Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_044410795.1 NA59_RS08125 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000934765.1:WP_044410795.1 Length = 392 Score = 176 bits (446), Expect = 1e-48 Identities = 123/376 (32%), Positives = 191/376 (50%), Gaps = 33/376 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PIT G A ++D G+ Y+D V GI V +LGH +P + A+ Q+ +L H + Sbjct: 13 PITFVEGEGATLYDEQGRAYLDAVSGIAVCSLGHAHPEIAHALCEQSKKLIHTS------ 66 Query: 75 GPYLALMEQL--SQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFD 126 Y + +QL + + +S NSGAEA E A+K+AR G T I+ + Sbjct: 67 NLYHVVNQQLLADELIRLSGMDKVFFGNSGAEANEGAIKIARKYGNDQGKTNPE-ILVME 125 Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGRT+ATL+ G Q+V E +H P S V + ++ S Sbjct: 126 NSFHGRTMATLSATGS-----QKVQE----GFH-PLVSGFVRVPFDDIAAVEQKIASHP- 174 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 ++ A + EPVQGEGG + +ALR CD+ +L++IDEIQ+G GRTG+ FAF Sbjct: 175 ---NLVAILVEPVQGEGGVHVPKDGYLKALRALCDQHNLLLMIDEIQTGVGRTGKWFAFQ 231 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 I PD+L LAK++ G+P+GA + R + L G G T+ GNP++CAA LA + + Sbjct: 232 HEDILPDVLSLAKALGNGVPIGACLARGKAAEVLAPGNHGTTFGGNPLACAAGLAVIKTI 291 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366 N + +Q + ++S ++ + +G+ + ++ G G M GI+ G L K Sbjct: 292 EHHNFIDYVAKQGEIMISDFKA-RLAGIE-QVKQVRGKGYMIGIQLDRPCGELVKRALDK 349 Query: 367 --VMEAARARGLLLMP 380 ++ R + L+P Sbjct: 350 NLLINVTRGDTIRLLP 365 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: 13 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: 392 Length adjustment: 31 Effective length of query: 385 Effective length of database: 361 Effective search space: 138985 Effective search space used: 138985 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