Align deoxynucleoside transporter, ATPase component (characterized)
to candidate HSERO_RS05090 HSERO_RS05090 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__HerbieS:HSERO_RS05090 Length = 501 Score = 669 bits (1726), Expect = 0.0 Identities = 331/494 (67%), Positives = 401/494 (81%) Query: 20 GVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPH 79 G+HKRF GVHALRGV L+ G+IYHLLGENGCGKSTLIKII+GAQPP EG++ I+G Sbjct: 3 GIHKRFAGVHALRGVDLTIHAGEIYHLLGENGCGKSTLIKIIAGAQPPSEGEIYIQGQRV 62 Query: 80 ARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAAR 139 A L+ L +L+ GIETVYQDLSLLPNMSVAENVAL+ +L H+GRLAR FDR L TAAR Sbjct: 63 AELTPLASLSLGIETVYQDLSLLPNMSVAENVALSEQLVHHQGRLARLFDRHALNQTAAR 122 Query: 140 ALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLI 199 AL AV LP +++F T +++LP+ATRQL+AIARAIA+ A+ VIMDEPTTSLTQKEVD L+ Sbjct: 123 ALRAVNLPADADFLDTRVDELPIATRQLIAIARAIATSARMVIMDEPTTSLTQKEVDALV 182 Query: 200 AVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGRH 259 V+ LRA GV VLFVSHKLDEC+AIGG+ IV RDG+K+AQGPI +FTKAQ+ +LMTG+ Sbjct: 183 KVINGLRANGVAVLFVSHKLDECFAIGGQAIVFRDGEKVAQGPIQQFTKAQLGQLMTGKQ 242 Query: 260 LSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAG 319 LS ERYR A +++VR R G F DVSF L GEILG+TGLLDSGRNELA ALAG Sbjct: 243 LSQERYRVDAQLHKPLMEVRALGRHGAFEDVSFALRQGEILGITGLLDSGRNELALALAG 302 Query: 320 VAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLR 379 V PA++G + L+GQ ++LR P DA H IGYVPEDR++EGLFLDK IRDN++T ++ LR Sbjct: 303 VEPARAGQITLEGQPLSLRNPGDAITHGIGYVPEDRISEGLFLDKSIRDNIVTTILRKLR 362 Query: 380 DRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILH 439 +FG +D Q + TV++LQIATP VD+PVQSLSGGNQQRVLIGRWLAI+PRVLILH Sbjct: 363 GKFGALDAAACQRFSTDTVRQLQIATPDVDRPVQSLSGGNQQRVLIGRWLAINPRVLILH 422 Query: 440 GPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRAD 499 GPTVGVDVGSKDIIYRI+Q L+QRG+G+ILISDDLPELLQNCD +L+MK+G + Y + Sbjct: 423 GPTVGVDVGSKDIIYRIIQDLAQRGLGVILISDDLPELLQNCDNLLLMKRGRIVRRYAVE 482 Query: 500 ELSEADLYHALLSE 513 L+E++L+H L+SE Sbjct: 483 GLAESELFHDLVSE 496 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: 790 Number of extensions: 27 Number of successful extensions: 3 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: 501 Length adjustment: 34 Effective length of query: 481 Effective length of database: 467 Effective search space: 224627 Effective search space used: 224627 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