Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011382577.1 AMB_RS00655 histidinol-phosphate aminotransferase family protein
Query= curated2:A5V022 (370 letters) >NCBI__GCF_000009985.1:WP_011382577.1 Length = 371 Score = 140 bits (354), Expect = 4e-38 Identities = 109/338 (32%), Positives = 165/338 (48%), Gaps = 19/338 (5%) Query: 42 LDANENPYGPSPHAL--AALAAVERDAPHRYAIYPDPDHVRLRAALSRYIGQPPERIICG 99 LD NEN P+ L + +A+V DA Y PD + L+ +G PP+ ++ Sbjct: 38 LDKNENT-DPAMIELVRSVIASVPADAGFTY-----PDLGPVYRKLAPMVGVPPQCLLLT 91 Query: 100 AGSDELIDLLMRATLRPGDTMIDCPPTFAMYSFDAALYGARVVPV---PRTDQFDVDIEG 156 GSD I + A + PGD ++ PTFAMY A +YGA+V + P + + Sbjct: 92 PGSDGAIRAVFEAYIAPGDKVLHTVPTFAMYGVYARMYGAQVTGLEYRPSNAGPVLHADD 151 Query: 157 VAEAVEREGAKLLFLAAPNNPTGTPLARSDVERLLDLP----IILAIDEAYAEFAGTSVV 212 V A+ KL+ L P++PTGT +++D+ R+++ ++ IDEAY F +V+ Sbjct: 152 VVAAIATSKPKLVGLPNPDSPTGTVFSQADLRRIIEAAGEGGALILIDEAYYPFHAETVL 211 Query: 213 DMVGACPNLVVLRTFSKWAGLAGLRIGYAAMHEDVAAYVWKIKQPYNVNVAAEVAAIASL 272 V P+LVV R+ K G+AG+R+GYAA H DVA + K++ Y V + L Sbjct: 212 PWVMEYPHLVVCRSTGKAWGMAGVRVGYAAAHPDVAVMLHKVRAMYEVGALSAAVFERML 271 Query: 273 DDLEERMATVARIVAERERLAAALAALPGFRVYPSAANFLLCRITGGAARARTICDGLAQ 332 D + +VARI A + AA+ L GF+ NFL ARA I LA Sbjct: 272 DHEDAMRESVARISAGKAHFLAAMDEL-GFQTLKGQGNFLHVAF---GARAEAIHAALAP 327 Query: 333 RGILIRYFNRPGLDDCIRISVGRPEQNDALLHALRELV 370 + + F P L R S E + ++ A+R++V Sbjct: 328 QVYYRKDFAEPCLKGFSRFSATTAELFNPVIEAIRDVV 365 Lambda K H 0.322 0.139 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: 346 Number of extensions: 15 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: 370 Length of database: 371 Length adjustment: 30 Effective length of query: 340 Effective length of database: 341 Effective search space: 115940 Effective search space used: 115940 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: 49 (23.5 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