GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_28585
          Length = 379

 Score =  334 bits (857), Expect = 2e-96
 Identities = 182/358 (50%), Positives = 240/358 (67%), Gaps = 11/358 (3%)

Query: 4   LLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFID 63
           L L ++ K  G   ++  + L+I  GEFVVFVGPSGCGKSTLLR+IAGL+ I GGD+ ID
Sbjct: 4   LKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63

Query: 64  GERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQL 123
           G RVND+ P +RG+ MVFQSYALYPHM+VYDN++FG+++A+  K  +  RV   A +LQL
Sbjct: 64  GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQL 123

Query: 124 TPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERM 183
              L R P+ LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA+LRV  R EIA+L  R+
Sbjct: 124 DKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRL 183

Query: 184 SDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVI 243
             +TMIYVTHDQVEAMTLAD+IVVL+ G IEQVG+P ELYERPA+ FVA F+GSP MN +
Sbjct: 184 G-STMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFL 242

Query: 244 PATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGT-- 301
            A +   G+ + V        +L   ++        S G+RPE + +  A     +GT  
Sbjct: 243 AAFLHTPGETSQVESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIALKAA-----QGTAG 297

Query: 302 --VSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNG 357
             VS VE LG  T ++++   +++P++ +    A    GD+V    D   LH+FDT+G
Sbjct: 298 IAVSGVEYLGSETYVHLD-TGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLHVFDTHG 354


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: 373
Number of extensions: 12
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: 362
Length of database: 379
Length adjustment: 30
Effective length of query: 332
Effective length of database: 349
Effective search space:   115868
Effective search space used:   115868
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.

Links

Downloads

Related tools

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