GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Shewanella loihica PV-4

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 5210768 Shew_3196 D-3-phosphoglycerate dehydrogenase (RefSeq)

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



>FitnessBrowser__PV4:5210768
          Length = 409

 Score =  146 bits (369), Expect = 7e-40
 Identities = 100/288 (34%), Positives = 150/288 (52%), Gaps = 11/288 (3%)

Query: 33  DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91
           +  +A++KDA   GI S  ++T A+L+ A +L ++    +G +Q D+A   + GI + N 
Sbjct: 45  EELLASIKDAHFVGIRSRTQLTKAVLDKAEKLVSIGCFCIGTNQVDLAAAEKLGIPVFNA 104

Query: 92  PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151
           P   T S A+ V   I+   R + +       G W  S   +    + +GKTLG++G G 
Sbjct: 105 PFSNTRSVAELVLGEIIMLLRGIPQRNALAHRGGWLKSANGSF---EARGKTLGVIGYGH 161

Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211
           IG  +   A     M+V++ +         A     +E  +LL+ AD V L VP TP+TK
Sbjct: 162 IGTQLGILAET-LGMRVIFFDIEDKLPLGNAQQIHSLE--QLLSLADVVSLHVPETPQTK 218

Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSD---- 267
           ++IG+ EL +M++ +ILINASRG  VD  AL EA++   I GA +DVF  EP  +D    
Sbjct: 219 NMIGSKELAAMRQGSILINASRGTVVDIDALAEAIRGDHIVGAAIDVFPVEPKSNDDEFV 278

Query: 268 SPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
           SPL  L NV+  PH+G +T E +  +    A  L    D   T   VN
Sbjct: 279 SPLRGLDNVLLTPHVGGSTQEAQENIGIEVAGKLAKYSDNGSTMTAVN 326


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: 260
Number of extensions: 14
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