Align BadI (characterized)
to candidate PfGW456L13_2433 Phenylacetate degradation enoyl-CoA hydratase PaaB (EC 4.2.1.17)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2433 Length = 263 Score = 123 bits (308), Expect = 4e-33 Identities = 91/270 (33%), Positives = 131/270 (48%), Gaps = 23/270 (8%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M FE +++ I GVA + +NRPD++N+F E+ +AL + + DV ++L G G R Sbjct: 1 MNFEHILFSIEAGVALLSLNRPDQLNSFNTQMHGEVKEALKQVRQNPDVRVLLLTGEG-R 59 Query: 61 AFCTGGDQSTHDGNYDGRGTV---GLPMEELHTAI----RDVPKPVIARVQGYAIGGGNV 113 FC G D S D N V G +E+ + + RD+P PVI V G A G G Sbjct: 60 GFCAGQDLS--DRNVAPGSAVPDLGESIEKFYNPLIRQLRDLPMPVICAVNGVAAGAGAN 117 Query: 114 LATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAE 173 + CDL + + A F Q K+G + GT L R+VG +A+ + + R S ++AE Sbjct: 118 IPLACDLVLAARSASFIQAFCKIGLIPDSGGTWTLPRLVGMARAKALALLGNRLSAEQAE 177 Query: 174 AMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKL 233 GL CV EL E K L + LA+ KRS N A ++ L+L Sbjct: 178 QWGLIYQCVEDAELRDEALKLARHLATQPTYGLALIKRSLN------ASMSNSFDEQLEL 231 Query: 234 YYD-------TDESREGVKALQEKRKPEFR 256 D +++ REGV A EKR P F+ Sbjct: 232 EKDLQRLAGRSEDYREGVGAFMEKRTPSFK 261 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: 185 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: 260 Length of database: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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