Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_037580293.1 BS73_RS19830 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000744815.1:WP_037580293.1 Length = 361 Score = 216 bits (550), Expect = 8e-61 Identities = 141/334 (42%), Positives = 183/334 (54%), Gaps = 11/334 (3%) Query: 38 KLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSND 97 KL+SNENP A AA E RYPD L A LS GVP + G GS Sbjct: 36 KLSSNENPYPPLPGVLDAAVAAAGEANRYPDMACAALIAELSGTLGVPESHIATGTGSVG 95 Query: 98 ILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPA-VKYGHDLDAMLAAVSDD 156 + + A G +VYA SF Y + TQ GAR++ VP HDLDAM AAV++ Sbjct: 96 VAQQLLQATAGPGDEVVYAWRSFEAYPIITQISGARSVRVPLRPDESHDLDAMAAAVNER 155 Query: 157 TRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRY 216 TRL+F+ PNNPTG + ++E FLD+VPR V+VVLDEAY E++ ++ D I R Sbjct: 156 TRLVFLCTPNNPTGNVLRREEIEGFLDRVPRDVLVVLDEAYLEFIRDKEAVDGIEIYRER 215 Query: 217 PNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDK-AF 275 PN+ V RTFSKA+GLAGLRVG+A+AQ + L + PF V+ LAQ AAI +L + A Sbjct: 216 PNVAVLRTFSKAYGLAGLRVGYAVAQEPVATALRQTAVPFGVSQLAQDAAIVSLRSREAL 275 Query: 276 LEKSAALNAQGYRRLTEAFDKLGLEYVP-SDGNFVLVRVGNDDAAGNRVNLELLKQGVIV 334 LE+ AL A+ R+ +A G VP S NFV +R+G AA E GV+V Sbjct: 276 LERVEALVAE-RERVLDALAAQGWPGVPRSQANFVWLRLGERTAAFAAACAE---AGVVV 331 Query: 335 RPVGNYGLPQWLRITIGLPEENEAFIAALERTLA 368 RP G +R++I N+ F+ R A Sbjct: 332 RPFEGEG----VRVSIAERPANDIFLEVASRFAA 361 Lambda K H 0.318 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: 385 Number of extensions: 16 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: 361 Length adjustment: 30 Effective length of query: 340 Effective length of database: 331 Effective search space: 112540 Effective search space used: 112540 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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