Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate RR42_RS02910 RR42_RS02910 2-aminoadipate aminotransferase
Query= reanno::acidovorax_3H11:Ac3H11_1015 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS02910 Length = 416 Score = 295 bits (755), Expect = 2e-84 Identities = 166/398 (41%), Positives = 230/398 (57%), Gaps = 9/398 (2%) Query: 3 FADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQ 62 FA + + S IRELF + P +ISFAGG+P A FD ++ A++ A+A LQ Sbjct: 10 FAPAMREPQGSPIRELFPYMSLPDMISFAGGYPSPASFDAAALQDAASKAMATNSAQCLQ 69 Query: 63 YGATEGYNPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGP 122 YG TEG LR+ L+A M +GA + + ++VT+GSQQ DLL + ++PG V VE P Sbjct: 70 YGPTEGMPALRQALSALMGERGAP-LPPEQVVVTSGSQQGFDLLVRAFVAPGTPVWVETP 128 Query: 123 TFLATIQCFRLYGAELISAPIDGNGVKTDELEKLIAE----HKPKFVYLIPTFGNPSGAM 178 T+ A +Q RL GA + + P D +G+ L ++A+ +P+ +YL+PTF NPSG Sbjct: 129 TYPAAVQALRLAGAAVRAIPSDQDGLCVQALAAMLADCPDAERPRLLYLVPTFANPSGRT 188 Query: 179 LSLERRKAVLEMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLS 238 L+L RR+AVL +A +H ++VEDDPYG L F P PSLL+L+A P +++ GS S Sbjct: 189 LALARRRAVLALAAQHRIVVVEDDPYGSLRFDGEPLPSLLSLAAQDPALTPWVIYLGSFS 248 Query: 239 KVLSPGLRVGWMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKV 298 K ++PGLR+GWM PAE+L +A + KQ D TS + Q A L+ G +P A + + Sbjct: 249 KTMAPGLRLGWMAGPAEILRRAVIAKQVCDLCTSPWLQLAMASCLEDGLLPRQTARIIDL 308 Query: 299 YAERAQAMGDALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFV 358 Y + M AL G A+ PQGG+F+W + G VAD L AI V +V Sbjct: 309 YRHKRDLMVRALADAFGPALRCEIPQGGMFLWCEIDG----VADAASLLPHAIAARVMYV 364 Query: 359 PGTPFFCANPDHATFRLSFATADVDKIREGVARLGQAV 396 PG F RLSFATA +I +GVARL QAV Sbjct: 365 PGASFGVDGQRSPALRLSFATASDAQIVQGVARLRQAV 402 Lambda K H 0.319 0.136 0.394 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: 477 Number of extensions: 25 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: 396 Length of database: 416 Length adjustment: 31 Effective length of query: 365 Effective length of database: 385 Effective search space: 140525 Effective search space used: 140525 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 (21.7 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