GapMind for catabolism of small carbon sources

 

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

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Pf1N1B4_2272 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2272 D-3-phosphoglycerate
           dehydrogenase (EC 1.1.1.95)
          Length = 409

 Score =  130 bits (328), Expect = 4e-35
 Identities = 96/279 (34%), Positives = 142/279 (50%), Gaps = 11/279 (3%)

Query: 45  GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104
           GI S  ++T  + + A +L A+    +G +Q D+     RGI + N P   T S A+ V 
Sbjct: 58  GIRSRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVL 117

Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164
           +  +   R + E       G W   I  A    +++GK LGIVG G IG  ++  A  G 
Sbjct: 118 AEAILLLRGIPEKNASCHRGGW---IKSAANSFEIRGKKLGIVGYGSIGTQLSVLAE-GL 173

Query: 165 NMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKK 224
            M+V + +         A   +   L ELL  +D V L VP T  T+ +IG  E++++KK
Sbjct: 174 GMQVYFYDTVTKLPLGNA--TQVGNLHELLGMSDIVTLHVPETAATQWMIGEKEIRAIKK 231

Query: 225 SAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPS----DSPLLKLANVVALP 280
             ILINA+RG  V+  AL +A+++  + GA +DVF  EP  +    +SPL  L NV+  P
Sbjct: 232 GGILINAARGTVVELDALADAIKDKHLIGAAIDVFPVEPRSNEEEFESPLRGLDNVILTP 291

Query: 281 HIGSATHETRHAMARNAAENLVAALD-GTLTSNIVNREV 318
           HIG +T E +  +    AE LV   D GT  S++   EV
Sbjct: 292 HIGGSTAEAQANIGLEVAEKLVKYSDNGTSVSSVNFPEV 330


Lambda     K      H
   0.317    0.131    0.366 

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: 270
Number of extensions: 15
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: 321
Length of database: 409
Length adjustment: 29
Effective length of query: 292
Effective length of database: 380
Effective search space:   110960
Effective search space used:   110960
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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