Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011764803.1 AZO_RS05420 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000061505.1:WP_011764803.1 Length = 365 Score = 454 bits (1167), Expect = e-132 Identities = 232/365 (63%), Positives = 281/365 (76%), Gaps = 4/365 (1%) Query: 3 ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62 AS P+Y+R+I PY GKPISE+ARE GL EA IVKLASNENPLGM A+ A A E Sbjct: 4 ASRAPAYIRSIQPYQPGKPISELAREMGLPEADIVKLASNENPLGMGAKARAAAEAAIRE 63 Query: 63 LGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAV 122 RYPD AF LKAAL+ ++GV A + +GNGSND+LEIAA F+ G S V++QYSFAV Sbjct: 64 AFRYPDGGAFALKAALARKFGVDAAQLVIGNGSNDVLEIAAQTFLAPGTSAVFSQYSFAV 123 Query: 123 YALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFL 182 Y LAT GAR I VPA YGHDLDAM AA++ DTR++F+ANPNNPTGTF+ G LEAFL Sbjct: 124 YPLATNARGARCIQVPAQAYGHDLDAMAAAIAPDTRIVFIANPNNPTGTFVGGAALEAFL 183 Query: 183 DKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQ 242 KVP V+VVLDEAYTE+L E+RYDS+AW+ R+PNLLVSRT KA+GLAGLRVG+AIA Sbjct: 184 AKVPEDVLVVLDEAYTEFLEPEQRYDSLAWLARFPNLLVSRTLCKAYGLAGLRVGYAIAH 243 Query: 243 PELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYV 302 P++ DL+NRVRQPFNV+ +A AAA AAL D F+ ++A +N +G ++LT+AF LGLE++ Sbjct: 244 PDVADLMNRVRQPFNVSAVALAAAEAALGDDDFVARTADINRRGKQQLTDAFASLGLEWI 303 Query: 303 PSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAA 362 PS GNFV VRVG DAA VNL LL+QGVIVRP+ YG+P+WLR++IGLPEEN FI A Sbjct: 304 PSAGNFVTVRVG--DAAA--VNLALLRQGVIVRPIAGYGMPEWLRVSIGLPEENARFITA 359 Query: 363 LERTL 367 L L Sbjct: 360 LRNAL 364 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: 490 Number of extensions: 20 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: 365 Length adjustment: 30 Effective length of query: 340 Effective length of database: 335 Effective search space: 113900 Effective search space used: 113900 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