Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate 16397 b2290 aspartate aminotransferase (NCBI)
Query= curated2:P63499 (429 letters) >FitnessBrowser__Keio:16397 Length = 405 Score = 523 bits (1348), Expect = e-153 Identities = 239/400 (59%), Positives = 319/400 (79%), Gaps = 1/400 (0%) Query: 30 QSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYA 89 +S+KL++V Y+IRGPV + A RLE EG+++LKLNIGNPAPFGF+APD I+ D+I+ LP A Sbjct: 6 KSSKLENVCYDIRGPVLKEAKRLEEEGNKVLKLNIGNPAPFGFDAPDEILVDVIRNLPTA 65 Query: 90 QGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLI 149 QGY DS+G+ SAR+A++ Y+ G V+D+Y+GNGVSELI +QALL++GD++L+ Sbjct: 66 QGYCDSKGLYSARKAIMQHYQ-ARGMRDVTVEDIYIGNGVSELIVQAMQALLNSGDEMLV 124 Query: 150 PSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAV 209 P+PDYPLWTA+ SL+ G VHYLCDE+ W PD+ D+ +KIT RT+ +V+INPNNPTGAV Sbjct: 125 PAPDYPLWTAAVSLSSGKAVHYLCDESSDWFPDLDDIRAKITPRTRGIVIINPNNPTGAV 184 Query: 210 YSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRV 269 YS E+L ++V++AR+H L++ ADEIYDKILYDDA+H S+A +APD+L +TFNGLSK YRV Sbjct: 185 YSKELLMEIVEIARQHNLIIFADEIYDKILYDDAEHHSIAPLAPDLLTITFNGLSKTYRV 244 Query: 270 AGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGG 329 AG+R GW+ + GPK+HA +IEG+ +LA+MRLC NVPAQHAIQ ALGG+QSI + + PGG Sbjct: 245 AGFRQGWMVLNGPKKHAKGYIEGLEMLASMRLCANVPAQHAIQTALGGYQSISEFITPGG 304 Query: 330 RLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVT 389 RL EQR+ AW +N+IPGVSCVKP GALY FP++D + ++I DD+++VLD LL EK+L+ Sbjct: 305 RLYEQRNRAWELINDIPGVSCVKPRGALYMFPKIDAKRFNIHDDQKMVLDFLLQEKVLLV 364 Query: 390 QGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 QGT FNWP PDH R+VTLP D+ ++ + FL Y Q Sbjct: 365 QGTAFNWPWPDHFRIVTLPRVDDIELSLSKFARFLSGYHQ 404 Lambda K H 0.320 0.138 0.419 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: 604 Number of extensions: 19 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: 429 Length of database: 405 Length adjustment: 31 Effective length of query: 398 Effective length of database: 374 Effective search space: 148852 Effective search space used: 148852 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 Aug 03 2021. The underlying query database was built on Aug 03 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