Align TreV, component of Trehalose porter (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 204 bits (519), Expect = 3e-57 Identities = 107/246 (43%), Positives = 161/246 (65%), Gaps = 2/246 (0%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 V++ + K++ + ++ +T I GE F +LG SG GKSTLL+ILAG E +G+++ D Sbjct: 21 VKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLD 80 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G +IT PP KR + M+FQ+YAL+P+M+V NIAF LK + EI ERV + KL+ + Sbjct: 81 GQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVHM 140 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 ++ +K Q+SGGQ+QRVALAR++ + P LLDEP+ LD ++R+ + EL I + + Sbjct: 141 AKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERV 200 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T I VTHDQ+EA+++A RIAI+ +G QV P +YE P + VA+FVG +N Sbjct: 201 GVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS--VNIFE 258 Query: 243 GELMKE 248 GE++ + Sbjct: 259 GEIVAD 264 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: 293 Number of extensions: 9 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 24 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