Align Trehalose transport system permease protein SugB (characterized)
to candidate 8499893 DvMF_0658 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= SwissProt::P9WG01 (274 letters) >FitnessBrowser__Miya:8499893 Length = 277 Score = 107 bits (266), Expect = 4e-28 Identities = 83/274 (30%), Positives = 137/274 (50%), Gaps = 9/274 (3%) Query: 2 GARRATYWAVLDTLVVGYALLPVLWIFSLSLKPTSTVKDGKLIPSTVTFDNYRGIFRGDL 61 G R A TL V +AL P+L+ + P S + + +T DN+R + Sbjct: 11 GLARVLDTAAAWTLAVLWAL-PLLYAVWTAFHP-SEFSTRFTLAAPLTLDNFRAAWDAAP 68 Query: 62 FSSALINSIGIGLITTVIA--VVLGAMAAYAVARLEFPGKRLLIGAALLITMFPSISLVT 119 F+ L+N++ L+T V+A +VL +AAYA A+ +FPGK +L L+ M LV Sbjct: 69 FARYLVNTVL--LVTMVLAGQLVLCTLAAYAFAKYDFPGKGILFALVLMQLMIMPDVLVV 126 Query: 120 PLFNIERAIGLFDTWPGLILPYITFALPLAIYTLSAFFREIPWDLEKAAKMDGATPGQAF 179 + AIG+ D+ + LPY+ A I+ L F+ IP +L++AA ++GA+ Q Sbjct: 127 ENYRTMSAIGVLDSTLAIGLPYMASA--FGIFLLRQTFKSIPKELDEAAAVEGASTLQIL 184 Query: 180 RKVIVPLAAPGLVTAAILVFIFAWNDLLLALSLTATKAAITAPVAIANFTGSSQFEEPTG 239 KV VPL P + A++ + WN+ L L +T T + V + F+ + Q + Sbjct: 185 WKVYVPLGKPVYLAYALVSVSYHWNNFLWPLIVTNTTNSRPLTVGLQVFSSTEQGVD-WS 243 Query: 240 SIAAGAIVITIPIIVFVLIFQRRIVAGLTSGAVK 273 I A ++ + P+++ L+FQR+ V +K Sbjct: 244 IITAATLMTSGPLLIGFLLFQRQFVQSFMRAGIK 277 Lambda K H 0.327 0.141 0.418 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: 224 Number of extensions: 9 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: 274 Length of database: 277 Length adjustment: 25 Effective length of query: 249 Effective length of database: 252 Effective search space: 62748 Effective search space used: 62748 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: 47 (22.7 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