Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 3608695 Dshi_2088 aminotransferase class I and II (RefSeq)
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Dino:3608695 Length = 372 Score = 152 bits (383), Expect = 2e-41 Identities = 114/372 (30%), Positives = 173/372 (46%), Gaps = 5/372 (1%) Query: 1 MTASFGPSYVRAIAPYIAGKP-ISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQA 59 MT + GP + A P + +E +L +NE+ G A AMA+A Sbjct: 1 MTHTPGPRFTPLAQSLPATVPFVGPETQERARGRPFAARLGANESAFGPSPRAVAAMAEA 60 Query: 60 ASELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYS 119 A+ Y D + +L+AAL+ + V + V +G G + +L V G ++V + + Sbjct: 61 ATGAWMYGDPESHDLRAALAAHHRVGMENVIVGEGIDGLLGYLVRLLVAPGDTVVTSAGA 120 Query: 120 FAVYALATQGLGARAIVVPAVKYGHDLDAML-AAVSDDTRLIFVANPNNPTGTFIEGPKL 178 + + G G VP D A+L A + D + I++ANP+NP G++ + Sbjct: 121 YPTFNYHVAGFGGTLHAVPYRDDHEDPQALLDMARAVDAKAIYLANPDNPMGSWHAAGVI 180 Query: 179 EAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGF 238 +D +P +++LDEAY E P + P ++ RTFSKA GLAG RVG+ Sbjct: 181 TDMIDALPPGCLLLLDEAYIELAPDGTAPEIAP---DDPRVIRLRTFSKARGLAGARVGY 237 Query: 239 AIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG 298 IA P L +VR F ++ ++QAAA+AAL D L K A A R+ E G Sbjct: 238 GIAAPGLISAFGKVRNHFGMSRVSQAAALAALQDSDHLAKVVAKTAAARTRIAEIGAAHG 297 Query: 299 LEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEA 358 L +PS NFV + G D A + L+ + + VR + +RI+ G PE + Sbjct: 298 LRALPSATNFVTLDCGGDGARAKAILEALIARDIFVRMPFVAPQDRCIRISCGTPEMLDL 357 Query: 359 FIAALERTLAAA 370 L LAAA Sbjct: 358 LAERLPDALAAA 369 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: 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: 372 Length adjustment: 30 Effective length of query: 340 Effective length of database: 342 Effective search space: 116280 Effective search space used: 116280 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