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 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= TCDB::Q48WG5 (631 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 153 bits (386), Expect = 2e-41 Identities = 126/419 (30%), Positives = 199/419 (47%), Gaps = 56/419 (13%) Query: 41 VLESPALNTGVFVGIIAGFVGATAYNKYYNYRKLPEVLTFFNGKRFVPFVVILRSIFVAL 100 VL L+TG+ G++ G V A ++ Y +LP + +FF G+R ++I ++ + Sbjct: 126 VLGMETLDTGIAGGMLIGGVTCFAV-RWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGY 184 Query: 101 ILVVVWPVIQSGINSFGMWIASSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPMNYTAL 160 +L +WP + I W + P +A +YG LERLL+P GLHH+ P Sbjct: 185 VLAHIWPSLSLLIERVSDWAVYQK---PAIAFGVYGALERLLIPLGLHHIWNAPFYLEV- 240 Query: 161 GGTYEVMTGAAAGTKVFGQDPLWLAWVTDLVHLKGSDASAYSHLMDSVTPARFKVGQMIG 220 G Y++ V G+ +LA +L G G +I Sbjct: 241 -GQYQLQDAEV----VRGEVARYLAGDPQAGNLAG--------------------GYLIK 275 Query: 221 ATGTLMGVALAMYRNVDADKKHTYKMMFISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYA 280 G L ALA++R D +++ + +SAAAA +LTGVTEP+E+ FMF A L++++ Sbjct: 276 MWG-LPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPLLFLIHV 334 Query: 281 LVQGASF---AMADLVNLRVHSFGNIELLTRTPMALKAGLGMDVINFVWVSVLFAVIMYF 337 ++ G ++ M D+ + V S G ++ ++ G F + L AVI Y Sbjct: 335 MLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGW------FAVLGPLTAVIYYI 388 Query: 338 IADMMIKKMHLATAGRLGNYDADILGDRNTQTRPTQVADSNSQVVQIVNLLGGAGNIDDV 397 + I +L T GRL Q+ T+ S + I+ LGG NI ++ Sbjct: 389 LFRGSILAFNLKTPGRL-------------QSDGTK--GSKESLRAIIAALGGRDNIVEL 433 Query: 398 DACMTRLRVTVKDPAKVGAEDDWKKAGAIGLIQKGNGVQAVYGPKADILKSDIQDLLDS 456 +AC+TRLR++V P V + + GA G+I G GVQ VYG KA+ L+ +Q LD+ Sbjct: 434 NACLTRLRLSVHSPELVN-KVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYLDT 491 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: 638 Number of extensions: 29 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: 499 Length adjustment: 36 Effective length of query: 595 Effective length of database: 463 Effective search space: 275485 Effective search space used: 275485 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