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_013403486.1 CALHY_RS08135 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000166355.1:WP_013403486.1 Length = 397 Score = 298 bits (764), Expect = 1e-85 Identities = 158/396 (39%), Positives = 239/396 (60%), Gaps = 2/396 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R +I S L I + A +K G+ VI GAGEPDFDTP+++K AA AI +G TKY Sbjct: 4 SQRALNISASPTLAIDSLAKKLKEAGENVIGFGAGEPDFDTPDNIKYAAISAIVKGYTKY 63 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T + G LK+AI + ++ + Y DE+ V+ GAK L N A L+ GDEV++P+PY Sbjct: 64 TPVAGISCLKEAIAKYYKENYEVDYSPDEVVVSNGAKHSLMNVFFALLNDGDEVLLPSPY 123 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W +Y +++ + GK V++ +++T LE T +T+ ++LNSPSNP+G Y+ Sbjct: 124 WVTYPELIKLAGGKVVVVPTTKEKNYKITLSDLEKYTTSKTKAIVLNSPSNPTGMVYTYE 183 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + + ++E + ++++ D++Y+ ++YDG + ++ A + K + VNGVSK+YAMT Sbjct: 184 ELKQIVEFCIER-EIFIVSDEIYDKLIYDGKKHISAASINEKAKEFVIVVNGVSKSYAMT 242 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGY +E K M+ +QS TS P+SI+Q A+ AL GPQD +K+ F++RRDL Sbjct: 243 GWRIGYTLSNKEFTKIMSNLQSHTTSNPNSIAQYAAYEALVGPQDSVKKMICEFEKRRDL 302 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 + + +N L PEGAFY + + +GK + GK I + F LLE VAVVP Sbjct: 303 IYSLVNDTKFLSALKPEGAFYIWVDISAAVGK-SFEGKLIDSANTFAKLLLEVEKVAVVP 361 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410 FG+ R+SYATSE ++E LERI ++LS Sbjct: 362 SEGFGMENHIRLSYATSEKNIREGLERIKRFVEKLS 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: 391 Number of extensions: 20 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 24 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