Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 173 bits (438), Expect = 9e-48 Identities = 122/395 (30%), Positives = 189/395 (47%), Gaps = 26/395 (6%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 A R++ I ++++ RA ++ +G+ +I + GEPDF TPE + AA + + G Y Sbjct: 5 APRLADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFY 64 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T G PEL++AI +++ G+A I + GA L A+ PG E ++ P Sbjct: 65 TPALGLPELREAISGFYRQRYGIAVPASRIAITAGASGALTLALACLAAPGSEWLLTDPG 124 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 + V EG PV I A+S F+ T LE RT L SP+NP+G AA Sbjct: 125 YPCNRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAA 184 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + + + +R L++D++Y + Y+G P L G + V SK + MT Sbjct: 185 ELADIAD-FVRQRQGQLIIDEIYHGLTYNG---DAPTALAAG--DNIFVVQSFSKYFQMT 238 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQD--FLKERTESFQRRR 312 GWR+G+ P ++ + + S+ +Q A++AA P+ L++R F+ RR Sbjct: 239 GWRLGWLVIPEPFVRDVEKLAQNLFISASTPAQHAALAAFQ-PETIALLEQRRAEFKARR 297 Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTD--FCAYLLEDAHV 370 D + L AI PEGAFY ++ C+ + TD F LLE+A V Sbjct: 298 DYLAPALEAIGFRITAQPEGAFYLYADCSTL------------TDDSFGFARRLLEEAGV 345 Query: 371 AVVPGSAF---GLSPFFRISYATSEAELKEALERI 402 A+ PG F G S R +Y ++A L E +ERI Sbjct: 346 AITPGIDFGNHGASSHVRFAYTNAQARLAEGVERI 380 Lambda K H 0.318 0.134 0.393 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: 407 Number of extensions: 23 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: 410 Length of database: 385 Length adjustment: 31 Effective length of query: 379 Effective length of database: 354 Effective search space: 134166 Effective search space used: 134166 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