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 N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 349 bits (896), Expect = e-101 Identities = 197/375 (52%), Positives = 251/375 (66%), Gaps = 29/375 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA V DK ++YP V + I DGE LVLVGPSGCGK+T LRM+AGLE ++GG Sbjct: 1 MAKVRLDKLRKVYPNGHV-GVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 + IG+R V + PKDRDIAMVFQNYALYPHMTVA+N+GF LK+ G PKAEI ++V EAA Sbjct: 60 TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 ++L+L Q LD +P ALSGGQRQRVA+GRA+VR+P+VFL+DEPLSNLDAKLR+S R +IA Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 + +RL T VYVTHDQ+EAMT+G R+ VL G++QQ+D+P N+YD PANLFVAGF+GSPA Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 241 MNLVE-VPITDGGVKFGNSVVPVNREALSAADKG-------DRTVTVGVRPEHFDVVELG 292 MNL+ + DGG K +P L +G DR + VG+RPE D++ Sbjct: 240 MNLLRGILYRDGGWKL---AMPQGELVLGELPQGAALEAWRDRDIVVGLRPE--DLLLCA 294 Query: 293 GAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKG 352 A A A LA + VVE +G + ++ GE+ LV R+ R++P G Sbjct: 295 DA-----------AGAALAAQLEVVEPVGNEVFLNLR---HGELA-LVSRMPPRELPAPG 339 Query: 353 STLHVVPRPGETHVF 367 STLH P H F Sbjct: 340 STLHFGFAPERLHFF 354 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: 412 Number of extensions: 22 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: 364 Length adjustment: 30 Effective length of query: 347 Effective length of database: 334 Effective search space: 115898 Effective search space used: 115898 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