Align MalF1; aka Maltose ABC transporter, permease 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_086508158.1 BZY95_RS01100 maltose ABC transporter permease MalF
Query= TCDB::Q9X0T0 (577 letters) >NCBI__GCF_002151265.1:WP_086508158.1 Length = 537 Score = 272 bits (696), Expect = 2e-77 Identities = 180/558 (32%), Positives = 291/558 (52%), Gaps = 54/558 (9%) Query: 12 LLAILNIALFWAGVFLFQNEYYELSIVLFSLLVLIDFFIINPRGYPYRYTIPALILLFVL 71 L+A L +AL W + N +++ L + +RY PA+ + + Sbjct: 30 LVAALVLALLWLVLAFHLNGQPIFALLFLVLGAALGVVFTRRTLMSHRYIFPAVASMALF 89 Query: 72 VLYPIYFTFKVAFTNYGTGHFMSRQEAIERLLYDPNFSYVVDSTPVSYKVFVVYDGLSPT 131 V++P+ +T ++F+NY + + +S + +LL + +Y +ST ++++ +G+ Sbjct: 90 VIFPLLYTVGISFSNYSSSNLLSEERVRAQLL---SRTYQEESTTFGFQLYSSDEGVR-- 144 Query: 132 DDFLILFKTGDTIFLGERPKPVVARGQEVLLSQFNLVPITGETISLNGDTFRIVPWPADL 191 ++L P E L + +L G + R V P L Sbjct: 145 ------------LYLEREGAPPTTGEAEAELEE-----------ALEGVS-RFVTGPLSL 180 Query: 192 SEINLVVRGEKTYKSFYSPDDEILRLNAPYFKSRIAQGYLVNAEYVLPDGKKLALRIAPD 251 + GE+ + + E + P + + L N P+G L LR+A Sbjct: 181 QD------GERRHVAIQPAAGEPVGEPLPMREVVAYRTALQNLVLATPEG--LELRMAGL 232 Query: 252 GEWRFMYVERLYRLAYKEIYDGVKMKITTTVVNNLTGREVVEREGAFYDVDENGNETFLV 311 + M ++R A +YD + T + E F+ +E E Sbjct: 233 RHYAPM-LDRYEVRADGSLYDRRDDLLLTA-----------DGETGFFVTEEG--ERITP 278 Query: 312 GFIDFVGWKNFLRIVKDPKVSGPFFRIFLWTFVWAVLSVVLSLAVGLPFALVLNNPRLKG 371 G+ VG N+ RI DP + GPF +IF+WTF +A L+V+ +L VG A +L +L+G Sbjct: 279 GWPVAVGLDNYARIFLDPDIRGPFIQIFVWTFAFAGLTVLFTLIVGFVLASLLQWDQLRG 338 Query: 372 RNLYRTLLIIPWAIPVFISALVWRNGLLNESYGVINKFLLPLFGLEPIKWFNDPFWARVG 431 + LYRTLLI+P+A+P FIS L+++ G+ N+ +G IN L LFG+ P WF DP+ AR Sbjct: 339 KALYRTLLILPYAVPAFISILIFK-GMFNQHFGEINLILDALFGVRP-DWFTDPWLARSM 396 Query: 432 VLLVNVWLTFPYMMTISLGALQSIPPELYEVAAIDGAGRFRRFVHITFPLLMTIIAPLLV 491 +L+VN WL +PYM+ + +G +QSIP +LYE +A+DG G IT PL++ + PLL+ Sbjct: 397 LLIVNTWLGYPYMLLLCMGLIQSIPRDLYEASAVDGGGPLTNLFQITLPLIIKPLTPLLI 456 Query: 492 SSFAFSFNNFTIIYLITGGGPPIPNSTTPTGYTDILISYVYKLAFEGGQGQDFGFASAIS 551 + FAF+FNNF +I L+TGG P I ++TP G TD+L+SY Y++AF+ GQ+FG A+AI+ Sbjct: 457 ACFAFNFNNFVLIALLTGGNPDILGASTPAGTTDLLVSYTYRIAFQDA-GQNFGLAAAIA 515 Query: 552 ILIFFLVGGISFVNFKLS 569 LIF LV G++ +N +L+ Sbjct: 516 TLIFLLVAGLALLNLRLA 533 Lambda K H 0.328 0.146 0.454 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: 897 Number of extensions: 54 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 577 Length of database: 537 Length adjustment: 36 Effective length of query: 541 Effective length of database: 501 Effective search space: 271041 Effective search space used: 271041 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 53 (25.0 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