GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lhgD in Pseudomonas fluorescens FW300-N2E2

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Pf6N2E2_261 Aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= SwissProt::Q9LES4
         (483 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_261 Aminobutyraldehyde
           dehydrogenase (EC 1.2.1.19)
          Length = 369

 Score =  348 bits (893), Expect = e-100
 Identities = 185/400 (46%), Positives = 251/400 (62%), Gaps = 40/400 (10%)

Query: 81  DTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAK 140
           + VV+GAGVVGLAVARE++  G +VL+++AA + G   SSRNSEV+HAGIYYP  SLKA+
Sbjct: 6   ECVVVGAGVVGLAVAREMARAGHDVLLIEAAEAIGMGISSRNSEVIHAGIYYPLGSLKAQ 65

Query: 141 FCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFE 200
            CV GR  LY YC  + +  +++GKLIVAT  +++  L+ L+  G +N V  LR+L+  +
Sbjct: 66  LCVEGRHRLYTYCESHGVATRRLGKLIVATDQAQVGGLETLLERGLKNGVDDLRLLDQEQ 125

Query: 201 AMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATF 260
           A  +EP L CV AL SP +GI+D+H+ ML+                  LQG+A+   A  
Sbjct: 126 AQALEPALACVAALYSPSTGIVDSHALMLA------------------LQGDAEAAGANI 167

Query: 261 SYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHG 320
           +++T +L  R+      L +  T          AQ+ L   L++N+AGL A ALA+R+ G
Sbjct: 168 AFHTPLLGARIITGGFILELGGT----------AQMTLSCRLLINAAGLQAPALARRIEG 217

Query: 321 LDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEW 380
           L+ ++VP     +G YF+L+G    PF  LVYP PE  GLG+H+T+DL G  +FGPD EW
Sbjct: 218 LEMQWVPEDFLCKGNYFSLAG--RAPFRHLVYPAPEAAGLGIHMTLDLAGQARFGPDTEW 275

Query: 381 IECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSP 440
           ++C           DYRV+P R+E FYP IR Y+P L D SL+P YSGIRPK+S P +  
Sbjct: 276 VDCE----------DYRVDPARAEAFYPAIRNYWPGLPDQSLQPAYSGIRPKISAPGEPA 325

Query: 441 ADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIANK 480
            DFVI  E  H VPGL+NL GIESPGLTS LAIA  +  +
Sbjct: 326 RDFVISSEAEHRVPGLINLLGIESPGLTSCLAIASRVRQR 365


Lambda     K      H
   0.318    0.136    0.401 

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: 471
Number of extensions: 22
Number of successful extensions: 4
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: 483
Length of database: 369
Length adjustment: 32
Effective length of query: 451
Effective length of database: 337
Effective search space:   151987
Effective search space used:   151987
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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