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_027720641.1 H589_RS0102885 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000425265.1:WP_027720641.1 Length = 391 Score = 258 bits (660), Expect = 2e-73 Identities = 137/388 (35%), Positives = 216/388 (55%), Gaps = 7/388 (1%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R+ S L + A+A ++ +GK ++ L GEPDF TP+HV +A A+ G +Y Sbjct: 4 SKRLMRAKPSATLAVNAKAQELRAQGKEIVSLAVGEPDFPTPQHVCEAMKKAVDDGFHRY 63 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 TA+ G PEL++A+ + + R G+ D ++ G KQ L+N MA +D GDEV+IP PY Sbjct: 64 TAVPGLPELRRAVADYYGRFYGVKATADNTIISNGGKQSLYNLFMALIDQGDEVLIPAPY 123 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY +V + +G PV++ A SGF + LEA T RT+ +++N+PSNP+G Y A Sbjct: 124 WVSYPAMVELADGVPVIVPTTAESGFLAQIKDLEACCTERTKLLVINTPSNPTGGHYPQA 183 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + + ++++ D++Y+ +VY + T + V +SK++ MT Sbjct: 184 HLDEIAN-WAKSKGIFIVSDEVYDRLVYAPAEYSTLSTFWEKNPEDVAIVGALSKSFCMT 242 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWR+G A +L+KAM +Q Q+TS ++++Q A++AA +G DF+ E + F RRRD+ Sbjct: 243 GWRVGTALAHPDLVKAMVKIQGQSTSNVNTMAQKAAIAAFDGSWDFIDEMRDVFHRRRDI 302 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 + + G+ C P+GAFY F + TP C +LE+ +A+VP Sbjct: 303 AHEIITSWPGVVCPKPDGAFYLFPVLENFYTEETPD------SASMCTKILEEVGIALVP 356 Query: 375 GSAFGLSPFFRISYATSEAELKEALERI 402 GSAFG R SYA + LK +L +I Sbjct: 357 GSAFGDDRCIRFSYAVDDEVLKTSLGKI 384 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: 395 Number of extensions: 20 Number of successful extensions: 4 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: 391 Length adjustment: 31 Effective length of query: 379 Effective length of database: 360 Effective search space: 136440 Effective search space used: 136440 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