Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 174 bits (441), Expect = 3e-48 Identities = 96/254 (37%), Positives = 152/254 (59%), Gaps = 10/254 (3%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 M+T+T + Y G + ++ +L + GE L+GPSGCGK+T L+ +AGL+ ++ G Sbjct: 1 MSTLTIEQVHSDYQG--QTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQG 58 Query: 61 AIFIGDKDV----THVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRV 116 I I + + T V R++ M+FQ+YAL+PH+TV EN+ F +K K+ + R+ Sbjct: 59 RISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQA--RL 116 Query: 117 DEAAATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRT 176 E A + L R P LSGGQ+QRV++ RA+ P++ L+DEP SN+DAK+R + Sbjct: 117 GEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMV 176 Query: 177 QIAALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFI 236 +I + ++ GV+ V+VTH + EA D++A+ KDG + Q G+ LY P + +VA F+ Sbjct: 177 EIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236 Query: 237 GSPAMNLGTFSVKD 250 G +N + VKD Sbjct: 237 GQ--VNYLSCEVKD 248 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: 313 Number of extensions: 21 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: 376 Length of database: 342 Length adjustment: 29 Effective length of query: 347 Effective length of database: 313 Effective search space: 108611 Effective search space used: 108611 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