Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate SMc04395 SMc04395 ABC transporter permease
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Smeli:SMc04395 Length = 292 Score = 261 bits (667), Expect = 1e-74 Identities = 128/286 (44%), Positives = 180/286 (62%) Query: 15 LRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWL 74 L+ L K+ P L +V G A+T S T+SK+LP FVG Y RLWA P W Sbjct: 7 LQELLPKLVLAPSFLIVLVFVYGFIAYTGFLSMTDSKMLPSYNFVGLSNYSRLWALPHWW 66 Query: 75 VSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWL 134 ++ NLA+F L + V+G LA L+DQKIR E R + LYP ALSFIVTG W+W Sbjct: 67 RAVSNLAIFATLYIAVCSVLGLALAILLDQKIRAEGFLRPVYLYPMALSFIVTGTAWKWF 126 Query: 135 LNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDED 194 L+P G+++ + GW SFSF+ + + N IY ++IAA+WQ TG +M + LAGLRG+D + Sbjct: 127 LDPGIGLENTMHLWGWESFSFNWIKDRNYAIYCVVIAAVWQSTGFIMAMFLAGLRGVDNE 186 Query: 195 IWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEV 254 I KAA++DG Y IIIP+MR VF++ V++A +K YDL++A T GGPG A+E+ Sbjct: 187 IIKAAQIDGATTPTIYRRIIIPLMRPVFLSAFVVLAHLAIKAYDLIIALTGGGPGQATEL 246 Query: 255 PAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLEFGGGRK 300 PA ++Y Y F + G +++ +MLV + IIVP+ Y E GG++ Sbjct: 247 PATFMYSYTFTRNQMAIGASSAIVMLVMIFSIIVPYLYSEVRGGKR 292 Lambda K H 0.329 0.142 0.449 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: 322 Number of extensions: 14 Number of successful extensions: 1 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: 302 Length of database: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 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 (21.8 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