Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= curated2:Q1AY33 (351 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 109 bits (272), Expect = 2e-28 Identities = 98/318 (30%), Positives = 144/318 (45%), Gaps = 26/318 (8%) Query: 47 AEAALAEALPRANRYPDRYAAALREAVAAANPGS-----DVANVLVGNGSSEVL-QNLLM 100 A +AL E P R ALREA+AA + NV+ G+ L L Sbjct: 54 AVSALREGDTHYTEIPGR--PALREAIAARYSKTLARALSAENVITVAGAQNALFVTSLC 111 Query: 101 LVERPGEVLFPWPTFTLYPSIAGTLGLRARRVPLTEEH--RVKPEALLSAVTGETRAVIL 158 L++ EVL P + Y + G RVP + E R+ + L +A+T TRA+ Sbjct: 112 LLQAGDEVLVLDPMYVTYEATLKASGATLVRVPCSPESGFRLDAQLLGAAITPRTRAIFF 171 Query: 159 CNPNNPTGTHLTLEEVSALAD-ALPEDVLLILDEAYQEFVADPAYHGSHALALERPNVAV 217 NPNNPTG L L+E+ A+AD A+ D+ +++DE Y+ V D YH AL V Sbjct: 172 SNPNNPTGVVLNLQELQAIADLAIARDLWVVVDEVYESLVFDGEYHSLAALPGMAERCVV 231 Query: 218 ARTFSKAHGLAGFRVGYGLASREIADYAERVRFPFSVNLAAQV--AATASMQAREKIRAR 275 + SK+H + G+R+G+ +A+ ++ +AE + L V AATA++ A + + Sbjct: 232 IGSLSKSHAMTGWRIGWIIATPQMVAHAETLVLSMLYGLPGFVMEAATAAVLAHDDVTQG 291 Query: 276 AEFVIRERERVERAFREA--GLNYVHSQ-GNFVLVETSPA----------LFERAGVLVR 322 + R R + A A G+ Q G FVLV+ LF AGV V Sbjct: 292 MREIYRRRRDLVMAGLSACPGIKVQAPQAGMFVLVDVRGTGLGSLDFAWRLFREAGVSVL 351 Query: 323 EGDPLGYPGWSRVTIGNT 340 + G P V + T Sbjct: 352 DAAAFGAPAQGFVRLSFT 369 Lambda K H 0.317 0.133 0.382 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: 438 Number of extensions: 19 Number of successful extensions: 3 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: 351 Length of database: 664 Length adjustment: 34 Effective length of query: 317 Effective length of database: 630 Effective search space: 199710 Effective search space used: 199710 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: 51 (24.3 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