Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013643724.1 METBO_RS00600 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000191585.1:WP_013643724.1 Length = 390 Score = 196 bits (498), Expect = 1e-54 Identities = 133/389 (34%), Positives = 191/389 (49%), Gaps = 32/389 (8%) Query: 14 HPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAP 73 H I L G++ VWD DG YID V GI V N+GH NP V EAI Q +L H + N Sbjct: 21 HKIALVKGKDTTVWDADGNSYIDCVAGIAVNNVGHSNPKVGEAICNQVKKLIHTS-NLYY 79 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRT 133 + L + L V VS NSGAEA E A+K+AR +GK II FHGRT Sbjct: 80 TEEQVTLAKLL---VDVSPHQKAFFCNSGAEANEGAIKLARKHSGKGEIITMINSFHGRT 136 Query: 134 LATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAA 193 + T+ G+ K PG Y PY + A+K E+ AA Sbjct: 137 ITTITATGQPKYQKGFEPLTPGFKY-APYGDIE-------AVK--------EMISPSTAA 180 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 + EPVQGE G + + + L+ C++ +L+I DE+Q+GFGRTG+ FA G+ PD Sbjct: 181 VLVEPVQGESGVIVPPEGYLKQLKEVCEDSNVLLIFDEVQTGFGRTGEMFASQTFGVTPD 240 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313 + LAK+IAGG P+GAV+ ++ + G T+ GNP+ CAAA AS+ + +E L Sbjct: 241 ITSLAKAIAGGFPMGAVLANNDVAESFVPGDHAATFGGNPLGCAAAKASINFILEEKLLD 300 Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARA 373 + V + K I + G G M G+E G +++ Sbjct: 301 KSKENGSYFVEKL--LKLQNQHELINEVRGKGLMVGVEMKTDCGC--------MVDELFK 350 Query: 374 RGLLLMPSGKARHIIRLLAPLTIEAEVLE 402 G+++ + A +++R + PLTI E ++ Sbjct: 351 EGIIV--NCAAGNVLRFVPPLTITKEQID 377 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: 345 Number of extensions: 11 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 385 Effective length of database: 359 Effective search space: 138215 Effective search space used: 138215 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