Align Fructose import permease protein FruG (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 227 bits (578), Expect = 4e-64 Identities = 135/327 (41%), Positives = 195/327 (59%), Gaps = 8/327 (2%) Query: 6 ANKVKAPKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIIL 65 A A ++ + R +P L +V+F+ M G L+ ++ +L ID+A+L I+ Sbjct: 8 ATSAAAGRRPWWRRRAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIV 67 Query: 66 AVAMTLPILTGGIDLSVGAIVAITAVVGLKLANA-GVPAFLVMIIMLLIGAVFGLLAGTL 124 AV MT IL GGIDLSVGA+VA + V+ +L G P + ++L +G FG G L Sbjct: 68 AVGMTFVILAGGIDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVL 127 Query: 125 IEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSF 184 I+ F +QPF+ TL+ MFLARG+A++IS DS+ Q ++++V + + Sbjct: 128 IQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQ----PWLASVANL--RLPLGGGSML 181 Query: 185 NVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAA 244 +VG ++AL VV G + + GRT+YAIGGS SSA LMGLPV T +Y S AA Sbjct: 182 SVGALVALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAA 241 Query: 245 LASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPL- 303 LA +VYT + S + +G ELDA+A+VVIGGT++ GG GYVLG++LG LV ++ L Sbjct: 242 LAGVVYTLYMLSGYSQHALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLI 301 Query: 304 TSDFGVPAEWTTIVIGLMILVFVVLQR 330 D + + WT IVIG ++L F +LQR Sbjct: 302 VFDGELSSWWTRIVIGALLLAFCLLQR 328 Lambda K H 0.327 0.142 0.400 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: 285 Number of extensions: 10 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: 340 Length of database: 337 Length adjustment: 28 Effective length of query: 312 Effective length of database: 309 Effective search space: 96408 Effective search space used: 96408 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 Apr 09 2024. 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