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_012169089.1 AZC_RS02835 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000010525.1:WP_012169089.1 Length = 394 Score = 237 bits (604), Expect = 5e-67 Identities = 135/386 (34%), Positives = 211/386 (54%), Gaps = 12/386 (3%) Query: 21 IGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGT 80 IG + ARA + +G+ +I LG G+PDF TPEH+ +AA A+ G+ YT G Sbjct: 11 IGEENAFAVLARATTLAAQGRDIINLGIGQPDFRTPEHIVEAAVKALKDGQHGYTPSVGI 70 Query: 81 PELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSD 140 L++A+ + + + + + G K ++ A++ +PG E++ P P + Y Sbjct: 71 QPLREAVARDLHKRFDVEVDPGLVMIMPGGKVTMYAAILLFGEPGAEILYPDPGFPIYRS 130 Query: 141 IVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLL 200 ++ P+ + +GF +AE+ A ITP+TR +++NSP+NP+G A+ L+ Sbjct: 131 MIEYTGATPIPVPIREENGFAFSAEETLALITPKTRLLIINSPANPTGGVTPKAEIDKLV 190 Query: 201 EVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGY 260 + L HPHV L+ D++Y+ ++DG R T P +++R + +NG SK YAMTGWR+GY Sbjct: 191 KGLADHPHVALMSDEIYDQFLFDGERHQT-LLAYPEIRDRLILLNGWSKTYAMTGWRLGY 249 Query: 261 AGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLN 320 + P+ L + + A SC ++ +Q A +AAL GPQ+ + F +RR LVV GLN Sbjct: 250 SIWPQALYDKVRKLSVNAWSCVNAATQYAGIAALEGPQEPVAAMLAEFDKRRRLVVEGLN 309 Query: 321 AIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGL 380 A+ G+ C P+GAFY F V S K + + LLEDA VA + G FG+ Sbjct: 310 ALPGVTCAKPKGAFYAF---PNVSRTGWTSAKAL------ASALLEDAGVATIGGPDFGV 360 Query: 381 --SPFFRISYATSEAELKEALERIAA 404 + R+SYA S + ALER+ A Sbjct: 361 HGEGYIRLSYANSAENIARALERMGA 386 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: 441 Number of extensions: 23 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: 394 Length adjustment: 31 Effective length of query: 379 Effective length of database: 363 Effective search space: 137577 Effective search space used: 137577 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