GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Mariniradius saccharolyticus AK6

Align Catabolic NAD-specific glutamate dehydrogenase RocG; NAD-GDH; Glutamate dehydrogenase; GlutDH; Trigger enzyme RocG; EC 1.4.1.2 (characterized)
to candidate WP_008623896.1 C943_RS02640 Glu/Leu/Phe/Val dehydrogenase

Query= SwissProt::P39633
         (424 letters)



>NCBI__GCF_000330725.2:WP_008623896.1
          Length = 425

 Score =  379 bits (973), Expect = e-110
 Identities = 189/398 (47%), Positives = 262/398 (65%), Gaps = 3/398 (0%)

Query: 28  ALRKLGYPGDMYELMKEPQRMLTVRIPVKMDNGSVKVFTGYRSQHNDAVGPTKGGVRFHP 87
           A +KLG   ++Y ++K P + + V +P+ MDNG +KVF G R  H++ +GP KGG+RF P
Sbjct: 26  AAQKLGLSEEVYNVLKNPAKQVIVSLPITMDNGKIKVFEGIRVIHSNILGPAKGGIRFAP 85

Query: 88  EVNEEEVKALSIWMTLKCGIANLPYGGGKGGIICDPRTMSFGELERLSRGYVRAISQIVG 147
           +V+ +EV+AL+ WMT KC + ++PYGGGKGG+ C+PR MS GE+ERL R Y  A+  + G
Sbjct: 86  DVHLDEVRALAAWMTWKCAVVDIPYGGGKGGVRCNPREMSAGEIERLVRAYTLAMIDVFG 145

Query: 148 PTKDIPAPDVYTNSQIMAWMMDEYSRLREFDSPGFITGKPLVLGGSQGRETATAQGVTIC 207
           P KDIPAPD+ T  + MAW+MDEYS+         +TGKPLVLGGS GR  AT +GV + 
Sbjct: 146 PDKDIPAPDMGTGPREMAWLMDEYSKAHGMTVNAVVTGKPLVLGGSLGRTEATGRGVMVT 205

Query: 208 IEEAVKKKGIKLQNARIIIQGFGNAGSFLAKFMHDAGAKVIGISDANGGLYNPDGLDIPY 267
              A++K  I    A   +QGFGN GS+ A+ + + G KV+ ISD +G  YN +G++I  
Sbjct: 206 ALAAMQKLKINPFQATCAVQGFGNVGSWAAQLLEERGLKVVSISDISGAYYNSNGINIQE 265

Query: 268 LLDKRDSFGMVTNLF--TDVITNE-ELLEKDCDILVPAAISNQITAKNAHNIQASIVVEA 324
            +  RD        +   + ++N  ELLE + D+LVPAA+ + IT  NA  I+A ++VE 
Sbjct: 266 AIAYRDGNKGTLEGYQGAEKLSNPMELLELEVDVLVPAAVEDVITIGNADKIKAKLIVEG 325

Query: 325 ANGPTTIDATKILNERGVLLVPDILASAGGVTVSYFEWVQNNQGYYWSEEEVAEKLRSVM 384
           ANGPT+  A  ILNE+G++ VPDILA+AGGVTVSYFEWVQN  GY W+ E V  +   +M
Sbjct: 326 ANGPTSAKADAILNEKGIMAVPDILANAGGVTVSYFEWVQNRLGYKWTAERVNRRSDRIM 385

Query: 385 VSSFETIYQTAATHKVDMRLAAYMTGIRKSAEASRFRG 422
             +F+ +YQ A  + V MR+AAY+  I K A+   FRG
Sbjct: 386 KDAFDHVYQAAVKYDVPMRIAAYIVAIDKVAKTYTFRG 423


Lambda     K      H
   0.317    0.134    0.390 

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: 509
Number of extensions: 15
Number of successful extensions: 2
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: 424
Length of database: 425
Length adjustment: 32
Effective length of query: 392
Effective length of database: 393
Effective search space:   154056
Effective search space used:   154056
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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