Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 134 bits (337), Expect = 3e-36 Identities = 77/221 (34%), Positives = 126/221 (57%), Gaps = 6/221 (2%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVT---HVAPRDR 77 ++ +L++A GE +V+ GPSG GKST +R + GLE +G I IG+ +V V R R Sbjct: 17 LRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRIR 76 Query: 78 D-IAMVFQNYALYPHMTVGENMGFA-LKIAGKSQDEINKRVDEAAATLGLTEFLERKPKA 135 + MVFQ++ L+PH+T+ EN A +K+ G ++D E + + + ++ P Sbjct: 77 ARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYPAQ 136 Query: 136 LSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHD 195 LSGGQ+QR A+ RA+ P++ L DEP S LDA++ + + AL + G+T + VTH+ Sbjct: 137 LSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GITMLCVTHE 195 Query: 196 QTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFI 236 A + DRI + G + + G+PR+ + P + F+ Sbjct: 196 MGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236 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: 216 Number of extensions: 8 Number of successful extensions: 4 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: 241 Length adjustment: 27 Effective length of query: 349 Effective length of database: 214 Effective search space: 74686 Effective search space used: 74686 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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