Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS16970 RR42_RS16970 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS16970 Length = 386 Score = 452 bits (1164), Expect = e-132 Identities = 225/339 (66%), Positives = 270/339 (79%), Gaps = 3/339 (0%) Query: 13 VALLVLPLILQSFG-NAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 + L P ++Q+ G N WVR+ D AL+Y++LALGLNIVVG+AGLLDLGY+AFYAVGAY+ Sbjct: 31 IIALCAPFLVQTLGGNYWVRVLDFALIYIMLALGLNIVVGFAGLLDLGYIAFYAVGAYMM 90 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL+ SPHLA+ F +FPNGLH S+W V+P+A L+AA FG +LGAPTLKLRGDYLAIV Sbjct: 91 ALLGSPHLANQFEWIHQLFPNGLHLSMWFVLPLAVLVAATFGVLLGAPTLKLRGDYLAIV 150 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191 TLGFGEIIRIFLNNLD P+N+TNGPKG+ +D V +FG D K E+FG V +YYY Sbjct: 151 TLGFGEIIRIFLNNLDRPLNITNGPKGITAVDPVHIFGFDFSKSHEIFGLKFTPVFMYYY 210 Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251 L +VLV+ V IC RLQ+SRIGRA++AIREDEIAAKAMGINTRN+KLLAF MGASFGG S Sbjct: 211 LLVVLVIAIVFICLRLQNSRIGRAFVAIREDEIAAKAMGINTRNIKLLAFAMGASFGGAS 270 Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311 GA+FGAFQGFVSPESF L ES+ I+A+VVLGG+GHIPGVILG +LL E+LR VA P Sbjct: 271 GAVFGAFQGFVSPESFVLWESIYILAIVVLGGMGHIPGVILGGILLVGFQELLRAVAEPA 330 Query: 312 QAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSP 348 Q M G +D+ +LRQLL LA++ +ML RP GLWPSP Sbjct: 331 QNMIFGHTIVDAEVLRQLLFGLALVGVMLYRPAGLWPSP 369 Lambda K H 0.328 0.144 0.430 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: 458 Number of extensions: 19 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: 358 Length of database: 386 Length adjustment: 30 Effective length of query: 328 Effective length of database: 356 Effective search space: 116768 Effective search space used: 116768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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