GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treC in Pseudomonas fluorescens FW300-N1B4

Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677 Trehalose synthase
           (EC 5.4.99.16)
          Length = 1113

 Score =  233 bits (595), Expect = 2e-65
 Identities = 172/560 (30%), Positives = 252/560 (45%), Gaps = 109/560 (19%)

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

Query: 65  YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE--SP 122
           YD+A Y  + P YGT+ D    + +A  RG+R+I ++V NHTS QHAWF+ A   +  S 
Sbjct: 74  YDIAEYRGVHPDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHAWFQRARKAKPGSA 133

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

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

Query: 239 DV---FTPRGLMTVGEMSSTSLEHCQRYAALT------GSELSMTFNFHHLKVDYPGGEK 289
           ++   +  R L+          E  Q Y   T      G E  M F+F  +   Y     
Sbjct: 241 EIDANYPDRMLLAEANQWP---EDTQLYFGNTDASGQKGDECHMAFHFPLMPRMY----- 292

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

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

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

Query: 436 LGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWK 495
               Y  +NVE    D  S+    ++L+A+RKQ      G  + L P++  +  Y RE+ 
Sbjct: 439 PLYGYLSVNVETQAGDPHSLLNWNRRLLAVRKQSKAFGRGTLKMLSPSNRRILAYTREFT 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: 1617
Number of extensions: 85
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: 1113
Length adjustment: 41
Effective length of query: 510
Effective length of database: 1072
Effective search space:   546720
Effective search space used:   546720
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 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