Align BadI (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__azobra:AZOBR_RS18155 Length = 248 Score = 120 bits (301), Expect = 3e-32 Identities = 88/247 (35%), Positives = 117/247 (47%), Gaps = 7/247 (2%) Query: 14 VAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQSTHDG 73 VA I ++RP K+NA +L+ A+ + D D+ +VL GAG RAFC G D D Sbjct: 5 VATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIRELD- 63 Query: 74 NYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIFGQVG 133 YD E+ AIR + KP IA V GYA GGG A CD+ I SE A FG Sbjct: 64 RYDTAWNFR-NREDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENAQFGAPE 122 Query: 134 PKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDELDAEVQK 193 K+G + G AFL+ +G A + +A A GL + VP D L A Q+ Sbjct: 123 IKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPADRLLARAQE 182 Query: 194 WGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLY---YDTDESREGVKALQEK 250 + R+P A AK N+ AH + Y L + T ++ EG A +EK Sbjct: 183 IAAIVASRAPIAAETAK--LNLKAAHTMPVEKAIEYERDLQTICFATADAAEGRAAFKEK 240 Query: 251 RKPEFRK 257 R P FR+ Sbjct: 241 RSPVFRR 247 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: 176 Number of extensions: 8 Number of successful extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 236 Effective length of database: 224 Effective search space: 52864 Effective search space used: 52864 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