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 WP_066599158.1 V473_RS00455 cell division ATP-binding protein FtsE
Query= TCDB::P96483 (377 letters) >NCBI__GCF_001046645.1:WP_066599158.1 Length = 236 Score = 114 bits (285), Expect = 3e-30 Identities = 69/199 (34%), Positives = 105/199 (52%), Gaps = 7/199 (3%) Query: 2 ATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGA 61 A V F+ Y G D + + ++ G F L G SG GK++ L++L + + G Sbjct: 3 AIVQFENVGLRY-GLDSETLSDVSFSLAGGGFYFLTGASGAGKTSLLKLLYLAQRPSRGV 61 Query: 62 IRIGDRDVTHLPPKD-----RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKV 116 IR+ DV LP K R I +VFQ++ L PH++ DN+ L+++G+ + EI V Sbjct: 62 IRLFGEDVVTLPRKRLPGFRRRIGVVFQDFRLVPHLSAYDNIALPLRVSGMEEGEIDAPV 121 Query: 117 EEAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRT 176 E + L +P LSGG++QRVA+ RA++ P++ + DEP N+DA + T Sbjct: 122 VEMLNWVGLGDRGQARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDADMARRLMT 181 Query: 177 QIASLQRRLGITTVYVTHD 195 +L RLG T V THD Sbjct: 182 LFEAL-NRLGTTIVVATHD 199 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: 235 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: 236 Length adjustment: 26 Effective length of query: 351 Effective length of database: 210 Effective search space: 73710 Effective search space used: 73710 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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