GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Williamsia sterculiae CPCC 203464

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_083709430.1 BW971_RS07470 polyprenol monophosphomannose synthase

Query= BRENDA::Q2PCE3
         (246 letters)



>NCBI__GCF_900156495.1:WP_083709430.1
          Length = 280

 Score = 84.7 bits (208), Expect = 2e-21
 Identities = 70/224 (31%), Positives = 112/224 (50%), Gaps = 20/224 (8%)

Query: 10  IVLATLNEIDNLPRLCSDIDSILKNTKIKYQLLFVDDNSSDGTREFIIEYCNKNKLSKY- 68
           +++ T NE +NLP +   +   L    +    L VDD+S DGT +        +   +  
Sbjct: 40  VIIPTFNERENLPVITERLLGSLPGITV----LVVDDDSPDGTGDLADRLAADDPAGRIK 95

Query: 69  IFNEYKKSTLIARY-----QGINNADGKYIIL-MDSDLQHPPKYLLNIYNSLLKHNDIVI 122
           + +   K  L   Y     QG++  DG  +++ MD+D  H P+ L  +   + +  D+VI
Sbjct: 96  VMHRTGKGGLGTAYLAGFRQGLD--DGFQVLVEMDADGSHAPEQLSRLLEKVNEGYDLVI 153

Query: 123 ASRYVKGGSTGNRKPIRGIISRGASLMAQLLLKSSRQIKDPISCYIGFRKG----LKLD- 177
            SRYV GG   N    R ++SRGA+L A+L L SS  + D  + Y  +R+     + LD 
Sbjct: 154 GSRYVPGGELVNWPRRRELLSRGANLYARLALGSS--VHDITAGYRAYRRAVLEKIALDT 211

Query: 178 IDEGWRGYEIGIFLRASNNNVKVKEIPYRFAERENGKSKVTSSV 221
           +D     ++I +  RA     +V E+P  F ERE G+SK++ SV
Sbjct: 212 VDSQGYCFQIDLAWRALQAGFRVGEVPITFTEREIGESKMSGSV 255


Lambda     K      H
   0.320    0.140    0.396 

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: 140
Number of extensions: 11
Number of successful extensions: 3
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: 246
Length of database: 280
Length adjustment: 25
Effective length of query: 221
Effective length of database: 255
Effective search space:    56355
Effective search space used:    56355
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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