Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011941059.1 GURA_RS21795 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000016745.1:WP_011941059.1 Length = 347 Score = 165 bits (418), Expect = 2e-45 Identities = 110/335 (32%), Positives = 173/335 (51%), Gaps = 16/335 (4%) Query: 32 DEATIVKLASNENPLG-MPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVT 90 D A +KL +NEN P+ + MA+ L RYPDA + + A + YG +W+ Sbjct: 22 DPAAYIKLNTNENAYPPSPKVLEAIMAEVGEGLRRYPDAASRAGREAAARLYGFLPEWIV 81 Query: 91 LGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAML 150 + NGS+++L AF ++G I Y S++ YA + GAR YG D L Sbjct: 82 MANGSDEVLNNLIRAFADEGDEIAYVYPSYSYYATLAEIQGARVKT-----YGLTDDWKL 136 Query: 151 AAVSD--DTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYD 208 A + D ++ F+ NPN P G +E +V +VV DE Y ++ Sbjct: 137 ANFPERYDGKIFFLTNPNAPYGFTFSREFIEELAGRVAGMLVV--DETYADFAGDT---- 190 Query: 209 SIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIA 268 ++ VR+Y N++V+RT SK++ LAG+R+G A+A+PE+ L+++R +N++ LAQAAA+A Sbjct: 191 ALDLVRKYENVVVTRTLSKSYSLAGMRLGLAVARPEVIAALDKIRDHYNLDRLAQAAAVA 250 Query: 269 ALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELL 328 AL D+ + ++ + + KL +PS GN+V + D G RV L Sbjct: 251 ALGDQDYFREAVRKICETRDWFSAELRKLRYSVIPSSGNYVFTTPPDRD--GARVYQGLF 308 Query: 329 KQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363 + ++VR + L LRI+IG EE E + AL Sbjct: 309 DRKILVRHFSDPNLAHGLRISIGTREEMEKTMEAL 343 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: 358 Number of extensions: 24 Number of successful extensions: 5 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: 347 Length adjustment: 29 Effective length of query: 341 Effective length of database: 318 Effective search space: 108438 Effective search space used: 108438 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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