GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Rhodobacter viridis JA737

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase

Query= BRENDA::Q5SLK3
         (254 letters)



>NCBI__GCF_003217355.1:WP_110804536.1
          Length = 258

 Score =  140 bits (354), Expect = 2e-38
 Identities = 89/250 (35%), Positives = 132/250 (52%)

Query: 2   VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61
           ++ E +DGV ++ LNRPE LNA+  +LL  L  ALK  + D  VR  +LTG+ +AF+AG 
Sbjct: 6   LIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGSDKAFAAGA 65

Query: 62  DLTEFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121
           D+ E  D+          +    +A+    KP++ AV G A G G  LA+  D  L A  
Sbjct: 66  DIKEMADKSFTDMFLQDFFGTEGDAILRTRKPIIAAVAGYALGGGCELAMMCDFILCAEN 125

Query: 122 ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEK 181
           A F    + +G+V   G +  L R VG +K+ E+ L    + A EA   GLV RV+P   
Sbjct: 126 AKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAERSGLVSRVLPLAD 185

Query: 182 LMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVR 241
           L+ EAL+ A+++A     A  + K  +   Y  +L E +  E  +      T+D +EG+ 
Sbjct: 186 LVPEALTTARKIAAKSAIATMVAKDCVNRAYETTLREGVLYERRVFHALFATEDQKEGMA 245

Query: 242 AFREKRPPRF 251
           AF EKRP +F
Sbjct: 246 AFTEKRPAKF 255


Lambda     K      H
   0.318    0.135    0.371 

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: 161
Number of extensions: 7
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: 254
Length of database: 258
Length adjustment: 24
Effective length of query: 230
Effective length of database: 234
Effective search space:    53820
Effective search space used:    53820
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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