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 GFF770 HP15_749 iron(III) ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Marino:GFF770 Length = 357 Score = 207 bits (526), Expect = 5e-58 Identities = 109/221 (49%), Positives = 145/221 (65%), Gaps = 6/221 (2%) Query: 21 VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVT----HLPPKD 76 V + A+ G+ L+GPSGCGKST LR LAG ++GG I + + ++ LPP+ Sbjct: 28 VKDVSFALSHGDIGCLLGPSGCGKSTILRALAGFLPLSGGEISLQSQAISLPGRTLPPEK 87 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R I MVFQ+YAL+PH+T+ADN+GF L+ + KAE RQKV E ++ L D P L Sbjct: 88 RRIGMVFQDYALFPHLTIADNVGFGLR--NLNKAEKRQKVMELLNVVHLQDLADNYPHEL 145 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQ+QRVA+ RA+ EP + L+DEP SNLDA LR + + + LGI+ + VTHDQ Sbjct: 146 SGGQQQRVALARALAPEPTLILLDEPFSNLDADLRRRLSLDVREILKTLGISAILVTHDQ 205 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIG 237 EA M D+VAVL+DG +QQ D P N+Y +PAN FVA F+G Sbjct: 206 QEAFAMCDQVAVLRDGRIQQWDVPYNLYHEPANRFVASFVG 246 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: 362 Number of extensions: 13 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: 357 Length adjustment: 30 Effective length of query: 347 Effective length of database: 327 Effective search space: 113469 Effective search space used: 113469 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