Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 146 bits (369), Expect = 7e-40 Identities = 79/235 (33%), Positives = 140/235 (59%), Gaps = 2/235 (0%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 +++R + K + V ALD V + GE V L G+NG+GKSTLIKIISG G + Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE-SKK 123 G++ + +P + + G+ I+QD +L P+L + NI +++ + L K + + + ++ Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 LD + ++I D++ +VE L Q+Q VA+ RA+ A++I+MDEPT AL+ E R++ + Sbjct: 130 ALDRIGVQI-DLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGI 188 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 R LK++G+ V+ ++H + + EV++++ VL GK + E + + +T MT Sbjct: 189 IRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMT 243 Score = 91.7 bits (226), Expect = 3e-23 Identities = 54/214 (25%), Positives = 111/214 (51%), Gaps = 5/214 (2%) Query: 12 KSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFN 71 + G + +S ++ GEV+ + G G G++++ K + G PD G ++ +G V Sbjct: 266 QGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDGSPVPLG 325 Query: 72 SPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAR--EVTNKIFLNKKKMMEESKKLLD 126 P A I + +D L I N+ + R T+ FL+ + +E+ L Sbjct: 326 DPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLR 385 Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186 L+++ PD+ V++LSGG +Q VA+AR + + ++++++ P+ + V + ++ R Sbjct: 386 RLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRE 445 Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 L ++G+GV++I+ ++ + R+ V+ G+II Sbjct: 446 LAREGIGVIVISDDLPELLATCHRVLVMREGRII 479 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: 238 Number of extensions: 12 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: 498 Length adjustment: 29 Effective length of query: 222 Effective length of database: 469 Effective search space: 104118 Effective search space used: 104118 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