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 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__Keio:15223 Length = 477 Score = 261 bits (666), Expect = 6e-74 Identities = 178/537 (33%), Positives = 281/537 (52%), Gaps = 75/537 (13%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69 QK GK+L++ V+V+P AG+++ +G SA ++ VM + G ++ N+ ++FA Sbjct: 10 QKVGKSLMLPVSVLPIAGILLGVG-----SANFSWLPAVVSHVMAEAGGSVFANMPLIFA 64 Query: 70 VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDY 129 + + + + A AA++A+ G+ + +A V + A ++ K Sbjct: 65 IGVALGFTNNDGVSALAAVVAY-----------GIMVKTMAVVAPLVLHLPAEEIASKHL 113 Query: 130 FTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWSTV 189 + GV GII+G + A ++N++Y KLP+ L FF GKRFVP + + + Sbjct: 114 ---------ADTGVLGGIISGAIAAYMFNRFYRI-KLPEYLGFFAGKRFVPIISGLAAIF 163 Query: 190 TAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNY 249 T +VLS +WP I S + F +W A P+VA +YG +ER L+PFGLHH+ +P Sbjct: 164 TGVVLSFIWPPIGSAIQTFSQWAAYQN---PVVAFGIYGFIERCLVPFGLHHIWNVPFQM 220 Query: 250 TELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAG 309 G YT + GQV G P ++A GD A +G Sbjct: 221 QI--GEYT----NAAGQVFHGDIPRYMA-----------GDPTAGK-----------LSG 252 Query: 310 QVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLY 369 + L A A++ + E RAK + +SAAL FLTG+TEPIEF FMF+AP+LY Sbjct: 253 GFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILY 312 Query: 370 VVYAITTGLAFALADLINLR---VHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFG 426 +++AI GLAF + L+ +R + G I+ I V +G + L F IV + + Sbjct: 313 IIHAILAGLAFPICILLGMRDGTSFSHGLIDFI------VLSGNSSKLWLFPIVGIGYAI 366 Query: 427 LNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADV 486 + +T+F LIK +L TPGR ++A+E +A ++ GGKENI ++ Sbjct: 367 VYYTIFRVLIKALDLKTPGR--------EDATEDAKATGTSEMAPALVAAFGGKENITNL 418 Query: 487 DACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543 DAC+TRLRV+V D+ V +A K+ GA G++V GVQA++G K+D LK+++ + + Sbjct: 419 DACITRLRVSVADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474 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: 652 Number of extensions: 34 Number of successful extensions: 5 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: 477 Length adjustment: 34 Effective length of query: 511 Effective length of database: 443 Effective search space: 226373 Effective search space used: 226373 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