GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Paraburkholderia bryophila 376MFSha3.1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate H281DRAFT_04333 H281DRAFT_04333 Lactate dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_04333
          Length = 329

 Score =  235 bits (599), Expect = 1e-66
 Identities = 137/308 (44%), Positives = 187/308 (60%), Gaps = 5/308 (1%)

Query: 1   MKKIVAWKSLPEDVLAYLQQHAQVV--QVDATQHDAFVAALKDADGGIGSSVKITPAMLE 58
           M+KI+  + +  DV+  L+Q+  V   Q D    +     L D DG + +   +   +L 
Sbjct: 1   MQKILVARPIFPDVIERLKQYFDVDWNQGDVLSAEELKRRLVDKDGALTAGDPVGAEVLA 60

Query: 59  GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
            A RL+ +S ++VG++ FD+A      ++  NTPDVL ESTAD  ++L++A+ARR+ E  
Sbjct: 61  AAPRLRVVSNMAVGYNNFDMAAFNAANVLGTNTPDVLNESTADFGWALMMAAARRIAESE 120

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS-ANP 177
            W++AG WQ        G D+ G TLG++G+GRIG A+ARRA  GFNM+V+Y NRS   P
Sbjct: 121 HWLRAGKWQKWAYDGFLGGDIHGSTLGVIGMGRIGQALARRAK-GFNMQVIYHNRSRVAP 179

Query: 178 QAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATV 237
           + E    A  V   +LL  AD V L +P T E  H IGAAEL  MK +A L N +RG  V
Sbjct: 180 EIEAELNAEYVSKQDLLRRADHVVLVLPYTKENHHTIGAAELALMKPTATLTNIARGGIV 239

Query: 238 DEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNA 297
           D+ AL+EAL++G I  AGLDVFE EP   +  LL + N+V  PHI SAT  TR AMA  A
Sbjct: 240 DDAALVEALRSGQIAAAGLDVFEGEP-NLNPDLLSVPNIVLTPHIASATEATRRAMANLA 298

Query: 298 AENLVAAL 305
           A+NL+A L
Sbjct: 299 ADNLIAGL 306


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: 236
Number of extensions: 12
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: 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