GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICB in Paraburkholderia bryophila 376MFSha3.1

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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