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_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033
          Length = 325

 Score =  173 bits (438), Expect = 6e-48
 Identities = 107/304 (35%), Positives = 163/304 (53%), Gaps = 3/304 (0%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+   L+A+V    V +  FL+ +   T+   +  + +++ GMT V+I  GIDLSVGS+L
Sbjct: 22  GLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVL 81

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A+  + + +   G S   + ++G+AV    G   G +    R+  FI +LG+L + RG
Sbjct: 82  ALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARG 141

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191
           LAY M+G    +   ++F      +   +    I   +I  IA   L  TV GR +  IG
Sbjct: 142 LAYQMTGS-RTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIGIG 200

Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251
            N EA +L GI      ILV+++ G LA  A     + L  A PNAG G EL VIAA VI
Sbjct: 201 TNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAAVVI 260

Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR--R 309
           GGTSL GG G+++  F G +I+ VL  G+  +G +   ++++ G VI++A+ +D  R  R
Sbjct: 261 GGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQR 320

Query: 310 AKER 313
           A  R
Sbjct: 321 ASRR 324


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: 279
Number of extensions: 9
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: 325
Length adjustment: 28
Effective length of query: 285
Effective length of database: 297
Effective search space:    84645
Effective search space used:    84645
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