Align Inositol transport system permease protein (characterized)
to candidate BWI76_RS14605 BWI76_RS14605 ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__Koxy:BWI76_RS14605 Length = 336 Score = 152 bits (384), Expect = 1e-41 Identities = 96/310 (30%), Positives = 148/310 (47%), Gaps = 39/310 (12%) Query: 59 NWSQI---SAQFMIIAVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILV 115 NW I SA +I+A L++ G DLSVGS + G L AI G P + +L Sbjct: 53 NWLNIIRQSAPLLIVATAMTLVITTGGIDLSVGSTLALVGALSAIALNNWGLPWPVVLLG 112 Query: 116 TFAIATAIGALNGFIVVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEG 175 + +GA+NGF + G+P+FIVTLA L ++RG A+ + Q G + Sbjct: 113 GLLLGGIVGAINGFFIAYEGIPAFIVTLATLAVVRGIALLVTQ---------GYSIPVPA 163 Query: 176 DWLAALFGGKILTGLFQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVIL 235 D L G W+ G+PM + I++++IGH++L Sbjct: 164 DSLFTFIG-------------RAWVV--------------GIPMPALIGIMILLIGHIVL 196 Query: 236 TKTRFGNWIFAAGGDAEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRG 295 RFG ++ A G +AE AR SG+ V + +++ + A + G S++G Sbjct: 197 NHMRFGRYVTAIGANAEGARRSGINTKAVTMKVYIISGMAAALAGMIITARLGSGSSNQG 256 Query: 296 LLKEFEAIIAVVIGGALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLIL 355 E + I AVV+G L GG+G+++G LGAL V+Q GL + + ++ G I+ Sbjct: 257 EGFELQVIAAVVLGSTSLFGGFGTIIGTLLGALSIAVIQNGLILSHISPFYTQIATGTII 316 Query: 356 LFAVILNTYI 365 L A+ LNT I Sbjct: 317 LLAIWLNTRI 326 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: 427 Number of extensions: 33 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 373 Length of database: 336 Length adjustment: 29 Effective length of query: 344 Effective length of database: 307 Effective search space: 105608 Effective search space used: 105608 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