Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 216 bits (551), Expect = 6e-61 Identities = 127/282 (45%), Positives = 171/282 (60%), Gaps = 12/282 (4%) Query: 5 TFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENV-TDGAIF 63 TF D +L+ ++ +L+I GE +VL+GPSGCGK+TTLR++AGLE G + Sbjct: 15 TFADGTLA--------LQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM 66 Query: 64 IGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATL 123 GD DVT + R + MVFQ+YAL+P+MTV EN+ + L++ +RVDE A + Sbjct: 67 FGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMM 126 Query: 124 GLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQR 183 L F ER+ LSGGQRQRVA+ RAI P+V L+DEPL+ LDAKLR R I L R Sbjct: 127 HLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLR 186 Query: 184 KLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNL 243 L +T VYVTHDQ EA+ +GDRI V+ G + Q G P+++Y PAN FVA FIG+ MN Sbjct: 187 SLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MN- 243 Query: 244 GTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPE 285 +V + DA + T A++ + R + FRPE Sbjct: 244 RLPAVLEADAWRVPGGLVPRHGTAASLAAAPSPRAELLFRPE 285 Lambda K H 0.316 0.135 0.380 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: 350 Number of extensions: 14 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: 376 Length of database: 357 Length adjustment: 30 Effective length of query: 346 Effective length of database: 327 Effective search space: 113142 Effective search space used: 113142 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 (21.6 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