Align ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein (characterized)
to candidate BPHYT_RS00415 BPHYT_RS00415 sugar ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc04259 (411 letters) >FitnessBrowser__BFirm:BPHYT_RS00415 Length = 422 Score = 257 bits (656), Expect = 5e-73 Identities = 135/349 (38%), Positives = 195/349 (55%), Gaps = 4/349 (1%) Query: 9 ALGATAALPFGAASATDLEVTHWWTSGGEAAAVAELAKAFDATGNKWVDGAIAGSGG-TA 67 ALG A L GAA + ++EV H+WTSGGEA + L + D G+ W D A+AG GG A Sbjct: 15 ALGVAAVLACGAARSAEVEVLHYWTSGGEAKSAQVLKQMLDEKGDTWKDFAVAGGGGGNA 74 Query: 68 RPIMISRITGGDPMAATQFNHGRQAEELVQAGLMRDLTDIATKENWKEIVKPSSLLDSCT 127 + +R+ G+P AA Q G +E G++ + D+A +E W +++ P + Sbjct: 75 MTALKTRVIAGNPPAAAQIK-GPAIQEWGDEGVLVSINDVAKREGWDKLIPPQ-ISGIMK 132 Query: 128 IEGKIYCAPVNIHSWQWLWLSNAAFKQAGVEVPKNWDEFVAAAPALEKAGIVPLAVGGQP 187 +G+ APVN+H LW++ A K+ + P WDEF A AL+KAGI P+A+GGQ Sbjct: 133 YKGQYVAAPVNVHRVNRLWINADALKKVNAQPPATWDEFFRTAEALQKAGITPVAIGGQQ 192 Query: 188 WQANGAFDVLMVAIAGKENFEKVFAQKDEEVAAGPEIAKVFKAADDARRMS-KGTNVQDW 246 WQ F+ + + + G +EK F Q D+ GP + K + + + K +DW Sbjct: 193 WQDAETFETVALGVGGAAFYEKAFVQLDQSTLRGPTMVKALETFKKIKAYTDKAQTGRDW 252 Query: 247 NQATNMVITGKAGGQIMGDWAQGEFQLAGQKAGVDYTCLPGLGVNEVISTGGDAFYFPLL 306 N AT MVI+GKA Q MGDWA+GEF +AG+ G DY C+P G + D+F F + Sbjct: 253 NLATGMVISGKAAMQFMGDWAKGEFSVAGKVPGKDYLCVPAPGSQNAYTFNVDSFAFFKV 312 Query: 307 EDEEKSKAQEVLASTLLKPETQVAFNLKKGSLPVRGDVDLAAANDCMKK 355 + K Q+ LAS LL P+ Q FNL KGS+PVR +DL+ + C ++ Sbjct: 313 RSADVEKGQKDLASLLLSPKFQEIFNLNKGSIPVRQGMDLSKFDTCAQR 361 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: 529 Number of extensions: 29 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: 422 Length adjustment: 31 Effective length of query: 380 Effective length of database: 391 Effective search space: 148580 Effective search space used: 148580 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