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:D8J112 (347 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 204 bits (520), Expect = 2e-57 Identities = 125/334 (37%), Positives = 188/334 (56%), Gaps = 21/334 (6%) Query: 26 ARLFNPAARQKLLAFAS-------LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAI 78 A L R LLAFA LLL++ F A+ F+ N ++IL ++ G++A+ Sbjct: 8 APLATDKPRFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAV 67 Query: 79 ACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLP----LGIAAAIFFGALSGWISG 134 T+VI+ GID++VG+++ F ++ A V+T P + + + G G++ G Sbjct: 68 GMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQG 127 Query: 135 MVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIY-FNDTEGFSAIAQDSLIGDLIPSLP 193 + L VP FI TLG M + +G +L+++ PI FND + + I LP Sbjct: 128 KAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWWGSGE-------ILFLP 180 Query: 194 IPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAIC 253 +P V+I LVA + L T +GR +A+G N EA RLSGV VDF +VY GA+ Sbjct: 181 VP--VVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALA 238 Query: 254 GIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNG 313 G++G ++++RL SA+ G GYEL IA+VVIGG SL+GG+G + GT++GA ++ VL NG Sbjct: 239 GLSGFLLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNG 298 Query: 314 LRIMSVAQEWQTVVTGVIIILAVYLDILRRRRRA 347 L ++ V Q VV G+II+ AV D R +A Sbjct: 299 LVMLHVTSYVQQVVIGLIIVAAVAFDHYARTHKA 332 Lambda K H 0.326 0.139 0.398 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: 241 Number of extensions: 17 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: 347 Length of database: 332 Length adjustment: 28 Effective length of query: 319 Effective length of database: 304 Effective search space: 96976 Effective search space used: 96976 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 (21.7 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