Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_011612205.1 TERY_RS12675 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000014265.1:WP_011612205.1 Length = 423 Score = 203 bits (517), Expect = 7e-57 Identities = 131/408 (32%), Positives = 212/408 (51%), Gaps = 34/408 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PI + G VWDT+GK Y+DFV GI LGH +P ++ + Q RL H + + Sbjct: 37 PIAIERGEGCRVWDTEGKEYLDFVAGIATCTLGHAHPVMMATVSEQIKRLHHVS-----N 91 Query: 75 GPYLALMEQLSQFVPVSYPLA--GMLTNSGAEAAENALKVARGATGKR------AIIAFD 126 Y+ + +L+Q++ + + A NSGAEA E A+K+AR ++ I+ Sbjct: 92 LYYIPVQGELAQWL-IQHSCADKAFFCNSGAEANEGAIKLARKYAHEKLNIENPTILTAH 150 Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGRTLAT+ G+ +K +PG Y++PY E A++ +D+ Sbjct: 151 ASFHGRTLATMTATGQPKYHKGFSPLMPG-FYYVPYNDI---AAIESAIEELDK------ 200 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 VAA + E +QGEGG D + + +R C+E+GIL+I+DE+Q+G GR+G+ + + Sbjct: 201 DKRQVAAIMLEALQGEGGIRPGDMTYFKRIREICNEKGILLILDEVQAGMGRSGKIWGYE 260 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 LGIEPD+ AK + GG+P+GA++ + P G T+ GNP +CA ALA + Sbjct: 261 NLGIEPDIFTSAKGLGGGIPIGAMLCKSHCDVFEP-GSHASTFGGNPFACAVALAVCHTL 319 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYI-GRLTGVGAMRGIEFANADGSPAPAQLA 365 ENL Q++ R E + P + + G G + G+E + A Sbjct: 320 EQENLL--ANVQQRGDELRIELKAIADKYPNLFSEVRGWGLINGLEL----NATATLTSI 373 Query: 366 KVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLA 413 +++AA GLL++P+G ++R + PL + ++E +D+L + +A Sbjct: 374 DIVKAAMNEGLLIVPAGP--KVLRFVPPLIVTETEVKEAMDLLAKAIA 419 Lambda K H 0.320 0.137 0.402 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: 385 Number of extensions: 17 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: 416 Length of database: 423 Length adjustment: 32 Effective length of query: 384 Effective length of database: 391 Effective search space: 150144 Effective search space used: 150144 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