Align TreV, component of Trehalose porter (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 203 bits (517), Expect = 4e-57 Identities = 117/296 (39%), Positives = 170/296 (57%), Gaps = 18/296 (6%) Query: 1 MTVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60 MT+ + + K++G+ +N + +I GE +LGPSG GK+TLL+ +AG+E D G+++ Sbjct: 1 MTIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL 60 Query: 61 ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMK----KEEIIERVEKA 116 DG D+T R V VFQ YAL+ +M+V NIAF L +R K K EI RVE+ Sbjct: 61 FDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEEL 120 Query: 117 AKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELK 176 KL+ + + + +Q+SGGQ+QRVAL+RA+ PS LLDEP LDA VR + R EL+ Sbjct: 121 LKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELR 180 Query: 177 RIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE- 235 R+ T I+VTHDQ+EAL LADR+AIL+ G+ EQ+ P +++ P+T +V FVGE Sbjct: 181 RVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGEA 240 Query: 236 -----------FPMNFL--PGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASG 278 F L P +K+ A RP + + ++E + G Sbjct: 241 NRFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFEVLIERAQVQG 296 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: 11 Number of successful extensions: 2 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: 339 Length adjustment: 28 Effective length of query: 296 Effective length of database: 311 Effective search space: 92056 Effective search space used: 92056 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