GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Acidovorax sp. GW101-3H11

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  177 bits (449), Expect = 8e-49
 Identities = 104/312 (33%), Positives = 162/312 (51%), Gaps = 21/312 (6%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+  +L  +V      +  F + E   T+   +  +A+M+ GMT V+I +GIDLSVGS++
Sbjct: 591 GLLAVLAGMVALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVM 650

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A+      + + G +   +  + LA G+  G   G +    RL  FI +LGML   RG
Sbjct: 651 ALAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRG 710

Query: 132 LAYVMSGG----------WPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYT 181
            AYV++            W  +PF            G +    +   V+ V+A + L  T
Sbjct: 711 SAYVVTDSRTQYVGDAISWLSAPF-----------FGGISFAFLLAVVLVVVAQLVLSRT 759

Query: 182 VTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGY 241
           V GR +  IG N EA +L G+    I ++V+ + G LA  AG + +A L  A PNAG G 
Sbjct: 760 VFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGM 819

Query: 242 ELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIA 301
           EL VIAA VIGGTSL GG G+++    G +I+ VL  G+  +G S   ++++ G VI+ A
Sbjct: 820 ELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAA 879

Query: 302 IAIDQIRRAKER 313
           + +D +R+ + +
Sbjct: 880 VIVDTLRQRRAK 891


Lambda     K      H
   0.328    0.145    0.421 

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: 522
Number of extensions: 25
Number of successful extensions: 2
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: 313
Length of database: 892
Length adjustment: 35
Effective length of query: 278
Effective length of database: 857
Effective search space:   238246
Effective search space used:   238246
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 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