Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 221 bits (562), Expect = 3e-62 Identities = 137/322 (42%), Positives = 194/322 (60%), Gaps = 22/322 (6%) Query: 19 LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDIEP---QNR 75 L+ +DLDI GE +VL+GPSGCGK+T LR +AGLE D+G + + G ND+ P + R Sbjct: 23 LQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVMFGD--NDVTPLPIEQR 80 Query: 76 DIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELS 135 + MVFQSYAL+P+MTVAEN+ +GL+++ + AA +RV+E+ ++ + +R+ +LS Sbjct: 81 GVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMMHLGPFAERRIDQLS 140 Query: 136 GGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQM 195 GGQRQRVAL RA++ Q V+L DEPL+ LDA LR +R +I +L + T +YVTHDQ Sbjct: 141 GGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLRSLHITAVYVTHDQA 200 Query: 196 EATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGAVLEKIPWPEA 255 EA LGDRI V+ G I Q GTP +IY P N F+A FIG+ MN L AVLE W Sbjct: 201 EAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNRLP-AVLEADAW--- 254 Query: 256 RKADQILGIRPDAFALNQGPLGTQEVALGDFQIDISE----NLGGQQMLHGTLAGNNVRI 311 R ++ A +L P E+ + +++ +LGG ++ GN R+ Sbjct: 255 RVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGG-SVVTALFLGNYTRL 313 Query: 312 LVDSMDNFSMKQTLPLKIDLTK 333 LVD + PL +D T+ Sbjct: 314 LVD------VGAPAPLVVDTTR 329 Lambda K H 0.318 0.136 0.383 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: 320 Number of extensions: 15 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: 347 Length of database: 357 Length adjustment: 29 Effective length of query: 318 Effective length of database: 328 Effective search space: 104304 Effective search space used: 104304 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: 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