GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Pseudomonas fluorescens GW456-L13

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate PfGW456L13_3396 Fumarylacetoacetate hydrolase family protein

Query= metacyc::MONOMER-16233
         (285 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3396
          Length = 283

 Score =  136 bits (343), Expect = 5e-37
 Identities = 93/250 (37%), Positives = 131/250 (52%), Gaps = 19/250 (7%)

Query: 37  ALAAAKGADVA-----SLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIPTEPM 91
           A+AA +G         SLPL   + R   P++ I ++V  G NY  H +E  L  P +P+
Sbjct: 38  AVAAGRGISSVRFAGPSLPL--SKVRLLPPIEPINRVVVAGANYAKHLVEFGLQAPAQPV 95

Query: 92  MFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDV 151
            F+KA  +L G ND +  P  +   D EVEL  VIG     +  +  L+ V GY + NDV
Sbjct: 96  AFLKAYGALIGANDSIRFPPLTEELDHEVELVAVIG--TEEIDLENPLACVLGYTVGNDV 153

Query: 152 SERFNQKQR----GTQWSKGKGHDTFCPVGPWLVTPDEV--GDPQDLDMHLNVNGTRMQT 205
           S R  Q+      G      K  D    +GPW+VT DE   G P+ L + L VNG   Q 
Sbjct: 154 SARDLQRSGPAGIGMDLFAAKSQDQTTGLGPWIVTKDEFPEGSPR-LRLTLKVNGEVRQD 212

Query: 206 GNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELGIEK 265
           G+T  M ++V QLI +V +  +   GD++ TG+P GVG G     ++LK GDV+E  +E 
Sbjct: 213 GSTGEMTWDVGQLIRFVQQRSSFASGDVLFTGSPAGVGMG---TGLFLKEGDVVEASVEG 269

Query: 266 LGTQRQQVSE 275
           +GT R  VS+
Sbjct: 270 IGTLRNVVSK 279


Lambda     K      H
   0.316    0.137    0.411 

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: 221
Number of extensions: 15
Number of successful extensions: 5
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
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: 42 (22.0 bits)
S2: 47 (22.7 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