Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate WP_068169202.1 HTA01S_RS08365 succinyldiaminopimelate transaminase
Query= curated2:Q2Y6Y6 (392 letters) >NCBI__GCF_001592305.1:WP_068169202.1 Length = 407 Score = 77.8 bits (190), Expect = 5e-19 Identities = 71/227 (31%), Positives = 109/227 (48%), Gaps = 22/227 (9%) Query: 38 IKLASNENPLGTSPMALNAMSKALDE-VSLYPDGSGFE-LKAA----LSERYGVTSD--- 88 I L E T M +A++ ALD ++ YP +G L+ A L RYGVT D Sbjct: 32 ISLGIGEPKHATPQMLKDALAAALDTGLTGYPATAGEPALREACAGWLQRRYGVTVDPAT 91 Query: 89 QIVLGNGSNDVLELAARVFL---KPGASTVYSQHAFAVYP---LVTKAVGGIGISVPARN 142 Q++ NGS + L A+ + +PGA+ V+ + +Y L+ A S PARN Sbjct: 92 QVLTVNGSREALFSFAQTVIDPTQPGATLVFPNPFYQIYEGAALLGGAQPYYVASDPARN 151 Query: 143 YGHDLDAMLDAVAPETRVVFIANPNNPTGTLLPADDVLRFLERVSP-DVLVVLDEAYNEY 201 + D D++ D V T+++F+ +P NPTG ++P D+ + E ++ DE Y+E Sbjct: 152 FAVDWDSVPDEVWARTQLIFVCSPGNPTGAVMPLDEWQKLFELSDRYGFVIASDECYSEI 211 Query: 202 L---PPALKGDSIA---WLKQFPNLLITRTFSKAYGMAGVRVGFGLG 242 P L G A F NL++ + SK + G+R GF G Sbjct: 212 YFRDEPPLGGLEAAVKLGRTDFKNLMMFTSLSKRSNVPGLRSGFVAG 258 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: 411 Number of extensions: 30 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: 392 Length of database: 407 Length adjustment: 31 Effective length of query: 361 Effective length of database: 376 Effective search space: 135736 Effective search space used: 135736 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 10 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