GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Pseudarthrobacter sulfonivorans Ar51

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_058929110.1 AU252_RS00885 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::Q5SLK3
         (254 letters)



>NCBI__GCF_001484605.1:WP_058929110.1
          Length = 258

 Score =  138 bits (348), Expect = 1e-37
 Identities = 82/249 (32%), Positives = 137/249 (55%), Gaps = 2/249 (0%)

Query: 8   DGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDLTEF 66
           DG+  + +NRPE++NA   E    L        +D  +R  ++TGAG +AFSAG DL + 
Sbjct: 10  DGIATIVMNRPERMNAFDAEAYKQLSEVWIRVRDDHAIRVAVITGAGEKAFSAGADLKDL 69

Query: 67  GDRKPD-YEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASFT 125
               P+ ++  L + ++++     + KP++ AVNG   G G+++    D+R+A   A+F 
Sbjct: 70  VPAPPELHDLWLTQKDQLLNRGLEIWKPVIAAVNGYCLGGGLTMLFATDIRIACHDATFG 129

Query: 126 TAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLMEE 185
            + V+ G++P +G +  +   V   +A E+LL    + A +AL  GL++ VV   +LME 
Sbjct: 130 LSEVKRGVLPGNGATQRVIDNVSYPRAMEMLLTGEPIDASKALEWGLINEVVDRARLMER 189

Query: 186 ALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRAFRE 245
           +L +A+++A     A   TK+L + +  + L   L LE VLQ     ++D  EG +AF E
Sbjct: 190 SLEIARQIAANAPLAVQATKELAVRSRSMDLASGLRLEQVLQRILQTSEDAVEGPKAFAE 249

Query: 246 KRPPRFQGR 254
           +RP  F GR
Sbjct: 250 RRPAVFGGR 258


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: 143
Number of extensions: 8
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: 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 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