GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Methylocapsa aurea KYG

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_036257477.1 DL86_RS01770 enoyl-CoA hydratase/isomerase family protein

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



>NCBI__GCF_000746085.1:WP_036257477.1
          Length = 354

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 66/203 (32%), Positives = 100/203 (49%), Gaps = 14/203 (6%)

Query: 13  RVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAGADIKEMAE 72
           R  +ITL+RP  LNAL   ++ E+ +AL   E+DP +  +++  + +AF AGADI+ + E
Sbjct: 13  RCGVITLDRPNVLNALTLNMVREIARALDLWESDPAVQTVLIRAAGRAFCAGADIRNLYE 72

Query: 73  LTYPQIYLDDF------FADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNAR 126
           L     Y D        +    RI    KP +A + G  +GGG  ++L    I A D+  
Sbjct: 73  LGRAGRYADQLAFWREEYCLNRRIKLYPKPYVALIDGIVMGGGAGVSLHGSHIVAGDDFN 132

Query: 127 FGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFP----- 181
           F  PEV +G  P +G T  L R  GK   + + LTG +M   +A    + A   P     
Sbjct: 133 FAMPEVGIGFFPDVGATFFLPRLPGKT-GVYLALTGARMTCGDALAFEVAAAYAPSARHA 191

Query: 182 --AESLLEETLKAARVIAEKSLP 202
             A+ L+E    +A + AE + P
Sbjct: 192 ALAQRLIEGEDPSAAIAAESAPP 214


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: 180
Number of extensions: 8
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: 257
Length of database: 354
Length adjustment: 27
Effective length of query: 230
Effective length of database: 327
Effective search space:    75210
Effective search space used:    75210
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: 48 (23.1 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