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 WP_086510093.1 BZY95_RS11660 ABC transporter substrate-binding protein
Query= TCDB::Q72H68 (429 letters) >NCBI__GCF_002151265.1:WP_086510093.1 Length = 421 Score = 399 bits (1025), Expect = e-116 Identities = 210/429 (48%), Positives = 278/429 (64%), Gaps = 11/429 (2%) Query: 1 MQRRTFLKKLGVGVAASLVLGPALVRAQSGPVIRVAGDSTAVGEGGRWMKEMVEAWGKKT 60 M ++T L L V A S AQ+ + G AVG + ++ V AW +KT Sbjct: 1 MYKKTLLSTLVVAGATSFS------HAQAADLTISCG---AVGAELQLCQQGVRAWEEKT 51 Query: 61 GTRVEYIDSPADTNDRLALYQQYWAARSPDVDVYMIDVIWPGIVAPHALDLKPYLTEAEL 120 G V+ + +P + +RL+LYQQ +A S D+D+ IDV+WPG++A H LDL+ L + Sbjct: 52 GYSVDVVSTPNSSTERLSLYQQILSANSTDIDIMQIDVVWPGLLANHLLDLREVLGDDAG 111 Query: 121 KEFFPRIVQNNTIRGKLTSLPFFTDAGILYYRKDLLEKYGYTSPPRTWNELEQMAERVME 180 + F IV+NNTI +L ++P+FTDAG+LYYR DLLE+YG+ PP TW EL ++A + Sbjct: 112 EGHFSAIVENNTIDDRLVAMPWFTDAGVLYYRADLLEQYGF-EPPETWEELTEVAREIQN 170 Query: 181 GERRAGNRDFWGFVFQGKPYEGLTCDALEWIYSHGGGRIVEPDGTISVNNGRAALALNRA 240 ER AGN GFVFQG+ YEGLTC+ALEW+ SHGGG IV+ DG I++NN +AA AL+ A Sbjct: 171 AEREAGNSRMHGFVFQGRAYEGLTCNALEWVASHGGGTIVDQDGEITINNPQAAAALDLA 230 Query: 241 HGWVGRIAPQGVTSYAEEEARNVWQQGNSLFMRNWPYAYALGQAEGSPIRGKFGVTVLPK 300 W+G I+P GV +Y EEEAR V+Q GN++FMRNWPYA+AL Q+EGS +RGK GVT LP Sbjct: 231 ASWIGDISPNGVLNYTEEEARGVFQGGNAVFMRNWPYAWALAQSEGSEVRGKVGVTQLP- 289 Query: 301 ASADAPNAATLGGWQLMVSAYSRYPKEAVDLVKYLASYEVQKDNAVRLSRLPTRPALYTD 360 S D AATLGGW L VS YS P+ A DLV +LA E QK A+ + PT ALY D Sbjct: 290 YSGDGSTAATLGGWNLAVSRYSENPELAADLVAFLAGEEEQKRRAIEGAYNPTLEALYQD 349 Query: 361 RDVLARNPWFRDLLPVFQNAVSRPSDVAGARYNQVSEAIWTEVHSVLTGRKKGEQAVRDL 420 +VL P+F +L F NAV+RPS G Y +VS A ++ H VL+G + GEQA+ DL Sbjct: 350 DEVLEAVPFFGELYETFVNAVARPSAPTGDAYGRVSNAFFSATHDVLSGNRSGEQAMSDL 409 Query: 421 EARIRRILR 429 + + R+ R Sbjct: 410 DHELARLKR 418 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: 514 Number of extensions: 26 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: 429 Length of database: 421 Length adjustment: 32 Effective length of query: 397 Effective length of database: 389 Effective search space: 154433 Effective search space used: 154433 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: 51 (24.3 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