GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pedobacter sp. GW460-11-11-14-LB5

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

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



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  126 bits (317), Expect = 5e-34
 Identities = 75/201 (37%), Positives = 111/201 (55%), Gaps = 8/201 (3%)

Query: 35  LKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAP------ 88
           LK + LD+  GEFV  +GPSG GKSTL+  +  L+  +SG+  ++G  V H++       
Sbjct: 25  LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84

Query: 89  AKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRPA 148
             + I  VFQ++ L P  T  DN+ L L  AG  K + + + A+A   + L   +  +P 
Sbjct: 85  RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144

Query: 149 ELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTH 208
           ELSGGQRQRVA+ RA++  P + L DEP  NLD    +     +  +H S   T+I VTH
Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIH-SKGNTIILVTH 203

Query: 209 DQVEAMTLADKIVVLNAGRIE 229
           ++ +    A +IV +  G IE
Sbjct: 204 EE-DIAQHAHRIVRMRDGLIE 223


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: 184
Number of extensions: 7
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: 352
Length of database: 252
Length adjustment: 26
Effective length of query: 326
Effective length of database: 226
Effective search space:    73676
Effective search space used:    73676
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: 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