GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treF in Pseudomonas fluorescens FW300-N2E2

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate Pf6N2E2_6094 Glucoamylase (EC 3.2.1.3)

Query= CAZy::ABK72415.1
         (668 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6094 Glucoamylase (EC
           3.2.1.3)
          Length = 529

 Score =  328 bits (841), Expect = 4e-94
 Identities = 197/493 (39%), Positives = 268/493 (54%), Gaps = 12/493 (2%)

Query: 154 ILLRTVRCVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTT 213
           +L+R V    G+    M C    DY R + T            A         P+LRL +
Sbjct: 30  VLMRKVHMTVGSATFRMRCAVRHDYARAATTARQDA-------AHICFEAPGQPSLRLCS 82

Query: 214 NLRIGIEGREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADKMWKTSEAWRQWINVGD 273
           +  + ++G  A A   L +G +    L     P  Q  + +A  + +T   WR WI    
Sbjct: 83  DQPMTLDGNAAVAEFTLAQGQSAEFLLGGIDDPRLQD-DVSAICLERTLAFWRGWIGQST 141

Query: 274 FPDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFAL 333
           +    WR  + RSAL LK LT    GA+LAA T  LPET  GERNWDYRY+WIRDS+F +
Sbjct: 142 YRGR-WREVVNRSALALKLLTSRKHGAILAAATFGLPETRGGERNWDYRYTWIRDSSFTV 200

Query: 334 WGLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSR 393
           +    LG   EA+ +  ++         +   L ++YG+ G   L E EL HLSG+ N+R
Sbjct: 201 YAFMRLGFVEEANAYMRWLRGRVSDCCDQPTKLNILYGLDGRLELPETELPHLSGFGNAR 260

Query: 394 PVRIGNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGI 453
           PVRIGN AY Q Q DI+G ++D+VYL  K  E I    W    + V++  K W++ D GI
Sbjct: 261 PVRIGNLAYKQVQLDIFGELMDAVYLVNKYGEAISHQGWKHTVDVVDQVCKVWQDKDVGI 320

Query: 454 WEVRGEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKR 512
           WE+RG+ QHF  S++MCWVA+DR  +LAE +   +   +W    + I  D+      D+ 
Sbjct: 321 WEMRGDKQHFLHSRLMCWVAVDRAIRLAEKRSLPAPFARWDETRQAIYQDIWTNFWNDEH 380

Query: 513 GVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-D 571
               QR G  ALD S+LL  L RF+ A DPR  +T+ AI   L  DG+V RYR +++  D
Sbjct: 381 QHFIQRLGSTALDGSMLLMPLVRFVSARDPRWLSTLDAIEKNLVRDGMVYRYRNDDSPID 440

Query: 572 GLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGN 631
           GL G EG+F  CSFW V  L   G + +A+   E+LL +A+PL LYAEE +   G HLGN
Sbjct: 441 GLRGIEGSFAACSFWYVECLARAGRVEKAQLEFEQLLRYANPLGLYAEEFDSH-GYHLGN 499

Query: 632 FPQAFTHLALINA 644
            PQA  HLALI+A
Sbjct: 500 TPQALPHLALISA 512


Lambda     K      H
   0.319    0.135    0.426 

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: 980
Number of extensions: 48
Number of successful extensions: 6
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: 668
Length of database: 529
Length adjustment: 37
Effective length of query: 631
Effective length of database: 492
Effective search space:   310452
Effective search space used:   310452
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 (21.7 bits)
S2: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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