Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012173138.1 AZC_RS23660 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000010525.1:WP_012173138.1 Length = 378 Score = 234 bits (597), Expect = 3e-66 Identities = 139/363 (38%), Positives = 206/363 (56%), Gaps = 9/363 (2%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V AI+ Y+ GK + G+++ + KL+SNE PLG A A A + L YPD Sbjct: 21 VLAISAYVPGK-----SHAAGVEK--VFKLSSNETPLGPSPKAIAAFQSAGTNLQDYPDG 73 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 ++ L+ A+ + G+ D + G GS++IL + AHA+V G ++ + F VY +AT G Sbjct: 74 SSTALREAIGKAMGIDPDRIICGAGSDEILNLIAHAYVGPGDEAIHCAHGFLVYKIATLG 133 Query: 130 LGARAIVVPAVK-YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 G +VVP + D+DA++ AV++ TR+IF+ANPNNPTGT++ ++ +P + Sbjct: 134 AGGVPVVVPDREDLQMDVDAIIGAVTERTRVIFLANPNNPTGTYLPFNEVRRLHAALPPN 193 Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248 V++VLD AY+EY+ + + N+++ RTFSK GLA LR+G+A+A + D Sbjct: 194 VLLVLDAAYSEYVRRNDYETGLELALSAENVIMCRTFSKIHGLAALRIGWAVASEAVIDA 253 Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNF 308 LNR+R PFN+N A AA AA+ D +E+S A N Q LT LGL PS GNF Sbjct: 254 LNRIRGPFNMNAPAIAAGAAAILDAEHVERSIAHNDQWLSWLTTELTALGLTVTPSVGNF 313 Query: 309 VLVRVGNDDA-AGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTL 367 VL+ + L ++G+I+R V +YGLP LR+TIG E N + AL L Sbjct: 314 VLIHFPKTPGRTAAEADAFLTRRGLILRAVASYGLPDSLRMTIGTEEANRLVVQALSDFL 373 Query: 368 AAA 370 + A Sbjct: 374 SGA 376 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: 360 Number of extensions: 12 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: 378 Length adjustment: 30 Effective length of query: 340 Effective length of database: 348 Effective search space: 118320 Effective search space used: 118320 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: 50 (23.9 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