GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pseudomonas putida KT2440

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Putida:PP_1484
          Length = 343

 Score =  233 bits (593), Expect = 7e-66
 Identities = 119/262 (45%), Positives = 167/262 (63%)

Query: 19  SLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQI 78
           ++Q   + + FG  + +  + +D+ DGEF   +GPSG GK+T LR IAG E  +SGS++I
Sbjct: 4   AVQFTQVSRTFGEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIRI 63

Query: 79  DGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLS 138
            GVE   + P +R +  VFQ YAL+PH+ V +N+  GLK  GV KAE   +  +A  M++
Sbjct: 64  QGVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAEEALAMVA 123

Query: 139 LEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRS 198
           L  Y AR+PA+LSGGQRQRVA+ RA+V  P++ L DEPL  LD  LR   + E+ +L R 
Sbjct: 124 LAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQ 183

Query: 199 LKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFI 258
           L  T I+VTHDQ EA++++D++ V N GRIEQV +P  LY +P+  FVA F+G+  +   
Sbjct: 184 LGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVGTSNVVRG 243

Query: 259 EAAKLGDGEAKTIGIRPEHIGL 280
           E A   +G      IRPE I L
Sbjct: 244 ELAMQINGSPAPFSIRPELIRL 265


Lambda     K      H
   0.320    0.137    0.393 

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: 263
Number of extensions: 8
Number of successful extensions: 1
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: 352
Length of database: 343
Length adjustment: 29
Effective length of query: 323
Effective length of database: 314
Effective search space:   101422
Effective search space used:   101422
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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