GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Desulfoscipio geothermicus DSM 3669

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_245779653.1 BM299_RS04985 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_900115975.1:WP_245779653.1
          Length = 471

 Score =  332 bits (851), Expect = 2e-95
 Identities = 179/389 (46%), Positives = 249/389 (64%), Gaps = 32/389 (8%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           D++G  ++D LGG+G  N+GH +P V+ AV+ Q+ + P   Q  +  + A L   LA +T
Sbjct: 64  DSEGNAYLDFLGGYGSLNIGHNHPRVIEAVE-QVRELPNILQASIPTITAALLHNLAVIT 122

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197
           PGKLK SF CNSG E+VE ALKLA+A     G+ TFI    +FHGKS GALS T +  +R
Sbjct: 123 PGKLKRSFLCNSGAEAVEGALKLARA---ATGRKTFIYCRNSFHGKSFGALSVTGREKYR 179

Query: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257
           + F PLL   R VPFG+I+A+R AL + +      AA I+EP+QGEGG+ +PP GYL+  
Sbjct: 180 ELFEPLLFDCREVPFGDIDALRKALRKYQ-----AAAFIVEPVQGEGGINMPPRGYLSEA 234

Query: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317
            + C + G L I DE+QTG GRTG MFAC+HENV+PD++CLAK+LGGG+MPIGA I  ++
Sbjct: 235 ARACRDAGTLFIADEIQTGFGRTGAMFACQHENVEPDVMCLAKSLGGGIMPIGAFITNDD 294

Query: 318 VFSVLF---DNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLA 374
           ++   +   +   LHT+TFGGN  A AA +A I VL+++ LPA A +KG   + G R L 
Sbjct: 295 IWQKAYGSVEKATLHTSTFGGNTWAAAAGIAAIEVLVKEKLPAAAAEKGTYFISGLRDLQ 354

Query: 375 REYPDLVQEARGKGMLMAIEF-----VDNEIGYNFASEMF--------------RQRVLV 415
           ++YP L+QE RG+G+L+ IE      + N+     AS++               R R++ 
Sbjct: 355 KKYP-LLQEVRGQGLLIGIELAQPGGLTNKATMGLASKLSHEYLGSMVAGELLNRHRIIT 413

Query: 416 AGTLNNAKTIRIEPPLTLTIEQCELVIKA 444
           A TLNN   IR+EPPLT+T E+ + V+ A
Sbjct: 414 AYTLNNPNVIRMEPPLTVTGEELDYVLNA 442


Lambda     K      H
   0.320    0.135    0.393 

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: 555
Number of extensions: 29
Number of successful extensions: 7
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: 459
Length of database: 471
Length adjustment: 33
Effective length of query: 426
Effective length of database: 438
Effective search space:   186588
Effective search space used:   186588
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 Apr 09 2024. 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