ G TYGGN ++ A A L Sbjct: 244 GHDHAGIVPDLVVSAKGLASGFPLSTFGAPAALMAQGRPGSQGGTYGGNAVSCAAALATL 303 Query: 288 DKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLAC--------GPAV 339 D V E G + + +G L D L + AV VRG+GLM+G+ G A Sbjct: 304 DVVAEEGLVARAEVLGDRLLDGLRRSTLDIDAV-GDVRGRGLMVGVELRDPEGAPDGAAA 362 Query: 340 GDVVVALRANGLLSVPAG--DNVVRLLPPLNIGEAEVEEAVAILAKTAKE 387 G V+ GLL + G VVRL+PPL + EA+V+ A+AI+ + ++ Sbjct: 363 GRVLKEAEQRGLLLLACGAYGQVVRLIPPLVVDEAQVDTAIAIVTEAIEK 412 Lambda K H 0.321 0.139 0.414 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: 487 Number of extensions: 30 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: 389 Length of database: 416 Length adjustment: 31 Effective length of query: 358 Effective length of database: 385 Effective search space: 137830 Effective search space used: 137830 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