Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BPHYT_RS25790 BPHYT_RS25790 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS25790 Length = 500 Score = 904 bits (2335), Expect = 0.0 Identities = 465/500 (93%), Positives = 486/500 (97%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 ++VVGVHKRFTGVHALRGVSLSF+RGQIYHLLGENGCGKSTLIKIISGAQPPDEG+LVIE Sbjct: 1 MQVVGVHKRFTGVHALRGVSLSFERGQIYHLLGENGCGKSTLIKIISGAQPPDEGELVIE 60 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 GV HARLSALE+LAAGIETVYQDLSLLPNM+VAENVALTSELATH+G+LARTFDRR LA Sbjct: 61 GVRHARLSALESLAAGIETVYQDLSLLPNMNVAENVALTSELATHQGKLARTFDRRELAR 120 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 TAARALEAVGLPGN+EFQ+TLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV Sbjct: 121 TAARALEAVGLPGNAEFQATLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 180 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA+FTKAQISELM Sbjct: 181 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAQFTKAQISELM 240 Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315 TGRHLSNERYRE AH +IVL+VRG+TRAGQFSDVSF LHGGEILG+TGLLDSGRNELAR Sbjct: 241 TGRHLSNERYREGAHEPNIVLEVRGYTRAGQFSDVSFGLHGGEILGITGLLDSGRNELAR 300 Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375 ALAGVAPAQSG V LDG+ I+LRTPSDAK HRIGYVPEDRLNEGLFLDKPIRDNVITAMI Sbjct: 301 ALAGVAPAQSGQVRLDGKSISLRTPSDAKNHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 360 Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435 SSLRDRFGQIDR RAQALAEQTVK+LQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV Sbjct: 361 SSLRDRFGQIDRVRAQALAEQTVKDLQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 420 Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAE 495 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKG V++E Sbjct: 421 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGRVASE 480 Query: 496 YRADELSEADLYHALLSEAA 515 Y+AD LSEADLYHALLSEAA Sbjct: 481 YQADTLSEADLYHALLSEAA 500 Lambda K H 0.319 0.135 0.376 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: 911 Number of extensions: 25 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: 515 Length of database: 500 Length adjustment: 34 Effective length of query: 481 Effective length of database: 466 Effective search space: 224146 Effective search space used: 224146 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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