Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate H281DRAFT_03731 H281DRAFT_03731 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__Burk376:H281DRAFT_03731 Length = 270 Score = 133 bits (335), Expect = 4e-36 Identities = 79/258 (30%), Positives = 130/258 (50%), Gaps = 1/258 (0%) Query: 42 VLTLASLVALFPVAWLVYLSLGPDKNDYLHPGRIWSKMTFDNYAFVLQDTNFFDWLKSSL 101 VL + L AL P+ W++ +SL ++ + +TF+NY + D +++ +S+ Sbjct: 12 VLVVYMLFALIPLYWMLSISLRTNEETMSTFATLPQHVTFENYKIIFTDPSWYWGYINSI 71 Query: 102 IVSLGTTVIGVLVAATTGYAVSRMRFPGYRKLMWVLLVTQMFPIAVLIVPMYQILSKLQL 161 I L TV+ VLVA YA SR RF G + + + LL +M P AV ++P +Q+ S + L Sbjct: 72 IYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLLPFFQLYSSVGL 131 Query: 162 IDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPFGTFFRLILPLARPG 221 D Y + L + VP W+L+G+ + EIDE +DG T F ++ LPL + G Sbjct: 132 TDTYIAVALAHMLFNVPLAVWILEGFMSGVSREIDETAYIDGYTFPAFFVKIFLPLIKSG 191 Query: 222 LAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEHDAQRNLMAATAVLVAIPV 281 + V F+ F+ ++ E+ A T + K AV + VS +++A VL +P Sbjct: 192 VGVTAFFCFMFSWVELLLARTLTSVNAKPIAAV-MTRTVSAAGMDWGVLSAAGVLTIVPG 250 Query: 282 SAFFYLVQKNLVTGLTAG 299 + Y V+ + G G Sbjct: 251 ALVIYFVRNYIAKGFAMG 268 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: 261 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 303 Length of database: 270 Length adjustment: 26 Effective length of query: 277 Effective length of database: 244 Effective search space: 67588 Effective search space used: 67588 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: 47 (22.7 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