Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 146 bits (369), Expect = 7e-40 Identities = 87/216 (40%), Positives = 132/216 (61%), Gaps = 4/216 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRG-DLV 62 LL +R++ K+F V+AL V + GEV AL+G+NGAGKSTL+KI+SG + D G + Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 63 FEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESK 122 +G++V + P AR LG+ IYQ+L+L P+L + NI+L R + + + + M+ Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 129 Query: 123 KLLDSLQIRI-PDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181 L L P N V +LS QRQ V +ARAV+F A++++MDEPT LS E ++ Sbjct: 130 PTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLF 187 Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRG 217 L R L+ +G+ +L I+H + + E+ADR+ VL G Sbjct: 188 ALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDG 223 Score = 80.5 bits (197), Expect = 7e-20 Identities = 59/229 (25%), Positives = 109/229 (47%), Gaps = 17/229 (7%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L +RDV + + G S ++ GEV+ L G GAG++ L +++ G RG++ Sbjct: 265 MLSVRDVADG----RRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRI 320 Query: 64 -----EGKKVIF--NSPNDARSLGIETIYQDL---ALIPDLPIYYNIFL---AREVTNKI 110 G V P A GI + +D L D ++ NI L AR+ Sbjct: 321 ANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLG 380 Query: 111 FLNKKKMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTA 170 LN+ + + +D+L IR+ + V LSGG +Q V ++R + +++++DEPT Sbjct: 381 RLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTR 440 Query: 171 ALSVVEARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI 219 + + ++ L L + G+ +L+I+ + + + DR+ V+ G + Sbjct: 441 GVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 489 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: 255 Number of extensions: 14 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: 537 Length adjustment: 30 Effective length of query: 221 Effective length of database: 507 Effective search space: 112047 Effective search space used: 112047 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