Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 218 bits (555), Expect = 2e-61 Identities = 128/306 (41%), Positives = 186/306 (60%), Gaps = 9/306 (2%) Query: 43 LLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAV 102 +LF L + + G F +A N +NIL +V+I ++A GMTFVIL GID++VGS+LA Sbjct: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 Query: 103 SAVLGMQVS---LGAAPG-WAIPMFIFS--GLVMGMVNGAMVALLNINAFVVTLGTMTAF 156 +++ V +G P W I + + + GL G V G V L++ AF+VTLG MT + Sbjct: 89 ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148 Query: 157 RGAAYLLADGTTVLN-NDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHI 215 RGA LL DG + ND ++ W G+G+ L +P + + V V LR T G + Sbjct: 149 RGATLLLNDGGPISGFND--AYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQV 206 Query: 216 YAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIA 275 YA+GGN +AARL+G+ V + VY+I G +GL+G + ++RL A G+GYEL IA Sbjct: 207 YAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIA 266 Query: 276 AVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKW 335 +VV+GG SL GG G + GTV+GAL+IGV++NGL +L ++S+ Q V G +IV AV D + Sbjct: 267 SVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326 Query: 336 RQKDAA 341 + A Sbjct: 327 ARTHKA 332 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: 352 Number of extensions: 16 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: 332 Length adjustment: 28 Effective length of query: 316 Effective length of database: 304 Effective search space: 96064 Effective search space used: 96064 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