Align TreV, component of Trehalose porter (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 245 bits (626), Expect = 1e-69 Identities = 137/332 (41%), Positives = 206/332 (62%), Gaps = 22/332 (6%) Query: 2 TVELIDIVKKYGKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60 +++L + K Y N+ + GI +I GEF V++GPSG GKSTLL+++AG+E + G + Sbjct: 3 SIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGTLK 62 Query: 61 ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120 D + D P +R++AMVFQNYALYP+M+V N+A+ LK RG+K+EEI RV AA +L Sbjct: 63 IDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAAML 122 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 I L++K ++SGGQ+QRVA+ RA+VR PS FL DEPLSNLDA++R R E+K++Q+ Sbjct: 123 EIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQLQR 182 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240 LK T +YVTHDQ EAL+L DR+ +L+ G EQV P +YE P + +VA F+G MN Sbjct: 183 RLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAMNM 242 Query: 241 LPGELMKEKAQE------------IGFRPEWVEVGKGN-----LSCMVESVEASGESRYL 283 LP ++E+ IG RP+ + + + ++ VE EA+G +L Sbjct: 243 LPVAYLRERGANGLLDHLAADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAESHL 302 Query: 284 ICNFKNNN----ITILSQEFYDVGQEVRFEII 311 + + ++ I ++ G+ +RF ++ Sbjct: 303 YVSLEGSDQPTVIRTSARPPVAEGETMRFHVL 334 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: 256 Number of extensions: 7 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: 354 Length adjustment: 28 Effective length of query: 296 Effective length of database: 326 Effective search space: 96496 Effective search space used: 96496 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