GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409
          Length = 322

 Score =  191 bits (484), Expect = 3e-53
 Identities = 106/297 (35%), Positives = 166/297 (55%), Gaps = 1/297 (0%)

Query: 13  IFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILG 72
           + L  + I V   +    FL+  N+  + L +S   I +  M   + +   DLSVGS++ 
Sbjct: 26  MLLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85

Query: 73  AASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGL 132
            A VV  ++M +   S FL V   L +G+  GL NG++I K R+   I+TL  + + RGL
Sbjct: 86  CAGVVAAVVMRDTD-SVFLGVSAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGL 144

Query: 133 AYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGG 192
           AY+ + G  +    E F V G G +  VPVP++   V  +     L YT  GR   AIGG
Sbjct: 145 AYIFANGKAVGVSQEQFFVFGNGQLFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGG 204

Query: 193 NMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIG 252
           N EA+ L G+  DR   L++ ++G + A AG +L + +   QP  GQG+EL VI+A V+G
Sbjct: 205 NQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLG 264

Query: 253 GTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRR 309
           G SLSGG G I     G +I+ ++ N M L  + +F+Q V+ G ++++A+ ID++++
Sbjct: 265 GVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQ 321


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: 294
Number of extensions: 19
Number of successful extensions: 2
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: 322
Length adjustment: 27
Effective length of query: 286
Effective length of database: 295
Effective search space:    84370
Effective search space used:    84370
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