Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Pf6N2E2_2862 Uncharacterized PLP-dependent aminotransferase YfdZ
Query= curated2:Q3A7R3 (347 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2862 Length = 405 Score = 77.8 bits (190), Expect = 5e-19 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 19/241 (7%) Query: 76 DPDW-VIMANGSDEVLNNLIRAFAGEGEEIAYVHPSYSYYSTLAEIQGAKVRTFLLDEGW 134 DP+ I+ GS E L +L+ A +G+ + +PSY + A I GA+VR+ L G Sbjct: 96 DPETEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPSYPIHIYGAVIAGAQVRSVPLVPGV 155 Query: 135 ALKDFPERYTG------KLFFLTNPNAPLGFCYPQEFIEE---LAGRVDGMLVVDEAYAD 185 ER K+ L P+ P C +F E LA + D +++ D AYAD Sbjct: 156 DFFAELERAIRGSIPKPKMMILGFPSNPTAQCVELDFFERVIALAKQYDVLVIHDLAYAD 215 Query: 186 FA----KENSLDLVRRLPNVVVTR-TFSKSYSLAGMRLGLAIAHPEVIAALNKIRDHYNL 240 K S+ V ++ V T SKSY++AG R+G + +PE++ AL +I+ +++ Sbjct: 216 IVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGWRIGFMVGNPELVNALARIKSYHDY 275 Query: 241 DRLA--QTACVAAL-ADQEYFQQCVSKIRETRDWFSAELRVLDWDV-IPSHGNFVFATPP 296 Q A +AAL DQ+ + + R+ R+ L L W V P +V+A P Sbjct: 276 GTFTPLQVAAIAALEGDQQCVRDIAEQYRQRRNVLVKGLHELGWMVENPKASMYVWAKIP 335 Query: 297 D 297 + Sbjct: 336 E 336 Lambda K H 0.320 0.137 0.413 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: 380 Number of extensions: 19 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: 347 Length of database: 405 Length adjustment: 30 Effective length of query: 317 Effective length of database: 375 Effective search space: 118875 Effective search space used: 118875 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 (21.8 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