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 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__SB2B:6936480 Length = 341 Score = 169 bits (429), Expect = 8e-47 Identities = 91/254 (35%), Positives = 151/254 (59%), Gaps = 8/254 (3%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVT----HLPPKDRDI 79 L++ + GE L+GPSGCGK+T LR +AGL+D++ G+I I + V+ + P+ R I Sbjct: 22 LNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAINGKTVSADGCFVAPEKRSI 81 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 M+FQ+YAL+PH+TVADN+ F ++ +R +EE ++ L R P LSGG Sbjct: 82 GMIFQDYALFPHLTVADNILFGVRQLDKQSRSVR--LEEMLSLVKLEGLGKRYPHELSGG 139 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 Q+QRV++ RA+ EP + L+DEP SN+DA++R + +I ++ + ++ V+VTH + EA Sbjct: 140 QQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRAILKARNVSAVFVTHSKDEA 199 Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSV 259 D +A+ + G + Q P +Y P +VA F+G A N ++V + G + Sbjct: 200 FAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLG--ASNYLDVRLEAGQLISTLGA 257 Query: 260 VPVNREALSAADKG 273 P+ ++ +A++ G Sbjct: 258 FPLPQDFKAASETG 271 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: 278 Number of extensions: 10 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 348 Effective length of database: 312 Effective search space: 108576 Effective search space used: 108576 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