Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_4864 PP_4864 High-affinity branched-chain amino acid transport ATP-binding protein BraF
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Putida:PP_4864 Length = 291 Score = 267 bits (682), Expect = 2e-76 Identities = 137/293 (46%), Positives = 197/293 (67%), Gaps = 27/293 (9%) Query: 9 MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68 MSDD +L V++L M+FGG+ A++D S + +R I ALIGPNGAGKTTVFNC+TGFYK + Sbjct: 1 MSDDIILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASG 60 Query: 69 GMITFNQKSGKQYLLERL------PDF------------------RITKEARVARTFQNI 104 G I N + +++ L DF + A +ARTFQNI Sbjct: 61 GRIELNVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNI 120 Query: 105 RLFSGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDR 164 RLF ++V+ENLLVAQH M + + G++ Y++ ++A++ A +WLE DL+D Sbjct: 121 RLFKEMSVVENLLVAQH---MWVNRNLLAGVLNTKAYRKAESDALDHAFYWLEVVDLVDC 177 Query: 165 ADDPAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTS 224 A+ AG+L YG QRRLEIARAMCT P+++CLDEPAAGLNP+E+ L+ +++ +R E + Sbjct: 178 ANRLAGELSYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDIT 237 Query: 225 ILLIEHDMSVVMEISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLGVEDEEV 277 ++LIEHDM +VM ISDH+VVL++G I++G P ++++P VIAAYLG ++EE+ Sbjct: 238 VVLIEHDMGMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGADEEEL 290 Lambda K H 0.318 0.136 0.386 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: 241 Number of extensions: 6 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: 292 Length of database: 291 Length adjustment: 26 Effective length of query: 266 Effective length of database: 265 Effective search space: 70490 Effective search space used: 70490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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