Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate WP_041101949.1 SUTH_RS07520 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q2Y6Y6 (392 letters) >NCBI__GCF_000828635.1:WP_041101949.1 Length = 408 Score = 70.5 bits (171), Expect = 8e-17 Identities = 68/236 (28%), Positives = 106/236 (44%), Gaps = 22/236 (9%) Query: 22 PISELAREMGMDEQSIIKL-ASNENPLG-TSPMALNA-MSKALDEVSLYPDGSG-FELKA 77 P+ A++M + IIKL N G SP + M + L + Y D G F + Sbjct: 20 PVLARAKQMEEEGHKIIKLNIGNLAAFGFDSPEEIQQDMIRNLPSAAGYVDSKGIFSARK 79 Query: 78 ALSERY------GVTSDQIVLGNGSNDVLELAARVFLKPGASTVYSQHAFAVYPLVTKAV 131 A+ GVT + I +GNG ++++ +A L G + YPL T AV Sbjct: 80 AVMHYTQQKHIKGVTIEDIYIGNGVSELIVMAMNALLDSGDEVLLPAPD---YPLWTAAV 136 Query: 132 GGIG------ISVPARNYGHDLDAMLDAVAPETRVVFIANPNNPTGTLLPADDVLRFLER 185 G + + DLD + + P+TR + I NPNNPTG + P D+VL+ + Sbjct: 137 SLSGGTPRHYLCDEGAGWLPDLDDIRAKITPQTRAIVIINPNNPTGAVYP-DEVLKEIIE 195 Query: 186 VS--PDVLVVLDEAYNEYLPPALKGDSIAWLKQFPNLLITRTFSKAYGMAGVRVGF 239 ++ D+++ DE Y++ L + SIA L + + SK Y G R G+ Sbjct: 196 IARQNDLIIYADEVYDKVLYDGVTHTSIAALSEDVLTITFNGLSKNYRSCGYRSGW 251 Lambda K H 0.317 0.135 0.385 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: 367 Number of extensions: 16 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: 392 Length of database: 408 Length adjustment: 31 Effective length of query: 361 Effective length of database: 377 Effective search space: 136097 Effective search space used: 136097 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: 50 (23.9 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