GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Herbaspirillum seropedicae SmR1

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 HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__HerbieS:HSERO_RS03645
          Length = 339

 Score =  207 bits (526), Expect = 4e-58
 Identities = 115/300 (38%), Positives = 186/300 (62%), Gaps = 6/300 (2%)

Query: 13  IFLILIAIVVFL-GVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           ++L+   + ++L G  T  F + EN   ++  V+   +++ GMT VI+T+GIDLSVGS+L
Sbjct: 36  LYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVL 95

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
            A S V+G+ +   G +P  ++ + +  G+  G+ NG ++    +  F+ TLG ++  RG
Sbjct: 96  -AVSAVLGMQVS-LGAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRG 153

Query: 132 LAYVMSGGWPI--SPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYA 189
            AY+++ G  +  +  P SF   G G    VP  +     + +++ + L+ TV G  IYA
Sbjct: 154 AAYLLADGTTVLNNDIP-SFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYA 212

Query: 190 IGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAAT 249
           IGGN++A++L GI+   +L+ VY+I+G  +  AG +  + L  A  N G GYELD IAA 
Sbjct: 213 IGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAV 272

Query: 250 VIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRR 309
           V+GGTSL GG G+I G  +GA+I+GV+ NG+ +LG+SSFWQ V  G VI++A+ +D+ R+
Sbjct: 273 VLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQ 332


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: 308
Number of extensions: 18
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: 313
Length of database: 339
Length adjustment: 28
Effective length of query: 285
Effective length of database: 311
Effective search space:    88635
Effective search space used:    88635
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 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