GapMind for catabolism of small carbon sources

 

Aligments for a candidate for antC in Marinobacter adhaerens HP15

Align Anthranilate 1,2-dioxygenase electron transfer component; EC 1.18.1.3 (characterized)
to candidate GFF4089 HP15_4029 oxidoreductase FAD/NAD(P)-binding domain protein

Query= SwissProt::O85675
         (343 letters)



>lcl|FitnessBrowser__Marino:GFF4089 HP15_4029 oxidoreductase
           FAD/NAD(P)-binding domain protein
          Length = 353

 Score =  164 bits (416), Expect = 2e-45
 Identities = 104/328 (31%), Positives = 171/328 (52%), Gaps = 14/328 (4%)

Query: 17  IAVQEDELLLDAAVRQGINLPLDCREGVCGTCQGTCETGIYEQEYVDEDALSERDLAKRK 76
           I V++ + +L AA+RQG+ LP  C  G C TC+     G  E       AL + +  + K
Sbjct: 14  IEVEDGQTILQAALRQGVWLPFACGHGTCATCKVQVLEGDVEIGDASPFALMDIERDEGK 73

Query: 77  MLACQTRVKSNAAFYFDHHSSICNAGETLKIATV-VTGVELVSETTAILHLDASQHVKQL 135
           +LAC   V+S+     D        G  ++  T  VTG+  +S T   +HL      + +
Sbjct: 74  VLACCATVESDVTIEADIDVDPDFEGYPVEDYTATVTGIVELSPTIRGVHLKLD---RPM 130

Query: 136 DFLPGQYARLQIPDTDDWRSYSFANRPNASNQLQFLIRLLPNGVMSNYLRERCQVGQTLI 195
            F  GQY  +++P  D  R++S AN P  +++++  +RL+  G  + Y+ E+ + G  L 
Sbjct: 131 TFQAGQYINIELPGVDGARAFSLANPPGKADEVELHVRLVEGGAATTYIHEQLKTGDALN 190

Query: 196 MEAPLGSFYLREVE-RPLVFIAGGTGLSAFLGMLDNIAEQPNQPSVHLYYGVNTEADLCE 254
           +  P G F++R  +   L+FIAGG+GLS+   M+ ++ EQ ++  + L+ G    A+L  
Sbjct: 191 LSGPYGQFFVRSSQPGDLIFIAGGSGLSSPQSMILDLLEQNDERKIVLFQGARNLAELYN 250

Query: 255 QKRLTTYAERIKNFSYHPIISKASE--QWQGKSGFIHE----HLDKNQLSEQSFDMYLCG 308
           ++          NF+Y P +S+A E  +WQG  G++H+    H D      ++   YLCG
Sbjct: 251 RELFEALDRDHDNFTYVPALSQAEEDAEWQGFRGYVHDAAKAHFDGRFAGNKA---YLCG 307

Query: 309 PPPMIEAVKTWLDEQAIADCHIYSEKFL 336
           PPPMI+A  T L +  + +  I+ EKFL
Sbjct: 308 PPPMIDAAITALMQGRLFERDIFMEKFL 335


Lambda     K      H
   0.319    0.134    0.401 

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: 278
Number of extensions: 17
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: 343
Length of database: 353
Length adjustment: 29
Effective length of query: 314
Effective length of database: 324
Effective search space:   101736
Effective search space used:   101736
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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