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_084056111.1 B9A12_RS02895 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_900176285.1:WP_084056111.1 Length = 398 Score = 363 bits (931), Expect = e-105 Identities = 186/397 (46%), Positives = 259/397 (65%), Gaps = 3/397 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R+S + S L I A+A A++ +GK VI G GEPDFDTP H+ QAA A+ RG+T+Y Sbjct: 4 SQRVSQVQPSATLSINAKAKALRAQGKKVISFGVGEPDFDTPHHIGQAAIQAVQRGQTRY 63 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 TA+ G PELK+AI + + + GL Y +E+ V+ G K L+N A LDPGD+VIIP PY Sbjct: 64 TAVQGIPELKEAIIDVVRADYGLDYSPEEVLVSCGGKHSLYNLFQAVLDPGDQVIIPAPY 123 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY D+V + +PV++ C S+ F+L + L AIT RTR ++LNSPSNP+G Y+ Sbjct: 124 WVSYPDMVRLAGAEPVIVDCPMSTSFKLEPQALREAITERTRMLILNSPSNPTGVHYTPE 183 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + R L +VLL H V ++ DD+Y ++Y G ++ A +EP LK+RT VNGVSK YAMT Sbjct: 184 ELRGLAQVLLDHEQVVIVSDDIYYRLLYKGAQWANMAMVEPRLKDRTFIVNGVSKTYAMT 243 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGY G ++IKA +QSQ+TS P S++Q A+VAAL G Q+ ++ ++F RRR+ Sbjct: 244 GWRIGYLLGDADVIKAAGKIQSQSTSNPCSVAQWAAVAALRGSQEDVQTMRQAFARRREY 303 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKR-IKTDTDFCAYLLEDAHVAVV 373 V+ L + G+ C P GAFY F + GK +G+R I+ D YL+E+AH+AVV Sbjct: 304 VMERLGRLPGVTCPDPNGAFYVFPNVSAYYGK--KAGERSIQGSLDLSDYLMEEAHLAVV 361 Query: 374 PGSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410 PG+AFG R+S+A S EL+E +R+ A RLS Sbjct: 362 PGAAFGEDRCIRLSFALSMEELEEGFDRLEKALGRLS 398 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: 430 Number of extensions: 22 Number of successful extensions: 2 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: 398 Length adjustment: 31 Effective length of query: 379 Effective length of database: 367 Effective search space: 139093 Effective search space used: 139093 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