GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaA in Burkholderia phytofirmans PsJN

Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate BPHYT_RS18250 BPHYT_RS18250 phenylacetate-CoA oxygenase subunit PaaA

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



>FitnessBrowser__BFirm:BPHYT_RS18250
          Length = 332

 Score =  449 bits (1156), Expect = e-131
 Identities = 210/305 (68%), Positives = 256/305 (83%), Gaps = 1/305 (0%)

Query: 22  EERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHSEIVGMLPEGNWVTRAPTLKRK 81
           E+  F   + A+ KIEA++WMP+AYR+TL+RQISQHAHSEIVGMLPEGNW+TRAP+LKRK
Sbjct: 23  EQVQFDAVMAADGKIEAQDWMPEAYRKTLVRQISQHAHSEIVGMLPEGNWITRAPSLKRK 82

Query: 82  LQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGKAKYSSIFNYPTLNWADMGAVG 141
             L+AK+QDEAGHGLYLYSA ETLG  RD+ IA LHSGKAKYSSIFNYPT  WAD+G +G
Sbjct: 83  AILLAKVQDEAGHGLYLYSAAETLGVSRDQLIAALHSGKAKYSSIFNYPTPTWADVGVIG 142

Query: 142 WLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQGYEILLTMMRHGTQAQKDMVQ 201
           WLVDGAAI+NQ+ L R +YGPY+RAMIRICKEESFHQRQG++ L++MM  GT+AQ+++VQ
Sbjct: 143 WLVDGAAIMNQIPLCRCTYGPYARAMIRICKEESFHQRQGFDALMSMMA-GTEAQRELVQ 201

Query: 202 DAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDELRQRFIDQTVPQLELLGCTAP 261
            A+NR WWP LMMFGPSD+ S +S QS  W IKR SND+LRQ+F+D TV Q ++LG T P
Sbjct: 202 QAVNRWWWPVLMMFGPSDKDSIHSNQSSKWGIKRISNDDLRQKFVDATVDQAKVLGVTLP 261

Query: 262 DPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIATRRNAIDNGAWVREAAVAHAR 321
           DP+LKWNE RGH+D+G IDW EF+ V+ G+GPCN ER+ATR  A D+GAWVREAA+AHA 
Sbjct: 262 DPDLKWNEARGHHDYGDIDWEEFWRVVNGDGPCNRERLATRVKAHDDGAWVREAALAHAE 321

Query: 322 KQQHK 326
           KQ+ +
Sbjct: 322 KQRQR 326


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: 432
Number of extensions: 12
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 (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