Align Fructose import permease protein FrcC (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 155 bits (391), Expect = 2e-42 Identities = 106/309 (34%), Positives = 162/309 (52%), Gaps = 14/309 (4%) Query: 53 IVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVL 112 I+ +L L+A +F +A IL +V+I GI+ T VIL GID++VG+++ Sbjct: 29 ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88 Query: 113 SSVIMGQF-TFRYGFPPA---LSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIV 168 +S+ T G PA ++++ +G GY+ G V + +P FIVTLG + Sbjct: 89 ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148 Query: 169 LASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYV-LNR 227 + L + I S +++G G +F VV+ LV +V L Sbjct: 149 RGATLLLNDGGPI-----SGFNDAYRWWGS----GEILFLPVPVVIFALVAAAGHVALRY 199 Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287 T +GR VYAVG + EAA+L+GVNV + S+Y + G + L+G+ L R+GS AG Sbjct: 200 TRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTG 259 Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347 + I +VVIGG SL GG G + G + GAL++GV S GL ++ ++IGL+I+ Sbjct: 260 YELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVA 319 Query: 348 AVAIDQWIR 356 AVA D + R Sbjct: 320 AVAFDHYAR 328 Lambda K H 0.327 0.141 0.420 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: 336 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: 360 Length of database: 332 Length adjustment: 29 Effective length of query: 331 Effective length of database: 303 Effective search space: 100293 Effective search space used: 100293 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