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_036257290.1 DL86_RS00860 enoyl-CoA hydratase-related protein

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



>NCBI__GCF_000746085.1:WP_036257290.1
          Length = 250

 Score =  112 bits (281), Expect = 6e-30
 Identities = 78/254 (30%), Positives = 120/254 (47%), Gaps = 12/254 (4%)

Query: 4   ETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAA 63
           E + ++    +  +T +RP+  NAL G +     +AL   + +  IG I++ GS  AF A
Sbjct: 3   EYVKIERDGAILCLTFDRPEKKNALTGAMYLAAAEALITADREESIGAILIGGSGGAFTA 62

Query: 64  GADIKEMAEL-----TYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDM 118
           G DI +  +       +P       FA    +A  + PLIAA+ G A+G G  + L CD+
Sbjct: 63  GNDIADFLQFGGEPGEFPA------FAFIKTLAASQTPLIAAIEGPAIGIGATMILHCDL 116

Query: 119 IFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVAR 178
            + A +A F  P V+LG++P    +  L R +G AKA +  L G    A EA R GL   
Sbjct: 117 AYVAPDATFRMPFVDLGLVPEAASSLLLPRRIGMAKASEFLLLGEPFGAQEAVRLGLANA 176

Query: 179 VFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATAD 238
           +  A+ L    ++ A+ IA K   A    +  +    +   A  I  E R+F     +A+
Sbjct: 177 IVAADRLRPFAIERAKWIAAKPREAIQATRRLLRGDVQEIRAR-IEEEARLFAGALQSAE 235

Query: 239 QKEGMAAFSEKRKP 252
            +   AAF  K KP
Sbjct: 236 ARAAFAAFLSKPKP 249


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: 131
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: 257
Length of database: 250
Length adjustment: 24
Effective length of query: 233
Effective length of database: 226
Effective search space:    52658
Effective search space used:    52658
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 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