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_042441707.1 TX73_RS22075 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000195775.1:WP_042441707.1 Length = 400 Score = 479 bits (1232), Expect = e-140 Identities = 230/395 (58%), Positives = 297/395 (75%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 A+ + + S + + +A +K G+ VI LG+GEPDFDTP ++K AA A+ G+TKY Sbjct: 5 ATALDRVKPSATIAVTDKARELKAAGRNVIGLGSGEPDFDTPANIKLAAIHAVEAGKTKY 64 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 TA+DG PELK+AI +KF+RENGL Y+ ++I V TG KQ+L+NA+MA+++PGDEVIIP PY Sbjct: 65 TAVDGIPELKQAIIDKFKRENGLTYKPNQIIVGTGGKQVLYNALMATINPGDEVIIPAPY 124 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY ++V + G+ V + C A GF+L LEAAITP+T+W++LNSPSNP+GAAYS A Sbjct: 125 WVSYPEMVALAGGESVPVVCTAEFGFKLQPAALEAAITPKTKWIILNSPSNPTGAAYSRA 184 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + + L +VL++HPHVW++ DDMYEH+VYD F F TPAQ+EP L +RTLTVNGVSK+Y MT Sbjct: 185 ELKALTDVLVKHPHVWVMTDDMYEHLVYDDFEFTTPAQIEPKLFDRTLTVNGVSKSYCMT 244 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGYAGGP ELIKAM+ +QSQ+TS P SI+Q A+V ALNGPQDF+ + F+ RRDL Sbjct: 245 GWRIGYAGGPAELIKAMSTIQSQSTSNPCSIAQWAAVEALNGPQDFIDAHNKVFKERRDL 304 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 VV+ LN G+DC PEGAFY + CAG +GK PSGK+I+TD DF LLE VAVV Sbjct: 305 VVSMLNQATGIDCPRPEGAFYVYPSCAGTIGKTAPSGKKIETDQDFVTELLEAEGVAVVQ 364 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409 GSAFGL P FRISYAT ++L++A +RI C L Sbjct: 365 GSAFGLGPAFRISYATKTSDLEDACKRIQRFCGNL 399 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: 518 Number of extensions: 12 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: 400 Length adjustment: 31 Effective length of query: 379 Effective length of database: 369 Effective search space: 139851 Effective search space used: 139851 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