Align Trehalose/maltose-binding protein aka TT_C1627, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate Pf1N1B4_5112 Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
Query= TCDB::Q72H68 (429 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5112 Length = 390 Score = 353 bits (907), Expect = e-102 Identities = 175/388 (45%), Positives = 244/388 (62%), Gaps = 1/388 (0%) Query: 42 VGEGGRWMKEMVEAWGKKTGTRVEYIDSPADTNDRLALYQQYWAARSPDVDVYMIDVIWP 101 VG + KE V+AW K+TG VE + +P +RL+ YQQ +A+S D+D+ ID++WP Sbjct: 1 VGAELQLCKEAVQAWSKQTGNNVEVVSTPNSATERLSFYQQILSAQSSDIDIIQIDMVWP 60 Query: 102 GIVAPHALDLKPYLTEAELKEFFPRIVQNNTIRGKLTSLPFFTDAGILYYRKDLLEKYGY 161 G++A H LDL+ L + +F V N T+ G+L ++P+FTD+G+LYYRKDLLEKY Sbjct: 61 GMLAKHLLDLREVLPANATQGYFQAQVDNATVNGRLVTMPWFTDSGLLYYRKDLLEKYNQ 120 Query: 162 TSPPRTWNELEQMAERVMEGERRAGNRDFWGFVFQGKPYEGLTCDALEWIYSHGGGRIVE 221 PRTW E+ A + + ER AGN + WG++FQG+ YEGLTC+ALEWI S G +V Sbjct: 121 -QVPRTWEEMTATARNIQQAERTAGNPNAWGYIFQGRAYEGLTCNALEWISSQPEGGLVN 179 Query: 222 PDGTISVNNGRAALALNRAHGWVGRIAPQGVTSYAEEEARNVWQQGNSLFMRNWPYAYAL 281 G I VN+ + AL A WVG I+P+GV +Y EEE R V+Q GN+LFMRNWPY +AL Sbjct: 180 SRGDIVVNSQASRTALTLAKSWVGDISPRGVLNYTEEEGRGVFQSGNALFMRNWPYVWAL 239 Query: 282 GQAEGSPIRGKFGVTVLPKASADAPNAATLGGWQLMVSAYSRYPKEAVDLVKYLASYEVQ 341 Q + S ++ K GV LP+ +A+TLGGW L VS YS +PK A +LV YL S + Q Sbjct: 240 VQGQDSAVKDKVGVAPLPRGGETGTHASTLGGWGLAVSRYSAHPKLAAELVSYLTSAQEQ 299 Query: 342 KDNAVRLSRLPTRPALYTDRDVLARNPWFRDLLPVFQNAVSRPSDVAGARYNQVSEAIWT 401 K A+ + P +LY D ++LA P++ L + + V RP+ + RY +VS A + Sbjct: 300 KHRALIGAYNPVIESLYQDPELLAAMPYYAQLHSILNDGVMRPASITADRYPRVSNAFFD 359 Query: 402 EVHSVLTGRKKGEQAVRDLEARIRRILR 429 VH VL G +QA+ +LE+ + RI R Sbjct: 360 RVHGVLAGELPVDQALAELESELTRIKR 387 Lambda K H 0.319 0.135 0.418 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: 461 Number of extensions: 22 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: 429 Length of database: 390 Length adjustment: 31 Effective length of query: 398 Effective length of database: 359 Effective search space: 142882 Effective search space used: 142882 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 (21.7 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