Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >FitnessBrowser__Marino:GFF1405 Length = 394 Score = 515 bits (1327), Expect = e-151 Identities = 261/396 (65%), Positives = 317/396 (80%), Gaps = 5/396 (1%) Query: 1 MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60 ++LS RVQAIKPSPTLAVT KAA L+A G++IIGLGAGEPDFDTP HIK AAI AI NG Sbjct: 3 LQLSSRVQAIKPSPTLAVTNKAAELRAAGQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQ 62 Query: 61 TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120 TKYTAV GT +LK+AII+KFKR+N L++ +ILVSSGGKQSFFNL LAT++PGDE IIP Sbjct: 63 TKYTAVDGTPALKKAIIAKFKRDNGLDYEANQILVSSGGKQSFFNLALATLNPGDEAIIP 122 Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180 APYWVSYPD+VL+AEGKPV I+TG E +FKI+P+QLE AIT RTR+FV+NSPSNPSG Y Sbjct: 123 APYWVSYPDMVLVAEGKPVIIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGMAY 182 Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240 +LEELQA+G VL+K+P+I+IATDDMYE IL +G F NILNA P+L RT VLNGVSKAY Sbjct: 183 TLEELQAIGEVLKKHPNIMIATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSKAY 242 Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300 +MTGWRIGY GPA II AM+ IQSQSTSNP SI+Q AA+AAL+GDQ C+ M++AF+ER Sbjct: 243 SMTGWRIGYAAGPAKIIGAMKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFKER 302 Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360 + +L ALN + G+ CL +G FY F + AI ++ S+D+ F +L A V Sbjct: 303 HDWLVEALNKLPGVECLNGDGTFYVFPSFQGAIDADSSV-----STDVEFAEKLLTDAGV 357 Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRIASLL 396 A VPGSAFGC G+MRLSFATSM+NL++AV+R+ L Sbjct: 358 ALVPGSAFGCPGHMRLSFATSMENLEKAVERLQKAL 393 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: 439 Number of extensions: 9 Number of successful extensions: 2 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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