GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Sinorhizobium meliloti 1021

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 SMc04398 SMc04398 enoyl-CoA hydratase

Query= SwissProt::Q9JLZ3
         (314 letters)



>FitnessBrowser__Smeli:SMc04398
          Length = 259

 Score =  140 bits (352), Expect = 4e-38
 Identities = 91/252 (36%), Positives = 129/252 (51%), Gaps = 8/252 (3%)

Query: 64  IVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGADLKERAK 123
           I ++ + R    NA   ++LK L  A D +++ + +R +I+  E    F AG D+K    
Sbjct: 14  IAIVTVARPEKLNAFDIDMLKALDSACDTVEARRDLRAVILTGEGKA-FSAGGDIKAWGG 72

Query: 124 MHSSEVG-PFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAKMGL 182
           M  +  G  +V     V   +A L +P IAA++G ALGGGLELA A DIR+A    K+GL
Sbjct: 73  MEPAAFGHDWVRFGHRVFERLATLRMPVIAALNGHALGGGLELAAAADIRLAEKQVKIGL 132

Query: 183 VETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAA 242
            ET L ++PG  GTQRL    G  + + ++    +    EA+A GLI  V+E      A 
Sbjct: 133 PETSLGMVPGWSGTQRLVARFGAQIVRRMVLGGEMFSAAEARAEGLIDAVVETG----AV 188

Query: 243 YRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTISTKDRLEGLLA 302
            + A D A     +GP A+ ++KL I      D   G A+E         T D  EG+ A
Sbjct: 189 MQAARDYAARVAGRGPAALEISKLMIASASGED--KGAAVEALGSILVAKTGDLKEGVAA 246

Query: 303 FKEKRPPRYKGE 314
           F EKR  R+KGE
Sbjct: 247 FSEKREARFKGE 258


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: 172
Number of extensions: 7
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: 314
Length of database: 259
Length adjustment: 26
Effective length of query: 288
Effective length of database: 233
Effective search space:    67104
Effective search space used:    67104
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