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::Q70HW1 (384 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 224 bits (571), Expect = 3e-63 Identities = 121/272 (44%), Positives = 165/272 (60%), Gaps = 11/272 (4%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 V +L I F +G SGCGKTTTLRMI+GLE T G +++GD+ V D P R + Sbjct: 34 VDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQDVTDRKPYRRPVN 93 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 VFQNYAL+PH+ +++N+AFGL+ R + + + V++ ++++ HL RKP LSGGQ Sbjct: 94 TVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLVELGHLARRKPTQLSGGQ 151 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 +QR+AL RA++ +PQV L+DEPL LD KLR QM+ E++++ + T ++VTHDQ EAM Sbjct: 152 QQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGLTFVHVTHDQEEAM 211 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ-DGDAFYFRA 259 TM D I VM G I+Q +P +Y P FVA F+G N I G + GD A Sbjct: 212 TMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNLIAGTVESVSGDVVQVAA 269 Query: 260 PSISLRLPEGRYGVLKASGAIGKPVVLGVRPE 291 SL LP R PV+LGVRPE Sbjct: 270 HGRSLALPAARCRTTSG------PVILGVRPE 295 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: 364 Number of extensions: 10 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: 386 Length adjustment: 30 Effective length of query: 354 Effective length of database: 356 Effective search space: 126024 Effective search space used: 126024 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: 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