Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 131 bits (329), Expect = 2e-35 Identities = 75/208 (36%), Positives = 122/208 (58%), Gaps = 3/208 (1%) Query: 34 TVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRV--NDVPPKDRDIAMVFQNYALYPH 91 T +G SG GK+T LR++ GLE G++ + R + +DV P R + V Q+ L+PH Sbjct: 40 TALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSDVLPLRRRVGYVIQDGGLFPH 99 Query: 92 MTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI-AHLLDRKPKALSGGQRQRVALGRAI 150 +T N+A + + I +R ++ A + + +L+R P LSGGQRQRVAL RA+ Sbjct: 100 LTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGVLERYPAELSGGQRQRVALMRAL 159 Query: 151 VREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMR 210 + +P L+DEPL LD +R +++ E++++ +L TVI VTHD EA +R+V++R Sbjct: 160 MADPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKTVIVVTHDLAEAAWFAERLVLLR 219 Query: 211 DGVIQQADTPQVVYSQPKNMFVAGFIGS 238 G + Q T + + +P + FV F+ + Sbjct: 220 QGAVLQDGTFRDLRERPADAFVNRFVAA 247 Lambda K H 0.321 0.138 0.395 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: 212 Number of extensions: 10 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: 384 Length of database: 255 Length adjustment: 27 Effective length of query: 357 Effective length of database: 228 Effective search space: 81396 Effective search space used: 81396 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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