Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_012968507.1 KVAR_RS15690 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000025465.1:WP_012968507.1 Length = 402 Score = 388 bits (996), Expect = e-112 Identities = 195/397 (49%), Positives = 265/397 (66%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 Q A R+ S+ S I + A++ GKPVI LG GE DF TP H+ A +AI +T Sbjct: 5 QIARRMQSVRPSPTAVISDQVRALEAAGKPVINLGEGELDFATPAHISYAGIEAIVHHQT 64 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132 KYTA+ GT LK+AI KF R+N L Y EI +GAKQ++FNA +A+LD G +VIIP Sbjct: 65 KYTAVSGTAALKEAIAAKFARDNQLHYRPQEIIAGSGAKQLIFNAFLATLDAGQQVIIPA 124 Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192 PYW SY D+V + +G+PV++ CD +G++LT E+L A+TP TRW++LNSP NP+GA YS Sbjct: 125 PYWVSYPDMVSLADGEPVIVPCDEQNGWKLTPEQLATALTPSTRWLILNSPGNPTGAIYS 184 Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252 + R L VL +P V ++ DD+YE + YD F T AQ P + +RTLTVNGVSK++A Sbjct: 185 EQELRALAAVLADYPQVLVMADDIYEPLRYDNIPFTTFAQAAPQMVSRTLTVNGVSKSHA 244 Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312 MTGWR+GYAGGP+ LI AM ++QSQ+TS PSSISQAA+VAALN +F +RR Sbjct: 245 MTGWRLGYAGGPQWLIAAMQILQSQSTSNPSSISQAAAVAALNHSANFFDGWLNVLDKRR 304 Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372 V+ + A DGL P+GAFY F+ C ++G++TP G+ ++ D+ +LLE VAV Sbjct: 305 QQVLGMIAATDGLSATAPQGAFYVFANCQALMGRMTPGGEILRNDSALANWLLEQTQVAV 364 Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409 + GSAFG+ + RI+YA + L +A +RIA AC +L Sbjct: 365 LHGSAFGMPGYLRIAYAIEDGLLTQACQRIAGACAQL 401 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: 481 Number of extensions: 14 Number of successful extensions: 1 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: 402 Length adjustment: 31 Effective length of query: 379 Effective length of database: 371 Effective search space: 140609 Effective search space used: 140609 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 10 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