Align TreV, component of Trehalose porter (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 224 bits (572), Expect = 2e-63 Identities = 124/333 (37%), Positives = 200/333 (60%), Gaps = 22/333 (6%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 VEL ++ K++G N VI+ I I G+ +LGPSG GK+T+L+++AG+EK +G+I D Sbjct: 7 VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G D+T + ++R++ MVFQ+YAL+P+MS+ +N+ + LKM G+ + E+ RV++A ++ + Sbjct: 67 GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDL 126 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 D+ V QISGGQQQRVALARA++ P L DEPLSNLDA +R + R +++ +QK+ Sbjct: 127 EGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQF 186 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE---FPMN 239 T +YVTHDQ EA +++D + +++KG Q+ P+ LY P ++++A F+G+ FP Sbjct: 187 DITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDANLFPAT 246 Query: 240 F-----------LPGELMKEKAQE--IGFRPEWVEV---GKGNLSCMVESVEASGESRYL 283 F LP L E +G RPE + + G+ + C++ V G + Sbjct: 247 FSDGYVDIYGYHLPRPLHFGTQGEGMVGVRPEAITLSDRGEESQRCVIRHVAYMGPQYEV 306 Query: 284 ICNFKNNNITI---LSQEFYDVGQEVRFEIIKY 313 + I + ++ DVG++ EI Y Sbjct: 307 TVEWHGQEILLQVNATRLQPDVGEQYYLEIHPY 339 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: 275 Number of extensions: 8 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: 348 Length adjustment: 28 Effective length of query: 296 Effective length of database: 320 Effective search space: 94720 Effective search space used: 94720 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