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 Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 197 bits (500), Expect = 1e-54 Identities = 172/550 (31%), Positives = 246/550 (44%), Gaps = 93/550 (16%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69 Q G+AL++ +AV+P AGL++ IG+ + ++A G AI NL ILFA Sbjct: 9 QPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAA----------GTAIFGNLGILFA 58 Query: 70 VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEM----LADSKAKVSSVLAGDLI 125 + + +A+D G A A + L + F + L D+ AKV + Sbjct: 59 IGVAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKV--------V 110 Query: 126 VKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIV 185 + + T + + V +GII+G +G YN++ LP+ LAFF G+RFVP + Sbjct: 111 AQAWATGQID----RLEVPIGIISGLIGGKFYNRFATI-ALPEYLAFFGGRRFVPIAAGI 165 Query: 186 WSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTI 245 + A VL + I S L+ + S + FVYG L RLLL GLHH+L Sbjct: 166 AGLLLAGVLGYGYAHISSALDAASHAVVESGGA----GMFVYGVLNRLLLVTGLHHLLNN 221 Query: 246 PMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPAR 305 + L G + TG DL A GD A Sbjct: 222 VAWF--LVGDFGGATG-------------------DLGRFFA-GDPNA----------GA 249 Query: 306 FKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIA 365 F +G L AM+ E+R M S A FLTGVTEPIEF FMF+A Sbjct: 250 FMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIEFTFMFLA 309 Query: 366 PVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVI------ 419 PVLY ++A+ TG+A L D++ +++ FGF +AGL ++NF + Sbjct: 310 PVLYAIHAVLTGVAMTLMDMLGIKL-GFGF-----------SAGLFDYVLNFKLSTRPWM 357 Query: 420 ---VSLVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGS-LATKVID 475 V + + +TLF F I+K +L TPGR + EA G G+ + Sbjct: 358 LLPVGAAYAVIYYTLFRFFIRKLDLATPGR------EKGEAVAAAGETAAGNERGAAFVK 411 Query: 476 LLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLI-VKDKGVQAVYGPKADV 534 LGG N+ VDAC TRLR+ V D V +A GA G+I Q V GP AD+ Sbjct: 412 ALGGAANLTSVDACTTRLRLIVADQSAV-DDAALNALGARGIIRPSANATQVVLGPIADL 470 Query: 535 LKSDIQDMLG 544 + +I+ +G Sbjct: 471 VAEEIRGAIG 480 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: 715 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 545 Length of database: 560 Length adjustment: 36 Effective length of query: 509 Effective length of database: 524 Effective search space: 266716 Effective search space used: 266716 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