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::Q70HW1 (384 letters) >FitnessBrowser__Cola:Echvi_2123 Length = 318 Score = 148 bits (373), Expect = 2e-40 Identities = 85/231 (36%), Positives = 142/231 (61%), Gaps = 10/231 (4%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVND-----VPPK 75 ++DF+L ++ VG SG GK++ LR+IAGLE + G +++GD+++ + VP Sbjct: 20 LEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHLGDQKILNPAQKLVPGY 79 Query: 76 DRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKA 135 D +I ++ Q Y LYP+ TV +N+A L L KA R E ++L + D+KP+ Sbjct: 80 D-EIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERTAEILELLSLRAFKDKKPRQ 136 Query: 136 LSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHD 195 LSGGQ+Q+VA+GRA+ EP+V L+DEP S+LDA + + E++++ L+ TVI+VTHD Sbjct: 137 LSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEIFDALEVTVIFVTHD 196 Query: 196 QTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRG 246 +A+ M + +++++ G + Q + V+ +P + +VA G +N I G Sbjct: 197 VDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLFG--YLNLIPG 245 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: 247 Number of extensions: 12 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: 318 Length adjustment: 29 Effective length of query: 355 Effective length of database: 289 Effective search space: 102595 Effective search space used: 102595 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