Align Inner-membrane translocator (characterized, see rationale)
to candidate H281DRAFT_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Burk376:H281DRAFT_04148 Length = 335 Score = 169 bits (429), Expect = 8e-47 Identities = 105/303 (34%), Positives = 173/303 (57%), Gaps = 12/303 (3%) Query: 64 WPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPV-ALLSIGMSLVIATGG 122 +P + L ++ + +F SF L G+ I+ + R + A++++GM+ VI TGG Sbjct: 38 YPFIGLLVVCIVMVFASDSF---------LSGANIENVLRQVSINAIIAVGMTCVILTGG 88 Query: 123 IDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVAT 182 IDLSVG+VMA+AG + A L+ V ++ + +A G+ VGL G NG V+F G+ PI+ T Sbjct: 89 IDLSVGSVMALAGTLAAGLM-VAGMNALAALAVGVAVGLGFGAANGFFVAFAGMPPIIVT 147 Query: 183 LLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTA 242 L M RG+A + G I + G G+ LG+ PV I+ + + +LL + Sbjct: 148 LATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGIQAPVVIMAVIYVIAWVLLERMP 207 Query: 243 LGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWL 302 G ++ A+G N +A+R G+ +KL Y IAGL ++ A ++ TA + S NAG+ Sbjct: 208 FGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSSFAAIVLTARLM-SGQPNAGVGF 266 Query: 303 ELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTV 362 ELDA+ AVV+GG +++GGR S+I +++GAL++ L + + G+ +IK +IL Sbjct: 267 ELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLA 326 Query: 363 LLL 365 + + Sbjct: 327 IYI 329 Lambda K H 0.323 0.136 0.379 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: 336 Number of extensions: 17 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: 405 Length of database: 335 Length adjustment: 30 Effective length of query: 375 Effective length of database: 305 Effective search space: 114375 Effective search space used: 114375 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 (22.0 bits) S2: 49 (23.5 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