GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Phaeobacter inhibens BS107

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 GFF2276 PGA1_c23080 ribose transport system permease protein RbsC

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__Phaeo:GFF2276
          Length = 324

 Score =  174 bits (442), Expect = 2e-48
 Identities = 98/297 (32%), Positives = 166/297 (55%), Gaps = 5/297 (1%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           GI +     ++   +   +FLT++N   V+ + + + +M+ G+T V+I+  +DLSVGS++
Sbjct: 17  GILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSMM 76

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             +++V+  L D+ G  P L++    A+ +  G   G L+   +L   I TLGMLS   G
Sbjct: 77  SFSTIVVLDLHDKLG--PTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSAIHG 134

Query: 132 LAYVMSGGWPISPFPES---FTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIY 188
           L    SGG  +    +    F + GQG +  +  P++    +  +  I L  T  GR++Y
Sbjct: 135 LTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFGRKVY 194

Query: 189 AIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAA 248
           A+GGN  A+   GI+  R++ L Y ++    A AG +  +    +Q   GQG EL+V+AA
Sbjct: 195 AVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELEVLAA 254

Query: 249 TVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAID 305
            ++GG SL GG GTI    +G +I+G ++NG++L+G+    Q VV  I+II+A+ +D
Sbjct: 255 VILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWLD 311


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: 326
Number of extensions: 22
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: 324
Length adjustment: 27
Effective length of query: 286
Effective length of database: 297
Effective search space:    84942
Effective search space used:    84942
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