Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate PfGW456L13_1928 Uncharacterized PLP-dependent aminotransferase YfdZ
Query= curated2:Q5P791 (356 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1928 Length = 405 Score = 72.0 bits (175), Expect = 3e-17 Identities = 83/279 (29%), Positives = 125/279 (44%), Gaps = 25/279 (8%) Query: 64 RLKAAIATRF------GVEPR-EVFVGNGSDEVLAHAFMALLKHERPLRFPDISYSFYPV 116 RL+ AI+ + ++P E V GS E LAH +A L + P+ SY + Sbjct: 78 RLRRAISNWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPSYPIHIY 137 Query: 117 YCGLYGIAFETVPLDD--DFAIRPDDYLPHGSVAAGGIIFPNPNAPTGRLMPLSDIERIV 174 + G +VPL DF + + +I P+ PT + + L ER++ Sbjct: 138 GAVIAGAQVRSVPLVPGVDFFAELERAIRGSIPKPKMMILGFPSNPTAQCVELDFFERVI 197 Query: 175 AGNPQ--CVVVIDEAYVD--FGGESAIPLVRHHPNLLVVQ----TLSKSRSLAGLRVGFA 226 A Q +VV D AY D + G A P + P + TLSKS ++AG R+GF Sbjct: 198 ALAKQYDVLVVHDLAYADIVYDGWKA-PSIMQVPGAKDIAVEFFTLSKSYNMAGWRIGFM 256 Query: 227 VGNPDLIEALDRVKDSFNSYPLDRLAIAGGVAAIEDEEHFQRTRMAVIATRER-LSADLA 285 VGNP+L+ AL R+K S++ Y +AA+E ++ R R L L Sbjct: 257 VGNPELVNALARIK-SYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQRRNVLVKGLH 315 Query: 286 SLGFDV-LPSAANFVFTRHP----HRDAGELAAQLRRRA 319 LG+ V P A+ +V+ + P H + E A +L A Sbjct: 316 ELGWMVENPKASMYVWAKIPEAYAHLGSLEFAKKLLAEA 354 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: 402 Number of extensions: 25 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: 356 Length of database: 405 Length adjustment: 30 Effective length of query: 326 Effective length of database: 375 Effective search space: 122250 Effective search space used: 122250 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 Jul 25 2024. The underlying query database was built on Jul 25 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