Align BadI (characterized)
to candidate GFF2642 PGA1_c26820 probable enoyl-CoA hydratase PaaG
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Phaeo:GFF2642 Length = 261 Score = 97.8 bits (242), Expect = 2e-25 Identities = 81/264 (30%), Positives = 118/264 (44%), Gaps = 18/264 (6%) Query: 4 EDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFC 63 E L+ E I +NRPD++N+F ++A +A D A++L GAG R FC Sbjct: 3 ETLLVEDHGTWVEITLNRPDRLNSFT-EEMHHALRAALEAARDGGARAVLLTGAG-RGFC 60 Query: 64 TGGDQSTHD-----GNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATIC 118 G D D G D TV L IR + PVI V G A G G LA C Sbjct: 61 AGQDLGDRDPRKMDGPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALAC 120 Query: 119 DLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178 D+ + +E A F Q K+G + G+ L R++GE +A+ + + K+AE GL Sbjct: 121 DVVLAAESAKFIQSFSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGLI 180 Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMG------MYALK 232 VP +EL AE + E+ L + K+ T A + + A+K Sbjct: 181 WKAVPDEELMAEARAMAEKFANGPTLGLGLTKQ-----TIQAAAVTTLSDQLEIEADAMK 235 Query: 233 LYYDTDESREGVKALQEKRKPEFR 256 ++ + EGV + EKR P F+ Sbjct: 236 TCGESADYAEGVASFLEKRVPAFK 259 Lambda K H 0.319 0.138 0.418 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: 175 Number of extensions: 15 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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