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 WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC
Query= TCDB::Q63GK8 (545 letters) >NCBI__GCF_000313915.1:WP_083848942.1 Length = 553 Score = 722 bits (1863), Expect = 0.0 Identities = 360/550 (65%), Positives = 432/550 (78%), Gaps = 10/550 (1%) Query: 2 KITSFDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAII 61 KI SF+FWQKFGKAL+VV+AVMPAAGLMISIGKLI M+ ++ TI V E+IGWAII Sbjct: 3 KIFSFEFWQKFGKALMVVIAVMPAAGLMISIGKLIAMA--QVSLAVTIGGVTENIGWAII 60 Query: 62 TNLHILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLA 121 NL ILFA+AIGGSWAK+RAGGAFA+ LAF+L NRITGA+FGV EMLA+ +A V ++ Sbjct: 61 GNLPILFALAIGGSWAKERAGGAFASGLAFILINRITGAVFGVTKEMLANPEATVHTIFG 120 Query: 122 GDLIVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPF 181 ++V YFTSVL APALNMGVFVGII GF GA +YNKYYN+ KLP L+FFNGKRFVPF Sbjct: 121 QKILVNGYFTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGKRFVPF 180 Query: 182 VVIVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHH 241 VVI+WS + A++LS+ WPF Q+G+NEFG+WIA S DSAP APF+YGTLERLLLPFGLHH Sbjct: 181 VVILWSVIIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLPFGLHH 240 Query: 242 MLTIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNV 301 MLTIPMNYT+LGGTY +LTG++ GQ V GQDPLWLAW+TDL NL GD Y+ LL ++ Sbjct: 241 MLTIPMNYTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQLLESI 300 Query: 302 VPARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMF 361 PARFK GQ+IGS+ LMG+ FAM+RNV+ +++ YK +FLSAALAVFLTGVTEP+EFMF Sbjct: 301 RPARFKVGQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEPLEFMF 360 Query: 362 MFIAPVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVS 421 MF LYVVYA+ G+AF LAD+I+LR+HAFG IEL+TR PM + AGL D+INF+I Sbjct: 361 MFAGIPLYVVYALLQGVAFGLADIIDLRLHAFGNIELLTRLPMSIKAGLGMDIINFIITC 420 Query: 422 LVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDE--------ASEGTGNVQDGSLATKV 473 +VFF L + + NF+IKKF++ TPGR GNYI+ D+ A+ T + + + Sbjct: 421 IVFFFLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTATSSTKPSEANNQVMNI 480 Query: 474 IDLLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKAD 533 I LLGGKENI DVDACMTRLRVTVKD VA E WK+ GA+GLI K+ GVQAVYGPKAD Sbjct: 481 IQLLGGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGLIHKNNGVQAVYGPKAD 540 Query: 534 VLKSDIQDML 543 VLKSDI D L Sbjct: 541 VLKSDINDYL 550 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: 879 Number of extensions: 39 Number of successful extensions: 4 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: 553 Length adjustment: 36 Effective length of query: 509 Effective length of database: 517 Effective search space: 263153 Effective search space used: 263153 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 24 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