Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_011372884.1 SUDEN_RS06570 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000012965.1:WP_011372884.1 Length = 394 Score = 167 bits (423), Expect = 5e-46 Identities = 126/404 (31%), Positives = 193/404 (47%), Gaps = 44/404 (10%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAAPHGPYL 78 G NA V D +GK+YIDF GI V ++GH N V +AI Q + +TH + + AP Sbjct: 26 GNNAIVVDANGKKYIDFASGIAVCSVGHANKRVNDAICKQLSNITHTSNLYYIAPQAKAA 85 Query: 79 ALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGR 132 + + S Y + NSGAEA E A+K+AR G + +I FHGR Sbjct: 86 QKIVEAS-----GYDMKCFFGNSGAEANEGAIKIARKFGEKDGELKRYKVITLQHSFHGR 140 Query: 133 TLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-V 191 T+ T+ G+ + Y PYP D + V V+D Sbjct: 141 TITTVKATGQEKMHN----------YFGPYPDG---------FVYADNIDHVASLVDDHT 181 Query: 192 AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIE 251 A + E VQGEGG LD Q L +F E+ +L+IIDE+Q+G RTG+ A I+ Sbjct: 182 CAVMIELVQGEGGVQPLDRDSVQKLAKFLKEKNVLLIIDEVQTGIYRTGKFLASNYYDIK 241 Query: 252 PDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENL 311 PD++ LAK + GG+P+G V+ L G G T+ GN +S AA + + + N Sbjct: 242 PDVVTLAKGLGGGVPIGVVM--TTLKDVFGAGDHGSTFGGNFLSTTAACEVVDILNEMNE 299 Query: 312 ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAA 371 + ++ S E++ + + ++ G+G M G+ + D L K++ A Sbjct: 300 SGELQKGIDYFDSELEKFYNAHRDIFTSKV-GIGMMCGLRVKDGD------TLTKIISNA 352 Query: 372 RARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 R G++++ +G R +RLL LTI E ++EG L + ++ L Sbjct: 353 REEGVIVLKAG--RDTLRLLPALTITKEEIDEGFTSLNRTISSL 394 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: 346 Number of extensions: 15 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: 416 Length of database: 394 Length adjustment: 31 Effective length of query: 385 Effective length of database: 363 Effective search space: 139755 Effective search space used: 139755 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