Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Putida:PP_2753 Length = 257 Score = 196 bits (498), Expect = 4e-55 Identities = 108/242 (44%), Positives = 153/242 (63%), Gaps = 8/242 (3%) Query: 11 LLQVNGVETYY-GNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQA-----R 64 LL V +E Y G I A+AGV + V +G+IV+L+GANGAGKST + I G QA Sbjct: 14 LLAVEDIEVIYDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAHVS 73 Query: 65 TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDN--LKHFAED 122 G + F+G+D + + +AR I EGR +F +T+ ENL+ G L N + +D Sbjct: 74 RGHIRFQGQDTAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLEQD 133 Query: 123 VEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGI 182 +E+I+ FPRLK + + G SGGEQQML+IGRALM +P+L+LLDEPS+GLAP+IV+ I Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVEEI 193 Query: 183 FEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 F + +LN +G++ + EQN ALR + AY++ NG+V GS EL A +++ YL Sbjct: 194 FAIVAQLNAQQGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHFYL 253 Query: 243 EG 244 G Sbjct: 254 GG 255 Lambda K H 0.320 0.137 0.387 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: 196 Number of extensions: 7 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: 247 Length of database: 257 Length adjustment: 24 Effective length of query: 223 Effective length of database: 233 Effective search space: 51959 Effective search space used: 51959 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 (21.8 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