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 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= TCDB::P96483 (377 letters) >MicrobesOnline__882:207786 Length = 397 Score = 166 bits (419), Expect = 1e-45 Identities = 90/248 (36%), Positives = 143/248 (57%), Gaps = 9/248 (3%) Query: 21 VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPP------ 74 VD+ +E+GE +V++G SG GKST +R L L + G + + RDVT +P Sbjct: 43 VDRASFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRL 102 Query: 75 KDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPK 134 + R MVFQN+AL+PH TV N F L+ GVP+AE ++ + + + L ++ +P Sbjct: 103 RQRSFGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPA 162 Query: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTH 194 LSGG +QRV + RA+ +P + LMDE S LD +R + ++ LQ L T V+++H Sbjct: 163 QLSGGMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFISH 222 Query: 195 DQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVK 254 D EA+ +GDR+ +++DG + Q+ +P ++ PA+ +VA F+G + V +T G V Sbjct: 223 DLDEALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVTKV---LTAGSVM 279 Query: 255 FGNSVVPV 262 + V V Sbjct: 280 KRSEAVAV 287 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: 361 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: 397 Length adjustment: 30 Effective length of query: 347 Effective length of database: 367 Effective search space: 127349 Effective search space used: 127349 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: 50 (23.9 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