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 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 207 bits (528), Expect = 6e-58 Identities = 164/539 (30%), Positives = 272/539 (50%), Gaps = 78/539 (14%) Query: 6 FDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHT-IARVMEDIGWAIITNL 64 F F Q+ +ALL+ +A++PAAG+MI G++ I + +A +M +G + + + Sbjct: 24 FKFAQRLSQALLLPIAILPAAGVMI------GLATNPIPFISADLATLMWTVGNLVFSMM 77 Query: 65 HILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDL 124 +LFAV I + +D+ AF+A+ + G F SS+ A Sbjct: 78 PMLFAVTIAIGFCRDQGIAAFSAVFGY-------GVFF--------------SSLSALAK 116 Query: 125 IVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVI 184 I +LG ++ G+ G++ G L K+ +LP +FF G+R P +++ Sbjct: 117 IYHLPTEMILGQATIDTGIAGGMMVGAF-TCLVVKHSERIRLPAVFSFFEGRRSAPLLML 175 Query: 185 VWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLT 244 + + A + LLWP + + + + W + P A VYG +ERLL+P GLHH+ Sbjct: 176 PMAILLAYLFLLLWPLLSNWIEQISNWAVYQE---PASAFAVYGMVERLLIPLGLHHIWN 232 Query: 245 IPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPA 304 P Y E+G + + V G+ +LA GD +A N Sbjct: 233 APF-YLEMGQYFNG------DEWVRGEVARYLA-----------GDPQAGN--------- 265 Query: 305 RFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFI 364 AG + L A A++R DK +R + + LSAA A +LTGVTEPIEF FMF+ Sbjct: 266 --LAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAFMFV 323 Query: 365 APVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVF 424 AP+L++++A+ TG+A+A+ +++ H+ F + +++ G +R++ F+I+ + Sbjct: 324 APLLFILHALMTGIAYAVTISLDIH-HSVVFSHGLVDFSLLL--GQSRNVEWFLILGPLT 380 Query: 425 FGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIA 484 + + +F I FNL TPGR EA G Q L + +I LGG++NI Sbjct: 381 AVIYYLVFRGAILAFNLKTPGRM--------EAGSG----QRAGLIS-MITALGGQDNIN 427 Query: 485 DVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543 ++ AC+TRLR++VK ++V +AQ + GA G+++ GVQ VYG KA+ ++ +Q L Sbjct: 428 ELTACLTRLRISVKHAELV-DKAQLNKLGAKGVVLVGNGVQLVYGTKAESIRRLLQRYL 485 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: 626 Number of extensions: 31 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: 490 Length adjustment: 35 Effective length of query: 510 Effective length of database: 455 Effective search space: 232050 Effective search space used: 232050 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: 52 (24.6 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