Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate 3607106 Dshi_0528 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Dino:3607106 Length = 334 Score = 241 bits (614), Expect = 3e-68 Identities = 136/303 (44%), Positives = 198/303 (65%), Gaps = 8/303 (2%) Query: 19 LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78 LLI+ V V + + LS +F+ NL SM Q PE +LAL + ++M++G GIDLS VG Sbjct: 16 LLIIMVFVFGLMSVLSPDRFLSSQNLTSMAFQFPEFAILALAMTIAMMTG--GIDLSVVG 73 Query: 79 LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIV----LMMGLLGGLLNGVVIARLRLTP 134 +ANLS +VAA+++ N + P ++++ AI L +G + GL+NG ++A L P Sbjct: 74 IANLSAVVAALILTHFSNAE-MPAAQSAIWLAIAITAALCIGAIAGLINGSLVAFFGLPP 132 Query: 135 ILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWL 194 IL TLG+ L+FTGFA+ ++ G++V + + + ++ IGN T+ VP+ +F +L + Sbjct: 133 ILATLGSGLVFTGFAIAMTGGSAV-MGFPDTVALIGNATLAGVPVPLILFAVLAFLLHLV 191 Query: 195 LKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDY 254 L R+ FGLR+ + G NP AA YA I RML+ Y + G+ AS+AGLI + +SAK DY Sbjct: 192 LTRTAFGLRVTMYGANPLAALYAAIDINRMLLKVYVIAGMFASVAGLIIMSRANSAKADY 251 Query: 255 GNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFL 314 G+SYLL+A+LIAV+GGVNP GG+GR+I V A +QFLSS N+LGVS F + WG L Sbjct: 252 GSSYLLLAVLIAVLGGVNPYGGYGRVIGVVLAVLSMQFLSSGLNMLGVSNFARELIWGAL 311 Query: 315 LLL 317 L+L Sbjct: 312 LIL 314 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: 322 Number of extensions: 17 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: 357 Length of database: 334 Length adjustment: 29 Effective length of query: 328 Effective length of database: 305 Effective search space: 100040 Effective search space used: 100040 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