GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Shewanella amazonensis SB2B

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate 6938708 Sama_2811 glycerate dehydrogenase (RefSeq)

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



>FitnessBrowser__SB2B:6938708
          Length = 317

 Score =  130 bits (327), Expect = 4e-35
 Identities = 97/292 (33%), Positives = 140/292 (47%), Gaps = 13/292 (4%)

Query: 28  DATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIV 87
           D T  +  ++    A   + +   +  A LE    L+ +  ++ G +  DVA   R GI 
Sbjct: 32  DRTPKELILSRAAGARFLLTNKTVLDAATLEAMPSLEYIGVLATGTNVVDVAAAKRLGIA 91

Query: 88  LANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV------DVQG 141
           + N P    ++ A   F+ +L    RV    + V  G W    G A F         + G
Sbjct: 92  VTNVPGYGPDAVAQMGFAHVLHHMSRVSAHHDAVTQGQWS---GQADFCFTLGQLESLSG 148

Query: 142 KTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVC 201
           KTLG+VG G I   +AR   + F MK+L  +RS      E  GA+ V L  L A +D + 
Sbjct: 149 KTLGLVGFGDIARQMAR-IGMAFGMKLLVHSRSKPTDLPE--GAKFVALDTLFAESDVLS 205

Query: 202 LQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFET 261
           L  PLT +T+ ++    L  MK+ A+LIN +RG  VDE AL +AL  G +  AG+DV  T
Sbjct: 206 LHCPLTDDTRDMVNRESLALMKQGALLINTARGGLVDEVALADALNAGRVR-AGVDVLST 264

Query: 262 EPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNI 313
           EP   ++PLL  AN+   PH   AT + R  +   A ENL A   G   + +
Sbjct: 265 EPPAPNNPLLHAANISITPHNAWATVKARQKLLDIAVENLRAFSRGESVNRV 316


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: 198
Number of extensions: 6
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: 317
Length adjustment: 28
Effective length of query: 293
Effective length of database: 289
Effective search space:    84677
Effective search space used:    84677
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