Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 133 bits (334), Expect = 8e-36 Identities = 101/305 (33%), Positives = 150/305 (49%), Gaps = 16/305 (5%) Query: 54 TVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAA 113 T+ +++ + GA N RF ++L + + A+G V+ GGIDV+ ++ A Sbjct: 28 TILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLA 87 Query: 114 LTMYGITKAVFAWWPDAP--FALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYL 171 V A D P + + L+ L G+ G V G V L P+ IVT+G + Sbjct: 88 FASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTV 147 Query: 172 YRG--LLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWW 229 +RG LLL G N + G I L +PV + ALVAAA Sbjct: 148 WRGATLLLNDGGPISGFNDAYRWWGSGEI----------LFLPVPVVIFALVAAAGHV-- 195 Query: 230 LLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPF 289 L T GR VYA+GG+ A G N+ I V+ G LAG++G L + A Sbjct: 196 ALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAV 255 Query: 290 DLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGA 349 G EL VIA+V++GGA +TGG+G V GT+LG +L+ ++ + L+++ V S Q+V+IG Sbjct: 256 AGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGL 315 Query: 350 FILLA 354 I+ A Sbjct: 316 IIVAA 320 Lambda K H 0.328 0.141 0.426 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: 301 Number of extensions: 16 Number of successful extensions: 4 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: 364 Length of database: 332 Length adjustment: 29 Effective length of query: 335 Effective length of database: 303 Effective search space: 101505 Effective search space used: 101505 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