Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_3037 Fructose ABC transporter, ATP-binding component FrcA
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3037 Length = 268 Score = 205 bits (522), Expect = 7e-58 Identities = 108/242 (44%), Positives = 159/242 (65%), Gaps = 7/242 (2%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +++ + + K +G V ALDG E+ GE++A++GDNGAGKS+LIK +SG PD G+++ Sbjct: 13 VMQAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKALSGATVPDEGEILL 72 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREV-------TNKIFLNKKK 116 +G+++ F SP +AR GIET+YQDLA+ P + I N+FL RE+ T L+KKK Sbjct: 73 DGQRIQFKSPIEARRAGIETVYQDLAVAPAMTIAENLFLGRELRRPGLLGTALRMLDKKK 132 Query: 117 MMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVE 176 M+EES + L++ I + VE LSGGQRQ VAVARA F+ +++MDEPTAAL V E Sbjct: 133 MLEESVARMAELKVGIRSMTQAVETLSGGQRQCVAVARAAAFARHVVIMDEPTAALGVKE 192 Query: 177 ARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEV 236 VLEL R ++ KGL V++I+HN+ +E+ADRI++ GK ++ ++ + V Sbjct: 193 GNMVLELIRRVRDKGLPVILISHNMPHVFEIADRIHIARLGKRAAVVNPKKISMSDTVAV 252 Query: 237 MT 238 MT Sbjct: 253 MT 254 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: 143 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 251 Length of database: 268 Length adjustment: 24 Effective length of query: 227 Effective length of database: 244 Effective search space: 55388 Effective search space used: 55388 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: 47 (22.7 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