Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AO356_24005 AO356_24005 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24005 Length = 403 Score = 193 bits (490), Expect = 8e-54 Identities = 127/363 (34%), Positives = 193/363 (53%), Gaps = 19/363 (5%) Query: 29 DVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYDA 88 D++ LT G+PDF TP H+K AA AI T YTP G LR AVQ ++ + +Y Sbjct: 33 DILDLTTGEPDFDTPAHIKQAAYAAIAAGATKYTPTPGVKALRVAVQRKLRTENQLDYPL 92 Query: 89 ESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSHGF 147 S I+I GA Q I AF L GDEV++P P +P + + G +PV ++ G Sbjct: 93 AS-IVIANGAKQIIFNAFAATLDDGDEVLVPTPYWPSFPDSVRFNGGEPVFIECGLDQGC 151 Query: 148 KLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NVFVLSDEIYSEL 206 KLT R +E + T+ ++L P NP+G SE EL+ +A +L+ +V +L DE+Y + Sbjct: 152 KLTPRQLEQHIGERTRWLILNSPGNPSGAVYSEAELQGLAQVLRRHAHVLILLDELYEHI 211 Query: 207 TYD-RPHYS---IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVS 262 +D RP + +A L+ + +++ G+SK+++MTGWRIGF P+ + + V + S Sbjct: 212 RFDGRPSQNLLNVAPDLQSRCLLVGGVSKTYAMTGWRIGFGAGPQALTDAMTVVQSQSTS 271 Query: 263 CASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSI 321 ASS+ Q AAL A G D Y++R D + L ++ GL+V++P G F++F Sbjct: 272 GASSVGQAAALAAFEGGLDFLPEQVAAYRQRRDVLVSTLRNVEGLEVLEPHGGFFVFVCC 331 Query: 322 KS-FGMTSFDFS--------MALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGL 372 G D +A L D GVA V GS++ + RLS A + +T+ E Sbjct: 332 AGLLGRYRPDGQRLEHDADVVAYLLDEGVAGVAGSAYGL--SPWFRLSIATATETVAEAG 389 Query: 373 DRL 375 R+ Sbjct: 390 RRI 392 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: 337 Number of extensions: 18 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: 393 Length of database: 403 Length adjustment: 31 Effective length of query: 362 Effective length of database: 372 Effective search space: 134664 Effective search space used: 134664 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