Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate BWI76_RS20495 BWI76_RS20495 alanine transaminase
Query= curated2:Q5FQA6 (355 letters) >FitnessBrowser__Koxy:BWI76_RS20495 Length = 412 Score = 70.1 bits (170), Expect = 1e-16 Identities = 69/235 (29%), Positives = 106/235 (45%), Gaps = 16/235 (6%) Query: 85 GSDEVLAHAFRALFHDDAPVLFSDVTYGFYPVYCGLFEQPFRHIPLND--DFAIDIDAYT 142 GS E LAH A VL + +Y + + R +PL + DF +++ Sbjct: 106 GSKEGLAHLMLATLDHGDTVLVPNPSYPIHIYGAVIAGAQVRSVPLVEGVDFFNELERAI 165 Query: 143 GDCGG----IIIANPNANTGIALPLEQIETL--LKRHPDRTVIIDEAYVD-----FGAQS 191 + +I+ P+ T + LE E + L + D V+ D AY D + A S Sbjct: 166 RESYPKPKMMILGFPSNPTAQCVELEFFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPS 225 Query: 192 AIELTHRYDNLLVVQTLSKSYALAGLRVGFAIGSPELIEGLIRVKDSFNSYPLSRPAQAG 251 +++ D + TLSKSY +AG R+GF +G+ L+ L R+K S++ Y P Q Sbjct: 226 IMQVPGARDVAVEFFTLSKSYNMAGWRIGFMVGNKTLVNALARIK-SYHDYGTFTPLQVA 284 Query: 252 AIAAIQ-DTDWLADITARVIASRDRLVPELQNLGFQV-LPSCANFVLVHHPAHKA 304 AIAA++ D + DI + RD LV L G+ V P + +V P A Sbjct: 285 AIAALEGDQQCVRDIAEQYKRRRDVLVKGLHEAGWMVECPKASMYVWAKIPEQYA 339 Lambda K H 0.323 0.139 0.417 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: 341 Number of extensions: 19 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: 355 Length of database: 412 Length adjustment: 30 Effective length of query: 325 Effective length of database: 382 Effective search space: 124150 Effective search space used: 124150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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