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 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 163 bits (413), Expect = 7e-45 Identities = 84/223 (37%), Positives = 134/223 (60%), Gaps = 6/223 (2%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD--- 76 AV +++I +GE V++G SG GKST LR + L G + I D+ + K+ Sbjct: 42 AVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQ 101 Query: 77 ---RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKP 133 +++AMVFQN+ L PH +V N+ F L++ GV K E QK E+ +++ L Y ++ Sbjct: 102 IRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLVGLKGYENQMV 161 Query: 134 KALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVT 193 LSGG +QRV + RA+ P+V LMDE S LD +RV + ++ +LQ ++ T V++T Sbjct: 162 SELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFIT 221 Query: 194 HDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI 236 HD EA+ +GDR+A++KDG + Q+ + + +PAN +V F+ Sbjct: 222 HDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 264 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: 305 Number of extensions: 12 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: 408 Length adjustment: 31 Effective length of query: 346 Effective length of database: 377 Effective search space: 130442 Effective search space used: 130442 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