Align deoxynucleoside transporter, ATPase component (characterized)
to candidate H281DRAFT_02174 H281DRAFT_02174 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Burk376:H281DRAFT_02174 Length = 550 Score = 323 bits (828), Expect = 1e-92 Identities = 196/516 (37%), Positives = 302/516 (58%), Gaps = 25/516 (4%) Query: 7 SSAPLSQPFL-EVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQ 65 S +P ++P L E+ + F GV ALRG +LS G+++ L+G+NG GKST+IKI++GA Sbjct: 15 SQSPATRPLLLEMQDIGISFGGVPALRGANLSVAAGEVHALIGQNGAGKSTMIKILTGAY 74 Query: 66 PPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA 125 G + EG + +A AGI T+YQ+++L+P SVAEN+ L GR Sbjct: 75 RRGSGSVRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFL--------GREP 126 Query: 126 RTF---DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVI 182 R F D R + AA L++ GL + + + + A +Q+VA+ARA++S+AK VI Sbjct: 127 RRFGLIDWRTVQHRAAALLDSFGLHIDVKKP---VGRYSTAIQQMVALARAVSSDAKMVI 183 Query: 183 MDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGP 242 MDE T+SL ++EV+ L V+ LR G V+FVSH+LDE YA+ V V+RDGQ +AQ Sbjct: 184 MDESTSSLDEREVELLFTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQST 243 Query: 243 IAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAG--------QFSDVSFKL 294 +AE K Q+ M GR L+ + + A A++ L RG + SDVS ++ Sbjct: 244 MAEMDKLQLVTTMLGRTLAAVVHDDPA-AREANLARRGKQAIAARDLGAHPKVSDVSLEV 302 Query: 295 HGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPED 354 H GE +G+ GLL SGR E R + G P + G V +DG + L++P DA + Y+ ED Sbjct: 303 HAGEAVGLAGLLGSGRTETMRLMFGADPLERGSVSIDGATVTLKSPQDAIARGLAYLTED 362 Query: 355 RLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQS 414 R EG+ + +RDN+ + +L R G +D + QA+ ++ + L I D+P++ Sbjct: 363 RKAEGIVPELSVRDNLTLVCLRTL-TRNGIVDVKKQQAIVDRFIASLGIKLRSADQPIRE 421 Query: 415 LSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDL 474 LSGGNQQ+VL+ RWLA +P +L+L PT G+DVG+K + +I++ L G+ +++ + +L Sbjct: 422 LSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKADVAKIVRELRDAGLAVLMSASEL 481 Query: 475 PELLQNCDRILMMKKGHVSAEYRADELSEADLYHAL 510 EL DR ++++ G AE E+SE+ + A+ Sbjct: 482 EELTAVSDRAVVIRDGRTVAELNGAEMSESAIMDAI 517 Score = 84.7 bits (208), Expect = 8e-21 Identities = 66/251 (26%), Positives = 124/251 (49%), Gaps = 11/251 (4%) Query: 24 RFTGVHA-LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARL 82 R G H + VSL G+ L G G G++ ++++ GA P + G + I+G Sbjct: 287 RDLGAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETMRLMFGADPLERGSVSIDGATVTLK 346 Query: 83 SALEALAAGIETVYQDLS---LLPNMSVAENVALTS-ELATHEGRLARTFDRRVLAATAA 138 S +A+A G+ + +D ++P +SV +N+ L T G + D + A Sbjct: 347 SPQDAIARGLAYLTEDRKAEGIVPELSVRDNLTLVCLRTLTRNGIV----DVKKQQAIVD 402 Query: 139 RALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNL 198 R + ++G+ S Q I +L +Q V +AR +A+E +++DEPT + ++ Sbjct: 403 RFIASLGIKLRSADQP--IRELSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKADV 460 Query: 199 IAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGR 258 ++ LR G+ VL + +L+E A+ +V+RDG+ +A+ AE +++ I + + Sbjct: 461 AKIVRELRDAGLAVLMSASELEELTAVSDRAVVIRDGRTVAELNGAEMSESAIMDAIAYG 520 Query: 259 HLSNERYRESA 269 S+ + E+A Sbjct: 521 GDSSSQLAEAA 531 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: 633 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 515 Length of database: 550 Length adjustment: 35 Effective length of query: 480 Effective length of database: 515 Effective search space: 247200 Effective search space used: 247200 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