Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF4565 PS417_23365 aminotransferase
Query= curated2:Q9KCA8 (369 letters) >FitnessBrowser__WCS417:GFF4565 Length = 364 Score = 165 bits (418), Expect = 2e-45 Identities = 108/355 (30%), Positives = 172/355 (48%), Gaps = 26/355 (7%) Query: 11 PPYKPGKPMEDVKRELGLETVVKLASNENPFGASPKVAEAIQEALHHTAIYPDGYARTLR 70 PP KP K V+L NE+P+G S EA+Q + YP L Sbjct: 30 PPEKPDK--------------VRLNYNESPYGPSGAAREAMQRGIATAGFYPYDSMYALA 75 Query: 71 DKVAHYVGVAPEELIFGNGSDEVIQILCRAFLNEQTNTVMAEPTFSQYKLNAVIEGAELR 130 A G+A E++ GS ++ AF E VMA P++ + A A ++ Sbjct: 76 GLFAQQQGIAEEQVAVFAGSMAALRYAVLAFTTESRGLVMAMPSYEVPRQAARSNKAPVK 135 Query: 131 EVPL-KDGVHDLDGMLEVIDENTRIVWVCNPNNPTGTYVSAEAFQSFLAKVPEDVLVVSD 189 EV L D HD+ ML D +++VCNPNNPTGT EA + LA P+ ++V D Sbjct: 136 EVSLGADHAHDIPAMLAA-DPQAGMLYVCNPNNPTGTITPTEAIRHALANKPKGSVLVVD 194 Query: 190 EAYVEYVTADDYPDTVPMIRTYKNLVVLRTFSKVFGLAALRIGYGVANQALIEKIEPVRP 249 EAY+++ D P V ++ + +L+VLRTFSK++G+A R+G + + AL+E++ Sbjct: 195 EAYIDFA---DVPSVVSWVKDHDDLLVLRTFSKIYGMAGARLGLAIGHPALLERLAVFGG 251 Query: 250 PFNNSTFSQVAAVAALEDEAFVQSSVEKNNEGMEQLTEWCSRMGLDYFPSQTNFLLIHVN 309 + S + +A+LED + NN+ ++ W G SQ N +I V Sbjct: 252 DNVPAGTSLLGGLASLEDVKLLPQRKALNNQLRDETVAWLKGRGFTCTASQANCFMIDVK 311 Query: 310 RSSDDVFNAMLKKGYIIRSGRAL-GYPAWIRITIGSKEQNDGCLAALADVLAEEL 363 + ++ V + +G +I GR +P W+R+T+G K + +A +V A ++ Sbjct: 312 QPAEQVIEKLATQGVMI--GRVFESWPQWVRVTVGDKRE----MARFREVFAAQV 360 Lambda K H 0.317 0.134 0.389 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: 322 Number of extensions: 13 Number of successful extensions: 5 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: 369 Length of database: 364 Length adjustment: 30 Effective length of query: 339 Effective length of database: 334 Effective search space: 113226 Effective search space used: 113226 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 (21.6 bits) S2: 49 (23.5 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