Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 223 bits (567), Expect = 9e-63 Identities = 128/322 (39%), Positives = 184/322 (57%), Gaps = 23/322 (7%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 +L IA G F L+G SGCGK+TTLRM++GLE T G I +GD+DVT P R + VFQ Sbjct: 38 DLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQDVTDRKPYRRPVNTVFQ 97 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 NYAL+PH+ + EN+ F L+ G + K V++ + L RKP LSGGQ+QR+ Sbjct: 98 NYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLVELGHLARRKPTQLSGGQQQRI 155 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 A+ RA++ PQV L+DEPL LD KLR Q + ++ +Q ++G+T V+VTHDQ EA+TM D Sbjct: 156 ALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGLTFVHVTHDQEEAMTMAD 215 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDA--TSGHARIKL 262 IAV+ G ++Q+G+P ELY+ P FVA F+G + GT GD + H R Sbjct: 216 TIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQSNLIAGTVESVSGDVVQVAAHGRSLA 275 Query: 263 SPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKLVG 322 P AA +G + +G RPE + I T+ +P + L GK+ Sbjct: 276 LP---AARCRTTSGPVILGVRPEKVRI----AKTEAEVP---------SGANHLTGKVTD 319 Query: 323 EGDLGSSSE---DVPESGQIVV 341 +G S++ ++P ++ V Sbjct: 320 ASFIGVSTQYLVELPSGEELAV 341 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: 366 Number of extensions: 14 Number of successful extensions: 2 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: 386 Length adjustment: 30 Effective length of query: 346 Effective length of database: 356 Effective search space: 123176 Effective search space used: 123176 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: 50 (23.9 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