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 18061 b4033 maltose transporter subunit (NCBI)
Query= TCDB::Q9X0T0 (577 letters) >FitnessBrowser__Keio:18061 Length = 514 Score = 295 bits (754), Expect = 4e-84 Identities = 189/565 (33%), Positives = 295/565 (52%), Gaps = 81/565 (14%) Query: 10 WFLLAILNIALFWAGVFLFQNEYYELSIVLFSLLVLIDFFIINPRGYPYRYTIPALILLF 69 W +L +L + + + V ++ Y +I L + N + Y +RY P + + Sbjct: 17 WSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANRKAYAWRYVYPGMAGMG 76 Query: 70 VLVLYPIYFTFKVAFTNYGTGHFMSRQEAIERLLYDPNFSYVVDSTPVSYKVFVVYD-GL 128 + VL+P+ T +AFTNY + + ++ + A + +L D S++ Y+ GL Sbjct: 77 LFVLFPLVCTIAIAFTNYSSTNQLTFERA-QEVLLDR-----------SWQAGKTYNFGL 124 Query: 129 SPT-DDFLILFKTGDTIFLGERPKPVVARGQEVLLSQFNLVPITGETISLNGDTFRIVPW 187 P D++ + G+T G+ L F GE Sbjct: 125 YPAGDEWQLALSDGET-------------GKNYLSDAFKF---GGEQ------------- 155 Query: 188 PADLSEINLVVRGEKTYKSFYSPDDEILRLNAPYFKSRIAQGYLVNAEYVLPDGKKLALR 247 L E GE+ + + + L + +LPDG K+ + Sbjct: 156 KLQLKETTAQPEGERANLRVITQNRQALS----------------DITAILPDGNKVMMS 199 Query: 248 IAPDGEWRFMYVERLYRLAYKEIYDGVKMKITTTVVNNLTGREVVERE--GAFYDVDENG 305 +F + LY L DG T+ NN +G + G + + +G Sbjct: 200 SLR----QFSGTQPLYTL------DG-----DGTLTNNQSGVKYRPNNQIGFYQSITADG 244 Query: 306 N---ETFLVGFIDFVGWKNFLRIVKDPKVSGPFFRIFLWTFVWAVLSVVLSLAVGLPFAL 362 N E G+ GWKNF R+ D + PF IF+WT V+++++V L++AVG+ A Sbjct: 245 NWGDEKLSPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLAC 304 Query: 363 VLNNPRLKGRNLYRTLLIIPWAIPVFISALVWRNGLLNESYGVINKFLLPLFGLEPIKWF 422 ++ L+G+ +YR LLI+P+A+P FIS L+++ GL N+S+G IN L LFG++P WF Sbjct: 305 LVQWEALRGKAVYRVLLILPYAVPSFISILIFK-GLFNQSFGEINMMLSALFGVKPA-WF 362 Query: 423 NDPFWARVGVLLVNVWLTFPYMMTISLGALQSIPPELYEVAAIDGAGRFRRFVHITFPLL 482 +DP AR +++VN WL +PYMM + +G L++IP +LYE +A+DGAG F+ F IT PLL Sbjct: 363 SDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLL 422 Query: 483 MTIIAPLLVSSFAFSFNNFTIIYLITGGGPPIPNSTTPTGYTDILISYVYKLAFEGGQGQ 542 + + PL+++SFAF+FNNF +I L+T GGP +TTP GYTD+L++Y Y++AFEGG GQ Sbjct: 423 IKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQ 482 Query: 543 DFGFASAISILIFFLVGGISFVNFK 567 DFG A+AI+ LIF LVG ++ VN K Sbjct: 483 DFGLAAAIATLIFLLVGALAIVNLK 507 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: 845 Number of extensions: 50 Number of successful extensions: 5 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: 514 Length adjustment: 35 Effective length of query: 542 Effective length of database: 479 Effective search space: 259618 Effective search space used: 259618 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: 52 (24.6 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