Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate PfGW456L13_1894 Glucose ABC transport system, periplasmic sugar-binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1894 Length = 432 Score = 216 bits (551), Expect = 8e-61 Identities = 144/422 (34%), Positives = 213/422 (50%), Gaps = 22/422 (5%) Query: 9 ALGATAALPFG---AASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSGG 65 +L + +ALP A S +EV HWWTSGGE AAV L + G W DGA+AG GG Sbjct: 12 SLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGG 71 Query: 66 -TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRD--LTDIATKENWKEIVKPSSL 122 TA ++ SR G+P Q G +E GL+ L D++ ENW ++ + Sbjct: 72 STAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDALKDVSKAENWDGLLS-KKV 129 Query: 123 LDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVE-VPKNWDEFVAAAPALEKAGIVPL 181 D+ EG PVNIH WLW++ FK+AG+E P +EF AA L+ AG + L Sbjct: 130 SDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIAL 189 Query: 182 AVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVF-KAADDARRMSKG 240 A GGQPWQ + F+ +++++ G + ++K D++ +GPE+ K F + M Sbjct: 190 AHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPN 249 Query: 241 TNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDA 300 +DWN A VI+GKAG Q+MGDWA+ E+ A + AG DY C+ G + + D+ Sbjct: 250 RAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDS 309 Query: 301 FYFPLLEDEEKS--KAQEVLASTLLKPETQVAFNLKKGSLPVRGD----VDLAAANDCMK 354 L+ + K AQ+ LA L + Q F++ KGS+PVR D +D ++C + Sbjct: 310 MAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQ 369 Query: 355 KGL-DILA--KGNVIQGT---DQLLSADSQKQKEDLFSEFFANHSMTPEDAQKRFADIIA 408 K D +A K +Q + + S Q D+ + F + P A + A + Sbjct: 370 KSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVK 429 Query: 409 AA 410 AA Sbjct: 430 AA 431 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: 551 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 411 Length of database: 432 Length adjustment: 32 Effective length of query: 379 Effective length of database: 400 Effective search space: 151600 Effective search space used: 151600 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