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) >lcl|FitnessBrowser__Keio:18062 b4034 maltose ABC transporter periplasmic protein (NCBI) 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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