Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8501895 DvMF_2610 ABC transporter related (RefSeq)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Miya:8501895 Length = 270 Score = 251 bits (641), Expect = 1e-71 Identities = 133/265 (50%), Positives = 177/265 (66%), Gaps = 6/265 (2%) Query: 2 TEKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTP 61 T + VL V IS FGGL+AL++V + +++G++ LIGPNGAGKTTFFN ITG+Y P Sbjct: 5 TANAAAAVLDVRSISMNFGGLRALNEVDLQVRQGEIVALIGPNGAGKTTFFNCITGIYVP 64 Query: 62 DAGTFELAGKPYEPTAVH-----EVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSG 116 GT + + V+ +V G++RTFQNIRLF M+ LENVM+GRH RT +G Sbjct: 65 TEGTVHVTPRDGRTVTVNGLKASQVTALGMSRTFQNIRLFPTMSVLENVMIGRHCRTRAG 124 Query: 117 LFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDP 176 + GA+ R +AEE I + + LL V + + +AR L YG QRRLEIARALAT+P Sbjct: 125 ILGALLRDPKTRAEEQRIVEESYALLKSVNLHQHYKDEARNLPYGAQRRLEIARALATEP 184 Query: 177 QLIALDEPAAGMNATEKVQLRELIDRIRNDNR-TILLIEHDVKLVMGLCDRVTVLDYGKQ 235 L+ LDEPAAGMN E +L+EL+ IR + ++LLIEHD+ +VM L DR+ V++YG + Sbjct: 185 FLLCLDEPAAGMNPQETHELKELVIEIRERHELSVLLIEHDMSMVMSLSDRIYVMEYGSK 244 Query: 236 IAEGNPAEVQKNEKVIEAYLGTGGH 260 IAEG P EV KN +VI+AYLG H Sbjct: 245 IAEGTPEEVSKNPRVIKAYLGEESH 269 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: 210 Number of extensions: 6 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: 270 Length adjustment: 25 Effective length of query: 235 Effective length of database: 245 Effective search space: 57575 Effective search space used: 57575 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