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 BWI76_RS01825 BWI76_RS01825 maltose ABC transporter permease MalF
Query= TCDB::Q9X0T0 (577 letters) >FitnessBrowser__Koxy:BWI76_RS01825 Length = 514 Score = 282 bits (722), Expect = 2e-80 Identities = 152/336 (45%), Positives = 217/336 (64%), Gaps = 22/336 (6%) Query: 237 VLPDGKKLALRIAPDGEWRFMYVERLYRLAYKEIYDGVKMKITTTVVNNLTGREV-VERE 295 VLPD K+ + +F + LY LA DG T+ NN +G + E Sbjct: 189 VLPDESKVIMSSLR----QFSGTQPLYALAN----DG-------TLTNNQSGVKYRPNAE 233 Query: 296 GAFYDVDEN----GNETFLVGFIDFVGWKNFLRIVKDPKVSGPFFRIFLWTFVWAVLSVV 351 FY G+E G+ +GW NF R+ +D + PFF IF+WT V++VL+V+ Sbjct: 234 VGFYQAINADGSWGSEKLSPGYTVTIGWDNFTRVFQDEGIQKPFFAIFVWTVVFSVLTVI 293 Query: 352 LSLAVGLPFALVLNNPRLKGRNLYRTLLIIPWAIPVFISALVWRNGLLNESYGVINKFLL 411 L++AVG+ A ++ LKG+ +YR LLI+P+A+P FIS L+++ GL N+S+G IN L Sbjct: 294 LTVAVGMVLACLVQWEALKGKAIYRVLLILPYAVPSFISILIFK-GLFNQSFGEINMMLS 352 Query: 412 PLFGLEPIKWFNDPFWARVGVLLVNVWLTFPYMMTISLGALQSIPPELYEVAAIDGAGRF 471 LFG++P WF+DP AR +++VN WL +PYMM + +G L++IP +LYE +A+DGA F Sbjct: 353 ALFGIKPA-WFSDPTTARTMIIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPF 411 Query: 472 RRFVHITFPLLMTIIAPLLVSSFAFSFNNFTIIYLITGGGPPIPNSTTPTGYTDILISYV 531 + F IT PLL+ + PL+++SFAF+FNNF +I L+T GGP +TTP GYTD+L+SY Sbjct: 412 QNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVSYT 471 Query: 532 YKLAFEGGQGQDFGFASAISILIFFLVGGISFVNFK 567 Y++AFEGG GQDFG A+AI+ LIF LVG ++ VN K Sbjct: 472 YRIAFEGGGGQDFGLAAAIATLIFLLVGLLAIVNLK 507 Score = 46.6 bits (109), Expect = 2e-09 Identities = 25/99 (25%), Positives = 53/99 (53%), Gaps = 1/99 (1%) Query: 10 WFLLAILNIALFWAGVFLFQNEYYELSIVLFSLLVLIDFFIINPRGYPYRYTIPALILLF 69 W ++ +L + + + V ++ Y +I+ L + + N + Y +RY P L + Sbjct: 17 WSVIGLLCLLVGYLVVLMYAQGEYLFAIMTLILSSVGLYIFSNRKAYAWRYVYPGLAGMG 76 Query: 70 VLVLYPIYFTFKVAFTNYGTGHFMSRQEAIERLLYDPNF 108 + VL+P+ T +AFTNY + + ++ + A +++L D +F Sbjct: 77 LFVLFPLICTIAIAFTNYSSTNQLTFERA-QQVLMDRSF 114 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: 825 Number of extensions: 47 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: 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