GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Escherichia coli BW25113

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 14182 b0036 crotonobetainyl CoA hydratase (RefSeq)

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__Keio:14182
          Length = 261

 Score =  141 bits (356), Expect = 1e-38
 Identities = 93/260 (35%), Positives = 136/260 (52%), Gaps = 6/260 (2%)

Query: 4   ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFA 62
           E++ +   G +  +TL+RPKA NA++     E+G     F  D  +   ++TG+ EK F+
Sbjct: 3   ESLHLTRNGSILEITLDRPKA-NAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEKFFS 61

Query: 63  AGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122
           AG D+   +     D   G         + ++ KP+IAAV G+A GGG ELA+  D I  
Sbjct: 62  AGWDLKAAAEGEAPDADFGPGGFAGLTEIFNLDKPVIAAVNGYAFGGGFELALAADFIVC 121

Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182
           AD A F  PE KLGI+P +GG  RLP+ +  A   ++ +T R M A EA R G+V+RV+ 
Sbjct: 122 ADNASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWGIVNRVVS 181

Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFER----RLFHSLFATE 238
            A L+D A   A  +      A+  +KE      E  + E   + R    + + S+  +E
Sbjct: 182 QAELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHSE 241

Query: 239 DQKEGMAAFVEKRKPVFKHR 258
           D  EG  AF EKR PV+K R
Sbjct: 242 DAIEGPLAFAEKRDPVWKGR 261


Lambda     K      H
   0.321    0.134    0.380 

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: 155
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: 258
Length of database: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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 (21.9 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