GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  124 bits (311), Expect = 3e-33
 Identities = 84/223 (37%), Positives = 120/223 (53%), Gaps = 17/223 (7%)

Query: 4   LLLKDIRKSYG-AVDVIHG---IDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59
           + +K+I + Y    +VIH    + LDI +GEFV  +GPSG GKSTL+ ++  L+  + G 
Sbjct: 6   ITIKEIGRKYVIGSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGT 65

Query: 60  MFIDGERVNDVPPS------KRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRR 113
             ++G  V+ +          + I  VFQ++ L P  T  DN+A  +  A  SK++ D R
Sbjct: 66  YVLNGTNVSHMSDDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDAR 125

Query: 114 VRGAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATR 173
              A + + L   +D  P  LSGGQRQRVA+ RA+  NP + L DEP  NLD      T 
Sbjct: 126 AARALENVGLGNRMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLD----TKTS 181

Query: 174 IEIAKLSERM--SDTTMIYVTHDQVEAMTLADRIVVLSAGHIE 214
           IEI  L E +     T+I VTH++ +    A RIV +  G IE
Sbjct: 182 IEIMGLLEEIHSKGNTIILVTHEE-DIAQHAHRIVRMRDGLIE 223


Lambda     K      H
   0.320    0.137    0.387 

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: 176
Number of extensions: 8
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: 362
Length of database: 252
Length adjustment: 27
Effective length of query: 335
Effective length of database: 225
Effective search space:    75375
Effective search space used:    75375
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