GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6094
          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:

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