Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 184 bits (468), Expect = 3e-51 Identities = 132/408 (32%), Positives = 204/408 (50%), Gaps = 41/408 (10%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAAP 73 + G A ++ DG+RY+DF G+ V LGHC+P +V+A+ AQA ++ H + + A Sbjct: 9 LAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTSNLYRVAG 68 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127 A + V S+ NSGAEA E ++K+AR G + II +G Sbjct: 69 QESVAA------KLVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEG 122 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGRTLAT+ G+ + + G H+PY + + AL+A Sbjct: 123 AFHGRTLATVAAGGQKKHLEGFAPAVDG-FDHVPYGNLN-------ALRAS--------I 166 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 E+ AA + EPVQGEGG + DP + + LR DE G+L+I DE+Q+G GRTG FA + Sbjct: 167 TEETAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQ 226 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307 GI PD++ +AK + GG P+GA + + + + G G T+ GNP++ A A L M Sbjct: 227 AGIAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMA 286 Query: 308 DENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367 + + + S+ E A+ + + G+G M GI+ P +A++ Sbjct: 287 EPGFLEHVQAMAALLRSKVED-TAARFPGVVEEVRGLGLMLGIK----PRMPNTEMVARL 341 Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 E GLL + +G +I+RLL PL I ++E + IL + E+ Sbjct: 342 AEG----GLLTVGAGD--NIVRLLPPLIINDAQVDEAVGILARAFDEV 383 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: 434 Number of extensions: 18 Number of successful extensions: 4 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: 384 Length adjustment: 31 Effective length of query: 385 Effective length of database: 353 Effective search space: 135905 Effective search space used: 135905 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