Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 303 bits (776), Expect = 4e-87 Identities = 163/346 (47%), Positives = 222/346 (64%), Gaps = 9/346 (2%) Query: 4 SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63 ++ ++ + K FG V+V++ VD+ + GEF++ VGPSGCGKSTLL +I GL++ + G Sbjct: 3 AITLSKVEKWFG----DVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRG 58 Query: 64 EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVA 123 + I G +V PP R + MVFQSYALYP +SV +N+GF+L+ P E ++++ A Sbjct: 59 AMLIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAA 118 Query: 124 AMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKR 183 A+L++ LDRRP LSGGQRQRVA+GR++ R P FLFDEPLSNLDA LRVEMR EI + Sbjct: 119 AVLKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAK 178 Query: 184 LHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPT 243 LHQ+ T +YVTHDQVEAMTL RI V++ G + Q+GTP E+Y PAN +VA FIGSP Sbjct: 179 LHQSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPK 238 Query: 244 MNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLV--MQETAPWRGRVSVVEP 301 MN++ G++ + + A V LG+RPEH+ T GRV VVE Sbjct: 239 MNVMPCTTDAGRYRLSAGRGGVFSGDRPA--VQLGIRPEHITPGAPGTGACDGRVDVVEY 296 Query: 302 TGPDTYVMVDTA-AGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFD 346 G DT +++D G VT+R T + PG+ VGL+ P +FD Sbjct: 297 LGADTLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFD 342 Lambda K H 0.318 0.135 0.388 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: 340 Number of extensions: 15 Number of successful extensions: 4 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: 355 Length of database: 349 Length adjustment: 29 Effective length of query: 326 Effective length of database: 320 Effective search space: 104320 Effective search space used: 104320 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