Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS01820 Length = 544 Score = 404 bits (1038), Expect = e-117 Identities = 225/501 (44%), Positives = 330/501 (65%), Gaps = 2/501 (0%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL++ + SF GV AL +L V GEVHAL+G+NGAGKST+IKIL+ A+ +G+V F Sbjct: 18 LLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYRRGSGSVRF 77 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 G+ +D R P + ++ GI+TIYQE NL P SVAEN++LGREPRR GL+DW ++ A Sbjct: 78 EGREVDFR-TPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWHAVQQRAA 136 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 ALL GL ++ PV + A QQMV +A+A++ +A+++IMDE T++L REV+ L + Sbjct: 137 ALLESFGLQIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDEREVELLFTV 196 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + L+ +VI+VSHRL E+ A+CDR TVMRDG+ VA +AD++ +V M+GR + Sbjct: 197 VRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTTMLGRTLA 256 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302 + A + + AA +LSA + VS GE VGLAGL+G+GRT+ Sbjct: 257 AVVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLGSGRTETM 316 Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362 RL+FGADP+ G + + + + L+SP+DAI G+ + EDRK +G + S+R NL+L Sbjct: 317 RLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVRDNLTLVC 376 Query: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422 L+ L+ G VD + ++ +V+ + L IK+ A+ I +LSGGNQQKVLL R +A P Sbjct: 377 LRTLAKNGV-VDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARWLAAEPS 435 Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482 +L++DEPTRGID+GAKAEV +++ +L D G+AV++ +SEL E+ AV+DR VV R+G VA Sbjct: 436 LLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIRDGRTVA 495 Query: 483 DLDAQTATEEGLMAYMATGTD 503 +L+ +E +M +A G+D Sbjct: 496 ELNGADMSETAIMDAIAYGSD 516 Lambda K H 0.320 0.136 0.380 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: 693 Number of extensions: 28 Number of successful extensions: 8 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 (21.8 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