Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS00415 BPHYT_RS00415 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS00415 Length = 422 Score = 515 bits (1327), Expect = e-151 Identities = 251/417 (60%), Positives = 302/417 (72%), Gaps = 4/417 (0%) Query: 3 KMTKIAAVAVGLAAAMSASAG---EVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAV 59 + K+ A+G+AA ++ A EVEVLHYWTSGGEAKS LK+++ KG TW+DFAV Sbjct: 7 RTAKLTVYALGVAAVLACGAARSAEVEVLHYWTSGGEAKSAQVLKQMLDEKGDTWKDFAV 66 Query: 60 AGGGGDSAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKV 119 AGGGG +AMT LK+RVI+GNPP+AAQ KGPAIQEW EGVL +++ +AK E WD+L+P Sbjct: 67 AGGGGGNAMTALKTRVIAGNPPAAAQIKGPAIQEWGDEGVLVSINDVAKREGWDKLIPPQ 126 Query: 120 VADVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVP 179 ++ +MKYKG YVAAPVNVHRVN +W +++ALKK A P TWDEFF A+ L+ AG+ P Sbjct: 127 ISGIMKYKGQYVAAPVNVHRVNRLWINADALKKVN-AQPPATWDEFFRTAEALQKAGITP 185 Query: 180 VAHGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDP 239 VA GGQ WQD TFE+V LGVGGA FY+ A V+LD + L TM K+LETF++IK YTD Sbjct: 186 VAIGGQQWQDAETFETVALGVGGAAFYEKAFVQLDQSTLRGPTMVKALETFKKIKAYTDK 245 Query: 240 GAPGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVD 299 GRDWNLAT M+I GKA Q MGDWAKGEF AGK PGKD+LC APGS NA+TFNVD Sbjct: 246 AQTGRDWNLATGMVISGKAAMQFMGDWAKGEFSVAGKVPGKDYLCVPAPGSQNAYTFNVD 305 Query: 300 SFILFKLKDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKD 359 SF FK++ A +K Q DLAS ++SP FQE+FNLNKGSIPVR G + KFD CA+ SA D Sbjct: 306 SFAFFKVRSADVEKGQKDLASLLLSPKFQEIFNLNKGSIPVRQGMDLSKFDTCAQRSAAD 365 Query: 360 FVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416 F G LVPS AH M PA EGA DV+ FWNDD S A K+A AAKT+ Sbjct: 366 FTSAQAKGTLVPSWAHDMVDTPAVEGAFYDVIGNFWNDDNESAQQAADKLAVAAKTR 422 Lambda K H 0.315 0.128 0.383 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: 636 Number of extensions: 26 Number of successful extensions: 2 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: 416 Length of database: 422 Length adjustment: 32 Effective length of query: 384 Effective length of database: 390 Effective search space: 149760 Effective search space used: 149760 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