GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudomonas stutzeri RCH2

Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate GFF1392 Psest_1429 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit

Query= metacyc::MONOMER-11683
         (330 letters)



>FitnessBrowser__psRCH2:GFF1392
          Length = 329

 Score =  163 bits (412), Expect = 6e-45
 Identities = 116/322 (36%), Positives = 161/322 (50%), Gaps = 17/322 (5%)

Query: 19  MYRTMLLARKIDERMWLLNRSGKIPFVISCQG-----------QEAAQVGAAFALDREMD 67
           MY  ML +R ++E +  +   GK P     +G           QE   VG    L+ E D
Sbjct: 12  MYEQMLTSRYMEESIERIYMEGKTPVFNMAKGPIPGEMHLSNGQEPCAVGVCAHLEAE-D 70

Query: 68  YVLPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTT 127
            V   +R   + +A G+   ++M   F KA    SGGR   GH      R+    S +  
Sbjct: 71  IVTATHRPHHIAVAKGVDLNEMMAEIFGKATGL-SGGRG--GHMHLFDGRVNFSCSGIIA 127

Query: 128 Q-VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYA 186
           + +  AVG AL+ +M+ K   A    GEG++NQG FHE  N AA+ KLPV+F+ E+N + 
Sbjct: 128 EGMGPAVGAALSRQMQGKPGVAVSFIGEGAANQGAFHETLNLAALWKLPVVFVIEDNAWG 187

Query: 187 ISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETIS 246
           ISV             RA  YGMPGV V  NDP  V++A  EA ERAR G GPTLIE  +
Sbjct: 188 ISVAKASATCIAQHHVRAAAYGMPGVFVENNDPDGVFRAAGEAIERARAGGGPTLIEIET 247

Query: 247 YRLTPHSSDDDDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVN 306
           YRL  H   D + +YR   E +   K DP+  Y+  L + G+LS+   + +       ++
Sbjct: 248 YRLAGHFMGDGE-TYRPEGEKDGLIKKDPIPGYRQRLIDEGVLSEAQAEDIAARARGRID 306

Query: 307 EATDEAENAPYAAPESALDYVY 328
           EA   A  +PY  PE AL+ V+
Sbjct: 307 EAVQFARESPYPRPEEALEKVF 328


Lambda     K      H
   0.316    0.132    0.377 

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: 245
Number of extensions: 10
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: 330
Length of database: 329
Length adjustment: 28
Effective length of query: 302
Effective length of database: 301
Effective search space:    90902
Effective search space used:    90902
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 (21.6 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