Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 127 bits (318), Expect = 6e-34 Identities = 69/217 (31%), Positives = 125/217 (57%), Gaps = 3/217 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 ++ + + KSFG V+A ++++I G + ALLG+NGAGKSTL+ I++G + D G +V Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 +G +F SP DA GI +YQ L+ + + N+ L + + + L +M +E Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQ--SPDMLLRPARMRDEVAA 146 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 L + + + D +V LS G+RQ V + + +Y ++++++DEPTA L+ E ++ E Sbjct: 147 LAERYGLAV-DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEA 205 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 + +G ++ I+H + + VAD I +L RG+++ Sbjct: 206 MWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVV 242 Score = 84.0 bits (206), Expect = 6e-21 Identities = 60/215 (27%), Positives = 107/215 (49%), Gaps = 8/215 (3%) Query: 20 LDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGK--KVIFNSPNDAR 77 L VS+++ +GE+VA+ G G G+ L++ I G +P+ G++ G+ + F P R Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350 Query: 78 SLG-IETIYQDLALIPDLPIYYNIFLA--REVTNKIFLNKKKMMEESKKLLDSLQIRIPD 134 L I Q LA L + N L + +FL++ + K+++ ++ D Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410 Query: 135 INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGL-G 193 I LSGG Q + + R + ++I+ + PT L + +V R L+ + G Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEV--WGRLLEARSTSG 468 Query: 194 VLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEET 228 VL++T ++ + E+ADRI V+ RG+ I K++T Sbjct: 469 VLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDT 503 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: 269 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