Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate Ac3H11_2062 ABC-type sugar transport system, periplasmic component
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2062 Length = 416 Score = 249 bits (635), Expect = 1e-70 Identities = 147/413 (35%), Positives = 224/413 (54%), Gaps = 20/413 (4%) Query: 4 RFLAAALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGS 63 + A A+G AA+ +ASA ++EV H+WTSGGEA +VAEL K G+ W D A+AG Sbjct: 6 KIAAVAVGLAAAM---SASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGG 62 Query: 64 GG-TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSL 122 GG +A ++ SR+ G+P +A Q G +E G++ ++ +A E W E++ P + Sbjct: 63 GGDSAMTVLKSRVISGNPPSAAQ-TKGPAIQEWASEGVLANMDTLAKAEKWDELL-PKVV 120 Query: 123 LDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVE-VPKNWDEFVAAAPALEKAGIVPL 181 D +G APVN+H W+W S+ A K+AGV +PK WDEF AAA L+ AG+VP+ Sbjct: 121 ADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPV 180 Query: 182 AVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMS--- 238 A GGQ WQ F+ +++ + G + ++ + D + K + + RR+ Sbjct: 181 AHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKK---SLETFRRIKGYT 237 Query: 239 -KGTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTG 297 G +DWN AT M+I GKAG Q+MGDWA+GEF AG+ G D+ C G + Sbjct: 238 DPGAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFN 297 Query: 298 GDAFYFPLLEDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKG- 356 D+F L+D KAQ LAS+++ P Q FNL KGS+PVR + +DC K Sbjct: 298 VDSFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASA 357 Query: 357 ---LDILAKGNVIQGT--DQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFA 404 +D G ++ ++ ++ +D+ S+F+ + ++ DA K+ A Sbjct: 358 KDFVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIA 410 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: 559 Number of extensions: 35 Number of successful extensions: 5 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: 416 Length adjustment: 31 Effective length of query: 380 Effective length of database: 385 Effective search space: 146300 Effective search space used: 146300 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