Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 228 bits (581), Expect = 5e-64 Identities = 172/536 (32%), Positives = 258/536 (48%), Gaps = 93/536 (17%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69 Q+ G+AL++ +A++P AGL++ +G D + ++ VM D G AI NL ++FA Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLG--------DTDLLNIA--VMHDAGQAIFANLALIFA 59 Query: 70 VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDY 129 + I +A+D G T + G ++ S KV Sbjct: 60 IGIAVGFARDNNG---------------TAGLAGAIGYLVMVSTLKVMDT---------- 94 Query: 130 FTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWSTV 189 ++NMG+ GI +G + LYN++ + KLP+ LAFF G+RFVP V + Sbjct: 95 --------SINMGMLAGIASGLMAGGLYNRFKDI-KLPEYLAFFGGRRFVPIVTGFSAVG 145 Query: 190 TAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNY 249 ++ L+WP IQ G+N FG + S + FV+G RLL+ GLHH+L M + Sbjct: 146 LGVIFGLIWPPIQHGINSFGVLLMESGS----LGAFVFGVFNRLLIVTGLHHILN-NMAW 200 Query: 250 TELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAG 309 G +TG+ VV G DL A GD K +F G Sbjct: 201 FVFGSFTDPVTGA----VVTG----------DLTRYFA-GDPKG----------GQFMTG 235 Query: 310 QVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLY 369 L AM+RN E+R +FLS AL FLTGVTEPIEF FMF+AP LY Sbjct: 236 MFPVMLFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLY 295 Query: 370 VVYAITTGLAFALADLINLRV---HAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFG 426 +++A+ TGL+ A+ +++N+ + + GFI+++ N L V L + Sbjct: 296 LIHAVLTGLSMAVTNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLV------FPVGLAYAL 349 Query: 427 LNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADV 486 + +++FN+ I+ FNL TPGR ED + D AT I LGG +N+ V Sbjct: 350 IYYSVFNYCIRHFNLKTPGR-------EDTQVVQAEAMSDNQRATAYIQALGGAQNLLSV 402 Query: 487 DACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKG--VQAVYGPKADVLKSDIQ 540 AC TRLR+ + D + A +A+ K GA+ ++ G +Q V GP AD + +I+ Sbjct: 403 GACTTRLRLDMVDRN-KAVDAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEIR 457 Lambda K H 0.325 0.140 0.416 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: 791 Number of extensions: 52 Number of successful extensions: 6 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: 545 Length of database: 568 Length adjustment: 36 Effective length of query: 509 Effective length of database: 532 Effective search space: 270788 Effective search space used: 270788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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