Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 149 bits (375), Expect = 1e-40 Identities = 82/221 (37%), Positives = 134/221 (60%), Gaps = 6/221 (2%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVA----PRD 76 ++ F+L++ G + +VG SG GKS+ LR++AGLE + G + +GD+ + + A P Sbjct: 20 LEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVPGY 79 Query: 77 RDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKAL 136 +I ++ Q Y LYP+ TV EN+ L + K+ + +R E L L F ++KP+ L Sbjct: 80 DEIQLIHQEYKLYPNSTVEENIARPLLLYDKAYQK--ERTAEILELLSLRAFKDKKPRQL 137 Query: 137 SGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQ 196 SGGQ+Q+VA+GRA+ P+V L+DEP S+LDA + ++ + L VT ++VTHD Sbjct: 138 SGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVTVIFVTHDV 197 Query: 197 TEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIG 237 +AL M + + +++ G L Q G RE++ +PA+ +VA G Sbjct: 198 DDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG 238 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: 241 Number of extensions: 7 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: 376 Length of database: 318 Length adjustment: 29 Effective length of query: 347 Effective length of database: 289 Effective search space: 100283 Effective search space used: 100283 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