Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 208 bits (530), Expect = 2e-58 Identities = 116/278 (41%), Positives = 164/278 (58%), Gaps = 13/278 (4%) Query: 19 PAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRD 78 PA++++D+ I DGE L L+GPSG GK+T LR +AGLE + G + +DVT+ R Sbjct: 16 PALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAAARR 75 Query: 79 IAMVFQNYALYPHMTVADNMGFALKIAG----VPKAEIRQKVEEAAKILDLTQYLDRKPK 134 + VFQ YAL+ HMTVA N+ F L + KAEI ++VEE K+++L R P Sbjct: 76 VGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVELEGLGGRYPS 135 Query: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTH 194 LSGGQRQRVA+ RA+ +P V L+DEP LDA +R S R ++ + G+TT++VTH Sbjct: 136 QLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDATGVTTIFVTH 195 Query: 195 DQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVK 254 DQ EA+ + DRVA+L +G ++Q+ +P ++D P FV GF+G N + ++ G K Sbjct: 196 DQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGE--ANRFDGQVSGGRFK 253 Query: 255 FGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELG 292 G VP A+ D T VRP F + E G Sbjct: 254 AGALTVP-------ASALKDGAATAYVRPHDFALDEAG 284 Lambda K H 0.317 0.135 0.379 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: 352 Number of extensions: 19 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: 377 Length of database: 339 Length adjustment: 29 Effective length of query: 348 Effective length of database: 310 Effective search space: 107880 Effective search space used: 107880 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 (21.6 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