GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Acidovorax sp. GW101-3H11

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ac3H11_2341 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2341
          Length = 322

 Score =  166 bits (419), Expect = 9e-46
 Identities = 110/278 (39%), Positives = 147/278 (52%), Gaps = 9/278 (3%)

Query: 28  DATQHDAFVAALKDADGGI--GSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRG 85
           D      F+AA      G+   +S+ +   ++     L+ +S+  VGFD  D+   T RG
Sbjct: 35  DQADPQGFLAAQGAEFSGVVTTASIGLQGEVIAALPHLQVISSFGVGFDALDIGTATARG 94

Query: 86  IVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLG 145
           + +  TP VL +  AD  F+L+L  +R +     +V+ G W  +      G  V GK LG
Sbjct: 95  VQVGYTPGVLNDCVADMAFALMLDVSRGIAASDRFVRQGQWPKA--RFALGTRVSGKRLG 152

Query: 146 IVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVP 205
           IVG+GRIG AVA RAA GF M+V Y NR        +Y      LA+    AD++ L V 
Sbjct: 153 IVGMGRIGQAVAERAA-GFRMEVSYHNRRPAEGCALSYFESLTALAQW---ADYLVLTVA 208

Query: 206 LTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLP 265
               T+HL+    L ++     LIN +RG+ VDE ALI+AL    I GAGLDVF+ EP  
Sbjct: 209 GGAGTRHLVNRDVLDALGPQGYLINVARGSVVDEAALIDALAERRIAGAGLDVFDNEP-Q 267

Query: 266 SDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVA 303
             + L+ L NVV  PH  SATHETR AMA    ENL A
Sbjct: 268 VPAALMALDNVVLTPHTASATHETRRAMADLVLENLHA 305


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: 218
Number of extensions: 10
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: 322
Length adjustment: 28
Effective length of query: 293
Effective length of database: 294
Effective search space:    86142
Effective search space used:    86142
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