Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Keio:1937256 Length = 500 Score = 160 bits (406), Expect = 4e-44 Identities = 84/235 (35%), Positives = 143/235 (60%), Gaps = 1/235 (0%) Query: 3 DLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62 ++L + K F VKALD V + +GE++ALLG+NGAGKSTLIK ++G + DRG + Sbjct: 8 EILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIW 67 Query: 63 FEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESK 122 EG+ + + A+ LGI T+YQ++ L+P++ + N+F+ RE L +K+M + + Sbjct: 68 LEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRAT 127 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +L+ S + D+ + S +Q VA+ RA+ SAK++++DEPTA+L E + + Sbjct: 128 ELMASYGFSL-DVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237 L R L+ +G+ ++ +TH + Q Y+V+DRI VL G + ++ E E+ ++M Sbjct: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241 Score = 90.5 bits (223), Expect = 6e-23 Identities = 60/233 (25%), Positives = 111/233 (47%), Gaps = 5/233 (2%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 K++G + +E+ GE+V L G G+G++ ++I G D G + +GK Sbjct: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 Query: 72 SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKIF--LNKKKMMEESKKLLD 126 SP+ A LGI +D +I + NI LA + +++K+ E +++ + Sbjct: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIR 387 Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186 L IR P +E LSGG +Q V ++R + + +++DEPT + V +++ L Sbjct: 388 QLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIET 447 Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTS 239 L GL +L+I+ + + ADR+ ++ K + E +V I + + Sbjct: 448 LCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAIAA 500 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: 249 Number of extensions: 14 Number of successful extensions: 4 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: 500 Length adjustment: 29 Effective length of query: 222 Effective length of database: 471 Effective search space: 104562 Effective search space used: 104562 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