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 18062 b4034 maltose ABC transporter periplasmic protein (NCBI)
Query= TCDB::Q9S5Y1 (393 letters) >FitnessBrowser__Keio:18062 Length = 396 Score = 204 bits (518), Expect = 5e-57 Identities = 133/387 (34%), Positives = 206/387 (53%), Gaps = 12/387 (3%) Query: 6 LVLMLVVVSALV-LSQTKLTIWCS-EKQVDILQKLGEEFKAKYGIPVEVQYVDFGSIKSK 63 L M+ SAL + + KL IW + +K + L ++G++F+ GI V V++ D ++ K Sbjct: 15 LTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPD--KLEEK 72 Query: 64 FLTAAPQGQGADIIVGAHDWVGELAVNGLIEPI-PNFSDLKNFYDTALKAFSYGGKLYGV 122 F A G G DII AHD G A +GL+ I P+ + Y A Y GKL Sbjct: 73 FPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAY 132 Query: 123 PYAMEAVALIYNKDYVDSVPKTMDELIEKAKQIDEEYGGEVRG-FIYDVANFYFSAPFIL 181 P A+EA++LIYNKD + + PKT +E+ +D+E + + ++++ YF+ P I Sbjct: 133 PIAVEALSLIYNKDLLPNPPKTWEEI----PALDKELKAKGKSALMFNLQEPYFTWPLIA 188 Query: 182 GYGGYVFKETPQGLDVTDIGLANEGAVKGAKLIKRMIDEGVLTPGDNYGTMDSMFKEGLA 241 GGY FK D+ D+G+ N GA G + +I + +Y ++ F +G Sbjct: 189 ADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGET 248 Query: 242 AMIINGLWAIKSYKDAGINYGVAPIPELEPGVPAKPFVGVQGFMINAKSPNKVIAMEFLT 301 AM ING WA + + +NYGV +P + G P+KPFVGV INA SPNK +A EFL Sbjct: 249 AMTINGPWAWSNIDTSKVNYGVTVLPTFK-GQPSKPFVGVLSAGINAASPNKELAKEFLE 307 Query: 302 NFIARKETMYKIYLADP-RLPARKDVLELVKDNPDVVAFTQSASMGTPMPNVPEMAPVWS 360 N++ E + + P A K E + +P + A ++A G MPN+P+M+ W Sbjct: 308 NYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWY 367 Query: 361 AMGDALSIIINGQASVEDALKEAVEKI 387 A+ A+ +G+ +V++ALK+A +I Sbjct: 368 AVRTAVINAASGRQTVDEALKDAQTRI 394 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: 410 Number of extensions: 25 Number of successful extensions: 5 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: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 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