GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Marinobacter adhaerens HP15

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2987 HP15_2931 glycerate dehydrogenase

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



>FitnessBrowser__Marino:GFF2987
          Length = 320

 Score =  155 bits (391), Expect = 2e-42
 Identities = 105/284 (36%), Positives = 149/284 (52%), Gaps = 9/284 (3%)

Query: 28  DATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIV 87
           D T  D  +  ++  D  + + V +T    +    LK ++ ++ G +  D A     GI 
Sbjct: 40  DRTTPDQILERIRGFDTVLVNKVVLTREHFDACPELKTIAVVATGLNNIDQAAAKDHGIK 99

Query: 88  LANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFG---VDVQGKTL 144
           + N  +    + A    +L+LA A R+++    V+AGHW  S    L     ++++G+TL
Sbjct: 100 VMNVTNYGRSTVAQHTMALMLALATRLLDYTRDVQAGHWGKSDMFCLMDHPIMELEGRTL 159

Query: 145 GIVGLGRIGGAVARRAALGFNMKVLYTNRSAN-PQAEEAYGARRVELAELLATADFVCLQ 203
           GIVG G +G  VA RAA  F MKVL   R    P   + Y   R+ L ELL  AD V L 
Sbjct: 160 GIVGYGDLGQGVAERAA-AFGMKVLLGARPGQEPGVVDGYS--RIPLDELLPQADVVSLH 216

Query: 204 VPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEP 263
             LT ET+ LIGA ELK MK  ++LIN SRG  V+E+AL +AL+ G I GAG DV   EP
Sbjct: 217 CLLTDETRDLIGARELKMMKPDSLLINTSRGGLVNEQALADALRAGEIGGAGFDVLTEEP 276

Query: 264 LPSDSPLL--KLANVVALPHIGSATHETRHAMARNAAENLVAAL 305
             + +PLL   + N++  PH   A+ E R  +    A NL + L
Sbjct: 277 PRNGNPLLADDIPNLIVTPHSAWASREARQRIVGITAVNLKSVL 320


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: 215
Number of extensions: 7
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: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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