GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26445
          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:

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