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 BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= TCDB::Q48WG5 (631 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 267 bits (683), Expect = 9e-76 Identities = 205/625 (32%), Positives = 308/625 (49%), Gaps = 65/625 (10%) Query: 11 GVSSTMLADPE--AKITSLLGTQMIVKDYFTSVLESPALNTGVFVGIIAGFVGATAYNKY 68 GV+S+ D A + +G ++ K T +PA+N GV GII G VG YN++ Sbjct: 59 GVASSWSKDSAGAAALAGAVGYFVLTKAMVTI---NPAINMGVLAGIITGLVGGAVYNRW 115 Query: 69 YNYRKLPEVLTFFNGKRFVPFVVILRSIFVALILVVVWPVIQSGINSFGMWIASSQDSAP 128 KLP+ L+FF GKRFVP + +A I VWP +Q+ I++ G WI A Sbjct: 116 SGI-KLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVG----AG 170 Query: 129 ILAPFLYGTLERLLLPFGLHHMLTIPMNYTALGGTYEVMTGAAAGTKVFGQDPLWLAWVT 188 L ++G + RLL+P GLH +L + + +G AAG G Sbjct: 171 ALGSGIFGFINRLLIPTGLHQVLNT-IAWFQIGEFTN-----AAGAVFHG---------- 214 Query: 189 DLVHLKGSDASAYSHLMDSVTPARFKVGQMIGATGTLMGVALAMYRNVDADKKHTYKMMF 248 D+ D +A M P M G L G ALAMY +++ M Sbjct: 215 DINRFYAGDGTA-GMFMSGFFPI-----MMFG----LPGAALAMYFAAPKERRPMVGGML 264 Query: 249 ISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYALVQGASFAMADLVNLRV---HSFGNIE- 304 +S A FLTGVTEPLE+LFMF A LY+++A++ G S +A + + S G I+ Sbjct: 265 LSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGISLFVATALGIHAGFSFSAGAIDY 324 Query: 305 -LLTRTPMALKAGLGMDVINFVWVSVLFAVIMYFIADMMIKKMHLATAGRLGNYDADILG 363 L+ P A K +V + + V+F VI + + +I+ +L T GR D + Sbjct: 325 VLMYSLPAASK-----NVWMLIVMGVVFFVIYFLLFSAVIRMFNLKTPGREDKVDDVVTE 379 Query: 364 DRNTQTRP--TQVADSNSQVVQIVNLLGGAGNIDDVDACMTRLRVTVKDPAKVGAEDDWK 421 + N+ T TQ+A + + +GG N+ +DAC+TRLR+TV D A V + K Sbjct: 380 EANSNTEEGLTQLATN------YIAAVGGTDNLKAIDACITRLRLTVADSALVN-DAACK 432 Query: 422 KAGAIGLIQKGNG-VQAVYGPKADILKSDIQDLLDSGALIPEVNMSQLTSKPTPAKDFKH 480 + GA G+++ +Q + G KA+ + +++ ++ G + S S P A+ K Sbjct: 433 RLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAASH--SAPVAAQAVKP 490 Query: 481 VTEDVLSVADGMVLPITG-------VKDQVFAAKMMGDGFAVEPTHGNIYAPVAGLVTSV 533 + +V PITG V D+ FA+K +GDG AV+PT + AP AG V + Sbjct: 491 QAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVVAPAAGTVVKI 550 Query: 534 FPTKHAFGLLTDNGLEVLVHVGLDTVALNGVPFSVKVSEGQRVHAGDLLVVADLAAIKSA 593 F T HAF L T+NG E++VH+G+DTVALNG F V EG V AG+ ++ DL + + Sbjct: 551 FNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPILELDLEFLNAN 610 Query: 594 ERETIIVVAFTNTTEIQDVTLTSLG 618 R I V +N+ + + + + G Sbjct: 611 ARSMISPVVCSNSDDYSALVIQATG 635 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: 894 Number of extensions: 42 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 631 Length of database: 650 Length adjustment: 38 Effective length of query: 593 Effective length of database: 612 Effective search space: 362916 Effective search space used: 362916 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: 54 (25.4 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