Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Dsui_2908 Dsui_2908 aspartate/tyrosine/aromatic aminotransferase
Query= curated2:Q2N7G6 (367 letters) >FitnessBrowser__PS:Dsui_2908 Length = 408 Score = 72.0 bits (175), Expect = 3e-17 Identities = 53/174 (30%), Positives = 79/174 (45%), Gaps = 18/174 (10%) Query: 70 AKLAEVHGLDAGRIVCGTGSDELLNLAAQAFAGPGDEVLFSTYSFSVYDIAARRCGATP- 128 A+ +V G+ I G G EL+ ++ A PGDEVL + ++ A TP Sbjct: 85 AQQKKVKGVGLEDIYVGNGVSELIVMSMNALLNPGDEVLVPAPDYPLWTAAVSLSSGTPR 144 Query: 129 --VEAPDADYAADVDALLAAVTDKTRVVFVANPNNPTGSFLPRD------EIARLHAGLP 180 + A + D+D + A +T+ TR + + NPNNPTG+ P D EIAR H Sbjct: 145 HYICDEGAGWLPDLDDIRAKITENTRAIVIINPNNPTGALYPDDLLKEIVEIARQH---- 200 Query: 181 QDVLFVLDQAYAEYLTPEEDDGGFALAAAHENVLVT--RTFSKAYGLAGERIGW 232 ++ D+ Y + L + A+ + E+VL SK Y G R GW Sbjct: 201 -HLIIYADEVYDKVLYDGVEH--TAIGSLSEDVLTISFNGLSKNYRSCGYRAGW 251 Lambda K H 0.317 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: 343 Number of extensions: 18 Number of successful extensions: 2 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: 367 Length of database: 408 Length adjustment: 30 Effective length of query: 337 Effective length of database: 378 Effective search space: 127386 Effective search space used: 127386 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 Aug 03 2021. The underlying query database was built on Aug 03 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