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 H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 241 bits (614), Expect = 7e-68 Identities = 173/547 (31%), Positives = 276/547 (50%), Gaps = 78/547 (14%) Query: 5 SFDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAV--HTIARVMEDIGWAIIT 62 +F QK GK+L++ VAV+P AGL L+G+ A D + + +M++ G I Sbjct: 5 AFGVLQKVGKSLMLPVAVLPVAGL------LLGLGATDFHGYVPAIVLALMKNAGDVIFA 58 Query: 63 NLHILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAG 122 NL ++FA+ + + ++ AA + +++ G I AKV + Sbjct: 59 NLPLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVI------------AKVEGI-EP 105 Query: 123 DLIVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFV 182 D+I +G P++ GVF GI+ G L A ++N+YY LP L FF GKRFVP V Sbjct: 106 DMI--------MGIPSIQTGVFGGILAGGLAAWMFNRYYRI-ALPAYLGFFAGKRFVPIV 156 Query: 183 VIVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHM 242 + S V +LS++WP I S + F +W A S P A VYG +ERLL+PFGLHH+ Sbjct: 157 TAIGSIVLGAILSVVWPPIGSAIKAFSQWAAVSD---PRTAATVYGFVERLLIPFGLHHI 213 Query: 243 LTIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVV 302 +P + E G TG +VV G D+ A T Sbjct: 214 WNVPF-FFEAGSFLDPTTG----KVVHG----------DITRFFAGDRT----------- 247 Query: 303 PARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFM 362 A AG + L A A++ E + M +SAAL FLTG+TEPIEF F+ Sbjct: 248 -AGILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFL 306 Query: 363 FIAPVLYVVYAITTGLAFALADLINLRV---HAFGFIELITRTPMMVNAGLTRDLINFV- 418 F+APVLY+++A A +A+ + +R+ + G I+ + ++ T F+ Sbjct: 307 FVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFN--LIGNKSTHAWYVFIL 364 Query: 419 --IVSLVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDL 476 I +++++G +F F+I +F+L TPGR + ++ ++ G G + +++ Sbjct: 365 GPIYAVIYYG----VFRFVITRFDLKTPGREDDTVETAKVSTAGV-----GGRSRELVLA 415 Query: 477 LGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLK 536 GG+ NI +DAC+TRLR++VK+ + E + K GA G++ GVQA++GP ++ +K Sbjct: 416 FGGRSNIDSLDACITRLRISVKN-PALVNEGKLKALGAAGVVRVGNGVQAIFGPLSENMK 474 Query: 537 SDIQDML 543 +D+ + L Sbjct: 475 TDMHEYL 481 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: 725 Number of extensions: 48 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: 596 Length adjustment: 36 Effective length of query: 509 Effective length of database: 560 Effective search space: 285040 Effective search space used: 285040 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