GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Burkholderia phytofirmans PsJN

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BPHYT_RS14520 BPHYT_RS14520 2-hydroxyacid dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS14520
          Length = 329

 Score =  236 bits (603), Expect = 4e-67
 Identities = 146/328 (44%), Positives = 195/328 (59%), Gaps = 9/328 (2%)

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

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

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS-ANP 177
            W++ G WQ     A  G D+ G TLG++G+GRIG A+ARRA  GF+M+V+Y NRS   P
Sbjct: 121 HWLRGGQWQKWAYDAFLGSDLHGSTLGVIGMGRIGQALARRAK-GFDMQVIYHNRSRVAP 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++  I  AGLDVFE EP   +  LL + NVV  PHI SAT  TR AMA  A
Sbjct: 240 DDAALVEALRSKQIAAAGLDVFEGEP-NLNQDLLSVPNVVLTPHIASATEATRRAMANLA 298

Query: 298 AENLVAAL-DGTLTS---NIVNREVLSK 321
           A+NL+A L +G       N VN EV+ K
Sbjct: 299 ADNLIAGLGEGPRAGRPPNPVNPEVIGK 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: 257
Number of extensions: 16
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