Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AO356_00960 AO356_00960 ABC transporter permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00960 Length = 325 Score = 185 bits (470), Expect = 1e-51 Identities = 118/314 (37%), Positives = 171/314 (54%), Gaps = 20/314 (6%) Query: 45 FYGLTLYLSGDG------------TSNFASAENTMNILRQVAINLVLAAGMTFVILTAGI 92 FYGL YL G +S+F S + + Q+ +VLA GMTF+++ GI Sbjct: 14 FYGLGTYLGLAGALLAMVALFSTLSSHFLSYDTFSTLANQIPDLMVLAVGMTFILIIGGI 73 Query: 93 DLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSGLVM----GMVNGAMVALLNINAFVV 148 DLSVGSVLA++A LG GW++ G+ + G V G++ I +F+V Sbjct: 74 DLSVGSVLALAASTVSVAVLGW--GWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIV 131 Query: 149 TLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRK 208 +LG + RG AY + T D SF W+ N + +A+ V+ ++ +L + Sbjct: 132 SLGVLEMARGLAYQMTGSRTAYIGD--SFAWLSNPIAFGISPSFIIALLVIFIAQAVLTR 189 Query: 209 TVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSG 268 TV G ++ IG N +A RL GI + V+S+ GL +G+A SRL A+ N GSG Sbjct: 190 TVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEAADPNAGSG 249 Query: 269 YELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVL 328 EL IAAVV+GGTSLMGG GS+ T G LII V+ GL +G + + + GAVIV+ Sbjct: 250 LELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVV 309 Query: 329 AVILDKWRQKDAAQ 342 AV+LD +R + A++ Sbjct: 310 AVVLDTYRSQRASR 323 Lambda K H 0.324 0.138 0.417 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: 288 Number of extensions: 16 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: 344 Length of database: 325 Length adjustment: 28 Effective length of query: 316 Effective length of database: 297 Effective search space: 93852 Effective search space used: 93852 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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