Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 3609562 Dshi_2946 histidinol-phosphate aminotransferase (RefSeq)
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Dino:3609562 Length = 361 Score = 234 bits (597), Expect = 3e-66 Identities = 141/342 (41%), Positives = 200/342 (58%), Gaps = 7/342 (2%) Query: 30 GLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWV 89 GLD T++KL+SNENPLG +A A AA EL RYP + L+ A++E YG+ + + Sbjct: 25 GLD--TVIKLSSNENPLGPSPAAIAAYKAAAGELHRYPSTDHAGLRGAIAEVYGLDPERI 82 Query: 90 TLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAM 149 G GS++I+ A+V G +++ ++ FA+Y ++T G + VP + D+DA+ Sbjct: 83 ICGAGSDEIIAFLCQAYVGPGDEVIHTEHGFAMYRISTLAAGGTPVEVPERERVTDVDAI 142 Query: 150 LAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDS 209 LA V+D TRL+F+ANPNNPTGT I G L D +P ++VLD AY EY+P YD+ Sbjct: 143 LAGVTDRTRLVFIANPNNPTGTMIGGNALARLADGLPEGCLLVLDGAYAEYVPD---YDA 199 Query: 210 -IAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIA 268 A V N++++RTFSK +GL LRVG+ + D+LNRVR PFN++T A AAA A Sbjct: 200 GKALVESRENVVMTRTFSKIYGLGALRVGWGYGPRHVIDVLNRVRGPFNLSTGALAAAEA 259 Query: 269 ALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELL 328 A+ D+A+ E A NA+ L LG+ S NFVL R + + AG + L Sbjct: 260 AVRDRAYTETCRAENAKWRGWLASELAALGIPSDTSSANFVLARFASPEEAGACDDF-LK 318 Query: 329 KQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLAAA 370 +G+IVR V Y LP LR+T+G E A + A+ A A Sbjct: 319 ARGIIVRRVSGYKLPAALRMTVGDAEGCRALVDAVAAFKAQA 360 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: 349 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 Aug 03 2021. The underlying query database was built on Aug 03 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