GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Rhizobium etli CFN 42

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase

Query= BRENDA::Q5SLK3
         (254 letters)



>NCBI__GCF_000092045.1:WP_042119745.1
          Length = 260

 Score =  120 bits (302), Expect = 2e-32
 Identities = 91/260 (35%), Positives = 140/260 (53%), Gaps = 12/260 (4%)

Query: 3   LKERQDG-VLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAG 60
           ++ R+DG VL + ++RP K NAI      A+    ++  +D E+R  +++GAG + F AG
Sbjct: 5   VRTRRDGAVLEVVIDRP-KANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAG 63

Query: 61  QDL--TEFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLA 118
            DL     GD   D +  +  +  + E L  L KP++ AVNG+  G G+ +AL  DL +A
Sbjct: 64  WDLKAAASGDAV-DGDYGVGGFGGLQE-LRDLNKPVICAVNGLCCGGGLEIALSTDLIIA 121

Query: 119 AVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVP 178
           A  A+F    +R G V D+  S  LP+ +    A ++LL    L   EA   G V+ VVP
Sbjct: 122 AEHATFALPEIRSGTVADAA-SIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVP 180

Query: 179 AEKLMEEALSLAKELAQGPTRAYALTKKLLLE----TYRLSLTEALALEAVLQGQAGQTQ 234
           AE+LME A  LA+ L  GP   YA  K+++ E    T++ ++ +    +     +   ++
Sbjct: 181 AERLMERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSE 240

Query: 235 DHEEGVRAFREKRPPRFQGR 254
           D  EG RAF EKR P ++GR
Sbjct: 241 DQLEGARAFAEKRSPIWKGR 260


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: 142
Number of extensions: 9
Number of successful extensions: 4
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: 260
Length adjustment: 24
Effective length of query: 230
Effective length of database: 236
Effective search space:    54280
Effective search space used:    54280
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 Apr 09 2024. 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