GapMind for catabolism of small carbon sources

 

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

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Pf6N2E2_5333 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= reanno::acidovorax_3H11:Ac3H11_2991
         (396 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5333
          Length = 378

 Score =  258 bits (660), Expect = 2e-73
 Identities = 149/373 (39%), Positives = 212/373 (56%), Gaps = 6/373 (1%)

Query: 19  DALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAMGYLAH 78
           +  RD+VR F + E  P  +  +K       LW K G+ G+L   +PE YGG    +L  
Sbjct: 12  ELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEAYGGLDADFLYS 71

Query: 79  MVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAMSEPG 138
            V +EEI R   + G+ +  HS++    I   G+EA K KYL KL+SGE V A+AM+EPG
Sbjct: 72  TVVIEEIGRLGLT-GIGFSLHSDIVAPYILHYGSEALKHKYLPKLVSGEMVTAIAMTEPG 130

Query: 139 AGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAFLIEKG 198
           AGSD+  +K  A   G  Y++NGSK +ITNG  AD ++V AKT+P+ GA+G + FL+E G
Sbjct: 131 AGSDLQGVKTTAVLDGDEYVINGSKTFITNGFLADLVIVVAKTDPKAGAKGTSLFLVEAG 190

Query: 199 MKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERAVLTGG 258
             GF   ++L+K+GM+   T EL FQDV VP EN+LG    G   LM  L  ER  +  G
Sbjct: 191 TLGFEKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLTVAIG 250

Query: 259 PLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAKNLDML 318
            L   ++ +   + Y  +RK FG+SI +FQ  + K+A+M T +Q GR F     + L + 
Sbjct: 251 GLASAEAALQWTLDYTRERKAFGKSIADFQNTRFKLAEMATEIQIGRVFVDRCLE-LHLQ 309

Query: 319 GTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEIGAG 378
           G   V       A    W  +    +  E VQ++GG G++ EYP+ R W DA++  I AG
Sbjct: 310 GKLDV----PTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAG 365

Query: 379 TSEIRRMLIGREL 391
           T+EI + +I R L
Sbjct: 366 TNEIMKEIIARSL 378


Lambda     K      H
   0.318    0.136    0.400 

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: 394
Number of extensions: 20
Number of successful extensions: 3
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: 396
Length of database: 378
Length adjustment: 30
Effective length of query: 366
Effective length of database: 348
Effective search space:   127368
Effective search space used:   127368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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