Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CA265_RS01140 CA265_RS01140 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Pedo557:CA265_RS01140 Length = 229 Score = 96.3 bits (238), Expect = 5e-25 Identities = 66/221 (29%), Positives = 105/221 (47%), Gaps = 25/221 (11%) Query: 7 EVVLKVAGISKRFGG----LQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPD 62 E +L + +SK + L L ++ +I G + GP+G+GKTT + GL Sbjct: 2 ESILNIRNVSKIYQSAGRELTVLDNINFSITAGSTVAITGPSGSGKTTLLGLCAGLDRAS 61 Query: 63 AGTFELAGKPYEPTAVHE---VAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFG 119 +GT EL G E E V + FQN +L +TALENVMV +R Sbjct: 62 SGTVELNGIALEKLNEDERAAVRNQYVGFIFQNFQLLPTLTALENVMVPLELRGAKN--- 118 Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179 I A ELLD VG+ + + LS G+Q+R+ +ARA + P ++ Sbjct: 119 --------------IRAHALELLDKVGLADRSHHYPVQLSGGEQQRVSLARAFSNQPAIL 164 Query: 180 ALDEPAAGMNA-TEKVQLRELIDRIRNDNRTILLIEHDVKL 219 DEP ++A T + ++ L D ++ T++++ HD++L Sbjct: 165 FADEPTGNLDAETSEKVIKLLFDLNKDAGTTLIIVTHDLEL 205 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: 154 Number of extensions: 16 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: 229 Length adjustment: 24 Effective length of query: 236 Effective length of database: 205 Effective search space: 48380 Effective search space used: 48380 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