Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_013402867.1 CALHY_RS04760 cell division ATP-binding protein FtsE
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000166355.1:WP_013402867.1 Length = 239 Score = 127 bits (318), Expect = 4e-34 Identities = 76/223 (34%), Positives = 125/223 (56%), Gaps = 8/223 (3%) Query: 8 HIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDR 67 ++ K YP + + NL I+ EF VG SG GK+T ++++ D TEG + +G+ Sbjct: 6 NVSKRYPNGVL-ALTNINLTIEKGEFVFLVGSSGAGKSTIVKLLLKEIDPTEGEIIVGEY 64 Query: 68 RVNDVPPKD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKI 122 ++ +P ++ R I +VFQ++ L P+ TVY+N+ F +++ P I R+V + Sbjct: 65 KLTQLPKREIPYYRRKIGIVFQDFRLLPNKTVYENVEFAMQITGAPAKIIRRQVPYVLSL 124 Query: 123 LDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLH 182 + +AH P LSGG++QRVAL RAIV +P + + DEP NLD ++ + ++ Sbjct: 125 VGLAHKAKCYPHELSGGEQQRVALARAIVNKPNLLVADEPTGNLDPDTSWEIMRLLEDIN 184 Query: 183 QRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYS 225 +R TTV+ TH + +M R+V + G I + D P+ VYS Sbjct: 185 KR-GTTVLVATHAKEIVDSMRKRVVAIDCGRIVK-DQPKGVYS 225 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: 206 Number of extensions: 9 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: 384 Length of database: 239 Length adjustment: 27 Effective length of query: 357 Effective length of database: 212 Effective search space: 75684 Effective search space used: 75684 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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