Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate Pf1N1B4_596 Glucose ABC transport system, periplasmic sugar-binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_596 Length = 435 Score = 216 bits (551), Expect = 8e-61 Identities = 133/367 (36%), Positives = 191/367 (52%), Gaps = 16/367 (4%) Query: 8 AALGATAALPFGAASAT---DLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSG 64 A+L AA P A +A +EV HWWTSGGE AAV L + G W DGA+AG G Sbjct: 14 ASLLPVAAFPVSALAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGG 73 Query: 65 G-TARPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRD--LTDIATKENWKEIVKPSS 121 G TA ++ SR G+P Q G +E GL+ L +++ E W ++ Sbjct: 74 GSTAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDTLKEVSKSEGWDNLLI-KK 131 Query: 122 LLDSCTIEGKIYCAPVNIHSWQWLWLSNAAFKQAGVE-VPKNWDEFVAAAPALEKAGIVP 180 + D+ EG PVNIH WLW++ FK+AG++ P +EF AA L+ AG + Sbjct: 132 VSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIDKAPTTLEEFYAAGDKLKAAGFIA 191 Query: 181 LAVGGQPWQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDAR-RMSK 239 LA GGQPWQ + F+ +++++ G + ++K D++ +GPE+AK F M Sbjct: 192 LAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMAKAFTELKKVTGYMDP 251 Query: 240 GTNVQDWNQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGD 299 +DWN A VI GKAG Q+MGDWA+ E+ A + AG DY C+P G + + D Sbjct: 252 NRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAKKVAGKDYQCVPFPGTEKAFTYNID 311 Query: 300 AFYFPLLEDEEKS--KAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKKGL 357 + L+ + K AQ+ LA L + Q F++ KGS+PVR D+ ND G Sbjct: 312 SMAVFKLKADRKGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDM----LNDMSGLGF 367 Query: 358 DILAKGN 364 D A+ + Sbjct: 368 DACAQAS 374 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: 538 Number of extensions: 29 Number of successful extensions: 6 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: 435 Length adjustment: 32 Effective length of query: 379 Effective length of database: 403 Effective search space: 152737 Effective search space used: 152737 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