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 CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__Caulo:CCNA_00572 Length = 582 Score = 217 bits (553), Expect = 9e-61 Identities = 175/545 (32%), Positives = 270/545 (49%), Gaps = 67/545 (12%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGK--LIG---MSAGDINAVHTIARVMEDIGWAIITNL 64 Q G+AL++ +AV+P A L++ IG+ L+G ++A ++A G AI +L Sbjct: 9 QPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAIFASL 68 Query: 65 HILFAVAIGGSWAKDRAGGA-FAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVL-AG 122 ++FA+ + A++ G A A ++ +V+ + GV A ++A + +V A Sbjct: 69 GLIFAIGVAVGLARENHGAAGLAGVVCYVIATK------GVEALLVAPPEVAAKAVEGAK 122 Query: 123 DLIVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFV 182 DL + + +G ++ +G+ G+I+G LYN+Y +LP+ LAFF G+RFVP V Sbjct: 123 DLAIAAWKAKEIGKLSIPVGILSGVISG----ALYNRYSTI-QLPEYLAFFGGRRFVPIV 177 Query: 183 VIVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHM 242 + V A++ W +++G++ + AS D + VYG L RLL+ GLHH+ Sbjct: 178 AGLAGVVLALLFGAFWSTLEAGVDGLSGLVTASGDLGLV----VYGLLNRLLIVTGLHHI 233 Query: 243 LTIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVV 302 L + + + G + +TG DLN A GD A Sbjct: 234 LNNVVWF--ILGDFNGVTG-------------------DLNRFAA-GDKTA--------- 262 Query: 303 PARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFM 362 F +G L AM E+R M S AL FLTGVTEPIEF FM Sbjct: 263 -GAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLGSLALTSFLTGVTEPIEFTFM 321 Query: 363 FIAPVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSL 422 F+APVL+ ++A+ TGL+ AL +++++++ FGF + + N TR L+ + V L Sbjct: 322 FLAPVLFAIHALLTGLSMALMNMLDVKL-GFGFSAGLFDYVLNFNKA-TRPLL-LIPVGL 378 Query: 423 VFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNV-QDGSLATKVIDLLGGKE 481 V+ L + +F F I +F+L TPGR EDEA V G ++ LGG Sbjct: 379 VYGALYYGVFRFAILRFDLKTPGR-------EDEAPPSAQAVTTGGGRGADMLAALGGAA 431 Query: 482 NIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLI-VKDKGVQAVYGPKADVLKSDIQ 540 N+ VDAC TRLR+ V D +V E K GA G++ DK +Q V GP AD + +I+ Sbjct: 432 NLVSVDACTTRLRLIVVDQGLV-NEPALKALGARGVVRPSDKALQVVLGPIADTVAGEIR 490 Query: 541 DMLGA 545 + A Sbjct: 491 HAISA 495 Score = 28.5 bits (62), Expect = 7e-04 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 2/65 (3%) Query: 470 ATKVIDLLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKG-VQAVY 528 A ++ LGG +N+ D+ +RLRV + D + V +A G G G V + Sbjct: 511 AKALLAALGGADNLRDLSVHASRLRVVLNDPERV-DQAALHTAGVRGFAAVAPGAVHIII 569 Query: 529 GPKAD 533 GP A+ Sbjct: 570 GPHAE 574 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: 786 Number of extensions: 41 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 545 Length of database: 582 Length adjustment: 36 Effective length of query: 509 Effective length of database: 546 Effective search space: 277914 Effective search space used: 277914 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 Apr 09 2024. 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