GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lhgD in Pseudomonas fluorescens FW300-N2C3

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate AO356_26445 AO356_26445 FAD-dependent oxidoreductase

Query= SwissProt::Q9LES4
         (483 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26445 AO356_26445
           FAD-dependent oxidoreductase
          Length = 368

 Score =  353 bits (907), Expect = e-102
 Identities = 185/398 (46%), Positives = 250/398 (62%), Gaps = 40/398 (10%)

Query: 80  VDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKA 139
           +D VV+GAGVVGLAVARE++L G EVL+++A  + G  TSSRNSEV+HAGIYYPP SLKA
Sbjct: 5   IDCVVVGAGVVGLAVAREMALAGHEVLVIEAGEAIGIGTSSRNSEVIHAGIYYPPGSLKA 64

Query: 140 KFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGF 199
           + CV GR  LY YC  + +  +K GKLIVA   +++ +L +L+  G  N V  LR+L+  
Sbjct: 65  QLCVEGRHALYAYCDSHGVSTRKTGKLIVAKDEAQVRQLQVLLERGLVNGVEDLRLLDRE 124

Query: 200 EAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHAT 259
           +A+ +EP L C+ AL SP +GI+D+H  ML+                  LQG+A+    T
Sbjct: 125 QALALEPALECIAALYSPSTGIVDSHGLMLA------------------LQGDAEAAGTT 166

Query: 260 FSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKRLH 319
            ++ + +++ RV      L V             A + L   L++N+AGL A ALA+R+ 
Sbjct: 167 IAFYSPLISARVTADGFLLDVG----------GAAPMVLSCRLLINAAGLKAPALARRME 216

Query: 320 GLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVE 379
           GL  + VP  +  +G YF+L+  K  PF  L+YP PE  GLGVH+T+DL G  +FGPD E
Sbjct: 217 GLAQQTVPRDYLCKGSYFSLA--KRAPFTHLIYPAPEAAGLGVHMTLDLGGQARFGPDTE 274

Query: 380 WIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQS 439
           W+E            DYRV+P R+  FY  IR Y+PDL D SL+PGYSGIRPK+S P + 
Sbjct: 275 WVEAE----------DYRVDPSRANAFYAAIRSYWPDLPDNSLQPGYSGIRPKISAPGEP 324

Query: 440 PADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477
            +DF+I  E  H VPGL+NLFGIESPGLT+ LAIA+ +
Sbjct: 325 ASDFLISSERLHNVPGLINLFGIESPGLTACLAIAKRV 362


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: 495
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: 368
Length adjustment: 32
Effective length of query: 451
Effective length of database: 336
Effective search space:   151536
Effective search space used:   151536
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 paper from 2022 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