Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_005457886.1 SACCYDRAFT_RS16640 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000244975.1:WP_005457886.1 Length = 395 Score = 202 bits (514), Expect = 1e-56 Identities = 138/387 (35%), Positives = 195/387 (50%), Gaps = 38/387 (9%) Query: 16 ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75 + L G A VWD DG+RY+DFV GI V LGH +PAVV A+ Q + H + N + Sbjct: 23 VNLVRGEGAVVWDADGRRYLDFVTGIAVNALGHAHPAVVSAVTRQIATIGHTS-NLYLNE 81 Query: 76 PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLA 135 P L L E+L + + NSGAEA E A K+AR TG+ ++A +GGFHGRT+ Sbjct: 82 PALTLAERLLELSGAGDGKV-LFCNSGAEAVEAAFKLAR-RTGRSTVVATEGGFHGRTMG 139 Query: 136 TLNLNG---KVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVA 192 L L G K AP++ V PG V H+P+ + A++R D A Sbjct: 140 ALALTGQPAKRAPFEPLV---PG-VRHVPFGD----------VPALERAID-----SDTA 180 Query: 193 AFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEP 252 AF+ EPVQGE G + + +A R G+L+++DE+Q+G GR G FA+ + GI+P Sbjct: 181 AFVVEPVQGENGVVVPGDDYLRAAREITRRHGVLLVVDEVQTGVGRLGSWFAYQQTGIQP 240 Query: 253 DLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLA 312 D++ LAK + GG+PLGA + E G G T+ GNP+ CAA LA L + L Sbjct: 241 DVVTLAKGLGGGLPLGACLAFGEAATLFEPGQHGTTFGGNPVCCAAGLAVLDTIAANGLL 300 Query: 313 TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAAR 372 + I + ER P + + G G + G+ +A A V AA+ Sbjct: 301 EHTAALGKEISAGLERLD----HPLVRTVRGAGLLLGVVLNSAVS-------AGVAAAAQ 349 Query: 373 ARGLLLMPSGKARHIIRLLAPLTIEAE 399 G L+ P ++RL PL + E Sbjct: 350 RAGFLVNP--VQPDVVRLAPPLVVSQE 374 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: 480 Number of extensions: 23 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: 395 Length adjustment: 31 Effective length of query: 385 Effective length of database: 364 Effective search space: 140140 Effective search space used: 140140 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