GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pedobacter sp. GW460-11-11-14-LB5

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate CA265_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS12240
          Length = 311

 Score =  132 bits (333), Expect = 8e-36
 Identities = 100/313 (31%), Positives = 148/313 (47%), Gaps = 26/313 (8%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKIT-------P 54
           K ++  +++ E+ LA LQ++  V     T +D   A LKD    +     IT        
Sbjct: 3   KNVLLLETIAEEALALLQENVNVF----TGYDE--AGLKDTLNNVEVHAIITRGKKHIDK 56

Query: 55  AMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRV 114
            +++    L+  +   VG D  DV + + R I + N P     + A+   +L+L   R +
Sbjct: 57  TLMDACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDM 116

Query: 115 VELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174
                 VK  +W      A  G ++ GKTLGI+GLG IG  VA+     F MKVL  +RS
Sbjct: 117 HRSVNHVKQNNWNWRNQYA--GDELNGKTLGILGLGNIGKRVAKLGD-AFGMKVLCWSRS 173

Query: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234
                        + L E+L  +D V L +PL+ ET  +IGA++L  MK  A LIN +RG
Sbjct: 174 VQD----------LPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTARG 223

Query: 235 ATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMA 294
           A +D  AL++AL  GTI G   DV   EP      +++  N +  PH  S T  T   M 
Sbjct: 224 ALIDHAALLDALNAGTIAGFAADVLPDEPPLQSLAVVQHPNALVTPHAASLTASTYKQMC 283

Query: 295 RNAAENLVAALDG 307
                N+++ L G
Sbjct: 284 LLTVRNVLSVLAG 296


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: 196
Number of extensions: 10
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: 311
Length adjustment: 27
Effective length of query: 294
Effective length of database: 284
Effective search space:    83496
Effective search space used:    83496
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