Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__Koxy:BWI76_RS06705 Length = 283 Score = 170 bits (430), Expect = 4e-47 Identities = 91/264 (34%), Positives = 150/264 (56%), Gaps = 3/264 (1%) Query: 42 VLTLASLVALFPVAWLVYLSLGPDKNDYLHPGRIWSKMTFDNYAFVLQ-DTNFFDWLKSS 100 V+ S + ++P+ W V SL N L I ++F +YA + + N+ W +S Sbjct: 21 VVIFVSTMIIYPLVWTVGASLNAG-NSLLSTSIIPENLSFQHYADLFNGNVNYLTWYWNS 79 Query: 101 LIVSLGTTVIGVLVAATTGYAVSRMRFPGYRKLMWVLLVTQMFPIAVLIVPMYQILSKLQ 160 + +S T V+ ++ + T YA SR RF G + + + L+ QM P ++ ++ + L Sbjct: 80 MKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALIAIFVLSQLLG 139 Query: 161 LIDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPFGTFFRLILPLARP 220 LI+++ L+L+Y +P WL+KGY D IP ++DE+ R+DG + F FF +I+PL++P Sbjct: 140 LINSHLALVLIYVGGMIPMNTWLMKGYLDAIPKDLDESARMDGASSFRIFFEIIMPLSKP 199 Query: 221 GLAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEH-DAQRNLMAATAVLVAI 279 LAV +SF G+ +ST + + KYT +GL + V++ A AA AVL+A+ Sbjct: 200 ILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGASYTTYAAGAVLIAV 259 Query: 280 PVSAFFYLVQKNLVTGLTAGGTKG 303 PV+ + +QK V+GLT+G TKG Sbjct: 260 PVAILYLALQKYFVSGLTSGSTKG 283 Lambda K H 0.326 0.139 0.422 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: 251 Number of extensions: 12 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: 303 Length of database: 283 Length adjustment: 26 Effective length of query: 277 Effective length of database: 257 Effective search space: 71189 Effective search space used: 71189 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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