GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Collimonas arenae Ter10

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_061531854.1 CAter10_RS00460 crotonase/enoyl-CoA hydratase family protein

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_001584165.1:WP_061531854.1
          Length = 270

 Score =  135 bits (340), Expect = 9e-37
 Identities = 83/269 (30%), Positives = 137/269 (50%), Gaps = 12/269 (4%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M +ET+      N+  + LNRPDK NA+N ++ +E+  A    ++ PE RV ++ G+GK 
Sbjct: 1   MTYETLSVSLAQNIAIVRLNRPDKANAMNMQMWQEIRTAFEWVDATPEARVAVLEGEGKT 60

Query: 61  FCAGADITQFNQL-----TPAEAWKFSKKGREIMDKIEALS------KPTIAMINGYALG 109
           F AG D+     L      P E  K       I++  +ALS      KP +A ++G  +G
Sbjct: 61  FTAGIDLQMMMGLGAQIQNPCEGRKREALRSIILNLQDALSSLERCRKPILAAVHGACVG 120

Query: 110 GGLELALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPG 169
           GG++L    D+R  + +A   + EI++G+    G  QRL ++IG+G A E+  T  ++  
Sbjct: 121 GGIDLITCADMRYCSSDAYFSIKEIDIGMTADVGTLQRLPKLIGEGMARELAYTARKVDA 180

Query: 170 KDAEKYGLVNRVVPLAN-LEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALE 228
            +A    LVNRV      L +   ++A  IA KSP+++  +KE++    D  +  GL   
Sbjct: 181 AEARDIHLVNRVFASREALREGVMEIAASIAAKSPLAIRGVKEMITYARDHSVADGLKYI 240

Query: 229 SVGWGVVFSTEDKKEGVSAFLEKREPTFK 257
           +     +  + D +E + A + KR   FK
Sbjct: 241 ATWNAAMLMSNDLQEAMMANVGKRPAEFK 269


Lambda     K      H
   0.315    0.135    0.382 

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: 132
Number of extensions: 10
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: 259
Length of database: 270
Length adjustment: 25
Effective length of query: 234
Effective length of database: 245
Effective search space:    57330
Effective search space used:    57330
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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