Align Glucose/galactose porter (characterized)
to candidate N515DRAFT_0592 N515DRAFT_0592 glucose/galactose transporter
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Dyella79:N515DRAFT_0592 Length = 430 Score = 207 bits (528), Expect = 4e-58 Identities = 137/403 (33%), Positives = 208/403 (51%), Gaps = 25/403 (6%) Query: 30 LLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKR 89 LLFF++GF+T LN LI +K F L+ + L+ F+ +YF ++LP+ ++KR K+ Sbjct: 26 LLFFIFGFVTWLNGPLITFVKLAFSLDDVNAFLVPMVFYCSYFFLALPSSAVLKRTGMKK 85 Query: 90 GIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAA 149 G+ +GL V AIG LF S RVY L LFV+ +G+ +LQ A+NPY++ILG ++AA Sbjct: 86 GMALGLFVMAIGAVLFGQFVSMRVYGGALAGLFVIGAGLALLQTASNPYISILGPIDSAA 145 Query: 150 SRLTLTQAFNSLGTTVAPVFGAVLILSA---------------ATDATVNAEADAVRFPY 194 R+ N + +AP L+LS A +A +N A V PY Sbjct: 146 QRIAFMGICNKVAGALAPFVFGWLVLSGIDTFDQQVKAAPTPEAREALLNTFAAKVHMPY 205 Query: 195 LLLALAFTVLAIIFAILKPPDVQ---EDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAE 251 L +A +LA+ P+++ + A +G+ + HL LG + +F+YVG E Sbjct: 206 LAMAGLLVLLAVWVLRSPLPEIKPSGANSEAEIGHAKGNLLSFPHLWLGVLCLFLYVGVE 265 Query: 252 VSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM--RYIDDGKALAFN 309 V G + + GL DA H F AM+ ++ + + I LA + Sbjct: 266 VMAGDAIGTYGQG---LGL-PLDATKHFTSFTLFAMLLGYLAGLVLIPKIISQQSYLAVS 321 Query: 310 AFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAI 369 A + + ATTG+ ++ V A+G N++M+P IF LA+ GLG T GS +L +AI Sbjct: 322 AVLGVAFTVGAWATTGYTSVGFVAALGFANAMMWPAIFPLAIKGLGRWTEAGSALLIMAI 381 Query: 370 VGGAIVPLIQGALADAIGIHLAFLMPII-CYAYIAFYGLIGSK 411 VGGA+VP L L F++ ++ CY YI FYGL G + Sbjct: 382 VGGALVPQAFVHLKQHYDFQLVFMLLMVPCYLYILFYGLRGHR 424 Lambda K H 0.328 0.141 0.420 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: 543 Number of extensions: 42 Number of successful extensions: 5 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: 412 Length of database: 430 Length adjustment: 32 Effective length of query: 380 Effective length of database: 398 Effective search space: 151240 Effective search space used: 151240 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: 50 (23.9 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