GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-2-hydroxyglutarate dehydrogenase (EC 1.1.99.2) (characterized)
to candidate Echvi_3348 Echvi_3348 Predicted dehydrogenase

Query= BRENDA::Q9H9P8
         (463 letters)



>FitnessBrowser__Cola:Echvi_3348
          Length = 400

 Score =  363 bits (932), Expect = e-105
 Identities = 189/415 (45%), Positives = 273/415 (65%), Gaps = 18/415 (4%)

Query: 48  SFDIVIVGGGIVGLASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPES 107
           ++DI IVGGGIVGLA+   +I + P L + +LEKE +LA HQTG+NSGVIHSG+YYKP S
Sbjct: 2   TYDIAIVGGGIVGLATGLKIIQQRPELKVVILEKEHELAKHQTGNNSGVIHSGLYYKPGS 61

Query: 108 LKAKLCVQGAALLYEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLI 167
           LKA  C+ G   L ++C+++ I ++  GK++VA + E++P LQ L ++GLQNG+ G R I
Sbjct: 62  LKATNCISGYHELIQFCEEENIPFEITGKVVVATKDEQLPLLQNLLKRGLQNGLKGTRQI 121

Query: 168 QQEDIKKKEPYCRGLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKE 227
             +++K+ EPYC+G+ A+  P TGIVDY++VAL++ + F+  GG +L + +VK I   K 
Sbjct: 122 TLDELKEYEPYCKGVAALHVPQTGIVDYKKVALAYGEKFKSLGGEILLDHQVKKIN-HKA 180

Query: 228 SPSRSIDGMQYPIVIKNTKGEEIRCQYVVTCAGLYSDRISELSG-CTPDPRIVPFRGDYL 286
           + +  I           T G+ I  + ++ CAGLYSD++++++G    D +I+PFRG+Y 
Sbjct: 181 NQTELI-----------TTGKTILSRLMINCAGLYSDKVADMNGELDLDVKIIPFRGEYY 229

Query: 287 LLKPEKCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSAT 346
            LK E+ YLVK  IYPVPD  FPFLGVHFT  M G +  GPNAV+AFKREGY+  DF+  
Sbjct: 230 KLKKEREYLVKNLIYPVPDPNFPFLGVHFTRMMKGGVEAGPNAVMAFKREGYKRTDFNLK 289

Query: 347 DVMDIIINSGLIKLASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRA 406
           +  + I   GL K+A++ +  G+ E Y++    A    LQ+ IP+I   D++ G AGVRA
Sbjct: 290 EFRESITWPGLQKVAAKYWKTGIGEYYRSFSKAAFTTALQELIPDIKEDDLVDGGAGVRA 349

Query: 407 QALDRDGNLVEDFVFDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEVQQRF 461
           QA DR G L++DF             ++V NAPSPAATSS++I G ++    +RF
Sbjct: 350 QACDRTGGLLDDFAITE-----NTHAINVLNAPSPAATSSLSIGGTVSARALKRF 399


Lambda     K      H
   0.321    0.140    0.420 

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: 479
Number of extensions: 14
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: 463
Length of database: 400
Length adjustment: 32
Effective length of query: 431
Effective length of database: 368
Effective search space:   158608
Effective search space used:   158608
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 (21.8 bits)
S2: 51 (24.3 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