GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaA in Sinorhizobium meliloti 1021

Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate SM_b21640 SM_b21640 phenylacetate-CoA oxygenase subunit PaaA

Query= metacyc::MONOMER-15947
         (330 letters)



>lcl|FitnessBrowser__Smeli:SM_b21640 SM_b21640 phenylacetate-CoA
           oxygenase subunit PaaA
          Length = 332

 Score =  496 bits (1277), Expect = e-145
 Identities = 234/322 (72%), Positives = 273/322 (84%), Gaps = 1/322 (0%)

Query: 1   MYAQLVETGVKRVKALEEMAPEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHS 60
           MYAQ+V+T   RVK+ ++M P+ERAFQERIDA  KIE K WMP+ YR+TLIRQISQHAHS
Sbjct: 1   MYAQMVKTDAPRVKSPDDMDPQERAFQERIDAGQKIEPKEWMPEGYRKTLIRQISQHAHS 60

Query: 61  EIVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGK 120
           EIVG LPEGNW+TRAPTL+RK  L+AK+QDEAGHGLYLY A ETLG  RD    +LH+GK
Sbjct: 61  EIVGQLPEGNWITRAPTLERKAILLAKVQDEAGHGLYLYCAAETLGVSRDALYEQLHTGK 120

Query: 121 AKYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQ 180
           AKYSSIFNYPTL+WAD+GA+GWLVDGAAI+NQV LQR SYGPYSRAMIRICKEESFHQRQ
Sbjct: 121 AKYSSIFNYPTLSWADIGAIGWLVDGAAIMNQVPLQRCSYGPYSRAMIRICKEESFHQRQ 180

Query: 181 GYEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDE 240
           GY+IL+ MM+ GT  Q+ MVQDA+NR WWP+LMMFGPSD+ S +SAQSMAWKIK+ SNDE
Sbjct: 181 GYDILIKMMK-GTPDQRAMVQDALNRWWWPSLMMFGPSDDASVHSAQSMAWKIKQNSNDE 239

Query: 241 LRQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIA 300
           LRQ+F++QTVPQ E LG T PDP+LKWNEE+G YDFG  DW+EF+EV+ GNGPCNAER+ 
Sbjct: 240 LRQKFVNQTVPQAEYLGLTVPDPDLKWNEEKGGYDFGEPDWNEFFEVIAGNGPCNAERLG 299

Query: 301 TRRNAIDNGAWVREAAVAHARK 322
            RR A ++GAW R+   AHA K
Sbjct: 300 ARRKAWEDGAWFRDGLTAHAEK 321


Lambda     K      H
   0.318    0.131    0.402 

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: 468
Number of extensions: 14
Number of successful extensions: 2
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: 330
Length of database: 332
Length adjustment: 28
Effective length of query: 302
Effective length of database: 304
Effective search space:    91808
Effective search space used:    91808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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