GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AO353_03840 AO353_03840 ABC transporter ATP-binding protein

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



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  255 bits (652), Expect = 1e-72
 Identities = 142/292 (48%), Positives = 195/292 (66%), Gaps = 9/292 (3%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           MTGL+L+++ K YG    +  ++L + EG+ V F+GPSGCGK+TLLRMIAGLE ++GG++
Sbjct: 1   MTGLILENVEKRYGTACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
            +D E + + P   R   MVFQS AL+PHMTV +N+A+ +++   SK +   RV    ++
Sbjct: 61  RLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELLEL 120

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           +QL   +DR    LSGGQRQRVAI RAI  +PK+ L DEPLS LDA LR + ++EI +L 
Sbjct: 121 IQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
           +R++ TT I VTHDQ EAMT+AD +VVL    ++QVG P+E+Y  PAN FVA FIGS   
Sbjct: 181 QRLNITT-IMVTHDQREAMTMADIVVVLGQNRVQQVGTPIEIYRHPANEFVADFIGSG-- 237

Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNAS-ENGKTASFGVRPEDLRVT 291
           N+ PAT    G+   V L GG +  L VP  +S   G+     VRPEDL+++
Sbjct: 238 NIFPATALGDGK---VGLPGGDA--LQVPICSSIVVGEKVKMLVRPEDLQLS 284


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: 309
Number of extensions: 10
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: 351
Length adjustment: 29
Effective length of query: 333
Effective length of database: 322
Effective search space:   107226
Effective search space used:   107226
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