Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 197 bits (500), Expect = 4e-55 Identities = 121/316 (38%), Positives = 182/316 (57%), Gaps = 16/316 (5%) Query: 31 RLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTA 90 R G+ P+ L ++ L++ + F + NI+ QV++ + A G TFVI+T+ Sbjct: 23 RSGIGPLFAALVIICIALSI-----ASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITS 77 Query: 91 GIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFS-------GLVMGMVNGAMVALLNI 143 GIDLSVGS++A++ ++ V G++PG AI + I G G +NG VA L + Sbjct: 78 GIDLSVGSLVALTGMVAATVMAGSSPG-AIGLGIAGLCAALAVGAAAGALNGLAVAWLRL 136 Query: 144 NAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPS-FEWIGNGDFLHVPWLIWVAVAVVLLS 202 F+VTL M RG ++DG T D P+ F G +P + V + + ++ Sbjct: 137 VPFIVTLAMMAMARGLTLAISDGRTKF--DFPNAFTAFGAKTVAGLPMPMIVMLVIFVIG 194 Query: 203 WVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGAN 262 V+LRKT G ++A+GGN +AARL GI V V+ Y ++G+ + +AG + A RL A Sbjct: 195 HVLLRKTTFGHQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSAL 254 Query: 263 GNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAK 322 + +G EL IAAVV+GGTSL GG GSI GT +G ++IGV+N GL++LG++ FW + Sbjct: 255 PSAANGLELQVIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQ 314 Query: 323 GAVIVLAVILDKWRQK 338 G VI AV+LD Q+ Sbjct: 315 GGVIFAAVLLDALSQR 330 Lambda K H 0.324 0.138 0.417 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: 327 Number of extensions: 22 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: 344 Length of database: 333 Length adjustment: 28 Effective length of query: 316 Effective length of database: 305 Effective search space: 96380 Effective search space used: 96380 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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