Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AO353_26890 AO353_26890 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26890 Length = 395 Score = 186 bits (471), Expect = 1e-51 Identities = 109/354 (30%), Positives = 188/354 (53%), Gaps = 5/354 (1%) Query: 26 QHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFN 85 Q DV+ L++G PDF TP + AA ++ T Y+ G LR ++ +++ Sbjct: 30 QGVDVLLLSVGDPDFDTPKPIVQAAIDSLLAGDTHYSEVRGTRSLRTSIARRHTRRSGQV 89 Query: 86 YDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPV-IVDTTS 144 DA+ +++ GA A+ + + +L PGDEV++ P+Y YE + CGAK V I Sbjct: 90 VDAD-HVLVLPGAQCAVYSVVQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPIAVRPE 148 Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204 +GF++ I +TP T+ ++L P+NP+G +LS +++A L +++++SDE+YS Sbjct: 149 NGFRVDPTDIAARITPRTRAILLNSPNNPSGASLSLAIWQALARLCVKHDLWLISDEVYS 208 Query: 205 ELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVS 262 EL Y+ H S A+ + ++T +N LSKSH+MTGWR+G++ PK + +H+ + + Sbjct: 209 ELLYEGEHISPASLPGMAERTATVNSLSKSHAMTGWRVGWVIGPKRLTEHLENLSLCMLF 268 Query: 263 CASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSI 321 Q AA A+ + +MR +Y+ R D V RL G+ V P G ++ + Sbjct: 269 GIPDFVQNAARVALEADLPELALMRNEYRARRDLVCARLGDCPGISPVIPDGGMFVMVDV 328 Query: 322 KSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375 + G+ + F+ LLE V+++ G +F G++R+ L E R+ Sbjct: 329 RQTGVGAQAFAEKLLEGYAVSVLAGEAFGPSAAGHIRIGLVLDQQRLAEACRRI 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: 13 Number of successful extensions: 6 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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