Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Cola:Echvi_1333 Length = 243 Score = 134 bits (336), Expect = 2e-36 Identities = 76/249 (30%), Positives = 136/249 (54%), Gaps = 15/249 (6%) Query: 8 VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67 ++L+ + K + G + ++++ + +++G++ GL+GPNGAGKTT F +I GL P++G Sbjct: 1 MILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVF 60 Query: 68 LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127 L + P ++ AK GI Q +F +++ EN+M AV Sbjct: 61 LDKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIM-------------AVLEMTNL 107 Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187 +AA ++ +ELL+ + LS G++RR EIARALA DP+ + LDEP AG Sbjct: 108 P--KAAQKEKMEELLEEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAG 165 Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 ++ +++ ++ +++N N IL+ +H+V + + DR ++ GK + G E+ + Sbjct: 166 VDPIAVEEIQTIVAKLKNKNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAAD 225 Query: 248 EKVIEAYLG 256 E+V + YLG Sbjct: 226 EQVRKVYLG 234 Lambda K H 0.319 0.137 0.384 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: 149 Number of extensions: 10 Number of successful extensions: 2 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: 243 Length adjustment: 24 Effective length of query: 236 Effective length of database: 219 Effective search space: 51684 Effective search space used: 51684 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: 46 (22.3 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