GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Lentibacillus jeotgali Grbi

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 WP_138919826.1 ON01_RS16060 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_000224785.1:WP_138919826.1
          Length = 292

 Score =  266 bits (679), Expect = 6e-76
 Identities = 138/289 (47%), Positives = 197/289 (68%), Gaps = 3/289 (1%)

Query: 20  IVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAASVVMG 79
           +V+FLG  +  F T++NI  ++  +S  A+++FGMT VI+T+GIDLSVGS+L   S +  
Sbjct: 1   MVIFLGFMSDAFFTLDNILNLLRQISVNALIAFGMTFVILTAGIDLSVGSLLALGSALTA 60

Query: 80  LLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAYVMSGG 139
            L+   G+ P L+V++GL +G+G G  NGL+ITK ++APFI+TL  ++V RG   V + G
Sbjct: 61  GLLTS-GMDPMLAVLLGLLIGLGLGAINGLIITKGKVAPFIATLATMTVYRGATLVYTDG 119

Query: 140 WPISPFPESFTVH--GQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNMEAS 197
            P++   +SF     G G V  +P PVI M  + +I    LK TV GR++YA+GGN E S
Sbjct: 120 MPVTGLSDSFAFEMIGGGYVFGIPFPVILMLAVFLILFFVLKKTVFGRQVYAVGGNEEVS 179

Query: 198 KLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGTSLS 257
            L GIK DR+ I VY++ G L+  AG +LT+ L  AQP AG+ +ELD IAA VIGGTSL 
Sbjct: 180 VLSGIKADRVKIWVYSLTGMLSVLAGLILTSRLNSAQPTAGEMFELDAIAAVVIGGTSLM 239

Query: 258 GGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQ 306
           GG G I G  +GA+I+GV+ NG+ L+ VSSF+QQ+V G VI++A+ +D+
Sbjct: 240 GGRGRITGTLIGALIIGVIDNGLNLMNVSSFYQQIVKGGVILLAVLLDR 288


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: 300
Number of extensions: 17
Number of successful extensions: 4
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: 292
Length adjustment: 27
Effective length of query: 286
Effective length of database: 265
Effective search space:    75790
Effective search space used:    75790
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: 48 (23.1 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