GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gudD in Pseudomonas fluorescens FW300-N2C3

Align Probable glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (uncharacterized)
to candidate AO356_25015 AO356_25015 glucarate dehydratase

Query= curated2:Q9RDE9
         (431 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_25015 AO356_25015
           glucarate dehydratase
          Length = 424

 Score =  385 bits (988), Expect = e-111
 Identities = 201/424 (47%), Positives = 272/424 (64%), Gaps = 8/424 (1%)

Query: 5   LTITAVHLTPILVADPPLLNTQGVHQPYTPRLIVEVETADGVTGVGETYGDAKYLELARP 64
           + I  V +TPI   DPPLLN  G+H+P+  R I+E+E+ +G  G+GE+YGDA  L + + 
Sbjct: 1   MKIKRVTVTPIAFRDPPLLNASGIHEPFALRSIIEIESDNGYIGLGESYGDAPALAIQQQ 60

Query: 65  FAAKLVGRQVSDLNGLFTLADEVAVDSSRVFGQVDVGGLRGVQTADKLRLSVVSGFEVAC 124
             ++L+G    +LN L  +    A  +++    V    L     A K   +  S FEVAC
Sbjct: 61  LQSQLIGLDPFNLNQLRAIVQ--ATVAAQKPASVAGAELAPGSHASKAVSNAYSAFEVAC 118

Query: 125 LDALGKALGLPVHALLGGKVRDAVEYSAYLFYKWADHPEGVASEKDDWGAAVDPAGVVAQ 184
           LD     L +P+  LLGG +RD + +SAYLF+K+A+H +      D WG A++   +VAQ
Sbjct: 119 LDLQAHYLNVPLVDLLGGAIRDEIPFSAYLFFKYAEHIDS-PYPPDSWGEALNEQQIVAQ 177

Query: 185 ARAFTERYGFTSFKLKGGVFPPEEEIAAVKALAEAFPGHPLRLDPNGAWSVETSLKVAAE 244
           AR   + YGF S KLK G   PE E+A +KAL +AFPG+PLR+DPN  WS+ETS+++A  
Sbjct: 178 ARRMIQDYGFKSIKLKAGALDPEHEVACIKALKQAFPGYPLRIDPNANWSLETSIRMAEL 237

Query: 245 LGDVLEYLEDPALGTPAMAEVAAKTGVPLATNMCVTTFAEIQEAFTKGAVQVVLSDHHYW 304
           LGD L+Y EDP  G   MAE+  +TG+PLATNM VT F E + +    +VQ+VL+DHHYW
Sbjct: 238 LGDDLQYYEDPTPGLEGMAELHKRTGLPLATNMVVTDFDEFRRSVALDSVQIVLADHHYW 297

Query: 305 GGLRNTQQLAAVCRTFGVGVSMHSNTHLGISLAAMTHVAATVPDLHHACDSHYPWQSED- 363
           GGLR+TQ LA +C TFG+GVSMHSN+HLGISL AM HVAA VP+L +ACD+HYPWQ  D 
Sbjct: 298 GGLRDTQALAKMCSTFGLGVSMHSNSHLGISLMAMAHVAAAVPNLDYACDTHYPWQEPDE 357

Query: 364 --VLTERLAFDGGKVAVSDAPGLGVALDRERLAFLHRRWLDDDGTLRDRDDAAAMRVADP 421
             +   +L    G V ++ APGLG+ LDR++L  LH ++L     +R RDD   M+   P
Sbjct: 358 EVIKGGKLPIVDGCVKITRAPGLGLELDRDQLGKLHDQFLSCG--IRQRDDVRQMQRYRP 415

Query: 422 EWVT 425
           EW T
Sbjct: 416 EWKT 419


Lambda     K      H
   0.319    0.135    0.410 

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: 525
Number of extensions: 20
Number of successful extensions: 4
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: 431
Length of database: 424
Length adjustment: 32
Effective length of query: 399
Effective length of database: 392
Effective search space:   156408
Effective search space used:   156408
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: 51 (24.3 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