Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PP_4863 PP_4863 high-affinity branched-chain amino acid transporter, ATP-binding
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Putida:PP_4863 Length = 238 Score = 281 bits (719), Expect = 8e-81 Identities = 145/235 (61%), Positives = 184/235 (78%), Gaps = 1/235 (0%) Query: 10 PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVV 69 P+L++ ++ +YG I+AL V +H+N+GE VSLIGANGAGKSTL+M+I G P+A +G +V Sbjct: 4 PILELKDLDVFYGPIQALKKVSMHINEGETVSLIGANGAGKSTLLMSIFGQPRAASGHIV 63 Query: 70 FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTL 129 + G DITR +H IA IAQSPEGRR+FP MTV ENL MG KH ED+++++ L Sbjct: 64 YRGTDITRKSSHYIASNGIAQSPEGRRVFPDMTVEENLMMGTIPIGDKHADEDMQRMYEL 123 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FPRLKER QR T+SGGEQQML+I RALM+RPKLLLLDEPSLGLAP++VK IF +R+L Sbjct: 124 FPRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFSTLREL 183 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 + G+T+FLVEQNA AL+LS RAYVMVNG++ M+G+G+ELL N EVR AYL G Sbjct: 184 AKT-GMTIFLVEQNANHALKLSDRAYVMVNGQIRMTGTGQELLVNEEVRNAYLGG 237 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: 223 Number of extensions: 4 Number of successful extensions: 2 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: 238 Length adjustment: 23 Effective length of query: 224 Effective length of database: 215 Effective search space: 48160 Effective search space used: 48160 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