GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas fluorescens FW300-N2E3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AO353_02740 AO353_02740 hydroxyacid dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_02740
          Length = 329

 Score =  136 bits (343), Expect = 6e-37
 Identities = 101/293 (34%), Positives = 143/293 (48%), Gaps = 25/293 (8%)

Query: 29  ATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVL 88
           A +H+   A + D       S  +   +  G TRL AL   S G++  D+A   R G+ +
Sbjct: 42  AERHEVVCAFIND-----DLSAPVLERLAAGGTRLIALR--SAGYNHVDLACAKRLGLSI 94

Query: 89  ANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVG 148
              P     + A+   +LILA  RR+       + G +       L G D+ GKT+G+VG
Sbjct: 95  VRVPAYSPHAVAEHAVALILALNRRLYRAYNRTREGDFSLH---GLTGFDLFGKTVGVVG 151

Query: 149 LGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTP 208
            G+IG AV  +   GF  K+L  +   NPQ + A G R + L ELLA A  + L  PLT 
Sbjct: 152 TGQIG-AVFAKIMTGFGCKLLAYDPFPNPQVQ-ALGVRYLPLPELLAEAQIISLHCPLTA 209

Query: 209 ETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETE------ 262
           ++KHLI +  L  ++  A+LIN  RG  VD  ALI+AL++G +   GLDV+E E      
Sbjct: 210 DSKHLINSQSLAHLQPGAMLINTGRGGLVDTPALIDALKSGQLGYLGLDVYEEEAQLFFE 269

Query: 263 -----PLPSD--SPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGT 308
                PL  D  + LL   NV+   H    THE   A+A    +N+     GT
Sbjct: 270 DRSDRPLQDDVLARLLTFPNVIITAHQAFLTHEALAAIAMTTLQNITDWAAGT 322


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: 216
Number of extensions: 12
Number of successful extensions: 4
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: 329
Length adjustment: 28
Effective length of query: 293
Effective length of database: 301
Effective search space:    88193
Effective search space used:    88193
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