Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Putida:PP_2753 Length = 257 Score = 210 bits (534), Expect = 2e-59 Identities = 114/232 (49%), Positives = 157/232 (67%), Gaps = 8/232 (3%) Query: 10 YYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQA-----ASGSIRYEGEE 64 Y G I A+ VS+ V +G+IV L+GANGAGKST L + G QA + G IR++G++ Sbjct: 24 YDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAHVSRGHIRFQGQD 83 Query: 65 LVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD--KVLELFPR 122 G+ ++ + R+ I V EGR VFS LT+EENL GGF + Q++ D ++ FPR Sbjct: 84 TAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLEQDLERIYAWFPR 143 Query: 123 LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR-R 181 LK + + +AG SGGEQQMLAIGRALM+KP+L+LLDEPS+GLAPII+++IF I+ QL + Sbjct: 144 LKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVEEIFAIVAQLNAQ 203 Query: 182 EGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233 +GV+ + EQN N AL+ A AY+LENGR+V + A L ++ YLGG Sbjct: 204 QGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHFYLGG 255 Lambda K H 0.318 0.136 0.374 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: 161 Number of extensions: 5 Number of successful extensions: 4 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: 233 Length of database: 257 Length adjustment: 24 Effective length of query: 209 Effective length of database: 233 Effective search space: 48697 Effective search space used: 48697 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: 46 (22.3 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