Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 194 bits (494), Expect = 2e-54 Identities = 106/270 (39%), Positives = 161/270 (59%), Gaps = 11/270 (4%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 +L I GE + L+GPSGCGK+T LR++AG+E +G + + TH+ R+R + VFQ Sbjct: 22 SLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHARERQVGFVFQ 81 Query: 85 NYALYPHMTVGENMGFALKIAGKSQ----DEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 +YAL+ HM V EN+ F L++ + + EI KRV + + + L +R P LSGGQ Sbjct: 82 HYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADRYPTQLSGGQ 141 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 RQR+A+ RA+ P+V L+DEP LD K+R + R + L ++ +++V+VTHDQ EAL Sbjct: 142 RQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVFVTHDQEEAL 201 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHAR- 259 + DR+ V+ G ++QVG+P E+Y PA+ FV F+G N+ F + A + AR Sbjct: 202 EVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLG----NVNVFHSRVHGAWAEVARD 257 Query: 260 -IKLSPETLAAMTPEDNGRITIGFRPEALE 288 + E +A + P D T+ PE+LE Sbjct: 258 DVPAGQEAVAFIRPHDIDIDTVA-TPESLE 286 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: 330 Number of extensions: 15 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: 376 Length of database: 360 Length adjustment: 30 Effective length of query: 346 Effective length of database: 330 Effective search space: 114180 Effective search space used: 114180 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 Apr 09 2024. 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