Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate BPHYT_RS06770 BPHYT_RS06770 aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >FitnessBrowser__BFirm:BPHYT_RS06770 Length = 390 Score = 171 bits (434), Expect = 3e-47 Identities = 115/374 (30%), Positives = 192/374 (51%), Gaps = 20/374 (5%) Query: 27 AEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGFTKYTAVGGTASLKQAIISKFKRENSL 86 A K + LG G PDF+ I DA A+R+G +Y +GG A L+QAI K + Sbjct: 32 AAEKGAVNLGQGFPDFNCDPRIVDAVANAMRDGHNQYPPMGGVAPLRQAISDKIESLYGR 91 Query: 87 EF-MPGEILVSSGGKQSFFNLVLATIDPGDEVIIPAPYWVSYPDIVLIAEGKPVFIDTGI 145 + EI V++G Q+ +L T+ PGDEVI+ P + SY + +A GKPVF+ Sbjct: 92 RYNATTEITVTAGATQALLTAILCTVHPGDEVIVVEPTYDSYLPSIELAGGKPVFVTLDA 151 Query: 146 EEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVYSLEELQALGAVLRKYPDILIATDDM 205 + + I D+L AITP+TR+ ++N+P NP+G+V+ ++++ L ++R ++LI +D++ Sbjct: 152 PD-YAIPFDKLAAAITPKTRLLLINTPHNPTGTVWRADDMRKLEEIVRG-TNVLILSDEV 209 Query: 206 YEHILLSGDGFVNILNACPDLKARTVVLNGVSKAYAMTGWRIGYCGGPAAIITAMENIQS 265 YEH++ G ++ P+L R+ V++ K Y +TGW++GY PAA+ + Sbjct: 210 YEHMVYDGAPHESVAR-YPELAQRSFVVSSFGKTYHVTGWKVGYVAAPAALTAEFRKVHQ 268 Query: 266 QSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRERNQFLTNALNSIAGIHCLLSEGAFYA 325 + N+ Q+ A D + + + ++++ F L + + L G ++ Sbjct: 269 FNVFTVNTPMQIGL-ADYMKDPAPYLDLPAFYQKKRDFFRAGLAN-SRFKLLPCTGTYFQ 326 Query: 326 FVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEVAAVPGSAFGCE----GYMRLSFATS 381 VD AIS L + F ++ + VAA+P SAF E G +R FA Sbjct: 327 CVDY-SAISDL---------PEAEFAQWLTGEIGVAAIPVSAFYHEAHESGVVRFCFAKQ 376 Query: 382 MDNLQEAVKRIASL 395 L A++R+A L Sbjct: 377 ESTLATALERLARL 390 Lambda K H 0.318 0.133 0.380 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: 322 Number of extensions: 19 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: 397 Length of database: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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