GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Haloterrigena daqingensis JX313

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_076581564.1 BB347_RS11510 enoyl-CoA hydratase/isomerase family protein

Query= reanno::psRCH2:GFF2389
         (257 letters)



>NCBI__GCF_001971705.1:WP_076581564.1
          Length = 261

 Score =  164 bits (414), Expect = 2e-45
 Identities = 107/266 (40%), Positives = 150/266 (56%), Gaps = 18/266 (6%)

Query: 2   TFETLLVDIQER--VALITLNRPQALNALNGQLISELNQALGQLEA--DPQIGC--IVLT 55
           +F+T  V+  E   V  +TLNRP ALNAL+GQL  ++ ++L  LE   D +I    +V++
Sbjct: 4   SFDTTTVEFDEDTGVGRVTLNRPDALNALSGQLREDIVESLRLLEEQNDDEIALRVVVVS 63

Query: 56  GSAKAFAAGADIKEMAELT---YPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCEL 112
           G+A  F AGADI E  + +    P+     F  D         P+IA + GY LGGG E 
Sbjct: 64  GAAGNFCAGADITEFEDASPGGSPERTHYQFIMDFP------VPVIAKIEGYCLGGGLET 117

Query: 113 ALLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAER 172
           A+ CD  FA ++AR G PEV+LG++PG GG Q ++   G A A ++ +TG  + A  A+ 
Sbjct: 118 AMACDFRFADEDARLGLPEVDLGIIPGAGGVQYISELAGPAAAKEIAMTGDHISATRADE 177

Query: 173 AGLVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHA 232
            G+V RV   + L E T K A  IA K   A   IK S   + +T+L EGI ++ +VF  
Sbjct: 178 LGIVNRV--PDDLDEATQKFAEKIASKPPLAIQTIKNSARISTQTSLKEGIDYDNKVFEP 235

Query: 233 VFATADQKEGMAAFSE-KRKPEFTNR 257
           + AT D KEG  AF+E   +PEF  R
Sbjct: 236 LLATEDHKEGARAFAEDDYEPEFKGR 261


Lambda     K      H
   0.321    0.135    0.375 

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: 152
Number of extensions: 7
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: 257
Length of database: 261
Length adjustment: 24
Effective length of query: 233
Effective length of database: 237
Effective search space:    55221
Effective search space used:    55221
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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