Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028997557.1 H537_RS0108415 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000430725.1:WP_028997557.1 Length = 269 Score = 256 bits (655), Expect = 3e-73 Identities = 133/249 (53%), Positives = 171/249 (68%), Gaps = 1/249 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIK-RGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67 +LK+A +S RFGGL L DV I + G ++GLIGPNGAGKTT FN+ITGL+ P G E Sbjct: 1 MLKLANVSMRFGGLHVLQDVNIELPPEGSIFGLIGPNGAGKTTVFNLITGLFRPTGGAIE 60 Query: 68 LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127 GK A HEV + GIARTFQNIR+F EM+ L+NV+VG H G G G +F + G Sbjct: 61 FGGKSLVGLAPHEVTRRGIARTFQNIRVFKEMSLLDNVVVGMHRHLGYGALGTLFSSPGV 120 Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187 +A E +RA ELL +V + A A +LSYG+QRRLE+ARALAT+P+L+ LDEP AG Sbjct: 121 RAAEKRARERALELLSWVRLDHKAGATADSLSYGEQRRLELARALATEPKLLLLDEPVAG 180 Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 MNA+EK +L I IR I +IEHD++ VMGLC+RV VL++G+ I + P VQ++ Sbjct: 181 MNASEKTELMHEIRNIRGRGYGIFMIEHDMRFVMGLCERVAVLNFGRIICDATPDVVQRD 240 Query: 248 EKVIEAYLG 256 +VIEAYLG Sbjct: 241 PQVIEAYLG 249 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: 241 Number of extensions: 7 Number of successful extensions: 1 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: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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 24 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