GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglC in Pseudomonas putida KT2440

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 PP_2456 PP_2456 D-ribose ABC transporter - permease subunit

Query= TCDB::G4FGN4
         (313 letters)



>lcl|FitnessBrowser__Putida:PP_2456 PP_2456 D-ribose ABC transporter
           - permease subunit
          Length = 331

 Score =  164 bits (414), Expect = 3e-45
 Identities = 103/297 (34%), Positives = 154/297 (51%), Gaps = 1/297 (0%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+   L+A++V     +  F +     T+   +  + +++ GMT V+I  GIDLSVGS+L
Sbjct: 28  GLAGALLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVL 87

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A+  + + +   G     S ++G+AV    G   G +    R+  FI +LG+L + RG
Sbjct: 88  ALAASTVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARG 147

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191
           LAY  +                    G  P  +I + VI V+A + L  TV GR +  IG
Sbjct: 148 LAYQFTDSRTAYIGDAYAWFSNPVAFGVSPAFIIALLVI-VLAQLVLTRTVFGRYLIGIG 206

Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251
            N EA +L GI      +LV+ + G LA  A     + L  A PNAG G EL VIAA VI
Sbjct: 207 TNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAAVVI 266

Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308
           GGTSL GG G+++  F G +I+ VL  G+  +G S   ++++ G VI+IA+ +D  R
Sbjct: 267 GGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTYR 323


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: 292
Number of extensions: 15
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: 331
Length adjustment: 28
Effective length of query: 285
Effective length of database: 303
Effective search space:    86355
Effective search space used:    86355
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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