Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_008411393.1 DESHY_RS06575 ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000315365.1:WP_008411393.1 Length = 227 Score = 192 bits (489), Expect = 6e-54 Identities = 96/212 (45%), Positives = 150/212 (70%), Gaps = 4/212 (1%) Query: 15 EVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGI 74 +++ + +++L + GE + +LG SG GK+T LR++AGLE+P G I I +K++ D Sbjct: 16 QLSTINKVNLSISRGEIIAILGQSGSGKSTILRLLAGLEKPCSGTIVIDNKVMFD--NNT 73 Query: 75 FVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLN 134 +V P++R + MVFQ YAL+PHMTV NI + L K+ R+E +R++EV L+ L E + Sbjct: 74 YVNPENRGVGMVFQDYALFPHMTVEKNIIYGLA--KLDRKERTKRLKEVLTLVNLEEFRD 131 Query: 135 RKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTI 194 R P ELSGGQ+QRVAL RA+ KP V L+DEP SNLDA LR ++R ELK++ + +G+T+I Sbjct: 132 RYPYELSGGQQQRVALARALAPKPAVLLLDEPFSNLDADLRCKIRDELKRIIKDVGITSI 191 Query: 195 YVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDE 226 +VTHDQ +A+++ DR+ +++G + +V + +E Sbjct: 192 FVTHDQEDAISLADRVVYLHKGTVLKVKTKEE 223 Lambda K H 0.323 0.142 0.406 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: 197 Number of extensions: 5 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: 372 Length of database: 227 Length adjustment: 26 Effective length of query: 346 Effective length of database: 201 Effective search space: 69546 Effective search space used: 69546 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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