Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 300 bits (769), Expect = 3e-86 Identities = 168/329 (51%), Positives = 210/329 (63%), Gaps = 7/329 (2%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA V K +Y G + + NL+I DGEF VLVGPSGCGKST LRML GLE ++ G Sbjct: 1 MAHVNIKQLRKTYDGRAD-VLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + IG + V H+ P +R IAMVFQ+YALYPHM V +NM F LK+AG S+ +I+ R+ AA Sbjct: 60 ELAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 A L + L+R P+ LSGGQRQRVA+GRAIVR P++FL DEPLSNLDA LRVQTR +IA Sbjct: 120 AILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAK 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L R+L T VYVTHDQ EA+T+GD+I V+ +G +QQ G P ELY +P N+FVAGFIGSP Sbjct: 180 LHRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPK 239 Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTP---EDNGRITIGFRPEALEIIPEGESTD 297 MN V D + I LA + P +T+G R E I EG Sbjct: 240 MNFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQ---IREGLGDG 296 Query: 298 LSIPIKLDFVEELGSDSFLYGKLVGEGDL 326 + ++ VE LG +FLY L G D+ Sbjct: 297 QPLHGVVNLVEHLGEANFLYVTLDGGHDI 325 Lambda K H 0.316 0.135 0.380 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: 384 Number of extensions: 12 Number of successful extensions: 1 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: 376 Length of database: 377 Length adjustment: 30 Effective length of query: 346 Effective length of database: 347 Effective search space: 120062 Effective search space used: 120062 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