Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS20240 RR42_RS20240 hypothetical protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS20240 Length = 595 Score = 209 bits (531), Expect = 1e-58 Identities = 111/257 (43%), Positives = 158/257 (61%), Gaps = 6/257 (2%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 ++ E++L V K FGGL A++DV ++ G++ GLIGPNGAGK+T FN++TG+ Sbjct: 338 QAGELILDVKAARKEFGGLVAVNDVSFQVRAGEIIGLIGPNGAGKSTTFNLVTGVLPATR 397 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTG----SGLFG 119 G G+ E+ K GI RTFQ++ L MT LENV +G H+R G+ Sbjct: 398 GEVLYRGEQISGLPSREIVKRGIGRTFQHVHLLPTMTVLENVAIGAHLRGDFAPQGGVTA 457 Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179 A+ R K EEA + A L+ VG+ +A +L+ G QR LEIARAL DP L+ Sbjct: 458 AILRMN--KNEEAKLLHEAARQLERVGLADCMYMEAGSLALGQQRILEIARALCCDPALL 515 Query: 180 ALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEG 239 LDEPAAG+ EK L EL+ +++ + ++LL+EHD+ VM L DR+ V+++G +IAEG Sbjct: 516 LLDEPAAGLRYKEKQALAELLKKLKGEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEG 575 Query: 240 NPAEVQKNEKVIEAYLG 256 P +VQK+ V+EAYLG Sbjct: 576 VPEDVQKDPAVLEAYLG 592 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: 397 Number of extensions: 18 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: 595 Length adjustment: 31 Effective length of query: 229 Effective length of database: 564 Effective search space: 129156 Effective search space used: 129156 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: 50 (23.9 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