Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_1113 Dsui_1113 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__PS:Dsui_1113 Length = 278 Score = 186 bits (472), Expect = 4e-52 Identities = 102/239 (42%), Positives = 147/239 (61%), Gaps = 8/239 (3%) Query: 12 LQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTG---- 66 L +N +E Y + I L GV + V KG+IV+L+GANGAGKST + I A G Sbjct: 16 LSINNIEVIYDHVILVLKGVSLTVPKGKIVALLGANGAGKSTTLKAISNLLHAERGDVTK 75 Query: 67 -SVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGL--DNLKHFAEDV 123 SV F+G + ++ +E+ + + Q EGR F +++ ENL GA ++ +++ Sbjct: 76 GSVEFKGTRVDQLTPNELVKRGVIQVMEGRHCFAHLSIEENLLTGAYTRGNSRAELKQNL 135 Query: 124 EKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIF 183 E ++ FPRLK R + G SGGEQQM +IGRALMA+P+++LLDEPS+GLAP IV+ IF Sbjct: 136 EMVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEEIF 195 Query: 184 EAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 E ++ LN E ++ L EQN ALR + Y++ NG+V M G KEL +N +V+ YL Sbjct: 196 EIVKDLNSRENVSFLLAEQNTMVALRYADLGYILENGRVVMEGDAKELASNEDVKEFYL 254 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: 183 Number of extensions: 14 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: 278 Length adjustment: 25 Effective length of query: 222 Effective length of database: 253 Effective search space: 56166 Effective search space used: 56166 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: 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