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_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 160 bits (406), Expect = 5e-44 Identities = 120/396 (30%), Positives = 187/396 (47%), Gaps = 24/396 (6%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 QP +++ +G + + AA + LG G PDF P+ + A + A+ G Sbjct: 2 QPQTKLPKVGTTIFTVMSQLAAE-----HGAVNLGQGFPDFSAPQRLIDATTAAMADGLN 56 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELD-EITVATGAKQILFNAMMASLDPGDEVIIP 131 +Y + G L++AI +K G + D EITV +GA + +FNA+ A + G+EVI+ Sbjct: 57 QYPPMTGVAPLRQAIAQKSLDLYGAQVDPDTEITVTSGATEAIFNAIHAVVRAGEEVIVL 116 Query: 132 TPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAY 191 P + Y + + + V + D + F + +++ AAITPRTR +++N+P NPSGA Sbjct: 117 DPAYDCYEPAIDLAGARAVHVPLDPQT-FAVDWDRVRAAITPRTRLLMVNTPHNPSGAML 175 Query: 192 SAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAY 251 + AD + L + LLR ++L+ D++YEHI+YDG R + A P L+ R ++ K Y Sbjct: 176 AEADLQALAD-LLRGTDIYLISDEVYEHIIYDGRRHES-ALRHPELRARAFVISSFGKTY 233 Query: 252 AMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRR 311 TGW+IGYA P L V T +Q A + E +Q + Sbjct: 234 HCTGWKIGYAIAPPALSAEFRKVHQYNTFTSFGPAQYGFAAMIRDEPQHHLELGAFYQAK 293 Query: 312 RDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVA 371 RD L + VP G F V S D +F +L + VA Sbjct: 294 RDRFREQLAQTRLVPLAVPGGYFQL----------VDYSAISDLPDHEFVKWLTIEKGVA 343 Query: 372 VVPGSAFGLSP-----FFRISYATSEAELKEALERI 402 +P S F +P R+ +A +EA L A+ER+ Sbjct: 344 AIPLSPFYEAPPVGQRIVRLCFAKNEATLDAAIERL 379 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: 344 Number of extensions: 20 Number of successful extensions: 5 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: 382 Length adjustment: 31 Effective length of query: 379 Effective length of database: 351 Effective search space: 133029 Effective search space used: 133029 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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