Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 3606961 Dshi_0388 ABC transporter related (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Dino:3606961 Length = 261 Score = 188 bits (478), Expect = 8e-53 Identities = 107/243 (44%), Positives = 158/243 (65%), Gaps = 8/243 (3%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L R++ K +G V ALD E+ GE++A++GDNGAGKS+LIK +SG PD G++ Sbjct: 9 ILAGRNLVKRYGRVTALDHCDFELYPGEILAVIGDNGAGKSSLIKAVSGAVIPDEGEVFL 68 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNK------KKM 117 EGK+V F SP DAR+ GIET+YQ LA+ P L I N+F+ RE+ + K + Sbjct: 69 EGKRVRFQSPLDARAAGIETVYQQLAMSPALSIADNMFMGRELRKPGWRGKWLRQLDRAA 128 Query: 118 MEE--SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVV 175 ME+ KL + + I +IN VE LSGGQRQ VAVARA F +K+I++DEPTAAL V Sbjct: 129 MEKFARDKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVIILDEPTAALGVK 188 Query: 176 EARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 E+R+VLEL +++ +G+ +++I+HN+ +EVADRI++ GK + ++ ++ + Sbjct: 189 ESRRVLELILDVRARGIPIVLISHNMPHVFEVADRIHIHRLGKRLCVIDPKDHDMSDAVA 248 Query: 236 VMT 238 MT Sbjct: 249 FMT 251 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: 136 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: 261 Length adjustment: 24 Effective length of query: 227 Effective length of database: 237 Effective search space: 53799 Effective search space used: 53799 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