Align Inner-membrane translocator (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 127 bits (318), Expect = 6e-34 Identities = 86/271 (31%), Positives = 146/271 (53%), Gaps = 7/271 (2%) Query: 98 IDILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLV-----PDISLVTV 152 ++IL+ + ++++GM+ VI GGID++VG+++A A A ++ P L+ + Sbjct: 53 LNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIAL 112 Query: 153 IAAGLIVGLLAGCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAI 212 + + LI GL G + G V++L + + TL M RG L+N G I+ + + Sbjct: 113 LVSTLI-GLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWW 171 Query: 213 GVGQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAY 272 G G+ L LP+PV I + + LR T G + AVG NA+A+R G+N I Y Sbjct: 172 GSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVY 231 Query: 273 GIAGLCAALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGAL 332 I G A L+G + +A + GS AG EL + +VVIGGA+LTGG + +V+GAL Sbjct: 232 AIIGALAGLSGFLLSARL-GSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGAL 290 Query: 333 IIQTLATTIIVSGLPAKFNLLIKAIVILTVL 363 +I L+ +++ + + ++ ++I+ + Sbjct: 291 LIGVLSNGLVMLHVTSYVQQVVIGLIIVAAV 321 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: 316 Number of extensions: 20 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: 332 Length adjustment: 30 Effective length of query: 375 Effective length of database: 302 Effective search space: 113250 Effective search space used: 113250 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