Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 150 bits (380), Expect = 4e-41 Identities = 104/310 (33%), Positives = 155/310 (50%), Gaps = 13/310 (4%) Query: 45 RLARNPEWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGI 104 RL R+P ++ +VV L++ + F + L ++ + ++ A+G V+ +GGI Sbjct: 25 RLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVILTGGI 84 Query: 105 DVSFTAIAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIV 164 D+S + AL+ + A P L + G L GV G+ NGL V L P +IV Sbjct: 85 DLSVGPVMALSGTLTAGLMVAGLPPG---LAIGAGMLIGVAFGIGNGLFVAYLHMPPIIV 141 Query: 165 TIGTQYLYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAA 224 T+ T + RGL L + +P FGR LF + V +L ++ Sbjct: 142 TLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFG----------IQVPILIMLLTY 191 Query: 225 VVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNR 284 +V + LL T +GR +YA+GG+ G L V+G +G+ A IAG++ S Sbjct: 192 LVAYVLLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLM 251 Query: 285 LANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQK 344 P V ELD IAAV+LGGA I GG G +VGTLLG +L+ ++ + L ++GV Q Sbjct: 252 SGQPNAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQS 311 Query: 345 VIIGAFILLA 354 VI G ILLA Sbjct: 312 VIKGGIILLA 321 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: 285 Number of extensions: 13 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: 364 Length of database: 330 Length adjustment: 29 Effective length of query: 335 Effective length of database: 301 Effective search space: 100835 Effective search space used: 100835 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