Align MalE1; 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 WP_061059304.1 M988_RS19105 maltose/maltodextrin ABC transporter substrate-binding protein MalE
Query= TCDB::Q9X0T1 (391 letters) >NCBI__GCF_001655005.1:WP_061059304.1 Length = 396 Score = 217 bits (553), Expect = 4e-61 Identities = 136/386 (35%), Positives = 214/386 (55%), Gaps = 12/386 (3%) Query: 7 IALLVVSLVVLA---QPKLTIWCS-EKQVDILQKLGEEFKAKYGVEVEVQYVNFQDIKSK 62 +A LV+S A + KL IW + +K + L ++G++F+ + G++V V++ + ++ K Sbjct: 15 LATLVLSSSAFAKIEEGKLVIWINGDKGYNGLAEIGKKFEKETGIKVLVEHPD--KLEEK 72 Query: 63 FLTAAPEGQGADIIVGAHDWVGELAVNGLIEPI-PNFSDLKNFYETALNAFSYGGKLYGI 121 + A G G DII AHD G A +GL+ I P+ + Y +A Y GKL Sbjct: 73 YPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEIHPSKAFQDKLYPFTWDAVRYNGKLIAY 132 Query: 122 PYAMEAIALIYNKDYVPEPPKTMDELIEIAKQIDEEFGGEVRGFITSAAEFYYIAPFIFG 181 P A+EA++LIYNKD +PEPPKT +E+ + K++ + + + + E Y+ P I Sbjct: 133 PVAVEALSLIYNKDILPEPPKTWEEIPALDKELRAKGKSAI---MWNLQEPYFTWPIIAA 189 Query: 182 YGGYVFKQTEKGLDVNDIGLANEGAIKGVKLLKRLVDEGILDPSDNYQIMDSMFREGQAA 241 GGY FK ++ D+G+ N G+ G++ + LV ++ +Y I ++ F +GQ A Sbjct: 190 DGGYAFKYDNGTYNIKDVGVNNAGSQAGLQFIVDLVKNKHINADTDYSIAEAAFNKGQTA 249 Query: 242 MIINGPWAIKAYKDAGIDYGVAPIPDLEPGVPARPFVGVQGFMVNAKSPNKLLAIEFLTS 301 M INGPWA + I+YGVA +P + G P++PFVGV +NA SPNK LA EFL + Sbjct: 250 MTINGPWAWSNIDKSNINYGVALLPTFK-GHPSKPFVGVLSAGINAASPNKELATEFLEN 308 Query: 302 FIAKKETMYRIYLGDP-RLPSRKDVLELVKDNPDVVGFTLSAANGIPMPNVPQMAAVWAA 360 ++ + +I P + K E ++ +P + +A G MPN+PQM+A W A Sbjct: 309 YLMTNAGLEQINKDKPLGAVALKSYQETLEKDPKIAATMQNAQKGEIMPNIPQMSAFWYA 368 Query: 361 MNDALNLVVNGKATVEEALKNAVERI 386 A+ VNG+ +V+EAL A +RI Sbjct: 369 ERSAIINAVNGRQSVKEALTGAEQRI 394 Lambda K H 0.319 0.139 0.404 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: 415 Number of extensions: 30 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: 391 Length of database: 396 Length adjustment: 31 Effective length of query: 360 Effective length of database: 365 Effective search space: 131400 Effective search space used: 131400 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: 50 (23.9 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