Align Inositol transport system permease protein (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 126 bits (316), Expect = 1e-33 Identities = 101/325 (31%), Positives = 150/325 (46%), Gaps = 41/325 (12%) Query: 46 AGDSGMFNSQGVMNWSQISAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTL 105 A + ++ +N + + IIAVG +++ G D++VGS++ FA + A + Sbjct: 41 AANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAFASIAAAYVVTAV 100 Query: 106 ---GWPVWL-AILVTFAIATAIGALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIE 161 G WL A+LV+ I A G + G V +P+FIVTL + + RG + L Sbjct: 101 VGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVWRGATLLLNDGGP 160 Query: 162 RKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLI 221 I G DA ++W+G + LP+ + Sbjct: 161 ----ISGFNDA------------------YRWWGSGEILF---------------LPVPV 183 Query: 222 VWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFAT 281 V L+ GHV L TR+G ++A GG+AEAAR SGV V+ + ++ A + Sbjct: 184 VIFALVAAAGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGF 243 Query: 282 CQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAG 341 G A + G E I +VVIGGA LTGG G V G LGAL+ GV+ GL Sbjct: 244 LLSARLGSAEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLH 303 Query: 342 VESSLFRVFLGLILLFAVILNTYIR 366 V S + +V +GLI++ AV + Y R Sbjct: 304 VTSYVQQVVIGLIIVAAVAFDHYAR 328 Lambda K H 0.330 0.145 0.443 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: 450 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 373 Length of database: 332 Length adjustment: 29 Effective length of query: 344 Effective length of database: 303 Effective search space: 104232 Effective search space used: 104232 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 (21.8 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