GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dyella japonica UNC79MFTsu3.2

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          Length = 411

 Score =  205 bits (521), Expect = 3e-57
 Identities = 139/386 (36%), Positives = 209/386 (54%), Gaps = 32/386 (8%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL---DPLRAMLAKTLA 134
           DT+G++++D   G  +  +GH++P +V A+  Q A++  HS  +     PL   LA+ L 
Sbjct: 39  DTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQ-ARKLWHSSNVFYTEPPLH--LAEELV 95

Query: 135 ALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKF----TFIATSGAFHGKSLGALSA 190
             + G  +  F CNSGTE+ EAA+KL + + + +G+       +   G+FHG++L A++A
Sbjct: 96  QAS-GFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGSFHGRTLAAVTA 154

Query: 191 TAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPP 250
           TA+  +++ + PL  GFR++ F ++  +  A  +      DVAAV+LEP+QGEGGV+   
Sbjct: 155 TAQPKYQENYEPLPGGFRYLDFNDVAGLEAAFAQ-----GDVAAVMLEPVQGEGGVLPAS 209

Query: 251 PGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIG 310
           P ++   R+LCD   AL++LDE+Q GMGRTG +FA   + V PDI+ LAKALG G  PIG
Sbjct: 210 PAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDGVTPDIVTLAKALGCG-FPIG 268

Query: 311 ATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGF 370
           A +A  +V  V+      H TTFGGNP+A A A   +  L    L A   ++   L DG 
Sbjct: 269 AMLAGPKVAEVM--QYGAHGTTFGGNPMAAAVARVALRKLASAELMANVAKQAQALRDGL 326

Query: 371 RQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQR------VLVAGTLNNAKT 424
             +  E   L  E RG+G+++     +   G   A E+          VL AG       
Sbjct: 327 AAIDGEL-KLFAEVRGRGLMLGAVLAEAYKGR--AGEVLDHAAAHGLLVLQAG----PDV 379

Query: 425 IRIEPPLTLTIEQCELVIKAARKALA 450
           +R  PPL +T       +   R ALA
Sbjct: 380 LRFVPPLNITDADLAEGLARLRAALA 405


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: 422
Number of extensions: 18
Number of successful extensions: 5
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: 411
Length adjustment: 32
Effective length of query: 427
Effective length of database: 379
Effective search space:   161833
Effective search space used:   161833
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