GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 63/181 (34%), Positives = 98/181 (54%), Gaps = 9/181 (4%)

Query: 18  LYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVTGMP------V 71
           L  +SL +  G    L+G + +GK++LM I+  LD P++G   ++G +V+ M       V
Sbjct: 25  LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84

Query: 72  RDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHIDMFLDRYPA 129
           R++ +  V+Q F   P      N+A PL   G  +K+ DAR       + +   +D  P 
Sbjct: 85  RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144

Query: 130 ELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATT 189
           ELSGGQ+QRVA+ARAL     ++L DEP  NLD K   E+   L ++ + G +T++  T 
Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSKG-NTIILVTH 203

Query: 190 E 190
           E
Sbjct: 204 E 204


Lambda     K      H
   0.318    0.133    0.375 

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: 155
Number of extensions: 7
Number of successful extensions: 3
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: 363
Length of database: 252
Length adjustment: 27
Effective length of query: 336
Effective length of database: 225
Effective search space:    75600
Effective search space used:    75600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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