Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate N515DRAFT_3233 N515DRAFT_3233 xylose ABC transporter membrane protein
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_3233 Length = 380 Score = 178 bits (451), Expect = 2e-49 Identities = 118/371 (31%), Positives = 187/371 (50%), Gaps = 59/371 (15%) Query: 33 ARQKLLAF--ASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGID 90 AR K+LA A + + F +F+ N+ ++ + A+ G+LA +VII ID Sbjct: 11 ARYKILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGMVFVIIAGEID 70 Query: 91 LSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLG 150 LSVG+++ + V+ N G P+ I A + G L G +G + +L+VP FI LG Sbjct: 71 LSVGSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRLRVPSFIVGLG 130 Query: 151 MMMLLKGLSLVISGTRPI--------YFNDTEGFSAIAQDSLIGDLIPSLPIPNAVL--- 199 M+ +G+ L + + I Y +G+ + +++G I ++ + AVL Sbjct: 131 GMLAFRGVLLGTTHSATIAPVPADLVYLG--QGYVSPLWSTVLGVAIFAVVVALAVLRRR 188 Query: 200 ---------------ILFLVAIGASI-----------------------------ILNKT 215 +L +VAIGA++ + ++T Sbjct: 189 RRAQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAVFSYLASQT 248 Query: 216 VFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGY 275 V GR+ +A+G N EA RLSGV V K+ V+ G +C AG++ +RL + P+ G Sbjct: 249 VLGRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAGSPSAGTNG 308 Query: 276 ELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILA 335 ELDAIAA IGG S+ GG GT+ G +IGA +M+ L NG+ +M V WQ +V G I++LA Sbjct: 309 ELDAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIVKGAILVLA 368 Query: 336 VYLDILRRRRR 346 V++D+L R +R Sbjct: 369 VWVDVLSRPQR 379 Score = 32.0 bits (71), Expect = 3e-05 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 2/70 (2%) Query: 280 IAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMS--VAQEWQTVVTGVIIILAVY 337 + + ++G + G +LGT A I V + + + V+ W TV+ I + V Sbjct: 122 VPSFIVGLGGMLAFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVVA 181 Query: 338 LDILRRRRRA 347 L +LRRRRRA Sbjct: 182 LAVLRRRRRA 191 Lambda K H 0.326 0.139 0.398 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: 300 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 347 Length of database: 380 Length adjustment: 29 Effective length of query: 318 Effective length of database: 351 Effective search space: 111618 Effective search space used: 111618 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