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 PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= TCDB::Q48WG5 (631 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 178 bits (452), Expect = 5e-49 Identities = 130/415 (31%), Positives = 198/415 (47%), Gaps = 59/415 (14%) Query: 45 PALNTGVFVGIIAGFVGATAYNKYYNYRKLPEVLTFFNGKRFVPFVVILRSIFVALILVV 104 P++N G+ GI++G + YN++ + KLPE L FF G+RFVP V ++ + ++ Sbjct: 94 PSINMGMLAGIVSGLMAGALYNRFKDI-KLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGY 152 Query: 105 VWPVIQSGINSFGMWIASSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPMNYTALGGTY 164 +WP IQ GINSFG + S F++G RLL+ GLHH+L M + G Sbjct: 153 IWPPIQHGINSFGTLMMESGS----FGAFVFGLFNRLLIVTGLHHILN-NMAWFVFGNFT 207 Query: 165 EVMTGAAAG---TKVFGQDPLWLAWVTDLVHLKGSDASAYSHLMDSVTPARFKVGQMIGA 221 + TGA ++ F DP KG +F G Sbjct: 208 DPTTGALVTGDLSRYFAGDP------------KGG---------------QFMTGMFPMM 240 Query: 222 TGTLMGVALAMYRNVDADKKHTYKMMFISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYAL 281 L LAMYRN ++ +F+S A FLTGVTEP+E+ FMF A L++++AL Sbjct: 241 IFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHAL 300 Query: 282 VQGASFAMADLVNLRV---HSFGNIELLTRTPMALKAGLGMDVINFVWVSVLFAVIMYFI 338 + G S A+ + +N+ + S G I+++ + L V + +AVI Y + Sbjct: 301 LTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFP------VGLAYAVIYYVV 354 Query: 339 ADMMIKKMHLATAGRLGNYDADILGDRNTQTRPTQVADSNSQVVQIVNLLGGAGNIDDVD 398 D I++ L T GR + + VAD N + + LGGA N+ V Sbjct: 355 FDFCIRRFDLKTPGR----------ETSADVEQVAVAD-NERAGAYIKALGGAENLITVG 403 Query: 399 ACMTRLRVTVKDPAKVGAEDDWKKAGAIGLIQ--KGNGVQAVYGPKADILKSDIQ 451 AC TRLR+ + D K ++ D K GA+ +++ KG +Q V GP AD + +I+ Sbjct: 404 ACTTRLRLDMVDRNK-ASDTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEIR 457 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: 836 Number of extensions: 46 Number of successful extensions: 5 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: 631 Length of database: 571 Length adjustment: 37 Effective length of query: 594 Effective length of database: 534 Effective search space: 317196 Effective search space used: 317196 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