Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_1109 Dsui_1109 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__PS:Dsui_1109 Length = 266 Score = 203 bits (516), Expect = 3e-57 Identities = 107/251 (42%), Positives = 153/251 (60%), Gaps = 1/251 (0%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 EV+L + IS RFGG++AL+D+ +K ++ +IGPNGAGK++ NVI G+Y P G Sbjct: 13 EVILDLQNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNVINGVYHPQEGRI 72 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 G+ + H A GIARTFQNI LF M+ L+N+M GR + G Sbjct: 73 VFHGEERKKMEPHMAATQGIARTFQNIALFKGMSVLDNIMTGRITKMKCGFLEQALYLGR 132 Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186 + EE A ++ +E++D++ I L YG Q+R+E+ RALA +P L+ LDEP A Sbjct: 133 AQKEELAHREKVEEVIDFLEIQHIRKTPVGRLPYGLQKRVELGRALAAEPSLLLLDEPMA 192 Query: 187 GMNATEKVQL-RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245 GMN EK + R ++D TI+LIEHD+ +VM + DR+ VLDYGK+I +G P +V+ Sbjct: 193 GMNVEEKQDMCRFILDVNDQFGTTIVLIEHDMGVVMDISDRMVVLDYGKKIGDGTPDDVR 252 Query: 246 KNEKVIEAYLG 256 N++VI AYLG Sbjct: 253 NNQEVISAYLG 263 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: 193 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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