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_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_900115975.1:WP_092483105.1 Length = 397 Score = 345 bits (885), Expect = 1e-99 Identities = 184/396 (46%), Positives = 253/396 (63%), Gaps = 2/396 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 A R +I S L I A+A M EG VI GAGEPDF TPE++KQA AI T+Y Sbjct: 4 AERAKNISPSPTLSIDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDMTRY 63 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T + G L++AI +K +NGL YE +I V+ GAK L+NA GDEVI+P PY Sbjct: 64 TPVAGIEPLRRAIVKKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILPAPY 123 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY + + + +PV+++ + F+LT ++L AITP TR ++LNSPSNP+GA Y+ Sbjct: 124 WVSYLEQIKLTGARPVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVYTGD 183 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + L E+L ++ + ++ D++YE ++YDG V+ A L PGLK T+ +NGVSK+YAMT Sbjct: 184 ELVALGEILEQN-KIAVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYAMT 242 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGYA P + KAMA +QS +TS P+SI+QAASV AL G Q+ +++ F +RRD Sbjct: 243 GWRIGYAAAPAPVAKAMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRRDY 302 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 +V LNA+ G++C P GAFY F +LGK + G +I + +D LLE AHVA+VP Sbjct: 303 MVERLNAMPGVNCNRPGGAFYVFPEIKPLLGK-SYEGVKIDSASDLAKVLLEKAHVAIVP 361 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410 G AFG FR+SYATS ++E L+RI +LS Sbjct: 362 GIAFGDDTCFRLSYATSMDNIREGLDRIEKVLQQLS 397 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: 450 Number of extensions: 26 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 Apr 09 2024. 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