GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2272
          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 (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