Align The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= TCDB::Q8DS05 (729 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 251 bits (642), Expect = 4e-71 Identities = 172/549 (31%), Positives = 286/549 (52%), Gaps = 80/549 (14%) 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 A+ +A+ ++ + L + A++ + Sbjct: 60 PLIFAIGVALGFTNNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIA--------AK 111 Query: 129 HVADYFINVLGQPALNMGVFVGIISGFVGATAYNKYYNFRKLPDVLSFFNGKRFVPFVVI 188 H+AD GV GIISG + A +N++Y KLP+ L FF GKRFVP + Sbjct: 112 HLAD------------TGVLGGIISGAIAAYMFNRFYRI-KLPEYLGFFAGKRFVPIISG 158 Query: 189 VRSTIVALILSVFWPIVQSGINGFGMWIASSQHTAPFLAPFLYGTLERLLLPFGLHHMLT 248 + + +ILS WP + + I F W A + P +A +YG +ER L+PFGLHH+ Sbjct: 159 LAAIFTGVILSFIWPPIGTAIQTFSQWAA---YQNPVVAFGIYGFIERCLVPFGLHHIWN 215 Query: 249 IPMNYTQLGGTYVVLTGAQAGKHVLGQDPLWLAWVQDLIHLKGAGHMSQYHHLLTSVTPA 308 +P Q+G T A AG+ G P ++A L G Y Sbjct: 216 VPFQM-QIGE----YTNA-AGQVFHGDIPRYMAGDPTAGKLSGGFLFKMYG--------- 260 Query: 309 RFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGMFLSAAVAVFLTGVTEPLEYMFMFA 368 L +A++ + P+ + K G+ +SAA+ FLTG+TEP+E+ FMF Sbjct: 261 -------------LPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFV 307 Query: 369 ALPLYLVYAVVQGLAFASADLIHLR---VHSFGNIEFLTRTPMAIKAGLAMDIVNFIVVS 425 A LY+++A++ GLAF L+ +R S G I+F+ + +G + + F +V Sbjct: 308 APILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFI------VLSGNSSKLWLFPIVG 361 Query: 426 VVFGVAMYFITNFMIKKFNLATSGRNGNYDTGDDASDETASNSNAGTANANSQIVKIINL 485 + + + Y + +IK +L T GR +DA++++ + + + A A +I Sbjct: 362 ICYAIVYYVVFRVLIKALDLKTPGR-------EDATEDSKAGATSEMAPA------LIAA 408 Query: 486 LGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAMGLIVKGNGVQAVYGPKADVLK 545 GGKENI+++DAC+TRLR++V DVAKV D+A KK GA G++V G+GVQA++G K+D LK Sbjct: 409 FGGKENITNLDACITRLRVSVADVAKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLK 467 Query: 546 SDIQDLLDS 554 +++ + + S Sbjct: 468 TEMDEYIRS 476 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: 818 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