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_015739359.1 ADEG_RS06970 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000024605.1:WP_015739359.1 Length = 398 Score = 357 bits (915), Expect = e-103 Identities = 182/387 (47%), Positives = 253/387 (65%), Gaps = 2/387 (0%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 A R + S L + +A + R+G+ VI GAGEPDFDTPEH+K+AA A+ +G TKY Sbjct: 5 AERAQKLSPSPTLSVDTKAKELLRQGERVINFGAGEPDFDTPEHIKEAAKRALDQGFTKY 64 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T + G L++AI EK R+N L Y +EI V+ GAK +FNA+ LDPGDEVIIP PY Sbjct: 65 TPVAGILPLREAICEKLYRDNQLEYSPNEIVVSCGAKHSIFNALQVLLDPGDEVIIPVPY 124 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 WTSY + V + G PV + + F+L E L AA+TPRTR ++LNSP+NP+G Y Sbjct: 125 WTSYPEQVKLAGGVPVFVPTSPENDFKLRPEDLRAAVTPRTRLLILNSPANPTGTVYRRE 184 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + L EV L +W+L D++YE ++YDG V+ A L+P +K RT+ VNGVSKAYAMT Sbjct: 185 ELIGLAEVAL-EADLWILSDEIYEKLIYDGMEHVSIAALDPEVKKRTIVVNGVSKAYAMT 243 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGYA PR + +AM +QS +TS P+S++QAA++AAL GPQ+ ++ +FQ+RRD Sbjct: 244 GWRIGYAAAPRPIAQAMTNLQSHSTSNPTSVAQAAALAALKGPQEPVENMRRAFQKRRDF 303 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 + LN++ G+ C P GAFY F +G+LG+ G+ I T +D +LLE+ VA V Sbjct: 304 IWQYLNSLPGVRCPKPLGAFYVFPEVSGLLGR-RLKGREIATASDLALFLLEEIKVATVA 362 Query: 375 GSAFGLSPFFRISYATSEAELKEALER 401 G+AFG + R SYA +++E ++R Sbjct: 363 GAAFGDDRYLRFSYALRLEDIEEGMQR 389 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: 451 Number of extensions: 28 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: 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