Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_038212056.1 Q392_RS21390 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000745855.1:WP_038212056.1 Length = 368 Score = 310 bits (794), Expect = 4e-89 Identities = 163/349 (46%), Positives = 221/349 (63%), Gaps = 4/349 (1%) Query: 7 PSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRY 66 P++V A+ PY+ G PIS VA GL IVKLASNENPLG A A++ A +L RY Sbjct: 8 PAHVAALKPYVPGLPISAVAARSGLAADRIVKLASNENPLGASPRALAALSSAGIDLSRY 67 Query: 67 PDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALA 126 PD++ L A++ + VP +W+ +G GS +L A +E G+S YAQYSF Y A Sbjct: 68 PDSDCAALSDAIARFHDVPREWIVVGAGSESVLGNVAACLLEPGRSTSYAQYSFQAYVNA 127 Query: 127 TQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVP 186 Q LGA + VV + + DL+ + ++ T L++VANP NPTGT ++ L++FL +VP Sbjct: 128 VQKLGAHSTVVASPDFTVDLEGLAGSILPSTSLVYVANPGNPTGTAVDPDALKSFLGRVP 187 Query: 187 RHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELT 246 HVVV+LDEAY E+LP ++R DS+AWVR + NL+V+RTFSKA+GLAGLRVG+ IAQP L Sbjct: 188 PHVVVLLDEAYVEFLPPDRRGDSVAWVREHANLVVTRTFSKAYGLAGLRVGYGIAQPGLA 247 Query: 247 DLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDG 306 D++ RVR PF ++ AQ AAIAAL D+ F+ ++ A QG L E + + + S Sbjct: 248 DVMRRVRSPFTISEPAQVAAIAALEDQDFIARTVAATRQGRTALVEGLASMDCQCLESHT 307 Query: 307 NFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEE 355 NFVL D G L + G+IVRPV +YGL W+RI+IG E Sbjct: 308 NFVLA----DVKGGADFARRLEQHGLIVRPVASYGLADWVRISIGTQPE 352 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: 392 Number of extensions: 13 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: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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 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