GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Escherichia coli BW25113

Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate 14182 b0036 crotonobetainyl CoA hydratase (RefSeq)

Query= SwissProt::G4V4T7
         (265 letters)



>lcl|FitnessBrowser__Keio:14182 b0036 crotonobetainyl CoA hydratase
           (RefSeq)
          Length = 261

 Score =  197 bits (502), Expect = 1e-55
 Identities = 117/271 (43%), Positives = 162/271 (59%), Gaps = 16/271 (5%)

Query: 1   MSETRVRYEKKDHVAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDR 60
           MSE+ +   +   +  +T+DRP   NA+D +   E+  ++ +   D  +R  ++TGAG++
Sbjct: 1   MSES-LHLTRNGSILEITLDRPKA-NAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEK 58

Query: 61  AFSVGQDLKERARLNESGVAPTT-FGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFE 119
            FS G DLK  A     G AP   FG GG AG   LT+ F L KPV+A V GYA GGGFE
Sbjct: 59  FFSAGWDLKAAAE----GEAPDADFGPGGFAG---LTEIFNLDKPVIAAVNGYAFGGGFE 111

Query: 120 LVLACDIVIAAEDAVFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATAL 179
           L LA D ++ A++A FALPE +LG++  +GGV RLP+ LP  +    ++TGRRM A  AL
Sbjct: 112 LALAADFIVCADNASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEAL 171

Query: 180 RHGLVNEVVPAAELDQCVADWTDSLVRAAPLSVRAIKEAALRSVDLPLEEAFT-----TS 234
           R G+VN VV  AEL     +    LV +APL++ A+KE    + ++P+EEA+        
Sbjct: 172 RWGIVNRVVSQAELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVL 231

Query: 235 YHWEERRRRSADAIEGVRAFAEKRDPIWTGQ 265
            H+      S DAIEG  AFAEKRDP+W G+
Sbjct: 232 KHYPS-VLHSEDAIEGPLAFAEKRDPVWKGR 261


Lambda     K      H
   0.320    0.136    0.399 

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: 184
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: 265
Length of database: 261
Length adjustment: 25
Effective length of query: 240
Effective length of database: 236
Effective search space:    56640
Effective search space used:    56640
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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