Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3115 HP15_3058 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Marino:GFF3115 Length = 251 Score = 217 bits (553), Expect = 2e-61 Identities = 104/249 (41%), Positives = 166/249 (66%), Gaps = 1/249 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L+V +S RFGGL A+ +V + ++ ++ +IGPNGAGKTT FN ++G Y P G Sbjct: 1 MLEVQNLSMRFGGLLAVDEVSLDVQEHEIVSIIGPNGAGKTTVFNCMSGFYKPTGGKILF 60 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 GK + +++++ G+ RTFQ++RLF++MT +EN++V +H + L + +T ++ Sbjct: 61 EGKEVQGKPDYKISRLGMVRTFQHVRLFSQMTVVENLLVAQHRHLNTNLISGLIQTPSYR 120 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 +E RA LD VG+ A+ +A L+YG QRRLEIAR + T+P+L+ LDEPAAG+ Sbjct: 121 KKEQKSLDRAAYWLDRVGLLDMANREAGNLAYGQQRRLEIARCMVTEPKLLMLDEPAAGL 180 Query: 189 NATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 N E +L +LI ++ D N +++LIEHD+ LVM + DR+ V++ G+ +A G P E+++N Sbjct: 181 NPAETKELNQLIISLKEDYNVSVVLIEHDMSLVMDISDRINVINQGRPLASGTPEEIRQN 240 Query: 248 EKVIEAYLG 256 + VI+AYLG Sbjct: 241 DDVIKAYLG 249 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: 8 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: 251 Length adjustment: 24 Effective length of query: 236 Effective length of database: 227 Effective search space: 53572 Effective search space used: 53572 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