GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Caulobacter crescentus NA1000

Align crotonase (EC 4.2.1.150) (characterized)
to candidate CCNA_02658 CCNA_02658 3-hydroxybutyryl-CoA dehydratase

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__Caulo:CCNA_02658
          Length = 265

 Score =  171 bits (434), Expect = 1e-47
 Identities = 103/262 (39%), Positives = 150/262 (57%), Gaps = 12/262 (4%)

Query: 6   IILEKDGNVASITLNRPKALNALNA-ATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAG 64
           I+ EK G++A +TLNRP A+NAL A     ++ AA   I +D ++  VI+TG+GKAF AG
Sbjct: 4   ILTEKRGHIAILTLNRPDAMNALGAPGDGDQVAAACEAINDDQDIRCVILTGAGKAFSAG 63

Query: 65  ADIAEMK---------DLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELS 115
            D+  MK          +   +G + ++  ++I R +  LE P IAA+NG A+G GC+++
Sbjct: 64  GDVKAMKAREGAFGGNGVKVRDGYRKNI--HRIVRAIYGLEVPSIAAVNGAAIGLGCDVA 121

Query: 116 LSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRI 175
              DIRIA+  A+FG   + LG+ PG GG   + R IG+  A EL++TG VI+A +A   
Sbjct: 122 CMTDIRIAADTARFGVTFLKLGLIPGDGGAWLMPRTIGMSRAAELLFTGDVIDAAKAAEW 181

Query: 176 GLVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGEC 235
           GL++K V    L+ EA AL + I    P A+RM K+ +  G     DT +   A      
Sbjct: 182 GLISKAVPAGDLMGEALALAERIAQQPPHALRMAKSLLKHGQTASYDTLMEMSAAAQAIA 241

Query: 236 FATEDRVEGMTAFVEKRDKAFK 257
             TED +EG+ A +EKR   FK
Sbjct: 242 HHTEDHMEGVDAILEKRSPVFK 263


Lambda     K      H
   0.318    0.136    0.376 

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: 185
Number of extensions: 12
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: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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 Sep 17 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