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 BWI76_RS01830 BWI76_RS01830 maltose ABC transporter substrate-binding protein MalE
Query= TCDB::Q9X0T1 (391 letters) >FitnessBrowser__Koxy:BWI76_RS01830 Length = 396 Score = 207 bits (526), Expect = 5e-58 Identities = 129/377 (34%), Positives = 205/377 (54%), Gaps = 9/377 (2%) Query: 13 SLVVLAQPKLTIWCS-EKQVDILQKLGEEFKAKYGVEVEVQYVNFQDIKSKFLTAAPEGQ 71 +L + + KL IW + +K + L ++G++F+ G++V V++ + ++ KF A G Sbjct: 24 ALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVSVEHPD--KLEEKFPQVAATGD 81 Query: 72 GADIIVGAHDWVGELAVNGLIEPI-PNFSDLKNFYETALNAFSYGGKLYGIPYAMEAIAL 130 G DII AHD G A +GL+ I P+ + Y +A Y GKL P A+EA++L Sbjct: 82 GPDIIFWAHDRFGGYAQSGLLAEISPDKAFQDKLYPFTWDAVRYNGKLIAYPVAVEALSL 141 Query: 131 IYNKDYVPEPPKTMDELIEIAKQIDEEFGGEVRGFITSAAEFYYIAPFIFGYGGYVFKQT 190 IYNKD VP PPKT +E+ + K++ + + + + E Y+ P I GGY FK Sbjct: 142 IYNKDLVPNPPKTWEEIPALDKELKAKGKSAL---MFNLQEPYFTWPLIAADGGYAFKFE 198 Query: 191 EKGLDVNDIGLANEGAIKGVKLLKRLVDEGILDPSDNYQIMDSMFREGQAAMIINGPWAI 250 DV ++G+ + GA G+ L L+ ++ +Y I ++ F +G+ AM INGPWA Sbjct: 199 NGKYDVKNVGVDSAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW 258 Query: 251 KAYKDAGIDYGVAPIPDLEPGVPARPFVGVQGFMVNAKSPNKLLAIEFLTSFIAKKETMY 310 + ++YGV +P + G ++PFVGV +NA SPNK LA EFL +++ + + Sbjct: 259 SNIDKSKVNYGVTLLPTFK-GNASKPFVGVLSAGINAASPNKELAKEFLENYLMTDQGLD 317 Query: 311 RIYLGDP-RLPSRKDVLELVKDNPDVVGFTLSAANGIPMPNVPQMAAVWAAMNDALNLVV 369 + P + K E ++ +P + +A G MPN+PQM+A W A+ A+ Sbjct: 318 EVNKDKPLGAVALKSFQEKLEKDPRIAATMANAQKGEIMPNIPQMSAFWYAVRTAVINAA 377 Query: 370 NGKATVEEALKNAVERI 386 +G+ TVE ALK+A RI Sbjct: 378 SGRQTVEAALKDAQSRI 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: 422 Number of extensions: 35 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 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