Align TreV, component of Trehalose porter (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 231 bits (589), Expect = 2e-65 Identities = 129/314 (41%), Positives = 187/314 (59%), Gaps = 32/314 (10%) Query: 13 GKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE 72 G ++ + +I GEF V++GPSG GKST L++LAG+E ++ G I D+T PP+ Sbjct: 16 GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75 Query: 73 KRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQ 132 R++AMVFQNYALYP+M+V DN+ F LK+ G+ K EI +VE+AAK+L ++E LD+K Sbjct: 76 DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135 Query: 133 ISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHD 192 +SGGQ+QRVA+ RAIVR P FL+DEPLSNLDA++R + R ++ +Q+ L T +YVTHD Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195 Query: 193 QKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP---------- 242 Q EA+++ DR+A+L G +QV P+ +Y+ P +VA F+G MN + Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVKF 255 Query: 243 ------------GELMK--EKAQEIGFRPEWVEVGKG--------NLSCMVESVEASGES 280 GE +K +G RPE +++ G L+ V VE G Sbjct: 256 GESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGAD 315 Query: 281 RYLICNFKNNNITI 294 Y+ + K TI Sbjct: 316 GYVYGSAKVGTETI 329 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: 286 Number of extensions: 13 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: 369 Length adjustment: 29 Effective length of query: 295 Effective length of database: 340 Effective search space: 100300 Effective search space used: 100300 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 Apr 09 2024. 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