Align MalE2; aka Maltose ABC transporter, periplasmic maltose-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate GFF849 Psest_0863 Maltose-binding periplasmic proteins/domains
Query= TCDB::Q9S5Y1 (393 letters) >FitnessBrowser__psRCH2:GFF849 Length = 395 Score = 261 bits (666), Expect = 3e-74 Identities = 148/374 (39%), Positives = 230/374 (61%), Gaps = 11/374 (2%) Query: 18 LSQTKLTIWCS-EKQVDILQKLGEEFKAKYGIPVEVQYVDFGSIKSKFLTAAPQGQGADI 76 + + KL +W + +K L ++G++F A+ GIPVEV + D S KF AA G G DI Sbjct: 27 IEEGKLVVWINGDKGYKGLAEVGKKFTAETGIPVEVAHPD--SATDKFQQAAATGNGPDI 84 Query: 77 IVGAHDWVGELAVNGLIEPIPNFSDLKN-FYDTALKAFSYGGKLYGVPYAMEAVALIYNK 135 + AHD +GE A +GL+ P+ +D K+ D + +A +Y KL+G P ++E + LIYNK Sbjct: 85 FIWAHDRIGEWAKSGLLTPVTPSADTKSGIADFSWQAVTYDNKLWGYPISVETIGLIYNK 144 Query: 136 DYVDSVPKTMDELIEKAKQIDEEYGGEVRGFIYDVANFYFSAPFILGYGGYVFKETPQGL 195 VD+ PKT D+++ +++ + R ++D N YF+ P + GGYVF+ G Sbjct: 145 ALVDTPPKTFDDVMALNEKLAAQ---GKRAILWDYNNTYFTWPLLSAKGGYVFEHADGGY 201 Query: 196 DVTDIGLANEGAVKGAKLIKRMIDEGVLTPGDNYGTMDSMFKEGLAAMIINGLWAIKSYK 255 DV G+ N GA GA++++ +ID+GV+ G +Y ++ F +G +AM+I+G WA + + Sbjct: 202 DVKSTGVNNAGAKAGAQVLRDLIDKGVMPKGADYSVAEAAFNKGDSAMMISGPWAWSNIE 261 Query: 256 DAGINYGVAPIPELEPGVPAKPFVGVQGFMINAKSPNKVIAMEFLTNFIARKETMYKIYL 315 +GI++GVAPIP ++ G P KPFVGV ++NA SPNK +A+EFL N++ + E + K Sbjct: 262 KSGIDFGVAPIPAID-GEPGKPFVGVAAALLNAASPNKDLAVEFLENYLLQVEGL-KTVN 319 Query: 316 ADPRLPARKDV--LELVKDNPDVVAFTQSASMGTPMPNVPEMAPVWSAMGDALSIIINGQ 373 AD L A + +E + NP + A ++A MG PMPNVPEM WS+M AL+ I +G+ Sbjct: 320 ADVPLGAVANTAYMEELSANPHIKATFENAQMGEPMPNVPEMGAFWSSMAAALTNITSGR 379 Query: 374 ASVEDALKEAVEKI 387 V+ AL +A ++I Sbjct: 380 QDVDAALDDAAKRI 393 Lambda K H 0.318 0.138 0.398 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: 424 Number of extensions: 17 Number of successful extensions: 6 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: 393 Length of database: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 (21.7 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