GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas putida KT2440

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PP_3376 PP_3376 putative phosphonate dehydrogenase

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



>FitnessBrowser__Putida:PP_3376
          Length = 320

 Score =  348 bits (892), Expect = e-100
 Identities = 186/317 (58%), Positives = 234/317 (73%), Gaps = 3/317 (0%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLE 58
           K+IV +K L +D++A LQ   +V  VD TQ DA      AL  A G +G+S+++  ++L+
Sbjct: 3   KRIVLYKRLSDDLMARLQDRVEVTWVDTTQPDALARLRDALPGAHGLLGASLRLDASLLD 62

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
            A +L+ +S++SVG D +D+A+L+RRG++L NTPDVLTE+TADT F+LILA+ARRVVELA
Sbjct: 63  LAPQLEVVSSVSVGVDNYDIAELSRRGVMLTNTPDVLTETTADTGFALILATARRVVELA 122

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178
            WV+ G WQ ++GPA FG DV GKTLGIVG+GRIG A+ARRAA GF M+VLY ++ A P+
Sbjct: 123 NWVRDGRWQANLGPAHFGSDVHGKTLGIVGMGRIGEALARRAAAGFGMRVLYHSQRAKPE 182

Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238
            E  Y A +  L ELL  ADFVCL VPL+  T+ LIGA EL  MK  AIL+N SRG  VD
Sbjct: 183 VEARYAACQCSLDELLQQADFVCLTVPLSASTEGLIGARELALMKPDAILVNISRGRVVD 242

Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298
           E+ALIEAL+   I GAGLDVF  EPLP DSPLL+L NVVA PHIGSAT ETR AMAR A 
Sbjct: 243 EQALIEALRARRIRGAGLDVFVHEPLPIDSPLLQLDNVVATPHIGSATEETRQAMARCAV 302

Query: 299 ENLVAALDGTLTSNIVN 315
           +NL++AL G    N+VN
Sbjct: 303 DNLLSALAGERPVNLVN 319


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: 243
Number of extensions: 5
Number of successful extensions: 2
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: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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: 48 (23.1 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