Align Maltose/Maltotriose PTS transporter, MalT (Shelburne et al., 2008) 631aas (68% identical to 4.A.1.1.11 from S. mutans (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= TCDB::Q48WG5 (631 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 206 bits (523), Expect = 3e-57 Identities = 152/452 (33%), Positives = 227/452 (50%), Gaps = 57/452 (12%) Query: 41 VLESPALNTGVFVGIIAGFVGATAYNKYYNYRKLPEVLTFFNGKRFVPFVVILRSIFVAL 100 ++ P++ TGVF GI+AG + A +N+YY LP L FF GKRFVP V + SI + Sbjct: 108 IMGIPSIQTGVFGGILAGGLAAWMFNRYYRIA-LPAYLGFFAGKRFVPIVTAIGSIVLGA 166 Query: 101 ILVVVWPVIQSGINSFGMWIASSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPMNYTAL 160 IL VVWP I S I +F W A S P A +YG +ERLL+PFGLHH+ +P + A Sbjct: 167 ILSVVWPPIGSAIKAFSQWAAVSD---PRTAATVYGFVERLLIPFGLHHIWNVPFFFEA- 222 Query: 161 GGTYEVMTGAAAGTKVFGQDPLWLAWVTDLVHLKGSDASAYSHLMDSVTPARFKVGQMIG 220 G + TG V G D+ D +A + F + +M G Sbjct: 223 GSFLDPTTGKV----VHG----------DITRFFAGDRTA------GILAGAF-LFKMFG 261 Query: 221 ATGTLMGVALAMYRNVDADKKHTYKMMFISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYA 280 L A+A++ + K M +SAA FLTG+TEP+E+ F+F A LY+++A Sbjct: 262 ----LPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFLFVAPVLYLIHA 317 Query: 281 LVQGASFAMADLVNLRV---HSFGNIELLTRTPMALKAGLGMDVINFVWVSVLFAVIMYF 337 + ++ +A+ + +R+ S G I+ L + K+ V F+ + ++AVI Y Sbjct: 318 CLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAWYV--FI-LGPIYAVIYYG 374 Query: 338 IADMMIKKMHLATAGRLGNYDADILGDRNTQTRPTQVADSNSQVVQIVNLLGGAGNIDDV 397 + +I + L T GR D +T A + ++V GG NID + Sbjct: 375 VFRFVITRFDLKTPGR---------EDDTVETAKVSTAGVGGRSRELVLAFGGRSNIDSL 425 Query: 398 DACMTRLRVTVKDPAKVGAEDDWKKAGAIGLIQKGNGVQAVYGPKADILKSDIQDLLDSG 457 DAC+TRLR++VK+PA V E K GA G+++ GNGVQA++GP ++ +K+D+ + L + Sbjct: 426 DACITRLRISVKNPALVN-EGKLKALGAAGVVRVGNGVQAIFGPLSENMKTDMHEYLKTA 484 Query: 458 ALIPEVNMSQLTSKPTPAKDFKHVTEDVLSVA 489 S+ A D K V E S A Sbjct: 485 G-----------SEADLAADGKAVAEAAASTA 505 Lambda K H 0.322 0.137 0.396 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: 803 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 631 Length of database: 596 Length adjustment: 37 Effective length of query: 594 Effective length of database: 559 Effective search space: 332046 Effective search space used: 332046 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