Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 342 bits (876), Expect = 2e-98 Identities = 178/397 (44%), Positives = 259/397 (65%), Gaps = 3/397 (0%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 Q + R++S+ S L + ++ +K +G VI L GEPDF+TP+H+K+AA AI + Sbjct: 3 QLSDRLNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFS 62 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132 +Y+ + G P L+ AI EK ++ENGL Y +I+ A GAKQ + NA++ ++PGDEVI+P Sbjct: 63 RYSPVPGYPALRNAIVEKLKKENGLEYTAAQISCANGAKQSVCNAILVLVNPGDEVIVPA 122 Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192 PYW SY ++V + EG PV+++ F++T ++LEAAITP+T+ ++L SPSNP+G+ YS Sbjct: 123 PYWVSYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYS 182 Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252 + L VL ++P V ++ D++YEHI Y G + AQ P +K RT+ VNGVSKAYA Sbjct: 183 KEELAGLAAVLAKYPQVVVIADEIYEHINYIG-AHQSIAQF-PEMKERTVIVNGVSKAYA 240 Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312 MTGWRIG+ GP ++KA +Q Q TS P S+SQ A+ AA G Q+ +KE ++F+RRR Sbjct: 241 MTGWRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEPVKEMQKAFERRR 300 Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372 DL+V + G + VP+GAFY F C+ GK + ++I+ D YLLEDAHVA Sbjct: 301 DLIVKLAKEVPGFEVNVPQGAFYLFPKCSYFFGK-SNGERKIENSDDLAMYLLEDAHVAC 359 Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409 V G++FG R+SYATS+ + EA+ RI A +L Sbjct: 360 VGGTSFGAPECIRMSYATSDENIVEAIRRIKEALAKL 396 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: 448 Number of extensions: 19 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 379 Effective length of database: 366 Effective search space: 138714 Effective search space used: 138714 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