Align Fructose import permease protein FruF (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 137 bits (345), Expect = 4e-37 Identities = 89/272 (32%), Positives = 146/272 (53%), Gaps = 12/272 (4%) Query: 59 ITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAMQTLS----NGMNVWL-SI 113 + +L E + Y +IA GMT VI GID++VGS++A A AA ++ +G WL ++ Sbjct: 53 LNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIAL 112 Query: 114 LIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVAG-NEP 172 L++ +GLA G V G V++L + FI TL M RG ++ G ++G N+ Sbjct: 113 LVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDG-----GPISGFNDA 167 Query: 173 LKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKIL 232 +W+ +G IL +P VI ++ + R T G + AVG N EA+R++G+ I Sbjct: 168 YRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFIT 227 Query: 233 FLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSA 292 VYAI G LA ++G +A + + V G E+ I +VVIGG SL GG + G+ Sbjct: 228 TSVYAIIGALAGLSGFLLSARLGSAEAV-AGTGYELRVIASVVIGGASLTGGSGGVGGTV 286 Query: 293 VGAVIIAMIRKTIITLGVNAEATPAFFAVVVI 324 +GA++I ++ ++ L V + ++++ Sbjct: 287 LGALLIGVLSNGLVMLHVTSYVQQVVIGLIIV 318 Lambda K H 0.325 0.136 0.384 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: 323 Number of extensions: 25 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: 356 Length of database: 332 Length adjustment: 29 Effective length of query: 327 Effective length of database: 303 Effective search space: 99081 Effective search space used: 99081 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