GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdhA in Acidovorax sp. GW101-3H11

Align NAD-specific glutamate dehydrogenase; NAD-GDH; EC 1.4.1.2; Surface-associated protein PGAG1 (uncharacterized)
to candidate Ac3H11_315 NADP-specific glutamate dehydrogenase (EC 1.4.1.4)

Query= curated2:B2RKJ1
         (445 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_315
          Length = 464

 Score =  502 bits (1292), Expect = e-146
 Identities = 252/434 (58%), Positives = 317/434 (73%), Gaps = 5/434 (1%)

Query: 13  KHPGESEFLQAVKEVLLSVEEVYNQHPEFEKNGIIERIVEPDRVFTFRVPWVDDQGKVQV 72
           ++PG+ EFLQAV EV+ S+     +HP + ++G++ER+VEP+R+  FRV WVDD G VQV
Sbjct: 33  RNPGQPEFLQAVTEVMESLWPFIAEHPRYAEHGLLERLVEPERIVMFRVSWVDDHGTVQV 92

Query: 73  NIGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLGFEQMFKNALTTLPMGGGKGGADFSPK 132
           N GYR+Q + AIGP+KGGIRFHPSVNLS+LKFL FEQ FKNALTTLPMGGGKGG+DF PK
Sbjct: 93  NRGYRIQHSMAIGPFKGGIRFHPSVNLSVLKFLAFEQTFKNALTTLPMGGGKGGSDFDPK 152

Query: 133 GKSEAEIMRFCQSFMTELWRNIGPDTDIPAGDIGVGGREVGYMFGMYKKLAREHTGTLTG 192
           G+S  E+MRFCQ+F++EL+R++G DTD+PAGDIGVGGREVG+M GM KKL+       TG
Sbjct: 153 GRSPGEVMRFCQAFVSELFRHVGADTDVPAGDIGVGGREVGFMAGMMKKLSNRADCVFTG 212

Query: 193 KGFEFGGSRLRPESTGFGAVYFVQNMCKQNGVDYKGKTLAISGFGNVAWGVAQKATELGI 252
           KG  FGGS +RPE+TG+G VYF Q M + NG    G  +++SG GNVA    +KA +LG 
Sbjct: 213 KGLSFGGSLIRPEATGYGTVYFAQEMLRANGRSLDGLRVSVSGSGNVAQYAVEKALQLGA 272

Query: 253 KVVTISGPDGYVYDPDGINTPEKFRCMLDLRDSGNDVVSDYVKRFPNAQFFPGKKPWEQK 312
           KV+T+S   G + D DG  TPEK   ++D+++     VSDY +R    +F  G +PW   
Sbjct: 273 KVITVSDSSGTIVDEDGF-TPEKLAILMDVKNHHYGRVSDYAER-TGVKFEAGVRPWHVP 330

Query: 313 VDFAMPCATQNEMNLEDAKTLHKNGVTLVAETSNMGCTAEASEYYVANKMLFAPGKAVNA 372
           VD A+PCATQNE++  DA TL KNGV  VAE +NM  T EA++ + A  +L+APGKA NA
Sbjct: 331 VDVALPCATQNELDARDAATLIKNGVVCVAEGANMPSTIEAAKVFEAAGVLYAPGKASNA 390

Query: 373 GGVSCSGLEMTQNAMHLVWTNEEVDKWLHQIMQDIHEQCVTYGK--DGNYIDYVKGANIA 430
           GGV+ SGLEM+QNA  L W  EEVD  L QIMQ IH  C+ YGK  DG  + YV GANIA
Sbjct: 391 GGVATSGLEMSQNAARLAWPREEVDARLLQIMQGIHAACLRYGKHADGR-VSYVDGANIA 449

Query: 431 GFMKVAKAMVAQGV 444
           GF+KVA AM+AQGV
Sbjct: 450 GFVKVADAMLAQGV 463


Lambda     K      H
   0.319    0.137    0.417 

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: 617
Number of extensions: 25
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: 445
Length of database: 464
Length adjustment: 33
Effective length of query: 412
Effective length of database: 431
Effective search space:   177572
Effective search space used:   177572
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: 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