Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 164 bits (415), Expect = 3e-45 Identities = 88/238 (36%), Positives = 144/238 (60%), Gaps = 2/238 (0%) Query: 1 MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60 M LL+++ + K+F VKAL G ++ + G V+AL+G+NGAGKST++K+++G + D G Sbjct: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 Query: 61 LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMME 119 L++ GK+ F P ++ GI I+Q+L LIP L I NIFL RE N+ ++ K M Sbjct: 61 LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 E+ KLL L +R + V +LS G +Q V +A+ + F +K+I+MDEPT AL+ E Sbjct: 121 EADKLLAKLNLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 + + R LK +G G++ I+H + + +E+ D + V G+ I ++ + + E+M Sbjct: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMM 237 Score = 96.7 bits (239), Expect = 8e-25 Identities = 62/233 (26%), Positives = 119/233 (51%), Gaps = 10/233 (4%) Query: 20 LDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSL 79 ++ VS + KGE++ + G GAG++ L+K++ G G + +G +V+ SP D + Sbjct: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327 Query: 80 GIETIYQDL---ALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLDSLQ---IRIP 133 GI I +D L+ + + N+ L K +E + + D ++ ++ P Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTP 387 Query: 134 DINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLG 193 + + LSGG +Q VA+AR + K++++DEPT + V +++ +L K GL Sbjct: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447 Query: 194 VLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFALGKVN 246 +++++ + + ++DRI V+ G H E T + EV+ + A+GK+N Sbjct: 448 IILVSSEMPEVLGMSDRIIVMHEG----HLSGEFTREQATQEVLMAAAVGKLN 496 Lambda K H 0.318 0.137 0.371 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: 264 Number of extensions: 17 Number of successful extensions: 5 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: 251 Length of database: 501 Length adjustment: 29 Effective length of query: 222 Effective length of database: 472 Effective search space: 104784 Effective search space used: 104784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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