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 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 207 bits (526), Expect = 1e-57 Identities = 167/540 (30%), Positives = 270/540 (50%), Gaps = 77/540 (14%) Query: 6 FDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARV-MEDIGWAIITNL 64 F F Q+ +ALL+ +A++PAAG+M+ G++ I + + V M +G I + Sbjct: 25 FKFAQRLSQALLIPIAILPAAGVML------GLTVSPIPFMPEVLNVLMLAVGKLIFAIM 78 Query: 65 HILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDL 124 ILFAVA+ + +D+ AF A+ + + A LAD + + Sbjct: 79 PILFAVAVAIGFCRDQGIAAFTAVFGYGVMTATLAA--------LADLYQLPTQL----- 125 Query: 125 IVKDYFTSVLGAPALNMGVFVGIITGFLGATLYN-KYYNYNKLPQALAFFNGKRFVPFVV 183 VLG L+ G+ G++ G G T + ++ Y +LP +FF G+R ++ Sbjct: 126 --------VLGMETLDTGIAGGMLIG--GVTCFAVRWSQYIRLPAIFSFFEGRRSASLLI 175 Query: 184 IVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHML 243 I + VL+ +WP + + W K P +A VYG LERLL+P GLHH+ Sbjct: 176 IPLAMGLGYVLAHIWPSLSLLIERVSDWAVYQK---PAIAFGVYGALERLLIPLGLHHIW 232 Query: 244 TIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVP 303 P Y E+G Y + + +VV G+ +LA GD +A N Sbjct: 233 NAPF-YLEVG-QYQL----QDAEVVRGEVARYLA-----------GDPQAGN-------- 267 Query: 304 ARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMF 363 AG + L A A++R D +R + + LSAA A +LTGVTEPIEF FMF Sbjct: 268 ---LAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMF 324 Query: 364 IAPVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLV 423 +AP+L++++ + +GLA+ + ++++ H+ F + ++ + L+R+ F ++ + Sbjct: 325 VAPLLFLIHVMLSGLAYFVCIMLDIH-HSIVFSHGLVDFTLLFS--LSRNTGWFAVLGPL 381 Query: 424 FFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENI 483 + + LF I FNL TPGR S+GT ++ A +I LGG++NI Sbjct: 382 TAVIYYILFRGSILAFNLKTPGRL---------QSDGTKGSKESLRA--IIAALGGRDNI 430 Query: 484 ADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543 +++AC+TRLR++V ++V + + Q GA G+IV KGVQ VYG KA+ L+ +Q L Sbjct: 431 VELNACLTRLRLSVHSPELV-NKVRLSQLGAKGVIVMGKGVQIVYGTKAETLRKVLQRYL 489 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: 616 Number of extensions: 31 Number of successful extensions: 7 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: 499 Length adjustment: 35 Effective length of query: 510 Effective length of database: 464 Effective search space: 236640 Effective search space used: 236640 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