Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Keio:16484 Length = 412 Score = 153 bits (386), Expect = 1e-41 Identities = 104/353 (29%), Positives = 167/353 (47%), Gaps = 9/353 (2%) Query: 28 EDVISLTIGQPDFFTPHH-VKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNY 86 ED+I ++G PD TP H V+ A + Y+ + G LR+A+ + + + D Sbjct: 36 EDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYSTSRGIPRLRRAISRWYQDRYDVEI 95 Query: 87 DAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPG--YEPIINLCGAKPVIVDTTS 144 D ESE I+T G+ + + L GD V++P P YP Y +I + V + Sbjct: 96 DPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPSYPIHIYGAVIAGAQVRSVPLVEGV 155 Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204 F R I ++ P K ++L +PSNPT + E + + AL K +V V+ D Y+ Sbjct: 156 DFFNELERAIRESY-PKPKMMILGFPSNPTAQCVELEFFEKVVALAKRYDVLVVHDLAYA 214 Query: 205 ELTYD---RPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNV 261 ++ YD P RD + LSKS++M GWRIGF+ K + + ++ Y+ Sbjct: 215 DIVYDGWKAPSIMQVPGARDVAVEFFTLSKSYNMAGWRIGFMVGNKTLVSALARIKSYHD 274 Query: 262 SCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPSI 321 + Q AA+ A+ + EQYK+R D + L G V P + Y++ I Sbjct: 275 YGTFTPLQVAAIAALEGDQQCVRDIAEQYKRRRDVLVKGLHEAGWMVEMPKASMYVWAKI 334 Query: 322 KS--FGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGL 372 M S +F+ LL +A V + PG F YG+ +VR + + D +R+ + Sbjct: 335 PEPYAAMGSLEFAKKLLNEAKVCVSPGIGFGDYGDTHVRFALIENRDRIRQAI 387 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: 344 Number of extensions: 13 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: 412 Length adjustment: 31 Effective length of query: 362 Effective length of database: 381 Effective search space: 137922 Effective search space used: 137922 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