GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Magnetospirillum magneticum AMB-1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000009985.1:WP_011383255.1
          Length = 388

 Score =  224 bits (572), Expect = 3e-63
 Identities = 130/381 (34%), Positives = 215/381 (56%), Gaps = 18/381 (4%)

Query: 66  VEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPL 125
           V ++ G    L  + G+ F+D   G  +  +GH +P +V+A++ Q  K    S     P 
Sbjct: 15  VIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCSNLYRVPG 74

Query: 126 RAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGK---FTFIATSGAFHG 182
           +  +A+ L  +       +FFCN+G E++E  +K+A+ Y    G+      +A +G+FHG
Sbjct: 75  QERVAERL--IKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGSFHG 132

Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242
           +++  L+A     + + F P+  GF HVP+G++EA R A+      G + AA+++EP+QG
Sbjct: 133 RTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAI------GSNTAALLVEPVQG 186

Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302
           EGG+    P YL  +R L D+FG L+++DEVQTG+GRTGK+FA E   + PD++ LAK L
Sbjct: 187 EGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVMGLAKGL 246

Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362
           GGG  P+GA +ATE+  S +   P  H  TFGGNPLA A A A ++ ++      + +  
Sbjct: 247 GGG-FPVGAVLATEKAASCM--TPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERVQAV 303

Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA 422
             +L      LAR YP  + + RG+G+++ ++ V   +   F +++F   +L  G  +N 
Sbjct: 304 AALLRGRLDDLARRYPGAIAQVRGQGLMLGLKTV--PVNTEFNAKLFAAGLLAVGAGDN- 360

Query: 423 KTIRIEPPLTLTIEQCELVIK 443
             +R+ PPL +   + E  ++
Sbjct: 361 -VVRLVPPLIIGEAEVERAVE 380


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: 440
Number of extensions: 27
Number of successful extensions: 6
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: 388
Length adjustment: 32
Effective length of query: 427
Effective length of database: 356
Effective search space:   152012
Effective search space used:   152012
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: 50 (23.9 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