Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_066599158.1 V473_RS00455 cell division ATP-binding protein FtsE
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_001046645.1:WP_066599158.1 Length = 236 Score = 102 bits (253), Expect = 1e-26 Identities = 62/199 (31%), Positives = 104/199 (52%), Gaps = 7/199 (3%) Query: 2 ARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGN 61 A V E++ Y G T+ D + + F G SG GKT+ L+++ + + G Sbjct: 3 AIVQFENVGLRY-GLDSETLSDVSFSLAGGGFYFLTGASGAGKTSLLKLLYLAQRPSRGV 61 Query: 62 LYIGDRRVNDVPPKD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRV 116 + + V +P K R I +VFQ++ L PH++ Y N+A L++ + + EID V Sbjct: 62 IRLFGEDVVTLPRKRLPGFRRRIGVVFQDFRLVPHLSAYDNIALPLRVSGMEEGEIDAPV 121 Query: 117 QEAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRA 176 E + + +P LSGG++QRVA+ RA++ P++ + DEP N+DA + ++ Sbjct: 122 VEMLNWVGLGDRGQARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDADMARRLMT 181 Query: 177 EIRKLHQRLQTTVIYVTHD 195 L+ RL TT++ THD Sbjct: 182 LFEALN-RLGTTIVVATHD 199 Lambda K H 0.321 0.138 0.395 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: 221 Number of extensions: 10 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: 384 Length of database: 236 Length adjustment: 27 Effective length of query: 357 Effective length of database: 209 Effective search space: 74613 Effective search space used: 74613 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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