Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8500413 DvMF_1163 ABC transporter related (RefSeq)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Miya:8500413 Length = 255 Score = 215 bits (547), Expect = 8e-61 Identities = 114/249 (45%), Positives = 163/249 (65%), Gaps = 1/249 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L++ G+++RFGGLQA+SD I+++ ++ LIGPNGAGKTT FN+++G Y P G Sbjct: 3 LLEMKGVTQRFGGLQAVSDFNISLEERKLIALIGPNGAGKTTVFNLVSGFYQPTEGQIIF 62 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 GKP H+V GIARTFQNIRL+ EM+ L+N+ + +H R G ++ A RT F Sbjct: 63 DGKPTAGLRPHQVTARGIARTFQNIRLWHEMSVLDNIRIAQHHRLGYTIWDAFLRTGRFT 122 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 E I A E+L+ + + A R L YG QRR+EIARA++ P+L+ LDEPAAG+ Sbjct: 123 RSEGNIDTIAWEMLEAMDLKDAAHELPRNLPYGLQRRVEIARAMSIRPKLLLLDEPAAGL 182 Query: 189 NATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 N+ + L +LI I ++ + I +IEH +K+VM LC+ + V+D+G IAEG P E+Q N Sbjct: 183 NSADVDGLIKLIRWIHDEFDIAIWMIEHQMKVVMSLCEWIKVIDFGSTIAEGTPEEIQSN 242 Query: 248 EKVIEAYLG 256 VI+AYLG Sbjct: 243 PVVIKAYLG 251 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: 186 Number of extensions: 7 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: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 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