Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1056 Psest_1089 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__psRCH2:GFF1056 Length = 258 Score = 167 bits (424), Expect = 2e-46 Identities = 97/251 (38%), Positives = 144/251 (57%), Gaps = 6/251 (2%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 E VL+ G++K F G A+ V + +++G ++ LIGPNGAGKTT FN++T TP G Sbjct: 4 EFVLETRGLTKEFRGFTAVDSVDLKVRQGHIHALIGPNGAGKTTVFNLLTKFLTPTRGEI 63 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 GK +E+A+ G+ R+FQ +F M+ LENV V + G+ +R++ Sbjct: 64 LYRGKNITSMKANEIARLGLVRSFQISAVFGHMSVLENVRVALQQKMGNSFH--FWRSER 121 Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186 E + + +LL V + FA A L YG +R LE+A LA DP ++ LDEP Sbjct: 122 SLRE---LDDQVMQLLAEVDLQSFAQTLAVELPYGRKRALELATTLALDPFVLLLDEPTQ 178 Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246 GM + + + EL+ R NRT+L++EH++ +V LCDR+TVL G +AEG+ V Sbjct: 179 GMGSEDVDMVVELV-RKAAANRTVLMVEHNLSVVSRLCDRITVLARGSVLAEGDYESVSA 237 Query: 247 NEKVIEAYLGT 257 N +V EAYLG+ Sbjct: 238 NPQVREAYLGS 248 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: 164 Number of extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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