Align The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized)
to candidate 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)
Query= TCDB::Q8DS05 (729 letters) >FitnessBrowser__Keio:15223 Length = 477 Score = 251 bits (640), Expect = 8e-71 Identities = 174/550 (31%), Positives = 285/550 (51%), Gaps = 86/550 (15%) Query: 9 SFEFWQKFGKCLMVVIAVMPAAGLMVSIGNSLALIDPKSTLLVTVANIIAQIGWGVINNL 68 +F QK GK LM+ ++V+P AG+++ +G++ S L V++++A+ G V N+ Sbjct: 5 AFANLQKVGKSLMLPVSVLPIAGILLGVGSANF-----SWLPAVVSHVMAEAGGSVFANM 59 Query: 69 HILFAVAIGGSWAKERAGGAFAAALAFILINLITGNFYGISLEMIADKTSYVHNIFGGKM 128 ++FA+ + + A AA +A YGI ++ +A V ++ ++ Sbjct: 60 PLIFAIGVALGFTNNDGVSALAAVVA-----------YGIMVKTMAVVAPLVLHLPAEEI 108 Query: 129 ---HVADYFINVLGQPALNMGVFVGIISGFVGATAYNKYYNFRKLPDVLSFFNGKRFVPF 185 H+AD GV GIISG + A +N++Y KLP+ L FF GKRFVP Sbjct: 109 ASKHLAD------------TGVLGGIISGAIAAYMFNRFYRI-KLPEYLGFFAGKRFVPI 155 Query: 186 VVIVRSTIVALILSVFWPIVQSGINGFGMWIASSQHTAPFLAPFLYGTLERLLLPFGLHH 245 + + + ++LS WP + S I F W A + P +A +YG +ER L+PFGLHH Sbjct: 156 ISGLAAIFTGVVLSFIWPPIGSAIQTFSQWAA---YQNPVVAFGIYGFIERCLVPFGLHH 212 Query: 246 MLTIPMNYTQLGGTYVVLTGAQAGKHVLGQDPLWLAWVQDLIHLKGAGHMSQYHHLLTSV 305 + +P Q+G T A AG+ G P ++A L G Y Sbjct: 213 IWNVPFQM-QIGE----YTNA-AGQVFHGDIPRYMAGDPTAGKLSGGFLFKMYG------ 260 Query: 306 TPARFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGMFLSAAVAVFLTGVTEPLEYMF 365 L +A++ + P+ + K G+ +SAA+ FLTG+TEP+E+ F Sbjct: 261 ----------------LPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSF 304 Query: 366 MFAALPLYLVYAVVQGLAFASADLIHLR---VHSFGNIEFLTRTPMAIKAGLAMDIVNFI 422 MF A LY+++A++ GLAF L+ +R S G I+F+ + +G + + F Sbjct: 305 MFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFI------VLSGNSSKLWLFP 358 Query: 423 VVSVVFGVAMYFITNFMIKKFNLATSGRNGNYDTGDDASDETASNSNAGTANANSQIVKI 482 +V + + + Y I +IK +L T GR +DA+++ + + A A + Sbjct: 359 IVGIGYAIVYYTIFRVLIKALDLKTPGR-------EDATEDAKATGTSEMAPA------L 405 Query: 483 INLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAMGLIVKGNGVQAVYGPKAD 542 + GGKENI+++DAC+TRLR++V DV+KV D+A KK GA G++V G+GVQA++G K+D Sbjct: 406 VAAFGGKENITNLDACITRLRVSVADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSD 464 Query: 543 VLKSDIQDLL 552 LK+++ + + Sbjct: 465 NLKTEMDEYI 474 Lambda K H 0.322 0.138 0.402 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: 809 Number of extensions: 42 Number of successful extensions: 7 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: 729 Length of database: 477 Length adjustment: 37 Effective length of query: 692 Effective length of database: 440 Effective search space: 304480 Effective search space used: 304480 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 (21.9 bits) S2: 53 (25.0 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