Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_1248 N515DRAFT_1248 ABC-2 type transport system ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_1248 Length = 315 Score = 115 bits (288), Expect = 1e-30 Identities = 78/239 (32%), Positives = 126/239 (52%), Gaps = 22/239 (9%) Query: 1 MTEKSNEV--VLKVAGISKRF-GGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITG 57 MTE++ + V GISK + GG QAL + + I+RG+++ L+GPNGAGKTT ++I G Sbjct: 1 MTEQATPTPHAVSVRGISKTYKGGFQALKSIDLDIRRGEIFALLGPNGAGKTTLISIICG 60 Query: 58 LYTPDAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGL 117 + P AGT G ++ + + +A I Q + A E V +R GL Sbjct: 61 IVKPSAGTVSADG--HDVLRDYRLTRAKIGLVPQEL----STDAFETVWAA--VRFSRGL 112 Query: 118 FGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQ 177 FG A + +++L + + + D K TLS G +RR+ IA+ALA +P Sbjct: 113 FG-----------RARDDRHIEKVLRDLSLWEKKDAKIMTLSGGMKRRVLIAKALAHEPS 161 Query: 178 LIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQI 236 ++ LDEP AG++ + + E++ R+R T++L H ++ + DRV V+ G+ I Sbjct: 162 ILFLDEPTAGVDVELRHDMWEMVRRLRATGVTVILTTHYIEEAEEMADRVGVITRGELI 220 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: 195 Number of extensions: 9 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: 315 Length adjustment: 26 Effective length of query: 234 Effective length of database: 289 Effective search space: 67626 Effective search space used: 67626 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