Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Synpcc7942_1794 Synpcc7942_1794 succinyldiaminopimelate transaminase
Query= curated2:Q5P791 (356 letters) >FitnessBrowser__SynE:Synpcc7942_1794 Length = 392 Score = 62.8 bits (151), Expect = 1e-14 Identities = 66/218 (30%), Positives = 100/218 (45%), Gaps = 21/218 (9%) Query: 74 GVEPR-EVFVGNGSDEVLAHAFMALLKHERPLRFPDISYSFYPVYCGLYGIAFETVPLDD 132 GV+P EV + GS E AH +A+++ D Y + L G +P Sbjct: 91 GVDPETEVLLLIGSQEGTAHLPLAVMEPGEIALLQDPGYPSHAGGVYLAGGEIYRLPTTA 150 Query: 133 DFAIRPD-DYLPHGSVAAGGI-IFPNPNAPTGRLMPLSDIERIVA--GNPQCVVVIDEAY 188 D PD +P ++ + + P+ PT + PL+ E VA + Q V+ D Y Sbjct: 151 DRGFLPDFSTIPTEILSRSRLLVLSYPHNPTTAIAPLAFFEEAVAFCRHHQLVLAHDFPY 210 Query: 189 VDFGGESA-IPLV----RHHPNLLVVQTLSKSRSLAGLRVGFAVGNPDLIEALDRVKD-- 241 D G + +P + R + +LSKS ++ G RVGFA+GN +LI AL R+K Sbjct: 211 PDLGFDGVEVPSIFQADRQKQQAIEFFSLSKSYNMGGFRVGFAIGNAELIGALRRLKAVV 270 Query: 242 SFNSYPLDRLAIAGGVAAIEDEEHFQRTRMAVIATRER 279 FN Y + +AG +AA+ + V ATR+R Sbjct: 271 DFNQY---QGILAGAIAALTGPQ------ACVEATRQR 299 Lambda K H 0.323 0.140 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: 399 Number of extensions: 17 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: 356 Length of database: 392 Length adjustment: 30 Effective length of query: 326 Effective length of database: 362 Effective search space: 118012 Effective search space used: 118012 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