Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BPHYT_RS05025 BPHYT_RS05025 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A165KPY4 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS05025 Length = 415 Score = 437 bits (1124), Expect = e-127 Identities = 238/412 (57%), Positives = 283/412 (68%), Gaps = 8/412 (1%) Query: 8 AAVAVGLAAAMSA--SAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGD 65 A A GL +SA +A +EVLH+WTSGGE+K+V LK M +G+TW+DFAVAGG G Sbjct: 9 ALCAAGLMCGVSAVQAAESIEVLHWWTSGGESKAVGVLKDDMTKQGYTWKDFAVAGGAGA 68 Query: 66 SAMTVLKSRVISGNPPSAAQTKGPAIQEWASEGVLANMDTLAKAEKWDELLPKVVADVMK 125 +AMT LK++VISGN PSAAQ KGP IQ+WAS+GVL +D A A W + LP + +M Sbjct: 69 AAMTALKTQVISGNAPSAAQIKGPLIQDWASQGVLVPID--AAAGDWKKNLPPEIDKIMH 126 Query: 126 YKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQ 185 G YVAAP +VHRVNW++ + AL KAG A P TW EFFA ADK+KAAG+ P+A GGQ Sbjct: 127 ADGHYVAAPFSVHRVNWLYINKAALDKAGGKA-PTTWPEFFAVADKMKAAGIQPIAMGGQ 185 Query: 186 NWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRD 245 WQD T +E VVL G A FY+ ALV LD LTSD M +T R+I+GY D G GRD Sbjct: 186 PWQDLTLWEDVVLSQG-ADFYKKALVDLDEKTLTSDKMVGVFDTVRKIQGYFDAGRTGRD 244 Query: 246 WNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFK 305 WNLATAM+I GKAG Q MGDWAKGEF AGK G D++CAA PG+ ++TFNVDSF+ F+ Sbjct: 245 WNLATAMVINGKAGMQFMGDWAKGEFANAGKKSGSDYICAAVPGTEKSYTFNVDSFVFFQ 304 Query: 306 LK-DAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKDFVDTA 364 K AA Q LA +IMSP FQE F+LNKGSIPVR G M KFDDCAK S D Sbjct: 305 QKGQKAATPGQLALAKTIMSPEFQEQFSLNKGSIPVRLGVSMAKFDDCAKKSYADEQVAI 364 Query: 365 KSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAKTK 416 KSGG VPS AHGMA A GAI DVV++F N + S A+ +A AAKTK Sbjct: 365 KSGGYVPSLAHGMAQPDAAAGAISDVVTKFMNSQQDS-KSAVAALAKAAKTK 415 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: 621 Number of extensions: 40 Number of successful extensions: 5 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: 416 Length of database: 415 Length adjustment: 31 Effective length of query: 385 Effective length of database: 384 Effective search space: 147840 Effective search space used: 147840 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