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_086510099.1 BZY95_RS11690 ABC transporter substrate-binding protein
Query= TCDB::Q72H68 (429 letters) >NCBI__GCF_002151265.1:WP_086510099.1 Length = 429 Score = 380 bits (976), Expect = e-110 Identities = 194/427 (45%), Positives = 267/427 (62%), Gaps = 6/427 (1%) Query: 3 RRTFLKKLGVGVAASLVLGPALVRAQSGPVIRVAGDSTAVGEGGRWMKEMVEAWGKKTGT 62 R T +++ G + L +AQ+ + GD G + E+ W ++TG Sbjct: 6 RTTLARQVLFGALVASGLTLVTTQAQAATITIACGD----GGSADFCPELARQWAQETGH 61 Query: 63 RVEYIDSPADTNDRLALYQQYWAARSPDVDVYMIDVIWPGIVAPHALDLKPYLTEAELKE 122 V + +P + L+LYQQ ++S D+DV M+D +WPG++A H +DL YL E + Sbjct: 62 EVAVVTTPQSGTETLSLYQQLLGSKSSDIDVLMVDTVWPGLLAAHLIDLADYLPEDASEG 121 Query: 123 FFPRIVQNNTIRGKLTSLPFFTDAGILYYRKDLLEKYGYTSPPRTWNELEQMAERVMEGE 182 FFP ++ NNT+ +L +LP+++DAG+LYYR+DLLEKY + P TW +L ++A + E Sbjct: 122 FFPAMIDNNTVDDRLLALPWYSDAGLLYYRRDLLEKYDH-DVPETWEQLTEIAREIQNAE 180 Query: 183 RRAGNRDFWGFVFQGKPYEGLTCDALEWIYSHGGGRIVEPDGTISVNNGRAALALNRAHG 242 R AGN GFVFQG+ YEGLT +ALEWI S+GGG IV+ DG I+VNN +AA AL A Sbjct: 181 REAGNERMHGFVFQGRAYEGLTTNALEWIASYGGGTIVDDDGNITVNNPQAAEALTLAAS 240 Query: 243 WVGRIAPQGVTSYAEEEARNVWQQGNSLFMRNWPYAYALGQAEGSPIRGKFGVTVLPKAS 302 WVG IAP+GV +Y EEEAR ++Q GN++FMRNWPYA+ALGQA+G+ I+GKFGV LP S Sbjct: 241 WVGDIAPRGVRNYMEEEARGLFQSGNAVFMRNWPYAWALGQADGTAIQGKFGVAPLPHGS 300 Query: 303 ADAPNAATLGGWQLMVSAYSRYPKEAVDLVKYLASYEVQKDNAVRLSRLPTRPALYTDRD 362 A + ATLGGW VS YS+ P A +LV YL + QK +A+R PTR LY D++ Sbjct: 301 A-GESVATLGGWSWAVSRYSKNPDLAAELVAYLTAEAQQKAHAIRFGMNPTRVTLYQDKE 359 Query: 363 VLARNPWFRDLLPVFQNAVSRPSDVAGARYNQVSEAIWTEVHSVLTGRKKGEQAVRDLEA 422 VL P+ +L + V RP++V G Y +VS A + VH VL+G EQA+ LE Sbjct: 360 VLEVQPFIGELYDTLVSGVPRPANVTGEHYTRVSNAFFNRVHDVLSGDLTAEQALGQLER 419 Query: 423 RIRRILR 429 + RI R Sbjct: 420 ELNRISR 426 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: 500 Number of extensions: 22 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: 429 Length adjustment: 32 Effective length of query: 397 Effective length of database: 397 Effective search space: 157609 Effective search space used: 157609 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