GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Dinoroseobacter shibae DFL-12

Align crotonase (EC 4.2.1.150) (characterized)
to candidate 3607639 Dshi_1048 Enoyl-CoA hydratase/isomerase (RefSeq)

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



>FitnessBrowser__Dino:3607639
          Length = 265

 Score =  145 bits (366), Expect = 8e-40
 Identities = 97/260 (37%), Positives = 139/260 (53%), Gaps = 10/260 (3%)

Query: 6   IILEKDGNVASITLNRPKALNALNAATLKEI-DAAINDIAEDDNVYAVIITGSG-KAFVA 63
           ++L+++G VA ITLN P  LNA+  A  + + D A+   A D  V  V++ G+G +AF A
Sbjct: 10  LLLDREGPVARITLNNPDRLNAMRLAMWQGLGDLAVELAASDARV--VVLRGAGDRAFCA 67

Query: 64  GADIAEMKDLTAV-EGRKFSVLGNKIFRKLENLEK---PVIAAINGFALGGGCELSLSCD 119
           GADI+E   + A  EG   +     + R LE L     PV+AAI G  +GGG E+++ CD
Sbjct: 68  GADISEFPQVRATPEG--VAAYNRTVARALEGLAALPMPVLAAIRGHCIGGGLEIAVRCD 125

Query: 120 IRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVN 179
           +R+AS  A+       LG+  G      LAR  G   A EL+YT + ++A  A R GLVN
Sbjct: 126 LRLASETARIAFTPAKLGLAIGADEVAALARIAGPAAAAELLYTAQPVDAARAERWGLVN 185

Query: 180 KVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATE 239
           + V  D L++EA AL   I  NAP+ +R  KA +    +       ++   +   CF + 
Sbjct: 186 RRVPEDMLMDEADALARTIAANAPLTLRAVKAGLAAFARPGDAAAASHADALVKTCFDSA 245

Query: 240 DRVEGMTAFVEKRDKAFKNK 259
           D  EG  AF EKR   FK +
Sbjct: 246 DYREGQRAFAEKRRPEFKGQ 265


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: 152
Number of extensions: 9
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