Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 184 bits (468), Expect = 2e-51 Identities = 92/268 (34%), Positives = 157/268 (58%), Gaps = 9/268 (3%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NLE+ +GE+ +++GP+G GK+ L +AG+ G I ++++ +AP R + V+Q Sbjct: 20 NLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFVYQ 79 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 +YAL+PH+TV EN+ F +I + I ++DE A LG+ L R P LSGG++QR Sbjct: 80 DYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQRT 139 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 A+ RA++ +P++ L+DEPLS LD + + + ++ + + L TT++VTHD EA+ + D Sbjct: 140 ALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYLAD 199 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARIKLSP 264 +I V+ G + QVG P+E++ +P N FVA F+G N+ V D ++ L+P Sbjct: 200 KIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVG--IENIFEGQVNDD-------KVSLAP 250 Query: 265 ETLAAMTPEDNGRITIGFRPEALEIIPE 292 + + G++ + PE + + E Sbjct: 251 DVDIFVNTGKQGKVKVAVPPEDIALSKE 278 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: 305 Number of extensions: 17 Number of successful extensions: 1 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: 344 Length adjustment: 29 Effective length of query: 347 Effective length of database: 315 Effective search space: 109305 Effective search space used: 109305 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 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