Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21385 Length = 521 Score = 157 bits (396), Expect = 5e-43 Identities = 88/243 (36%), Positives = 148/243 (60%), Gaps = 2/243 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LLEI +V K F V AL V + + G V+AL+G+NGAGKSTL+KII+G ++PD G+L Sbjct: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122 GK V F++P A GI I+Q+L L+P + I NI++ RE N ++ ++M + Sbjct: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +LL+ L+I + D +V NLS +RQ V +A+AV + + +++MDEPT+A++ E + Sbjct: 147 QLLERLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFS 205 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 + +LK +G G++ ITH + + + +AD + V G I ++ + + + + +M L Sbjct: 206 IIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 265 Query: 243 GKV 245 ++ Sbjct: 266 SQL 268 Score = 92.0 bits (227), Expect = 2e-23 Identities = 55/244 (22%), Positives = 123/244 (50%), Gaps = 9/244 (3%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 L+ +RD+ G K GVS +++ GE++ + G G+G++ + + I G D G++ Sbjct: 280 LMSVRDLRLD-GVFK---GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICL 335 Query: 64 EGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA--REVTNKIFLNKKKMM 118 +G+ V + P+ A G + +D L P L + N+ +A F+ +K + Sbjct: 336 DGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALR 395 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 + + L+++ P + ++ LSGG +Q +AR + + +++++DEPT + V Sbjct: 396 ALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKA 455 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 ++ L L +G+ V++I+ + + ++DR+ V+ G ++ + E E + ++ + Sbjct: 456 EIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLAS 515 Query: 239 SFAL 242 ++ Sbjct: 516 GMSV 519 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: 258 Number of extensions: 11 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: 521 Length adjustment: 29 Effective length of query: 222 Effective length of database: 492 Effective search space: 109224 Effective search space used: 109224 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