Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 130 bits (328), Expect = 3e-35 Identities = 91/291 (31%), Positives = 146/291 (50%), Gaps = 16/291 (5%) Query: 24 AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQ---FVGLKNYEELLNPHDPL 80 A+ +L+PAL+ + + +LP+ + +S T+++ + FV L NY ELL H PL Sbjct: 7 AWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELL--HRPL 64 Query: 81 SNLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISM 140 F TL + L L+ + L A+LLN+ R + L+RT L P + Sbjct: 65 ---FWSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVA 121 Query: 141 LAWQGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGAL 200 + W+ L N +YG N L G+ G+ + WL WA +I+ VW F Y M + L AL Sbjct: 122 VIWRYLFNTKYGLANYALGGL-GIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAAL 180 Query: 201 QSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGP 260 Q+IP D YEAA IDGA+ + FR++T+P + L + I + S F F +++T GGP Sbjct: 181 QAIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGP 240 Query: 261 PNSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMR 311 L T + Y+ + + ++ LLF+++ ++ V +R Sbjct: 241 -------LQSTTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLR 284 Lambda K H 0.327 0.140 0.451 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: 311 Number of extensions: 21 Number of successful extensions: 3 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: 321 Length of database: 292 Length adjustment: 27 Effective length of query: 294 Effective length of database: 265 Effective search space: 77910 Effective search space used: 77910 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: 48 (23.1 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