Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 207 bits (528), Expect = 2e-58 Identities = 109/236 (46%), Positives = 151/236 (63%), Gaps = 4/236 (1%) Query: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 I I + K +G AL ++L+I DGE + +GPSG GK+TLLRT+AGLE +G++ Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVN-GFEPDLRKE---RIAEAAR 119 G+DVT A R + VFQ YAL+ HMTV +N+ FG+ V G + + E R+ E + Sbjct: 63 GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +++LE R P QLSGGQRQRVA+ RA+ PSV L DEP LDA +R +R EL + Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIG 235 H G T I+VTHDQ EA+ +AD++ +LN GRIEQ+G+P ++ P + FV F+G Sbjct: 183 HDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG 238 Lambda K H 0.320 0.139 0.396 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: 346 Number of extensions: 18 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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