GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treC in Pseudomonas fluorescens FW300-N2E2

Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate Pf6N2E2_2118 Trehalose synthase (EC 5.4.99.16)

Query= CAZy::AAC77196.1
         (551 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2118
          Length = 1114

 Score =  226 bits (576), Expect = 4e-63
 Identities = 167/560 (29%), Positives = 250/560 (44%), Gaps = 109/560 (19%)

Query: 5   PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNG 64
           P W+++ VIYQ++ KS+ D+   G GD  G+I+ LDY+  LGV+ IWL PFY SP+ D+G
Sbjct: 14  PLWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIEKLDYIADLGVNTIWLLPFYPSPRRDDG 73

Query: 65  YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE--SP 122
           YD+A Y  +   YGT+ D    + +A  R +R+I ++V NHTS QH WF+ A   +  S 
Sbjct: 74  YDIAEYRGVSADYGTMADARRFIAEAHKRNLRVITELVINHTSDQHPWFQRARKAKPGSK 133

Query: 123 YRQFYIWRDGEPETPPNNWRSKF---GGSAWRWHAESEQYYLHLFAPEQADLNWENPAVR 179
            R FY+W D + +   +  R  F     S W W   + QY+ H F   Q DLN++NP V 
Sbjct: 134 ARDFYVWSDDDHKY--DGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVI 191

Query: 180 AELKKVCEFWADRGVDGLRLDVV-NLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNR 238
             +  V  +W D G+DGLRLD +  LI +D    E+L           P  H+ L  +  
Sbjct: 192 KAVLSVMRYWLDMGIDGLRLDAIPYLIERDGTNNENL-----------PETHDVLKLIRA 240

Query: 239 DV---FTPRGLMTVGEMSSTSLEHCQRY------AALTGSELSMTFNFHHLKVDYPGGEK 289
           ++   +  R L+          E  Q Y        + G E  M F+F  +   Y     
Sbjct: 241 EIDANYPDRMLLAEANQWP---EDTQLYFGDVDAQGMNGDECHMAFHFPLMPRMY----- 292

Query: 290 WTLAKPDFVALKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEY---------- 339
             LA+ D   +  + R   +   N  W A+F  NHD+  +      E +Y          
Sbjct: 293 MALAQEDRFPITDILRQTPEIPANCQW-AIFLRNHDELTLEMVTDKERDYLWNYYAADRR 351

Query: 340 -RV----------------PAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDV 382
            R+                   ++L  +L  M GTP +Y G+EIGM +            
Sbjct: 352 ARINLGIRRRLAPLVERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD------------ 399

Query: 383 ESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWSNGDNAGFTAGE-------PWIG 435
              N++                     RD  RTPMQWS   N GF+  +       P + 
Sbjct: 400 ---NIYL------------------GDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMD 438

Query: 436 LGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWK 495
               YQ +NVE    D  S+    ++++A+RKQ      G  + L P++  +  Y RE+ 
Sbjct: 439 PQYGYQSVNVETQAGDPHSLLNWTRRMLAVRKQSKAFGRGTLKMLSPSNRRILAYTREYT 498

Query: 496 G-----QTLLVIANLSREIQ 510
           G     + +L +AN+SR  Q
Sbjct: 499 GPDGKHEIILCVANVSRSAQ 518


Lambda     K      H
   0.320    0.136    0.448 

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: 1623
Number of extensions: 82
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 1114
Length adjustment: 41
Effective length of query: 510
Effective length of database: 1073
Effective search space:   547230
Effective search space used:   547230
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: 55 (25.8 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