Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate H281DRAFT_00166 H281DRAFT_00166 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__Burk376:H281DRAFT_00166 Length = 415 Score = 206 bits (524), Expect = 1e-57 Identities = 130/365 (35%), Positives = 194/365 (53%), Gaps = 20/365 (5%) Query: 1 MNLRFLAAALGATAALPFGAAS---ATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVD 57 M R + AL A A L G ++ A +EV HWWTSGGE+ AV L G W D Sbjct: 1 MKFRAIMGALCA-AGLMCGVSAVQAAESVEVLHWWTSGGESKAVGVLKDDMTKQGYTWKD 59 Query: 58 GAIAGSGGTARPIMI-SRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEI 116 A+AG G A + +++ G+ +A Q G ++ G++ + +A +WK+ Sbjct: 60 FAVAGGAGAAAMTALKTQVISGNAPSAAQIK-GPLIQDWASQGVLVPIDSVAG--DWKKN 116 Query: 117 VKPSSLLDSCT-IEGKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEK 175 + P +D +G AP ++H WL+++ AA +AG +VP W EF A A ++ Sbjct: 117 LPPE--IDKIMHADGHYVAAPFSVHRVNWLYINKAALDKAGGKVPTTWPEFFAVADKMKA 174 Query: 176 AGIVPLAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDAR 235 AGI P+A+GGQPWQ ++ ++++ G + ++K DE+ ++ VF D R Sbjct: 175 AGIQPIAMGGQPWQDLTLWEDVVLS-QGADFYKKALVDLDEKTLTSDKMVGVF---DTVR 230 Query: 236 RMS----KGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVN 291 ++ G +DWN AT MVI GKAG Q MGDWA+GEF AG+K+G DY C G Sbjct: 231 KIQGYFDAGRTGRDWNLATAMVINGKAGMQFMGDWAKGEFANAGKKSGSDYVCAAVPGTE 290 Query: 292 EVISTGGDAF-YFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAAN 350 + + D+F +F + + Q LA T++ PE Q F+L KGS+PVR V +A + Sbjct: 291 KAYTFNVDSFVFFQQKGQKAATPGQLALAKTIMSPEFQEQFSLNKGSIPVRLGVSMAKFD 350 Query: 351 DCMKK 355 DC KK Sbjct: 351 DCAKK 355 Lambda K H 0.315 0.131 0.389 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: 512 Number of extensions: 30 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: 411 Length of database: 415 Length adjustment: 31 Effective length of query: 380 Effective length of database: 384 Effective search space: 145920 Effective search space used: 145920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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