Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate SMc02031 SMc02031 permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 128 bits (322), Expect = 2e-34 Identities = 91/307 (29%), Positives = 160/307 (52%), Gaps = 11/307 (3%) Query: 24 VLVVLVATWLS--RGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVGLAN 81 + +VL+ +L+ F+ +DNL ++ Q + +LA+G +++G GIDLS +A Sbjct: 34 IALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILTG--GIDLSVAAIAA 91 Query: 82 LSGMVAAMLV--PRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCTL 139 LS + A+L+ P ++ G D + + I +++G+ G LNG +I++ ++ + TL Sbjct: 92 LSASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFIATL 151 Query: 140 GTQLLFTGFAVVISNGASVHV-----DYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWL 194 GT F G A+++++G V E L +G G + VP++ I L ++ Sbjct: 152 GTMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVSALIALLCAAAGWYV 211 Query: 195 LKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDY 254 L+ + G +Y +G N AA +GI +R I TYA+ G+LA++AG+I +SA Sbjct: 212 LRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRLNSANALM 271 Query: 255 GNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFL 314 + L +I V+GG N GG G + A ++ L + NLL VS F+ A G + Sbjct: 272 ADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQRIAQGVV 331 Query: 315 LLLSLAF 321 +++ + F Sbjct: 332 IVVVVIF 338 Lambda K H 0.327 0.143 0.429 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: 339 Number of extensions: 17 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: 1 Length of query: 357 Length of database: 349 Length adjustment: 29 Effective length of query: 328 Effective length of database: 320 Effective search space: 104960 Effective search space used: 104960 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