Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF2492 PGA1_c25240 histidinol-phosphate aminotransferase HisC
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Phaeo:GFF2492 Length = 361 Score = 221 bits (563), Expect = 2e-62 Identities = 129/332 (38%), Positives = 192/332 (57%), Gaps = 5/332 (1%) Query: 34 ATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGN 93 + + KL+SNENPLG A AM A SE+ RYP ++ L+ A+ E YG+P + + G Sbjct: 27 SNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYPSSDHSGLRQAIGEVYGLPMEQIICGA 86 Query: 94 GSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAV 153 GS++I+ A+ G +++ ++ FA+Y ++ GA + V D+DA+LA Sbjct: 87 GSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISALAAGATPVEVAERDRVTDVDALLAGC 146 Query: 154 SDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDS-IAW 212 ++ TRL+F+ANPNNPTGT I L D +P+ ++VLD AY EY+ + YD+ A Sbjct: 147 TERTRLVFIANPNNPTGTMIGMADLARLADGLPKGALLVLDGAYAEYV---EGYDAGAAL 203 Query: 213 VRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALND 272 V N++++RTFSK +GL G RVG+ A + D+LNRVR PFN+++ A A A AA+ D Sbjct: 204 VANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVLNRVRGPFNLSSTALAGAEAAVRD 263 Query: 273 KAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGV 332 + E NA+ L EA +LG+ S NF+L R + + AG + L +G+ Sbjct: 264 TDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFILARFASPEEAG-ACDAFLQSRGL 322 Query: 333 IVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 IVR V Y LP LRIT+G A +AA++ Sbjct: 323 IVRRVTGYKLPAALRITVGDETACNALVAAMK 354 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: 337 Number of extensions: 9 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: 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 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