GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Caulobacter crescentus NA1000

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate CCNA_01794 CCNA_01794 enoyl-CoA hydratase/isomerase family

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Caulo:CCNA_01794
          Length = 256

 Score =  151 bits (381), Expect = 1e-41
 Identities = 89/233 (38%), Positives = 131/233 (56%), Gaps = 13/233 (5%)

Query: 6   VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAG 65
           +++E+ G +A+VT+NRP+A+NAL+      +   I +++ D +V  VILTGAG+++F AG
Sbjct: 2   LLIERRGAIAIVTLNRPEAMNALSKALRLALHDAIVQLDQDPDVSVVILTGAGDRAFTAG 61

Query: 66  ADISE-------MKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMS 118
            D+ E       M   N  + R   +      R +E   KPVI A+NG A+ GG E+A++
Sbjct: 62  LDLKELGGDPAAMGAANDQDARSNPV------RAVETCRKPVIGAINGVAITGGFELALA 115

Query: 119 CDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGL 178
           CD+ +AS NARF      +GI PG+G +Q+LSRL+G   AK+L  T   + A  A   GL
Sbjct: 116 CDVLLASENARFADTHARVGIMPGWGLSQKLSRLIGPYRAKELSLTGNFLDARTAADWGL 175

Query: 179 VNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESE 231
           VN+V   SEL+ TA  +A  + S    A+   K  I+ G        LA E E
Sbjct: 176 VNRVTTASELLPTALRMAQDMASIPVEALSFYKSLIDDGYAVAFGEGLALEHE 228


Lambda     K      H
   0.317    0.134    0.365 

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: 169
Number of extensions: 5
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: 261
Length of database: 256
Length adjustment: 24
Effective length of query: 237
Effective length of database: 232
Effective search space:    54984
Effective search space used:    54984
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 (21.6 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