Align TreV, component of Trehalose porter (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 202 bits (513), Expect = 1e-56 Identities = 102/233 (43%), Positives = 157/233 (67%), Gaps = 2/233 (0%) Query: 18 INGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEKRNVA 77 ++ ++ I GE F +LG SG GKSTLL++LAG E+ +G+I DG DITD PP +R + Sbjct: 36 VDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYERPIN 95 Query: 78 MVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQ 137 M+FQ+YAL+P+M+V NIAF LK M K +I +RV++ KL+ + + +K Q+SGGQ Sbjct: 96 MMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQ 155 Query: 138 QQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEAL 197 +QRVALAR++ + P LLDEP+ LD ++RT + E+ I + + T + VTHDQ+EA+ Sbjct: 156 RQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAM 215 Query: 198 SLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGELMKEKA 250 ++A RIAI+ G QV P +YE P ++ +A+F+G +N E+++++A Sbjct: 216 TMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIG--TVNLFDCEIIEDEA 266 Lambda K H 0.318 0.137 0.385 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: 291 Number of extensions: 10 Number of successful extensions: 1 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: 324 Length of database: 378 Length adjustment: 29 Effective length of query: 295 Effective length of database: 349 Effective search space: 102955 Effective search space used: 102955 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