Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >MicrobesOnline__882:209225 Length = 354 Score = 161 bits (407), Expect = 3e-44 Identities = 96/239 (40%), Positives = 133/239 (55%), Gaps = 16/239 (6%) Query: 6 LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65 +E + +T G+ + D NL E VGPSG GKTT LR IAGL+ EG + + Sbjct: 5 VEGLGRTLAGRE--VLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRV- 61 Query: 66 DRRVNDVPPKDRD--IAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKIL 123 PP+ + +VFQ+Y L+PH++V++N+AFG + R V A + RV + Sbjct: 62 ------TPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAF 115 Query: 124 -----DIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEI 178 D+AH+ R P LS GQRQRVAL RA+V +P V L+DEP +NLD LR +M A + Sbjct: 116 RLDTDDLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFV 175 Query: 179 RKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237 R + +R + VTHD EA +GDR+ VM G + Q P VY P + A F+G Sbjct: 176 RDVVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG 234 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: 365 Number of extensions: 24 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: 354 Length adjustment: 30 Effective length of query: 354 Effective length of database: 324 Effective search space: 114696 Effective search space used: 114696 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: 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