Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate H281DRAFT_02176 H281DRAFT_02176 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Burk376:H281DRAFT_02176 Length = 321 Score = 105 bits (261), Expect = 2e-27 Identities = 95/307 (30%), Positives = 146/307 (47%), Gaps = 21/307 (6%) Query: 19 LLIVNVLVVLVATWLSRGQ-FVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGV 77 L I+ LV LV L R + F N+ S L+++G+ +++G GIDLS Sbjct: 5 LPILLALVALVVLGLVRYEHFASAYNITSFWRYNSMFALISVGMAFVIITG--GIDLSVG 62 Query: 78 GLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILC 137 +A +S +VAA+ +G V+ CA GL G+LNGV+I RL++ P + Sbjct: 63 TVAAMSSVVAALAS---AHGGWVAVVAG---CAA----GLAVGVLNGVIITRLKILPFIV 112 Query: 138 TLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWLLKR 197 TL T L G A+++ +V + ++ G G + +PI I A V V GWL R Sbjct: 113 TLATSLGAHGVALLLGKNDAVSIASDSNFANFGQGDLFGLPIP-GIVAALVAVAGWLALR 171 Query: 198 SP-FGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYGN 256 S FG +G + +AA G+ R L+ YA+ G+LA +AG+I A + + + G Sbjct: 172 STRFGRHSLAIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGV 231 Query: 257 SYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFN------LLGVSQFFGDCA 310 + L AI V+GG GG G I +L + +L N + +S ++ Sbjct: 232 GWELFAISAVVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVI 291 Query: 311 WGFLLLL 317 G LLL Sbjct: 292 RGVFLLL 298 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: 316 Number of extensions: 18 Number of successful extensions: 2 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: 321 Length adjustment: 28 Effective length of query: 329 Effective length of database: 293 Effective search space: 96397 Effective search space used: 96397 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