GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Sinorhizobium meliloti 1021

Align LacI family transcriptional regulator, 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 SMc03813 SMc03813 periplasmic binding ABC transporter protein

Query= TCDB::G4FGN5
         (343 letters)



>FitnessBrowser__Smeli:SMc03813
          Length = 337

 Score =  143 bits (361), Expect = 6e-39
 Identities = 99/286 (34%), Positives = 149/286 (52%), Gaps = 20/286 (6%)

Query: 22  DMTILLAPKSLNNPYWFAVENGMKDAAEKLG-IKAIFDAPVEADAAKQAEKILSYIVKGV 80
           D    L  K LNN +   ++ G + AA+KLG +   +  P E D AKQ +     + +GV
Sbjct: 29  DREFALVFKVLNNAFSPPIQQGCEAAAKKLGDVTCTYLGPTEYDEAKQVQLAQDMVTRGV 88

Query: 81  DGIGISPNDPEGIKVVVKRALDKGIPVIMFDSD--SPDSG-RYAYIGTNNYNAGYEAGKL 137
            G+G+S  +P+ +  ++K A DKGIPV+ FD+D    D+G R  YIGT+N    YE G  
Sbjct: 89  AGLGVSAGNPKAMARIMKMAQDKGIPVVTFDTDVLPEDAGLRSTYIGTDN----YEFGIA 144

Query: 138 MAQLIEKYKAEKKTIRLAILTGGLAALNLNERIRGFKDALEDYSKRSGKEIVY----VAD 193
           +AQ + + K +  T+   I +G  A+ NL  R++G +D L   +K  G E +       +
Sbjct: 145 LAQKVLESKKDGGTV--CIQSGAPASENLKARVQGIRDTLAGVTKDKGAEKLTGQNGWTE 202

Query: 194 PFPC----DDDSAKAIQIIRDVTRKYTDLDGWFMSGGWPLFAPK--ETVISALGGPERMK 247
           P  C    +DD   A Q +RDV     +L  +   GGW  +AP+  +  +  L      K
Sbjct: 203 PAGCPVYNNDDITLAAQQVRDVMTNNPELSAFVAVGGWAQYAPQAYKQAMEPLKARLDSK 262

Query: 248 DLLVVGFDTLLPELELVKAGAVKGLVGQRPYDMGYLSVLVLYNMAK 293
           DL+VV  D   P+L L+  G     +GQRPYDMGY +++ L  + K
Sbjct: 263 DLVVVFGDNFGPQLPLLAEGLSHYNIGQRPYDMGYETIMALDKLTK 308


Lambda     K      H
   0.318    0.139    0.398 

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: 276
Number of extensions: 18
Number of successful extensions: 5
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: 343
Length of database: 337
Length adjustment: 28
Effective length of query: 315
Effective length of database: 309
Effective search space:    97335
Effective search space used:    97335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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