GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaC in Cupriavidus basilensis 4G11

Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate RR42_RS23735 RR42_RS23735 phenylacetic acid degradation protein

Query= metacyc::MONOMER-15949
         (253 letters)



>FitnessBrowser__Cup4G11:RR42_RS23735
          Length = 266

 Score =  211 bits (538), Expect = 9e-60
 Identities = 125/266 (46%), Positives = 156/266 (58%), Gaps = 18/266 (6%)

Query: 3   PNHDLIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAA-- 60
           P H  + Y+LRL D+ALI GQR  EWC + PALEE++AL N+ LDL+GQAR    +AA  
Sbjct: 4   PQH--LSYVLRLADNALILGQRNSEWCSQGPALEEDIALANISLDLIGQARLLYSHAATL 61

Query: 61  -ELLADGRDA-DHLAFRRDERAYRNLLLVEQPN-----------GDFAVTMAKQFLYDAW 107
            E L   R   D  A+ R ER + N  LVE P+            D+AVT+ + FLY A 
Sbjct: 62  DEALNGARKTEDSYAYFRAEREFANYTLVELPHFGPLAGTARAERDYAVTITRNFLYSAL 121

Query: 108 HFQVLDGLSRSGDARVAGIAAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLW 167
              +   L  S D  +A IAAK+LKE  YHL  + +W+ R GDGTEESHRR QAA+  L 
Sbjct: 122 MGHLWTALQSSTDTHLAAIAAKSLKETRYHLTHAADWLIRFGDGTEESHRRAQAALDYLM 181

Query: 168 RFTVEMSDGDEVEQRLCEAGIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRR 227
            +T E    D VE  +  AGI P  A +  AWQA VA   A ATL LP  A +   +G+ 
Sbjct: 182 PYTREFFAADAVETAVAAAGIGPLMADLQPAWQADVAATVAQATLTLPSEAKHI-TTGKH 240

Query: 228 GLHSEHLGLLLAEMQFLQRAYPDATW 253
           G HSEH+G LL+EMQ L R +P ATW
Sbjct: 241 GEHSEHMGYLLSEMQSLARQHPGATW 266


Lambda     K      H
   0.321    0.136    0.421 

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: 184
Number of extensions: 11
Number of successful extensions: 3
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: 253
Length of database: 266
Length adjustment: 24
Effective length of query: 229
Effective length of database: 242
Effective search space:    55418
Effective search space used:    55418
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 (21.9 bits)
S2: 47 (22.7 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