Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Putida:PP_2753 Length = 257 Score = 186 bits (473), Expect = 3e-52 Identities = 103/241 (42%), Positives = 161/241 (66%), Gaps = 8/241 (3%) Query: 9 LLQVKGLKVAYGG-IQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLS-----MN 62 LL V+ ++V Y G I AV GV V +G++V+L+G+NGAGK+TT+KAI+G + ++ Sbjct: 14 LLAVEDIEVIYDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAHVS 73 Query: 63 DGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKD-KAGILAD 121 G+I + G+ G A L ++G+V V EGR VF+ +TI ENL+ G ++R + + D Sbjct: 74 RGHIRFQGQDTAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLEQD 133 Query: 122 IEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKI 181 +E+++ FPRL+ ++ AG SGGEQQMLA+GRALM++P+++LLDEPSMGL+PI+V++I Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVEEI 193 Query: 182 FEVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 F +V + A GV+ ++ EQN + AL A Y++E+G + G +L ++ YL Sbjct: 194 FAIVAQLNAQQGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHFYL 253 Query: 241 G 241 G Sbjct: 254 G 254 Lambda K H 0.317 0.136 0.373 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: 162 Number of extensions: 8 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: 242 Length of database: 257 Length adjustment: 24 Effective length of query: 218 Effective length of database: 233 Effective search space: 50794 Effective search space used: 50794 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