GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Limnohabitans curvus MWH-C5

Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate WP_108401500.1 B9Z44_RS01330 enoyl-CoA hydratase

Query= SwissProt::Q9JLZ3
         (314 letters)



>NCBI__GCF_003063475.1:WP_108401500.1
          Length = 258

 Score =  147 bits (370), Expect = 3e-40
 Identities = 98/258 (37%), Positives = 135/258 (52%), Gaps = 10/258 (3%)

Query: 57  LEEENRGIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 116
           L E    + VL +NR    NAL+  L+  L  A+ AL +D  +  I+I       F AGA
Sbjct: 7   LSERQGRVGVLTLNRPEQLNALNDTLMDALGAALLALDADDGIGAIVITGSDKA-FAAGA 65

Query: 117 DLKERAKMHSSEV--GPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVA 174
           D+   A     +V    F+++    I  +     P IAA+ G A+GGG ELALACD+ VA
Sbjct: 66  DIAAMADWGYMDVFSSAFITRNWETIRQVRK---PVIAAVAGFAMGGGCELALACDLIVA 122

Query: 175 ASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLE 234
           A SAK  L E KLA++PG GGTQRLPRAIG + A ++  SAR+L  +EA   GL+S V+ 
Sbjct: 123 AESAKFALPEVKLAMLPGAGGTQRLPRAIGKAKAMDMCLSARMLSAEEADRYGLVSRVV- 181

Query: 235 QNQEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTK 294
                DA   + L LA         A+   K ++N+  E  L  G+  E        ++ 
Sbjct: 182 ---PSDALMAETLKLANTIAGFSLPALIAIKESVNRAWEGSLTEGVKFERHALYARFASA 238

Query: 295 DRLEGLLAFKEKRPPRYK 312
           D  EG+ AF EKR P ++
Sbjct: 239 DAHEGMHAFLEKRKPTFQ 256


Lambda     K      H
   0.318    0.135    0.377 

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: 154
Number of extensions: 7
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: 314
Length of database: 258
Length adjustment: 26
Effective length of query: 288
Effective length of database: 232
Effective search space:    66816
Effective search space used:    66816
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 24 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