Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS01820 Length = 544 Score = 322 bits (824), Expect = 3e-92 Identities = 193/519 (37%), Positives = 302/519 (58%), Gaps = 25/519 (4%) Query: 4 QEVSSAPLSQ-PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIIS 62 +E +PL++ P LE+ + F GV ALR +LS G+++ L+G+NG GKST+IKI++ Sbjct: 6 KETPHSPLTRSPLLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILT 65 Query: 63 GAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEG 122 GA G + EG + +A AGI T+YQ+++L+P SVAEN+ L G Sbjct: 66 GAYRRGSGSVRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFL--------G 117 Query: 123 RLARTF---DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAK 179 R R F D + AA LE+ GL + + + + A +Q+VA+ARA++S+AK Sbjct: 118 REPRRFGLIDWHAVQQRAAALLESFGLQIDVKKP---VGRYSTAIQQMVALARAVSSDAK 174 Query: 180 FVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMA 239 VIMDE T+SL ++EV+ L V+ LR G V+FVSH+LDE YA+ V V+RDGQ +A Sbjct: 175 MVIMDESTSSLDEREVELLFTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVA 234 Query: 240 QGPIAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRG--------FTRAGQFSDVS 291 Q +A+ K Q+ M GR L+ ++ A A++ L RG + + SDVS Sbjct: 235 QSTMADMDKLQLVTTMLGRTLAAV-VQDDAEAREANLARRGKQMIAATQLSAHPKVSDVS 293 Query: 292 FKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYV 351 ++H GE +G+ GLL SGR E R + G P + G + + G+ +AL++P DA + Y+ Sbjct: 294 LEVHAGEAVGLAGLLGSGRTETMRLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYL 353 Query: 352 PEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKP 411 EDR EG+ + +RDN+ + +L G +D + QA+ ++ + L I D+P Sbjct: 354 TEDRKAEGIVPELSVRDNLTLVCLRTLAKN-GVVDVKKQQAIVDRFIASLGIKLRSADQP 412 Query: 412 VQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILIS 471 ++ LSGGNQQ+VL+ RWLA +P +L+L PT G+DVG+K + +I++ L G+ ++L + Sbjct: 413 IRELSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSA 472 Query: 472 DDLPELLQNCDRILMMKKGHVSAEYRADELSEADLYHAL 510 +L EL DR ++++ G AE ++SE + A+ Sbjct: 473 SELEELTAVADRAVVIRDGRTVAELNGADMSETAIMDAI 511 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: 606 Number of extensions: 30 Number of successful extensions: 7 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: 544 Length adjustment: 35 Effective length of query: 480 Effective length of database: 509 Effective search space: 244320 Effective search space used: 244320 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